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%% This BibTeX bibliography file was created using BibDesk. |
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%% Created for Dan Gezelter at 2010-10-18 12:52:34 -0400 |
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@string{acp = {Adv. Chem. Phys.}} |
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@string{bj = {Biophys. J.}} |
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@string{ccp5 = {CCP5 Information Quarterly}} |
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@string{cp = {Chem. Phys.}} |
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@string{cpl = {Chem. Phys. Lett.}} |
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@string{jacs = {J. Am. Chem. Soc.}} |
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@string{jcc = {J. Comp. Chem.}} |
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@string{jcop = {J. Comp. Phys.}} |
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@string{jcp = {J. Chem. Phys.}} |
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@string{jmb = {J. Mol. Bio.}} |
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@string{jml = {J. Mol. Liq.}} |
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@string{jpc = {J. Phys. Chem.}} |
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@string{jpca = {J. Phys. Chem. A}} |
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@string{jpcb = {J. Phys. Chem. B}} |
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@string{mp = {Mol. Phys.}} |
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@string{pams = {Proc. Am. Math Soc.}} |
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@string{pccp = {Phys. Chem. Chem. Phys.}} |
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@string{pnas = {Proc. Natl. Acad. Sci. USA}} |
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@string{pr = {Phys. Rev.}} |
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@string{pra = {Phys. Rev. A}} |
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@string{prb = {Phys. Rev. B}} |
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@string{pre = {Phys. Rev. E}} |
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@string{prl = {Phys. Rev. Lett.}} |
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@string{rmp = {Rev. Mod. Phys.}} |
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@misc{openmd, |
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Author = {J. Daniel Gezelter and Shenyu Kuang and James Marr and Kelsey Stocker and Chunlei Li and Charles F. Vardeman and Teng Lin and Christopher J. Fennell and Xiuquan Sun and Kyle Daily and Yang Zheng and Matthew A. Meineke}, |
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Date-Added = {2010-10-18 12:51:55 -0400}, |
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Date-Modified = {2010-10-18 12:51:55 -0400}, |
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Howpublished = {Available at {\tt http://openmd.net}}, |
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Title = {{OpenMD, an open source engine for molecular dynamics}}} |
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@article{Fine1973, |
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Author = {Fine, Rana A. and Millero, Frank J.}, |
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Date-Added = {2010-09-22 15:53:25 -0400}, |
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Date-Modified = {2010-09-22 15:53:25 -0400}, |
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Journal = {J. Chem. Phys.}, |
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Keywords = {water; isothermal compressibility; experiment}, |
73 |
Number = {10}, |
74 |
Pages = {5529-5536}, |
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Title = {Compressibility of water as a function of temperature and pressure}, |
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Volume = {59}, |
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Year = {1973}, |
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Bdsk-File-1 = {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}} |
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|
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@article{Pi2009, |
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Author = {Pi, Helena L. and Aragones, Juan L. and Vega, Carlos and Noya, Eva G. and Abascal, Jose L.F. and Gonzalez, Miguel A. and McBride,, Carl}, |
82 |
Date-Added = {2010-09-22 15:53:20 -0400}, |
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Date-Modified = {2010-09-22 15:53:20 -0400}, |
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Journal = {Mol. Phys.}, |
85 |
Keywords = {water; isothermal compressibility; density}, |
86 |
Number = {4}, |
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Pages = {365-374}, |
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Title = {Anomalies in water as obtained from computer simulations of the TIP4P/2005 model: Density maxima, and density, isothermal compressibility and heat capacity minima}, |
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Volume = {107}, |
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Year = {2009}, |
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|
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@article{Grote1995, |
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Author = {Grote, Marcus J. and Keller, Joseph B.}, |
95 |
Date-Added = {2010-09-08 16:48:01 -0400}, |
96 |
Date-Modified = {2010-09-08 16:48:01 -0400}, |
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Keywords = {boundary}, |
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Title = {On nonreflecting boundary conditions}, |
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Year = {1995}, |
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|
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@article{Warshel1978, |
103 |
Author = {A. Warshel}, |
104 |
Date-Added = {2010-09-08 16:48:01 -0400}, |
105 |
Date-Modified = {2010-09-08 16:48:01 -0400}, |
106 |
Journal = {Chem. Phys. Lett.}, |
107 |
Keywords = {boundary; SCSSD}, |
108 |
Month = {May}, |
109 |
Number = {3}, |
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Pages = {454-458}, |
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Title = {A microscopic model for calculations of chemical processes in aqueous solutions}, |
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Volume = {55}, |
113 |
Year = {1978}, |
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|
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@article{Belch1985, |
117 |
Abstract = {The structure in a water cluster restrictedby a hydrophobic wall was studied as a function of the distance from the wall. Significant orientational preference was observed near the surface. This preference is very similar to that present in liquid water near planar hydrophobic surfaces of infinite extend.}, |
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Author = {Belch, A.C. and Berkowitz, M.}, |
119 |
Date-Added = {2010-09-08 16:48:01 -0400}, |
120 |
Date-Modified = {2010-09-08 16:48:01 -0400}, |
121 |
Journal = {Chem. Phys. Lett.}, |
122 |
Keywords = {dewetting; boundary}, |
123 |
Month = {January}, |
124 |
Number = {3}, |
125 |
Pages = {278-282}, |
126 |
Title = {Molecular dynamics simulations of TIPS2 water restricted by a spherical hydrophobic boundary}, |
127 |
Volume = {113}, |
128 |
Year = {1985}, |
129 |
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|
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@article{King1989, |
132 |
Abstract = {A consistent simulation of ionic or strongly polar solutes in polar solvents presents a major challenge from both fundamental and practical aspects. The frequently used method of periodic boundary conditions (PBC) does not correctly take into account the symmetry of the solute field. Instead of using PBC, it is natural to model this type of system as a sphere (with the solute at the origin), but the boundary conditions to be used in such a model are not obvious. Early calculations performed with our surface constrained soft sphere dipoles (SCSSD) model indicated that the dipoles near the surface ofthe sphere will show unusual orientational preferences (they will overpolarize) unless a corrective force is included in the model, and thus we implemented polarization constraints in this spherical model of polar solutions. More recent approaches that treated the surface with stochastic dynamics, but did not take into account the surface polarization effects, were also found to exhibit these nonphysical orientational preferences. The present work develops a surface constrained all- atom solvent (SCAAS) model in order to consistently treat the surface polarization effects in all-atom molecular dynamics simulations. The SCAAS model, which was presented in a preliminary way in previous works, introduces surface constraints as boundary conditions in order to make the necessarily finite system behave as if it was part of an infinite system. The performance of the model with regard to various properties of bulk water is examined by comparing its results to those obtained by PBC simulations. The results obtained from SCAAS models of different sizes are found to be similar to each other and to the corresponding PBC results. The performance of the model in simulations of solvated ions is emphasized and a comparison of the results obtained with spheres of different sizes demonstrates that the model does not possess significant size dependence. This indicates that the model can be used with a relatively small number of solvent molecules for convergent simulation of structure, energetics, and dynamics of polar solutions. The much simpler fixed center Langevin dipoles (FCLD) model is also examined and found to provide a powerful tool for estimating solvation free energies. Finally, a preliminary study of the dielectric properties of the SCAAS model is reported and the potential of this model for exploring the correct implementation of the solvent reaction field is discussed.}, |
133 |
Author = {King, G. and Warshel, A.}, |
134 |
Date-Added = {2010-09-08 16:48:01 -0400}, |
135 |
Date-Modified = {2010-09-08 16:48:01 -0400}, |
136 |
Journal = {J. Chem. Phys.}, |
137 |
Keywords = {dewetting; boundary}, |
138 |
Month = {September}, |
139 |
Number = {6}, |
140 |
Pages = {3647-3661}, |
141 |
Title = {A surface constrained all-atom solvent model for effective simulations of polar solutions}, |
142 |
Volume = {91}, |
143 |
Year = {1989}, |
144 |
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|
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@article{Lee1984, |
147 |
Abstract = {Molecular dynamics simulations have been carried out for liquid water between flat hydrophobic s~rf~ces. The surfaces p.rodu~edensity oscillations that extend at lea~t 10 A into the liquid, and slgmficant molecular onentatlOnal preferences that extend at least 7 A into the liquid. The liquid structure nearest the surface is characterized by "dangling" hydrogen bonds; i.e., a typical water molecule at the surface has one potentially hydrogen-bonding group oriented toward the hydrophobic surface. This surface arrangement represents a balance between the tendencies of the liquid to maximize the number of hydrogen bonds on the one hand, and to maximize the packing density of the molecules on the other. A detailed analysis shows that the structural properties of the liquid farther from the surface can be understood as effects imposed by this surface structure. These results show that the hydration structure of large hydrophobic surfaces |
148 |
can be very different from that of small hydrophobic molecules.}, |
149 |
Author = {Lee, C.Y. and McCammon, J.A. and Rossky, P.J.}, |
150 |
Date-Added = {2010-09-08 16:48:01 -0400}, |
151 |
Date-Modified = {2010-09-08 16:48:01 -0400}, |
152 |
Journal = {J. Chem. Phys.}, |
153 |
Keywords = {dewetting; boundary}, |
154 |
Month = {May}, |
155 |
Number = {9}, |
156 |
Pages = {4448-4455}, |
157 |
Title = {The structure of liquid water at an extended hydrophobic surface}, |
158 |
Volume = {80}, |
159 |
Year = {1984}, |
160 |
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|
162 |
@article{Beglov1994, |
163 |
Abstract = {An approach is developed to obtain statistical properties similar to those of an infinite bulk system from computer simulations of a finite cluster. A rigorous theoretical formulation is given for the solvent boundary potential which takes the influence of the surrounding bulk into account. The solvent boundary potential is the configuration-dependent solvation free energy of an effective cluster composed of an arbitrary solute and a finite number of explicit solvent molecules embedded inside a hard sphere of variable radius; the hard sphere does not act directly on the solute or the explicit solvent molecules, and its radius varies according to the instantaneous configurations. The formulation follows from an exact separation of the multidimensional configurational Boltzmann integral in terms of the solvent molecules nearest to the solute and the remaining bulk solvent molecules. An approximation to the solvent boundary potential is constructed for simulations of bulk water at constant pressure, including the influence of van der Waals and electrostatic interactions. The approximation is illustrated with calculations of the solvation free energy of a water molecule and of sodium and potassium ions. The influence of bulk solvent on the conformational equilibrium of molecular solutes is illustrated by performing umbrella sampling calculations of n-butane and alanine dipeptide in water. The boundary potential is tested to examine the dependence of the results on the number of water molecules included explicitly in the simulations. It is observed that bulk-like results are obtained, even when only the waters in the first hydration shell are included explicitly.}, |
164 |
Author = {Beglov, D. and Roux, B.}, |
165 |
Date-Added = {2010-09-08 16:48:01 -0400}, |
166 |
Date-Modified = {2010-09-08 16:48:01 -0400}, |
167 |
Journal = {J. Chem. Phys.}, |
168 |
Keywords = {dewetting; boundary}, |
169 |
Month = {June}, |
170 |
Number = {12}, |
171 |
Pages = {9050-9063}, |
172 |
Title = {Finite representations of an infinite bulk system: Solvent boundary potential for computer simulations}, |
173 |
Volume = {100}, |
174 |
Year = {1994}, |
175 |
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176 |
|
177 |
@article{Choudhury2007, |
178 |
Author = {Niharendu Choudhury and B. Montgomery Pettitt}, |
179 |
Date-Added = {2010-09-08 16:48:01 -0400}, |
180 |
Date-Modified = {2010-09-08 16:48:01 -0400}, |
181 |
Journal = {J. Am. Chem. Soc.}, |
182 |
Keywords = {dewetting; hydrophobic}, |
183 |
Number = {15}, |
184 |
Pages = {4847-4852}, |
185 |
Title = {The dewetting transition and the hydrophobic effect}, |
186 |
Volume = {129}, |
187 |
Year = {2007}, |
188 |
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189 |
|
190 |
@article{Du1994, |
191 |
Author = {Quan Du and Eric Freysz and Y. Ron Shen}, |
192 |
Date-Added = {2010-09-08 16:48:01 -0400}, |
193 |
Date-Modified = {2010-09-08 16:48:01 -0400}, |
194 |
Journal = {Science}, |
195 |
Keywords = {dewetting; hydrophobic boundary}, |
196 |
Month = {May}, |
197 |
Pages = {826-828}, |
198 |
Title = {Surface vibrational spectroscopic studies of hydrogen bonding and hydrophobicity}, |
199 |
Volume = {264}, |
200 |
Year = {1994}, |
201 |
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202 |
|
203 |
@article{Lee1994, |
204 |
Author = {Song Hi Lee and Peter J. Rossky}, |
205 |
Date-Added = {2010-09-08 16:48:01 -0400}, |
206 |
Date-Modified = {2010-09-08 16:48:01 -0400}, |
207 |
Journal = {J. Chem. Phys.}, |
208 |
Keywords = {dewetting; hydrophobic boundary; hydrophilic boundary}, |
209 |
Month = {February}, |
210 |
Number = {4}, |
211 |
Pages = {3334-3345}, |
212 |
Title = {A comparison of the structure and dynamics of liquid water at hydrophobic and hydrophilic surfaces - a molecular dynamics simulation study}, |
213 |
Volume = {100}, |
214 |
Year = {1994}, |
215 |
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216 |
|
217 |
@article{Taylor1996, |
218 |
Author = {Ramona S. Taylor and Liem X. Dang and Bruce C. Garrett}, |
219 |
Date-Added = {2010-09-08 16:48:01 -0400}, |
220 |
Date-Modified = {2010-09-08 16:48:01 -0400}, |
221 |
Journal = {J. Phys. Chem.}, |
222 |
Keywords = {dewetting; SPC/E}, |
223 |
Pages = {11720-11725}, |
224 |
Title = {Molecular dynamics simulations of the liquid/vapor interface of SPC/E water}, |
225 |
Volume = {100}, |
226 |
Year = {1996}, |
227 |
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228 |
|
229 |
@article{Du1993, |
230 |
Author = {Q. Du and R. Superfine and E. Freysz and Y.R. Shen}, |
231 |
Date-Added = {2010-09-08 16:48:01 -0400}, |
232 |
Date-Modified = {2010-09-08 16:48:01 -0400}, |
233 |
Journal = {Phys. Rev. Lett.}, |
234 |
Keywords = {dewetting; water; experiment; hydrophobic boundary}, |
235 |
Month = {April}, |
236 |
Number = {15}, |
237 |
Pages = {2313-2316}, |
238 |
Title = {Vibrational spectroscopy of water at the vapor/water interface}, |
239 |
Volume = {70}, |
240 |
Year = {1993}, |
241 |
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242 |
|
243 |
@article{Li2005, |
244 |
Abstract = {A new approach is developed to study the dynamics of the localized process in solutions and other condensed phase systems. The approach employs a fluctuating elastic boundary (FEB) model which encloses the simulated system in an elastic bag that mimics the effects of the bulk solvent. This alleviates the need for periodic boundary conditions and allows for a reduction in the number of solvent molecules that need to be included in the simulation. The boundary bag is modeled as a mesh of quasi-particles connected by elastic bonds. The FEB model allows for volume and density fluctuations characteristic of the bulk system, and the shape of the boundary fluctuates during the course of the simulation to adapt to the configuration fluctuations of the explicit solute-solvent system inside. The method is applied to the simulation of a Lennard-Jones model of liquid argon. Various structural and dynamical quantities are computed and compared with those obtained from conventional periodic boundary simulations. The agreement between the two is excellent in most cases, thus validating the viability of the FEB method.}, |
245 |
Author = {Li, Y. and Krilov, G. and Berne, B.J.}, |
246 |
Date-Added = {2010-09-08 16:48:01 -0400}, |
247 |
Date-Modified = {2010-09-08 16:48:01 -0400}, |
248 |
Journal = {J. Phys. Chem. B}, |
249 |
Keywords = {Elastic bag; dewetting}, |
250 |
Pages = {463-470}, |
251 |
Title = {Elastic bag model for molecular dynamics simulations of solvated systems: Application to liquid argon}, |
252 |
Volume = {109}, |
253 |
Year = {2005}, |
254 |
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255 |
|
256 |
@article{Debenedetti1986, |
257 |
Author = {Debenedetti, P.G.}, |
258 |
Date-Added = {2010-09-08 16:48:01 -0400}, |
259 |
Date-Modified = {2010-09-08 16:48:01 -0400}, |
260 |
Journal = {J. Chem. Phys.}, |
261 |
Keywords = {fluctuation dissipation}, |
262 |
Month = {February}, |
263 |
Number = {3}, |
264 |
Pages = {1778-1787}, |
265 |
Title = {On the relationship between principal fluctuations and stability coefficients in multicomponent systems}, |
266 |
Volume = {84}, |
267 |
Year = {1986}, |
268 |
Bdsk-File-1 = {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}} |
269 |
|
270 |
@article{Bagchi1997, |
271 |
Abstract = {Constant temperature and constant pressure molecular dynamics calculations have been performed on the extended simple point charge (SPC/E) model water to understand the effects of pressure on its structural and dynamical properties. The effect of pressure is to increase the presence of interstitial water molecules, which is shown to be responsible for the experimentally observed increase in the first x-ray diffraction peak and a broadening of the OdOO bond angle distribution. These structural changes lead to weaker hydrogen bonding and the observed minimum in the rotational correlation time as a function of pressure. The weak maximum in the measured translational diffusion coefficient at around 1.5 kbar was not reproduced. The temperature of the density maximum was estimated to occur at 2454 K, which suggests that structural changes with increasing pressure and decreasing temperature are not quantitatively reproduced by the SPC/E model. {\copyright} 1997 American Institute of Physics. [S0021-9606(97)51644-8]}, |
272 |
Author = {Bagchi, K. and Balasubramanian, S. and Klein, M.L.}, |
273 |
Date-Added = {2010-09-08 16:48:01 -0400}, |
274 |
Date-Modified = {2010-09-08 16:48:01 -0400}, |
275 |
Journal = {J. Chem. Phys.}, |
276 |
Keywords = {g(r); SPC/E; pressure}, |
277 |
Month = {November}, |
278 |
Number = {22}, |
279 |
Pages = {8561-8567}, |
280 |
Title = {The effects of pressure on structural and dynamical properties of associated liquids: Molecular dynamics calculations for the extended simple point charge model of water}, |
281 |
Volume = {20}, |
282 |
Year = {1997}, |
283 |
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284 |
|
285 |
@article{Minceva-Sukarova1984, |
286 |
Author = {Minceva-Sukarova, B. and Sherman, W.F. and Wilkinson, G.R.}, |
287 |
Date-Added = {2010-09-08 16:48:01 -0400}, |
288 |
Date-Modified = {2010-09-08 16:48:01 -0400}, |
289 |
Journal = {J. Phys. C: Solid State Phys.}, |
290 |
Keywords = {ice; structure; pressure}, |
291 |
Pages = {5833-5850}, |
292 |
Title = {The raman spectra of ice (Ih, II, III, V, VI and IX) as functions of pressure and temperature}, |
293 |
Volume = {17}, |
294 |
Year = {1984}, |
295 |
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296 |
|
297 |
@article{Hummer2000, |
298 |
Author = {G. Hummer and S. Garde and A.E. Garc{\'\i}a and L.R. Pratt}, |
299 |
Date-Added = {2010-09-08 16:48:01 -0400}, |
300 |
Date-Modified = {2010-09-08 16:48:01 -0400}, |
301 |
Journal = {Chemical Physics}, |
302 |
Keywords = {interface; hydrophobic boundary; structure}, |
303 |
Pages = {349-370}, |
304 |
Title = {New perspectives on hydrophobic effects}, |
305 |
Volume = {258}, |
306 |
Year = {2000}, |
307 |
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308 |
|
309 |
@article{Perera1991, |
310 |
Author = {Perera, Lalith and Berkowitz, Max L.}, |
311 |
Date-Added = {2010-09-08 16:48:01 -0400}, |
312 |
Date-Modified = {2010-09-08 16:48:01 -0400}, |
313 |
Journal = {J. Chem. Phys.}, |
314 |
Keywords = {ions; polarizable}, |
315 |
Month = {August}, |
316 |
Number = {3}, |
317 |
Pages = {1954-1963}, |
318 |
Title = {Many-body effects in molecular dynamics simulations of Na+(H2O)n and Cl-(H2O)n clusters}, |
319 |
Volume = {95}, |
320 |
Year = {1991}, |
321 |
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322 |
|
323 |
@article{Stuart1996, |
324 |
Abstract = {Polarizable and nonpolarizable potential models for both water and chloride are used to address the issue of surfaceVsinteriorsolvationofthechlorideioninCl(H2O)n-clusters,fornupto255. Wefindthat,evenfor the largest clusters, simulations with polarizable water models show that the chloride ion is preferentially solvated near the surface of the cluster. This behavior is not observed with a nonpolarizable model. The many-body effects are not directly responsible for this solvation behavior; polarizability appears to be important primarilyforitsroleinfacilitatingalargeraveragedipolemomentonthewatermodel. Polarizabilityonthe chloride ion is not found to have a substantial effect on the structure of the clusters.}, |
325 |
Author = {Stuart, S.J. and Berne, B.J.}, |
326 |
Date-Added = {2010-09-08 16:48:01 -0400}, |
327 |
Date-Modified = {2010-09-08 16:48:01 -0400}, |
328 |
Journal = {J. Phys. Chem.}, |
329 |
Keywords = {ions; polarizable; chloride}, |
330 |
Pages = {11934-11943}, |
331 |
Title = {Effects of polarizability on the hydration of the chloride ion}, |
332 |
Volume = {100}, |
333 |
Year = {1996}, |
334 |
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335 |
|
336 |
@article{Motakabbir1990, |
337 |
Abstract = {Molecular dynamics computer simulations on rigid SPC/E water molecules were performed. The goal of the simulations is to study the behavior of isothermal compressibility, which was calculated in the simulations at T = 298, 273, and 248 K. Thecalculatedisothermalcompressibilitiesatthesetemperaturesdisplayatrendcontrarytotheexperimentalobservations. The hydrogen-bonded network in water was also investigated. No correlation between the temperature dependence of isothermal compressibility and the number of hydrogen-bonded pentagons was observed.}, |
338 |
Author = {Motakabbir, K.A. and Berkowitz, M.}, |
339 |
Date-Added = {2010-09-08 16:48:01 -0400}, |
340 |
Date-Modified = {2010-09-08 16:48:01 -0400}, |
341 |
Journal = {J. Phys. Chem.}, |
342 |
Keywords = {isothermal compressibility; SPC/E; Pa}, |
343 |
Pages = {8359-8362}, |
344 |
Title = {Isothermal compressibility of SPC/E water}, |
345 |
Volume = {94}, |
346 |
Year = {1990}, |
347 |
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348 |
|
349 |
@article{Vedamuthu1995, |
350 |
Author = {Vedamuthu, Mary and Singh, Surjit and Robinson, G. Wilse}, |
351 |
Date-Added = {2010-09-08 16:48:01 -0400}, |
352 |
Date-Modified = {2010-09-08 16:48:01 -0400}, |
353 |
Journal = {J. Phys. Chem.}, |
354 |
Keywords = {isothermal compressibility; water}, |
355 |
Pages = {9263-9267}, |
356 |
Title = {Properties of liquid water. 4. The isothermal compressibility minimum near 50 C}, |
357 |
Volume = {99}, |
358 |
Year = {1995}, |
359 |
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360 |
|
361 |
@article{Brancato2009, |
362 |
Author = {Giuseppe Brancato and Nadia Rega and Vincenzo Barone}, |
363 |
Date-Added = {2010-09-08 16:48:01 -0400}, |
364 |
Date-Modified = {2010-09-08 16:48:01 -0400}, |
365 |
Journal = {Chem. Phys. Lett}, |
366 |
Keywords = {non-periodic boundary conditions}, |
367 |
Pages = {177-181}, |
368 |
Title = {Molecular dynamics simulations in a NpT ensemble using non-periodic boundary conditions}, |
369 |
Volume = {483}, |
370 |
Year = {2009}, |
371 |
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372 |
|
373 |
@article{Baltazar2006, |
374 |
Author = {S.E. Baltazar and A.H. Romero and J.L. Rodr{\'\i}guez-L{\'o}pez and H. Terrones and R. Marto{\v n}{\'a}k}, |
375 |
Date-Added = {2010-09-08 16:48:01 -0400}, |
376 |
Date-Modified = {2010-09-08 16:48:01 -0400}, |
377 |
Journal = {Computational Materials Science}, |
378 |
Keywords = {NPT}, |
379 |
Pages = {526-536}, |
380 |
Title = {Assessment of isobaric-isothermal (NPT) simulations for finite systems}, |
381 |
Volume = {37}, |
382 |
Year = {2006}, |
383 |
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384 |
|
385 |
@article{Urquidi1999, |
386 |
Author = {J. Urquidi and S. Singh and C.H. Cho and G.W. Robinson}, |
387 |
Date-Added = {2010-09-08 16:48:01 -0400}, |
388 |
Date-Modified = {2010-09-08 16:48:01 -0400}, |
389 |
Journal = {Phys. Rev. Lett.}, |
390 |
Keywords = {pressure; structure}, |
391 |
Month = {September}, |
392 |
Number = {12}, |
393 |
Pages = {2348-2350}, |
394 |
Title = {Origin of temperature and pressure effects on the radial distribution function of water}, |
395 |
Volume = {83}, |
396 |
Year = {1999}, |
397 |
Bdsk-File-1 = {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}} |
398 |
|
399 |
@article{Robinson1999, |
400 |
Author = {G. Wilse Robinson and Chul Hee Cho and Jacob Urquidi}, |
401 |
Date-Added = {2010-09-08 16:48:01 -0400}, |
402 |
Date-Modified = {2010-09-08 16:48:01 -0400}, |
403 |
Journal = {J. Chem. Phys.}, |
404 |
Keywords = {pressure; structure}, |
405 |
Month = {July}, |
406 |
Number = {2}, |
407 |
Pages = {698-702}, |
408 |
Title = {Isobestic points in liquid water: Further strong evidence for the two-state mixture model}, |
409 |
Volume = {111}, |
410 |
Year = {1999}, |
411 |
Bdsk-File-1 = {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}} |
412 |
|
413 |
@article{Gorbaty1999, |
414 |
Author = {Yu. E. Gorbaty and G.V. Bondarenko and A.G. Kalinichev and A.V. Okhulkov}, |
415 |
Date-Added = {2010-09-08 16:48:01 -0400}, |
416 |
Date-Modified = {2010-09-08 16:48:01 -0400}, |
417 |
Journal = {Mol. Phys.}, |
418 |
Keywords = {pressure; structure}, |
419 |
Number = {11}, |
420 |
Pages = {1659-1665}, |
421 |
Title = {The effect of pressure on hydrogen bonding in water: IR study of νOD HDO at pressures of up to 1500 bar}, |
422 |
Volume = {96}, |
423 |
Year = {1999}, |
424 |
Bdsk-File-1 = {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}} |
425 |
|
426 |
@article{Stillinger1974, |
427 |
Abstract = {The technique of computer simulation by molecular dynamics has been used to investigate highly compressed water at mass density 1.346 glcm3. The calculations involve 216 rigid molecules, subject to an additive interaction (the "ST2 potential") whose strong anisotropic character has been shown to describe the hydrogen bond phenomenon. In the light of previous calculations on the same model at ordinary pressures, substantial restructuring of the liquid in response to compression is obvious. No evidence arises to support description of the liquid in terms of crystal structures of ices VI and VII, the solid forms that might be expected to be relevant at the chosen density. The calculations indicate that the initial effect of pressure increase (at I atm) leads to increased fluidity, as is known to be the case for real water.}, |
428 |
Author = {Frank H. Stillinger and Aneesur Rahman}, |
429 |
Date-Added = {2010-09-08 16:48:01 -0400}, |
430 |
Date-Modified = {2010-09-08 16:48:01 -0400}, |
431 |
Journal = {J. Chem. Phys.}, |
432 |
Keywords = {pressure; structure; water}, |
433 |
Month = {December}, |
434 |
Number = {12}, |
435 |
Pages = {4973-4980}, |
436 |
Title = {Molecular dynamics study of liquid water under high compression}, |
437 |
Volume = {61}, |
438 |
Year = {1974}, |
439 |
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440 |
|
441 |
@article{Impey1981, |
442 |
Author = {R.W. Impey and M.L. Klein and I.R. McDonald}, |
443 |
Date-Added = {2010-09-08 16:48:01 -0400}, |
444 |
Date-Modified = {2010-09-08 16:48:01 -0400}, |
445 |
Journal = {J. Chem. Phys.}, |
446 |
Keywords = {pressure; structure; water}, |
447 |
Number = {1}, |
448 |
Pages = {647-652}, |
449 |
Title = {Molecular dynamics studies of the structure of water at high temperatures and density}, |
450 |
Volume = {74}, |
451 |
Year = {1981}, |
452 |
Bdsk-File-1 = {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}} |
453 |
|
454 |
@article{Wang2006, |
455 |
Author = {Jiyao Wang and Yuqing Deng and Beno{\^\i}t Roux}, |
456 |
Date-Added = {2010-09-08 16:48:01 -0400}, |
457 |
Date-Modified = {2010-09-08 16:48:01 -0400}, |
458 |
Journal = {Biophysical Journal}, |
459 |
Keywords = {restraining potential}, |
460 |
Month = {October}, |
461 |
Pages = {2798-2814}, |
462 |
Title = {Absolute binding free energy calculations using molecular dynamics simulations with restraining potentials}, |
463 |
Volume = {91}, |
464 |
Year = {2006}, |
465 |
Bdsk-File-1 = {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}} |
466 |
|
467 |
@article{Warshel1979, |
468 |
Author = {Warshel, Arieh}, |
469 |
Date-Added = {2010-09-08 16:48:01 -0400}, |
470 |
Date-Modified = {2010-09-08 16:48:01 -0400}, |
471 |
Journal = {J. Phys. Chem.}, |
472 |
Keywords = {SCSSD; boundary; water}, |
473 |
Number = {12}, |
474 |
Pages = {1640-1652}, |
475 |
Title = {Calculations of chemical processes in solutions}, |
476 |
Volume = {83}, |
477 |
Year = {1979}, |
478 |
Bdsk-File-1 = {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}} |
479 |
|
480 |
@article{Campo2010, |
481 |
Author = {M.G. Campo}, |
482 |
Date-Added = {2010-09-08 16:48:01 -0400}, |
483 |
Date-Modified = {2010-09-08 16:48:01 -0400}, |
484 |
Journal = {Papers in Physics}, |
485 |
Keywords = {SPC/E}, |
486 |
Number = {article 020001}, |
487 |
Pages = {020001-1 - 020001-7}, |
488 |
Title = {Structural and dynamic properties of SPC/E water}, |
489 |
Volume = {2}, |
490 |
Year = {2010}, |
491 |
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492 |
|
493 |
@article{Berendsen1987, |
494 |
Author = {H.J.C. Berendsen and J.R. Grigera and T.P. Straatsma}, |
495 |
Date-Added = {2010-09-08 16:48:01 -0400}, |
496 |
Date-Modified = {2010-09-08 16:48:01 -0400}, |
497 |
Journal = {J. Phys. Chem.}, |
498 |
Keywords = {SPC/E}, |
499 |
Pages = {6269-6271}, |
500 |
Title = {The missing term in effective pair potentials}, |
501 |
Volume = {91}, |
502 |
Year = {1987}, |
503 |
Bdsk-File-1 = {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}} |
504 |
|
505 |
@article{Jorgensen1998, |
506 |
Abstract = {Monte Carlo statistical mechanics simulations have been carried out with the TIP3P, SPC, and TIP4P models for liquid water at 13 temperatures from 50C to 100C at 1 atm. Long runs with 512 water molecules provided definitive results for densities. Although the TIP4P model yields a flat region in the density profile and a temperature of maximum density near 15C, the SPC and TIP3P models show monotonically increasing density with decreasing temperature. Results for heats of vaporization, isothermal compressibilities, and coefficients of thermal expansion and their convergence characteristics are also reported. 1998 John Wiley & Sons, Inc. J Comput Chem 19: 11791186, 1998}, |
507 |
Author = {Jorgensen, W.L. and Jenson, C.}, |
508 |
Date-Added = {2010-09-08 16:48:01 -0400}, |
509 |
Date-Modified = {2010-09-08 16:48:01 -0400}, |
510 |
Journal = {Journal of Computational Chemistry}, |
511 |
Keywords = {SPC/E; density; water models; structure; g(r)}, |
512 |
Number = {10}, |
513 |
Pages = {1179-1186}, |
514 |
Title = {Temperature dependence of TIP3P, SPC, and TIP4P water from NPT Monte Carlo simulations: Seeking temperatures of maximum density}, |
515 |
Volume = {19}, |
516 |
Year = {1998}, |
517 |
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518 |
|
519 |
@article{Peltz2003, |
520 |
Author = {Csaba Peltz and Andr{\'a}s Baranyai and Ariel A. Chialvo and Peter T. Cummings}, |
521 |
Date-Added = {2010-09-08 16:48:01 -0400}, |
522 |
Date-Modified = {2010-09-08 16:48:01 -0400}, |
523 |
Journal = {Molecular Simulation}, |
524 |
Keywords = {SPC/E; structure}, |
525 |
Number = {1}, |
526 |
Pages = {13-21}, |
527 |
Title = {Microstructure of water at the level of three-particle correlation functions as predicted by classical intermolecular models}, |
528 |
Volume = {29}, |
529 |
Year = {2003}, |
530 |
Bdsk-File-1 = {YnBsaXN0MDDUAQIDBAUIJidUJHRvcFgkb2JqZWN0c1gkdmVyc2lvblkkYXJjaGl2ZXLRBgdUcm9vdIABqAkKFRYXGyIjVSRudWxs0wsMDQ4RFFpOUy5vYmplY3RzV05TLmtleXNWJGNsYXNzog8QgASABqISE4ACgAOAB1lhbGlhc0RhdGFccmVsYXRpdmVQYXRo0hgNGRpXTlMuZGF0YU8RAZQAAAAAAZQAAgAACFNlcmVuaXR5AAAAAAAAAAAAAAAAAAAAAAAAAMiiw+JIKwAAABJC+Q1QZWx0ejIwMDMucGRmAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAEkMkyC6gXAAAAAAAAAAAAAEABAAACSAAAAAAAAAAAAAAAAAAAAAGUGFwZXJzABAACAAAyKL8IgAAABEACAAAyC7YnAAAAAEAFAASQvkAEkLjABI4nQASOJAAAJHaAAIAP1NlcmVuaXR5OlVzZXJzOmtzdG9ja2UxOkRvY3VtZW50czpSZXNlYXJjaDpQYXBlcnM6UGVsdHoyMDAzLnBkZgAADgAcAA0AUABlAGwAdAB6ADIAMAAwADMALgBwAGQAZgAPABIACABTAGUAcgBlAG4AaQB0AHkAEgA2VXNlcnMva3N0b2NrZTEvRG9jdW1lbnRzL1Jlc2VhcmNoL1BhcGVycy9QZWx0ejIwMDMucGRmABMAAS8AABUAAgAP//8AAIAF0hwdHh9YJGNsYXNzZXNaJGNsYXNzbmFtZaMfICFdTlNNdXRhYmxlRGF0YVZOU0RhdGFYTlNPYmplY3RfECouLi9Eb2N1bWVudHMvUmVzZWFyY2gvUGFwZXJzL1BlbHR6MjAwMy5wZGbSHB0kJaIlIVxOU0RpY3Rpb25hcnkSAAGGoF8QD05TS2V5ZWRBcmNoaXZlcgAIABEAFgAfACgAMgA1ADoAPABFAEsAUgBdAGUAbABvAHEAcwB2AHgAegB8AIYAkwCYAKACOAI6Aj8CSAJTAlcCZQJsAnUCogKnAqoCtwK8AAAAAAAAAgEAAAAAAAAAKAAAAAAAAAAAAAAAAAAAAs4=}} |
531 |
|
532 |
@article{Kratky1980, |
533 |
Author = {K.W. Kratky}, |
534 |
Date-Added = {2010-09-08 16:48:01 -0400}, |
535 |
Date-Modified = {2010-09-08 16:48:01 -0400}, |
536 |
Journal = {Journal of Computational Physics}, |
537 |
Keywords = {spherical boundary conditions}, |
538 |
Pages = {205-217}, |
539 |
Title = {New boundary conditions for computer experiments of thermodynamic systems}, |
540 |
Volume = {37}, |
541 |
Year = {1980}, |
542 |
Bdsk-File-1 = {YnBsaXN0MDDUAQIDBAUIJidUJHRvcFgkb2JqZWN0c1gkdmVyc2lvblkkYXJjaGl2ZXLRBgdUcm9vdIABqAkKFRYXGyIjVSRudWxs0wsMDQ4RFFpOUy5vYmplY3RzV05TLmtleXNWJGNsYXNzog8QgASABqISE4ACgAOAB1lhbGlhc0RhdGFccmVsYXRpdmVQYXRo0hgNGRpXTlMuZGF0YU8RAZgAAAAAAZgAAgAACFNlcmVuaXR5AAAAAAAAAAAAAAAAAAAAAAAAAMiiw+JIKwAAABJC+Q5LcmF0a3kxOTgwLnBkZgAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAEkMryDQQLQAAAAAAAAAAAAEABAAACSAAAAAAAAAAAAAAAAAAAAAGUGFwZXJzABAACAAAyKL8IgAAABEACAAAyDRIbQAAAAEAFAASQvkAEkLjABI4nQASOJAAAJHaAAIAQFNlcmVuaXR5OlVzZXJzOmtzdG9ja2UxOkRvY3VtZW50czpSZXNlYXJjaDpQYXBlcnM6S3JhdGt5MTk4MC5wZGYADgAeAA4ASwByAGEAdABrAHkAMQA5ADgAMAAuAHAAZABmAA8AEgAIAFMAZQByAGUAbgBpAHQAeQASADdVc2Vycy9rc3RvY2tlMS9Eb2N1bWVudHMvUmVzZWFyY2gvUGFwZXJzL0tyYXRreTE5ODAucGRmAAATAAEvAAAVAAIAD///AACABdIcHR4fWCRjbGFzc2VzWiRjbGFzc25hbWWjHyAhXU5TTXV0YWJsZURhdGFWTlNEYXRhWE5TT2JqZWN0XxArLi4vRG9jdW1lbnRzL1Jlc2VhcmNoL1BhcGVycy9LcmF0a3kxOTgwLnBkZtIcHSQloiUhXE5TRGljdGlvbmFyeRIAAYagXxAPTlNLZXllZEFyY2hpdmVyAAgAEQAWAB8AKAAyADUAOgA8AEUASwBSAF0AZQBsAG8AcQBzAHYAeAB6AHwAhgCTAJgAoAI8Aj4CQwJMAlcCWwJpAnACeQKnAqwCrwK8AsEAAAAAAAACAQAAAAAAAAAoAAAAAAAAAAAAAAAAAAAC0w==}} |
543 |
|
544 |
@article{Kratky1982, |
545 |
Author = {K.W. Kratky and W. Schreiner}, |
546 |
Date-Added = {2010-09-08 16:48:01 -0400}, |
547 |
Date-Modified = {2010-09-08 16:48:01 -0400}, |
548 |
Journal = {J. Chem. Phys.}, |
549 |
Keywords = {spherical boundary conditions}, |
550 |
Pages = {313-320}, |
551 |
Title = {Computational techniques for spherical boundary conditions}, |
552 |
Volume = {47}, |
553 |
Year = {1982}, |
554 |
Bdsk-File-1 = {YnBsaXN0MDDUAQIDBAUIJidUJHRvcFgkb2JqZWN0c1gkdmVyc2lvblkkYXJjaGl2ZXLRBgdUcm9vdIABqAkKFRYXGyIjVSRudWxs0wsMDQ4RFFpOUy5vYmplY3RzV05TLmtleXNWJGNsYXNzog8QgASABqISE4ACgAOAB1lhbGlhc0RhdGFccmVsYXRpdmVQYXRo0hgNGRpXTlMuZGF0YU8RAZgAAAAAAZgAAgAACFNlcmVuaXR5AAAAAAAAAAAAAAAAAAAAAAAAAMiiw+JIKwAAABJC+Q5LcmF0a3kxOTgyLnBkZgAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAEkMmyDQQ7gAAAAAAAAAAAAEABAAACSAAAAAAAAAAAAAAAAAAAAAGUGFwZXJzABAACAAAyKL8IgAAABEACAAAyDRJLgAAAAEAFAASQvkAEkLjABI4nQASOJAAAJHaAAIAQFNlcmVuaXR5OlVzZXJzOmtzdG9ja2UxOkRvY3VtZW50czpSZXNlYXJjaDpQYXBlcnM6S3JhdGt5MTk4Mi5wZGYADgAeAA4ASwByAGEAdABrAHkAMQA5ADgAMgAuAHAAZABmAA8AEgAIAFMAZQByAGUAbgBpAHQAeQASADdVc2Vycy9rc3RvY2tlMS9Eb2N1bWVudHMvUmVzZWFyY2gvUGFwZXJzL0tyYXRreTE5ODIucGRmAAATAAEvAAAVAAIAD///AACABdIcHR4fWCRjbGFzc2VzWiRjbGFzc25hbWWjHyAhXU5TTXV0YWJsZURhdGFWTlNEYXRhWE5TT2JqZWN0XxArLi4vRG9jdW1lbnRzL1Jlc2VhcmNoL1BhcGVycy9LcmF0a3kxOTgyLnBkZtIcHSQloiUhXE5TRGljdGlvbmFyeRIAAYagXxAPTlNLZXllZEFyY2hpdmVyAAgAEQAWAB8AKAAyADUAOgA8AEUASwBSAF0AZQBsAG8AcQBzAHYAeAB6AHwAhgCTAJgAoAI8Aj4CQwJMAlcCWwJpAnACeQKnAqwCrwK8AsEAAAAAAAACAQAAAAAAAAAoAAAAAAAAAAAAAAAAAAAC0w==}} |
555 |
|
556 |
@article{Schreiner1983, |
557 |
Author = {W. Schreiner and K.W. Kratky}, |
558 |
Date-Added = {2010-09-08 16:48:01 -0400}, |
559 |
Date-Modified = {2010-09-08 16:48:01 -0400}, |
560 |
Journal = {Mol. Phys.}, |
561 |
Keywords = {spherical boundary conditions}, |
562 |
Number = {3}, |
563 |
Pages = {435-452}, |
564 |
Title = {Finiteness effects in computer simulation of fluids with spherical boundary conditions}, |
565 |
Volume = {50}, |
566 |
Year = {1983}, |
567 |
Bdsk-File-1 = {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}} |
568 |
|
569 |
@article{Brooks1983a, |
570 |
Author = {Brooks, C.L III and Karplus, M.}, |
571 |
Date-Added = {2010-09-08 16:48:01 -0400}, |
572 |
Date-Modified = {2010-09-08 16:48:38 -0400}, |
573 |
Journal = {J. Chem. Phys.}, |
574 |
Keywords = {stochastic boundary conditions}, |
575 |
Month = {December}, |
576 |
Number = {12}, |
577 |
Pages = {6312-6325}, |
578 |
Title = {Deformable stochastic boundaries in molecular dynamics}, |
579 |
Volume = {79}, |
580 |
Year = {1983}, |
581 |
Bdsk-File-1 = {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}} |
582 |
|
583 |
@article{Berkowitz1982, |
584 |
Author = {Max Berkowitz and J. Andrew McCammon}, |
585 |
Date-Added = {2010-09-08 16:48:01 -0400}, |
586 |
Date-Modified = {2010-09-08 16:48:01 -0400}, |
587 |
Journal = {Chem. Phys. Lett.}, |
588 |
Keywords = {stochastic boundary conditions}, |
589 |
Month = {July}, |
590 |
Number = {3}, |
591 |
Pages = {215-217}, |
592 |
Title = {Molecular dynamics with stochastic boundary conditions}, |
593 |
Volume = {90}, |
594 |
Year = {1982}, |
595 |
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596 |
|
597 |
@article{Paolantoni2009, |
598 |
Author = {M. Paolantoni and N. Faginas Lago and M. Albert{\'\i} and A. Lagan{\'a}}, |
599 |
Date-Added = {2010-09-08 16:48:01 -0400}, |
600 |
Date-Modified = {2010-09-08 16:48:01 -0400}, |
601 |
Journal = {J. Phys. Chem. A}, |
602 |
Keywords = {tetrahedrality, q}, |
603 |
Pages = {15100-15105}, |
604 |
Title = {Tetrahedral ordering in water: Raman profiles and their temperature dependence}, |
605 |
Volume = {113}, |
606 |
Year = {2009}, |
607 |
Bdsk-File-1 = {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}} |
608 |
|
609 |
@article{Chau1998, |
610 |
Author = {P.L. Chau and A.J. Hardwick}, |
611 |
Date-Added = {2010-09-08 16:48:01 -0400}, |
612 |
Date-Modified = {2010-09-08 16:48:01 -0400}, |
613 |
Journal = {Mol. Phys.}, |
614 |
Keywords = {tetrahedrality; q; structure}, |
615 |
Number = {3}, |
616 |
Pages = {511-518}, |
617 |
Title = {A new order parameter for tetrahedral configurations}, |
618 |
Volume = {93}, |
619 |
Year = {1998}, |
620 |
Bdsk-File-1 = {YnBsaXN0MDDUAQIDBAUIJidUJHRvcFgkb2JqZWN0c1gkdmVyc2lvblkkYXJjaGl2ZXLRBgdUcm9vdIABqAkKFRYXGyIjVSRudWxs0wsMDQ4RFFpOUy5vYmplY3RzV05TLmtleXNWJGNsYXNzog8QgASABqISE4ACgAOAB1lhbGlhc0RhdGFccmVsYXRpdmVQYXRo0hgNGRpXTlMuZGF0YU8RAZAAAAAAAZAAAgAACFNlcmVuaXR5AAAAAAAAAAAAAAAAAAAAAAAAAMiiw+JIKwAAABJC+QxDaGF1MTk5OC5wZGYAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAEkMAyD6T+gAAAAAAAAAAAAEABAAACSAAAAAAAAAAAAAAAAAAAAAGUGFwZXJzABAACAAAyKL8IgAAABEACAAAyD7MOgAAAAEAFAASQvkAEkLjABI4nQASOJAAAJHaAAIAPlNlcmVuaXR5OlVzZXJzOmtzdG9ja2UxOkRvY3VtZW50czpSZXNlYXJjaDpQYXBlcnM6Q2hhdTE5OTgucGRmAA4AGgAMAEMAaABhAHUAMQA5ADkAOAAuAHAAZABmAA8AEgAIAFMAZQByAGUAbgBpAHQAeQASADVVc2Vycy9rc3RvY2tlMS9Eb2N1bWVudHMvUmVzZWFyY2gvUGFwZXJzL0NoYXUxOTk4LnBkZgAAEwABLwAAFQACAA///wAAgAXSHB0eH1gkY2xhc3Nlc1okY2xhc3NuYW1lox8gIV1OU011dGFibGVEYXRhVk5TRGF0YVhOU09iamVjdF8QKS4uL0RvY3VtZW50cy9SZXNlYXJjaC9QYXBlcnMvQ2hhdTE5OTgucGRm0hwdJCWiJSFcTlNEaWN0aW9uYXJ5EgABhqBfEA9OU0tleWVkQXJjaGl2ZXIACAARABYAHwAoADIANQA6ADwARQBLAFIAXQBlAGwAbwBxAHMAdgB4AHoAfACGAJMAmACgAjQCNgI7AkQCTwJTAmECaAJxAp0CogKlArICtwAAAAAAAAIBAAAAAAAAACgAAAAAAAAAAAAAAAAAAALJ}} |
621 |
|
622 |
@article{Scatena2001, |
623 |
Author = {Scatena, L.F. and Brown, M.G. and Richmond, G.L.}, |
624 |
Date-Added = {2010-09-08 16:48:01 -0400}, |
625 |
Date-Modified = {2010-09-08 16:48:01 -0400}, |
626 |
Journal = {Science}, |
627 |
Keywords = {water; experiment; dewetting; hydrophobic boundary}, |
628 |
Month = {May}, |
629 |
Pages = {908-912}, |
630 |
Title = {Water at hydrophobic surfaces: Weak hydrogen bonding and strong orientation effects}, |
631 |
Volume = {292}, |
632 |
Year = {2001}, |
633 |
Bdsk-File-1 = {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}} |
634 |
|
635 |
@article{Vega2005, |
636 |
Abstract = {The melting point of ice Ih for the TIP3P, SPC, SPC/E, TIP4P, TIP4P/Ew and TIP5P models has been determined by computer simulation. It has been found that the melting points of ice Ih for these models are 146, 190, 215, 232, 245 and 274 K respectively. Thus from the models of water available so far only TIP5P reproduces the experimental melting point of water. The relative stability of ice II with respect to ice Ih at the normal melting point has also been considered. Ice II is more stable than ice Ih for the TIP3P, SPC, SPC/E and TIP5P models. Only for the TIP4P and TIP4P/Ew models is ice Ih more stable than ice II at low pressures. The complete phase diagram for the SPC/E, TIP4P and TIP5P models has been computed. It has been found that SPC/E and TIP5P do not correctly describe the phase diagram of water. However, TIP4P provides a qualitatively correct description of the phase diagram of water. A slight modification of the parameters of the TIP4P model yields a new model, denoted as TIP4P/ice, which reproduces the experimental melting point of water and provides an excellent description of the densities of all ice phases.}, |
637 |
Author = {Vega, C. and Abascal, J.L.F. and MacDowell, L.G. and McBride, C.}, |
638 |
Date-Added = {2010-09-08 16:48:01 -0400}, |
639 |
Date-Modified = {2010-09-08 16:48:01 -0400}, |
640 |
Journal = {J. Phys.: Condes. Matter}, |
641 |
Keywords = {water; model}, |
642 |
Pages = {S3283-S3288}, |
643 |
Title = {Can simple models describe the phase diagram of water?}, |
644 |
Volume = {17}, |
645 |
Year = {2005}, |
646 |
Bdsk-File-1 = {YnBsaXN0MDDUAQIDBAUIJidUJHRvcFgkb2JqZWN0c1gkdmVyc2lvblkkYXJjaGl2ZXLRBgdUcm9vdIABqAkKFRYXGyIjVSRudWxs0wsMDQ4RFFpOUy5vYmplY3RzV05TLmtleXNWJGNsYXNzog8QgASABqISE4ACgAOAB1lhbGlhc0RhdGFccmVsYXRpdmVQYXRo0hgNGRpXTlMuZGF0YU8RAZAAAAAAAZAAAgAACFNlcmVuaXR5AAAAAAAAAAAAAAAAAAAAAAAAAMiiw+JIKwAAABJC+QxWZWdhMjAwNS5wZGYAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAEkMQx+yo4AAAAAAAAAAAAAEABAAACSAAAAAAAAAAAAAAAAAAAAAGUGFwZXJzABAACAAAyKL8IgAAABEACAAAx+zhIAAAAAEAFAASQvkAEkLjABI4nQASOJAAAJHaAAIAPlNlcmVuaXR5OlVzZXJzOmtzdG9ja2UxOkRvY3VtZW50czpSZXNlYXJjaDpQYXBlcnM6VmVnYTIwMDUucGRmAA4AGgAMAFYAZQBnAGEAMgAwADAANQAuAHAAZABmAA8AEgAIAFMAZQByAGUAbgBpAHQAeQASADVVc2Vycy9rc3RvY2tlMS9Eb2N1bWVudHMvUmVzZWFyY2gvUGFwZXJzL1ZlZ2EyMDA1LnBkZgAAEwABLwAAFQACAA///wAAgAXSHB0eH1gkY2xhc3Nlc1okY2xhc3NuYW1lox8gIV1OU011dGFibGVEYXRhVk5TRGF0YVhOU09iamVjdF8QKS4uL0RvY3VtZW50cy9SZXNlYXJjaC9QYXBlcnMvVmVnYTIwMDUucGRm0hwdJCWiJSFcTlNEaWN0aW9uYXJ5EgABhqBfEA9OU0tleWVkQXJjaGl2ZXIACAARABYAHwAoADIANQA6ADwARQBLAFIAXQBlAGwAbwBxAHMAdgB4AHoAfACGAJMAmACgAjQCNgI7AkQCTwJTAmECaAJxAp0CogKlArICtwAAAAAAAAIBAAAAAAAAACgAAAAAAAAAAAAAAAAAAALJ}} |
647 |
|
648 |
@article{Jhon2006, |
649 |
Author = {Jhon, Young In and No, Kyoung Tai and Jhon, Mu Shik}, |
650 |
Date-Added = {2010-09-08 16:48:01 -0400}, |
651 |
Date-Modified = {2010-09-08 16:48:01 -0400}, |
652 |
Journal = {Fluid Phase Equilibria}, |
653 |
Keywords = {water; q; tetrahedrality}, |
654 |
Pages = {160-166}, |
655 |
Title = {The molecular-level relationship between the properties of liquid water molecules and orientational order}, |
656 |
Volume = {244}, |
657 |
Year = {2006}, |
658 |
Bdsk-File-1 = {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}} |
659 |
|
660 |
@article{Ohtaki1997, |
661 |
Author = {Hitoshi Ohtaki and Tam{\'a}s Radnai and Toshio Yamaguchi}, |
662 |
Date-Added = {2010-09-08 16:48:01 -0400}, |
663 |
Date-Modified = {2010-09-08 16:48:01 -0400}, |
664 |
Journal = {Chemical Society Reviews}, |
665 |
Keywords = {water; structure}, |
666 |
Pages = {41-51}, |
667 |
Title = {Structure of water under subcritical and supercritical conditions studied by solution X-ray diffraction}, |
668 |
Year = {1997}, |
669 |
Bdsk-File-1 = {YnBsaXN0MDDUAQIDBAUIJidUJHRvcFgkb2JqZWN0c1gkdmVyc2lvblkkYXJjaGl2ZXLRBgdUcm9vdIABqAkKFRYXGyIjVSRudWxs0wsMDQ4RFFpOUy5vYmplY3RzV05TLmtleXNWJGNsYXNzog8QgASABqISE4ACgAOAB1lhbGlhc0RhdGFccmVsYXRpdmVQYXRo0hgNGRpXTlMuZGF0YU8RAZgAAAAAAZgAAgAACFNlcmVuaXR5AAAAAAAAAAAAAAAAAAAAAAAAAMiiw+JIKwAAABJC+Q5PaHRha2kxOTk3LnBkZgAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAEkMGyDvR8gAAAAAAAAAAAAEABAAACSAAAAAAAAAAAAAAAAAAAAAGUGFwZXJzABAACAAAyKL8IgAAABEACAAAyDwKMgAAAAEAFAASQvkAEkLjABI4nQASOJAAAJHaAAIAQFNlcmVuaXR5OlVzZXJzOmtzdG9ja2UxOkRvY3VtZW50czpSZXNlYXJjaDpQYXBlcnM6T2h0YWtpMTk5Ny5wZGYADgAeAA4ATwBoAHQAYQBrAGkAMQA5ADkANwAuAHAAZABmAA8AEgAIAFMAZQByAGUAbgBpAHQAeQASADdVc2Vycy9rc3RvY2tlMS9Eb2N1bWVudHMvUmVzZWFyY2gvUGFwZXJzL09odGFraTE5OTcucGRmAAATAAEvAAAVAAIAD///AACABdIcHR4fWCRjbGFzc2VzWiRjbGFzc25hbWWjHyAhXU5TTXV0YWJsZURhdGFWTlNEYXRhWE5TT2JqZWN0XxArLi4vRG9jdW1lbnRzL1Jlc2VhcmNoL1BhcGVycy9PaHRha2kxOTk3LnBkZtIcHSQloiUhXE5TRGljdGlvbmFyeRIAAYagXxAPTlNLZXllZEFyY2hpdmVyAAgAEQAWAB8AKAAyADUAOgA8AEUASwBSAF0AZQBsAG8AcQBzAHYAeAB6AHwAhgCTAJgAoAI8Aj4CQwJMAlcCWwJpAnACeQKnAqwCrwK8AsEAAAAAAAACAQAAAAAAAAAoAAAAAAAAAAAAAAAAAAAC0w==}} |
670 |
|
671 |
@article{Tanaka1987, |
672 |
Author = {Hideki Tanaka and Iwao Ohmine}, |
673 |
Date-Added = {2010-09-08 16:48:01 -0400}, |
674 |
Date-Modified = {2010-09-08 16:48:01 -0400}, |
675 |
Journal = {J. Chem. Phys.}, |
676 |
Keywords = {water; structure}, |
677 |
Number = {10}, |
678 |
Pages = {6128-6139}, |
679 |
Title = {Large local energy fluctuations in water}, |
680 |
Volume = {87}, |
681 |
Year = {1987}, |
682 |
Bdsk-File-1 = {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}} |
683 |
|
684 |
@article{Kalinichev1999, |
685 |
Abstract = {Monte Carlo computer simulations with the TIP4P intermolecular potential are performed in 9 thermodynamic states of compressed liquid water along the 298 K isotherm. Two distinct pressure ranges are found in the pressure dependence of the O-O near-neighbor distances in qualitative agreement with the X-ray diffraction data. Nevertheless, the experimentally observed minimum in this dependence is not reproduced by the present simulations. The evolution of hydrogen-bonded network in liquid water under gradual compression is quantitatively analyzed using the combined geometric and energetic criterion of hydrogen bonding. Despite some bending and weakening of the existing hydrogen bonds, the average topology of the H-bonded network remains intact, and the average number of hydrogen bonds per a water molecule remains constant ((nrm) = 3.2) over the whole pressure range studied, while the increase in density is mainly achieved by an increased packing efficiency of non-bonded nearest and second nearest neighbors.}, |
686 |
Author = {Kalinichev, A.G. and Gorbaty, Yu.E. and Okhulkov, A.V.}, |
687 |
Date-Added = {2010-09-08 16:48:01 -0400}, |
688 |
Date-Modified = {2010-09-08 16:48:01 -0400}, |
689 |
Journal = {Journal of Molecular Liquids}, |
690 |
Keywords = {water; structure; g(r); pressure; TIP4P}, |
691 |
Pages = {57-72}, |
692 |
Title = {Structure and hydrogen bonding of liquid water at high hydrostatic pressures: Monte Carlo NPT-ensemble simulations up to 10 kbar}, |
693 |
Volume = {82}, |
694 |
Year = {1999}, |
695 |
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696 |
|
697 |
@article{Mishima1998, |
698 |
Author = {Osamu Mishima and H. Eugene Stanley}, |
699 |
Date-Added = {2010-09-08 16:48:01 -0400}, |
700 |
Date-Modified = {2010-09-08 16:48:01 -0400}, |
701 |
Journal = {Nature}, |
702 |
Keywords = {water; structure; liquid-liquid transition}, |
703 |
Month = {March}, |
704 |
Pages = {164-168}, |
705 |
Title = {Decompression-induced melting of ice IV and the liquid-liquid transition in water}, |
706 |
Volume = {392}, |
707 |
Year = {1998}, |
708 |
Bdsk-File-1 = {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}} |
709 |
|
710 |
@article{Jancso1984, |
711 |
Abstract = {Molecular dynamics simulations of liquid water at densities of 0.9718 and 1.346 g/cm3. and at temperatures of 63 and 77'T have been performed employing a modified version of the central-force model of water. The structural changes observed are in reasonably good agreement with recent high-pressure neutron scattering studies. The self-diffusion coefficient has been found to decrease by = 35% on compression. The OH stretching frequency underwent a shift of 10 cm-' in the directionof lower frequencies and was accompanied by an increase in the average O-H bond length.}, |
712 |
Author = {Jancs{\'o}, G. and Bopp, P. and Heinzinger, K.}, |
713 |
Date-Added = {2010-09-08 16:48:01 -0400}, |
714 |
Date-Modified = {2010-09-08 16:48:01 -0400}, |
715 |
Journal = {Chemical Physics}, |
716 |
Keywords = {water; structure; pressure}, |
717 |
Pages = {377-387}, |
718 |
Title = {Molecular dynamics study of high-density liquid water using a modified central-force potential}, |
719 |
Volume = {85}, |
720 |
Year = {1984}, |
721 |
Bdsk-File-1 = {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}} |
722 |
|
723 |
@article{Kumar, |
724 |
Author = {Pradeep Kumar and Sergey V. Buldyrev and H. Eugene Stanley}, |
725 |
Date-Added = {2010-09-08 16:48:01 -0400}, |
726 |
Date-Modified = {2010-09-08 16:48:01 -0400}, |
727 |
Journal = {arXiv:0807.4699v1}, |
728 |
Keywords = {water; structure; q; tetrahedrality}, |
729 |
Title = {Space-Time Correlations in the Orientational Order Parameter and the Orientational Entropy of Water}, |
730 |
Bdsk-File-1 = {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}} |
731 |
|
732 |
@article{Errington2001, |
733 |
Author = {Jeffrey R. Errington and Pablo G. Debenedetti}, |
734 |
Date-Added = {2010-09-08 16:48:01 -0400}, |
735 |
Date-Modified = {2010-09-08 16:48:01 -0400}, |
736 |
Journal = {Nature}, |
737 |
Keywords = {water; structure; q; tetrahedrality}, |
738 |
Month = {January}, |
739 |
Pages = {318-321}, |
740 |
Title = {Relationship between structural order and the anomalies of liquid water}, |
741 |
Volume = {409}, |
742 |
Year = {2001}, |
743 |
Bdsk-File-1 = {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}} |
744 |
|
745 |
@article{cite-key, |
746 |
Date-Added = {2010-08-27 15:57:54 -0400}, |
747 |
Date-Modified = {2010-08-27 15:57:54 -0400}} |
748 |
|
749 |
@article{Glattli2002, |
750 |
Author = {A. Gl{\"a}ttli and X. Daura and W.F. van Gunsteren}, |
751 |
Date-Added = {2010-08-27 15:54:36 -0400}, |
752 |
Date-Modified = {2010-08-27 15:57:25 -0400}, |
753 |
Journal = {J. Chem. Phys.}, |
754 |
Keywords = {isothermal compressibility; SPC/E, atm}, |
755 |
Month = {June}, |
756 |
Number = {22}, |
757 |
Pages = {9811-9828}, |
758 |
Title = {Derivation of an improved single point charge model for liquid water: SPC/A and SPC/L}, |
759 |
Volume = {116}, |
760 |
Year = {2002}} |
761 |
|
762 |
@article{Jeffrey:2006dk, |
763 |
Author = {Jeffrey,D. J. and Onishi,Y.}, |
764 |
Date-Added = {2008-04-30 12:15:31 -0400}, |
765 |
Date-Modified = {2008-04-30 12:15:31 -0400}, |
766 |
Journal = {Journal of Fluid Mechanics Digital Archive}, |
767 |
M3 = {10.1017/S0022112084000355}, |
768 |
Number = {-1}, |
769 |
Pages = {261--290}, |
770 |
Title = {Calculation of the resistance and mobility functions for two unequal rigid spheres in low-Reynolds-number flow}, |
771 |
Ty = {JOUR}, |
772 |
Volume = {139}, |
773 |
Year = {2006}} |
774 |
|
775 |
@article{Goldman:1966ph, |
776 |
Abstract = { Bipolar coordinates are employed to determine the terminal settling motion of two, identical, homogeneous, unconstrained spheres in an unbounded fluid at small Reynolds numbers. Exact numerical values are obtained for the linear and angular velocities of the spheres as a function of their relative separation and of the orientation of their line-of-centers relative to the direction of gravity. Comparison with published experimental data indicates good agreement, especially when wall effects are taken into account.}, |
777 |
Author = {Goldman, A. J. and Cox, R. G. and Brenner, H.}, |
778 |
Date-Added = {2008-04-30 12:12:54 -0400}, |
779 |
Date-Modified = {2008-04-30 12:12:54 -0400}, |
780 |
Journal = {Chemical Engineering Science}, |
781 |
Number = {12}, |
782 |
Pages = {1151--1170}, |
783 |
Title = {The slow motion of two identical arbitrarily oriented spheres through a viscous fluid}, |
784 |
Ty = {JOUR}, |
785 |
Url = {http://www.sciencedirect.com/science/article/B6TFK-44360XJ-D0/1/c14cf5c48fab65f0aaa096e60d15fa87}, |
786 |
Volume = {21}, |
787 |
Year = {1966}, |
788 |
Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B6TFK-44360XJ-D0/1/c14cf5c48fab65f0aaa096e60d15fa87}} |
789 |
|
790 |
@article{Brenner:1972th, |
791 |
Abstract = { A general theory is presented for determining the quasistatic Stokes resistance of a particle or an aggregate of particles of arbitrary shape which move with arbitrary translational and rotational velocities in an infinite viscous fluid subjected to a general linear shear flow in the absence of the particles. It is shown that the hydrodynamic resistance of the particles may be characterized by two intrinsic matrices-the grand resistance matrix and the shear resistance matrix, the elements of each matrix being dependent only upon the instantaneous geometrical configuration of the multiparticle system. Explicit expressions for these matrix elements are given for a single ellipsoidal particle and for two spheres. Analytical, closed-form expressions are given for the case where the spheres are widely spaced compared with their radii. When the separation between the spheres is arbitrary, the matrix elements are only determinate numerically for specified ratios of sphere radii and center-to-center separation distances. These numerical values are derived from available bipolar-coordinate system solutions for two spheres. Besides providing a compact and systematic representation of the intrinsic Stokes resistance of multiparticle systems subjected to shear, which does not depend upon the precise velocities of the particles or on the nature of the shear flow, it is demonstrated (by way of example) that the matrix representation permits an immediate determination of the translational and rotational velocities of the individual particles in a neutrally buoyant multiparticle system.}, |
792 |
Author = {Brenner, Howard and O'Neill, Michael E.}, |
793 |
Date-Added = {2008-04-30 12:12:49 -0400}, |
794 |
Date-Modified = {2008-04-30 12:12:49 -0400}, |
795 |
Journal = {Chemical Engineering Science}, |
796 |
Number = {7}, |
797 |
Pages = {1421--1439}, |
798 |
Title = {On the Stokes resistance of multiparticle systems in a linear shear field}, |
799 |
Ty = {JOUR}, |
800 |
Url = {http://www.sciencedirect.com/science/article/B6TFK-444GW12-16J/1/ba6bda9d1e50c88fea6cd92aac2f6bd7}, |
801 |
Volume = {27}, |
802 |
Year = {1972}, |
803 |
Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B6TFK-444GW12-16J/1/ba6bda9d1e50c88fea6cd92aac2f6bd7}} |
804 |
|
805 |
@article{GarciadelaTorreJjp0647941, |
806 |
Affiliation = {Departamento de Qu{\'\i}mica F{\'\i}sica, Facultad de Qu{\'\i}mica, Universidad de Murcia, 30071 Murcia, Spain}, |
807 |
Author = {{Garc\'{i}a de la Torre}, Jose and del Rio Echenique, G. and Ortega, A.}, |
808 |
Date-Added = {2008-04-30 10:14:50 -0400}, |
809 |
Date-Modified = {2008-04-30 10:14:50 -0400}, |
810 |
Issn = {1520-6106}, |
811 |
Journal = jpcb, |
812 |
Number = {5}, |
813 |
Pages = {955-961}, |
814 |
Title = {Improved Calculation of Rotational Diffusion and Intrinsic Viscosity of Bead Models for Macromolecules and Nanoparticles}, |
815 |
Url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp0647941}, |
816 |
Volume = {111}, |
817 |
Year = {2007}, |
818 |
Bdsk-Url-1 = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp0647941}} |
819 |
|
820 |
@article{Garcia-de-la-Torre:2001wd, |
821 |
Abstract = { The calculation of hydrodynamic and other solution properties of rigid macromolecules, using bead-shell model methodologies, requires the specification of the macromolecular shape in a format that can be interfaced with existing programs for hydrodynamic computations. Here, a procedure is presented for such a structural specification that is applicable to arbitrarily shaped particles. A computer program (), in which the user inserts the code needed to determine the structure, produces an structural file that is interpreted by another program () which is in charge of the computation of properties. As simple and yet illustrative examples we consider two cases: (1) dimeric structures composed of ellipsoidal subunits; and (2) toroidal structures, presenting simple equations that predict the properties of toroids with varying radial ratios.}, |
822 |
Author = {{Garc\'{i}a de la Torre}, Jose}, |
823 |
Date-Added = {2008-04-29 15:11:32 -0400}, |
824 |
Date-Modified = {2008-04-29 15:11:32 -0400}, |
825 |
Journal = {Biophysical Chemistry}, |
826 |
Keywords = {Rigid macromolecules; Hydrodynamic properties; Bead-shell model; Three-dimensional structure}, |
827 |
Number = {3}, |
828 |
Pages = {265--274}, |
829 |
Title = {Building hydrodynamic bead-shell models for rigid bioparticles of arbitrary shape}, |
830 |
Ty = {JOUR}, |
831 |
Url = {http://www.sciencedirect.com/science/article/B6TFB-44XJKW6-8/1/376af59f3b89aecd8486b1c6186b0953}, |
832 |
Volume = {94}, |
833 |
Year = {2001}, |
834 |
Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B6TFB-44XJKW6-8/1/376af59f3b89aecd8486b1c6186b0953}} |
835 |
|
836 |
@article{Peters:1999uq, |
837 |
Abstract = {The Fokker-Planck (FP) equation describing the dynamics of a single Brownian particle near a fixed external surface is derived using the multiple-time-scales perturbation method, previously used by Cukier and Deutch and Nienhuis in the absence of any external surfaces, and Piasecki ei LII. for two Brownian spheres in a hard fluid. The FP equation includes an explicit expression for the (time-independent) particle friction tensor in terms of the force autocorrelation Function and equilibrium average force on the particle by the surrounding fluid and in the presence of a fixed external surface. such as an adsorbate. The scaling and perturbation analysis given here also shows that the Force autocorrelation function must decay rapidly on the zeroth-order time scale tau(0), which physically requires N-Kn much less than 1, where N-Kn is the Knudsen number (ratio of the length scale for fluid intermolecular interactions to the Brownian particle length scale). This restricts the theory given here to liquid systems where N-Kn much less than 1. For a specified particle configuration with respect to the external surface, equilibrium canonical molecular dynamics (MD) calculations are conducted, as shown here, in order to obtain numerical values of the friction tensor from the force autocorrelation expression. Molecular dynamics computations of the friction tensor for a single spherical particle in the absence of a fixed external surface are shown to recover Stokes' law for various types of fluid molecule-particle interaction potentials. Analytical studies of the static force correlation function also demonstrate the remarkable principle of force-time parity whereby the particle friction coefficient is nearly independent of the fluid molecule-particle interaction potential. Molecular dynamics computations of the friction tensor for a single spherical particle near a fixed external spherical surface (adsorbate) demonstrate a breakdown in continuum hydrodynamic results at close particle surface separation distances on the order of several molecular diameters.}, |
838 |
Author = {Peters, MH}, |
839 |
Date-Added = {2008-03-13 16:54:59 -0400}, |
840 |
Date-Modified = {2008-03-13 16:56:54 -0400}, |
841 |
Journal = {Journal of Statistical Physics}, |
842 |
Keywords = {Brownian particle; Fokker Planck equation; adsorption; molecular friction; force autocorrelation function; molecular dynamics}, |
843 |
Pages = {557-586}, |
844 |
Timescited = {0}, |
845 |
Title = {Fokker-Planck equation, molecular friction, and molecular dynamics for Brownian particle transport near external solid surfaces}, |
846 |
Volume = {94}, |
847 |
Year = {1999}} |
848 |
|
849 |
@article{Peters:1999qy, |
850 |
Abstract = {The Fokker-Planck equation and molecular-based grand friction tensor are derived for the problem of rotational and translational motions of a structured Brownian particle, including the presence of a structured wall. Using the method of multiple time scales, it is shown that the time independent, grand friction tensor for the Brownian particle includes, in a general way, terms that account fur the fluid molecular mediated interactions with the wall. The resulting Fokker-Planck equation has important applications in processes involving site-specific adsorption of macromolecules, such as affinity chromotography, biological separations, and numerous cellular processes involving attachment of macromolecules. (C) 1999 American Institute of Physics. [S0021-9606(98)51748-5].}, |
851 |
Author = {Peters, MH}, |
852 |
Date-Added = {2008-03-13 16:54:59 -0400}, |
853 |
Date-Modified = {2008-03-13 16:56:44 -0400}, |
854 |
Journal = jcp, |
855 |
Pages = {528-538}, |
856 |
Timescited = {0}, |
857 |
Title = {Fokker-Planck equation and the grand molecular friction tensor for coupled rotational and translational motions of structured Brownian particles near structured surfaces}, |
858 |
Volume = {110}, |
859 |
Year = {1999}} |
860 |
|
861 |
@article{Peters:2000fk, |
862 |
Abstract = {Beginning with the molecular-based Fokker-Planck equation obtained previously [M. H. Peters, J. Chem. Phys. 110, 528 (1999); J. Stat. Phys. 94, 557 (1999)], the Smoluchowski diffusion equation is derived here to describe the spatial and orientational dynamics of molecularly structured macromolecules near molecularly structured surfaces. The formal scaling and perturbation methods employed allow the establishment of definite limits on the use of the Smoluchowski equation when surfaces are present. It is shown that the Smoluchowski equation reduces to that given previously [D. W. Condiff and J. S. Dahler, J. Chem. Phys. 44, 3988 (1966)] in the absence of external surfaces. A specific example application is given involving a spherical macromolecule with electrostatic charge segments near a planar surface with an arbitrary charge distribution. Finally, we show that the short-time solution to the Smoluchowski equation obtained here yields a Brownian dynamics method consistent with that given previously [E. Dickinson, S. A. Allison, and J. A. McCammon, J. Chem. Soc. Faraday Trans. 2 81, 591 (1985)] for orientable, interacting Brownian particles. This study has applications to problems involving site-specific adsorption of orientable, structured Brownian particles, such as association or adsorption of biological macromolecules to cellular surfaces and enzyme-substrate docking kinetics, to name a few. (C) 2000 American Institute of Physics. [S0021-9606(00)50112-3].}, |
863 |
Author = {Peters, MH}, |
864 |
Date-Added = {2008-03-13 16:54:59 -0400}, |
865 |
Date-Modified = {2008-03-13 16:56:20 -0400}, |
866 |
Journal = jcp, |
867 |
Pages = {5488-5498}, |
868 |
Timescited = {0}, |
869 |
Title = {The Smoluchowski diffusion equation for structured macromolecules near structured surfaces}, |
870 |
Volume = {112}, |
871 |
Year = {2000}} |
872 |
|
873 |
@article{Nienhuis:1970lr, |
874 |
Abstract = { A quantummechanical system consisting of N light bath particles and one heavy Brownian linear rotator is considered. By employing the multiple time scale technique and the Wigner representation of quantummechanics, a Fokker-Planck equation for the motion of the Brownian particle is derived. Some properties of this equation are briefly discussed.}, |
875 |
Author = {Nienhuis, G.}, |
876 |
Date-Added = {2008-03-13 16:53:44 -0400}, |
877 |
Date-Modified = {2008-03-13 16:53:44 -0400}, |
878 |
Journal = {Physica}, |
879 |
Number = {1}, |
880 |
Pages = {26--48}, |
881 |
Title = {On the microscopic theory of Brownian motion with a rotational degree of freedom}, |
882 |
Ty = {JOUR}, |
883 |
Url = {http://www.sciencedirect.com/science/article/B6X42-46D224N-BW/2/0e1b39b5a20e979c5fa5e1f560de6413}, |
884 |
Volume = {49}, |
885 |
Year = {1970}, |
886 |
Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B6X42-46D224N-BW/2/0e1b39b5a20e979c5fa5e1f560de6413}} |
887 |
|
888 |
@article{SunX._jp0762020, |
889 |
Affiliation = {Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556}, |
890 |
Author = {Sun, X. and Gezelter, J.D.}, |
891 |
Date-Added = {2008-02-15 13:48:18 -0500}, |
892 |
Date-Modified = {2008-02-15 13:48:18 -0500}, |
893 |
Issn = {1520-6106}, |
894 |
Journal = jpcb, |
895 |
Number = {7}, |
896 |
Pages = {1968-1975}, |
897 |
Title = {Dipolar Ordering in the Ripple Phases of Molecular-Scale Models of Lipid Membranes}, |
898 |
Url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp0762020}, |
899 |
Volume = {112}, |
900 |
Year = {2008}, |
901 |
Bdsk-Url-1 = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp0762020}} |
902 |
|
903 |
@book{Schlick2002, |
904 |
Address = {Secaucus, NJ, USA}, |
905 |
Author = {Tamar Schlick}, |
906 |
Date-Added = {2008-02-12 16:52:19 -0500}, |
907 |
Date-Modified = {2008-02-12 16:53:15 -0500}, |
908 |
Isbn = {038795404X}, |
909 |
Publisher = {Springer-Verlag New York, Inc.}, |
910 |
Title = {Molecular Modeling and Simulation: An Interdisciplinary Guide}, |
911 |
Year = {2002}} |
912 |
|
913 |
@article{Chun:2000fj, |
914 |
Abstract = {A modeling approach that can significantly speed up the dynamics simulation of large molecular systems is presented herein. A multigranular modeling approach, whereby different parts of the molecule are modeled at different levels of detail, is enabled by substructuring. Substructuring the molecular system is accomplished by collecting groups of atoms into rigid or flexible bodies. Body flexibility is modeled by a truncated set of body-based modes. This approach allows for the elimination of the high-frequency harmonic motion while capturing the low-frequency anharmonic motion of interest. This results in the use of larger integration step sizes, substantially reducing the computational time required for a given dynamic simulation. The method also includes the use of a multiple time scale (MTS) integration scheme. Speed increases of 5- to 30-fold over atomistic simulations have been realized in various applications of the method. (C) 2000 John Wiley \& Sons, Inc.}, |
915 |
Author = {Chun, HM and Padilla, CE and Chin, DN and Watanabe, M and Karlov, VI and Alper, HE and Soosaar, K and Blair, KB and Becker, OM and Caves, LSD and Nagle, R and Haney, DN and Farmer, BL}, |
916 |
Date-Added = {2008-01-22 10:38:33 -0500}, |
917 |
Date-Modified = {2008-01-22 10:38:49 -0500}, |
918 |
Journal = jcc, |
919 |
Keywords = {molecular dynamics; normal modes; anharmonicity; macromolecules; numerical integrators}, |
920 |
Pages = {159--184}, |
921 |
Timescited = 0, |
922 |
Title = {{MBO(N)D:} A multibody method for long-time molecular dynamics simulations}, |
923 |
Volume = 21, |
924 |
Year = 2000} |
925 |
|
926 |
@article{Fogolari:1996lr, |
927 |
Abstract = {In an effort to reduce the number of degrees of freedom necessary to describe a polypeptide chain we analyze the statistical behavior of polypeptide chains when represented as C alpha chains, C alpha chains with C beta atoms attached, and C alpha chains with rotational ellipsoids as models of side chains. A statistical analysis on a restricted data set of 75 unrelated protein structures is performed. The comparison of the database distributions with those obtained by model calculation on very short polypeptide stretches allows the dissection of local versus nonlocal features of the distributions. The database distribution of the bend angles of polypeptide chains of pseudo bonded C alpha atoms spans a restricted range of values and shows a bimodal structure. On the other hand, the torsion angles of the C alpha chain may assume almost all possible values. The distribution is bimodal, but with a much broader probability distribution than for bend angles. The C alpha - C beta vectors may be taken as representative of the orientation of the lateral chain, as the direction of the bond is close to the direction of the vector joining C alpha to the ad hoc defined center of the "steric mass" of the side chain. Interestingly, both the bend angle defined by C alpha i-C alpha i+1-C beta i+1 and the torsional angle offset of the pseudo-dihedral C alpha i-C alpha i+1-C alpha i+2-C beta i+2 with respect to C alpha i-C alpha i+1-C alpha i+2-C alpha i+3 span a limited range of values. The latter results show that it is possible to give a more realistic representation of polypeptide chains without introducing additional degrees of freedom, i.e., by just adding to the C alpha chain a C beta with given side-chain properties. However, a more realistic description of side chains may be attained by modeling side chains as rotational ellipsoids that have roughly the same orientation and steric hindrance. To this end, we define the steric mass of an atom as proportional to its van der Waals volume and we calculate the side-chain inertia ellipsoid assuming that the steric mass of each atom is uniformly distributed within its van der Waals volume. Finally, we define the rotational ellipsoid representing the side chain as the uniform density ellipsoid possessing the same rotationally averaged inertia tensor of the side chain. The statistics of ellipsoid parameters support the possibility of representing a side chain via an ellipsoid, independently of the local conformation. To make this description useful for molecular modeling we describe ellipsoid-ellipsoid interactions via a Lennard-Jones potential that preserves the repulsive core of the interacting ellipsoids and takes into account their mutual orientation. Tests are performed for two different forms of the interaction potential on a set of high-resolution protein structures. Results are encouraging, in view of the drastic simplifications that were introduced.}, |
928 |
Address = {Dipartimento di Scienze e Tecnologie Biomediche, Universita di Udine, Italy.}, |
929 |
Au = {Fogolari, F and Esposito, G and Viglino, P and Cattarinussi, S}, |
930 |
Author = {Fogolari, F and Esposito, G and Viglino, P and Cattarinussi, S}, |
931 |
Da = {19960924}, |
932 |
Date-Added = {2008-01-22 10:19:04 -0500}, |
933 |
Date-Modified = {2008-01-22 10:19:09 -0500}, |
934 |
Dcom = {19960924}, |
935 |
Edat = {1996/03/01}, |
936 |
Issn = {0006-3495 (Print)}, |
937 |
Jid = {0370626}, |
938 |
Journal = {Biophys J}, |
939 |
Jt = {Biophysical journal}, |
940 |
Language = {eng}, |
941 |
Lr = {20071115}, |
942 |
Mh = {Amino Acids/chemistry; Biophysics; Carbon/chemistry; Databases, Factual; Evaluation Studies as Topic; *Models, Molecular; Molecular Structure; Peptides/*chemistry; *Protein Conformation; Software; Thermodynamics}, |
943 |
Mhda = {1996/03/01 00:01}, |
944 |
Number = {3}, |
945 |
Own = {NLM}, |
946 |
Pages = {1183--1197}, |
947 |
Pl = {UNITED STATES}, |
948 |
Pmid = {8785277}, |
949 |
Pst = {ppublish}, |
950 |
Pt = {Journal Article}, |
951 |
Pubm = {Print}, |
952 |
Rn = {0 (Amino Acids); 0 (Peptides); 7440-44-0 (Carbon)}, |
953 |
Sb = {IM}, |
954 |
So = {Biophys J. 1996 Mar;70(3):1183-97.}, |
955 |
Stat = {MEDLINE}, |
956 |
Title = {Modeling of polypeptide chains as C alpha chains, C alpha chains with C beta, and C alpha chains with ellipsoidal lateral chains.}, |
957 |
Volume = {70}, |
958 |
Year = {1996}} |
959 |
|
960 |
@inbook{Ramachandran1996, |
961 |
Address = {Providence, Rhode Island}, |
962 |
Author = {Gomathi Ramachandran and Tamar Schlick}, |
963 |
Chapter = {Beyond optimization: Simulating the dynamics of supercoiled DNA by a macroscopic model}, |
964 |
Date-Added = {2008-01-22 10:03:42 -0500}, |
965 |
Date-Modified = {2008-01-22 10:06:57 -0500}, |
966 |
Editor = {P. M. Pardalos and D. Shalloway and G. Xue}, |
967 |
Pages = {215-231}, |
968 |
Publisher = {American Mathematical Society}, |
969 |
Series = {DIMACS Series in Discrete Mathematics and Theoretical Computer Science}, |
970 |
Title = {Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding}, |
971 |
Volume = {23}, |
972 |
Year = {1996}} |
973 |
|
974 |
@article{FIXMAN:1986lr, |
975 |
Author = {Fixman, M}, |
976 |
Date-Added = {2008-01-22 09:59:29 -0500}, |
977 |
Date-Modified = {2008-01-22 09:59:35 -0500}, |
978 |
Journal = {Macromolecules}, |
979 |
Pages = {1204-1207}, |
980 |
Timescited = {0}, |
981 |
Title = {CONSTRUCTION OF LANGEVIN FORCES IN THE SIMULATION OF HYDRODYNAMIC INTERACTION}, |
982 |
Volume = {19}, |
983 |
Year = {1986}} |
984 |
|
985 |
@article{Berendsen87, |
986 |
Author = {H.~J.~C. Berendsen and J.~R. Grigera and T.~P. Straatsma}, |
987 |
Date-Added = {2008-01-22 09:53:15 -0500}, |
988 |
Date-Modified = {2008-01-22 09:53:15 -0500}, |
989 |
Journal = jpc, |
990 |
Pages = {6269-6271}, |
991 |
Title = {The Missing Term in Effective Pair Potentials}, |
992 |
Volume = 91, |
993 |
Year = 1987} |
994 |
|
995 |
@incollection{Berendsen81, |
996 |
Address = {Dordrecht}, |
997 |
Author = {H.~J.~C. Berendsen and J.~P.~M. Postma and W.~F. {van~Gunsteren} and J. Hermans}, |
998 |
Booktitle = {Intermolecular Forces}, |
999 |
Date-Added = {2008-01-22 09:52:49 -0500}, |
1000 |
Date-Modified = {2008-01-22 09:52:49 -0500}, |
1001 |
Editor = {B. Pullman}, |
1002 |
Pages = {331-342}, |
1003 |
Publisher = {Reidel}, |
1004 |
Title = {Simple Point Charge Water}, |
1005 |
Year = 1981} |
1006 |
|
1007 |
@article{Stillinger74, |
1008 |
Author = {F.~H. Stillinger and A. Rahman}, |
1009 |
Date-Added = {2008-01-22 09:51:43 -0500}, |
1010 |
Date-Modified = {2008-01-22 09:51:43 -0500}, |
1011 |
Journal = jcp, |
1012 |
Number = 4, |
1013 |
Pages = {1545-1557}, |
1014 |
Title = {Improved simulation of liquid water by molecular dynamics}, |
1015 |
Volume = 60, |
1016 |
Year = 1974} |
1017 |
|
1018 |
@article{Torre:1983lr, |
1019 |
Author = {{Garc\'{i}a de la Torre}, Jose and Rodes, Vicente}, |
1020 |
Date-Added = {2008-01-11 16:16:43 -0500}, |
1021 |
Date-Modified = {2008-01-11 16:16:43 -0500}, |
1022 |
Journal = jcp, |
1023 |
Journal1 = {The Journal of Chemical Physics}, |
1024 |
Journal2 = {J. Chem. Phys.}, |
1025 |
Keywords = {polymers; molecular models; hydrodynamics; rotation; interactions; macromolecules}, |
1026 |
Number = 5, |
1027 |
Pages = {2454--2460}, |
1028 |
Publisher = {AIP}, |
1029 |
Title = {Effects from bead size and hydrodynamic interactions on the translational and rotational coefficients of macromolecular bead models}, |
1030 |
Ty = {JOUR}, |
1031 |
Url = {http://link.aip.org/link/?JCP/79/2454/1}, |
1032 |
Volume = 79, |
1033 |
Year = 1983, |
1034 |
Bdsk-Url-1 = {http://link.aip.org/link/?JCP/79/2454/1}} |
1035 |
|
1036 |
@article{PhysRev.119.53, |
1037 |
Author = {Favro, L. Dale}, |
1038 |
Date-Added = {2008-01-09 16:57:02 -0500}, |
1039 |
Date-Modified = {2008-01-09 16:57:02 -0500}, |
1040 |
Doi = {10.1103/PhysRev.119.53}, |
1041 |
Journal = {Phys. Rev.}, |
1042 |
Month = {Jul}, |
1043 |
Number = 1, |
1044 |
Numpages = 9, |
1045 |
Pages = {53--62}, |
1046 |
Publisher = {American Physical Society}, |
1047 |
Title = {Theory of the Rotational Brownian Motion of a Free Rigid Body}, |
1048 |
Volume = 119, |
1049 |
Year = 1960, |
1050 |
Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRev.119.53}} |
1051 |
|
1052 |
@article{hess:209, |
1053 |
Author = {Berk Hess}, |
1054 |
Date-Added = {2008-01-08 16:41:06 -0500}, |
1055 |
Date-Modified = {2008-01-08 16:41:06 -0500}, |
1056 |
Doi = {10.1063/1.1421362}, |
1057 |
Journal = jcp, |
1058 |
Keywords = {viscosity; molecular dynamics method; liquid theory; shear flow}, |
1059 |
Number = 1, |
1060 |
Pages = {209-217}, |
1061 |
Publisher = {AIP}, |
1062 |
Title = {Determining the shear viscosity of model liquids from molecular dynamics simulations}, |
1063 |
Url = {http://link.aip.org/link/?JCP/116/209/1}, |
1064 |
Volume = 116, |
1065 |
Year = 2002, |
1066 |
Bdsk-Url-1 = {http://link.aip.org/link/?JCP/116/209/1}, |
1067 |
Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.1421362}} |
1068 |
|
1069 |
@article{Garcia-de-la-Torre:1997qy, |
1070 |
Abstract = {Single-valued hydrodynamic coefficients of a rigid particle can be calculated from existing theories and computer programs for either bead models or ellipsoids. Starting from these coefficients, we review the procedures for the calculation of complex solution properties depending on rotational diffusion, such as the decays of electric birefringence and fluorescence anisotropy. We also describe the calculation of the scattering from factor of bead models. The hydrodynamic coefficients and solution properties can be combined to give universal, shape-dependent functions, which were initially intended for ellipsoidal particles, and are extended here for the most general case. We have implemented all three developments in a new computer program. SOLPRO, for calculation of SOLution PROperties, which can be linked to existing software for bead models or ellipsoids.}, |
1071 |
Address = {Departamento de Quimica Fisica Universidad de Murcia, Spain. jgt{\char64}fcu,um.es}, |
1072 |
Au = {{Garc\'{i}a de la Torre}, Jose and Carrasco, B and Harding, SE}, |
1073 |
Author = {{Garc\'{i}a de la Torre}, Jose and Carrasco, B and Harding, S E}, |
1074 |
Da = 19970709, |
1075 |
Date-Added = {2008-01-08 15:45:31 -0500}, |
1076 |
Date-Modified = {2008-01-08 15:46:57 -0500}, |
1077 |
Dcom = 19970709, |
1078 |
Edat = {1997/01/01}, |
1079 |
Issn = {0175-7571 (Print)}, |
1080 |
Jid = 8409413, |
1081 |
Journal = {Eur Biophys J}, |
1082 |
Jt = {European biophysics journal : EBJ}, |
1083 |
Keywords = {Birefringence; Fluorescence Polarization; Humans; Immunoglobulin G/chemistry; Models, Structural; *Protein Conformation; Proteins/*chemistry; Scattering, Radiation; *Software; Ultracentrifugation/methods}, |
1084 |
Language = {eng}, |
1085 |
Lr = 20061115, |
1086 |
Mhda = {1997/01/01 00:01}, |
1087 |
Number = {5-6}, |
1088 |
Own = {NLM}, |
1089 |
Pages = {361--372}, |
1090 |
Pl = {GERMANY}, |
1091 |
Pmid = 9213556, |
1092 |
Pst = {ppublish}, |
1093 |
Pt = {Journal Article; Research Support, Non-U.S. Gov't}, |
1094 |
Pubm = {Print}, |
1095 |
Rn = {0 (Immunoglobulin G); 0 (Proteins)}, |
1096 |
Sb = {IM}, |
1097 |
So = {Eur Biophys J. 1997;25(5-6):361-72.}, |
1098 |
Stat = {MEDLINE}, |
1099 |
Title = {SOLPRO: theory and computer program for the prediction of SOLution PROperties of rigid macromolecules and bioparticles.}, |
1100 |
Volume = 25, |
1101 |
Year = 1997} |
1102 |
|
1103 |
@article{Ravichandran:1999fk, |
1104 |
Abstract = {Detailed molecular dynamics simulations of the rotational and the translational motions of Gay-Berne ellipsoids in a sea of Lennard-Jones spheres have been carried out. It is found that while the translational motion of an ellipsoid is isotropic at low density, it becomes increasingly anisotropic with density until the ratio of the parallel to the perpendicular diffusion coefficients becomes nearly equal to the value of the aspect ratio at high density. The latter is in agreement with the prediction of Navier-Stokes hydrodynamics with slip boundary condition. The product of the translational diffusion coefficient and the rotational correlation time also attains a hydrodynamic-like density independent behavior only at high density. The reorientational correlation function becomes nonexponential at high density and low temperature where it also develops a slow decay. The perpendicular component of the velocity time correlation function exhibits a clear double minimum, only at high density, which becomes more pronounced as the aspect ratio is increased. (C) 1999 American Institute of Physics. [S0021-9606(99)51440-2].}, |
1105 |
Author = {Ravichandran, S and Bagchi, B}, |
1106 |
Date-Added = {2008-01-08 15:24:48 -0500}, |
1107 |
Date-Modified = {2008-01-08 15:25:41 -0500}, |
1108 |
Journal = jcp, |
1109 |
Pages = {7505-7511}, |
1110 |
Title = {Anisotropic diffusion of nonspherical molecules in dense liquids: A molecular dynamics simulation of isolated ellipsoids in the sea of spheres}, |
1111 |
Volume = 111, |
1112 |
Year = 1999} |
1113 |
|
1114 |
@article{TANG:1993lr, |
1115 |
Abstract = {Translational friction coefficients of hard prolate ellipsoids (having aspect ratios of 1-10) have been calculated by solving the linearized Navier-Stokes equations of hydrodynamics, using the method of Faxen's theorem. When the stick boundary condition was used, the present results reproduce the famous work of Lamb. The new information derived from this study arises from the analysis of the friction under the influence of the slip hydrodynamic boundary condition. It was found that the slip friction perpendicular to the long axis of the prolate ellipsoid increases monotonically with aspect ratio, whereas the parallel component of the friction decreases monotonically to an apparent limiting value. The ratio f(perpendicular to)/f(parallel to) of friction coefficients perpendicular and parallel to the long axis of the particle, calculated using slip hydrodynamics, scales roughly as the aspect ratio of the ellipsoid, in accord with the findings from an Enskog (uncorrelated binary collision) kinetic theory of hard ellipsoids and from the estimate derived from molecular dynamics. In contrast, f(perpendicular to)/f(parallel to) derived by means of stick hydrodynamics shows a weak dependence on the aspect ratio and disagrees with kinetic theory and molecular dynamics findings.}, |
1116 |
Author = {TANG, SA and EVANS, GT}, |
1117 |
Date-Added = {2008-01-08 15:23:42 -0500}, |
1118 |
Date-Modified = {2008-01-08 15:24:09 -0500}, |
1119 |
Journal = mp, |
1120 |
Pages = {1443-1457}, |
1121 |
Title = {A CRITIQUE OF SLIP AND STICK HYDRODYNAMICS FOR ELLIPSOIDAL BODIES}, |
1122 |
Volume = 80, |
1123 |
Year = 1993} |
1124 |
|
1125 |
@article{Schmidt:2003kx, |
1126 |
Abstract = {Using molecular dynamics computer simulation, we have calculated the velocity autocorrelation function and diffusion constant for a spherical solute in a dense fluid of spherical solvent particles. The size and mass of the solute particle are related in such a way that we can naturally approach the Brownian limit (when the solute becomes much larger and more massive than the solvent particles). We find that as long as the solute radius is interpreted as an effective hydrodynamic radius, the Stokes-Einstein law with slip boundary conditions is satisfied as the Brownian limit is approached (specifically, when the solute is roughly 100 times more massive than the solvent particles). In contrast, the Stokes-Einstein law is not satisfied for a tagged particle of the neat solvent. We also find that in the Brownian limit the amplitude of the long-time tail of the solute's velocity autocorrelation function is in good agreement with theoretical hydrodynamic predictions. When the solvent density is substantially lower than the triple density, the Stokes-Einstein law is no longer satisfied, and the amplitude of the long-time tail is not in good agreement with theoretical predictions, signaling the breakdown of hydrodynamics. (C) 2003 American Institute of Physics.}, |
1127 |
Author = {Schmidt, JR and Skinner, JL}, |
1128 |
Date-Added = {2008-01-08 15:12:53 -0500}, |
1129 |
Date-Modified = {2008-01-08 15:13:21 -0500}, |
1130 |
Doi = {DOI 10.1063/1.1610442}, |
1131 |
Journal = jcp, |
1132 |
Pages = {8062-8068}, |
1133 |
Title = {Hydrodynamic boundary conditions, the Stokes-Einstein law, and long-time tails in the Brownian limit}, |
1134 |
Volume = 119, |
1135 |
Year = 2003, |
1136 |
Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.1610442}} |
1137 |
|
1138 |
@article{Schmidt:2004fj, |
1139 |
Abstract = {Using molecular dynamics computer simulation, we have calculated the velocity autocorrelation function and diffusion constant for a variety of solutes in a dense fluid of spherical solvent particles. We explore the effects of surface roughness of the solute on the resulting hydrodynamic boundary condition as we naturally approach the Brownian limit (when the solute becomes much larger and more massive than the solvent particles). We find that when the solute and solvent interact through a purely repulsive isotropic potential, in the Brownian limit the Stokes-Einstein law is satisfied with slip boundary conditions. However, when surface roughness is introduced through an anisotropic solute-solvent interaction potential, we find that the Stokes-Einstein law is satisfied with stick boundary conditions. In addition, when the attractive strength of a short-range isotropic solute-solvent potential is increased, the solute becomes dressed with solvent particles, making it effectively rough, and so stick boundary conditions are again recovered.}, |
1140 |
Author = {Schmidt, JR and Skinner, JL}, |
1141 |
Date-Added = {2008-01-08 15:12:53 -0500}, |
1142 |
Date-Modified = {2008-01-08 15:13:20 -0500}, |
1143 |
Doi = {DOI 10.1021/jp037185r}, |
1144 |
Journal = jpcb, |
1145 |
Pages = {6767-6771}, |
1146 |
Title = {Brownian motion of a rough sphere and the Stokes-Einstein Law}, |
1147 |
Volume = 108, |
1148 |
Year = 2004, |
1149 |
Bdsk-Url-1 = {http://dx.doi.org/10.1021/jp037185r}} |
1150 |
|
1151 |
@article{Klein01, |
1152 |
Author = {J.~C. Shelley andf M.~Y. Shelley and R.~C. Reeder and S. Bandyopadhyay and M.~L. Klein}, |
1153 |
Date-Added = {2008-01-08 14:58:56 -0500}, |
1154 |
Date-Modified = {2008-01-08 14:58:56 -0500}, |
1155 |
Journal = {J. Phys. Chem. B}, |
1156 |
Pages = {4464-4470}, |
1157 |
Title = {A Coarse Grain Model for Phospholipid Simulations}, |
1158 |
Volume = 105, |
1159 |
Year = 2001} |
1160 |
|
1161 |
@article{Berardi98, |
1162 |
Author = {R. Berardi and C. Fava and C. Zannoni}, |
1163 |
Date-Added = {2008-01-08 14:58:56 -0500}, |
1164 |
Date-Modified = {2008-01-08 14:58:56 -0500}, |
1165 |
Journal = cpl, |
1166 |
Pages = {8-14}, |
1167 |
Title = {A Gay-Berne potential for dissimilar biaxial particles}, |
1168 |
Volume = 297, |
1169 |
Year = 1998} |
1170 |
|
1171 |
@article{Hura00, |
1172 |
Author = {G. Hura and J.~M. Sorenson and R.~M. Glaeser and T. Head-Gordon}, |
1173 |
Date-Added = {2008-01-08 14:58:56 -0500}, |
1174 |
Date-Modified = {2008-01-08 14:58:56 -0500}, |
1175 |
Journal = {J. Chem. Phys.}, |
1176 |
Pages = {9140-9148}, |
1177 |
Title = {A high-quality x-ray scattering experiment on liquid water at ambient conditions}, |
1178 |
Volume = 113, |
1179 |
Year = 2000} |
1180 |
|
1181 |
@article{Peker93, |
1182 |
Author = {A. Peker and W.~L. Johnson}, |
1183 |
Date-Added = {2008-01-08 14:58:56 -0500}, |
1184 |
Date-Modified = {2008-01-08 14:58:56 -0500}, |
1185 |
Journal = {Appl. Phys. Lett.}, |
1186 |
Pages = {2342-2344}, |
1187 |
Title = {A highly processable metallic-glass - $\mbox{Zr}_{41.2}\mbox{Ti}_{13.8}\mbox{Cu}_{12.5}\mbox{Ni}_{10.0}\mbox{Be}_{22.5}$}, |
1188 |
Volume = 63, |
1189 |
Year = 1993} |
1190 |
|
1191 |
@article{Raphael2000, |
1192 |
Author = {Robert M. Raphael and Aleksander S. Popel and William E. Brownell}, |
1193 |
Date-Added = {2008-01-08 14:58:56 -0500}, |
1194 |
Date-Modified = {2008-01-08 14:58:56 -0500}, |
1195 |
Journal = bj, |
1196 |
Pages = {2844-2862}, |
1197 |
Title = {A Membrane Bending Model of Outer Hair Cell Electromotility}, |
1198 |
Volume = 78, |
1199 |
Year = 2000} |
1200 |
|
1201 |
@article{Heimburg00, |
1202 |
Author = {Thomas Heimburg}, |
1203 |
Date-Added = {2008-01-08 14:58:56 -0500}, |
1204 |
Date-Modified = {2008-01-08 14:58:56 -0500}, |
1205 |
Journal = bj, |
1206 |
Pages = {1154-1165}, |
1207 |
Title = {A Model for the Lipid Pretransition: Coupling of Ripple Formation with the Chain-Melting Transition}, |
1208 |
Volume = 78, |
1209 |
Year = 2000} |
1210 |
|
1211 |
@article{Tieleman98, |
1212 |
Author = {D.~P. Tieleman and H.~J.~C. Berendsen}, |
1213 |
Date-Added = {2008-01-08 14:58:56 -0500}, |
1214 |
Date-Modified = {2008-01-08 14:58:56 -0500}, |
1215 |
Journal = {Biophys. J.}, |
1216 |
Pages = {2786-2801}, |
1217 |
Title = {A molecular dynamics study of the pores formed by Escherichia coli OmpF porin in a fully hydrated palmitoyloleoylphosphatidylcholine bilayer}, |
1218 |
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Abstract = {The plasma membrane of cells is an ordered environment, giving rise to anisotropic orientation and restricted motion of molecules and proteins residing in the membrane. At the same time as being an organized matrix of defined structure, the cell membrane is heterogeneous and dynamic. Here we present a method where we use fluorescence imaging of linear dichroism to measure the orientation of molecules relative to the cell membrane. By detecting linear dichroism as well as fluorescence anisotropy, the orientation parameters are separated from dynamic properties such as rotational diffusion and homo energy transfer (energy migration). The sensitivity of the technique is enhanced by using two-photon excitation for higher photo-selection compared to single photon excitation. We show here that we can accurately image lipid organization in whole cell membranes and in delicate structures such as membrane nanotubes connecting two cells. The speed of our wide-field imaging system makes it possible to image changes in orientation and anisotropy occurring on a subsecond timescale. This is demonstrated by time-lapse studies showing that cholesterol depletion rapidly disrupts the orientation of a fluorophore located within the hydrophobic region of the cell membrane but not of a surface bound probe. This is consistent with cholesterol having an important role in stabilizing and ordering the lipid tails within the plasma membrane. }, |
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Abstract = {Quantitative structures of the fully hydrated fluid phases of dimyristoylphosphatidylcholine (DMPC) and dilauroylphosphatidylcholine (DLPC) were obtained at 30{degrees}C. Data for the relative form factors F(qz) for DMPC were obtained using a combination of four methods. 1), Volumetric data provided F(0). 2), Diffuse x-ray scattering from oriented stacks of bilayers provided relative form factors |F(qz)| for high qz, 0.22 < qz < 0.8 A-1. 3), X-ray scattering from extruded unilamellar vesicles with diameter 600 A provided |F(qz)| for low qz, 0.1 < qz < 0.3 A-1. 4), Previous measurements using a liquid crystallographic x-ray method provided |F(2{pi}h/D)| for h = 1 and 2 for a range of nearly fully hydrated D-spacings. The data from method 4 overlap and validate the new unilamellar vesicles data for DMPC, so method 4 is not required for DLPC or future studies. We used hybrid electron density models to obtain structural results from these form factors. Comparison of the model electron density profiles with that of gel phase DMPC provides areas per lipid A, 60.6 {+/-} 0.5 A2 for DMPC and 63.2 {+/-} 0.5 A2 for DLPC. Constraints on the model provided by volume measurements and component volumes obtained from simulations put the electron density profiles {rho}(z) and the corresponding form factors F(qz) on absolute scales. Various thicknesses, such as the hydrophobic thickness and the steric thickness, are obtained and compared to literature values. |
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Ty = {JOUR}, |
4121 |
Url = {http://www.sciencedirect.com/science/article/B6TFK-445H8BM-84/2/b34951283900cdde792ec1309ec51565}, |
4122 |
Volume = 24, |
4123 |
Year = 1969, |
4124 |
Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B6TFK-445H8BM-84/2/b34951283900cdde792ec1309ec51565}} |
4125 |
|
4126 |
@article{Stimson:1926qy, |
4127 |
Author = {Stimson, M and Jeffery, GB}, |
4128 |
Date-Added = {2008-01-08 14:51:23 -0500}, |
4129 |
Date-Modified = {2008-01-08 14:51:35 -0500}, |
4130 |
Journal = {Proceedings of the Royal Society of London Series A-Containing Papers of a Mathematical and Physical Character}, |
4131 |
Pages = {110-116}, |
4132 |
Title = {The motion of two spheres in a viscous fluid}, |
4133 |
Volume = 111, |
4134 |
Year = 1926} |
4135 |
|
4136 |
@article{Orlandi:2006fk, |
4137 |
Abstract = {Liquid crystal phases formed by bent-shaped (or {\tt{}"{}}banana{\tt{}"{}}) molecules are currently of great interest. Here we investigate by Monte Carlo computer simulations the phases formed by rigid banana molecules modeled combining three Gay-Berne sites and containing either one central or two lateral and transversal dipoles. We show that changing the dipole position and orientation has a profound effect on the mesophase stability and molecular organization. In particular, we find a uniaxial nematic phase only for off-center dipolar models and tilted phases only for the one with terminal dipoles.}, |
4138 |
Address = {Dipartimento di Chimica Fisica e Inorganica, and INSTM, Universita di Bologna, Viale Risorgimento 4, 40136 Bologna, Italy.}, |
4139 |
Au = {Orlandi, S and Berardi, R and Steltzer, J and Zannoni, C}, |
4140 |
Author = {Orlandi, Silvia and Berardi, Roberto and Steltzer, Joachim and Zannoni, Claudio}, |
4141 |
Da = 20060407, |
4142 |
Date-Added = {2008-01-08 14:47:56 -0500}, |
4143 |
Date-Modified = {2008-01-08 14:48:06 -0500}, |
4144 |
Dcom = 20070727, |
4145 |
Doi = {10.1063/1.2176622}, |
4146 |
Edat = {2006/04/08 09:00}, |
4147 |
Issn = {0021-9606 (Print)}, |
4148 |
Jid = 0375360, |
4149 |
Journal = {J Chem Phys}, |
4150 |
Jt = {The Journal of chemical physics}, |
4151 |
Language = {eng}, |
4152 |
Mhda = {2006/04/08 09:01}, |
4153 |
Number = 12, |
4154 |
Own = {NLM}, |
4155 |
Pages = 124907, |
4156 |
Pl = {United States}, |
4157 |
Pmid = 16599725, |
4158 |
Pst = {ppublish}, |
4159 |
Pt = {Journal Article}, |
4160 |
Pubm = {Print}, |
4161 |
So = {J Chem Phys. 2006 Mar 28;124(12):124907.}, |
4162 |
Stat = {PubMed-not-MEDLINE}, |
4163 |
Title = {A Monte Carlo study of the mesophases formed by polar bent-shaped molecules.}, |
4164 |
Volume = 124, |
4165 |
Year = 2006, |
4166 |
Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.2176622}} |
4167 |
|
4168 |
@article{sun:031602, |
4169 |
Author = {Xiuquan Sun and J. Daniel Gezelter}, |
4170 |
Date-Added = {2008-01-08 14:42:33 -0500}, |
4171 |
Date-Modified = {2008-01-08 14:42:33 -0500}, |
4172 |
Doi = {10.1103/PhysRevE.75.031602}, |
4173 |
Eid = 031602, |
4174 |
Journal = {Physical Review E (Statistical, Nonlinear, and Soft Matter Physics)}, |
4175 |
Keywords = {lattice theory; membranes}, |
4176 |
Number = 3, |
4177 |
Numpages = 7, |
4178 |
Pages = 031602, |
4179 |
Publisher = {APS}, |
4180 |
Title = {Spontaneous corrugation of dipolar membranes}, |
4181 |
Url = {http://link.aps.org/abstract/PRE/v75/e031602}, |
4182 |
Volume = 75, |
4183 |
Year = 2007, |
4184 |
Bdsk-Url-1 = {http://link.aps.org/abstract/PRE/v75/e031602}, |
4185 |
Bdsk-Url-2 = {http://dx.doi.org/10.1103/PhysRevE.75.031602}} |
4186 |
|
4187 |
@article{Ortega:2007lr, |
4188 |
Abstract = {The equivalent radius for any solution property is the radius of a spherical particle having the same value of solution property as that of the macromolecule under consideration. Equivalent radii for different properties present a dependence on size and shape that are more similar than the values of the properties themselves. Furthermore, the ratios of equivalent radii of two properties depend on the conformation (shape or flexibility), but not on the absolute sizes. We define equivalent radii and their ratios, and describe their evaluation for some common models of rigid and flexible macromolecules. Using radii and ratios, we have devised procedures to fit macromolecular models to experimental properties, allowing the determination of the model parameters. Using these quantities, we can construct target functions for an equilibrated, unbiased optimization. The procedures, which have been implemented in public-domain computer programs, are illustrated for rigid, globular proteins, and the rodlike tobacco mosaic virus, and for semiflexible, wormlike heparin molecules.}, |
4189 |
Address = {Departamento de Quimica Fisica, Facultad de Quimica, Universidad de Murcia, 30071 Murcia, Spain.}, |
4190 |
Au = {Ortega, A and {Garc\'{i}a de la Torre}, Jose}, |
4191 |
Author = {Ortega, A and {Garc\'{i}a de la Torre}, Jose}, |
4192 |
Da = 20070813, |
4193 |
Date-Added = {2008-01-08 14:38:03 -0500}, |
4194 |
Date-Modified = {2008-01-08 14:38:49 -0500}, |
4195 |
Dcom = 20071017, |
4196 |
Dep = 20070724, |
4197 |
Doi = {10.1021/bm700473f}, |
4198 |
Edat = {2007/07/25 09:00}, |
4199 |
Issn = {1525-7797 (Print)}, |
4200 |
Jid = 100892849, |
4201 |
Journal = {Biomacromolecules}, |
4202 |
Jt = {Biomacromolecules}, |
4203 |
Keywords = {Computer Simulation; Heparin/chemistry; Macromolecular Substances/*chemistry; *Models, Chemical; *Models, Molecular; Molecular Conformation; Particle Size; Protein Conformation; Proteins/chemistry; Software; Solutions}, |
4204 |
Language = {eng}, |
4205 |
Mhda = {2007/10/18 09:00}, |
4206 |
Number = 8, |
4207 |
Own = {NLM}, |
4208 |
Pages = {2464--2475}, |
4209 |
Phst = {2007/07/24 {$[$}aheadofprint{$]$}}, |
4210 |
Pl = {United States}, |
4211 |
Pmid = 17645309, |
4212 |
Pst = {ppublish}, |
4213 |
Pt = {Journal Article; Research Support, Non-U.S. Gov't}, |
4214 |
Pubm = {Print-Electronic}, |
4215 |
Rn = {0 (Macromolecular Substances); 0 (Proteins); 0 (Solutions); 9005-49-6 (Heparin)}, |
4216 |
Sb = {IM}, |
4217 |
So = {Biomacromolecules. 2007 Aug;8(8):2464-75. Epub 2007 Jul 24.}, |
4218 |
Stat = {MEDLINE}, |
4219 |
Title = {Equivalent radii and ratios of radii from solution properties as indicators of macromolecular conformation, shape, and flexibility.}, |
4220 |
Volume = 8, |
4221 |
Year = 2007, |
4222 |
Bdsk-Url-1 = {http://dx.doi.org/10.1021/bm700473f}} |
4223 |
|
4224 |
@article{Torre2003, |
4225 |
Abstract = {While the prediction of hydrodynamic properties of rigid particles |
4226 |
is nowadays feasible using simple and efficient computer programs, |
4227 |
the calculation of such properties and, in general, the dynamic |
4228 |
behavior of flexible macromolecules has not reached a similar situation. |
4229 |
Although the theories are available, usually the computational work |
4230 |
is done using solutions specific for each problem. We intend to |
4231 |
develop computer programs that would greatly facilitate the task |
4232 |
of predicting solution behavior of flexible macromolecules. In this |
4233 |
paper, we first present an overview of the two approaches that are |
4234 |
most practical: the Monte Carlo rigid-body treatment, and the Brownian |
4235 |
dynamics simulation technique. The Monte Carlo procedure is based |
4236 |
on the calculation of properties for instantaneous conformations |
4237 |
of the macromolecule that are regarded as if they were instantaneously |
4238 |
rigid. We describe how a Monte Carlo program can be interfaced to |
4239 |
the programs in the HYDRO suite for rigid particles, and provide |
4240 |
an example of such calculation, for a hypothetical particle: a protein |
4241 |
with two domains connected by a flexible linker. We also describe |
4242 |
briefly the essentials of Brownian dynamics, and propose a general |
4243 |
mechanical model that includes several kinds of intramolecular interactions, |
4244 |
such as bending, internal rotation, excluded volume effects, etc. |
4245 |
We provide an example of the application of this methodology to |
4246 |
the dynamics of a semiflexible, wormlike DNA.}, |
4247 |
Annote = {724XK Times Cited:6 Cited References Count:64}, |
4248 |
Author = {{Garc\'{i}a de la Torre}, Jose and H. E. Sanchez and A. Ortega and J. G. Hernandez and M. X. Fernandes and F. G. Diaz and M. C. L. Martinez}, |
4249 |
Issn = {0175-7571}, |
4250 |
Journal = {European Biophysics Journal with Biophysics Letters}, |
4251 |
Month = {Aug}, |
4252 |
Number = 5, |
4253 |
Pages = {477-486}, |
4254 |
Title = {Calculation of the solution properties of flexible macromolecules: methods and applications}, |
4255 |
Uri = {<Go to ISI>://000185513400011}, |
4256 |
Volume = 32, |
4257 |
Year = 2003} |
4258 |
|
4259 |
@article{Alakent2005, |
4260 |
Abstract = {Time series analysis tools are employed on the principal modes obtained |
4261 |
from the C-alpha trajectories from two independent molecular-dynamics |
4262 |
simulations of alpha-amylase inhibitor (tendamistat). Fluctuations |
4263 |
inside an energy minimum (intraminimum motions), transitions between |
4264 |
minima (interminimum motions), and relaxations in different hierarchical |
4265 |
energy levels are investigated and compared with those encountered |
4266 |
in vacuum by using different sampling window sizes and intervals. |
4267 |
The low-frequency low-indexed mode relationship, established in |
4268 |
vacuum, is also encountered in water, which shows the reliability |
4269 |
of the important dynamics information offered by principal components |
4270 |
analysis in water. It has been shown that examining a short data |
4271 |
collection period (100 ps) may result in a high population of overdamped |
4272 |
modes, while some of the low-frequency oscillations (< 10 cm(-1)) |
4273 |
can be captured in water by using a longer data collection period |
4274 |
(1200 ps). Simultaneous analysis of short and long sampling window |
4275 |
sizes gives the following picture of the effect of water on protein |
4276 |
dynamics. Water makes the protein lose its memory: future conformations |
4277 |
are less dependent on previous conformations due to the lowering |
4278 |
of energy barriers in hierarchical levels of the energy landscape. |
4279 |
In short-time dynamics (< 10 ps), damping factors extracted from |
4280 |
time series model parameters are lowered. For tendamistat, the friction |
4281 |
coefficient in the Langevin equation is found to be around 40-60 |
4282 |
cm(-1) for the low-indexed modes, compatible with literature. The |
4283 |
fact that water has increased the friction and that on the other |
4284 |
hand has lubrication effect at first sight contradicts. However, |
4285 |
this comes about because water enhances the transitions between |
4286 |
minima and forces the protein to reduce its already inherent inability |
4287 |
to maintain oscillations observed in vacuum. Some of the frequencies |
4288 |
lower than 10 cm(-1) are found to be overdamped, while those higher |
4289 |
than 20 cm(-1) are slightly increased. As for the long-time dynamics |
4290 |
in water, it is found that random-walk motion is maintained for |
4291 |
approximately 200 ps (about five times of that in vacuum) in the |
4292 |
low-indexed modes, showing the lowering of energy barriers between |
4293 |
the higher-level minima.}, |
4294 |
Annote = {973OH Times Cited:1 Cited References Count:33}, |
4295 |
Author = {B. Alakent and M. C. Camurdan and P. Doruker}, |
4296 |
Issn = {0021-9606}, |
4297 |
Journal = jcp, |
4298 |
Month = {Oct 8}, |
4299 |
Number = 14, |
4300 |
Pages = {-}, |
4301 |
Title = {Hierarchical structure of the energy landscape of proteins revisited by time series analysis. II. Investigation of explicit solvent effects}, |
4302 |
Uri = {<Go to ISI>://000232532000064}, |
4303 |
Volume = 123, |
4304 |
Year = 2005} |
4305 |
|
4306 |
@book{Alexander1987, |
4307 |
Address = {New York}, |
4308 |
Author = {C. Alexander}, |
4309 |
Publisher = {Oxford University Press}, |
4310 |
Title = {A Pattern Language: Towns, Buildings, Construction}, |
4311 |
Year = 1987} |
4312 |
|
4313 |
@book{Allen1987, |
4314 |
Address = {New York}, |
4315 |
Author = {M.~P. Allen and D.~J. Tildesley}, |
4316 |
Publisher = {Oxford University Press}, |
4317 |
Title = {Computer Simulations of Liquids}, |
4318 |
Year = 1987} |
4319 |
|
4320 |
@article{Allison1991, |
4321 |
Abstract = {A Brownian dynamics algorithm is developed to simulate dynamics experiments |
4322 |
of rigid macromolecules. It is applied to polarized dynamic light |
4323 |
scattering from rodlike sturctures and from a model of a DNA fragment |
4324 |
(762 base pairs). A number of rod cases are examined in which the |
4325 |
translational anisotropy is increased form zero to a large value. |
4326 |
Simulated first cumulants as well as amplitudes and lifetimes of |
4327 |
the dynamic form factor are compared with predictions of analytic |
4328 |
theories and found to be in very good agreement with them. For DNA |
4329 |
fragments 762 base pairs in length or longer, translational anisotropy |
4330 |
does not contribute significantly to dynamic light scattering. In |
4331 |
a comparison of rigid and flexible simulations on semistiff models |
4332 |
of this fragment, it is shown directly that flexing contributes |
4333 |
to the faster decay processes probed by light scattering and that |
4334 |
the flexible model studies are in good agreement with experiment.}, |
4335 |
Annote = {Eu814 Times Cited:8 Cited References Count:32}, |
4336 |
Author = {S. A. Allison}, |
4337 |
Issn = {0024-9297}, |
4338 |
Journal = {Macromolecules}, |
4339 |
Month = {Jan 21}, |
4340 |
Number = 2, |
4341 |
Pages = {530-536}, |
4342 |
Title = {A Brownian Dynamics Algorithm for Arbitrary Rigid Bodies - Application to Polarized Dynamic Light-Scattering}, |
4343 |
Uri = {<Go to ISI>://A1991EU81400029}, |
4344 |
Volume = 24, |
4345 |
Year = 1991} |
4346 |
|
4347 |
@article{Andersen1983, |
4348 |
Annote = {Rq238 Times Cited:559 Cited References Count:14}, |
4349 |
Author = {H. C. Andersen}, |
4350 |
Issn = {0021-9991}, |
4351 |
Journal = jcop, |
4352 |
Number = 1, |
4353 |
Pages = {24-34}, |
4354 |
Title = {Rattle - a Velocity Version of the Shake Algorithm for Molecular-Dynamics Calculations}, |
4355 |
Uri = {<Go to ISI>://A1983RQ23800002}, |
4356 |
Volume = 52, |
4357 |
Year = 1983} |
4358 |
|
4359 |
@article{Auerbach2005, |
4360 |
Abstract = {Acetylcholine receptor channels (AChRs) are proteins that switch between |
4361 |
stable #closed# and #open# conformations. In patch clamp recordings, |
4362 |
diliganded AChR gating appears to be a simple, two-state reaction. |
4363 |
However, mutagenesis studies indicate that during gating dozens |
4364 |
of residues across the protein move asynchronously and are organized |
4365 |
into rigid body gating domains (#blocks#). Moreover, there is an |
4366 |
upper limit to the apparent channel opening rate constant. These |
4367 |
observations suggest that the gating reaction has a broad, corrugated |
4368 |
transition state region, with the maximum opening rate reflecting, |
4369 |
in part, the mean first-passage time across this ensemble. Simulations |
4370 |
reveal that a flat, isotropic energy profile for the transition |
4371 |
state can account for many of the essential features of AChR gating. |
4372 |
With this mechanism, concerted, local structural transitions that |
4373 |
occur on the broad transition state ensemble give rise to fractional |
4374 |
measures of reaction progress (Phi values) determined by rate-equilibrium |
4375 |
free energy relationship analysis. The results suggest that the |
4376 |
coarse-grained AChR gating conformational change propagates through |
4377 |
the protein with dynamics that are governed by the Brownian motion |
4378 |
of individual gating blocks.}, |
4379 |
Annote = {895QF Times Cited:9 Cited References Count:33}, |
4380 |
Author = {A. Auerbach}, |
4381 |
Issn = {0027-8424}, |
4382 |
Journal = pnas, |
4383 |
Month = {Feb 1}, |
4384 |
Number = 5, |
4385 |
Pages = {1408-1412}, |
4386 |
Title = {Gating of acetylcholine receptor channels: Brownian motion across a broad transition state}, |
4387 |
Uri = {<Go to ISI>://000226877300030}, |
4388 |
Volume = 102, |
4389 |
Year = 2005} |
4390 |
|
4391 |
@article{Baber1995, |
4392 |
Abstract = {The effect of the general anesthetics halothane, enflurane, and isoflurane |
4393 |
on hydrocarbon chain packing in palmitoyl(d(31))oleoylphosphatidylcholine |
4394 |
membranes in the liquid crystalline phase was investigated using |
4395 |
H-2 NMR. Upon the addition of the anesthetics, the first five methylene |
4396 |
units near the interface generally show a very small increase in |
4397 |
segmental order, while segments deeper within the bilayer show a |
4398 |
small decrease in segmental order. From the H-2 NMR results, the |
4399 |
chain length for the perdeuterated palmitoyl chain in the absence |
4400 |
of anesthetic was found to be 12.35 Angstrom. Upon the addition |
4401 |
of halothane enflurane, or isoflurane, the acyl chain undergoes |
4402 |
slight contractions of 0.11, 0.20, or 0.16 Angstrom, respectively, |
4403 |
at 50 mol % anesthetic. A simple model was used to estimate the |
4404 |
relative amounts of anesthetic located near the interface and deeper |
4405 |
in the bilayer hydrocarbon region, and only a slight preference |
4406 |
for an interfacial location was observed. Intermolecular H-1-H-1 |
4407 |
nuclear Overhauser effects (NOEs) were measured between phospholipid |
4408 |
and halothane protons. These NOEs are consistent with the intramembrane |
4409 |
location of the anesthetics suggested by the H-2 NMR data. In addition, |
4410 |
the NOE data indicate that anesthetics prefer the interfacial and |
4411 |
hydrocarbon regions of the membrane and are not found in high concentrations |
4412 |
in the phospholipid headgroup.}, |
4413 |
Annote = {Qz716 Times Cited:38 Cited References Count:37}, |
4414 |
Author = {J. Baber and J. F. Ellena and D. S. Cafiso}, |
4415 |
Issn = {0006-2960}, |
4416 |
Journal = {Biochemistry}, |
4417 |
Month = {May 16}, |
4418 |
Number = 19, |
4419 |
Pages = {6533-6539}, |
4420 |
Title = {Distribution of General-Anesthetics in Phospholipid-Bilayers Determined Using H-2 Nmr and H-1-H-1 Noe Spectroscopy}, |
4421 |
Uri = {<Go to ISI>://A1995QZ71600035}, |
4422 |
Volume = 34, |
4423 |
Year = 1995} |
4424 |
|
4425 |
@article{Banerjee2004, |
4426 |
Abstract = {Based on a coherent state representation of noise operator and an |
4427 |
ensemble averaging procedure using Wigner canonical thermal distribution |
4428 |
for harmonic oscillators, a generalized quantum Langevin equation |
4429 |
has been recently developed [Phys. Rev. E 65, 021109 (2002); 66, |
4430 |
051106 (2002)] to derive the equations of motion for probability |
4431 |
distribution functions in c-number phase-space. We extend the treatment |
4432 |
to explore several systematic approximation schemes for the solutions |
4433 |
of the Langevin equation for nonlinear potentials for a wide range |
4434 |
of noise correlation, strength and temperature down to the vacuum |
4435 |
limit. The method is exemplified by an analytic application to harmonic |
4436 |
oscillator for arbitrary memory kernel and with the help of a numerical |
4437 |
calculation of barrier crossing, in a cubic potential to demonstrate |
4438 |
the quantum Kramers' turnover and the quantum Arrhenius plot. (C) |
4439 |
2004 American Institute of Physics.}, |
4440 |
Annote = {816YY Times Cited:8 Cited References Count:35}, |
4441 |
Author = {D. Banerjee and B. C. Bag and S. K. Banik and D. S. Ray}, |
4442 |
Issn = {0021-9606}, |
4443 |
Journal = jcp, |
4444 |
Month = {May 15}, |
4445 |
Number = 19, |
4446 |
Pages = {8960-8972}, |
4447 |
Title = {Solution of quantum Langevin equation: Approximations, theoretical and numerical aspects}, |
4448 |
Uri = {<Go to ISI>://000221146400009}, |
4449 |
Volume = 120, |
4450 |
Year = 2004} |
4451 |
|
4452 |
@article{Barojas1973, |
4453 |
Author = {J. Barojas and D. Levesque}, |
4454 |
Journal = {Phys. Rev. A}, |
4455 |
Pages = {1092-1105}, |
4456 |
Title = {Simulation of Diatomic Homonuclear Liquids}, |
4457 |
Volume = 7, |
4458 |
Year = 1973} |
4459 |
|
4460 |
@article{Barth1998, |
4461 |
Abstract = {We present an efficient new method termed LN for propagating biomolecular |
4462 |
dynamics according to the Langevin equation that arose fortuitously |
4463 |
upon analysis of the range of harmonic validity of our normal-mode |
4464 |
scheme LIN. LN combines force linearization with force splitting |
4465 |
techniques and disposes of LIN'S computationally intensive minimization |
4466 |
(anharmonic correction) component. Unlike the competitive multiple-timestepping |
4467 |
(MTS) schemes today-formulated to be symplectic and time-reversible-LN |
4468 |
merges the slow and fast forces via extrapolation rather than impulses; |
4469 |
the Langevin heat bath prevents systematic energy drifts. This combination |
4470 |
succeeds in achieving more significant speedups than these MTS methods |
4471 |
which are Limited by resonance artifacts to an outer timestep less |
4472 |
than some integer multiple of half the period of the fastest motion |
4473 |
(around 4-5 fs for biomolecules). We show that LN achieves very |
4474 |
good agreement with small-timestep solutions of the Langevin equation |
4475 |
in terms of thermodynamics (energy means and variances), geometry, |
4476 |
and dynamics (spectral densities) for two proteins in vacuum and |
4477 |
a large water system. Significantly, the frequency of updating the |
4478 |
slow forces extends to 48 fs or more, resulting in speedup factors |
4479 |
exceeding 10. The implementation of LN in any program that employs |
4480 |
force-splitting computations is straightforward, with only partial |
4481 |
second-derivative information required, as well as sparse Hessian/vector |
4482 |
multiplication routines. The linearization part of LN could even |
4483 |
be replaced by direct evaluation of the fast components. The application |
4484 |
of LN to biomolecular dynamics is well suited for configurational |
4485 |
sampling, thermodynamic, and structural questions. (C) 1998 American |
4486 |
Institute of Physics.}, |
4487 |
Annote = {105HH Times Cited:29 Cited References Count:49}, |
4488 |
Author = {E. Barth and T. Schlick}, |
4489 |
Issn = {0021-9606}, |
4490 |
Journal = jcp, |
4491 |
Month = {Aug 1}, |
4492 |
Number = 5, |
4493 |
Pages = {1617-1632}, |
4494 |
Title = {Overcoming stability limitations in biomolecular dynamics. I. Combining force splitting via extrapolation with Langevin dynamics in LN}, |
4495 |
Uri = {<Go to ISI>://000075066300006}, |
4496 |
Volume = 109, |
4497 |
Year = 1998} |
4498 |
|
4499 |
@article{Batcho2001, |
4500 |
Abstract = {We present an analysis for a simple two-component harmonic oscillator |
4501 |
that compares the use of position-Verlet to velocity-Verlet for |
4502 |
multiple-time step integration. The numerical stability analysis |
4503 |
based on the impulse-Verlet splitting shows that position-Verlet |
4504 |
has enhanced stability, in terms of the largest allowable time step, |
4505 |
for cases where an ample separation of time scales exists. Numerical |
4506 |
investigations confirm the advantages of the position-Verlet scheme |
4507 |
when used for the fastest time scales of the system. Applications |
4508 |
to a biomolecule. a solvated protein, for both Newtonian and Langevin |
4509 |
dynamics echo these trends over large outer time-step regimes. (C) |
4510 |
2001 American Institute of Physics.}, |
4511 |
Annote = {469KV Times Cited:6 Cited References Count:30}, |
4512 |
Author = {P. F. Batcho and T. Schlick}, |
4513 |
Issn = {0021-9606}, |
4514 |
Journal = jcp, |
4515 |
Month = {Sep 1}, |
4516 |
Number = 9, |
4517 |
Pages = {4019-4029}, |
4518 |
Title = {Special stability advantages of position-Verlet over velocity-Verlet in multiple-time step integration}, |
4519 |
Uri = {<Go to ISI>://000170813800005}, |
4520 |
Volume = 115, |
4521 |
Year = 2001} |
4522 |
|
4523 |
@article{Bates2005, |
4524 |
Abstract = {Inspired by recent claims that compounds composed of V-shaped molecules |
4525 |
can exhibit the elusive biaxial nematic phase, we have developed |
4526 |
a generic simulation model for such systems. This contains the features |
4527 |
of the molecule that are essential to its liquid crystal behavior, |
4528 |
namely the anisotropies of the two arms and the angle between them. |
4529 |
The behavior of the model has been investigated using Monte Carlo |
4530 |
simulations for a wide range of these structural parameters. This |
4531 |
allows us to establish the relationship between the V-shaped molecule |
4532 |
and its ability to form a biaxial nematic phase. Of particular importance |
4533 |
are the criteria of geometry and the relative anisotropy necessary |
4534 |
for the system to exhibit a Landau point, at which the biaxial nematic |
4535 |
is formed directly from the isotropic phase. The simulations have |
4536 |
also been used to determine the orientational order parameters for |
4537 |
a selection of molecular axes. These are especially important because |
4538 |
they reveal the phase symmetry and are connected to the experimental |
4539 |
determination of this. The simulation results show that, whereas |
4540 |
some positions are extremely sensitive to the phase biaxiality, |
4541 |
others are totally blind to this.}, |
4542 |
Annote = {Part 1 988LQ Times Cited:0 Cited References Count:38}, |
4543 |
Author = {M. A. Bates and G. R. Luckhurst}, |
4544 |
Issn = {1539-3755}, |
4545 |
Journal = {Physical Review E}, |
4546 |
Month = {Nov}, |
4547 |
Number = 5, |
4548 |
Pages = {-}, |
4549 |
Title = {Biaxial nematic phases and V-shaped molecules: A Monte Carlo simulation study}, |
4550 |
Uri = {<Go to ISI>://000233603100030}, |
4551 |
Volume = 72, |
4552 |
Year = 2005} |
4553 |
|
4554 |
@article{Beard2003, |
4555 |
Abstract = {We introduce an unbiased protocol for performing rotational moves |
4556 |
in rigid-body dynamics simulations. This approach - based on the |
4557 |
analytic solution for the rotational equations of motion for an |
4558 |
orthogonal coordinate system at constant angular velocity - removes |
4559 |
deficiencies that have been largely ignored in Brownian dynamics |
4560 |
simulations, namely errors for finite rotations that result from |
4561 |
applying the noncommuting rotational matrices in an arbitrary order. |
4562 |
Our algorithm should thus replace standard approaches to rotate |
4563 |
local coordinate frames in Langevin and Brownian dynamics simulations.}, |
4564 |
Annote = {736UA Times Cited:0 Cited References Count:11}, |
4565 |
Author = {D. A. Beard and T. Schlick}, |
4566 |
Issn = {0006-3495}, |
4567 |
Journal = bj, |
4568 |
Month = {Nov 1}, |
4569 |
Number = 5, |
4570 |
Pages = {2973-2976}, |
4571 |
Title = {Unbiased rotational moves for rigid-body dynamics}, |
4572 |
Uri = {<Go to ISI>://000186190500018}, |
4573 |
Volume = 85, |
4574 |
Year = 2003} |
4575 |
|
4576 |
@article{Beloborodov1998, |
4577 |
Abstract = {Using the Green function of arbitrary rigid Brownian diffusion (Goldstein, |
4578 |
Biopolymers 33, 409-436, 1993), it was analytically shown that coupling |
4579 |
between translation and rotation diffusion degrees of freedom does |
4580 |
not affect the correlation functions relevant to the NMR intramolecular |
4581 |
relaxation. It follows that spectral densities usually used for |
4582 |
the anisotropic rotation diffusion (Woessner, J. Chem. Phys. 37, |
4583 |
647-654, 1962) can be regarded as exact in respect to the rotation-translation |
4584 |
coupling for the spin system connected with a rigid body. (C) 1998 |
4585 |
Academic Press.}, |
4586 |
Annote = {Zu605 Times Cited:2 Cited References Count:6}, |
4587 |
Author = {I. S. Beloborodov and V. Y. Orekhov and A. S. Arseniev}, |
4588 |
Issn = {1090-7807}, |
4589 |
Journal = {Journal of Magnetic Resonance}, |
4590 |
Month = {Jun}, |
4591 |
Number = 2, |
4592 |
Pages = {328-329}, |
4593 |
Title = {Effect of coupling between rotational and translational Brownian motions on NMR spin relaxation: Consideration using green function of rigid body diffusion}, |
4594 |
Uri = {<Go to ISI>://000074214800017}, |
4595 |
Volume = 132, |
4596 |
Year = 1998} |
4597 |
|
4598 |
@article{Berardi1996, |
4599 |
Abstract = {We demonstrate that the overall molecular dipole organization in a |
4600 |
smectic liquid crystal formed of polar molecules can be strongly |
4601 |
influenced by the position of the dipole in the molecule. We study |
4602 |
by large scale Monte Carlo simulations systems of attractive-repulsive |
4603 |
''Gay-Berne'' elongated ellipsoids with an axial dipole at the center |
4604 |
or near the end of the molecule and we show that monolayer smectic |
4605 |
liquid crystals and modulated antiferroelectric bilayer stripe domains |
4606 |
similar to the experimentally observed ''antiphase'' structures |
4607 |
are obtained in the two cases.}, |
4608 |
Annote = {Vn637 Times Cited:49 Cited References Count:26}, |
4609 |
Author = {R. Berardi and S. Orlandi and C. Zannoni}, |
4610 |
Issn = {0009-2614}, |
4611 |
Journal = {Chemical Physics Letters}, |
4612 |
Month = {Oct 18}, |
4613 |
Number = 3, |
4614 |
Pages = {357-362}, |
4615 |
Title = {Antiphase structures in polar smectic liquid crystals and their molecular origin}, |
4616 |
Uri = {<Go to ISI>://A1996VN63700023}, |
4617 |
Volume = 261, |
4618 |
Year = 1996} |
4619 |
|
4620 |
@article{Berkov2005, |
4621 |
Abstract = {In this paper a detailed numerical study (in frames of the Slonczewski |
4622 |
formalism) of magnetization oscillations driven by a spin-polarized |
4623 |
current through a thin elliptical nanoelement is presented. We show |
4624 |
that a sophisticated micromagnetic model, where a polycrystalline |
4625 |
structure of a nanoelement is taken into account, can explain qualitatively |
4626 |
all most important features of the magnetization oscillation spectra |
4627 |
recently observed experimentally [S. I. Kiselev , Nature 425, 380 |
4628 |
(2003)], namely, existence of several equidistant spectral bands, |
4629 |
sharp onset and abrupt disappearance of magnetization oscillations |
4630 |
with increasing current, absence of the out-of-plane regime predicted |
4631 |
by a macrospin model, and the relation between frequencies of so-called |
4632 |
small-angle and quasichaotic oscillations. However, a quantitative |
4633 |
agreement with experimental results (especially concerning the frequency |
4634 |
of quasichaotic oscillations) could not be achieved in the region |
4635 |
of reasonable parameter values, indicating that further model refinement |
4636 |
is necessary for a complete understanding of the spin-driven magnetization |
4637 |
precession even in this relatively simple experimental situation.}, |
4638 |
Annote = {969IT Times Cited:2 Cited References Count:55}, |
4639 |
Author = {D. V. Berkov and N. L. Gorn}, |
4640 |
Issn = {1098-0121}, |
4641 |
Journal = {Physical Review B}, |
4642 |
Month = {Sep}, |
4643 |
Number = 9, |
4644 |
Pages = {-}, |
4645 |
Title = {Magnetization precession due to a spin-polarized current in a thin nanoelement: Numerical simulation study}, |
4646 |
Uri = {<Go to ISI>://000232228500058}, |
4647 |
Volume = 72, |
4648 |
Year = 2005} |
4649 |
|
4650 |
@article{Berkov2005a, |
4651 |
Abstract = {Numerical simulations of fast remagnetization processes using stochastic |
4652 |
dynamics are widely used to study various magnetic systems. In this |
4653 |
paper, we first address several crucial methodological problems |
4654 |
of such simulations: (i) the influence of finite-element discretization |
4655 |
on simulated dynamics, (ii) choice between Ito and Stratonovich |
4656 |
stochastic calculi by the solution of micromagnetic stochastic equations |
4657 |
of motion and (iii) non-trivial correlation properties of the random |
4658 |
(thermal) field. Next, we discuss several examples to demonstrate |
4659 |
the great potential of the Langevin dynamics for studying fast remagnetization |
4660 |
processes in technically relevant applications: we present numerical |
4661 |
analysis of equilibrium magnon spectra in patterned structures, |
4662 |
study thermal noise effects on the magnetization dynamics of nanoelements |
4663 |
in pulsed fields and show some results for a remagnetization dynamics |
4664 |
induced by a spin-polarized current. (c) 2004 Elsevier B.V. All |
4665 |
rights reserved.}, |
4666 |
Annote = {Part 1 Sp. Iss. SI 922KU Times Cited:2 Cited References Count:25}, |
4667 |
Author = {D. V. Berkov and N. L. Gorn}, |
4668 |
Issn = {0304-8853}, |
4669 |
Journal = {Journal of Magnetism and Magnetic Materials}, |
4670 |
Month = {Apr}, |
4671 |
Pages = {442-448}, |
4672 |
Title = {Stochastic dynamic simulations of fast remagnetization processes: recent advances and applications}, |
4673 |
Uri = {<Go to ISI>://000228837600109}, |
4674 |
Volume = 290, |
4675 |
Year = 2005} |
4676 |
|
4677 |
@article{Berkov2002, |
4678 |
Abstract = {We report on recent progress achieved by the development of numerical |
4679 |
methods based on the stochastic (Langevin) dynamics applied to systems |
4680 |
of interacting magnetic nanoparticles. The method enables direct |
4681 |
simulations of the trajectories of magnetic moments taking into |
4682 |
account (i) all relevant interactions, (ii) precession dynamics, |
4683 |
and (iii) temperature fluctuations included via the random (thermal) |
4684 |
field. We present several novel results obtained using new methods |
4685 |
developed for the solution of the Langevin equations. In particular, |
4686 |
we have investigated magnetic nanodots and disordered granular systems |
4687 |
of single-domain magnetic particles. For the first case we have |
4688 |
calculated the spectrum and the spatial distribution of spin excitations. |
4689 |
For the second system the complex ac susceptibility chi(omega, T) |
4690 |
for various particle concentrations and particle anisotropies were |
4691 |
computed and compared with numerous experimental results.}, |
4692 |
Annote = {526TF Times Cited:4 Cited References Count:37}, |
4693 |
Author = {D. V. Berkov and N. L. Gorn and P. Gornert}, |
4694 |
Issn = {0031-8965}, |
4695 |
Journal = {Physica Status Solidi a-Applied Research}, |
4696 |
Month = {Feb 16}, |
4697 |
Number = 2, |
4698 |
Pages = {409-421}, |
4699 |
Title = {Magnetization dynamics in nanoparticle systems: Numerical simulation using Langevin dynamics}, |
4700 |
Uri = {<Go to ISI>://000174145200026}, |
4701 |
Volume = 189, |
4702 |
Year = 2002} |
4703 |
|
4704 |
@article{Bernal1980, |
4705 |
Author = {J.M. Bernal and {Garc\'{i}a de la Torre}, Jose}, |
4706 |
Journal = {Biopolymers}, |
4707 |
Pages = {751-766}, |
4708 |
Title = {Transport Properties and Hydrodynamic Centers of Rigid Macromolecules with Arbitrary Shape}, |
4709 |
Volume = 19, |
4710 |
Year = 1980} |
4711 |
|
4712 |
@article{Brenner1967, |
4713 |
Author = {H. Brenner}, |
4714 |
Journal = {J. Collid. Int. Sci.}, |
4715 |
Pages = {407-436}, |
4716 |
Title = {Coupling between the Translational and Rotational Brownian Motions of Rigid Particles of Arbitrary shape}, |
4717 |
Volume = 23, |
4718 |
Year = 1967} |
4719 |
|
4720 |
@article{Brooks1983, |
4721 |
Annote = {Qp423 Times Cited:6414 Cited References Count:96}, |
4722 |
Author = {B. R. Brooks and R. E. Bruccoleri and B. D. Olafson and D. J. States and S. Swaminathan and M. Karplus}, |
4723 |
Issn = {0192-8651}, |
4724 |
Journal = jcc, |
4725 |
Number = 2, |
4726 |
Pages = {187-217}, |
4727 |
Title = {Charmm - a Program for Macromolecular Energy, Minimization, and Dynamics Calculations}, |
4728 |
Uri = {<Go to ISI>://A1983QP42300010}, |
4729 |
Volume = 4, |
4730 |
Year = 1983} |
4731 |
|
4732 |
@article{Brunger1984, |
4733 |
Annote = {Sm173 Times Cited:143 Cited References Count:22}, |
4734 |
Author = {A. Brunger and C. L. Brooks and M. Karplus}, |
4735 |
Issn = {0009-2614}, |
4736 |
Journal = {Chemical Physics Letters}, |
4737 |
Number = 5, |
4738 |
Pages = {495-500}, |
4739 |
Title = {Stochastic Boundary-Conditions for Molecular-Dynamics Simulations of St2 Water}, |
4740 |
Uri = {<Go to ISI>://A1984SM17300007}, |
4741 |
Volume = 105, |
4742 |
Year = 1984} |
4743 |
|
4744 |
@article{Budd1999, |
4745 |
Abstract = {This paper examines a synthesis of adaptive mesh methods with the |
4746 |
use of symmetry to study a partial differential equation. In particular, |
4747 |
it considers methods which admit discrete self-similar solutions, |
4748 |
examining the convergence of these to the true self-similar solution |
4749 |
as well as their stability. Special attention is given to the nonlinear |
4750 |
diffusion equation describing flow in a porous medium.}, |
4751 |
Annote = {199EE Times Cited:4 Cited References Count:14}, |
4752 |
Author = {C. J. Budd and G. J. Collins and W. Z. Huang and R. D. Russell}, |
4753 |
Issn = {1364-503X}, |
4754 |
Journal = {Philosophical Transactions of the Royal Society of London Series a-Mathematical Physical and Engineering Sciences}, |
4755 |
Month = {Apr 15}, |
4756 |
Number = 1754, |
4757 |
Pages = {1047-1077}, |
4758 |
Title = {Self-similar numerical solutions of the porous-medium equation using moving mesh methods}, |
4759 |
Uri = {<Go to ISI>://000080466800005}, |
4760 |
Volume = 357, |
4761 |
Year = 1999} |
4762 |
|
4763 |
@article{Camp1999, |
4764 |
Abstract = {Fluids of hard bent-core molecules have been studied using theory |
4765 |
and computer simulation. The molecules are composed of two hard |
4766 |
spherocylinders, with length-to-breadth ratio L/D, joined by their |
4767 |
ends at an angle 180 degrees - gamma. For L/D = 2 and gamma = 0,10,20 |
4768 |
degrees, the simulations show isotropic, nematic, smectic, and solid |
4769 |
phases. For L/D = 2 and gamma = 30 degrees, only isotropic, nematic, |
4770 |
and solid phases are in evidence, which suggests that there is a |
4771 |
nematic-smectic-solid triple point at an angle in the range 20 degrees |
4772 |
< gamma < 30 degrees. In all of the orientationally ordered fluid |
4773 |
phases the order is purely uniaxial. For gamma = 10 degrees and |
4774 |
20 degrees, at the studied densities, the solid is also uniaxially |
4775 |
ordered, whilst for gamma = 30 degrees the solid layers are biaxially |
4776 |
ordered. For L/D = 2 and gamma = 60 degrees and 90 degrees we find |
4777 |
no spontaneous orientational ordering. This is shown to be due to |
4778 |
the interlocking of dimer pairs which precludes alignment. We find |
4779 |
similar results for L/D = 9.5 and gamma = 72 degrees, where an isotropic-biaxial |
4780 |
nematic transition is predicted by Onsager theory. Simulations in |
4781 |
the biaxial nematic phase show it to be at least mechanically stable |
4782 |
with respect to the isotropic phase, however. We have compared the |
4783 |
quasi-exact simulation results in the isotropic phase with the predicted |
4784 |
equations of state from three theories: the virial expansion containing |
4785 |
the second and third virial coefficients; the Parsons-Lee equation |
4786 |
of state; an application of Wertheim's theory of associating fluids |
4787 |
in the limit of infinite attractive association energy. For all |
4788 |
of the molecule elongations and geometries we have simulated, the |
4789 |
Wertheim theory proved to be the most accurate. Interestingly, the |
4790 |
isotropic equation of state is virtually independent of the dimer |
4791 |
bond angle-a feature that is also reflected in the lack of variation |
4792 |
with angle of the calculated second and third virial coefficients. |
4793 |
(C) 1999 American Institute of Physics. [S0021-9606(99)50445-5].}, |
4794 |
Annote = {255TC Times Cited:24 Cited References Count:38}, |
4795 |
Author = {P. J. Camp and M. P. Allen and A. J. Masters}, |
4796 |
Issn = {0021-9606}, |
4797 |
Journal = jcp, |
4798 |
Month = {Dec 1}, |
4799 |
Number = 21, |
4800 |
Pages = {9871-9881}, |
4801 |
Title = {Theory and computer simulation of bent-core molecules}, |
4802 |
Uri = {<Go to ISI>://000083685400056}, |
4803 |
Volume = 111, |
4804 |
Year = 1999} |
4805 |
|
4806 |
@article{Care2005, |
4807 |
Abstract = {A review is presented of molecular and mesoscopic computer simulations |
4808 |
of liquid crystalline systems. Molecular simulation approaches applied |
4809 |
to such systems are described, and the key findings for bulk phase |
4810 |
behaviour are reported. Following this, recently developed lattice |
4811 |
Boltzmann approaches to the mesoscale modelling of nemato-dynanics |
4812 |
are reviewed. This paper concludes with a discussion of possible |
4813 |
areas for future development in this field.}, |
4814 |
Annote = {989TU Times Cited:2 Cited References Count:258}, |
4815 |
Author = {C. M. Care and D. J. Cleaver}, |
4816 |
Issn = {0034-4885}, |
4817 |
Journal = {Reports on Progress in Physics}, |
4818 |
Month = {Nov}, |
4819 |
Number = 11, |
4820 |
Pages = {2665-2700}, |
4821 |
Title = {Computer simulation of liquid crystals}, |
4822 |
Uri = {<Go to ISI>://000233697600004}, |
4823 |
Volume = 68, |
4824 |
Year = 2005} |
4825 |
|
4826 |
@article{Carrasco1999, |
4827 |
Abstract = {The hydrodynamic properties of rigid particles are calculated from |
4828 |
models composed of spherical elements (beads) using theories developed |
4829 |
by Kirkwood, Bloomfield, and their coworkers. Bead models have usually |
4830 |
been built in such a way that the beads fill the volume occupied |
4831 |
by the particles. Sometimes the beads are few and of varying sizes |
4832 |
(bead models in the strict sense), and other times there are many |
4833 |
small beads (filling models). Because hydrodynamic friction takes |
4834 |
place at the molecular surface, another possibility is to use shell |
4835 |
models, as originally proposed by Bloomfield. In this work, we have |
4836 |
developed procedures to build models of the various kinds, and we |
4837 |
describe the theory and methods for calculating their hydrodynamic |
4838 |
properties, including approximate methods that may be needed to |
4839 |
treat models with a very large number of elements. By combining |
4840 |
the various possibilities of model building and hydrodynamic calculation, |
4841 |
several strategies can be designed. We have made a quantitative |
4842 |
comparison of the performance of the various strategies by applying |
4843 |
them to some test cases, for which the properties are known a priori. |
4844 |
We provide guidelines and computational tools for bead modeling.}, |
4845 |
Annote = {200TT Times Cited:46 Cited References Count:57}, |
4846 |
Author = {B. Carrasco and {Garc\'{i}a de la Torre}, Jose}, |
4847 |
Issn = {0006-3495}, |
4848 |
Journal = bj, |
4849 |
Month = {Jun}, |
4850 |
Number = 6, |
4851 |
Pages = {3044-3057}, |
4852 |
Title = {Hydrodynamic properties of rigid particles: Comparison of different modeling and computational procedures}, |
4853 |
Uri = {<Go to ISI>://000080556700016}, |
4854 |
Volume = 76, |
4855 |
Year = 1999} |
4856 |
|
4857 |
@article{Chandra1999, |
4858 |
Abstract = {Dynamical properties of the soft sticky dipole (SSD) model of water |
4859 |
are calculated by means of molecular dynamics simulations. Since |
4860 |
this is not a simple point model, the forces and torques arising |
4861 |
from the SSD potential are derived here. Simulations are carried |
4862 |
out in the microcanonical ensemble employing the Ewald method for |
4863 |
the electrostatic interactions. Various time correlation functions |
4864 |
and dynamical quantities associated with the translational and rotational |
4865 |
motion of water molecules are evaluated and compared with those |
4866 |
of two other commonly used models of liquid water, namely the transferable |
4867 |
intermolecular potential-three points (TIP3P) and simple point charge/extended |
4868 |
(SPC/E) models, and also with experiments. The dynamical properties |
4869 |
of the SSD water model are found to be in good agreement with the |
4870 |
experimental results and appear to be better than the TIP3P and |
4871 |
SPC/E models in most cases, as has been previously shown for its |
4872 |
thermodynamic, structural, and dielectric properties. Also, molecular |
4873 |
dynamics simulations of the SSD model are found to run much faster |
4874 |
than TIP3P, SPC/E, and other multisite models. (C) 1999 American |
4875 |
Institute of Physics. [S0021-9606(99)51430-X].}, |
4876 |
Annote = {221EN Times Cited:14 Cited References Count:66}, |
4877 |
Author = {A. Chandra and T. Ichiye}, |
4878 |
Issn = {0021-9606}, |
4879 |
Journal = jcp, |
4880 |
Month = {Aug 8}, |
4881 |
Number = 6, |
4882 |
Pages = {2701-2709}, |
4883 |
Title = {Dynamical properties of the soft sticky dipole model of water: Molecular dynamics simulations}, |
4884 |
Uri = {<Go to ISI>://000081711200038}, |
4885 |
Volume = 111, |
4886 |
Year = 1999} |
4887 |
|
4888 |
@article{Channell1990, |
4889 |
Annote = {Dk631 Times Cited:152 Cited References Count:34}, |
4890 |
Author = {P. J. Channell and C. Scovel}, |
4891 |
Issn = {0951-7715}, |
4892 |
Journal = {Nonlinearity}, |
4893 |
Month = {may}, |
4894 |
Number = 2, |
4895 |
Pages = {231-259}, |
4896 |
Title = {Symplectic Integration of Hamiltonian-Systems}, |
4897 |
Uri = {<Go to ISI>://A1990DK63100001}, |
4898 |
Volume = 3, |
4899 |
Year = 1990} |
4900 |
|
4901 |
@article{Chen2003, |
4902 |
Abstract = {We investigate the asymptotic behavior of systems of nonlinear differential |
4903 |
equations and introduce a family of mixed methods from combinations |
4904 |
of explicit Runge-Kutta methods. These methods have better stability |
4905 |
behavior than traditional Runge-Kutta methods and generally extend |
4906 |
the range of validity of the calculated solutions. These methods |
4907 |
also give a way of determining if the numerical solutions are real |
4908 |
or spurious. Emphasis is put on examples coming from mathematical |
4909 |
models in ecology. (C) 2002 IMACS. Published by Elsevier Science |
4910 |
B.V. All rights reserved.}, |
4911 |
Annote = {633ZD Times Cited:0 Cited References Count:9}, |
4912 |
Author = {B. Chen and F. Solis}, |
4913 |
Issn = {0168-9274}, |
4914 |
Journal = {Applied Numerical Mathematics}, |
4915 |
Month = {Jan}, |
4916 |
Number = {1-2}, |
4917 |
Pages = {21-30}, |
4918 |
Title = {Explicit mixed finite order Runge-Kutta methods}, |
4919 |
Uri = {<Go to ISI>://000180314200002}, |
4920 |
Volume = 44, |
4921 |
Year = 2003} |
4922 |
|
4923 |
@article{Cheung2004, |
4924 |
Abstract = {Equilibrium molecular dynamics calculations have been performed for |
4925 |
the liquid crystal molecule n-4-(trans-4-n-pentylcyclohexyl)benzonitrile |
4926 |
(PCH5) using a fully atomistic model. Simulation data have been |
4927 |
obtained for a series of temperatures in the nematic phase. The |
4928 |
simulation data have been used to calculate the flexoelectric coefficients |
4929 |
e(s) and e(b) using the linear response formalism of Osipov and |
4930 |
Nemtsov [M. A. Osipov and V. B. Nemtsov, Sov. Phys. Crstallogr. |
4931 |
31, 125 (1986)]. The temperature and order parameter dependence |
4932 |
of e(s) and e(b) are examined, as are separate contributions from |
4933 |
different intermolecular interactions. Values of e(s) and e(b) calculated |
4934 |
from simulation are consistent with those found from experiment. |
4935 |
(C) 2004 American Institute of Physics.}, |
4936 |
Annote = {866UM Times Cited:4 Cited References Count:61}, |
4937 |
Author = {D. L. Cheung and S. J. Clark and M. R. Wilson}, |
4938 |
Issn = {0021-9606}, |
4939 |
Journal = jcp, |
4940 |
Month = {Nov 8}, |
4941 |
Number = 18, |
4942 |
Pages = {9131-9139}, |
4943 |
Title = {Calculation of flexoelectric coefficients for a nematic liquid crystal by atomistic simulation}, |
4944 |
Uri = {<Go to ISI>://000224798900053}, |
4945 |
Volume = 121, |
4946 |
Year = 2004} |
4947 |
|
4948 |
@article{Cheung2002, |
4949 |
Abstract = {Equilibrium molecular dynamics calculations have been performed for |
4950 |
the liquid crystal molecule n-4-(trans-4-npentylcyclohexyl)benzonitrile |
4951 |
(PCH5) using a fully atomistic model. Simulation data has been obtained |
4952 |
for a series of temperatures in the nematic phase. The rotational |
4953 |
viscosity co-efficient gamma(1), has been calculated using the angular |
4954 |
velocity correlation function of the nematic director, n, the mean |
4955 |
squared diffusion of n and statistical mechanical methods based |
4956 |
on the rotational diffusion co-efficient. We find good agreement |
4957 |
between the first two methods and experimental values. (C) 2002 |
4958 |
Published by Elsevier Science B.V.}, |
4959 |
Annote = {547KF Times Cited:8 Cited References Count:31}, |
4960 |
Author = {D. L. Cheung and S. J. Clark and M. R. Wilson}, |
4961 |
Issn = {0009-2614}, |
4962 |
Journal = {Chemical Physics Letters}, |
4963 |
Month = {Apr 15}, |
4964 |
Number = {1-2}, |
4965 |
Pages = {140-146}, |
4966 |
Title = {Calculation of the rotational viscosity of a nematic liquid crystal}, |
4967 |
Uri = {<Go to ISI>://000175331000020}, |
4968 |
Volume = 356, |
4969 |
Year = 2002} |
4970 |
|
4971 |
@article{Chin2004, |
4972 |
Abstract = {Current molecular dynamics simulations of biomolecules using multiple |
4973 |
time steps to update the slowly changing force are hampered by instabilities |
4974 |
beginning at time steps near the half period of the fastest vibrating |
4975 |
mode. These #resonance# instabilities have became a critical barrier |
4976 |
preventing the long time simulation of biomolecular dynamics. Attempts |
4977 |
to tame these instabilities by altering the slowly changing force |
4978 |
and efforts to damp them out by Langevin dynamics do not address |
4979 |
the fundamental cause of these instabilities. In this work, we trace |
4980 |
the instability to the nonanalytic character of the underlying spectrum |
4981 |
and show that a correct splitting of the Hamiltonian, which renders |
4982 |
the spectrum analytic, restores stability. The resulting Hamiltonian |
4983 |
dictates that in addition to updating the momentum due to the slowly |
4984 |
changing force, one must also update the position with a modified |
4985 |
mass. Thus multiple-time stepping must be done dynamically. (C) |
4986 |
2004 American Institute of Physics.}, |
4987 |
Annote = {757TK Times Cited:1 Cited References Count:22}, |
4988 |
Author = {S. A. Chin}, |
4989 |
Issn = {0021-9606}, |
4990 |
Journal = jcp, |
4991 |
Month = {Jan 1}, |
4992 |
Number = 1, |
4993 |
Pages = {8-13}, |
4994 |
Title = {Dynamical multiple-time stepping methods for overcoming resonance instabilities}, |
4995 |
Uri = {<Go to ISI>://000187577400003}, |
4996 |
Volume = 120, |
4997 |
Year = 2004} |
4998 |
|
4999 |
@article{Cook2000, |
5000 |
Abstract = {The Kirkwood correlation factor g(1) determines the preference for |
5001 |
local parallel or antiparallel dipole association in the isotropic |
5002 |
phase. Calamitic mesogens with longitudinal dipole moments and Kirkwood |
5003 |
factors greater than 1 have an enhanced effective dipole moment |
5004 |
along the molecular long axis. This leads to higher values of Delta |
5005 |
epsilon in the nematic phase. This paper describes state-of-the-art |
5006 |
molecular dynamics simulations of two calamitic mesogens 4-(trans-4-n-pentylcyclohexyl)benzonitrile |
5007 |
(PCH5) and 4-(trans-4-n-pentylcyclohexyl) chlorobenzene (PCH5-Cl) |
5008 |
in the isotropic liquid phase using an all-atom force field and |
5009 |
taking long range electrostatics into account using an Ewald summation. |
5010 |
Using this methodology, PCH5 is seen to prefer antiparallel dipole |
5011 |
alignment with a negative g(1) and PCH5-Cl is seen to prefer parallel |
5012 |
dipole alignment with a positive g(1); this is in accordance with |
5013 |
experimental dielectric measurements. Analysis of the molecular |
5014 |
dynamics trajectories allows an assessment of why these molecules |
5015 |
behave differently.}, |
5016 |
Annote = {376BF Times Cited:10 Cited References Count:16}, |
5017 |
Author = {M. J. Cook and M. R. Wilson}, |
5018 |
Issn = {0267-8292}, |
5019 |
Journal = {Liquid Crystals}, |
5020 |
Month = {Dec}, |
5021 |
Number = 12, |
5022 |
Pages = {1573-1583}, |
5023 |
Title = {Simulation studies of dipole correlation in the isotropic liquid phase}, |
5024 |
Uri = {<Go to ISI>://000165437800002}, |
5025 |
Volume = 27, |
5026 |
Year = 2000} |
5027 |
|
5028 |
@article{Cui2003, |
5029 |
Abstract = {All-atom Langevin dynamics simulations have been performed to study |
5030 |
the folding pathways of the 18-residue binding domain fragment E6ap |
5031 |
of the human papillomavirus E6 interacting peptide. Six independent |
5032 |
folding trajectories, with a total duration of nearly 2 mus, all |
5033 |
lead to the same native state in which the E6ap adopts a fluctuating |
5034 |
a-helix structure in the central portion (Ser-4-Leu-13) but with |
5035 |
very flexible N and C termini. Simulations starting from different |
5036 |
core configurations exhibit the E6ap folding dynamics as either |
5037 |
a two- or three-state folder with an intermediate misfolded state. |
5038 |
The essential leucine hydrophobic core (Leu-9, Leu-12, and Leu-13) |
5039 |
is well conserved in the native-state structure but absent in the |
5040 |
intermediate structure, suggesting that the leucine core is not |
5041 |
only essential for the binding activity of E6ap but also important |
5042 |
for the stability of the native structure. The free energy landscape |
5043 |
reveals a significant barrier between the basins separating the |
5044 |
native and misfolded states. We also discuss the various underlying |
5045 |
forces that drive the peptide into its native state.}, |
5046 |
Annote = {689LC Times Cited:3 Cited References Count:48}, |
5047 |
Author = {B. X. Cui and M. Y. Shen and K. F. Freed}, |
5048 |
Issn = {0027-8424}, |
5049 |
Journal = pnas, |
5050 |
Month = {Jun 10}, |
5051 |
Number = 12, |
5052 |
Pages = {7087-7092}, |
5053 |
Title = {Folding and misfolding of the papillomavirus E6 interacting peptide E6ap}, |
5054 |
Uri = {<Go to ISI>://000183493500037}, |
5055 |
Volume = 100, |
5056 |
Year = 2003} |
5057 |
|
5058 |
@article{Denisov2003, |
5059 |
Abstract = {We study the slow phase of thermally activated magnetic relaxation |
5060 |
in finite two-dimensional ensembles of dipolar interacting ferromagnetic |
5061 |
nanoparticles whose easy axes of magnetization are perpendicular |
5062 |
to the distribution plane. We develop a method to numerically simulate |
5063 |
the magnetic relaxation for the case that the smallest heights of |
5064 |
the potential barriers between the equilibrium directions of the |
5065 |
nanoparticle magnetic moments are much larger than the thermal energy. |
5066 |
Within this framework, we analyze in detail the role that the correlations |
5067 |
of the nanoparticle magnetic moments and the finite size of the |
5068 |
nanoparticle ensemble play in magnetic relaxation.}, |
5069 |
Annote = {642XH Times Cited:11 Cited References Count:31}, |
5070 |
Author = {S. I. Denisov and T. V. Lyutyy and K. N. Trohidou}, |
5071 |
Issn = {1098-0121}, |
5072 |
Journal = {Physical Review B}, |
5073 |
Month = {Jan 1}, |
5074 |
Number = 1, |
5075 |
Pages = {-}, |
5076 |
Title = {Magnetic relaxation in finite two-dimensional nanoparticle ensembles}, |
5077 |
Uri = {<Go to ISI>://000180830400056}, |
5078 |
Volume = 67, |
5079 |
Year = 2003} |
5080 |
|
5081 |
@article{Derreumaux1998, |
5082 |
Abstract = {To explore the origin of the large-scale motion of triosephosphate |
5083 |
isomerase's flexible loop (residues 166 to 176) at the active site, |
5084 |
several simulation protocols are employed both for the free enzyme |
5085 |
in vacuo and for the free enzyme with some solvent modeling: high-temperature |
5086 |
Langevin dynamics simulations, sampling by a #dynamics##driver# |
5087 |
approach, and potential-energy surface calculations. Our focus is |
5088 |
on obtaining the energy barrier to the enzyme's motion and establishing |
5089 |
the nature of the loop movement. Previous calculations did not determine |
5090 |
this energy barrier and the effect of solvent on the barrier. High-temperature |
5091 |
molecular dynamics simulations and crystallographic studies have |
5092 |
suggested a rigid-body motion with two hinges located at both ends |
5093 |
of the loop; Brownian dynamics simulations at room temperature pointed |
5094 |
to a very flexible behavior. The present simulations and analyses |
5095 |
reveal that although solute/solvent hydrogen bonds play a crucial |
5096 |
role in lowering the energy along the pathway, there still remains |
5097 |
a high activation barrier, This finding clearly indicates that, |
5098 |
if the loop opens and closes in the absence of a substrate at standard |
5099 |
conditions (e.g., room temperature, appropriate concentration of |
5100 |
isomerase), the time scale for transition is not in the nanosecond |
5101 |
but rather the microsecond range. Our results also indicate that |
5102 |
in the context of spontaneous opening in the free enzyme, the motion |
5103 |
is of rigid-body type and that the specific interaction between |
5104 |
residues Ala(176) and Tyr(208) plays a crucial role in the loop |
5105 |
opening/closing mechanism.}, |
5106 |
Annote = {Zl046 Times Cited:30 Cited References Count:29}, |
5107 |
Author = {P. Derreumaux and T. Schlick}, |
5108 |
Issn = {0006-3495}, |
5109 |
Journal = bj, |
5110 |
Month = {Jan}, |
5111 |
Number = 1, |
5112 |
Pages = {72-81}, |
5113 |
Title = {The loop opening/closing motion of the enzyme triosephosphate isomerase}, |
5114 |
Uri = {<Go to ISI>://000073393400009}, |
5115 |
Volume = 74, |
5116 |
Year = 1998} |
5117 |
|
5118 |
@article{Dullweber1997, |
5119 |
Abstract = {Rigid body molecular models possess symplectic structure and time-reversal |
5120 |
symmetry. Standard numerical integration methods destroy both properties, |
5121 |
introducing nonphysical dynamical behavior such as numerically induced |
5122 |
dissipative states and drift in the energy during long term simulations. |
5123 |
This article describes the construction, implementation, and practical |
5124 |
application of fast explicit symplectic-reversible integrators for |
5125 |
multiple rigid body molecular simulations, These methods use a reduction |
5126 |
to Euler equations for the free rigid body, together with a symplectic |
5127 |
splitting technique. In every time step, the orientational dynamics |
5128 |
of each rigid body is integrated by a sequence of planar rotations. |
5129 |
Besides preserving the symplectic and reversible structures of the |
5130 |
flow, this scheme accurately conserves the total angular momentum |
5131 |
of a system of interacting rigid bodies. Excellent energy conservation |
5132 |
fan be obtained relative to traditional methods, especially in long-time |
5133 |
simulations. The method is implemented in a research code, ORIENT |
5134 |
and compared with a quaternion/extrapolation scheme for the TIP4P |
5135 |
model of water. Our experiments show that the symplectic-reversible |
5136 |
scheme is far superior to the more traditional quaternion method. |
5137 |
(C) 1997 American Institute of Physics.}, |
5138 |
Annote = {Ya587 Times Cited:35 Cited References Count:32}, |
5139 |
Author = {A. Dullweber and B. Leimkuhler and R. McLachlan}, |
5140 |
Issn = {0021-9606}, |
5141 |
Journal = jcp, |
5142 |
Month = {Oct 15}, |
5143 |
Number = 15, |
5144 |
Pages = {5840-5851}, |
5145 |
Title = {Symplectic splitting methods for rigid body molecular dynamics}, |
5146 |
Uri = {<Go to ISI>://A1997YA58700024}, |
5147 |
Volume = 107, |
5148 |
Year = 1997} |
5149 |
|
5150 |
@book{Gamma1994, |
5151 |
Address = {London}, |
5152 |
Author = {E. Gamma, R. Helm, R. Johnson and J. Vlissides}, |
5153 |
Chapter = 7, |
5154 |
Publisher = {Perason Education}, |
5155 |
Title = {Design Patterns: Elements of Reusable Object-Oriented Software}, |
5156 |
Year = 1994} |
5157 |
|
5158 |
@article{Edwards2005, |
5159 |
Abstract = {Using the Langevin dynamics technique, we have carried out simulations |
5160 |
of a single-chain flexible diblock copolymer. The polymer consists |
5161 |
of two blocks of equal length, one very poorly solvated and the |
5162 |
other close to theta-conditions. We study what happens when such |
5163 |
a polymer is stretched, for a range of different stretching speeds, |
5164 |
and correlate our observations with features in the plot of force |
5165 |
vs extension. We find that at slow speeds this force profile does |
5166 |
not increase monotonically, in disagreement with earlier predictions, |
5167 |
and that at high speeds there is a strong dependence on which end |
5168 |
of the polymer is pulled, as well as a high level of hysteresis.}, |
5169 |
Annote = {992EC Times Cited:0 Cited References Count:13}, |
5170 |
Author = {S. A. Edwards and D. R. M. Williams}, |
5171 |
Issn = {0024-9297}, |
5172 |
Journal = {Macromolecules}, |
5173 |
Month = {Dec 13}, |
5174 |
Number = 25, |
5175 |
Pages = {10590-10595}, |
5176 |
Title = {Stretching a single diblock copolymer in a selective solvent: Langevin dynamics simulations}, |
5177 |
Uri = {<Go to ISI>://000233866200035}, |
5178 |
Volume = 38, |
5179 |
Year = 2005} |
5180 |
|
5181 |
@article{Egberts1988, |
5182 |
Annote = {Q0188 Times Cited:219 Cited References Count:43}, |
5183 |
Author = {E. Egberts and H. J. C. Berendsen}, |
5184 |
Issn = {0021-9606}, |
5185 |
Journal = jcp, |
5186 |
Month = {Sep 15}, |
5187 |
Number = 6, |
5188 |
Pages = {3718-3732}, |
5189 |
Title = {Molecular-Dynamics Simulation of a Smectic Liquid-Crystal with Atomic Detail}, |
5190 |
Uri = {<Go to ISI>://A1988Q018800036}, |
5191 |
Volume = 89, |
5192 |
Year = 1988} |
5193 |
|
5194 |
@article{Ermak1978, |
5195 |
Annote = {Fp216 Times Cited:785 Cited References Count:42}, |
5196 |
Author = {D. L. Ermak and J. A. Mccammon}, |
5197 |
Issn = {0021-9606}, |
5198 |
Journal = jcp, |
5199 |
Number = 4, |
5200 |
Pages = {1352-1360}, |
5201 |
Title = {Brownian Dynamics with Hydrodynamic Interactions}, |
5202 |
Uri = {<Go to ISI>://A1978FP21600004}, |
5203 |
Volume = 69, |
5204 |
Year = 1978} |
5205 |
|
5206 |
@article{Evans1977, |
5207 |
Annote = {Ds757 Times Cited:271 Cited References Count:18}, |
5208 |
Author = {D. J. Evans}, |
5209 |
Issn = {0026-8976}, |
5210 |
Journal = mp, |
5211 |
Number = 2, |
5212 |
Pages = {317-325}, |
5213 |
Title = {Representation of Orientation Space}, |
5214 |
Uri = {<Go to ISI>://A1977DS75700002}, |
5215 |
Volume = 34, |
5216 |
Year = 1977} |
5217 |
|
5218 |
@article{Fennell2004, |
5219 |
Abstract = {The density maximum and temperature dependence of the self-diffusion |
5220 |
constant were investigated for the soft sticky dipole (SSD) water |
5221 |
model and two related reparametrizations of this single-point model. |
5222 |
A combination of microcanonical and isobaric-isothermal molecular |
5223 |
dynamics simulations was used to calculate these properties, both |
5224 |
with and without the use of reaction field to handle long-range |
5225 |
electrostatics. The isobaric-isothermal simulations of the melting |
5226 |
of both ice-I-h and ice-I-c showed a density maximum near 260 K. |
5227 |
In most cases, the use of the reaction field resulted in calculated |
5228 |
densities which were significantly lower than experimental densities. |
5229 |
Analysis of self-diffusion constants shows that the original SSD |
5230 |
model captures the transport properties of experimental water very |
5231 |
well in both the normal and supercooled liquid regimes. We also |
5232 |
present our reparametrized versions of SSD for use both with the |
5233 |
reaction field or without any long-range electrostatic corrections. |
5234 |
These are called the SSD/RF and SSD/E models, respectively. These |
5235 |
modified models were shown to maintain or improve upon the experimental |
5236 |
agreement with the structural and transport properties that can |
5237 |
be obtained with either the original SSD or the density-corrected |
5238 |
version of the original model (SSD1). Additionally, a novel low-density |
5239 |
ice structure is presented which appears to be the most stable ice |
5240 |
structure for the entire SSD family. (C) 2004 American Institute |
5241 |
of Physics.}, |
5242 |
Annote = {816YY Times Cited:5 Cited References Count:39}, |
5243 |
Author = {C. J. Fennell and J. D. Gezelter}, |
5244 |
Issn = {0021-9606}, |
5245 |
Journal = jcp, |
5246 |
Month = {May 15}, |
5247 |
Number = 19, |
5248 |
Pages = {9175-9184}, |
5249 |
Title = {On the structural and transport properties of the soft sticky dipole and related single-point water models}, |
5250 |
Uri = {<Go to ISI>://000221146400032}, |
5251 |
Volume = 120, |
5252 |
Year = 2004} |
5253 |
|
5254 |
@article{Fernandes2002, |
5255 |
Abstract = {We have developed a Brownian dynamics simulation algorithm to generate |
5256 |
Brownian trajectories of an isolated, rigid particle of arbitrary |
5257 |
shape in the presence of electric fields or any other external agents. |
5258 |
Starting from the generalized diffusion tensor, which can be calculated |
5259 |
with the existing HYDRO software, the new program BROWNRIG (including |
5260 |
a case-specific subprogram for the external agent) carries out a |
5261 |
simulation that is analyzed later to extract the observable dynamic |
5262 |
properties. We provide a variety of examples of utilization of this |
5263 |
method, which serve as tests of its performance, and also illustrate |
5264 |
its applicability. Examples include free diffusion, transport in |
5265 |
an electric field, and diffusion in a restricting environment.}, |
5266 |
Annote = {633AD Times Cited:2 Cited References Count:43}, |
5267 |
Author = {M. X. Fernandes and {Garc\'{i}a de la Torre}, Jose}, |
5268 |
Issn = {0006-3495}, |
5269 |
Journal = bj, |
5270 |
Month = {Dec}, |
5271 |
Number = 6, |
5272 |
Pages = {3039-3048}, |
5273 |
Title = {Brownian dynamics simulation of rigid particles of arbitrary shape in external fields}, |
5274 |
Uri = {<Go to ISI>://000180256300012}, |
5275 |
Volume = 83, |
5276 |
Year = 2002} |
5277 |
|
5278 |
@book{Frenkel1996, |
5279 |
Address = {New York}, |
5280 |
Author = {D. Frenkel and B. Smit}, |
5281 |
Publisher = {Academic Press}, |
5282 |
Title = {Understanding Molecular Simulation : From Algorithms to Applications}, |
5283 |
Year = 1996} |
5284 |
|
5285 |
@article{Gay1981, |
5286 |
Annote = {Lj347 Times Cited:482 Cited References Count:13}, |
5287 |
Author = {J. G. Gay and B. J. Berne}, |
5288 |
Issn = {0021-9606}, |
5289 |
Journal = jcp, |
5290 |
Number = 6, |
5291 |
Pages = {3316-3319}, |
5292 |
Title = {Modification of the Overlap Potential to Mimic a Linear Site-Site Potential}, |
5293 |
Uri = {<Go to ISI>://A1981LJ34700029}, |
5294 |
Volume = 74, |
5295 |
Year = 1981} |
5296 |
|
5297 |
@article{Gelin1999, |
5298 |
Abstract = {To investigate the influence of inertial effects on the dynamics of |
5299 |
an assembly of beads subjected to rigid constraints and placed in |
5300 |
a buffer medium, a convenient method to introduce suitable generalized |
5301 |
coordinates is presented. Without any restriction on the nature |
5302 |
of the soft forces involved (both stochastic and deterministic), |
5303 |
pertinent Langevin equations are derived. Provided that the Brownian |
5304 |
forces are Gaussian and Markovian, the corresponding Fokker-Planck |
5305 |
equation (FPE) is obtained in the complete phase space of generalized |
5306 |
coordinates and momenta. The correct short time behavior for correlation |
5307 |
functions (CFs) of generalized coordinates is established, and the |
5308 |
diffusion equation with memory (DEM) is deduced from the FPE in |
5309 |
the high friction Limit. The DEM is invoked to perform illustrative |
5310 |
calculations in two dimensions of the orientational CFs for once |
5311 |
broken nonrigid rods immobilized on a surface. These calculations |
5312 |
reveal that the CFs under certain conditions exhibit an oscillatory |
5313 |
behavior, which is irreproducible within the standard diffusion |
5314 |
equation. Several methods are considered for the approximate solution |
5315 |
of the DEM, and their application to three dimensional DEMs is discussed.}, |
5316 |
Annote = {257MM Times Cited:2 Cited References Count:82}, |
5317 |
Author = {M. F. Gelin}, |
5318 |
Issn = {1022-1344}, |
5319 |
Journal = {Macromolecular Theory and Simulations}, |
5320 |
Month = {Nov}, |
5321 |
Number = 6, |
5322 |
Pages = {529-543}, |
5323 |
Title = {Inertial effects in the Brownian dynamics with rigid constraints}, |
5324 |
Uri = {<Go to ISI>://000083785700002}, |
5325 |
Volume = 8, |
5326 |
Year = 1999} |
5327 |
|
5328 |
@article{Goetz1998, |
5329 |
Author = {R. Goetz and R. Lipowsky}, |
5330 |
Journal = jcp, |
5331 |
Number = 17, |
5332 |
Pages = 7397, |
5333 |
Title = {Computer simulations of bilayer membranes: Self-assembly and interfacial tension}, |
5334 |
Volume = 108, |
5335 |
Year = 1998} |
5336 |
|
5337 |
@book{Goldstein2001, |
5338 |
Address = {San Francisco}, |
5339 |
Author = {H. Goldstein and C. Poole and J. Safko}, |
5340 |
Edition = {3rd}, |
5341 |
Publisher = {Addison Wesley}, |
5342 |
Title = {Classical Mechanics}, |
5343 |
Year = 2001} |
5344 |
|
5345 |
@article{Gray2003, |
5346 |
Abstract = {Protein-protein docking algorithms provide a means to elucidate structural |
5347 |
details for presently unknown complexes. Here, we present and evaluate |
5348 |
a new method to predict protein-protein complexes from the coordinates |
5349 |
of the unbound monomer components. The method employs a low-resolution, |
5350 |
rigid-body, Monte Carlo search followed by simultaneous optimization |
5351 |
of backbone displacement and side-chain conformations using Monte |
5352 |
Carlo minimization. Up to 10(5) independent simulations are carried |
5353 |
out, and the resulting #decoys# are ranked using an energy function |
5354 |
dominated by van der Waals interactions, an implicit solvation model, |
5355 |
and an orientation-dependent hydrogen bonding potential. Top-ranking |
5356 |
decoys are clustered to select the final predictions. Small-perturbation |
5357 |
studies reveal the formation of binding funnels in 42 of 54 cases |
5358 |
using coordinates derived from the bound complexes and in 32 of |
5359 |
54 cases using independently determined coordinates of one or both |
5360 |
monomers. Experimental binding affinities correlate with the calculated |
5361 |
score function and explain the predictive success or failure of |
5362 |
many targets. Global searches using one or both unbound components |
5363 |
predict at least 25% of the native residue-residue contacts in 28 |
5364 |
of the 32 cases where binding funnels exist. The results suggest |
5365 |
that the method may soon be useful for generating models of biologically |
5366 |
important complexes from the structures of the isolated components, |
5367 |
but they also highlight the challenges that must be met to achieve |
5368 |
consistent and accurate prediction of protein-protein interactions. |
5369 |
(C) 2003 Elsevier Ltd. All rights reserved.}, |
5370 |
Annote = {704QL Times Cited:48 Cited References Count:60}, |
5371 |
Author = {J. J. Gray and S. Moughon and C. Wang and O. Schueler-Furman and B. Kuhlman and C. A. Rohl and D. Baker}, |
5372 |
Issn = {0022-2836}, |
5373 |
Journal = jmb, |
5374 |
Month = {Aug 1}, |
5375 |
Number = 1, |
5376 |
Pages = {281-299}, |
5377 |
Title = {Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations}, |
5378 |
Uri = {<Go to ISI>://000184351300022}, |
5379 |
Volume = 331, |
5380 |
Year = 2003} |
5381 |
|
5382 |
@article{Greengard1994, |
5383 |
Abstract = {Some of the recently developed fast summation methods that have arisen |
5384 |
in scientific computing are described. These methods require an |
5385 |
amount of work proportional to N or N log N to evaluate all pairwise |
5386 |
interactions in an ensemble of N particles. Traditional methods, |
5387 |
by contrast, require an amount of work proportional to N-2. AS a |
5388 |
result, large-scale simulations can be carried out using only modest |
5389 |
computer resources. In combination with supercomputers, it is possible |
5390 |
to address questions that were previously out of reach. Problems |
5391 |
from diffusion, gravitation, and wave propagation are considered.}, |
5392 |
Annote = {Pb499 Times Cited:99 Cited References Count:44}, |
5393 |
Author = {L. Greengard}, |
5394 |
Issn = {0036-8075}, |
5395 |
Journal = {Science}, |
5396 |
Month = {Aug 12}, |
5397 |
Number = 5174, |
5398 |
Pages = {909-914}, |
5399 |
Title = {Fast Algorithms for Classical Physics}, |
5400 |
Uri = {<Go to ISI>://A1994PB49900031}, |
5401 |
Volume = 265, |
5402 |
Year = 1994} |
5403 |
|
5404 |
@article{Greengard1987, |
5405 |
Annote = {L0498 Times Cited:899 Cited References Count:7}, |
5406 |
Author = {L. Greengard and V. Rokhlin}, |
5407 |
Issn = {0021-9991}, |
5408 |
Journal = jcop, |
5409 |
Month = {Dec}, |
5410 |
Number = 2, |
5411 |
Pages = {325-348}, |
5412 |
Title = {A Fast Algorithm for Particle Simulations}, |
5413 |
Uri = {<Go to ISI>://A1987L049800006}, |
5414 |
Volume = 73, |
5415 |
Year = 1987} |
5416 |
|
5417 |
@article{Hairer1997, |
5418 |
Abstract = {Backward error analysis is a useful tool for the study of numerical |
5419 |
approximations to ordinary differential equations. The numerical |
5420 |
solution is formally interpreted as the exact solution of a perturbed |
5421 |
differential equation, given as a formal and usually divergent series |
5422 |
in powers of the step size. For a rigorous analysis, this series |
5423 |
has to be truncated. In this article we study the influence of this |
5424 |
truncation to the difference between the numerical solution and |
5425 |
the exact solution of the perturbed differential equation. Results |
5426 |
on the long-time behaviour of numerical solutions are obtained in |
5427 |
this way. We present applications to the numerical phase portrait |
5428 |
near hyperbolic equilibrium points, to asymptotically stable periodic |
5429 |
orbits and Hopf bifurcation, and to energy conservation and approximation |
5430 |
of invariant tori in Hamiltonian systems.}, |
5431 |
Annote = {Xj488 Times Cited:50 Cited References Count:19}, |
5432 |
Author = {E. Hairer and C. Lubich}, |
5433 |
Issn = {0029-599X}, |
5434 |
Journal = {Numerische Mathematik}, |
5435 |
Month = {Jun}, |
5436 |
Number = 4, |
5437 |
Pages = {441-462}, |
5438 |
Title = {The life-span of backward error analysis for numerical integrators}, |
5439 |
Uri = {<Go to ISI>://A1997XJ48800002}, |
5440 |
Volume = 76, |
5441 |
Year = 1997} |
5442 |
|
5443 |
@article{Hao1993, |
5444 |
Abstract = {A new procedure for studying the folding and unfolding of proteins, |
5445 |
with an application to bovine pancreatic trypsin inhibitor (BPTI), |
5446 |
is reported. The unfolding and refolding of the native structure |
5447 |
of the protein are characterized by the dimensions of the protein, |
5448 |
expressed in terms of the three principal radii of the structure |
5449 |
considered as an ellipsoid. A dynamic equation, describing the variations |
5450 |
of the principal radii on the unfolding path, and a numerical procedure |
5451 |
to solve this equation are proposed. Expanded and distorted conformations |
5452 |
are refolded to the native structure by a dimensional-constraint |
5453 |
energy minimization procedure. A unique and reproducible unfolding |
5454 |
pathway for an intermediate of BPTI lacking the [30,51] disulfide |
5455 |
bond is obtained. The resulting unfolded conformations are extended; |
5456 |
they contain near-native local structure, but their longest principal |
5457 |
radii are more than 2.5 times greater than that of the native structure. |
5458 |
The most interesting finding is that the majority of expanded conformations, |
5459 |
generated under various conditions, can be refolded closely to the |
5460 |
native structure, as measured by the correct overall chain fold, |
5461 |
by the rms deviations from the native structure of only 1.9-3.1 |
5462 |
angstrom, and by the energy differences of about 10 kcal/mol from |
5463 |
the native structure. Introduction of the [30,51] disulfide bond |
5464 |
at this stage, followed by minimization, improves the closeness |
5465 |
of the refolded structures to the native structure, reducing the |
5466 |
rms deviations to 0.9-2.0 angstrom. The unique refolding of these |
5467 |
expanded structures over such a large conformational space implies |
5468 |
that the folding is strongly dictated by the interactions in the |
5469 |
amino acid sequence of BPTI. The simulations indicate that, under |
5470 |
conditions that favor a compact structure as mimicked by the volume |
5471 |
constraints in our algorithm; the expanded conformations have a |
5472 |
strong tendency to move toward the native structure; therefore, |
5473 |
they probably would be favorable folding intermediates. The results |
5474 |
presented here support a general model for protein folding, i.e., |
5475 |
progressive formation of partially folded structural units, followed |
5476 |
by collapse to the compact native structure. The general applicability |
5477 |
of the procedure is also discussed.}, |
5478 |
Annote = {Ly294 Times Cited:27 Cited References Count:57}, |
5479 |
Author = {M. H. Hao and M. R. Pincus and S. Rackovsky and H. A. Scheraga}, |
5480 |
Issn = {0006-2960}, |
5481 |
Journal = {Biochemistry}, |
5482 |
Month = {Sep 21}, |
5483 |
Number = 37, |
5484 |
Pages = {9614-9631}, |
5485 |
Title = {Unfolding and Refolding of the Native Structure of Bovine Pancreatic Trypsin-Inhibitor Studied by Computer-Simulations}, |
5486 |
Uri = {<Go to ISI>://A1993LY29400014}, |
5487 |
Volume = 32, |
5488 |
Year = 1993} |
5489 |
|
5490 |
@article{Hinsen2000, |
5491 |
Abstract = {The slow dynamics of proteins around its native folded state is usually |
5492 |
described by diffusion in a strongly anharmonic potential. In this |
5493 |
paper, we try to understand the form and origin of the anharmonicities, |
5494 |
with the principal aim of gaining a better understanding of the |
5495 |
principal motion types, but also in order to develop more efficient |
5496 |
numerical methods for simulating neutron scattering spectra of large |
5497 |
proteins. First, we decompose a molecular dynamics (MD) trajectory |
5498 |
of 1.5 ns for a C-phycocyanin dimer surrounded by a layer of water |
5499 |
into three contributions that we expect to be independent: the global |
5500 |
motion of the residues, the rigid-body motion of the sidechains |
5501 |
relative to the backbone, and the internal deformations of the sidechains. |
5502 |
We show that they are indeed almost independent by verifying the |
5503 |
factorization of the incoherent intermediate scattering function. |
5504 |
Then, we show that the global residue motions, which include all |
5505 |
large-scale backbone motions, can be reproduced by a simple harmonic |
5506 |
model which contains two contributions: a short-time vibrational |
5507 |
term, described by a standard normal mode calculation in a local |
5508 |
minimum, and a long-time diffusive term, described by Brownian motion |
5509 |
in an effective harmonic potential. The potential and the friction |
5510 |
constants were fitted to the MD data. The major anharmonic contribution |
5511 |
to the incoherent intermediate scattering function comes from the |
5512 |
rigid-body diffusion of the sidechains. This model can be used to |
5513 |
calculate scattering functions for large proteins and for long-time |
5514 |
scales very efficiently, and thus provides a useful complement to |
5515 |
MD simulations, which are best suited for detailed studies on smaller |
5516 |
systems or for shorter time scales. (C) 2000 Elsevier Science B.V. |
5517 |
All rights reserved.}, |
5518 |
Annote = {Sp. Iss. SI 368MT Times Cited:16 Cited References Count:31}, |
5519 |
Author = {K. Hinsen and A. J. Petrescu and S. Dellerue and M. C. Bellissent-Funel and G. R. Kneller}, |
5520 |
Issn = {0301-0104}, |
5521 |
Journal = {Chemical Physics}, |
5522 |
Month = {Nov 1}, |
5523 |
Number = {1-2}, |
5524 |
Pages = {25-37}, |
5525 |
Title = {Harmonicity in slow protein dynamics}, |
5526 |
Uri = {<Go to ISI>://000090121700003}, |
5527 |
Volume = 261, |
5528 |
Year = 2000} |
5529 |
|
5530 |
@article{Ho1992, |
5531 |
Abstract = {Evidence has been found for the existence water at the protein-lipid |
5532 |
hydrophobic interface ot the membrane proteins, gramicidin and apocytochrome |
5533 |
C, using two related fluorescence spectroscopic approaches. The |
5534 |
first approach exploited the fact that the presence of water in |
5535 |
the excited state solvent cage of a fluorophore increases the rate |
5536 |
of decay. For 1,6-diphenyl-1,3,5-hexatriene (DPH) and 1-palmitoyl-2-[[2-[4-(6-phenyl-trans-1,3,5-hexatrienyl) |
5537 |
phenyl]ethyl]carbonyl]-3-sn-PC (DPH-PC), where the fluorophores |
5538 |
are located in the hydrophobic core of the lipid bilayer, the introduction |
5539 |
of gramicidin reduced the fluorescence lifetime, indicative of an |
5540 |
increased presence of water in the bilayer. Since a high protein:lipid |
5541 |
ratio was used, the fluorophores were forced to be adjacent to the |
5542 |
protein hydrophobic surface, hence the presence of water in this |
5543 |
region could be inferred. Cholesterol is known to reduce the water |
5544 |
content of lipid bilayers and this effect was maintained at the |
5545 |
protein-lipid interface with both gramicidin and apocytochrome C, |
5546 |
again suggesting hydration in this region. The second approach was |
5547 |
to use the fluorescence enhancement induced by exchanging deuterium |
5548 |
oxide (D2O) for H2O. Both the fluorescence intensities of trimethylammonium-DPH, |
5549 |
located in the lipid head group region, and of the gramicidin intrinsic |
5550 |
tryptophans were greater in a D2O buffer compared with H2O, showing |
5551 |
that the fluorophores were exposed to water in the bilayer at the |
5552 |
protein-lipid interface. In the presence of cholesterol the fluorescence |
5553 |
intensity ratio of D2O to H2O decreased, indicating a removal of |
5554 |
water by the cholesterol, in keeping with the lifetime data. Altered |
5555 |
hydration at the protein-lipid interface could affect conformation, |
5556 |
thereby offering a new route by which membrane protein functioning |
5557 |
may be modified.}, |
5558 |
Annote = {Ju251 Times Cited:55 Cited References Count:44}, |
5559 |
Author = {C. Ho and C. D. Stubbs}, |
5560 |
Issn = {0006-3495}, |
5561 |
Journal = bj, |
5562 |
Month = {Oct}, |
5563 |
Number = 4, |
5564 |
Pages = {897-902}, |
5565 |
Title = {Hydration at the Membrane Protein-Lipid Interface}, |
5566 |
Uri = {<Go to ISI>://A1992JU25100002}, |
5567 |
Volume = 63, |
5568 |
Year = 1992} |
5569 |
|
5570 |
@book{Hockney1981, |
5571 |
Address = {New York}, |
5572 |
Author = {R.W. Hockney and J.W. Eastwood}, |
5573 |
Publisher = {McGraw-Hill}, |
5574 |
Title = {Computer Simulation Using Particles}, |
5575 |
Year = 1981} |
5576 |
|
5577 |
@article{Hoover1985, |
5578 |
Annote = {Acr30 Times Cited:1809 Cited References Count:11}, |
5579 |
Author = {W. G. Hoover}, |
5580 |
Issn = {1050-2947}, |
5581 |
Journal = {Physical Review A}, |
5582 |
Number = 3, |
5583 |
Pages = {1695-1697}, |
5584 |
Title = {Canonical Dynamics - Equilibrium Phase-Space Distributions}, |
5585 |
Uri = {<Go to ISI>://A1985ACR3000056}, |
5586 |
Volume = 31, |
5587 |
Year = 1985} |
5588 |
|
5589 |
@article{Huh2004, |
5590 |
Abstract = {Racemic fluids of chiral calamitic molecules are investigated with |
5591 |
molecular dynamics simulations. In particular, the phase behavior |
5592 |
as a function of density is examined for eight racemates. The relationship |
5593 |
between chiral discrimination and orientational order in the phase |
5594 |
is explored. We find that the transition from the isotropic phase |
5595 |
to a liquid crystal phase is accompanied by an increase in chiral |
5596 |
discrimination, as measured by differences in radial distributions. |
5597 |
Among ordered phases, discrimination is largest for smectic phases |
5598 |
with a significant preference for heterochiral contact within the |
5599 |
layers. (C) 2004 American Institute of Physics.}, |
5600 |
Annote = {870FJ Times Cited:0 Cited References Count:63}, |
5601 |
Author = {Y. Huh and N. M. Cann}, |
5602 |
Issn = {0021-9606}, |
5603 |
Journal = jcp, |
5604 |
Month = {Nov 22}, |
5605 |
Number = 20, |
5606 |
Pages = {10299-10308}, |
5607 |
Title = {Discrimination in isotropic, nematic, and smectic phases of chiral calamitic molecules: A computer simulation study}, |
5608 |
Uri = {<Go to ISI>://000225042700059}, |
5609 |
Volume = 121, |
5610 |
Year = 2004} |
5611 |
|
5612 |
@article{Humphrey1996, |
5613 |
Abstract = {VMD is a molecular graphics program designed for the display and analysis |
5614 |
of molecular assemblies, in particular biopolymers such as proteins |
5615 |
and nucleic acids. VMD can simultaneously display any number of |
5616 |
structures using a wide variety of rendering styles and coloring |
5617 |
methods. Molecules are displayed as one or more ''representations,'' |
5618 |
in which each representation embodies a particular rendering method |
5619 |
and coloring scheme for a selected subset of atoms. The atoms displayed |
5620 |
in each representation are chosen using an extensive atom selection |
5621 |
syntax, which includes Boolean operators and regular expressions. |
5622 |
VMD provides a complete graphical user interface for program control, |
5623 |
as well as a text interface using the Tcl embeddable parser to allow |
5624 |
for complex scripts with variable substitution, control loops, and |
5625 |
function calls. Full session logging is supported, which produces |
5626 |
a VMD command script for later playback. High-resolution raster |
5627 |
images of displayed molecules may be produced by generating input |
5628 |
scripts for use by a number of photorealistic image-rendering applications. |
5629 |
VMD has also been expressly designed with the ability to animate |
5630 |
molecular dynamics (MD) simulation trajectories, imported either |
5631 |
from files or from a direct connection to a running MD simulation. |
5632 |
VMD is the visualization component of MDScope, a set of tools for |
5633 |
interactive problem solving in structural biology, which also includes |
5634 |
the parallel MD program NAMD, and the MDCOMM software used to connect |
5635 |
the visualization and simulation programs. VMD is written in C++, |
5636 |
using an object-oriented design; the program, including source code |
5637 |
and extensive documentation, is freely available via anonymous ftp |
5638 |
and through the World Wide Web.}, |
5639 |
Annote = {Uh515 Times Cited:1418 Cited References Count:19}, |
5640 |
Author = {W. Humphrey and A. Dalke and K. Schulten}, |
5641 |
Issn = {0263-7855}, |
5642 |
Journal = {Journal of Molecular Graphics}, |
5643 |
Month = {Feb}, |
5644 |
Number = 1, |
5645 |
Pages = {33-\&}, |
5646 |
Title = {VMD: Visual molecular dynamics}, |
5647 |
Uri = {<Go to ISI>://A1996UH51500005}, |
5648 |
Volume = 14, |
5649 |
Year = 1996} |
5650 |
|
5651 |
@article{Izaguirre2001, |
5652 |
Abstract = {In this paper we show the possibility of using very mild stochastic |
5653 |
damping to stabilize long time step integrators for Newtonian molecular |
5654 |
dynamics. More specifically, stable and accurate integrations are |
5655 |
obtained for damping coefficients that are only a few percent of |
5656 |
the natural decay rate of processes of interest, such as the velocity |
5657 |
autocorrelation function. Two new multiple time stepping integrators, |
5658 |
Langevin Molly (LM) and Brunger-Brooks-Karplus-Molly (BBK-M), are |
5659 |
introduced in this paper. Both use the mollified impulse method |
5660 |
for the Newtonian term. LM uses a discretization of the Langevin |
5661 |
equation that is exact for the constant force, and BBK-M uses the |
5662 |
popular Brunger-Brooks-Karplus integrator (BBK). These integrators, |
5663 |
along with an extrapolative method called LN, are evaluated across |
5664 |
a wide range of damping coefficient values. When large damping coefficients |
5665 |
are used, as one would for the implicit modeling of solvent molecules, |
5666 |
the method LN is superior, with LM closely following. However, with |
5667 |
mild damping of 0.2 ps(-1), LM produces the best results, allowing |
5668 |
long time steps of 14 fs in simulations containing explicitly modeled |
5669 |
flexible water. With BBK-M and the same damping coefficient, time |
5670 |
steps of 12 fs are possible for the same system. Similar results |
5671 |
are obtained for a solvated protein-DNA simulation of estrogen receptor |
5672 |
ER with estrogen response element ERE. A parallel version of BBK-M |
5673 |
runs nearly three times faster than the Verlet-I/r-RESPA (reversible |
5674 |
reference system propagator algorithm) when using the largest stable |
5675 |
time step on each one, and it also parallelizes well. The computation |
5676 |
of diffusion coefficients for flexible water and ER/ERE shows that |
5677 |
when mild damping of up to 0.2 ps-1 is used the dynamics are not |
5678 |
significantly distorted. (C) 2001 American Institute of Physics.}, |
5679 |
Annote = {397CQ Times Cited:14 Cited References Count:36}, |
5680 |
Author = {J. A. Izaguirre and D. P. Catarello and J. M. Wozniak and R. D. Skeel}, |
5681 |
Issn = {0021-9606}, |
5682 |
Journal = jcp, |
5683 |
Month = {Feb 1}, |
5684 |
Number = 5, |
5685 |
Pages = {2090-2098}, |
5686 |
Title = {Langevin stabilization of molecular dynamics}, |
5687 |
Uri = {<Go to ISI>://000166676100020}, |
5688 |
Volume = 114, |
5689 |
Year = 2001} |
5690 |
|
5691 |
@article{Torre1977, |
5692 |
Author = {{Garc\'{i}a de la Torre}, Jose and V.~A. Bloomfield}, |
5693 |
Journal = {Biopolymers}, |
5694 |
Pages = {1747-1763}, |
5695 |
Title = {Hydrodynamic properties of macromolecular complexes. I. Translation}, |
5696 |
Volume = 16, |
5697 |
Year = 1977} |
5698 |
|
5699 |
@article{Kale1999, |
5700 |
Abstract = {Molecular dynamics programs simulate the behavior of biomolecular |
5701 |
systems, leading to understanding of their functions. However, the |
5702 |
computational complexity of such simulations is enormous. Parallel |
5703 |
machines provide the potential to meet this computational challenge. |
5704 |
To harness this potential, it is necessary to develop a scalable |
5705 |
program. It is also necessary that the program be easily modified |
5706 |
by application-domain programmers. The NAMD2 program presented in |
5707 |
this paper seeks to provide these desirable features. It uses spatial |
5708 |
decomposition combined with force decomposition to enhance scalability. |
5709 |
It uses intelligent periodic load balancing, so as to maximally |
5710 |
utilize the available compute power. It is modularly organized, |
5711 |
and implemented using Charm++, a parallel C++ dialect, so as to |
5712 |
enhance its modifiability. It uses a combination of numerical techniques |
5713 |
and algorithms to ensure that energy drifts are minimized, ensuring |
5714 |
accuracy in long running calculations. NAMD2 uses a portable run-time |
5715 |
framework called Converse that also supports interoperability among |
5716 |
multiple parallel paradigms. As a result, different components of |
5717 |
applications can be written in the most appropriate parallel paradigms. |
5718 |
NAMD2 runs on most parallel machines including workstation clusters |
5719 |
and has yielded speedups in excess of 180 on 220 processors. This |
5720 |
paper also describes the performance obtained on some benchmark |
5721 |
applications. (C) 1999 Academic Press.}, |
5722 |
Annote = {194FM Times Cited:373 Cited References Count:51}, |
5723 |
Author = {L. Kale and R. Skeel and M. Bhandarkar and R. Brunner and A. Gursoy and N. Krawetz and J. Phillips and A. Shinozaki and K. Varadarajan and K. Schulten}, |
5724 |
Issn = {0021-9991}, |
5725 |
Journal = jcop, |
5726 |
Month = {May 1}, |
5727 |
Number = 1, |
5728 |
Pages = {283-312}, |
5729 |
Title = {NAMD2: Greater scalability for parallel molecular dynamics}, |
5730 |
Uri = {<Go to ISI>://000080181500013}, |
5731 |
Volume = 151, |
5732 |
Year = 1999} |
5733 |
|
5734 |
@article{Kane2000, |
5735 |
Abstract = {The purpose of this work is twofold. First, we demonstrate analytically |
5736 |
that the classical Newmark family as well as related integration |
5737 |
algorithms are variational in the sense of the Veselov formulation |
5738 |
of discrete mechanics. Such variational algorithms are well known |
5739 |
to be symplectic and momentum preserving and to often have excellent |
5740 |
global energy behaviour. This analytical result is verified through |
5741 |
numerical examples and is believed to be one of the primary reasons |
5742 |
that this class of algorithms performs so well. Second, we develop |
5743 |
algorithms for mechanical systems with forcing, and in particular, |
5744 |
for dissipative systems. In this case, we develop integrators that |
5745 |
are based on a discretization of the Lagrange d'Alembert principle |
5746 |
as well as on a variational formulation of dissipation. It is demonstrated |
5747 |
that these types of structured integrators have good numerical behaviour |
5748 |
in terms of obtaining the correct amounts by which the energy changes |
5749 |
over the integration run. Copyright (C) 2000 John Wiley & Sons, |
5750 |
Ltd.}, |
5751 |
Annote = {373CJ Times Cited:30 Cited References Count:41}, |
5752 |
Author = {C. Kane and J. E. Marsden and M. Ortiz and M. West}, |
5753 |
Issn = {0029-5981}, |
5754 |
Journal = {International Journal for Numerical Methods in Engineering}, |
5755 |
Month = {Dec 10}, |
5756 |
Number = 10, |
5757 |
Pages = {1295-1325}, |
5758 |
Title = {Variational integrators and the Newmark algorithm for conservative and dissipative mechanical systems}, |
5759 |
Uri = {<Go to ISI>://000165270600004}, |
5760 |
Volume = 49, |
5761 |
Year = 2000} |
5762 |
|
5763 |
@article{Klimov1997, |
5764 |
Abstract = {The viscosity (eta) dependence of the folding rates for four sequences |
5765 |
(the native state of three sequences is a beta sheet, while the |
5766 |
fourth forms an alpha helix) is calculated for off-lattice models |
5767 |
of proteins. Assuming that the dynamics is given by the Langevin |
5768 |
equation, we show that the folding rates increase linearly at low |
5769 |
viscosities eta, decrease as 1/eta at large eta, and have a maximum |
5770 |
at intermediate values. The Kramers' theory of barrier crossing |
5771 |
provides a quantitative fit of the numerical results. By mapping |
5772 |
the simulation results to real proteins we estimate that for optimized |
5773 |
sequences the time scale for forming a four turn alpha-helix topology |
5774 |
is about 500 ns, whereas for beta sheet it is about 10 mu s.}, |
5775 |
Annote = {Xk293 Times Cited:77 Cited References Count:17}, |
5776 |
Author = {D. K. Klimov and D. Thirumalai}, |
5777 |
Issn = {0031-9007}, |
5778 |
Journal = prl, |
5779 |
Month = {Jul 14}, |
5780 |
Number = 2, |
5781 |
Pages = {317-320}, |
5782 |
Title = {Viscosity dependence of the folding rates of proteins}, |
5783 |
Uri = {<Go to ISI>://A1997XK29300035}, |
5784 |
Volume = 79, |
5785 |
Year = 1997} |
5786 |
|
5787 |
@article{Kol1997, |
5788 |
Abstract = {Rigid-body molecular dynamics simulations typically are performed |
5789 |
in a quaternion representation. The nonseparable form of the Hamiltonian |
5790 |
in quaternions prevents the use of a standard leapfrog (Verlet) |
5791 |
integrator, so nonsymplectic Runge-Kutta, multistep, or extrapolation |
5792 |
methods are generally used, This is unfortunate since symplectic |
5793 |
methods like Verlet exhibit superior energy conservation in long-time |
5794 |
integrations. In this article, we describe an alternative method, |
5795 |
which we call RSHAKE (for rotation-SHAKE), in which the entire rotation |
5796 |
matrix is evolved (using the scheme of McLachlan and Scovel [J. |
5797 |
Nonlin. Sci, 16 233 (1995)]) in tandem with the particle positions. |
5798 |
We employ a fast approximate Newton solver to preserve the orthogonality |
5799 |
of the rotation matrix. We test our method on a system of soft-sphere |
5800 |
dipoles and compare with quaternion evolution using a 4th-order |
5801 |
predictor-corrector integrator, Although the short-time error of |
5802 |
the quaternion algorithm is smaller for fixed time step than that |
5803 |
for RSHAKE, the quaternion scheme exhibits an energy drift which |
5804 |
is not observed in simulations with RSHAKE, hence a fixed energy |
5805 |
tolerance can be achieved by using a larger time step, The superiority |
5806 |
of RSHAKE increases with system size. (C) 1997 American Institute |
5807 |
of Physics.}, |
5808 |
Annote = {Xq332 Times Cited:11 Cited References Count:18}, |
5809 |
Author = {A. Kol and B. B. Laird and B. J. Leimkuhler}, |
5810 |
Issn = {0021-9606}, |
5811 |
Journal = jcp, |
5812 |
Month = {Aug 15}, |
5813 |
Number = 7, |
5814 |
Pages = {2580-2588}, |
5815 |
Title = {A symplectic method for rigid-body molecular simulation}, |
5816 |
Uri = {<Go to ISI>://A1997XQ33200046}, |
5817 |
Volume = 107, |
5818 |
Year = 1997} |
5819 |
|
5820 |
@article{Lansac2001, |
5821 |
Abstract = {Cyanobiphenyls (nCB's) represent a useful and intensively studied |
5822 |
class of mesogens. Many of the peculiar properties of nCB's (e.g., |
5823 |
the occurence of the partial bilayer smectic-A(d) phase) are thought |
5824 |
to be a manifestation of short-range antiparallel association of |
5825 |
neighboring molecules, resulting from strong dipole-dipole interactions |
5826 |
between cyano groups. To test and extend existing models of microscopic |
5827 |
ordering in nCB's, we carry out large-scale atomistic simulation |
5828 |
studies of the microscopic structure and dynamics of the Sm-A(d) |
5829 |
phase of 4-octyl-4'-cyanobiphenyl (8CB). We compute a variety of |
5830 |
thermodynamic, structural, and dynamical properties for this material, |
5831 |
and make a detailed comparison of our results with experimental |
5832 |
measurements in order to validate our molecular model. Semiquantitative |
5833 |
agreement with experiment is found: the smectic layer spacing and |
5834 |
mass density are well reproduced, translational diffusion constants |
5835 |
are similar to experiment, but the orientational ordering of alkyl |
5836 |
chains is overestimated. This simulation provides a detailed picture |
5837 |
of molecular conformation, smectic layer structure, and intermolecular |
5838 |
correlations in Sm-A(d) 8CB, and demonstrates that pronounced short-range |
5839 |
antiparallel association of molecules arising from dipole-dipole |
5840 |
interactions plays a dominant role in determining the molecular-scale |
5841 |
structure of 8CB.}, |
5842 |
Annote = {Part 1 496QF Times Cited:10 Cited References Count:60}, |
5843 |
Author = {Y. Lansac and M. A. Glaser and N. A. Clark}, |
5844 |
Issn = {1063-651X}, |
5845 |
Journal = {Physical Review E}, |
5846 |
Month = {Nov}, |
5847 |
Number = 5, |
5848 |
Pages = {-}, |
5849 |
Title = {Microscopic structure and dynamics of a partial bilayer smectic liquid crystal}, |
5850 |
Uri = {<Go to ISI>://000172406900063}, |
5851 |
Volume = 6405, |
5852 |
Year = 2001} |
5853 |
|
5854 |
@article{Lansac2003, |
5855 |
Abstract = {Recently, a new class of smectic liquid crystal phases characterized |
5856 |
by the spontaneous formation of macroscopic chiral domains from |
5857 |
achiral bent-core molecules has been discovered. We have carried |
5858 |
out Monte Carlo simulations of a minimal hard spherocylinder dimer |
5859 |
model to investigate the role of excluded volume interactions in |
5860 |
determining the phase behavior of bent-core materials and to probe |
5861 |
the molecular origins of polar and chiral symmetry breaking. We |
5862 |
present the phase diagram of hard spherocylinder dimers of length-diameter |
5863 |
ratio of 5 as a function of pressure or density and dimer opening |
5864 |
angle psi. With decreasing psi, a transition from a nonpolar to |
5865 |
a polar smectic A phase is observed near psi=167degrees, and the |
5866 |
nematic phase becomes thermodynamically unstable for psi<135degrees. |
5867 |
Free energy calculations indicate that the antipolar smectic A (SmAP(A)) |
5868 |
phase is more stable than the polar smectic A phase (SmAP(F)). No |
5869 |
chiral smectic or biaxial nematic phases were found.}, |
5870 |
Annote = {Part 1 646CM Times Cited:15 Cited References Count:38}, |
5871 |
Author = {Y. Lansac and P. K. Maiti and N. A. Clark and M. A. Glaser}, |
5872 |
Issn = {1063-651X}, |
5873 |
Journal = {Physical Review E}, |
5874 |
Month = {Jan}, |
5875 |
Number = 1, |
5876 |
Pages = {-}, |
5877 |
Title = {Phase behavior of bent-core molecules}, |
5878 |
Uri = {<Go to ISI>://000181017300042}, |
5879 |
Volume = 67, |
5880 |
Year = 2003} |
5881 |
|
5882 |
@book{Leach2001, |
5883 |
Address = {Harlow, England}, |
5884 |
Author = {A. Leach}, |
5885 |
Edition = {2nd}, |
5886 |
Publisher = {Pearson Educated Limited}, |
5887 |
Title = {Molecular Modeling: Principles and Applications}, |
5888 |
Year = 2001} |
5889 |
|
5890 |
@article{Leimkuhler1999, |
5891 |
Abstract = {Reversible and adaptive integration methods based on Kustaanheimo-Stiefel |
5892 |
regularization and modified Sundman transformations are applied |
5893 |
to simulate general perturbed Kepler motion and to compute classical |
5894 |
trajectories of atomic systems (e.g. Rydberg atoms). The new family |
5895 |
of reversible adaptive regularization methods also conserves angular |
5896 |
momentum and exhibits superior energy conservation and numerical |
5897 |
stability in long-time integrations. The schemes are appropriate |
5898 |
for scattering, for astronomical calculations of escape time and |
5899 |
long-term stability, and for classical and semiclassical studies |
5900 |
of atomic dynamics. The components of an algorithm for trajectory |
5901 |
calculations are described. Numerical experiments illustrate the |
5902 |
effectiveness of the reversible approach.}, |
5903 |
Annote = {199EE Times Cited:11 Cited References Count:48}, |
5904 |
Author = {B. Leimkuhler}, |
5905 |
Issn = {1364-503X}, |
5906 |
Journal = {Philosophical Transactions of the Royal Society of London Series a-Mathematical Physical and Engineering Sciences}, |
5907 |
Month = {Apr 15}, |
5908 |
Number = 1754, |
5909 |
Pages = {1101-1133}, |
5910 |
Title = {Reversible adaptive regularization: perturbed Kepler motion and classical atomic trajectories}, |
5911 |
Uri = {<Go to ISI>://000080466800007}, |
5912 |
Volume = 357, |
5913 |
Year = 1999} |
5914 |
|
5915 |
@book{Leimkuhler2004, |
5916 |
Address = {Cambridge}, |
5917 |
Author = {B. Leimkuhler and S. Reich}, |
5918 |
Publisher = {Cambridge University Press}, |
5919 |
Title = {Simulating Hamiltonian Dynamics}, |
5920 |
Year = 2004} |
5921 |
|
5922 |
@article{Levelut1981, |
5923 |
Annote = {Ml751 Times Cited:96 Cited References Count:16}, |
5924 |
Author = {A. M. Levelut and R. J. Tarento and F. Hardouin and M. F. Achard and G. Sigaud}, |
5925 |
Issn = {1050-2947}, |
5926 |
Journal = {Physical Review A}, |
5927 |
Number = 4, |
5928 |
Pages = {2180-2186}, |
5929 |
Title = {Number of Sa Phases}, |
5930 |
Uri = {<Go to ISI>://A1981ML75100057}, |
5931 |
Volume = 24, |
5932 |
Year = 1981} |
5933 |
|
5934 |
@article{Lieb1982, |
5935 |
Annote = {Nu461 Times Cited:40 Cited References Count:28}, |
5936 |
Author = {W. R. Lieb and M. Kovalycsik and R. Mendelsohn}, |
5937 |
Issn = {0006-3002}, |
5938 |
Journal = {Biochimica Et Biophysica Acta}, |
5939 |
Number = 2, |
5940 |
Pages = {388-398}, |
5941 |
Title = {Do Clinical-Levels of General-Anesthetics Affect Lipid Bilayers - Evidence from Raman-Scattering}, |
5942 |
Uri = {<Go to ISI>://A1982NU46100012}, |
5943 |
Volume = 688, |
5944 |
Year = 1982} |
5945 |
|
5946 |
@article{Link1997, |
5947 |
Abstract = {A smectic liquid-crystal phase made from achiral molecules with bent |
5948 |
cores was found to have fluid layers that exhibit two spontaneous |
5949 |
symmetry-breaking instabilities: polar molecular orientational ordering |
5950 |
about the layer normal and molecular tilt. These instabilities combine |
5951 |
to form a chiral layer structure with a handedness that depends |
5952 |
on the sign of the tilt. The bulk states are either antiferroelectric-racemic, |
5953 |
with the layer polar direction and handedness alternating in sign |
5954 |
from layer to layer, or antiferroelectric-chiral, which is of uniform |
5955 |
layer handedness. Both states exhibit an electric field-induced |
5956 |
transition from antiferroelectric to ferroelectric.}, |
5957 |
Annote = {Yl002 Times Cited:407 Cited References Count:25}, |
5958 |
Author = {D. R. Link and G. Natale and R. Shao and J. E. Maclennan and N. A. Clark and E. Korblova and D. M. Walba}, |
5959 |
Issn = {0036-8075}, |
5960 |
Journal = {Science}, |
5961 |
Month = {Dec 12}, |
5962 |
Number = 5345, |
5963 |
Pages = {1924-1927}, |
5964 |
Title = {Spontaneous formation of macroscopic chiral domains in a fluid smectic phase of achiral molecules}, |
5965 |
Uri = {<Go to ISI>://A1997YL00200028}, |
5966 |
Volume = 278, |
5967 |
Year = 1997} |
5968 |
|
5969 |
@article{Liwo2005, |
5970 |
Annote = {Suppl. 1 005MG Times Cited:0 Cited References Count:0}, |
5971 |
Author = {A. Liwo and M. Khalili and H. A. Scheraga}, |
5972 |
Issn = {1742-464X}, |
5973 |
Journal = {Febs Journal}, |
5974 |
Month = {Jul}, |
5975 |
Pages = {359-360}, |
5976 |
Title = {Ab initio simulations of protein folding pathways by molecular dynamics with the united-residue (UNRES) model of polypeptide chains}, |
5977 |
Uri = {<Go to ISI>://000234826102043}, |
5978 |
Volume = 272, |
5979 |
Year = 2005} |
5980 |
|
5981 |
@article{Luty1994, |
5982 |
Abstract = {We compare the Particle-Particle Particle-Mesh (PPPM) and Ewald methods |
5983 |
for calculating electrostatic interactions in periodic molecular |
5984 |
systems. A brief comparison of the theories shows that the methods |
5985 |
are very similar differing mainly in the technique which is used |
5986 |
to perform the ''k-space'' or mesh calculation. Because the PPPM |
5987 |
utilizes the highly efficient numerical Fast Fourier Transform (FFT) |
5988 |
method it requires significantly less computational effort than |
5989 |
the Ewald method and scale's almost linearly with system size.}, |
5990 |
Annote = {Qf464 Times Cited:50 Cited References Count:20}, |
5991 |
Author = {B. A. Luty and M. E. Davis and I. G. Tironi and W. F. Vangunsteren}, |
5992 |
Issn = {0892-7022}, |
5993 |
Journal = {Molecular Simulation}, |
5994 |
Number = 1, |
5995 |
Pages = {11-20}, |
5996 |
Title = {A Comparison of Particle-Particle, Particle-Mesh and Ewald Methods for Calculating Electrostatic Interactions in Periodic Molecular-Systems}, |
5997 |
Uri = {<Go to ISI>://A1994QF46400002}, |
5998 |
Volume = 14, |
5999 |
Year = 1994} |
6000 |
|
6001 |
@book{Marion1990, |
6002 |
Address = {New York}, |
6003 |
Author = {J.~B. Marion}, |
6004 |
Edition = {2rd}, |
6005 |
Publisher = {Academic Press}, |
6006 |
Title = {Classical Dynamics of Particles and Systems}, |
6007 |
Year = 1990} |
6008 |
|
6009 |
@article{Marrink1994, |
6010 |
Abstract = {To obtain insight in the process of water permeation through a lipid |
6011 |
membrane, we performed molecular dynamics simulations on a phospholipid |
6012 |
(DPPC)/water system with atomic detail. Since the actual process |
6013 |
of permeation is too slow to be studied directly, we deduced the |
6014 |
permeation rate indirectly via computation of the free energy and |
6015 |
diffusion rate profiles of a water molecule across the bilayer. |
6016 |
We conclude that the permeation of water through a lipid membrane |
6017 |
cannot be described adequately by a simple homogeneous solubility-diffusion |
6018 |
model. Both the excess free energy and the diffusion rate strongly |
6019 |
depend on the position in the membrane, as a result from the inhomogeneous |
6020 |
nature of the membrane. The calculated excess free energy profile |
6021 |
has a shallow slope and a maximum height of 26 kJ/mol. The diffusion |
6022 |
rate is highest in the middle of the membrane where the lipid density |
6023 |
is low. In the interfacial region almost all water molecules are |
6024 |
bound by the lipid headgroups, and the diffusion turns out to be |
6025 |
1 order of magnitude smaller. The total transport process is essentially |
6026 |
determined by the free energy barrier. The rate-limiting step is |
6027 |
the permeation through the dense part of the lipid tails, where |
6028 |
the resistance is highest. We found a permeation rate of 7(+/-3) |
6029 |
x 10(-2) cm/s at 350 K, comparable to experimental values for DPPC |
6030 |
membranes, if corrected for the temperature of the simulation. Taking |
6031 |
the inhomogeneity of the membrane into account, we define a new |
6032 |
''four-region'' model which seems to be more realistic than the |
6033 |
''two-phase'' solubility-diffusion model.}, |
6034 |
Annote = {Ng219 Times Cited:187 Cited References Count:25}, |
6035 |
Author = {S. J. Marrink and H. J. C. Berendsen}, |
6036 |
Issn = {0022-3654}, |
6037 |
Journal = {Journal of Physical Chemistry}, |
6038 |
Month = {Apr 14}, |
6039 |
Number = 15, |
6040 |
Pages = {4155-4168}, |
6041 |
Title = {Simulation of Water Transport through a Lipid-Membrane}, |
6042 |
Uri = {<Go to ISI>://A1994NG21900040}, |
6043 |
Volume = 98, |
6044 |
Year = 1994} |
6045 |
|
6046 |
@article{Marrink2004, |
6047 |
Author = {S.~J. Marrink and A.~H. de~Vries and A.~E. Mark}, |
6048 |
Journal = {J. Phys. Chem. B}, |
6049 |
Pages = {750-760}, |
6050 |
Title = {Coarse Grained Model for Semiquantitative Lipid Simulations}, |
6051 |
Volume = 108, |
6052 |
Year = 2004} |
6053 |
|
6054 |
@article{Marsden1998, |
6055 |
Abstract = {This paper presents a geometric-variational approach to continuous |
6056 |
and discrete mechanics and field theories. Using multisymplectic |
6057 |
geometry, we show that the existence of the fundamental geometric |
6058 |
structures as well as their preservation along solutions can be |
6059 |
obtained directly from the variational principle. In particular, |
6060 |
we prove that a unique multisymplectic structure is obtained by |
6061 |
taking the derivative of an action function, and use this structure |
6062 |
to prove covariant generalizations of conservation of symplecticity |
6063 |
and Noether's theorem. Natural discretization schemes for PDEs, |
6064 |
which have these important preservation properties, then follow |
6065 |
by choosing a discrete action functional. In the case of mechanics, |
6066 |
we recover the variational symplectic integrators of Veselov type, |
6067 |
while for PDEs we obtain covariant spacetime integrators which conserve |
6068 |
the corresponding discrete multisymplectic form as well as the discrete |
6069 |
momentum mappings corresponding to symmetries. We show that the |
6070 |
usual notion of symplecticity along an infinite-dimensional space |
6071 |
of fields can be naturally obtained by making a spacetime split. |
6072 |
All of the aspects of our method are demonstrated with a nonlinear |
6073 |
sine-Gordon equation, including computational results and a comparison |
6074 |
with other discretization schemes.}, |
6075 |
Annote = {154RH Times Cited:88 Cited References Count:36}, |
6076 |
Author = {J. E. Marsden and G. W. Patrick and S. Shkoller}, |
6077 |
Issn = {0010-3616}, |
6078 |
Journal = {Communications in Mathematical Physics}, |
6079 |
Month = {Dec}, |
6080 |
Number = 2, |
6081 |
Pages = {351-395}, |
6082 |
Title = {Multisymplectic geometry, variational integrators, and nonlinear PDEs}, |
6083 |
Uri = {<Go to ISI>://000077902200006}, |
6084 |
Volume = 199, |
6085 |
Year = 1998} |
6086 |
|
6087 |
@article{Matthey2004, |
6088 |
Abstract = {PROTOMOL is a high-performance framework in C++ for rapid prototyping |
6089 |
of novel algorithms for molecular dynamics and related applications. |
6090 |
Its flexibility is achieved primarily through the use of inheritance |
6091 |
and design patterns (object-oriented programming): Performance is |
6092 |
obtained by using templates that enable generation of efficient |
6093 |
code for sections critical to performance (generic programming). |
6094 |
The framework encapsulates important optimizations that can be used |
6095 |
by developers, such as parallelism in the force computation. Its |
6096 |
design is based on domain analysis of numerical integrators for |
6097 |
molecular dynamics (MD) and of fast solvers for the force computation, |
6098 |
particularly due to electrostatic interactions. Several new and |
6099 |
efficient algorithms are implemented in PROTOMOL. Finally, it is |
6100 |
shown that PROTOMOL'S sequential performance is excellent when compared |
6101 |
to a leading MD program, and that it scales well for moderate number |
6102 |
of processors. Binaries and source codes for Windows, Linux, Solaris, |
6103 |
IRIX, HP-UX, and AIX platforms are available under open source license |
6104 |
at http://protomol.sourceforge.net.}, |
6105 |
Annote = {860EP Times Cited:2 Cited References Count:52}, |
6106 |
Author = {T. Matthey and T. Cickovski and S. Hampton and A. Ko and Q. Ma and M. Nyerges and T. Raeder and T. Slabach and J. A. Izaguirre}, |
6107 |
Issn = {0098-3500}, |
6108 |
Journal = {Acm Transactions on Mathematical Software}, |
6109 |
Month = {Sep}, |
6110 |
Number = 3, |
6111 |
Pages = {237-265}, |
6112 |
Title = {ProtoMol, an object-oriented framework for prototyping novel algorithms for molecular dynamics}, |
6113 |
Uri = {<Go to ISI>://000224325600001}, |
6114 |
Volume = 30, |
6115 |
Year = 2004} |
6116 |
|
6117 |
@article{McLachlan1993, |
6118 |
Author = {R.~I McLachlan}, |
6119 |
Journal = {prl}, |
6120 |
Pages = {3043-3046}, |
6121 |
Title = {Explicit Lie-Poisson integration and the Euler equations}, |
6122 |
Volume = 71, |
6123 |
Year = 1993} |
6124 |
|
6125 |
@article{McLachlan1998, |
6126 |
Abstract = {We give a survey and some new examples of generating functions for |
6127 |
systems with symplectic structure, systems with a first integral, |
6128 |
systems that preserve volume, and systems with symmetries and/or |
6129 |
time-reversing symmetries. Both ODEs and maps are treated, and we |
6130 |
discuss how generating functions may be used in the structure-preserving |
6131 |
numerical integration of ODEs with the above properties.}, |
6132 |
Annote = {Yt049 Times Cited:7 Cited References Count:26}, |
6133 |
Author = {R. I. McLachlan and G. R. W. Quispel}, |
6134 |
Issn = {0167-2789}, |
6135 |
Journal = {Physica D}, |
6136 |
Month = {Jan 15}, |
6137 |
Number = {1-2}, |
6138 |
Pages = {298-309}, |
6139 |
Title = {Generating functions for dynamical systems with symmetries, integrals, and differential invariants}, |
6140 |
Uri = {<Go to ISI>://000071558900021}, |
6141 |
Volume = 112, |
6142 |
Year = 1998} |
6143 |
|
6144 |
@article{McLachlan1998a, |
6145 |
Abstract = {We consider properties of flows, the relationships between them, and |
6146 |
whether numerical integrators can be made to preserve these properties. |
6147 |
This is done in the context of automorphisms and antiautomorphisms |
6148 |
of a certain group generated by maps associated to vector fields. |
6149 |
This new framework unifies several known constructions. We also |
6150 |
use the concept of #covariance# of a numerical method with respect |
6151 |
to a group of coordinate transformations. The main application is |
6152 |
to explore the relationship between spatial symmetries, reversing |
6153 |
symmetries, and time symmetry of flows and numerical integrators.}, |
6154 |
Annote = {Zc449 Times Cited:14 Cited References Count:33}, |
6155 |
Author = {R. I. McLachlan and G. R. W. Quispel and G. S. Turner}, |
6156 |
Issn = {0036-1429}, |
6157 |
Journal = {Siam Journal on Numerical Analysis}, |
6158 |
Month = {Apr}, |
6159 |
Number = 2, |
6160 |
Pages = {586-599}, |
6161 |
Title = {Numerical integrators that preserve symmetries and reversing symmetries}, |
6162 |
Uri = {<Go to ISI>://000072580500010}, |
6163 |
Volume = 35, |
6164 |
Year = 1998} |
6165 |
|
6166 |
@article{McLachlan2005, |
6167 |
Abstract = {In this paper we revisit the Moser-Veselov description of the free |
6168 |
rigid body in body coordinates, which, in the 3 x 3 case, can be |
6169 |
implemented as an explicit, second-order, integrable approximation |
6170 |
of the continuous solution. By backward error analysis, we study |
6171 |
the modified vector field which is integrated exactly by the discrete |
6172 |
algorithm. We deduce that the discrete Moser-Veselov (DMV) is well |
6173 |
approximated to higher order by time reparametrizations of the continuous |
6174 |
equations (modified vector field). We use the modified vector field |
6175 |
to scale the initial data of the DMV to improve the order of the |
6176 |
approximation and show the equivalence of the DMV and the RATTLE |
6177 |
algorithm. Numerical integration with these preprocessed initial |
6178 |
data is several orders of magnitude more accurate than the original |
6179 |
DMV and RATTLE approach.}, |
6180 |
Annote = {911NS Times Cited:0 Cited References Count:14}, |
6181 |
Author = {R. I. McLachlan and A. Zanna}, |
6182 |
Issn = {1615-3375}, |
6183 |
Journal = {Foundations of Computational Mathematics}, |
6184 |
Month = {Feb}, |
6185 |
Number = 1, |
6186 |
Pages = {87-123}, |
6187 |
Title = {The discrete Moser-Veselov algorithm for the free rigid body, revisited}, |
6188 |
Uri = {<Go to ISI>://000228011900003}, |
6189 |
Volume = 5, |
6190 |
Year = 2005} |
6191 |
|
6192 |
@article{Meineke2005, |
6193 |
Abstract = {OOPSE is a new molecular dynamics simulation program that is capable |
6194 |
of efficiently integrating equations of motion for atom types with |
6195 |
orientational degrees of freedom (e.g. #sticky# atoms and point |
6196 |
dipoles). Transition metals can also be simulated using the embedded |
6197 |
atom method (EAM) potential included in the code. Parallel simulations |
6198 |
are carried out using the force-based decomposition method. Simulations |
6199 |
are specified using a very simple C-based meta-data language. A |
6200 |
number of advanced integrators are included, and the basic integrator |
6201 |
for orientational dynamics provides substantial improvements over |
6202 |
older quaternion-based schemes. (C) 2004 Wiley Periodicals, Inc.}, |
6203 |
Annote = {891CF Times Cited:1 Cited References Count:56}, |
6204 |
Author = {M. A. Meineke and C. F. Vardeman and T. Lin and C. J. Fennell and J. D. Gezelter}, |
6205 |
Issn = {0192-8651}, |
6206 |
Journal = jcc, |
6207 |
Month = {Feb}, |
6208 |
Number = 3, |
6209 |
Pages = {252-271}, |
6210 |
Title = {OOPSE: An object-oriented parallel simulation engine for molecular dynamics}, |
6211 |
Uri = {<Go to ISI>://000226558200006}, |
6212 |
Volume = 26, |
6213 |
Year = 2005} |
6214 |
|
6215 |
@article{Melchionna1993, |
6216 |
Abstract = {In this paper we write down equations of motion (following the approach |
6217 |
pioneered by Hoover) for an exact isothermal-isobaric molecular |
6218 |
dynamics simulation, and we extend them to multiple thermostating |
6219 |
rates, to a shape-varying cell and to molecular systems, coherently |
6220 |
with the previous 'extended system method'. An integration scheme |
6221 |
is proposed together with a numerical illustration of the method.}, |
6222 |
Annote = {Kq355 Times Cited:172 Cited References Count:17}, |
6223 |
Author = {S. Melchionna and G. Ciccotti and B. L. Holian}, |
6224 |
Issn = {0026-8976}, |
6225 |
Journal = mp, |
6226 |
Month = {Feb 20}, |
6227 |
Number = 3, |
6228 |
Pages = {533-544}, |
6229 |
Title = {Hoover Npt Dynamics for Systems Varying in Shape and Size}, |
6230 |
Uri = {<Go to ISI>://A1993KQ35500002}, |
6231 |
Volume = 78, |
6232 |
Year = 1993} |
6233 |
|
6234 |
@article{Memmer2002, |
6235 |
Abstract = {The phase behaviour of achiral banana-shaped molecules was studied |
6236 |
by computer simulation. The banana-shaped molecules were described |
6237 |
by model intermolecular interactions based on the Gay-Berne potential. |
6238 |
The characteristic molecular structure was considered by joining |
6239 |
two calamitic Gay-Berne particles through a bond to form a biaxial |
6240 |
molecule of point symmetry group C-2v with a suitable bending angle. |
6241 |
The dependence on temperature of systems of N=1024 rigid banana-shaped |
6242 |
molecules with bending angle phi=140degrees has been studied by |
6243 |
means of Monte Carlo simulations in the isobaric-isothermal ensemble |
6244 |
(NpT). On cooling an isotropic system, two phase transitions characterized |
6245 |
by phase transition enthalpy, entropy and relative volume change |
6246 |
have been observed. For the first time by computer simulation of |
6247 |
a many-particle system of banana-shaped molecules, at low temperature |
6248 |
an untilted smectic phase showing a global phase biaxiality and |
6249 |
a spontaneous local polarization in the layers, i.e. a local polar |
6250 |
arrangement of the steric dipoles, with an antiferroelectric-like |
6251 |
superstructure could be proven, a phase structure which recently |
6252 |
has been discovered experimentally. Additionally, at intermediate |
6253 |
temperature a nematic-like phase has been proved, whereas close |
6254 |
to the transition to the smectic phase hints of a spontaneous achiral |
6255 |
symmetry breaking have been determined. Here, in the absence of |
6256 |
a layered structure a helical superstructure has been formed. All |
6257 |
phases have been characterized by visual representations of selected |
6258 |
configurations, scalar and pseudoscalar correlation functions, and |
6259 |
order parameters.}, |
6260 |
Annote = {531HT Times Cited:12 Cited References Count:37}, |
6261 |
Author = {R. Memmer}, |
6262 |
Issn = {0267-8292}, |
6263 |
Journal = {Liquid Crystals}, |
6264 |
Month = {Apr}, |
6265 |
Number = 4, |
6266 |
Pages = {483-496}, |
6267 |
Title = {Liquid crystal phases of achiral banana-shaped molecules: a computer simulation study}, |
6268 |
Uri = {<Go to ISI>://000174410500001}, |
6269 |
Volume = 29, |
6270 |
Year = 2002} |
6271 |
|
6272 |
@article{Metropolis1949, |
6273 |
Author = {N. Metropolis and S. Ulam}, |
6274 |
Journal = {J. Am. Stat. Ass.}, |
6275 |
Pages = {335-341}, |
6276 |
Title = {The $\mbox{Monte Carlo}$ Method}, |
6277 |
Volume = 44, |
6278 |
Year = 1949} |
6279 |
|
6280 |
@article{Mielke2004, |
6281 |
Abstract = {The torque generated by RNA polymerase as it tracks along double-stranded |
6282 |
DNA can potentially induce long-range structural deformations integral |
6283 |
to mechanisms of biological significance in both prokaryotes and |
6284 |
eukaryotes. In this paper, we introduce a dynamic computer model |
6285 |
for investigating this phenomenon. Duplex DNA is represented as |
6286 |
a chain of hydrodynamic beads interacting through potentials of |
6287 |
linearly elastic stretching, bending, and twisting, as well as excluded |
6288 |
volume. The chain, linear when relaxed, is looped to form two open |
6289 |
but topologically constrained subdomains. This permits the dynamic |
6290 |
introduction of torsional stress via a centrally applied torque. |
6291 |
We simulate by Brownian dynamics the 100 mus response of a 477-base |
6292 |
pair B-DNA template to the localized torque generated by the prokaryotic |
6293 |
transcription ensemble. Following a sharp rise at early times, the |
6294 |
distributed twist assumes a nearly constant value in both subdomains, |
6295 |
and a succession of supercoiling deformations occurs as superhelical |
6296 |
stress is increasingly partitioned to writhe. The magnitude of writhe |
6297 |
surpasses that of twist before also leveling off when the structure |
6298 |
reaches mechanical equilibrium with the torsional load. Superhelicity |
6299 |
is simultaneously right handed in one subdomain and left handed |
6300 |
in the other, as predicted by the #transcription-induced##twin-supercoiled-domain# |
6301 |
model [L. F. Liu and J. C. Wang, Proc. Natl. Acad. Sci. U.S.A. 84, |
6302 |
7024 (1987)]. The properties of the chain at the onset of writhing |
6303 |
agree well with predictions from theory, and the generated stress |
6304 |
is ample for driving secondary structural transitions in physiological |
6305 |
DNA. (C) 2004 American Institute of Physics.}, |
6306 |
Annote = {861ZF Times Cited:3 Cited References Count:34}, |
6307 |
Author = {S. P. Mielke and W. H. Fink and V. V. Krishnan and N. Gronbech-Jensen and C. J. Benham}, |
6308 |
Issn = {0021-9606}, |
6309 |
Journal = jcp, |
6310 |
Month = {Oct 22}, |
6311 |
Number = 16, |
6312 |
Pages = {8104-8112}, |
6313 |
Title = {Transcription-driven twin supercoiling of a DNA loop: A Brownian dynamics study}, |
6314 |
Uri = {<Go to ISI>://000224456500064}, |
6315 |
Volume = 121, |
6316 |
Year = 2004} |
6317 |
|
6318 |
@article{Naess2001, |
6319 |
Abstract = {The three Eulerian angles constitute the classical choice of generalized |
6320 |
coordinates used to describe the three degrees of rotational freedom |
6321 |
of a rigid body, but it has long been known that this choice yields |
6322 |
singular equations of motion. The latter is also true when Eulerian |
6323 |
angles are used in Brownian dynamics analyses of the angular orientation |
6324 |
of single rigid bodies and segmented polymer chains. Starting from |
6325 |
kinetic theory we here show that by instead employing the three |
6326 |
components of Cartesian rotation vectors as the generalized coordinates |
6327 |
describing angular orientation, no singularity appears in the configuration |
6328 |
space diffusion equation and the associated Brownian dynamics algorithm. |
6329 |
The suitability of Cartesian rotation vectors in Brownian dynamics |
6330 |
simulations of segmented polymer chains with spring-like or ball-socket |
6331 |
joints is discussed. (C) 2001 Elsevier Science B.V. All rights reserved.}, |
6332 |
Annote = {433TA Times Cited:7 Cited References Count:19}, |
6333 |
Author = {S. N. Naess and H. M. Adland and A. Mikkelsen and A. Elgsaeter}, |
6334 |
Issn = {0378-4371}, |
6335 |
Journal = {Physica A}, |
6336 |
Month = {May 15}, |
6337 |
Number = {3-4}, |
6338 |
Pages = {323-339}, |
6339 |
Title = {Brownian dynamics simulation of rigid bodies and segmented polymer chains. Use of Cartesian rotation vectors as the generalized coordinates describing angular orientations}, |
6340 |
Uri = {<Go to ISI>://000168774800005}, |
6341 |
Volume = 294, |
6342 |
Year = 2001} |
6343 |
|
6344 |
@article{Niori1996, |
6345 |
Abstract = {The synthesis of a banana-shaped molecule is reported and it is found |
6346 |
that the smectic phase which it forms is biaxial with the molecules |
6347 |
packed in the best,direction into a layer. Because of this characteristic |
6348 |
packing, spontaneous polarization appears parallel to the layer |
6349 |
and switches on reversal of an applied electric field. This is the |
6350 |
first obvious example of ferroelectricity in an achiral smectic |
6351 |
phase and is ascribed to the C-2v symmetry of the molecular packing.}, |
6352 |
Annote = {Ux855 Times Cited:447 Cited References Count:18}, |
6353 |
Author = {T. Niori and T. Sekine and J. Watanabe and T. Furukawa and H. Takezoe}, |
6354 |
Issn = {0959-9428}, |
6355 |
Journal = {Journal of Materials Chemistry}, |
6356 |
Month = {Jul}, |
6357 |
Number = 7, |
6358 |
Pages = {1231-1233}, |
6359 |
Title = {Distinct ferroelectric smectic liquid crystals consisting of banana shaped achiral molecules}, |
6360 |
Uri = {<Go to ISI>://A1996UX85500025}, |
6361 |
Volume = 6, |
6362 |
Year = 1996} |
6363 |
|
6364 |
@article{Noguchi2002, |
6365 |
Abstract = {We Studied the structural changes of bilayer vesicles induced by mechanical |
6366 |
forces using a Brownian dynamics simulation. Two nanoparticles, |
6367 |
which interact repulsively with amphiphilic molecules, are put inside |
6368 |
a vesicle. The position of one nanoparticle is fixed, and the other |
6369 |
is moved by a constant force as in optical-trapping experiments. |
6370 |
First, the pulled vesicle stretches into a pear or tube shape. Then |
6371 |
the inner monolayer in the tube-shaped region is deformed, and a |
6372 |
cylindrical structure is formed between two vesicles. After stretching |
6373 |
the cylindrical region, fission occurs near the moved vesicle. Soon |
6374 |
after this the cylindrical region shrinks. The trapping force similar |
6375 |
to 100 pN is needed to induce the formation of the cylindrical structure |
6376 |
and fission.}, |
6377 |
Annote = {Part 1 568PX Times Cited:5 Cited References Count:39}, |
6378 |
Author = {H. Noguchi and M. Takasu}, |
6379 |
Issn = {1063-651X}, |
6380 |
Journal = {Physical Review E}, |
6381 |
Month = {may}, |
6382 |
Number = 5, |
6383 |
Pages = {-}, |
6384 |
Title = {Structural changes of pulled vesicles: A Brownian dynamics simulation}, |
6385 |
Uri = {<Go to ISI>://000176552300084}, |
6386 |
Volume = 65, |
6387 |
Year = 2002} |
6388 |
|
6389 |
@article{Noguchi2001, |
6390 |
Abstract = {We studied the fusion dynamics of vesicles using a Brownian dynamics |
6391 |
simulation. Amphiphilic molecules spontaneously form vesicles with |
6392 |
a bilayer structure. Two vesicles come into contact and form a stalk |
6393 |
intermediate, in which a necklike structure only connects the outer |
6394 |
monolayers, as predicted by the stalk hypothesis. We have found |
6395 |
a new pathway of pore opening from stalks at high temperature: the |
6396 |
elliptic stalk bends and contact between the ends of the arc-shaped |
6397 |
stalk leads to pore opening. On the other hand, we have clarified |
6398 |
that the pore-opening process at low temperature agrees with the |
6399 |
modified stalk model: a pore is induced by contact between the inner |
6400 |
monolayers inside the stalk. (C) 2001 American Institute of Physics.}, |
6401 |
Annote = {491UW Times Cited:48 Cited References Count:25}, |
6402 |
Author = {H. Noguchi and M. Takasu}, |
6403 |
Issn = {0021-9606}, |
6404 |
Journal = jcp, |
6405 |
Month = {Nov 22}, |
6406 |
Number = 20, |
6407 |
Pages = {9547-9551}, |
6408 |
Title = {Fusion pathways of vesicles: A Brownian dynamics simulation}, |
6409 |
Uri = {<Go to ISI>://000172129300049}, |
6410 |
Volume = 115, |
6411 |
Year = 2001} |
6412 |
|
6413 |
@book{Olver1986, |
6414 |
Address = {New York}, |
6415 |
Author = {P.J. Olver}, |
6416 |
Publisher = {Springer}, |
6417 |
Title = {Applications of Lie groups to differential equatitons}, |
6418 |
Year = 1986} |
6419 |
|
6420 |
@article{Omelyan1998, |
6421 |
Abstract = {A revised version of the quaternion approach for numerical integration |
6422 |
of the equations of motion for rigid polyatomic molecules is proposed. |
6423 |
The modified approach is based on a formulation of the quaternion |
6424 |
dynamics with constraints. This allows one to resolve the rigidity |
6425 |
problem rigorously using constraint forces. It is shown that the |
6426 |
procedure for preservation of molecular rigidity can be realized |
6427 |
particularly simply within the Verlet algorithm in velocity form. |
6428 |
We demonstrate that the method presented leads to an improved numerical |
6429 |
stability with respect to the usual quaternion rescaling scheme |
6430 |
and it is roughly as good as the cumbersome atomic-constraint technique. |
6431 |
(C) 1998 American Institute of Physics.}, |
6432 |
Annote = {Yx279 Times Cited:12 Cited References Count:28}, |
6433 |
Author = {I. P. Omelyan}, |
6434 |
Issn = {0894-1866}, |
6435 |
Journal = {Computers in Physics}, |
6436 |
Month = {Jan-Feb}, |
6437 |
Number = 1, |
6438 |
Pages = {97-103}, |
6439 |
Title = {On the numerical integration of motion for rigid polyatomics: The modified quaternion approach}, |
6440 |
Uri = {<Go to ISI>://000072024300025}, |
6441 |
Volume = 12, |
6442 |
Year = 1998} |
6443 |
|
6444 |
@article{Omelyan1998a, |
6445 |
Abstract = {An algorithm for numerical integration of the rigid-body equations |
6446 |
of motion is proposed. The algorithm uses the leapfrog scheme and |
6447 |
the quantities involved are angular velocities and orientational |
6448 |
variables that can be expressed in terms of either principal axes |
6449 |
or quaternions. Due to specific features of the algorithm, orthonormality |
6450 |
and unit norms of the orientational variables are integrals of motion, |
6451 |
despite an approximate character of the produced trajectories. It |
6452 |
is shown that the method presented appears to be the most efficient |
6453 |
among all such algorithms known.}, |
6454 |
Annote = {101XL Times Cited:8 Cited References Count:22}, |
6455 |
Author = {I. P. Omelyan}, |
6456 |
Issn = {1063-651X}, |
6457 |
Journal = {Physical Review E}, |
6458 |
Month = {Jul}, |
6459 |
Number = 1, |
6460 |
Pages = {1169-1172}, |
6461 |
Title = {Algorithm for numerical integration of the rigid-body equations of motion}, |
6462 |
Uri = {<Go to ISI>://000074893400151}, |
6463 |
Volume = 58, |
6464 |
Year = 1998} |
6465 |
|
6466 |
@article{Owren1992, |
6467 |
Abstract = {Continuous, explicit Runge-Kutta methods with the minimal number of |
6468 |
stages are considered. These methods are continuously differentiable |
6469 |
if and only if one of the stages is the FSAL evaluation. A characterization |
6470 |
of a subclass of these methods is developed for orders 3, 4, and |
6471 |
5. It is shown how the free parameters of these methods can be used |
6472 |
either to minimize the continuous truncation error coefficients |
6473 |
or to maximize the stability region. As a representative for these |
6474 |
methods the fifth-order method with minimized error coefficients |
6475 |
is chosen, supplied with an error estimation method, and analysed |
6476 |
by using the DETEST software. The results are compared with a similar |
6477 |
implementation of the Dormand-Prince 5(4) pair with interpolant, |
6478 |
showing a significant advantage in the new method for the chosen |
6479 |
problems.}, |
6480 |
Annote = {Ju936 Times Cited:25 Cited References Count:20}, |
6481 |
Author = {B. Owren and M. Zennaro}, |
6482 |
Issn = {0196-5204}, |
6483 |
Journal = {Siam Journal on Scientific and Statistical Computing}, |
6484 |
Month = {Nov}, |
6485 |
Number = 6, |
6486 |
Pages = {1488-1501}, |
6487 |
Title = {Derivation of Efficient, Continuous, Explicit Runge-Kutta Methods}, |
6488 |
Uri = {<Go to ISI>://A1992JU93600013}, |
6489 |
Volume = 13, |
6490 |
Year = 1992} |
6491 |
|
6492 |
@article{Palacios1998, |
6493 |
Abstract = {The stochastic Landau-Lifshitz-Gilbert equation of motion for a classical |
6494 |
magnetic moment is numerically solved (properly observing the customary |
6495 |
interpretation of it as a Stratonovich stochastic differential equation), |
6496 |
in order to study the dynamics of magnetic nanoparticles. The corresponding |
6497 |
Langevin-dynamics approach allows for the study of the fluctuating |
6498 |
trajectories of individual magnetic moments, where we have encountered |
6499 |
remarkable phenomena in the overbarrier rotation process, such as |
6500 |
crossing-back or multiple crossing of the potential barrier, rooted |
6501 |
in the gyromagnetic nature of the system. Concerning averaged quantities, |
6502 |
we study the linear dynamic response of the archetypal ensemble |
6503 |
of noninteracting classical magnetic moments with axially symmetric |
6504 |
magnetic anisotropy. The results are compared with different analytical |
6505 |
expressions used to model the relaxation of nanoparticle ensembles, |
6506 |
assessing their accuracy. It has been found that, among a number |
6507 |
of heuristic expressions for the linear dynamic susceptibility, |
6508 |
only the simple formula proposed by Shliomis and Stepanov matches |
6509 |
the coarse features of the susceptibility reasonably. By comparing |
6510 |
the numerical results with the asymptotic formula of Storonkin {Sov. |
6511 |
Phys. Crystallogr. 30, 489 (1985) [Kristallografiya 30, 841 (1985)]}, |
6512 |
the effects of the intra-potential-well relaxation modes on the |
6513 |
low-temperature longitudinal dynamic response have been assessed, |
6514 |
showing their relatively small reflection in the susceptibility |
6515 |
curves but their dramatic influence on the phase shifts. Comparison |
6516 |
of the numerical results with the exact zero-damping expression |
6517 |
for the transverse susceptibility by Garanin, Ishchenko, and Panina |
6518 |
{Theor. Math. Phys. (USSR) 82, 169 (1990) [Teor. Mat. Fit. 82, 242 |
6519 |
(1990)]}, reveals a sizable contribution of the spread of the precession |
6520 |
frequencies of the magnetic moment in the anisotropy field to the |
6521 |
dynamic response at intermediate-to-high temperatures. [S0163-1829 |
6522 |
(98)00446-9].}, |
6523 |
Annote = {146XW Times Cited:66 Cited References Count:45}, |
6524 |
Author = {J. L. Garcia-Palacios and F. J. Lazaro}, |
6525 |
Issn = {0163-1829}, |
6526 |
Journal = {Physical Review B}, |
6527 |
Month = {Dec 1}, |
6528 |
Number = 22, |
6529 |
Pages = {14937-14958}, |
6530 |
Title = {Langevin-dynamics study of the dynamical properties of small magnetic particles}, |
6531 |
Uri = {<Go to ISI>://000077460000052}, |
6532 |
Volume = 58, |
6533 |
Year = 1998} |
6534 |
|
6535 |
@article{Parr1995, |
6536 |
Abstract = {Despite the parsing power of LR/LALR algorithms, e.g. YACC, programmers |
6537 |
often choose to write recursive-descent parsers by hand to obtain |
6538 |
increased flexibility, better error handling, and ease of debugging. |
6539 |
We introduce ANTLR, a public-domain parser generator that combines |
6540 |
the flexibility of hand-coded parsing with the convenience of a |
6541 |
parser generator, which is a component of PCCTS. ANTLR has many |
6542 |
features that make it easier to use than other language tools. Most |
6543 |
important, ANTLR provides predicates which let the programmer systematically |
6544 |
direct the parse via arbitrary expressions using semantic and syntactic |
6545 |
context; in practice, the use of predicates eliminates the need |
6546 |
to hand-tweak the ANTLR output, even for difficult parsing problems. |
6547 |
ANTLR also integrates the description of lexical and syntactic analysis, |
6548 |
accepts LL(k) grammars for k > 1 with extended BNF notation, and |
6549 |
can automatically generate abstract syntax trees. ANTLR is widely |
6550 |
used, with over 1000 registered industrial and academic users in |
6551 |
37 countries. It has been ported to many popular systems such as |
6552 |
the PC, Macintosh, and a variety of UNIX platforms; a commercial |
6553 |
C++ front-end has been developed as a result of one of our industrial |
6554 |
collaborations.}, |
6555 |
Annote = {Rk104 Times Cited:19 Cited References Count:10}, |
6556 |
Author = {T. J. Parr and R. W. Quong}, |
6557 |
Issn = {0038-0644}, |
6558 |
Journal = {Software-Practice \& Experience}, |
6559 |
Month = {Jul}, |
6560 |
Number = 7, |
6561 |
Pages = {789-810}, |
6562 |
Title = {Antlr - a Predicated-Ll(K) Parser Generator}, |
6563 |
Uri = {<Go to ISI>://A1995RK10400004}, |
6564 |
Volume = 25, |
6565 |
Year = 1995} |
6566 |
|
6567 |
@article{Pastor1988, |
6568 |
Annote = {T1302 Times Cited:61 Cited References Count:26}, |
6569 |
Author = {R. W. Pastor and B. R. Brooks and A. Szabo}, |
6570 |
Issn = {0026-8976}, |
6571 |
Journal = mp, |
6572 |
Month = {Dec 20}, |
6573 |
Number = 6, |
6574 |
Pages = {1409-1419}, |
6575 |
Title = {An Analysis of the Accuracy of Langevin and Molecular-Dynamics Algorithms}, |
6576 |
Uri = {<Go to ISI>://A1988T130200011}, |
6577 |
Volume = 65, |
6578 |
Year = 1988} |
6579 |
|
6580 |
@article{Pelzl1999, |
6581 |
Annote = {220RC Times Cited:313 Cited References Count:49}, |
6582 |
Author = {G. Pelzl and S. Diele and W. Weissflog}, |
6583 |
Issn = {0935-9648}, |
6584 |
Journal = {Advanced Materials}, |
6585 |
Month = {Jul 5}, |
6586 |
Number = 9, |
6587 |
Pages = {707-724}, |
6588 |
Title = {Banana-shaped compounds - A new field of liquid crystals}, |
6589 |
Uri = {<Go to ISI>://000081680400007}, |
6590 |
Volume = 11, |
6591 |
Year = 1999} |
6592 |
|
6593 |
@article{Perram1985, |
6594 |
Annote = {Akb93 Times Cited:71 Cited References Count:12}, |
6595 |
Author = {J. W. Perram and M. S. Wertheim}, |
6596 |
Issn = {0021-9991}, |
6597 |
Journal = jcop, |
6598 |
Number = 3, |
6599 |
Pages = {409-416}, |
6600 |
Title = {Statistical-Mechanics of Hard Ellipsoids .1. Overlap Algorithm and the Contact Function}, |
6601 |
Uri = {<Go to ISI>://A1985AKB9300008}, |
6602 |
Volume = 58, |
6603 |
Year = 1985} |
6604 |
|
6605 |
@article{Rotne1969, |
6606 |
Author = {F. Perrin}, |
6607 |
Journal = {J. Chem. Phys.}, |
6608 |
Pages = {4831-4837}, |
6609 |
Title = {Variational treatment of hydrodynamic interaction in polymers}, |
6610 |
Volume = 50, |
6611 |
Year = 1969} |
6612 |
|
6613 |
@article{Perrin1936, |
6614 |
Author = {F. Perrin}, |
6615 |
Journal = {J. Phys. Radium}, |
6616 |
Pages = {1-11}, |
6617 |
Title = {Mouvement brownien d'un ellipsoid(II). Rotation libre et depolarisation des fluorescences. Translation et diffusion de moleculese ellipsoidales}, |
6618 |
Volume = 7, |
6619 |
Year = 1936} |
6620 |
|
6621 |
@article{Perrin1934, |
6622 |
Author = {F. Perrin}, |
6623 |
Journal = {J. Phys. Radium}, |
6624 |
Pages = {497-511}, |
6625 |
Title = {Mouvement brownien d'un ellipsoid(I). Dispersion dielectrique pour des molecules ellipsoidales}, |
6626 |
Volume = 5, |
6627 |
Year = 1934} |
6628 |
|
6629 |
@article{Petrache2000, |
6630 |
Author = {H.~I. Petrache and S.~W. Dodd and M.~F. Brown}, |
6631 |
Journal = bj, |
6632 |
Pages = {3172-3192}, |
6633 |
Title = {Area per Lipid and Acyl Length Distributions in Fluid Phosphatidylcholines Determined by $^2\text{H}$ {\sc nmr} Spectroscopy}, |
6634 |
Volume = 79, |
6635 |
Year = 2000} |
6636 |
|
6637 |
@article{Petrache1998, |
6638 |
Abstract = {X-ray diffraction data taken at high instrumental resolution were |
6639 |
obtained for EPC and DMPC under various osmotic pressures, primarily |
6640 |
at T = 30 degrees C. The headgroup thickness D-HH was obtained from |
6641 |
relative electron density profiles. By using volumetric results |
6642 |
and by comparing to gel phase DPPC we obtain areas A(EPC)(F) = 69.4 |
6643 |
+/- 1.1 Angstrom(2) and A(DMPC)(F) = 59.7 +/- 0.2 Angstrom(2). The |
6644 |
analysis also gives estimates for the areal compressibility K-A. |
6645 |
The A(F) results lead to other structural results regarding membrane |
6646 |
thickness and associated waters. Using the recently determined absolute |
6647 |
electrons density profile of DPPC, the AF results also lead to absolute |
6648 |
electron density profiles and absolute continuous transforms \F(q)\ |
6649 |
for EPC and DMPC, Limited measurements of temperature dependence |
6650 |
show directly that fluctuations increase with increasing temperature |
6651 |
and that a small decrease in bending modulus K-c accounts for the |
6652 |
increased water spacing reported by Simon et al. (1995) Biophys. |
6653 |
J. 69, 1473-1483. (C) 1998 Elsevier Science Ireland Ltd. All rights |
6654 |
reserved.}, |
6655 |
Annote = {130AT Times Cited:98 Cited References Count:39}, |
6656 |
Author = {H. I. Petrache and S. Tristram-Nagle and J. F. Nagle}, |
6657 |
Issn = {0009-3084}, |
6658 |
Journal = {Chemistry and Physics of Lipids}, |
6659 |
Month = {Sep}, |
6660 |
Number = 1, |
6661 |
Pages = {83-94}, |
6662 |
Title = {Fluid phase structure of EPC and DMPC bilayers}, |
6663 |
Uri = {<Go to ISI>://000076497600007}, |
6664 |
Volume = 95, |
6665 |
Year = 1998} |
6666 |
|
6667 |
@article{Powles1973, |
6668 |
Author = {J.~G. Powles}, |
6669 |
Journal = {Advan. Phys.}, |
6670 |
Pages = {1-56}, |
6671 |
Title = {A general ellipsoid can not always serve as a modle for the rotational diffusion properties of arbitrary shaped rigid molecules}, |
6672 |
Volume = 22, |
6673 |
Year = 1973} |
6674 |
|
6675 |
@article{Recio2004, |
6676 |
Abstract = {Protein recognition is one of the most challenging and intriguing |
6677 |
problems in structural biology. Despite all the available structural, |
6678 |
sequence and biophysical information about protein-protein complexes, |
6679 |
the physico-chemical patterns, if any, that make a protein surface |
6680 |
likely to be involved in protein-protein interactions, remain elusive. |
6681 |
Here, we apply protein docking simulations and analysis of the interaction |
6682 |
energy landscapes to identify protein-protein interaction sites. |
6683 |
The new protocol for global docking based on multi-start global |
6684 |
energy optimization of an allatom model of the ligand, with detailed |
6685 |
receptor potentials and atomic solvation parameters optimized in |
6686 |
a training set of 24 complexes, explores the conformational space |
6687 |
around the whole receptor without restrictions. The ensembles of |
6688 |
the rigid-body docking solutions generated by the simulations were |
6689 |
subsequently used to project the docking energy landscapes onto |
6690 |
the protein surfaces. We found that highly populated low-energy |
6691 |
regions consistently corresponded to actual binding sites. The procedure |
6692 |
was validated on a test set of 21 known protein-protein complexes |
6693 |
not used in the training set. As much as 81% of the predicted high-propensity |
6694 |
patch residues were located correctly in the native interfaces. |
6695 |
This approach can guide the design of mutations on the surfaces |
6696 |
of proteins, provide geometrical details of a possible interaction, |
6697 |
and help to annotate protein surfaces in structural proteomics. |
6698 |
(C) 2003 Elsevier Ltd. All rights reserved.}, |
6699 |
Annote = {763GQ Times Cited:21 Cited References Count:59}, |
6700 |
Author = {J. Fernandez-Recio and M. Totrov and R. Abagyan}, |
6701 |
Issn = {0022-2836}, |
6702 |
Journal = jmb, |
6703 |
Month = {Jan 16}, |
6704 |
Number = 3, |
6705 |
Pages = {843-865}, |
6706 |
Title = {Identification of protein-protein interaction sites from docking energy landscapes}, |
6707 |
Uri = {<Go to ISI>://000188066900016}, |
6708 |
Volume = 335, |
6709 |
Year = 2004} |
6710 |
|
6711 |
@article{Reddy2006, |
6712 |
Abstract = {An overview on the recent developments in the field of liquid crystalline |
6713 |
bent-core molecules (so-called banana liquid crystals) is given. |
6714 |
After some basic issues, dealing with general aspects of the systematisation |
6715 |
of the mesophases, development of polar order and chirality in this |
6716 |
class of LC systems and explaining some general structure-property |
6717 |
relationships, we focus on fascinating new developments in this |
6718 |
field, such as modulated, undulated and columnar phases, so-called |
6719 |
B7 phases, phase biaxiality, ferroelectric and antiferroelectric |
6720 |
polar order in smectic and columnar phases, amplification and switching |
6721 |
of chirality and the spontaneous formation of superstructural and |
6722 |
supramolecular chirality.}, |
6723 |
Annote = {021NS Times Cited:2 Cited References Count:316}, |
6724 |
Author = {R. A. Reddy and C. Tschierske}, |
6725 |
Issn = {0959-9428}, |
6726 |
Journal = {Journal of Materials Chemistry}, |
6727 |
Number = 10, |
6728 |
Pages = {907-961}, |
6729 |
Title = {Bent-core liquid crystals: polar order, superstructural chirality and spontaneous desymmetrisation in soft matter systems}, |
6730 |
Uri = {<Go to ISI>://000235990500001}, |
6731 |
Volume = 16, |
6732 |
Year = 2006} |
6733 |
|
6734 |
@article{Reich1999, |
6735 |
Abstract = {Backward error analysis has become an important tool for understanding |
6736 |
the long time behavior of numerical integration methods. This is |
6737 |
true in particular for the integration of Hamiltonian systems where |
6738 |
backward error analysis can be used to show that a symplectic method |
6739 |
will conserve energy over exponentially long periods of time. Such |
6740 |
results are typically based on two aspects of backward error analysis: |
6741 |
(i) It can be shown that the modified vector fields have some qualitative |
6742 |
properties which they share with the given problem and (ii) an estimate |
6743 |
is given for the difference between the best interpolating vector |
6744 |
field and the numerical method. These aspects have been investigated |
6745 |
recently, for example, by Benettin and Giorgilli in [J. Statist. |
6746 |
Phys., 74 (1994), pp. 1117-1143], by Hairer in [Ann. Numer. Math., |
6747 |
1 (1994), pp. 107-132], and by Hairer and Lubich in [Numer. Math., |
6748 |
76 (1997), pp. 441-462]. In this paper we aim at providing a unifying |
6749 |
framework and a simplification of the existing results and corresponding |
6750 |
proofs. Our approach to backward error analysis is based on a simple |
6751 |
recursive definition of the modified vector fields that does not |
6752 |
require explicit Taylor series expansion of the numerical method |
6753 |
and the corresponding flow maps as in the above-cited works. As |
6754 |
an application we discuss the long time integration of chaotic Hamiltonian |
6755 |
systems and the approximation of time averages along numerically |
6756 |
computed trajectories.}, |
6757 |
Annote = {237HV Times Cited:43 Cited References Count:41}, |
6758 |
Author = {S. Reich}, |
6759 |
Issn = {0036-1429}, |
6760 |
Journal = {Siam Journal on Numerical Analysis}, |
6761 |
Month = {Sep 8}, |
6762 |
Number = 5, |
6763 |
Pages = {1549-1570}, |
6764 |
Title = {Backward error analysis for numerical integrators}, |
6765 |
Uri = {<Go to ISI>://000082650600010}, |
6766 |
Volume = 36, |
6767 |
Year = 1999} |
6768 |
|
6769 |
@article{Ros2005, |
6770 |
Abstract = {The recent literature in the field of liquid crystals shows that banana-shaped |
6771 |
mesogenic materials represent a bewitching and stimulating field |
6772 |
of research that is interesting both academically and in terms of |
6773 |
applications. Numerous topics are open to investigation in this |
6774 |
area because of the rich phenomenology and new possibilities that |
6775 |
these materials offer. The principal concepts in this area are reviewed |
6776 |
along with recent results. In addition, new directions to stimulate |
6777 |
further research activities are highlighted.}, |
6778 |
Annote = {990XA Times Cited:3 Cited References Count:72}, |
6779 |
Author = {M. B. Ros and J. L. Serrano and M. R. {de la Fuente} and C. L. Folcia}, |
6780 |
Issn = {0959-9428}, |
6781 |
Journal = {Journal of Materials Chemistry}, |
6782 |
Number = 48, |
6783 |
Pages = {5093-5098}, |
6784 |
Title = {Banana-shaped liquid crystals: a new field to explore}, |
6785 |
Uri = {<Go to ISI>://000233775500001}, |
6786 |
Volume = 15, |
6787 |
Year = 2005} |
6788 |
|
6789 |
@article{Roux1991, |
6790 |
Abstract = {The mobility of water, Na+. and K+ has been calculated inside a periodic |
6791 |
poly-(L,D)-alanine beta-helix, a model for the interior of the gramicidin |
6792 |
channel. Because of the different dynamical regimes for the three |
6793 |
species (high barrier for Na+, low barrier for K+, almost free diffusion |
6794 |
for water), different methods are used to calculate the mobilities. |
6795 |
By use of activated dynamics and a potential of mean force determined |
6796 |
previously (Roux, B.; Karplus, M. Biophys. J. 1991, 59, 961), the |
6797 |
barrier crossing rate of Na+ ion is determined. The motion of Na+ |
6798 |
at the transition state is controlled by local interactions and |
6799 |
collisions with the neighboring carbonyls and the two nearest water |
6800 |
molecules. There are significant deviations from transition-state |
6801 |
theory; the transmission coefficient is equal to 0.11. The water |
6802 |
and K+ motions are found to be well described by a diffusive model; |
6803 |
the motion of K+ appears to be controlled by the diffusion of water. |
6804 |
The time-dependent friction functions of Na+ and K+ ions in the |
6805 |
periodic beta-helix are calculated and analyzed by using a generalized |
6806 |
Langevin equation approach. Both Na+ and K+ suffer many rapid collisions, |
6807 |
and their dynamics is overdamped and noninertial. Thus, the selectivity |
6808 |
sequence of ions in the beta-helix is not influenced strongly by |
6809 |
their masses.}, |
6810 |
Annote = {Fr756 Times Cited:97 Cited References Count:65}, |
6811 |
Author = {B. Roux and M. Karplus}, |
6812 |
Issn = {0022-3654}, |
6813 |
Journal = {Journal of Physical Chemistry}, |
6814 |
Month = {Jun 13}, |
6815 |
Number = 12, |
6816 |
Pages = {4856-4868}, |
6817 |
Title = {Ion-Transport in a Gramicidin-Like Channel - Dynamics and Mobility}, |
6818 |
Uri = {<Go to ISI>://A1991FR75600049}, |
6819 |
Volume = 95, |
6820 |
Year = 1991} |
6821 |
|
6822 |
@article{Roy2005, |
6823 |
Abstract = {A vast majority of compounds with bent core or banana shaped molecules |
6824 |
exhibit the phase sequence B-6-B-1-B-2 as the chain length is increased |
6825 |
in a homologous series. The B-6 phase has an intercalated fluid |
6826 |
lamellar structure with a layer spacing of half the molecular length. |
6827 |
The B-1 phase has a two dimensionally periodic rectangular columnar |
6828 |
structure. The B-2 phase has a monolayer fluid lamellar structure |
6829 |
with molecules tilted with respect to the layer normal. Neglecting |
6830 |
the tilt order of the molecules in the B-2 phase, we have developed |
6831 |
a frustrated packing model to describe this phase sequence qualitatively. |
6832 |
The model has some analogy with that of the frustrated smectics |
6833 |
exhibited by highly polar rod like molecules.}, |
6834 |
Annote = {985FW Times Cited:0 Cited References Count:30}, |
6835 |
Author = {A. Roy and N. V. Madhusudana}, |
6836 |
Issn = {1292-8941}, |
6837 |
Journal = {European Physical Journal E}, |
6838 |
Month = {Nov}, |
6839 |
Number = 3, |
6840 |
Pages = {253-258}, |
6841 |
Title = {A frustrated packing model for the B-6-B-1-SmAP(A) sequence of phases in banana shaped molecules}, |
6842 |
Uri = {<Go to ISI>://000233363300002}, |
6843 |
Volume = 18, |
6844 |
Year = 2005} |
6845 |
|
6846 |
@article{Ryckaert1977, |
6847 |
Annote = {Cz253 Times Cited:3680 Cited References Count:7}, |
6848 |
Author = {J. P. Ryckaert and G. Ciccotti and H. J. C. Berendsen}, |
6849 |
Issn = {0021-9991}, |
6850 |
Journal = jcop, |
6851 |
Number = 3, |
6852 |
Pages = {327-341}, |
6853 |
Title = {Numerical-Integration of Cartesian Equations of Motion of a System with Constraints - Molecular-Dynamics of N-Alkanes}, |
6854 |
Uri = {<Go to ISI>://A1977CZ25300007}, |
6855 |
Volume = 23, |
6856 |
Year = 1977} |
6857 |
|
6858 |
@article{Sagui1999, |
6859 |
Abstract = {Current computer simulations of biomolecules typically make use of |
6860 |
classical molecular dynamics methods, as a very large number (tens |
6861 |
to hundreds of thousands) of atoms are involved over timescales |
6862 |
of many nanoseconds. The methodology for treating short-range bonded |
6863 |
and van der Waals interactions has matured. However, long-range |
6864 |
electrostatic interactions still represent a bottleneck in simulations. |
6865 |
In this article, we introduce the basic issues for an accurate representation |
6866 |
of the relevant electrostatic interactions. In spite of the huge |
6867 |
computational time demanded by most biomolecular systems, it is |
6868 |
no longer necessary to resort to uncontrolled approximations such |
6869 |
as the use of cutoffs. In particular, we discuss the Ewald summation |
6870 |
methods, the fast particle mesh methods, and the fast multipole |
6871 |
methods. We also review recent efforts to understand the role of |
6872 |
boundary conditions in systems with long-range interactions, and |
6873 |
conclude with a short perspective on future trends.}, |
6874 |
Annote = {213KJ Times Cited:126 Cited References Count:73}, |
6875 |
Author = {C. Sagui and T. A. Darden}, |
6876 |
Issn = {1056-8700}, |
6877 |
Journal = {Annual Review of Biophysics and Biomolecular Structure}, |
6878 |
Pages = {155-179}, |
6879 |
Title = {Molecular dynamics simulations of biomolecules: Long-range electrostatic effects}, |
6880 |
Uri = {<Go to ISI>://000081271400008}, |
6881 |
Volume = 28, |
6882 |
Year = 1999} |
6883 |
|
6884 |
@article{Sandu1999, |
6885 |
Abstract = {Numerical resonance artifacts have become recognized recently as a |
6886 |
limiting factor to increasing the timestep in multiple-timestep |
6887 |
(MTS) biomolecular dynamics simulations. At certain timesteps correlated |
6888 |
to internal motions (e.g., 5 fs, around half the period of the fastest |
6889 |
bond stretch, T-min), visible inaccuracies or instabilities can |
6890 |
occur. Impulse-MTS schemes are vulnerable to these resonance errors |
6891 |
since large energy pulses are introduced to the governing dynamics |
6892 |
equations when the slow forces are evaluated. We recently showed |
6893 |
that such resonance artifacts can be masked significantly by applying |
6894 |
extrapolative splitting to stochastic dynamics. Theoretical and |
6895 |
numerical analyses of force-splitting integrators based on the Verlet |
6896 |
discretization are reported here for linear models to explain these |
6897 |
observations and to suggest how to construct effective integrators |
6898 |
for biomolecular dynamics that balance stability with accuracy. |
6899 |
Analyses for Newtonian dynamics demonstrate the severe resonance |
6900 |
patterns of the Impulse splitting, with this severity worsening |
6901 |
with the outer timestep. Delta t: Constant Extrapolation is generally |
6902 |
unstable, but the disturbances do not grow with Delta t. Thus. the |
6903 |
stochastic extrapolative combination can counteract generic instabilities |
6904 |
and largely alleviate resonances with a sufficiently strong Langevin |
6905 |
heat-bath coupling (gamma), estimates for which are derived here |
6906 |
based on the fastest and slowest motion periods. These resonance |
6907 |
results generally hold for nonlinear test systems: a water tetramer |
6908 |
and solvated protein. Proposed related approaches such as Extrapolation/Correction |
6909 |
and Midpoint Extrapolation work better than Constant Extrapolation |
6910 |
only for timesteps less than T-min/2. An effective extrapolative |
6911 |
stochastic approach for biomolecules that balances long-timestep |
6912 |
stability with good accuracy for the fast subsystem is then applied |
6913 |
to a biomolecule using a three-class partitioning: the medium forces |
6914 |
are treated by Midpoint Extrapolation via position Verlet, and the |
6915 |
slow forces are incorporated by Constant Extrapolation. The resulting |
6916 |
algorithm (LN) performs well on a solvated protein system in terms |
6917 |
of thermodynamic properties and yields an order of magnitude speedup |
6918 |
with respect to single-timestep Langevin trajectories. Computed |
6919 |
spectral density functions also show how the Newtonian modes can |
6920 |
be approximated by using a small gamma in the range Of 5-20 ps(-1). |
6921 |
(C) 1999 Academic Press.}, |
6922 |
Annote = {194FM Times Cited:14 Cited References Count:32}, |
6923 |
Author = {A. Sandu and T. Schlick}, |
6924 |
Issn = {0021-9991}, |
6925 |
Journal = jcop, |
6926 |
Month = {May 1}, |
6927 |
Number = 1, |
6928 |
Pages = {74-113}, |
6929 |
Title = {Masking resonance artifacts in force-splitting methods for biomolecular simulations by extrapolative Langevin dynamics}, |
6930 |
Uri = {<Go to ISI>://000080181500004}, |
6931 |
Volume = 151, |
6932 |
Year = 1999} |
6933 |
|
6934 |
@article{Sasaki2004, |
6935 |
Abstract = {Tris(2-aminoethyl) amine derivatives with appended urea and sulfonamide |
6936 |
groups are shown to facilitate the translocation of fluorescent |
6937 |
phospholipid probes and endogenous phosphatidylserine across vesicle |
6938 |
and erythrocyte cell membranes. The synthetic translocases appear |
6939 |
to operate by binding to the phospholipid head groups and forming |
6940 |
lipophilic supramolecular complexes which diffuse through the non-polar |
6941 |
interior of the bilayer membrane.}, |
6942 |
Annote = {760PX Times Cited:8 Cited References Count:25}, |
6943 |
Author = {Y. Sasaki and R. Shukla and B. D. Smith}, |
6944 |
Issn = {1477-0520}, |
6945 |
Journal = {Organic \& Biomolecular Chemistry}, |
6946 |
Number = 2, |
6947 |
Pages = {214-219}, |
6948 |
Title = {Facilitated phosphatidylserine flip-flop across vesicle and cell membranes using urea-derived synthetic translocases}, |
6949 |
Uri = {<Go to ISI>://000187843800012}, |
6950 |
Volume = 2, |
6951 |
Year = 2004} |
6952 |
|
6953 |
@article{Satoh1996, |
6954 |
Abstract = {The effects of dipole-dipole interaction on mesophase formation are |
6955 |
investigated with a Monte Carlo simulation using the dipolar Gay-Berne |
6956 |
potential. It is shown that the dipole moment at the end of a molecule |
6957 |
causes a shift in the nematic-isotropic transition toward higher |
6958 |
temperature and a spread of the temperature range of the nematic |
6959 |
phase and that layer structures with various interdigitations are |
6960 |
formed in the smectic phase.}, |
6961 |
Annote = {Uq975 Times Cited:32 Cited References Count:33}, |
6962 |
Author = {K. Satoh and S. Mita and S. Kondo}, |
6963 |
Issn = {0009-2614}, |
6964 |
Journal = {Chemical Physics Letters}, |
6965 |
Month = {Jun 7}, |
6966 |
Number = {1-3}, |
6967 |
Pages = {99-104}, |
6968 |
Title = {Monte Carlo simulations using the dipolar Gay-Berne model: Effect of terminal dipole moment on mesophase formation}, |
6969 |
Uri = {<Go to ISI>://A1996UQ97500017}, |
6970 |
Volume = 255, |
6971 |
Year = 1996} |
6972 |
|
6973 |
@article{Schaps1999, |
6974 |
Annote = {163EC Times Cited:0 Cited References Count:0}, |
6975 |
Author = {G. L. Schaps}, |
6976 |
Issn = {1044-789X}, |
6977 |
Journal = {Dr Dobbs Journal}, |
6978 |
Month = {Mar}, |
6979 |
Number = 3, |
6980 |
Pages = {84-+}, |
6981 |
Title = {Compiler construction with ANTLR and Java - Tools for building tools}, |
6982 |
Uri = {<Go to ISI>://000078389200023}, |
6983 |
Volume = 24, |
6984 |
Year = 1999} |
6985 |
|
6986 |
@article{Shen2002, |
6987 |
Abstract = {Met-enkephalin is one of the smallest opiate peptides. Yet, its dynamical |
6988 |
structure and receptor docking mechanism are still not well understood. |
6989 |
The conformational dynamics of this neuron peptide in liquid water |
6990 |
are studied here by using all-atom molecular dynamics (MID) and |
6991 |
implicit water Langevin dynamics (LD) simulations with AMBER potential |
6992 |
functions and the three-site transferable intermolecular potential |
6993 |
(TIP3P) model for water. To achieve the same simulation length in |
6994 |
physical time, the full MID simulations require 200 times as much |
6995 |
CPU time as the implicit water LID simulations. The solvent hydrophobicity |
6996 |
and dielectric behavior are treated in the implicit solvent LD simulations |
6997 |
by using a macroscopic solvation potential, a single dielectric |
6998 |
constant, and atomic friction coefficients computed using the accessible |
6999 |
surface area method with the TIP3P model water viscosity as determined |
7000 |
here from MID simulations for pure TIP3P water. Both the local and |
7001 |
the global dynamics obtained from the implicit solvent LD simulations |
7002 |
agree very well with those from the explicit solvent MD simulations. |
7003 |
The simulations provide insights into the conformational restrictions |
7004 |
that are associated with the bioactivity of the opiate peptide dermorphin |
7005 |
for the delta-receptor.}, |
7006 |
Annote = {540MH Times Cited:36 Cited References Count:45}, |
7007 |
Author = {M. Y. Shen and K. F. Freed}, |
7008 |
Issn = {0006-3495}, |
7009 |
Journal = bj, |
7010 |
Month = {Apr}, |
7011 |
Number = 4, |
7012 |
Pages = {1791-1808}, |
7013 |
Title = {Long time dynamics of met-enkephalin: Comparison of explicit and implicit solvent models}, |
7014 |
Uri = {<Go to ISI>://000174932400010}, |
7015 |
Volume = 82, |
7016 |
Year = 2002} |
7017 |
|
7018 |
@article{Shillcock2005, |
7019 |
Annote = {901QJ Times Cited:9 Cited References Count:23}, |
7020 |
Author = {J. C. Shillcock and R. Lipowsky}, |
7021 |
Issn = {1476-1122}, |
7022 |
Journal = {Nature Materials}, |
7023 |
Month = {Mar}, |
7024 |
Number = 3, |
7025 |
Pages = {225-228}, |
7026 |
Title = {Tension-induced fusion of bilayer membranes and vesicles}, |
7027 |
Uri = {<Go to ISI>://000227296700019}, |
7028 |
Volume = 4, |
7029 |
Year = 2005} |
7030 |
|
7031 |
@article{Shimada1993, |
7032 |
Abstract = {To make improved treatments of electrostatic interactions in biomacromolecular |
7033 |
simulations, two possibilities are considered. The first is the |
7034 |
famous particle-particle and particle-mesh (PPPM) method developed |
7035 |
by Hockney and Eastwood, and the second is a new one developed here |
7036 |
in their spirit but by the use of the multipole expansion technique |
7037 |
suggested by Ladd. It is then numerically found that the new PPPM |
7038 |
method gives more accurate results for a two-particle system at |
7039 |
small separation of particles. Preliminary numerical examination |
7040 |
of the various computational methods for a single configuration |
7041 |
of a model BPTI-water system containing about 24,000 particles indicates |
7042 |
that both of the PPPM methods give far more accurate values with |
7043 |
reasonable computational cost than do the conventional truncation |
7044 |
methods. It is concluded the two PPPM methods are nearly comparable |
7045 |
in overall performance for the many-particle systems, although the |
7046 |
first method has the drawback that the accuracy in the total electrostatic |
7047 |
energy is not high for configurations of charged particles randomly |
7048 |
generated.}, |
7049 |
Annote = {Lh164 Times Cited:27 Cited References Count:47}, |
7050 |
Author = {J. Shimada and H. Kaneko and T. Takada}, |
7051 |
Issn = {0192-8651}, |
7052 |
Journal = jcc, |
7053 |
Month = {Jul}, |
7054 |
Number = 7, |
7055 |
Pages = {867-878}, |
7056 |
Title = {Efficient Calculations of Coulombic Interactions in Biomolecular Simulations with Periodic Boundary-Conditions}, |
7057 |
Uri = {<Go to ISI>://A1993LH16400011}, |
7058 |
Volume = 14, |
7059 |
Year = 1993} |
7060 |
|
7061 |
@article{Skeel2002, |
7062 |
Abstract = {The best simple method for Newtonian molecular dynamics is indisputably |
7063 |
the leapfrog Stormer-Verlet method. The appropriate generalization |
7064 |
to simple Langevin dynamics is unclear. An analysis is presented |
7065 |
comparing an 'impulse method' (kick; fluctuate; kick), the 1982 |
7066 |
method of van Gunsteren and Berendsen, and the Brunger-Brooks-Karplus |
7067 |
(BBK) method. It is shown how the impulse method and the van Gunsteren-Berendsen |
7068 |
methods can be implemented as efficiently as the BBK method. Other |
7069 |
considerations suggest that the impulse method is the best basic |
7070 |
method for simple Langevin dynamics, with the van Gunsteren-Berendsen |
7071 |
method a close contender.}, |
7072 |
Annote = {633RX Times Cited:8 Cited References Count:22}, |
7073 |
Author = {R. D. Skeel and J. A. Izaguirre}, |
7074 |
Issn = {0026-8976}, |
7075 |
Journal = mp, |
7076 |
Month = {Dec 20}, |
7077 |
Number = 24, |
7078 |
Pages = {3885-3891}, |
7079 |
Title = {An impulse integrator for Langevin dynamics}, |
7080 |
Uri = {<Go to ISI>://000180297200014}, |
7081 |
Volume = 100, |
7082 |
Year = 2002} |
7083 |
|
7084 |
@article{Skeel1997, |
7085 |
Abstract = {The following integration methods for special second-order ordinary |
7086 |
differential equations are studied: leapfrog, implicit midpoint, |
7087 |
trapezoid, Stormer-Verlet, and Cowell-Numerov. We show that all |
7088 |
are members, or equivalent to members, of a one-parameter family |
7089 |
of schemes. Some methods have more than one common form, and we |
7090 |
discuss a systematic enumeration of these forms. We also present |
7091 |
a stability and accuracy analysis based on the idea of ''modified |
7092 |
equations'' and a proof of symplecticness. It follows that Cowell-Numerov |
7093 |
and ''LIM2'' (a method proposed by Zhang and Schlick) are symplectic. |
7094 |
A different interpretation of the values used by these integrators |
7095 |
leads to higher accuracy and better energy conservation. Hence, |
7096 |
we suggest that the straightforward analysis of energy conservation |
7097 |
is misleading.}, |
7098 |
Annote = {We981 Times Cited:30 Cited References Count:35}, |
7099 |
Author = {R. D. Skeel and G. H. Zhang and T. Schlick}, |
7100 |
Issn = {1064-8275}, |
7101 |
Journal = {Siam Journal on Scientific Computing}, |
7102 |
Month = {Jan}, |
7103 |
Number = 1, |
7104 |
Pages = {203-222}, |
7105 |
Title = {A family of symplectic integrators: Stability, accuracy, and molecular dynamics applications}, |
7106 |
Uri = {<Go to ISI>://A1997WE98100012}, |
7107 |
Volume = 18, |
7108 |
Year = 1997} |
7109 |
|
7110 |
@article{Tao2005, |
7111 |
Abstract = {Recently a microscopic theory for the dynamics of suspensions of long |
7112 |
thin rigid rods was presented, confirming and expanding the well-known |
7113 |
theory by Doi and Edwards [The Theory of Polymer Dynamics (Clarendon, |
7114 |
Oxford, 1986)] and Kuzuu [J. Phys. Soc. Jpn. 52, 3486 (1983)]. Here |
7115 |
this theory is put to the test by comparing it against computer |
7116 |
simulations. A Brownian dynamics simulation program was developed |
7117 |
to follow the dynamics of the rods, with a length over a diameter |
7118 |
ratio of 60, on the Smoluchowski time scale. The model accounts |
7119 |
for excluded volume interactions between rods, but neglects hydrodynamic |
7120 |
interactions. The self-rotational diffusion coefficients D-r(phi) |
7121 |
of the rods were calculated by standard methods and by a new, more |
7122 |
efficient method based on calculating average restoring torques. |
7123 |
Collective decay of orientational order was calculated by means |
7124 |
of equilibrium and nonequilibrium simulations. Our results show |
7125 |
that, for the currently accessible volume fractions, the decay times |
7126 |
in both cases are virtually identical. Moreover, the observed decay |
7127 |
of diffusion coefficients with volume fraction is much quicker than |
7128 |
predicted by the theory, which is attributed to an oversimplification |
7129 |
of dynamic correlations in the theory. (c) 2005 American Institute |
7130 |
of Physics.}, |
7131 |
Annote = {943DN Times Cited:3 Cited References Count:26}, |
7132 |
Author = {Y. G. Tao and W. K. {den Otter} and J. T. Padding and J. K. G. Dhont and W. J. Briels}, |
7133 |
Issn = {0021-9606}, |
7134 |
Journal = jcp, |
7135 |
Month = {Jun 22}, |
7136 |
Number = 24, |
7137 |
Pages = {-}, |
7138 |
Title = {Brownian dynamics simulations of the self- and collective rotational diffusion coefficients of rigid long thin rods}, |
7139 |
Uri = {<Go to ISI>://000230332400077}, |
7140 |
Volume = 122, |
7141 |
Year = 2005} |
7142 |
|
7143 |
@book{Tolman1979, |
7144 |
Address = {New York}, |
7145 |
Author = {R.~C. Tolman}, |
7146 |
Chapter = 2, |
7147 |
Pages = {19-22}, |
7148 |
Publisher = {Dover Publications, Inc.}, |
7149 |
Title = {The Principles of Statistical Mechanics}, |
7150 |
Year = 1979} |
7151 |
|
7152 |
@article{Tu1995, |
7153 |
Abstract = {We report a constant pressure and temperature molecular dynamics simulation |
7154 |
of a fully hydrated liquid crystal (L(alpha) phase bilayer of dipalmitoylphosphatidylcholine |
7155 |
at 50 degrees C and 28 water molecules/lipid. We have shown that |
7156 |
the bilayer is stable throughout the 1550-ps simulation and have |
7157 |
demonstrated convergence of the system dimensions. Several important |
7158 |
aspects of the bilayer structure have been investigated and compared |
7159 |
favorably with experimental results. For example, the average positions |
7160 |
of specific carbon atoms along the bilayer normal agree well with |
7161 |
neutron diffraction data, and the electron density profile is in |
7162 |
accord with x-ray diffraction results. The hydrocarbon chain deuterium |
7163 |
order parameters agree reasonably well with NMR results for the |
7164 |
middles of the chains, but the simulation predicts too much order |
7165 |
at the chain ends. In spite of the deviations in the order parameters, |
7166 |
the hydrocarbon chain packing density appears to be essentially |
7167 |
correct, inasmuch as the area/lipid and bilayer thickness are in |
7168 |
agreement with the most refined experimental estimates. The deuterium |
7169 |
order parameters for the glycerol and choline groups, as well as |
7170 |
the phosphorus chemical shift anisotropy, are in qualitative agreement |
7171 |
with those extracted from NMR measurements.}, |
7172 |
Annote = {Tv018 Times Cited:108 Cited References Count:34}, |
7173 |
Author = {K. Tu and D. J. Tobias and M. L. Klein}, |
7174 |
Issn = {0006-3495}, |
7175 |
Journal = bj, |
7176 |
Month = {Dec}, |
7177 |
Number = 6, |
7178 |
Pages = {2558-2562}, |
7179 |
Title = {Constant pressure and temperature molecular dynamics simulation of a fully hydrated liquid crystal phase dipalmitoylphosphatidylcholine bilayer}, |
7180 |
Uri = {<Go to ISI>://A1995TV01800037}, |
7181 |
Volume = 69, |
7182 |
Year = 1995} |
7183 |
|
7184 |
@article{Tuckerman1992, |
7185 |
Abstract = {The Trotter factorization of the Liouville propagator is used to generate |
7186 |
new reversible molecular dynamics integrators. This strategy is |
7187 |
applied to derive reversible reference system propagator algorithms |
7188 |
(RESPA) that greatly accelerate simulations of systems with a separation |
7189 |
of time scales or with long range forces. The new algorithms have |
7190 |
all of the advantages of previous RESPA integrators but are reversible, |
7191 |
and more stable than those methods. These methods are applied to |
7192 |
a set of paradigmatic systems and are shown to be superior to earlier |
7193 |
methods. It is shown how the new RESPA methods are related to predictor-corrector |
7194 |
integrators. Finally, we show how these methods can be used to accelerate |
7195 |
the integration of the equations of motion of systems with Nose |
7196 |
thermostats.}, |
7197 |
Annote = {Je891 Times Cited:680 Cited References Count:19}, |
7198 |
Author = {M. Tuckerman and B. J. Berne and G. J. Martyna}, |
7199 |
Issn = {0021-9606}, |
7200 |
Journal = jcp, |
7201 |
Month = {Aug 1}, |
7202 |
Number = 3, |
7203 |
Pages = {1990-2001}, |
7204 |
Title = {Reversible Multiple Time Scale Molecular-Dynamics}, |
7205 |
Uri = {<Go to ISI>://A1992JE89100044}, |
7206 |
Volume = 97, |
7207 |
Year = 1992} |
7208 |
|
7209 |
@book{Varadarajan1974, |
7210 |
Address = {New York}, |
7211 |
Author = {V.S. Varadarajan}, |
7212 |
Publisher = {Prentice-Hall}, |
7213 |
Title = {Lie groups, Lie algebras, and their representations}, |
7214 |
Year = 1974} |
7215 |
|
7216 |
@article{Vincent1995, |
7217 |
Abstract = {We have implemented a portable parallel version of the macromolecular |
7218 |
modeling package AMBER4. The message passing paradigm was used. |
7219 |
All message passing constructs are compliant with the Message Passing |
7220 |
Interface (MPI) standard. The molecular dynamics/minimization module |
7221 |
MINMD and the free-energy perturbation module Gibbs have been implemented |
7222 |
in parallel on a number of machines, including a Gray T3D, an IBM |
7223 |
SP1/SP2, and a collection of networked workstations. In addition, |
7224 |
the code has been tested with an MPI implementation from Argonne |
7225 |
National Laboratories/Mississippi State University which runs on |
7226 |
many parallel machines. The goal of this work is to decrease the |
7227 |
amount of time required to perform molecular dynamics simulations. |
7228 |
Performance results for a Lipid bilayer molecular dynamics simulation |
7229 |
on a Gray T3D, an IBM SP1/SPZ and a Gray C90 are compared. (C) 1995 |
7230 |
by John Wiley & Sons, Inc.}, |
7231 |
Annote = {Ta403 Times Cited:16 Cited References Count:23}, |
7232 |
Author = {J. J. Vincent and K. M. Merz}, |
7233 |
Issn = {0192-8651}, |
7234 |
Journal = jcc, |
7235 |
Month = {Nov}, |
7236 |
Number = 11, |
7237 |
Pages = {1420-1427}, |
7238 |
Title = {A Highly Portable Parallel Implementation of Amber4 Using the Message-Passing Interface Standard}, |
7239 |
Uri = {<Go to ISI>://A1995TA40300009}, |
7240 |
Volume = 16, |
7241 |
Year = 1995} |
7242 |
|
7243 |
@article{Wegener1979, |
7244 |
Author = {W.~A. Wegener, V.~J. Koester and R.~M. Dowben}, |
7245 |
Journal = {Proc. Natl. Acad. Sci.}, |
7246 |
Number = 12, |
7247 |
Pages = {6356-6360}, |
7248 |
Title = {A general ellipsoid can not always serve as a modle for the rotational diffusion properties of arbitrary shaped rigid molecules}, |
7249 |
Volume = 76, |
7250 |
Year = 1979} |
7251 |
|
7252 |
@article{Wilson2006, |
7253 |
Author = {G.~V. Wilson}, |
7254 |
Journal = {American Scientist}, |
7255 |
Title = {Where's the Real Bottleneck in Scientific Computing?}, |
7256 |
Volume = 94, |
7257 |
Year = 2006} |
7258 |
|
7259 |
@article{Withers2003, |
7260 |
Abstract = {The effects of longitudinal quadrupole moments on the formation of |
7261 |
liquid crystalline phases are studied by means of constant NPT Monte |
7262 |
Carlo simulation methods. The popular Gay-Berne model mesogen is |
7263 |
used as the reference fluid, which displays the phase sequences |
7264 |
isotropic-smectic A-smectic B and isotropic-smectic B at high (T*=2.0) |
7265 |
and low (T*=1.5) temperatures, respectively. With increasing quadrupole |
7266 |
magnitude the smectic phases are observed to be stabilized with |
7267 |
respect to the isotropic liquid, while the smectic B is destabilized |
7268 |
with respect to the smectic A. At the lower temperature, a sufficiently |
7269 |
large quadrupole magnitude results in the injection of the smectic |
7270 |
A phase into the phase sequence and the replacement of the smectic |
7271 |
B phase by the tilted smectic J phase. The nematic phase is also |
7272 |
injected into the phase sequence at both temperatures considered, |
7273 |
and ultimately for sufficiently large quadrupole magnitudes no coherent |
7274 |
layered structures were observed. The stabilization of the smectic |
7275 |
A phase supports the commonly held belief that, while the inclusion |
7276 |
of polar groups is not a prerequisite for the formation of the smectic |
7277 |
A phase, quadrupolar interactions help to increase the temperature |
7278 |
and pressure range for which the smectic A phase is observed. The |
7279 |
quality of the layered structure is worsened with increasing quadrupole |
7280 |
magnitude. This behavior, along with the injection of the nematic |
7281 |
phase into the phase sequence, indicate that the general tendency |
7282 |
of the quadrupolar interactions is to destabilize the layered structure. |
7283 |
A pressure dependence upon the smectic layer spacing is observed. |
7284 |
This behavior is in much closer agreement with experimental findings |
7285 |
than has been observed previously for nonpolar Gay-Berne and hard |
7286 |
spherocylinder models. (C) 2003 American Institute of Physics.}, |
7287 |
Annote = {738EF Times Cited:3 Cited References Count:43}, |
7288 |
Author = {I. M. Withers}, |
7289 |
Issn = {0021-9606}, |
7290 |
Journal = jcp, |
7291 |
Month = {Nov 15}, |
7292 |
Number = 19, |
7293 |
Pages = {10209-10223}, |
7294 |
Title = {Effects of longitudinal quadrupoles on the phase behavior of a Gay-Berne fluid}, |
7295 |
Uri = {<Go to ISI>://000186273200027}, |
7296 |
Volume = 119, |
7297 |
Year = 2003} |
7298 |
|
7299 |
@article{Wolf1999, |
7300 |
Abstract = {Based on a recent result showing that the net Coulomb potential in |
7301 |
condensed ionic systems is rather short ranged, an exact and physically |
7302 |
transparent method permitting the evaluation of the Coulomb potential |
7303 |
by direct summation over the r(-1) Coulomb pair potential is presented. |
7304 |
The key observation is that the problems encountered in determining |
7305 |
the Coulomb energy by pairwise, spherically truncated r(-1) summation |
7306 |
are a direct consequence of the fact that the system summed over |
7307 |
is practically never neutral. A simple method is developed that |
7308 |
achieves charge neutralization wherever the r(-1) pair potential |
7309 |
is truncated. This enables the extraction of the Coulomb energy, |
7310 |
forces, and stresses from a spherically truncated, usually charged |
7311 |
environment in a manner that is independent of the grouping of the |
7312 |
pair terms. The close connection of our approach with the Ewald |
7313 |
method is demonstrated and exploited, providing an efficient method |
7314 |
for the simulation of even highly disordered ionic systems by direct, |
7315 |
pairwise r(-1) summation with spherical truncation at rather short |
7316 |
range, i.e., a method which fully exploits the short-ranged nature |
7317 |
of the interactions in ionic systems. The method is validated by |
7318 |
simulations of crystals, liquids, and interfacial systems, such |
7319 |
as free surfaces and grain boundaries. (C) 1999 American Institute |
7320 |
of Physics. [S0021-9606(99)51517-1].}, |
7321 |
Annote = {189PD Times Cited:70 Cited References Count:34}, |
7322 |
Author = {D. Wolf and P. Keblinski and S. R. Phillpot and J. Eggebrecht}, |
7323 |
Issn = {0021-9606}, |
7324 |
Journal = jcp, |
7325 |
Month = {May 1}, |
7326 |
Number = 17, |
7327 |
Pages = {8254-8282}, |
7328 |
Title = {Exact method for the simulation of Coulombic systems by spherically truncated, pairwise r(-1) summation}, |
7329 |
Uri = {<Go to ISI>://000079913000008}, |
7330 |
Volume = 110, |
7331 |
Year = 1999} |
7332 |
|
7333 |
@article{Yoshida1990, |
7334 |
Annote = {Ej798 Times Cited:492 Cited References Count:9}, |
7335 |
Author = {H. Yoshida}, |
7336 |
Issn = {0375-9601}, |
7337 |
Journal = {Physics Letters A}, |
7338 |
Month = {Nov 12}, |
7339 |
Number = {5-7}, |
7340 |
Pages = {262-268}, |
7341 |
Title = {Construction of Higher-Order Symplectic Integrators}, |
7342 |
Uri = {<Go to ISI>://A1990EJ79800009}, |
7343 |
Volume = 150, |
7344 |
Year = 1990} |
7345 |
|
7346 |
@article{Blum1972, |
7347 |
Author = {L. Blum and A.~J. Torruella}, |
7348 |
Journal = jcp, |
7349 |
Number = 1, |
7350 |
Pages = {303-309}, |
7351 |
Title = {Computer simulations of bilayer membranes: Self-assembly and interfacial tension}, |
7352 |
Volume = 56, |
7353 |
Year = 1972} |
7354 |
|
7355 |
@article{Stone1978, |
7356 |
Author = {A.~J. Stone}, |
7357 |
Journal = mp, |
7358 |
Number = 1, |
7359 |
Pages = {241-256}, |
7360 |
Title = {The description of bimolecular potentials, forces and torques: the S and V function expansions}, |
7361 |
Volume = 36, |
7362 |
Year = 1978} |
7363 |
|
7364 |
@article{Berardi2003, |
7365 |
Author = {R. Berardi, M. Cecchini and C. Zannoni}, |
7366 |
Journal = jcp, |
7367 |
Number = 18, |
7368 |
Pages = {9933-9946}, |
7369 |
Title = {A Monte Carlo study of the chiral columnar organizations of dissymmetric discotic mesogens}, |
7370 |
Volume = 119, |
7371 |
Year = 2003} |
7372 |
|
7373 |
@article{Beard2000, |
7374 |
Author = {D. A. Beard and T. Schlick}, |
7375 |
Journal = jcp, |
7376 |
Number = 17, |
7377 |
Pages = {7313-7322}, |
7378 |
Title = {Inertial Stochastic Dynamics. I. Long-time-step Methods for Langevin Dynamics}, |
7379 |
Volume = 112, |
7380 |
Year = 2000} |
7381 |
|
7382 |
@book{Hirsch1997, |
7383 |
Address = {New York}, |
7384 |
Author = {M.W. Hirsch}, |
7385 |
Publisher = {Springer}, |
7386 |
Title = {Differential Topology}, |
7387 |
Year = 1997} |
7388 |
|
7389 |
@book{Jost2002, |
7390 |
Address = {Berlin}, |
7391 |
Author = {J. Jost}, |
7392 |
Publisher = {Springer-Verlag}, |
7393 |
Title = {Riemannian Geometry and Geometric Analysis}, |
7394 |
Year = 2002} |
7395 |
|
7396 |
@book{McDuff1998, |
7397 |
Address = {Oxford}, |
7398 |
Author = {D. McDuff and D. Salamon}, |
7399 |
Publisher = {Oxford Mathematical Monographs}, |
7400 |
Title = {Introduction to Symplectic Topology}, |
7401 |
Year = 1998} |
7402 |
|
7403 |
@article{Matubayasi1999, |
7404 |
Author = {N. Matubayasi and M. Nakahara}, |
7405 |
Journal = jcp, |
7406 |
Number = 7, |
7407 |
Pages = {3291-3301}, |
7408 |
Title = {Reversible molecular dynamics for rigid bodies and hybrid Monte Carlo}, |
7409 |
Volume = 110, |
7410 |
Year = 1999} |
7411 |
|
7412 |
@article{Miller2002, |
7413 |
Author = {T.F. Miller III, M. Eleftheriou}, |
7414 |
Journal = jcp, |
7415 |
Number = 20, |
7416 |
Pages = {8649-8659}, |
7417 |
Title = {Symplectic quaternion scheme for biophysical molecular dynamics}, |
7418 |
Volume = 116, |
7419 |
Year = 1999} |
7420 |
|
7421 |
@article{McMillan1971, |
7422 |
Author = {W.L. McMillan}, |
7423 |
Journal = jcp, |
7424 |
Number = 3, |
7425 |
Pages = {1238-1246}, |
7426 |
Title = {Simple Molecular Model for the Smectic A Phase of Liquid Crystals}, |
7427 |
Volume = 4, |
7428 |
Year = 1971} |
7429 |
|
7430 |
@article{Gilmore1974, |
7431 |
Author = {R. Gilmore}, |
7432 |
Journal = {Journal of Mathematical Physics}, |
7433 |
Number = 12, |
7434 |
Pages = {2090-2092}, |
7435 |
Title = {Baker-Campbell-Hausdorff Formulas}, |
7436 |
Volume = 15, |
7437 |
Year = 1974} |
7438 |
|
7439 |
@article{Strang1968, |
7440 |
Author = {G. Strang}, |
7441 |
Journal = {SIAM Journal on Numerical Analysis}, |
7442 |
Number = 3, |
7443 |
Pages = {506-517}, |
7444 |
Title = {On the construction and comparision of difference schemes}, |
7445 |
Volume = 5, |
7446 |
Year = 1968} |
7447 |
|
7448 |
@article{Trotter1959, |
7449 |
Author = {H.F. Trotter}, |
7450 |
Journal = {SIAM Journal on Numerical Analysis}, |
7451 |
Number = 14, |
7452 |
Pages = {545-551}, |
7453 |
Title = {On the product of semi-groups of operators}, |
7454 |
Volume = 10, |
7455 |
Year = 1959} |
7456 |
|
7457 |
@article{Cartwright1992, |
7458 |
Author = {J.H.E. Cartwright and O. Piro}, |
7459 |
Journal = {International Journal of Bifurcation and Chaos}, |
7460 |
Number = 3, |
7461 |
Pages = {427-449}, |
7462 |
Title = {The Dynamics of Runge-Kutta Methods}, |
7463 |
Volume = 2, |
7464 |
Year = 1992} |
7465 |
|
7466 |
@article{HuseyinKaya07012005, |
7467 |
Abstract = {It has been demonstrated that a "near-Levinthal" cooperative mechanism, whereby the common G[o] interaction scheme is augmented by an extra favorability for the native state as a whole, can lead to apparent two-state folding/unfolding kinetics over a broad range of native stabilities in lattice models of proteins. Here such a mechanism is shown to be generalizable to a simplified continuum (off-lattice) Langevin dynamics model with a C{alpha} protein chain representation, with the resulting chevron plots exhibiting an extended quasilinear regime reminiscent of that of apparent two-state real proteins. Similarly high degrees of cooperativity are possible in G[o]-like continuum models with rudimentary pairwise desolvation barriers as well. In these models, cooperativity increases with increasing desolvation barrier height, suggesting strongly that two-state-like folding/unfolding kinetics would be achievable when the pairwise desolvation barrier becomes sufficiently high. Besides cooperativity, another generic folding property of interest that has emerged from published experiments on several apparent two-state proteins is that their folding relaxation under constant native stability (isostability) conditions is essentially Arrhenius, entailing high intrinsic enthalpic folding barriers of [~]17-30 kcal/mol. Based on a new analysis of published data on barnase, here we propose that a similar property should also apply to a certain class of non-two-state proteins that fold with chevron rollovers. However, several continuum G[o]-like constructs considered here fail to predict any significant intrinsic enthalpic folding barrier under isostability conditions; thus the physical origin of such barriers in real proteins remains to be elucidated. |
7468 |
}, |
7469 |
Author = {Kaya, Huseyin and Liu, Zhirong and Chan, Hue Sun}, |
7470 |
Doi = {10.1529/biophysj.104.057471}, |
7471 |
Eprint = {http://www.biophysj.org/cgi/reprint/89/1/520.pdf}, |
7472 |
Journal = {Biophys. J.}, |
7473 |
Number = 1, |
7474 |
Pages = {520-535}, |
7475 |
Title = {{Chevron Behavior and Isostable Enthalpic Barriers in Protein Folding: Successes and Limitations of Simple Go-like Modeling}}, |
7476 |
Url = {http://www.biophysj.org/cgi/content/abstract/89/1/520}, |
7477 |
Volume = 89, |
7478 |
Year = 2005, |
7479 |
Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/89/1/520}, |
7480 |
Bdsk-Url-2 = {http://dx.doi.org/10.1529/biophysj.104.057471}} |
7481 |
|
7482 |
@article{JoseGarciadelaTorre02012000, |
7483 |
Abstract = {The solution properties, including hydrodynamic quantities and the radius of gyration, of globular proteins are calculated from their detailed, atomic-level structure, using bead-modeling methodologies described in our previous article (Carrasco and Garcia de la Torre, 1999, Biophys. J. 76:3044-3057). We review how this goal has been pursued by other authors in the past. Our procedure starts from a list of atomic coordinates, from which we build a primary hydrodynamic model by replacing nonhydrogen atoms with spherical elements of some fixed radius. The resulting particle, consisting of overlapping spheres, is in turn represented by a shell model treated as described in our previous work. We have applied this procedure to a set of 13 proteins. For each protein, the atomic element radius is adjusted, to fit all of the hydrodynamic properties, taking values close to 3 A, with deviations that fall within the error of experimental data. Some differences are found in the atomic element radius found for each protein, which can be explained in terms of protein hydration. A computational shortcut makes the procedure feasible, even in personal computers. All of the model-building and calculations are carried out with a HYDROPRO public-domain computer program. |
7484 |
}, |
7485 |
Author = {{Garc\'{i}a de la Torre}, Jose and Huertas, Maria L. and Carrasco, Beatriz}, |
7486 |
Eprint = {http://www.biophysj.org/cgi/reprint/78/2/719.pdf}, |
7487 |
Journal = bj, |
7488 |
Number = {2}, |
7489 |
Pages = {719-730}, |
7490 |
Title = {{Calculation of Hydrodynamic Properties of Globular Proteins from Their Atomic-Level Structure}}, |
7491 |
Url = {http://www.biophysj.org/cgi/content/abstract/78/2/719}, |
7492 |
Volume = {78}, |
7493 |
Year = {2000}, |
7494 |
Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/78/2/719}} |
7495 |
|
7496 |
@article{GarciadelaTorreJ2002, |
7497 |
Affiliation = {Departamento de Qu{\'\i}mica F{\'\i}sica, Facultad de Qu{\'\i}mica, Universidad de Murcia, 30071 Murcia, Spain}, |
7498 |
Author = {{Garc\'{i}a de la Torre}, Jose and Carrasco, B.}, |
7499 |
Journal = {Biopolymers}, |
7500 |
Number = {3}, |
7501 |
Pages = {163-167}, |
7502 |
Title = {Hydrodynamic Properties of Rigid Macromolecules Composed of Ellipsoidal and Cylindrical Subunits}, |
7503 |
Volume = {63}, |
7504 |
Year = {2002}} |