--- trunk/langevin/langevin.bib 2008/01/11 22:08:57 3310 +++ trunk/langevin/langevin.bib 2008/04/30 14:50:53 3390 @@ -2,83 +2,346 @@ %% http://bibdesk.sourceforge.net/ -%% Created for Dan Gezelter at 2008-01-11 16:20:18 -0500 +%% Created for Xiuquan Sun at 2008-04-30 10:19:14 -0400 %% Saved with string encoding Western (ASCII) +@string{acp = {Adv. Chem. Phys.}} +@string{bj = {Biophys. J.}} + +@string{ccp5 = {CCP5 Information Quarterly}} + +@string{cp = {Chem. Phys.}} + +@string{cpl = {Chem. Phys. Lett.}} + +@string{jacs = {J. Am. Chem. Soc.}} + +@string{jcc = {J. Comp. Chem.}} + +@string{jcop = {J. Comp. Phys.}} + +@string{jcp = {J. Chem. Phys.}} + +@string{jmb = {J. Mol. Bio.}} + +@string{jml = {J. Mol. Liq.}} + +@string{jpc = {J. Phys. Chem.}} + +@string{jpca = {J. Phys. Chem. A}} + +@string{jpcb = {J. Phys. Chem. B}} + +@string{mp = {Mol. Phys.}} + +@string{pams = {Proc. Am. Math Soc.}} + +@string{pccp = {Phys. Chem. Chem. Phys.}} + +@string{pnas = {Proc. Natl. Acad. Sci. USA}} + +@string{pr = {Phys. Rev.}} + +@string{pra = {Phys. Rev. A}} + +@string{prb = {Phys. Rev. B}} + +@string{pre = {Phys. Rev. E}} + +@string{prl = {Phys. Rev. Lett.}} + +@string{rmp = {Rev. Mod. Phys.}} + + +@article{GarciadelaTorreJjp0647941, + Affiliation = {Departamento de Qu{\'\i}mica F{\'\i}sica, Facultad de Qu{\'\i}mica, Universidad de Murcia, 30071 Murcia, Spain}, + Author = {{Garc\'{i}a de la Torre}, Jose and del Rio Echenique, G. and Ortega, A.}, + Date-Added = {2008-04-30 10:14:50 -0400}, + Date-Modified = {2008-04-30 10:14:50 -0400}, + Issn = {1520-6106}, + Journal = jpcb, + Number = {5}, + Pages = {955-961}, + Title = {Improved Calculation of Rotational Diffusion and Intrinsic Viscosity of Bead Models for Macromolecules and Nanoparticles}, + Url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp0647941}, + Volume = {111}, + Year = {2007}} + +@article{Garcia-de-la-Torre:2001wd, + 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.}, + Author = {{Garc\'{i}a de la Torre}, Jose }, + Date-Added = {2008-04-29 15:11:32 -0400}, + Date-Modified = {2008-04-29 15:11:32 -0400}, + Journal = {Biophysical Chemistry}, + Keywords = {Rigid macromolecules; Hydrodynamic properties; Bead-shell model; Three-dimensional structure}, + Number = {3}, + Pages = {265--274}, + Title = {Building hydrodynamic bead-shell models for rigid bioparticles of arbitrary shape}, + Ty = {JOUR}, + Url = {http://www.sciencedirect.com/science/article/B6TFB-44XJKW6-8/1/376af59f3b89aecd8486b1c6186b0953}, + Volume = {94}, + Year = {2001}} + +@article{Peters:1999uq, + 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.}, + Author = {Peters, MH}, + Date-Added = {2008-03-13 16:54:59 -0400}, + Date-Modified = {2008-03-13 16:56:54 -0400}, + Journal = {Journal of Statistical Physics}, + Keywords = {Brownian particle; Fokker Planck equation; adsorption; molecular friction; force autocorrelation function; molecular dynamics}, + Pages = {557-586}, + Timescited = {0}, + Title = {Fokker-Planck equation, molecular friction, and molecular dynamics for Brownian particle transport near external solid surfaces}, + Volume = {94}, + Year = {1999}} + +@article{Peters:1999qy, + 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].}, + Author = {Peters, MH}, + Date-Added = {2008-03-13 16:54:59 -0400}, + Date-Modified = {2008-03-13 16:56:44 -0400}, + Journal = jcp, + Pages = {528-538}, + Timescited = {0}, + Title = {Fokker-Planck equation and the grand molecular friction tensor for coupled rotational and translational motions of structured Brownian particles near structured surfaces}, + Volume = {110}, + Year = {1999}} + +@article{Peters:2000fk, + 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].}, + Author = {Peters, MH}, + Date-Added = {2008-03-13 16:54:59 -0400}, + Date-Modified = {2008-03-13 16:56:20 -0400}, + Journal = jcp, + Pages = {5488-5498}, + Timescited = {0}, + Title = {The Smoluchowski diffusion equation for structured macromolecules near structured surfaces}, + Volume = {112}, + Year = {2000}} + +@article{Nienhuis:1970lr, + 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.}, + Author = {Nienhuis, G. }, + Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B6X42-46D224N-BW/2/0e1b39b5a20e979c5fa5e1f560de6413}, + Date-Added = {2008-03-13 16:53:44 -0400}, + Date-Modified = {2008-03-13 16:53:44 -0400}, + Journal = {Physica}, + Number = {1}, + Pages = {26--48}, + Title = {On the microscopic theory of Brownian motion with a rotational degree of freedom}, + Ty = {JOUR}, + Url = {http://www.sciencedirect.com/science/article/B6X42-46D224N-BW/2/0e1b39b5a20e979c5fa5e1f560de6413}, + Volume = {49}, + Year = {1970}} + +@article{SunX._jp0762020, + Affiliation = {Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556}, + Author = {Sun, X. and Gezelter, J.D.}, + Bdsk-Url-1 = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp0762020}, + Date-Added = {2008-02-15 13:48:18 -0500}, + Date-Modified = {2008-02-15 13:48:18 -0500}, + Issn = {1520-6106}, + Journal = jpcb, + Number = {7}, + Pages = {1968-1975}, + Title = {Dipolar Ordering in the Ripple Phases of Molecular-Scale Models of Lipid Membranes}, + Url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp0762020}, + Volume = {112}, + Year = {2008}} + +@book{Schlick2002, + Address = {Secaucus, NJ, USA}, + Author = {Tamar Schlick}, + Date-Added = {2008-02-12 16:52:19 -0500}, + Date-Modified = {2008-02-12 16:53:15 -0500}, + Isbn = {038795404X}, + Publisher = {Springer-Verlag New York, Inc.}, + Title = {Molecular Modeling and Simulation: An Interdisciplinary Guide}, + Year = {2002}} + +@article{Chun:2000fj, + 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.}, + 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}, + Date-Added = {2008-01-22 10:38:33 -0500}, + Date-Modified = {2008-01-22 10:38:49 -0500}, + Journal = jcc, + Keywords = {molecular dynamics; normal modes; anharmonicity; macromolecules; numerical integrators}, + Pages = {159--184}, + Timescited = 0, + Title = {{MBO(N)D:} A multibody method for long-time molecular dynamics simulations}, + Volume = 21, + Year = 2000} + +@article{Fogolari:1996lr, + 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.}, + Address = {Dipartimento di Scienze e Tecnologie Biomediche, Universita di Udine, Italy.}, + Au = {Fogolari, F and Esposito, G and Viglino, P and Cattarinussi, S}, + Author = {Fogolari, F and Esposito, G and Viglino, P and Cattarinussi, S}, + Da = {19960924}, + Date-Added = {2008-01-22 10:19:04 -0500}, + Date-Modified = {2008-01-22 10:19:09 -0500}, + Dcom = {19960924}, + Edat = {1996/03/01}, + Issn = {0006-3495 (Print)}, + Jid = {0370626}, + Journal = {Biophys J}, + Jt = {Biophysical journal}, + Language = {eng}, + Lr = {20071115}, + Mh = {Amino Acids/chemistry; Biophysics; Carbon/chemistry; Databases, Factual; Evaluation Studies as Topic; *Models, Molecular; Molecular Structure; Peptides/*chemistry; *Protein Conformation; Software; Thermodynamics}, + Mhda = {1996/03/01 00:01}, + Number = {3}, + Own = {NLM}, + Pages = {1183--1197}, + Pl = {UNITED STATES}, + Pmid = {8785277}, + Pst = {ppublish}, + Pt = {Journal Article}, + Pubm = {Print}, + Rn = {0 (Amino Acids); 0 (Peptides); 7440-44-0 (Carbon)}, + Sb = {IM}, + So = {Biophys J. 1996 Mar;70(3):1183-97. }, + Stat = {MEDLINE}, + Title = {Modeling of polypeptide chains as C alpha chains, C alpha chains with C beta, and C alpha chains with ellipsoidal lateral chains.}, + Volume = {70}, + Year = {1996}} + +@inbook{Ramachandran1996, + Address = {Providence, Rhode Island}, + Author = {Gomathi Ramachandran and Tamar Schlick}, + Chapter = {Beyond optimization: Simulating the dynamics of supercoiled DNA by a macroscopic model}, + Date-Added = {2008-01-22 10:03:42 -0500}, + Date-Modified = {2008-01-22 10:06:57 -0500}, + Editor = {P. M. Pardalos and D. Shalloway and G. Xue}, + Pages = {215-231}, + Publisher = {American Mathematical Society}, + Series = {DIMACS Series in Discrete Mathematics and Theoretical Computer Science}, + Title = {Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding}, + Volume = {23}, + Year = {1996}} + +@article{FIXMAN:1986lr, + Author = {Fixman, M}, + Date-Added = {2008-01-22 09:59:29 -0500}, + Date-Modified = {2008-01-22 09:59:35 -0500}, + Journal = {Macromolecules}, + Pages = {1204-1207}, + Timescited = {0}, + Title = {CONSTRUCTION OF LANGEVIN FORCES IN THE SIMULATION OF HYDRODYNAMIC INTERACTION}, + Volume = {19}, + Year = {1986}} + +@article{Berendsen87, + Author = {H.~J.~C. Berendsen and J.~R. Grigera and T.~P. Straatsma}, + Date-Added = {2008-01-22 09:53:15 -0500}, + Date-Modified = {2008-01-22 09:53:15 -0500}, + Journal = jpc, + Pages = {6269-6271}, + Title = {The Missing Term in Effective Pair Potentials}, + Volume = 91, + Year = 1987} + +@incollection{Berendsen81, + Address = {Dordrecht}, + Author = {H.~J.~C. Berendsen and J.~P.~M. Postma and W.~F. {van~Gunsteren} and J. Hermans}, + Booktitle = {Intermolecular Forces}, + Date-Added = {2008-01-22 09:52:49 -0500}, + Date-Modified = {2008-01-22 09:52:49 -0500}, + Editor = {B. Pullman}, + Pages = {331-342}, + Publisher = {Reidel}, + Title = {Simple Point Charge Water}, + Year = 1981} + +@article{Stillinger74, + Author = {F.~H. Stillinger and A. Rahman}, + Date-Added = {2008-01-22 09:51:43 -0500}, + Date-Modified = {2008-01-22 09:51:43 -0500}, + Journal = jcp, + Number = 4, + Pages = {1545-1557}, + Title = {Improved simulation of liquid water by molecular dynamics}, + Volume = 60, + Year = 1974} + @article{Torre:1983lr, - Author = {de la Torre, Jose Garcia and Rodes, Vicente}, + Author = {{Garc\'{i}a de la Torre}, Jose and Rodes, Vicente}, + Bdsk-Url-1 = {http://link.aip.org/link/?JCP/79/2454/1}, Date-Added = {2008-01-11 16:16:43 -0500}, Date-Modified = {2008-01-11 16:16:43 -0500}, - Journal = {The Journal of Chemical Physics}, + Journal = jcp, Journal1 = {The Journal of Chemical Physics}, Journal2 = {J. Chem. Phys.}, Keywords = {polymers; molecular models; hydrodynamics; rotation; interactions; macromolecules}, - Number = {5}, + Number = 5, Pages = {2454--2460}, Publisher = {AIP}, Title = {Effects from bead size and hydrodynamic interactions on the translational and rotational coefficients of macromolecular bead models}, Ty = {JOUR}, Url = {http://link.aip.org/link/?JCP/79/2454/1}, - Volume = {79}, - Year = {1983}} + Volume = 79, + Year = 1983} @article{PhysRev.119.53, Author = {Favro, L. Dale}, + Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRev.119.53}, Date-Added = {2008-01-09 16:57:02 -0500}, Date-Modified = {2008-01-09 16:57:02 -0500}, Doi = {10.1103/PhysRev.119.53}, Journal = {Phys. Rev.}, Month = {Jul}, - Number = {1}, - Numpages = {9}, + Number = 1, + Numpages = 9, Pages = {53--62}, Publisher = {American Physical Society}, Title = {Theory of the Rotational Brownian Motion of a Free Rigid Body}, - Volume = {119}, - Year = {1960}} + Volume = 119, + Year = 1960} @article{hess:209, Author = {Berk Hess}, + Bdsk-Url-1 = {http://link.aip.org/link/?JCP/116/209/1}, + Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.1421362}, Date-Added = {2008-01-08 16:41:06 -0500}, Date-Modified = {2008-01-08 16:41:06 -0500}, Doi = {10.1063/1.1421362}, - Journal = {The Journal of Chemical Physics}, + Journal = jcp, Keywords = {viscosity; molecular dynamics method; liquid theory; shear flow}, - Number = {1}, + Number = 1, Pages = {209-217}, Publisher = {AIP}, Title = {Determining the shear viscosity of model liquids from molecular dynamics simulations}, Url = {http://link.aip.org/link/?JCP/116/209/1}, - Volume = {116}, - Year = {2002}} + Volume = 116, + Year = 2002} @article{Garcia-de-la-Torre:1997qy, 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.}, Address = {Departamento de Quimica Fisica Universidad de Murcia, Spain. jgt{\char64}fcu,um.es}, - Au = {Garcia de la Torre, J and Carrasco, B and Harding, SE}, - Author = {Garcia de la Torre, J and Carrasco, B and Harding, S E}, - Da = {19970709}, + Au = {{Garc\'{i}a de la Torre}, Jose and Carrasco, B and Harding, SE}, + Author = {{Garc\'{i}a de la Torre}, Jose and Carrasco, B and Harding, S E}, + Da = 19970709, Date-Added = {2008-01-08 15:45:31 -0500}, Date-Modified = {2008-01-08 15:46:57 -0500}, - Dcom = {19970709}, + Dcom = 19970709, Edat = {1997/01/01}, Issn = {0175-7571 (Print)}, - Jid = {8409413}, + Jid = 8409413, Journal = {Eur Biophys J}, Jt = {European biophysics journal : EBJ}, Keywords = {Birefringence; Fluorescence Polarization; Humans; Immunoglobulin G/chemistry; Models, Structural; *Protein Conformation; Proteins/*chemistry; Scattering, Radiation; *Software; Ultracentrifugation/methods}, Language = {eng}, - Lr = {20061115}, + Lr = 20061115, Mhda = {1997/01/01 00:01}, Number = {5-6}, Own = {NLM}, Pages = {361--372}, Pl = {GERMANY}, - Pmid = {9213556}, + Pmid = 9213556, Pst = {ppublish}, Pt = {Journal Article; Research Support, Non-U.S. Gov't}, Pubm = {Print}, @@ -87,54 +350,56 @@ So = {Eur Biophys J. 1997;25(5-6):361-72.}, Stat = {MEDLINE}, Title = {SOLPRO: theory and computer program for the prediction of SOLution PROperties of rigid macromolecules and bioparticles.}, - Volume = {25}, - Year = {1997}} + Volume = 25, + Year = 1997} @article{Ravichandran:1999fk, 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].}, Author = {Ravichandran, S and Bagchi, B}, Date-Added = {2008-01-08 15:24:48 -0500}, Date-Modified = {2008-01-08 15:25:41 -0500}, - Journal = {Journal of Chemical Physics}, + Journal = jcp, Pages = {7505-7511}, Title = {Anisotropic diffusion of nonspherical molecules in dense liquids: A molecular dynamics simulation of isolated ellipsoids in the sea of spheres}, - Volume = {111}, - Year = {1999}} + Volume = 111, + Year = 1999} @article{TANG:1993lr, 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.}, Author = {TANG, SA and EVANS, GT}, Date-Added = {2008-01-08 15:23:42 -0500}, Date-Modified = {2008-01-08 15:24:09 -0500}, - Journal = {Molecular Physics}, + Journal = mp, Pages = {1443-1457}, Title = {A CRITIQUE OF SLIP AND STICK HYDRODYNAMICS FOR ELLIPSOIDAL BODIES}, - Volume = {80}, - Year = {1993}} + Volume = 80, + Year = 1993} @article{Schmidt:2003kx, 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.}, Author = {Schmidt, JR and Skinner, JL}, + Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.1610442}, Date-Added = {2008-01-08 15:12:53 -0500}, Date-Modified = {2008-01-08 15:13:21 -0500}, Doi = {DOI 10.1063/1.1610442}, - Journal = {Journal of Chemical Physics}, + Journal = jcp, Pages = {8062-8068}, Title = {Hydrodynamic boundary conditions, the Stokes-Einstein law, and long-time tails in the Brownian limit}, - Volume = {119}, - Year = {2003}} + Volume = 119, + Year = 2003} @article{Schmidt:2004fj, 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.}, Author = {Schmidt, JR and Skinner, JL}, + Bdsk-Url-1 = {http://dx.doi.org/10.1021/jp037185r}, Date-Added = {2008-01-08 15:12:53 -0500}, Date-Modified = {2008-01-08 15:13:20 -0500}, Doi = {DOI 10.1021/jp037185r}, - Journal = {Journal of Physical Chemistry B}, + Journal = jpcb, Pages = {6767-6771}, Title = {Brownian motion of a rough sphere and the Stokes-Einstein Law}, - Volume = {108}, - Year = {2004}} + Volume = 108, + Year = 2004} @article{Klein01, Author = {J.~C. Shelley andf M.~Y. Shelley and R.~C. Reeder and S. Bandyopadhyay and M.~L. Klein}, @@ -274,11 +539,11 @@ Date-Modified = {2008-01-08 14:58:56 -0500}, Journal = {J. Chem. Phys.}, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Essmann_SmoothPME_95.pdf}, - Number = {19}, + Number = 19, Pages = {8577-8593}, Title = {A smooth particle mesh Ewald method}, - Volume = {103}, - Year = {1995}} + Volume = 103, + Year = 1995} @article{Ricci94, Author = {S.~M. Ricci and J. Talbot and G. Tarjus and P. Viot}, @@ -328,8 +593,8 @@ Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Karasawa_LatticSumConvergence_89.pdf}, Pages = {7320-7327}, Title = {Acceleration of Convergence for Lattice Sums}, - Volume = {93}, - Year = {1989}} + Volume = 93, + Year = 1989} @article{Petersen95, Author = {H.~G. Petersen}, @@ -338,11 +603,11 @@ Journal = {J. Chem. Phys.}, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Petersen_AccuracyofPME_95.pdf}, Month = {September}, - Number = {9}, + Number = 9, Pages = {3668-3679}, Title = {Accuracy and efficiency of the particle mesh Ewald method}, - Volume = {103}, - Year = {1995}} + Volume = 103, + Year = 1995} @article{Duncan06, Author = {Peter D. Duncan and Philip J. Camp}, @@ -428,7 +693,7 @@ Year = 2003} @article{Cascales98, - Author = {J.~J.~L. Cascales and J.~G.~H. Cifre and J.~G. de~la~Torre}, + Author = {J.~J.~L. Cascales and J.~G.~H. Cifre and {Garc\'{i}a de la Torre}, Jose}, Date-Added = {2008-01-08 14:58:56 -0500}, Date-Modified = {2008-01-08 14:58:57 -0500}, Journal = {J. Phys. Chem. B}, @@ -475,8 +740,8 @@ Journal = {Phil. Mag. A}, Pages = {1057-1066}, Title = {Applications of the embedded-atom method to glass formation and crystallization of liquid and glass transition-metal nickel}, - Volume = {75}, - Year = {1997}} + Volume = 75, + Year = 1997} @inproceedings{Gotze89, Address = {Amsterdam}, @@ -529,8 +794,8 @@ Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Roberts_BoundryConditionsIonWater_95.pdf}, Pages = {1322-1331}, Title = {Boundary Conditions in Sumulations of Aqueous Ionic Solutions: A Systematic Study}, - Volume = {99}, - Year = {1995}} + Volume = 99, + Year = 1995} @article{Ayton02, Author = {G. Ayton and G.~A. Voth}, @@ -607,17 +872,19 @@ Abstract = {X-ray data are presented for the benchmark dipalmitoylphosphatidylcholine lipid bilayer in the most biologically relevant state in which the bilayers are fully hydrated and in the fluid (liquid-crystalline) phase. Form factors F(qz) are obtained from a combination of two sample preparations, oriented stacks of bilayers for qz extending to 0.85 A-1 and unilamellar vesicles for smaller qz. Modeling obtains the electron density profile and values for the area per molecule, for the locations of the component groups, and for the different types of thicknesses of the bilayer, such as the hydrocarbon thickness and the steric thickness. }, Author = {Kucerka, Norbert and Tristram-Nagle, Stephanie and Nagle, John F.}, + Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/90/11/L83}, + Bdsk-Url-2 = {http://dx.doi.org/10.1529/biophysj.106.086017}, Date-Added = {2008-01-08 14:58:56 -0500}, Date-Modified = {2008-01-08 14:58:57 -0500}, Doi = {10.1529/biophysj.106.086017}, Eprint = {http://www.biophysj.org/cgi/reprint/90/11/L83.pdf}, Journal = {Biophys. J.}, - Number = {11}, + Number = 11, Pages = {L83-85}, Title = {{Closer Look at Structure of Fully Hydrated Fluid Phase DPPC Bilayers}}, Url = {http://www.biophysj.org/cgi/content/abstract/90/11/L83}, - Volume = {90}, - Year = {2006}} + Volume = 90, + Year = 2006} @article{deJoannis06, Author = {J. de~Joannis and F.~Y. Jiang and J.~T. Kindt}, @@ -747,8 +1014,8 @@ Journal = {Mol. Simul.}, Pages = {351-368}, Title = {Cutoff Errors in the Ewald. Summation Formulae for Point Charge Systems}, - Volume = {9}, - Year = {1992}} + Volume = 9, + Year = 1992} @article{Tlusty00, Author = {T. Tlusty and S.~A. Safran}, @@ -762,18 +1029,19 @@ @article{Seung1988, Author = {Seung, H. S. and Nelson, David R.}, + Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRevA.38.1005}, Date-Added = {2008-01-08 14:58:56 -0500}, Date-Modified = {2008-01-08 14:58:58 -0500}, Doi = {10.1103/PhysRevA.38.1005}, Journal = {Phys. Rev. A}, Month = {Jul}, - Number = {2}, - Numpages = {13}, + Number = 2, + Numpages = 13, Pages = {1005--1018}, Publisher = {American Physical Society}, Title = {Defects in flexible membranes with crystalline order}, - Volume = {38}, - Year = {1988}} + Volume = 38, + Year = 1988} @article{Monroe95, Author = {C. Monroe and D.~M. Meekhof and B.~E. King and W.~M. Itano and D.~J. Wineland}, @@ -834,8 +1102,8 @@ Journal = {Ann. Physik}, Pages = {253-287}, Title = {Die Berechnung optischer und elektrostatischer Gitterpotential}, - Volume = {64}, - Year = {1921}} + Volume = 64, + Year = 1921} @article{Zwanzig88, Author = {R. Zwanzig}, @@ -882,10 +1150,10 @@ Date-Added = {2008-01-08 14:58:56 -0500}, Date-Modified = {2008-01-08 14:58:58 -0500}, Journal = prl, - Pages = {3649}, + Pages = 3649, Title = {Direct Observation of Stretched-Exponential Relaxation in Low-Temperature Lennard-Jones Systems Using the Cage Correlation Function}, Volume = 82, - Year = {1999}} + Year = 1999} @article{Ngai81, Author = {K.~L. Ngai and F.-S. Liu}, @@ -935,8 +1203,8 @@ Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/McCammon_ArtificialEwaldPeriodicity_99.pdf}, Pages = {69-88}, Title = {Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: a continuum electrostatics study}, - Volume = {78}, - Year = {1999}} + Volume = 78, + Year = 1999} @article{Spohr97, Author = {E. Spohr}, @@ -944,17 +1212,17 @@ Date-Modified = {2008-01-08 14:58:58 -0500}, Journal = {J. Chem. Phys.}, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Spohr_2DElectrostatics_97.pdf}, - Number = {16}, + Number = 16, Pages = {6342-6348}, Title = {Effect of electrostatic boundary conditions and system size on the interfacial properties of water and aqueous solutions}, - Volume = {107}, - Year = {1997}} + Volume = 107, + Year = 1997} @article{Marrink01b, Author = {S.~J. Marrink and A.~E. Mark}, Date-Added = {2008-01-08 14:58:56 -0500}, Date-Modified = {2008-01-08 14:58:58 -0500}, - Journal = {Journal of Physical Chemistry B}, + Journal = jpcb, Pages = {6122-6127}, Title = {Effect of undulations on surface tension in simulated bilayers}, Volume = 105, @@ -1047,8 +1315,8 @@ Journal = {Mol. Phys.}, Pages = {1313-1327}, Title = {Electrostatic Lattice Sums for Semi-Infinite Lattices}, - Volume = {37}, - Year = {1979}} + Volume = 37, + Year = 1979} @article{Heyes81, Author = {D.~M. Heyes}, @@ -1057,11 +1325,11 @@ Journal = {J. Chem. Phys.}, Keywords = {Empty Keywords}, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Heyes_CoulombChargeSpreading_81.pdf}, - Number = {3}, + Number = 3, Pages = {1924-1929}, Title = {Electrostatic potentials and fields in infinite point charge lattices}, - Volume = {74}, - Year = {1981}} + Volume = 74, + Year = 1981} @article{Tsonchev04, Author = {Stefan Tsonchev and George C. Schatz and Mark A. Ratner}, @@ -1081,34 +1349,36 @@ Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Tobias_ElectrostaticsCalculations_01.pdf}, Pages = {253-261}, Title = {Electrostatics calculations: recent methodological advances and applications to membranes}, - Volume = {11}, - Year = {2001}} + Volume = 11, + Year = 2001} @article{Arnold02, Author = {A. Arnold and J. {de Joannis} and C. Holm}, + Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.149195}, Date-Added = {2008-01-08 14:58:56 -0500}, Date-Modified = {2008-01-08 14:58:58 -0500}, Doi = {10.1063/1.149195}, Journal = {J. Chem. Phys.}, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Arnold_SlabElectrostatics_02.pdf}, - Number = {6}, + Number = 6, Pages = {2496-2502}, Title = {Electrostatics in periodic slab geometries. I}, - Volume = {117}, - Year = {2002}} + Volume = 117, + Year = 2002} @article{deJoannis02, Author = {J. {de Joannis} and A. Arnold and C. Holm}, + Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.149195}, Date-Added = {2008-01-08 14:58:56 -0500}, Date-Modified = {2008-01-08 14:58:58 -0500}, Doi = {10.1063/1.149195}, Journal = {J. Chem. Phys.}, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Joannis_SlabElectrostatics_02.pdf}, - Number = {6}, + Number = 6, Pages = {2503-2512}, Title = {Electrostatics in periodic slab geometries. II}, - Volume = {117}, - Year = {2002}} + Volume = 117, + Year = 2002} @article{Barenco95, Author = {A. Barenco and C.~H. Bennett and R. Cleve and D.~P. DiVincenzo and N. Margolus and P. Shor and T. Sleator and J.~A. Smolin and H. Weinfurter}, @@ -1158,11 +1428,11 @@ Date-Modified = {2008-01-08 14:58:58 -0500}, Journal = {J. Phys. Chem. B}, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/WolfApplications/Zahn_enhancedWolfH2O_02.pdf}, - Number = {41}, + Number = 41, Pages = {10725-10732}, Title = {Enhancement of the Wolf Damped Coulomb Potential: Static, Dynamic, and Dielectric Properties of Liquid Water from Molecular Simulation}, - Volume = {106}, - Year = {2002}} + Volume = 106, + Year = 2002} @article{Metropolis53, Author = {N. Metropolis and A.~W. Rosenbluth and M.~N. Rosenbluth and A.~H. Teller and E. Teller}, @@ -1180,10 +1450,10 @@ Date-Added = {2008-01-08 14:58:56 -0500}, Date-Modified = {2008-01-08 14:58:58 -0500}, Journal = {Surf. Sci.}, - Pages = {195}, + Pages = 195, Title = {Errata: The electrostatic potential in the surface region of an ionic crystal}, - Volume = {54}, - Year = {1976}} + Volume = 54, + Year = 1976} @article{Steane96, Author = {A.~M. Steane}, @@ -1211,11 +1481,11 @@ Date-Modified = {2008-01-08 14:58:59 -0500}, Journal = {J. Chem. Phys.}, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Hunenberger_IonSolutionEwaldArtifacts_99.pdf}, - Number = {4}, + Number = 4, Pages = {1856-1872}, Title = {Ewald artifacts in computer simulations of ionic solvation and ion -- ion interaction: A continuum electrostatics study}, - Volume = {110}, - Year = {1999}} + Volume = 110, + Year = 1999} @article{Rhee89, Author = {Y.-J. Rhee and J.~W. Halley and J. Hautman and A. Rahman}, @@ -1223,11 +1493,11 @@ Date-Modified = {2008-01-08 14:58:59 -0500}, Journal = {Phys. Rev. B}, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Rhee_finiteDimensionEwald_88.pdf}, - Number = {1}, + Number = 1, Pages = {36-42}, Title = {Ewald methods in molecular dynamics for systems of finite extent in one of three dimensions}, - Volume = {40}, - Year = {1989}} + Volume = 40, + Year = 1989} @article{Yeh99, Author = {I.-C. Yeh and M.~L. Berkowitz}, @@ -1235,14 +1505,15 @@ Date-Modified = {2008-01-08 14:58:59 -0500}, Journal = {J. Chem. Phys.}, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Yeh_SlabCorrectionEwald_99.pdf}, - Number = {7}, + Number = 7, Pages = {3155-3162}, Title = {Ewald summation for systems with slab geometry}, - Volume = {111}, - Year = {1999}} + Volume = 111, + Year = 1999} @article{Brodka04, Author = {A. Br\'{o}dka}, + Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.cplett.2004.10.086}, Date-Added = {2008-01-08 14:58:56 -0500}, Date-Modified = {2008-01-08 14:58:59 -0500}, Doi = {10.1016/j.cplett.2004.10.086}, @@ -1250,8 +1521,8 @@ Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Brodka_PointDipoleSlabEwald_04.pdf}, Pages = {62-67}, Title = {Ewald summation method with electrostatic layer correction for interactions of point dipoles in slab geometry}, - Volume = {400}, - Year = {2004}} + Volume = 400, + Year = 2004} @article{Chuang98, Author = {I. Chuang and N. Gershenfeld and M. Kubinec}, @@ -1319,17 +1590,18 @@ 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. }, Annote = {10.1529/biophysj.104.050096}, Author = {Benninger, Richard K. P. and Onfelt, Bjorn and Neil, Mark A. A. and Davis, Daniel M. and French, Paul M. W.}, + Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/88/1/609}, Date-Added = {2008-01-08 14:58:56 -0500}, Date-Modified = {2008-01-08 14:58:59 -0500}, - Journal = {Biophysical Journal}, + Journal = bj, Journal1 = {Biophys. J.}, - Number = {1}, + Number = 1, Pages = {609--622}, Title = {Fluorescence Imaging of Two-Photon Linear Dichroism: Cholesterol Depletion Disrupts Molecular Orientation in Cell Membranes}, Ty = {JOUR}, Url = {http://www.biophysj.org/cgi/content/abstract/88/1/609}, - Volume = {88}, - Year = {2005}} + Volume = 88, + Year = 2005} @inbook{Blumen86, Address = {Amsterdam}, @@ -1380,7 +1652,7 @@ Date-Added = {2008-01-08 14:58:56 -0500}, Date-Modified = {2008-01-08 14:58:59 -0500}, Eid = 157802, - Journal = {Physical Review Letters}, + Journal = prl, Number = 15, Numpages = 4, Pages = 157802, @@ -1447,11 +1719,11 @@ Date-Modified = {2008-01-08 14:58:59 -0500}, Journal = {J. Chem. Phys.}, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Roberts_IonSolventEwaldProbs_94.pdf}, - Number = {6}, + Number = 6, Pages = {5024-5031}, Title = {How the unit cell surface charge distriubution affects the energetics of ion-solvent interactions in simulations}, - Volume = {101}, - Year = {1994}} + Volume = 101, + Year = 1994} @article{Stillinger85, Author = {F.~H. Stillinger and T.~A. Weber}, @@ -1472,8 +1744,8 @@ Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/WolfApplications/Kast_dampedCoulomb_03.pdf}, Pages = {398-404}, Title = {Integral equation theory for correcting truncation errors in molecular simulations}, - Volume = {367}, - Year = {2003}} + Volume = 367, + Year = 2003} @article{Ayton01, Author = {Gary Ayton and Scott G. Bardenhagen and Patrick McMurty and Deborah Sulsky and Gregory A. Voth}, @@ -1532,11 +1804,11 @@ Date-Modified = {2008-01-08 14:58:59 -0500}, Journal = {J. Chem. Phys.}, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Luty_LatticeSumElectrostatics_95.pdf}, - Number = {8}, + Number = 8, Pages = {3014-3021}, Title = {Lattice-sum methods for calculating electrostatic interactions in molecular simulations}, - Volume = {103}, - Year = {1995}} + Volume = 103, + Year = 1995} @article{Wan94, Author = {Yi. Wan and R.~M. Stratt}, @@ -1572,7 +1844,7 @@ Author = {E. Lindahl and O. Edholm}, Date-Added = {2008-01-08 14:58:56 -0500}, Date-Modified = {2008-01-08 14:58:59 -0500}, - Journal = {Biophysical Journal}, + Journal = bj, Month = {July}, Pages = {426-433}, Title = {Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations}, @@ -1600,6 +1872,7 @@ @article{Goldstein88, Author = {Raymond E. Goldstein and Stanislas Leibler}, + Bdsk-File-1 = {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}, Date-Added = {2008-01-08 14:58:56 -0500}, Date-Modified = {2008-01-08 14:58:59 -0500}, Journal = prl, @@ -1624,11 +1897,11 @@ Date-Added = {2008-01-08 14:58:56 -0500}, Date-Modified = {2008-01-08 14:58:59 -0500}, Journal = {J. Chem. Soc., Faraday Trans. II}, - Number = {7}, + Number = 7, Pages = {1485-1496}, Title = {Molecular dynamics computer simulation of surface properties of crystalline potassium chloride}, - Volume = {73}, - Year = {1977}} + Volume = 73, + Year = 1977} @article{Vuilleumier97, Author = {Rodolphe Vuilleumier and Daniel Borgis}, @@ -1663,7 +1936,7 @@ Author = {A.~M. Smondyrev and M.~L. Berkowitz}, Date-Added = {2008-01-08 14:58:56 -0500}, Date-Modified = {2008-01-08 14:59:00 -0500}, - Journal = {Biophysical Journal}, + Journal = bj, Pages = {2472-2478}, Title = {Molecular Dynamics Simulation of {\sc dppc} Bilayer in {\sc dmso}}, Volume = 76, @@ -1673,7 +1946,7 @@ Author = {S.~J. Marrink and D.~P. Teileman}, Date-Added = {2008-01-08 14:58:56 -0500}, Date-Modified = {2008-01-08 14:59:00 -0500}, - Journal = {Biophysical Journal}, + Journal = bj, Pages = {2386-2392}, Title = {Molecular Dynamics Simulation of Spontaneous Membrane Fusion during a Cubic-Hexagonal Phase Transition}, Volume = 83, @@ -1712,16 +1985,17 @@ @article{Weber00, Author = {W. Weber and P.~H. H\"{u}nenberger and J.~A. McCammon}, + Bdsk-Url-1 = {http://dx.doi.org/10.1021/jp9937757}, Date-Added = {2008-01-08 14:58:56 -0500}, Date-Modified = {2008-01-08 14:59:00 -0500}, Doi = {10.1021/jp9937757}, Journal = {J. Phys. Chem. B}, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/McCammon_ArtificialEwaldPeriodicityMD_00.pdf}, - Number = {15}, + Number = 15, Pages = {3668-3675}, Title = {Molecular Dynamics Simulations of a Polyalanine Octapeptide under Ewald Boundary Conditions: Influence of Artificial Periodicity on Peptide Conformation}, - Volume = {104}, - Year = {2000}} + Volume = 104, + Year = 2000} @article{Venable00, Author = {R.~M. Venable and B.~R. Brooks and R.~W. Pastor}, @@ -1738,7 +2012,7 @@ Author = {M. Patra and M. Karttunen and M.~T. Hyv\"{o}nen and E. Falk and P. Lindqvist and I. Vattulainen}, Date-Added = {2008-01-08 14:58:56 -0500}, Date-Modified = {2008-01-08 14:59:00 -0500}, - Journal = {Biophysical Journal}, + Journal = bj, Pages = {3636-3645}, Title = {Molecular Dynamics Simulations of Lipid Bilayers: Major Artifacts Due to Truncating Electrostatic Interactions}, Volume = 84, @@ -1761,17 +2035,17 @@ Journal = {J. Chem. Phys.}, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/WaterSimulation/Rahman_MDWater_71.pdf}, Month = {October}, - Number = {7}, + Number = 7, Pages = {3336-3359}, Title = {Molecular Dynamics Study of Liquid Water}, - Volume = {55}, - Year = {1971}} + Volume = 55, + Year = 1971} @article{Sum03, Author = {A.~K. Sum and J.~J. de~Pablo}, Date-Added = {2008-01-08 14:58:56 -0500}, Date-Modified = {2008-01-08 14:59:00 -0500}, - Journal = {Biophysical Journal}, + Journal = bj, Pages = {3636-3645}, Title = {Molecular Simulation Study on the influence of Dimethylsulfoxide on the structure of Phospholipid Bilayers}, Volume = 85, @@ -1826,8 +2100,8 @@ Journal = {Mol. Phys.}, Pages = {789-792}, Title = {Monte Carlo studies of the dielectric properties of water-like models}, - Volume = {26}, - Year = {1973}} + Volume = 26, + Year = 1973} @article{Brush66, Author = {S.~G. Brush and H.~L. Sahlin and E. Teller}, @@ -1836,11 +2110,11 @@ Journal = {J. Chem. Phys.}, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Brush_MCEwaldApplication_66.pdf}, Month = {September}, - Number = {6}, + Number = 6, Pages = {2102-2118}, Title = {Monte Carlo Study of a One-Component Plasma. I}, - Volume = {45}, - Year = {1966}} + Volume = 45, + Year = 1966} @article{Tenchov2001, Author = {Boris Tenchov and Rumiana Koynova and Gert Rapp}, @@ -1854,15 +2128,16 @@ @article{Steinbach94, Author = {P.~J. Steinbach and B.~R. Brooks}, + Bdsk-Url-1 = {http://dx.doi.org/10.1002/jcc.540150702}, Date-Added = {2008-01-08 14:58:56 -0500}, Date-Modified = {2008-01-08 14:59:00 -0500}, Doi = {10.1002/jcc.540150702}, Journal = {J. Comput. Chem.}, - Number = {7}, + Number = 7, Pages = {667-683}, Title = {New spherical-cutoff methods for long-range forces in macromolecular simulation}, - Volume = {15}, - Year = {1994}} + Volume = 15, + Year = 1994} @article{McKinnon92, Author = {S.~J. McKinnon and S.~L. Whittenburg and B. Brooks}, @@ -1959,7 +2234,7 @@ Author = {J. Norberg and L. Nilsson}, Date-Added = {2008-01-08 14:58:56 -0500}, Date-Modified = {2008-01-08 14:59:00 -0500}, - Journal = {Biophysical Journal}, + Journal = bj, Pages = {1537-1553}, Title = {On the truncation of Long-Range Electrostatic Interactions in {\sc dna}}, Volume = 79, @@ -1994,11 +2269,11 @@ Date-Modified = {2008-01-08 14:59:00 -0500}, Journal = {J. Chem. Phys.}, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Jones_ChargeShapeFunctions_56.pdf}, - Number = {5}, + Number = 5, Pages = {1062-1063}, Title = {Optimum Atomic Shape for Bertaut Series}, - Volume = {25}, - Year = {1956}} + Volume = 25, + Year = 1956} @article{Renard1966, Author = {R\'emi Renard and Carl W. Garland}, @@ -2136,11 +2411,11 @@ Volume = 51, Year = 1995} -@book{Cevc87, +@book{Cevc80, Address = {New York}, Author = {Gregor Cevc and Derek Marsh}, Date-Added = {2008-01-08 14:58:56 -0500}, - Date-Modified = {2008-01-08 14:59:01 -0500}, + Date-Modified = {2008-03-20 12:27:15 -0400}, Publisher = {Wiley-Interscience}, Title = {Phospholipid Bilayers}, Year = 1980} @@ -2263,8 +2538,8 @@ Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Kawata_Rapid2DEwald_01.pdf}, Pages = {157-164}, Title = {Rapid calculation of two-dimensional Ewald summation}, - Volume = {340}, - Year = {2001}} + Volume = 340, + Year = 2001} @inproceedings{Barker80, Author = {J.~A. Barker}, @@ -2467,11 +2742,11 @@ Date-Modified = {2008-01-08 14:59:01 -0500}, Journal = {Proc. R. Soc. London Ser. A}, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/deLeeuw_EwaldSum_80.pdf}, - Number = {1752}, + Number = 1752, Pages = {27-56}, Title = {Simulation of Electostatic Systems in Periodic Boundary Conditions. I. Lattice Sums and Dielectric Constants}, - Volume = {373}, - Year = {1980}} + Volume = 373, + Year = 1980} @article{Ercolessi88, Author = {F. Ercolessi and M. Parrinello and E. Tosatti}, @@ -2579,17 +2854,19 @@ 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. }, Author = {Kucerka, Norbert and Liu, Yufeng and Chu, Nanjun and Petrache, Horia I. and Tristram-Nagle, Stephanie and Nagle, John F.}, + Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/88/4/2626}, + Bdsk-Url-2 = {http://dx.doi.org/10.1529/biophysj.104.056606}, Date-Added = {2008-01-08 14:58:56 -0500}, Date-Modified = {2008-01-08 14:59:02 -0500}, Doi = {10.1529/biophysj.104.056606}, Eprint = {http://www.biophysj.org/cgi/reprint/88/4/2626.pdf}, Journal = {Biophys. J.}, - Number = {4}, + Number = 4, Pages = {2626-2637}, Title = {{Structure of Fully Hydrated Fluid Phase DMPC and DLPC Lipid Bilayers Using X-Ray Scattering from Oriented Multilamellar Arrays and from Unilamellar Vesicles}}, Url = {http://www.biophysj.org/cgi/content/abstract/88/4/2626}, - Volume = {88}, - Year = {2005}} + Volume = 88, + Year = 2005} @article{Lenz07, Author = {Olaf Lenz and Friederike Schmid}, @@ -2699,11 +2976,11 @@ Date-Added = {2008-01-08 14:58:56 -0500}, Date-Modified = {2008-01-08 14:59:02 -0500}, Journal = {Mol. Phys.}, - Number = {2}, + Number = 2, Pages = {387-400}, Title = {The computer simulation of polar liquids}, - Volume = {38}, - Year = {1979}} + Volume = 38, + Year = 1979} @article{Pense92, Author = {A. W. Pense}, @@ -2743,8 +3020,8 @@ Journal = {Surf. Sci.}, Pages = {433-440}, Title = {The electrostatic potential in the surface region of an ionic crystal}, - Volume = {49}, - Year = {1975}} + Volume = 49, + Year = 1975} @article{Daw93, Author = {M.~S. Daw and S.~M. Foiles and M.~I. Baskes}, @@ -2792,11 +3069,11 @@ Date-Modified = {2008-01-08 14:59:02 -0500}, Journal = {J. Chem. Phys.}, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/WaterSimulation/Andrea_LongRangeForcesInWater_83.pdf}, - Number = {9}, + Number = 9, Pages = {4576-4584}, Title = {The role of long ranged forces in determining the structure and properties of liquid water}, - Volume = {79}, - Year = {1983}} + Volume = 79, + Year = 1983} @article{Brannigan04b, Author = {G. Brannigan and A.~C. Tamboli and F.~L.~H. Brown}, @@ -3000,18 +3277,19 @@ @article{Mutz1991, Author = {Mutz, M. and Bensimon, D. and Brienne, M. J.}, + Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRevLett.67.923}, Date-Added = {2008-01-08 14:58:56 -0500}, Date-Modified = {2008-01-08 14:59:03 -0500}, Doi = {10.1103/PhysRevLett.67.923}, Journal = {Phys. Rev. Lett.}, Month = {Aug}, - Number = {7}, - Numpages = {3}, + Number = 7, + Numpages = 3, Pages = {923--926}, Publisher = {American Physical Society}, Title = {Wrinkling transition in partially polymerized vesicles}, - Volume = {67}, - Year = {1991}} + Volume = 67, + Year = 1991} @article{Wendt78, Author = {H. Wendt and F.~F. Abraham}, @@ -3027,7 +3305,7 @@ Date-Added = {2008-01-08 14:58:56 -0500}, Date-Modified = {2008-01-08 14:59:03 -0500}, Note = {private correspondence}, - Year = {2000}} + Year = 2000} @article{Dwyer1977, Author = {D.~J. Dwyer and G.~W. Simmons and R.~P. Wei}, @@ -3086,16 +3364,17 @@ @article{Davis:1969uq, Abstract = { Exact solutions of the Stokes equations are derived for the case of two unequal spheres slowly rotating or translating perpendicular to their line of centers in a quiescent, unbounded viscous fluid, following Wakiya[16]. Numerical results are presented for the force and torque coefficients for size ratios from 1[middle dot]0 to 10[middle dot]0, and separations down to 0[middle dot]001 times the radius of the smaller.}, Author = {Davis, M. H.}, + Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B6TFK-445H8BM-84/2/b34951283900cdde792ec1309ec51565}, Date-Added = {2008-01-08 14:57:14 -0500}, Date-Modified = {2008-01-08 14:57:14 -0500}, Journal = {Chemical Engineering Science}, - Number = {12}, + Number = 12, Pages = {1769--1776}, Title = {The slow translation and rotation of two unequal spheres in a viscous fluid}, Ty = {JOUR}, Url = {http://www.sciencedirect.com/science/article/B6TFK-445H8BM-84/2/b34951283900cdde792ec1309ec51565}, - Volume = {24}, - Year = {1969}} + Volume = 24, + Year = 1969} @article{Stimson:1926qy, Author = {Stimson, M and Jeffery, GB}, @@ -3104,82 +3383,86 @@ Journal = {Proceedings of the Royal Society of London Series A-Containing Papers of a Mathematical and Physical Character}, Pages = {110-116}, Title = {The motion of two spheres in a viscous fluid}, - Volume = {111}, - Year = {1926}} + Volume = 111, + Year = 1926} @article{Orlandi:2006fk, 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.}, Address = {Dipartimento di Chimica Fisica e Inorganica, and INSTM, Universita di Bologna, Viale Risorgimento 4, 40136 Bologna, Italy.}, Au = {Orlandi, S and Berardi, R and Steltzer, J and Zannoni, C}, Author = {Orlandi, Silvia and Berardi, Roberto and Steltzer, Joachim and Zannoni, Claudio}, - Da = {20060407}, + Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.2176622}, + Da = 20060407, Date-Added = {2008-01-08 14:47:56 -0500}, Date-Modified = {2008-01-08 14:48:06 -0500}, - Dcom = {20070727}, + Dcom = 20070727, Doi = {10.1063/1.2176622}, Edat = {2006/04/08 09:00}, Issn = {0021-9606 (Print)}, - Jid = {0375360}, + Jid = 0375360, Journal = {J Chem Phys}, Jt = {The Journal of chemical physics}, Language = {eng}, Mhda = {2006/04/08 09:01}, - Number = {12}, + Number = 12, Own = {NLM}, - Pages = {124907}, + Pages = 124907, Pl = {United States}, - Pmid = {16599725}, + Pmid = 16599725, Pst = {ppublish}, Pt = {Journal Article}, Pubm = {Print}, So = {J Chem Phys. 2006 Mar 28;124(12):124907.}, Stat = {PubMed-not-MEDLINE}, Title = {A Monte Carlo study of the mesophases formed by polar bent-shaped molecules.}, - Volume = {124}, - Year = {2006}} + Volume = 124, + Year = 2006} @article{sun:031602, Author = {Xiuquan Sun and J. Daniel Gezelter}, + Bdsk-Url-1 = {http://link.aps.org/abstract/PRE/v75/e031602}, + Bdsk-Url-2 = {http://dx.doi.org/10.1103/PhysRevE.75.031602}, Date-Added = {2008-01-08 14:42:33 -0500}, Date-Modified = {2008-01-08 14:42:33 -0500}, Doi = {10.1103/PhysRevE.75.031602}, - Eid = {031602}, + Eid = 031602, Journal = {Physical Review E (Statistical, Nonlinear, and Soft Matter Physics)}, Keywords = {lattice theory; membranes}, - Number = {3}, - Numpages = {7}, - Pages = {031602}, + Number = 3, + Numpages = 7, + Pages = 031602, Publisher = {APS}, Title = {Spontaneous corrugation of dipolar membranes}, Url = {http://link.aps.org/abstract/PRE/v75/e031602}, - Volume = {75}, - Year = {2007}} + Volume = 75, + Year = 2007} @article{Ortega:2007lr, 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.}, Address = {Departamento de Quimica Fisica, Facultad de Quimica, Universidad de Murcia, 30071 Murcia, Spain.}, - Au = {Ortega, A and Garcia de la Torre, J}, - Author = {Ortega, A and Garcia de la Torre, J}, - Da = {20070813}, + Au = {Ortega, A and {Garc\'{i}a de la Torre}, Jose}, + Author = {Ortega, A and {Garc\'{i}a de la Torre}, Jose}, + Bdsk-Url-1 = {http://dx.doi.org/10.1021/bm700473f}, + Da = 20070813, Date-Added = {2008-01-08 14:38:03 -0500}, Date-Modified = {2008-01-08 14:38:49 -0500}, - Dcom = {20071017}, - Dep = {20070724}, + Dcom = 20071017, + Dep = 20070724, Doi = {10.1021/bm700473f}, Edat = {2007/07/25 09:00}, Issn = {1525-7797 (Print)}, - Jid = {100892849}, + Jid = 100892849, Journal = {Biomacromolecules}, Jt = {Biomacromolecules}, Keywords = {Computer Simulation; Heparin/chemistry; Macromolecular Substances/*chemistry; *Models, Chemical; *Models, Molecular; Molecular Conformation; Particle Size; Protein Conformation; Proteins/chemistry; Software; Solutions}, Language = {eng}, Mhda = {2007/10/18 09:00}, - Number = {8}, + Number = 8, Own = {NLM}, Pages = {2464--2475}, Phst = {2007/07/24 {$[$}aheadofprint{$]$}}, Pl = {United States}, - Pmid = {17645309}, + Pmid = 17645309, Pst = {ppublish}, Pt = {Journal Article; Research Support, Non-U.S. Gov't}, Pubm = {Print-Electronic}, @@ -3188,8 +3471,8 @@ So = {Biomacromolecules. 2007 Aug;8(8):2464-75. Epub 2007 Jul 24.}, Stat = {MEDLINE}, Title = {Equivalent radii and ratios of radii from solution properties as indicators of macromolecular conformation, shape, and flexibility.}, - Volume = {8}, - Year = {2007}} + Volume = 8, + Year = 2007} @article{Torre2003, Abstract = {While the prediction of hydrodynamic properties of rigid particles @@ -3215,16 +3498,16 @@ We provide an example of the application of this methodology to the dynamics of a semiflexible, wormlike DNA.}, Annote = {724XK Times Cited:6 Cited References Count:64}, - Author = {J. G. {de la Torre} and H. E. Sanchez and A. Ortega and J. G. Hernandez and M. X. Fernandes and F. G. Diaz and M. C. L. Martinez}, + 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}, Issn = {0175-7571}, Journal = {European Biophysics Journal with Biophysics Letters}, Month = {Aug}, - Number = {5}, + Number = 5, Pages = {477-486}, Title = {Calculation of the solution properties of flexible macromolecules: methods and applications}, Uri = {://000185513400011}, - Volume = {32}, - Year = {2003}} + Volume = 32, + Year = 2003} @article{Alakent2005, Abstract = {Time series analysis tools are employed on the principal modes obtained @@ -3264,28 +3547,28 @@ Annote = {973OH Times Cited:1 Cited References Count:33}, Author = {B. Alakent and M. C. Camurdan and P. Doruker}, Issn = {0021-9606}, - Journal = {Journal of Chemical Physics}, + Journal = jcp, Month = {Oct 8}, - Number = {14}, + Number = 14, Pages = {-}, Title = {Hierarchical structure of the energy landscape of proteins revisited by time series analysis. II. Investigation of explicit solvent effects}, Uri = {://000232532000064}, - Volume = {123}, - Year = {2005}} + Volume = 123, + Year = 2005} @book{Alexander1987, Address = {New York}, Author = {C. Alexander}, Publisher = {Oxford University Press}, Title = {A Pattern Language: Towns, Buildings, Construction}, - Year = {1987}} + Year = 1987} @book{Allen1987, Address = {New York}, Author = {M.~P. Allen and D.~J. Tildesley}, Publisher = {Oxford University Press}, Title = {Computer Simulations of Liquids}, - Year = {1987}} + Year = 1987} @article{Allison1991, Abstract = {A Brownian dynamics algorithm is developed to simulate dynamics experiments @@ -3307,24 +3590,24 @@ Issn = {0024-9297}, Journal = {Macromolecules}, Month = {Jan 21}, - Number = {2}, + Number = 2, Pages = {530-536}, Title = {A Brownian Dynamics Algorithm for Arbitrary Rigid Bodies - Application to Polarized Dynamic Light-Scattering}, Uri = {://A1991EU81400029}, - Volume = {24}, - Year = {1991}} + Volume = 24, + Year = 1991} @article{Andersen1983, Annote = {Rq238 Times Cited:559 Cited References Count:14}, Author = {H. C. Andersen}, Issn = {0021-9991}, - Journal = {Journal of Computational Physics}, - Number = {1}, + Journal = jcop, + Number = 1, Pages = {24-34}, Title = {Rattle - a Velocity Version of the Shake Algorithm for Molecular-Dynamics Calculations}, Uri = {://A1983RQ23800002}, - Volume = {52}, - Year = {1983}} + Volume = 52, + Year = 1983} @article{Auerbach2005, Abstract = {Acetylcholine receptor channels (AChRs) are proteins that switch between @@ -3349,14 +3632,14 @@ Annote = {895QF Times Cited:9 Cited References Count:33}, Author = {A. Auerbach}, Issn = {0027-8424}, - Journal = {Proceedings of the National Academy of Sciences of the United States of America}, + Journal = pnas, Month = {Feb 1}, - Number = {5}, + Number = 5, Pages = {1408-1412}, Title = {Gating of acetylcholine receptor channels: Brownian motion across a broad transition state}, Uri = {://000226877300030}, - Volume = {102}, - Year = {2005}} + Volume = 102, + Year = 2005} @article{Baber1995, Abstract = {The effect of the general anesthetics halothane, enflurane, and isoflurane @@ -3385,12 +3668,12 @@ Issn = {0006-2960}, Journal = {Biochemistry}, Month = {May 16}, - Number = {19}, + Number = 19, Pages = {6533-6539}, Title = {Distribution of General-Anesthetics in Phospholipid-Bilayers Determined Using H-2 Nmr and H-1-H-1 Noe Spectroscopy}, Uri = {://A1995QZ71600035}, - Volume = {34}, - Year = {1995}} + Volume = 34, + Year = 1995} @article{Banerjee2004, Abstract = {Based on a coherent state representation of noise operator and an @@ -3410,22 +3693,22 @@ Annote = {816YY Times Cited:8 Cited References Count:35}, Author = {D. Banerjee and B. C. Bag and S. K. Banik and D. S. Ray}, Issn = {0021-9606}, - Journal = {Journal of Chemical Physics}, + Journal = jcp, Month = {May 15}, - Number = {19}, + Number = 19, Pages = {8960-8972}, Title = {Solution of quantum Langevin equation: Approximations, theoretical and numerical aspects}, Uri = {://000221146400009}, - Volume = {120}, - Year = {2004}} + Volume = 120, + Year = 2004} @article{Barojas1973, Author = {J. Barojas and D. Levesque}, Journal = {Phys. Rev. A}, Pages = {1092-1105}, Title = {Simulation of Diatomic Homonuclear Liquids}, - Volume = {7}, - Year = {1973}} + Volume = 7, + Year = 1973} @article{Barth1998, Abstract = {We present an efficient new method termed LN for propagating biomolecular @@ -3457,14 +3740,14 @@ Annote = {105HH Times Cited:29 Cited References Count:49}, Author = {E. Barth and T. Schlick}, Issn = {0021-9606}, - Journal = {Journal of Chemical Physics}, + Journal = jcp, Month = {Aug 1}, - Number = {5}, + Number = 5, Pages = {1617-1632}, Title = {Overcoming stability limitations in biomolecular dynamics. I. Combining force splitting via extrapolation with Langevin dynamics in LN}, Uri = {://000075066300006}, - Volume = {109}, - Year = {1998}} + Volume = 109, + Year = 1998} @article{Batcho2001, Abstract = {We present an analysis for a simple two-component harmonic oscillator @@ -3481,14 +3764,14 @@ Annote = {469KV Times Cited:6 Cited References Count:30}, Author = {P. F. Batcho and T. Schlick}, Issn = {0021-9606}, - Journal = {Journal of Chemical Physics}, + Journal = jcp, Month = {Sep 1}, - Number = {9}, + Number = 9, Pages = {4019-4029}, Title = {Special stability advantages of position-Verlet over velocity-Verlet in multiple-time step integration}, Uri = {://000170813800005}, - Volume = {115}, - Year = {2001}} + Volume = 115, + Year = 2001} @article{Bates2005, Abstract = {Inspired by recent claims that compounds composed of V-shaped molecules @@ -3514,12 +3797,12 @@ Issn = {1539-3755}, Journal = {Physical Review E}, Month = {Nov}, - Number = {5}, + Number = 5, Pages = {-}, Title = {Biaxial nematic phases and V-shaped molecules: A Monte Carlo simulation study}, Uri = {://000233603100030}, - Volume = {72}, - Year = {2005}} + Volume = 72, + Year = 2005} @article{Beard2003, Abstract = {We introduce an unbiased protocol for performing rotational moves @@ -3534,14 +3817,14 @@ Annote = {736UA Times Cited:0 Cited References Count:11}, Author = {D. A. Beard and T. Schlick}, Issn = {0006-3495}, - Journal = {Biophysical Journal}, + Journal = bj, Month = {Nov 1}, - Number = {5}, + Number = 5, Pages = {2973-2976}, Title = {Unbiased rotational moves for rigid-body dynamics}, Uri = {://000186190500018}, - Volume = {85}, - Year = {2003}} + Volume = 85, + Year = 2003} @article{Beloborodov1998, Abstract = {Using the Green function of arbitrary rigid Brownian diffusion (Goldstein, @@ -3558,12 +3841,12 @@ Issn = {1090-7807}, Journal = {Journal of Magnetic Resonance}, Month = {Jun}, - Number = {2}, + Number = 2, Pages = {328-329}, Title = {Effect of coupling between rotational and translational Brownian motions on NMR spin relaxation: Consideration using green function of rigid body diffusion}, Uri = {://000074214800017}, - Volume = {132}, - Year = {1998}} + Volume = 132, + Year = 1998} @article{Berardi1996, Abstract = {We demonstrate that the overall molecular dipole organization in a @@ -3580,12 +3863,12 @@ Issn = {0009-2614}, Journal = {Chemical Physics Letters}, Month = {Oct 18}, - Number = {3}, + Number = 3, Pages = {357-362}, Title = {Antiphase structures in polar smectic liquid crystals and their molecular origin}, Uri = {://A1996VN63700023}, - Volume = {261}, - Year = {1996}} + Volume = 261, + Year = 1996} @article{Berkov2005, Abstract = {In this paper a detailed numerical study (in frames of the Slonczewski @@ -3610,12 +3893,12 @@ Issn = {1098-0121}, Journal = {Physical Review B}, Month = {Sep}, - Number = {9}, + Number = 9, Pages = {-}, Title = {Magnetization precession due to a spin-polarized current in a thin nanoelement: Numerical simulation study}, Uri = {://000232228500058}, - Volume = {72}, - Year = {2005}} + Volume = 72, + Year = 2005} @article{Berkov2005a, Abstract = {Numerical simulations of fast remagnetization processes using stochastic @@ -3641,8 +3924,8 @@ Pages = {442-448}, Title = {Stochastic dynamic simulations of fast remagnetization processes: recent advances and applications}, Uri = {://000228837600109}, - Volume = {290}, - Year = {2005}} + Volume = 290, + Year = 2005} @article{Berkov2002, Abstract = {We report on recent progress achieved by the development of numerical @@ -3664,52 +3947,52 @@ Issn = {0031-8965}, Journal = {Physica Status Solidi a-Applied Research}, Month = {Feb 16}, - Number = {2}, + Number = 2, Pages = {409-421}, Title = {Magnetization dynamics in nanoparticle systems: Numerical simulation using Langevin dynamics}, Uri = {://000174145200026}, - Volume = {189}, - Year = {2002}} + Volume = 189, + Year = 2002} @article{Bernal1980, - Author = {J.M. Bernal and J. G. {de la Torre}}, + Author = {J.M. Bernal and {Garc\'{i}a de la Torre}, Jose}, Journal = {Biopolymers}, Pages = {751-766}, Title = {Transport Properties and Hydrodynamic Centers of Rigid Macromolecules with Arbitrary Shape}, - Volume = {19}, - Year = {1980}} + Volume = 19, + Year = 1980} @article{Brenner1967, Author = {H. Brenner}, Journal = {J. Collid. Int. Sci.}, Pages = {407-436}, Title = {Coupling between the Translational and Rotational Brownian Motions of Rigid Particles of Arbitrary shape}, - Volume = {23}, - Year = {1967}} + Volume = 23, + Year = 1967} @article{Brooks1983, Annote = {Qp423 Times Cited:6414 Cited References Count:96}, Author = {B. R. Brooks and R. E. Bruccoleri and B. D. Olafson and D. J. States and S. Swaminathan and M. Karplus}, Issn = {0192-8651}, - Journal = {Journal of Computational Chemistry}, - Number = {2}, + Journal = jcc, + Number = 2, Pages = {187-217}, Title = {Charmm - a Program for Macromolecular Energy, Minimization, and Dynamics Calculations}, Uri = {://A1983QP42300010}, - Volume = {4}, - Year = {1983}} + Volume = 4, + Year = 1983} @article{Brunger1984, Annote = {Sm173 Times Cited:143 Cited References Count:22}, Author = {A. Brunger and C. L. Brooks and M. Karplus}, Issn = {0009-2614}, Journal = {Chemical Physics Letters}, - Number = {5}, + Number = 5, Pages = {495-500}, Title = {Stochastic Boundary-Conditions for Molecular-Dynamics Simulations of St2 Water}, Uri = {://A1984SM17300007}, - Volume = {105}, - Year = {1984}} + Volume = 105, + Year = 1984} @article{Budd1999, Abstract = {This paper examines a synthesis of adaptive mesh methods with the @@ -3723,12 +4006,12 @@ Issn = {1364-503X}, Journal = {Philosophical Transactions of the Royal Society of London Series a-Mathematical Physical and Engineering Sciences}, Month = {Apr 15}, - Number = {1754}, + Number = 1754, Pages = {1047-1077}, Title = {Self-similar numerical solutions of the porous-medium equation using moving mesh methods}, Uri = {://000080466800005}, - Volume = {357}, - Year = {1999}} + Volume = 357, + Year = 1999} @article{Camp1999, Abstract = {Fluids of hard bent-core molecules have been studied using theory @@ -3764,14 +4047,14 @@ Annote = {255TC Times Cited:24 Cited References Count:38}, Author = {P. J. Camp and M. P. Allen and A. J. Masters}, Issn = {0021-9606}, - Journal = {Journal of Chemical Physics}, + Journal = jcp, Month = {Dec 1}, - Number = {21}, + Number = 21, Pages = {9871-9881}, Title = {Theory and computer simulation of bent-core molecules}, Uri = {://000083685400056}, - Volume = {111}, - Year = {1999}} + Volume = 111, + Year = 1999} @article{Care2005, Abstract = {A review is presented of molecular and mesoscopic computer simulations @@ -3786,12 +4069,12 @@ Issn = {0034-4885}, Journal = {Reports on Progress in Physics}, Month = {Nov}, - Number = {11}, + Number = 11, Pages = {2665-2700}, Title = {Computer simulation of liquid crystals}, Uri = {://000233697600004}, - Volume = {68}, - Year = {2005}} + Volume = 68, + Year = 2005} @article{Carrasco1999, Abstract = {The hydrodynamic properties of rigid particles are calculated from @@ -3813,16 +4096,16 @@ them to some test cases, for which the properties are known a priori. We provide guidelines and computational tools for bead modeling.}, Annote = {200TT Times Cited:46 Cited References Count:57}, - Author = {B. Carrasco and J. G. {de la Torre}}, + Author = {B. Carrasco and {Garc\'{i}a de la Torre}, Jose}, Issn = {0006-3495}, - Journal = {Biophysical Journal}, + Journal = bj, Month = {Jun}, - Number = {6}, + Number = 6, Pages = {3044-3057}, Title = {Hydrodynamic properties of rigid particles: Comparison of different modeling and computational procedures}, Uri = {://000080556700016}, - Volume = {76}, - Year = {1999}} + Volume = 76, + Year = 1999} @article{Chandra1999, Abstract = {Dynamical properties of the soft sticky dipole (SSD) model of water @@ -3846,14 +4129,14 @@ Annote = {221EN Times Cited:14 Cited References Count:66}, Author = {A. Chandra and T. Ichiye}, Issn = {0021-9606}, - Journal = {Journal of Chemical Physics}, + Journal = jcp, Month = {Aug 8}, - Number = {6}, + Number = 6, Pages = {2701-2709}, Title = {Dynamical properties of the soft sticky dipole model of water: Molecular dynamics simulations}, Uri = {://000081711200038}, - Volume = {111}, - Year = {1999}} + Volume = 111, + Year = 1999} @article{Channell1990, Annote = {Dk631 Times Cited:152 Cited References Count:34}, @@ -3861,12 +4144,12 @@ Issn = {0951-7715}, Journal = {Nonlinearity}, Month = {may}, - Number = {2}, + Number = 2, Pages = {231-259}, Title = {Symplectic Integration of Hamiltonian-Systems}, Uri = {://A1990DK63100001}, - Volume = {3}, - Year = {1990}} + Volume = 3, + Year = 1990} @article{Chen2003, Abstract = {We investigate the asymptotic behavior of systems of nonlinear differential @@ -3887,8 +4170,8 @@ Pages = {21-30}, Title = {Explicit mixed finite order Runge-Kutta methods}, Uri = {://000180314200002}, - Volume = {44}, - Year = {2003}} + Volume = 44, + Year = 2003} @article{Cheung2004, Abstract = {Equilibrium molecular dynamics calculations have been performed for @@ -3906,14 +4189,14 @@ Annote = {866UM Times Cited:4 Cited References Count:61}, Author = {D. L. Cheung and S. J. Clark and M. R. Wilson}, Issn = {0021-9606}, - Journal = {Journal of Chemical Physics}, + Journal = jcp, Month = {Nov 8}, - Number = {18}, + Number = 18, Pages = {9131-9139}, Title = {Calculation of flexoelectric coefficients for a nematic liquid crystal by atomistic simulation}, Uri = {://000224798900053}, - Volume = {121}, - Year = {2004}} + Volume = 121, + Year = 2004} @article{Cheung2002, Abstract = {Equilibrium molecular dynamics calculations have been performed for @@ -3935,8 +4218,8 @@ Pages = {140-146}, Title = {Calculation of the rotational viscosity of a nematic liquid crystal}, Uri = {://000175331000020}, - Volume = {356}, - Year = {2002}} + Volume = 356, + Year = 2002} @article{Chin2004, Abstract = {Current molecular dynamics simulations of biomolecules using multiple @@ -3957,14 +4240,14 @@ Annote = {757TK Times Cited:1 Cited References Count:22}, Author = {S. A. Chin}, Issn = {0021-9606}, - Journal = {Journal of Chemical Physics}, + Journal = jcp, Month = {Jan 1}, - Number = {1}, + Number = 1, Pages = {8-13}, Title = {Dynamical multiple-time stepping methods for overcoming resonance instabilities}, Uri = {://000187577400003}, - Volume = {120}, - Year = {2004}} + Volume = 120, + Year = 2004} @article{Cook2000, Abstract = {The Kirkwood correlation factor g(1) determines the preference for @@ -3988,12 +4271,12 @@ Issn = {0267-8292}, Journal = {Liquid Crystals}, Month = {Dec}, - Number = {12}, + Number = 12, Pages = {1573-1583}, Title = {Simulation studies of dipole correlation in the isotropic liquid phase}, Uri = {://000165437800002}, - Volume = {27}, - Year = {2000}} + Volume = 27, + Year = 2000} @article{Cui2003, Abstract = {All-atom Langevin dynamics simulations have been performed to study @@ -4016,14 +4299,14 @@ Annote = {689LC Times Cited:3 Cited References Count:48}, Author = {B. X. Cui and M. Y. Shen and K. F. Freed}, Issn = {0027-8424}, - Journal = {Proceedings of the National Academy of Sciences of the United States of America}, + Journal = pnas, Month = {Jun 10}, - Number = {12}, + Number = 12, Pages = {7087-7092}, Title = {Folding and misfolding of the papillomavirus E6 interacting peptide E6ap}, Uri = {://000183493500037}, - Volume = {100}, - Year = {2003}} + Volume = 100, + Year = 2003} @article{Denisov2003, Abstract = {We study the slow phase of thermally activated magnetic relaxation @@ -4041,12 +4324,12 @@ Issn = {1098-0121}, Journal = {Physical Review B}, Month = {Jan 1}, - Number = {1}, + Number = 1, Pages = {-}, Title = {Magnetic relaxation in finite two-dimensional nanoparticle ensembles}, Uri = {://000180830400056}, - Volume = {67}, - Year = {2003}} + Volume = 67, + Year = 2003} @article{Derreumaux1998, Abstract = {To explore the origin of the large-scale motion of triosephosphate @@ -4076,14 +4359,14 @@ Annote = {Zl046 Times Cited:30 Cited References Count:29}, Author = {P. Derreumaux and T. Schlick}, Issn = {0006-3495}, - Journal = {Biophysical Journal}, + Journal = bj, Month = {Jan}, - Number = {1}, + Number = 1, Pages = {72-81}, Title = {The loop opening/closing motion of the enzyme triosephosphate isomerase}, Uri = {://000073393400009}, - Volume = {74}, - Year = {1998}} + Volume = 74, + Year = 1998} @article{Dullweber1997, Abstract = {Rigid body molecular models possess symplectic structure and time-reversal @@ -4108,22 +4391,22 @@ Annote = {Ya587 Times Cited:35 Cited References Count:32}, Author = {A. Dullweber and B. Leimkuhler and R. McLachlan}, Issn = {0021-9606}, - Journal = {Journal of Chemical Physics}, + Journal = jcp, Month = {Oct 15}, - Number = {15}, + Number = 15, Pages = {5840-5851}, Title = {Symplectic splitting methods for rigid body molecular dynamics}, Uri = {://A1997YA58700024}, - Volume = {107}, - Year = {1997}} + Volume = 107, + Year = 1997} @book{Gamma1994, Address = {London}, Author = {E. Gamma, R. Helm, R. Johnson and J. Vlissides}, - Chapter = {7}, + Chapter = 7, Publisher = {Perason Education}, Title = {Design Patterns: Elements of Reusable Object-Oriented Software}, - Year = {1994}} + Year = 1994} @article{Edwards2005, Abstract = {Using the Langevin dynamics technique, we have carried out simulations @@ -4141,49 +4424,49 @@ Issn = {0024-9297}, Journal = {Macromolecules}, Month = {Dec 13}, - Number = {25}, + Number = 25, Pages = {10590-10595}, Title = {Stretching a single diblock copolymer in a selective solvent: Langevin dynamics simulations}, Uri = {://000233866200035}, - Volume = {38}, - Year = {2005}} + Volume = 38, + Year = 2005} @article{Egberts1988, Annote = {Q0188 Times Cited:219 Cited References Count:43}, Author = {E. Egberts and H. J. C. Berendsen}, Issn = {0021-9606}, - Journal = {Journal of Chemical Physics}, + Journal = jcp, Month = {Sep 15}, - Number = {6}, + Number = 6, Pages = {3718-3732}, Title = {Molecular-Dynamics Simulation of a Smectic Liquid-Crystal with Atomic Detail}, Uri = {://A1988Q018800036}, - Volume = {89}, - Year = {1988}} + Volume = 89, + Year = 1988} @article{Ermak1978, Annote = {Fp216 Times Cited:785 Cited References Count:42}, Author = {D. L. Ermak and J. A. Mccammon}, Issn = {0021-9606}, - Journal = {Journal of Chemical Physics}, - Number = {4}, + Journal = jcp, + Number = 4, Pages = {1352-1360}, Title = {Brownian Dynamics with Hydrodynamic Interactions}, Uri = {://A1978FP21600004}, - Volume = {69}, - Year = {1978}} + Volume = 69, + Year = 1978} @article{Evans1977, Annote = {Ds757 Times Cited:271 Cited References Count:18}, Author = {D. J. Evans}, Issn = {0026-8976}, - Journal = {Molecular Physics}, - Number = {2}, + Journal = mp, + Number = 2, Pages = {317-325}, Title = {Representation of Orientation Space}, Uri = {://A1977DS75700002}, - Volume = {34}, - Year = {1977}} + Volume = 34, + Year = 1977} @article{Fennell2004, Abstract = {The density maximum and temperature dependence of the self-diffusion @@ -4212,14 +4495,14 @@ Annote = {816YY Times Cited:5 Cited References Count:39}, Author = {C. J. Fennell and J. D. Gezelter}, Issn = {0021-9606}, - Journal = {Journal of Chemical Physics}, + Journal = jcp, Month = {May 15}, - Number = {19}, + Number = 19, Pages = {9175-9184}, Title = {On the structural and transport properties of the soft sticky dipole and related single-point water models}, Uri = {://000221146400032}, - Volume = {120}, - Year = {2004}} + Volume = 120, + Year = 2004} @article{Fernandes2002, Abstract = {We have developed a Brownian dynamics simulation algorithm to generate @@ -4234,35 +4517,35 @@ its applicability. Examples include free diffusion, transport in an electric field, and diffusion in a restricting environment.}, Annote = {633AD Times Cited:2 Cited References Count:43}, - Author = {M. X. Fernandes and J. G. {de la Torre}}, + Author = {M. X. Fernandes and {Garc\'{i}a de la Torre}, Jose}, Issn = {0006-3495}, - Journal = {Biophysical Journal}, + Journal = bj, Month = {Dec}, - Number = {6}, + Number = 6, Pages = {3039-3048}, Title = {Brownian dynamics simulation of rigid particles of arbitrary shape in external fields}, Uri = {://000180256300012}, - Volume = {83}, - Year = {2002}} + Volume = 83, + Year = 2002} @book{Frenkel1996, Address = {New York}, Author = {D. Frenkel and B. Smit}, Publisher = {Academic Press}, Title = {Understanding Molecular Simulation : From Algorithms to Applications}, - Year = {1996}} + Year = 1996} @article{Gay1981, Annote = {Lj347 Times Cited:482 Cited References Count:13}, Author = {J. G. Gay and B. J. Berne}, Issn = {0021-9606}, - Journal = {Journal of Chemical Physics}, - Number = {6}, + Journal = jcp, + Number = 6, Pages = {3316-3319}, Title = {Modification of the Overlap Potential to Mimic a Linear Site-Site Potential}, Uri = {://A1981LJ34700029}, - Volume = {74}, - Year = {1981}} + Volume = 74, + Year = 1981} @article{Gelin1999, Abstract = {To investigate the influence of inertial effects on the dynamics of @@ -4288,21 +4571,21 @@ Issn = {1022-1344}, Journal = {Macromolecular Theory and Simulations}, Month = {Nov}, - Number = {6}, + Number = 6, Pages = {529-543}, Title = {Inertial effects in the Brownian dynamics with rigid constraints}, Uri = {://000083785700002}, - Volume = {8}, - Year = {1999}} + Volume = 8, + Year = 1999} @article{Goetz1998, Author = {R. Goetz and R. Lipowsky}, - Journal = {Journal of Chemical Physics}, - Number = {17}, - Pages = {7397}, + Journal = jcp, + Number = 17, + Pages = 7397, Title = {Computer simulations of bilayer membranes: Self-assembly and interfacial tension}, - Volume = {108}, - Year = {1998}} + Volume = 108, + Year = 1998} @book{Goldstein2001, Address = {San Francisco}, @@ -4310,7 +4593,7 @@ Edition = {3rd}, Publisher = {Addison Wesley}, Title = {Classical Mechanics}, - Year = {2001}} + Year = 2001} @article{Gray2003, Abstract = {Protein-protein docking algorithms provide a means to elucidate structural @@ -4340,14 +4623,14 @@ Annote = {704QL Times Cited:48 Cited References Count:60}, Author = {J. J. Gray and S. Moughon and C. Wang and O. Schueler-Furman and B. Kuhlman and C. A. Rohl and D. Baker}, Issn = {0022-2836}, - Journal = {Journal of Molecular Biology}, + Journal = jmb, Month = {Aug 1}, - Number = {1}, + Number = 1, Pages = {281-299}, Title = {Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations}, Uri = {://000184351300022}, - Volume = {331}, - Year = {2003}} + Volume = 331, + Year = 2003} @article{Greengard1994, Abstract = {Some of the recently developed fast summation methods that have arisen @@ -4364,25 +4647,25 @@ Issn = {0036-8075}, Journal = {Science}, Month = {Aug 12}, - Number = {5174}, + Number = 5174, Pages = {909-914}, Title = {Fast Algorithms for Classical Physics}, Uri = {://A1994PB49900031}, - Volume = {265}, - Year = {1994}} + Volume = 265, + Year = 1994} @article{Greengard1987, Annote = {L0498 Times Cited:899 Cited References Count:7}, Author = {L. Greengard and V. Rokhlin}, Issn = {0021-9991}, - Journal = {Journal of Computational Physics}, + Journal = jcop, Month = {Dec}, - Number = {2}, + Number = 2, Pages = {325-348}, Title = {A Fast Algorithm for Particle Simulations}, Uri = {://A1987L049800006}, - Volume = {73}, - Year = {1987}} + Volume = 73, + Year = 1987} @article{Hairer1997, Abstract = {Backward error analysis is a useful tool for the study of numerical @@ -4403,12 +4686,12 @@ Issn = {0029-599X}, Journal = {Numerische Mathematik}, Month = {Jun}, - Number = {4}, + Number = 4, Pages = {441-462}, Title = {The life-span of backward error analysis for numerical integrators}, Uri = {://A1997XJ48800002}, - Volume = {76}, - Year = {1997}} + Volume = 76, + Year = 1997} @article{Hao1993, Abstract = {A new procedure for studying the folding and unfolding of proteins, @@ -4450,12 +4733,12 @@ Issn = {0006-2960}, Journal = {Biochemistry}, Month = {Sep 21}, - Number = {37}, + Number = 37, Pages = {9614-9631}, Title = {Unfolding and Refolding of the Native Structure of Bovine Pancreatic Trypsin-Inhibitor Studied by Computer-Simulations}, Uri = {://A1993LY29400014}, - Volume = {32}, - Year = {1993}} + Volume = 32, + Year = 1993} @article{Hinsen2000, Abstract = {The slow dynamics of proteins around its native folded state is usually @@ -4494,8 +4777,8 @@ Pages = {25-37}, Title = {Harmonicity in slow protein dynamics}, Uri = {://000090121700003}, - Volume = {261}, - Year = {2000}} + Volume = 261, + Year = 2000} @article{Ho1992, Abstract = {Evidence has been found for the existence water at the protein-lipid @@ -4528,33 +4811,33 @@ Annote = {Ju251 Times Cited:55 Cited References Count:44}, Author = {C. Ho and C. D. Stubbs}, Issn = {0006-3495}, - Journal = {Biophysical Journal}, + Journal = bj, Month = {Oct}, - Number = {4}, + Number = 4, Pages = {897-902}, Title = {Hydration at the Membrane Protein-Lipid Interface}, Uri = {://A1992JU25100002}, - Volume = {63}, - Year = {1992}} + Volume = 63, + Year = 1992} @book{Hockney1981, Address = {New York}, Author = {R.W. Hockney and J.W. Eastwood}, Publisher = {McGraw-Hill}, Title = {Computer Simulation Using Particles}, - Year = {1981}} + Year = 1981} @article{Hoover1985, Annote = {Acr30 Times Cited:1809 Cited References Count:11}, Author = {W. G. Hoover}, Issn = {1050-2947}, Journal = {Physical Review A}, - Number = {3}, + Number = 3, Pages = {1695-1697}, Title = {Canonical Dynamics - Equilibrium Phase-Space Distributions}, Uri = {://A1985ACR3000056}, - Volume = {31}, - Year = {1985}} + Volume = 31, + Year = 1985} @article{Huh2004, Abstract = {Racemic fluids of chiral calamitic molecules are investigated with @@ -4570,14 +4853,14 @@ Annote = {870FJ Times Cited:0 Cited References Count:63}, Author = {Y. Huh and N. M. Cann}, Issn = {0021-9606}, - Journal = {Journal of Chemical Physics}, + Journal = jcp, Month = {Nov 22}, - Number = {20}, + Number = 20, Pages = {10299-10308}, Title = {Discrimination in isotropic, nematic, and smectic phases of chiral calamitic molecules: A computer simulation study}, Uri = {://000225042700059}, - Volume = {121}, - Year = {2004}} + Volume = 121, + Year = 2004} @article{Humphrey1996, Abstract = {VMD is a molecular graphics program designed for the display and analysis @@ -4611,12 +4894,12 @@ Issn = {0263-7855}, Journal = {Journal of Molecular Graphics}, Month = {Feb}, - Number = {1}, + Number = 1, Pages = {33-\&}, Title = {VMD: Visual molecular dynamics}, Uri = {://A1996UH51500005}, - Volume = {14}, - Year = {1996}} + Volume = 14, + Year = 1996} @article{Izaguirre2001, Abstract = {In this paper we show the possibility of using very mild stochastic @@ -4649,22 +4932,22 @@ Annote = {397CQ Times Cited:14 Cited References Count:36}, Author = {J. A. Izaguirre and D. P. Catarello and J. M. Wozniak and R. D. Skeel}, Issn = {0021-9606}, - Journal = {Journal of Chemical Physics}, + Journal = jcp, Month = {Feb 1}, - Number = {5}, + Number = 5, Pages = {2090-2098}, Title = {Langevin stabilization of molecular dynamics}, Uri = {://000166676100020}, - Volume = {114}, - Year = {2001}} + Volume = 114, + Year = 2001} @article{Torre1977, - Author = {Jose Garcia De La Torre, V.A. Bloomfield}, + Author = {{Garc\'{i}a de la Torre}, Jose and V.~A. Bloomfield}, Journal = {Biopolymers}, Pages = {1747-1763}, Title = {Hydrodynamic properties of macromolecular complexes. I. Translation}, - Volume = {16}, - Year = {1977}} + Volume = 16, + Year = 1977} @article{Kale1999, Abstract = {Molecular dynamics programs simulate the behavior of biomolecular @@ -4692,14 +4975,14 @@ Annote = {194FM Times Cited:373 Cited References Count:51}, 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}, Issn = {0021-9991}, - Journal = {Journal of Computational Physics}, + Journal = jcop, Month = {May 1}, - Number = {1}, + Number = 1, Pages = {283-312}, Title = {NAMD2: Greater scalability for parallel molecular dynamics}, Uri = {://000080181500013}, - Volume = {151}, - Year = {1999}} + Volume = 151, + Year = 1999} @article{Kane2000, Abstract = {The purpose of this work is twofold. First, we demonstrate analytically @@ -4723,12 +5006,12 @@ Issn = {0029-5981}, Journal = {International Journal for Numerical Methods in Engineering}, Month = {Dec 10}, - Number = {10}, + Number = 10, Pages = {1295-1325}, Title = {Variational integrators and the Newmark algorithm for conservative and dissipative mechanical systems}, Uri = {://000165270600004}, - Volume = {49}, - Year = {2000}} + Volume = 49, + Year = 2000} @article{Klimov1997, Abstract = {The viscosity (eta) dependence of the folding rates for four sequences @@ -4745,14 +5028,14 @@ Annote = {Xk293 Times Cited:77 Cited References Count:17}, Author = {D. K. Klimov and D. Thirumalai}, Issn = {0031-9007}, - Journal = {Physical Review Letters}, + Journal = prl, Month = {Jul 14}, - Number = {2}, + Number = 2, Pages = {317-320}, Title = {Viscosity dependence of the folding rates of proteins}, Uri = {://A1997XK29300035}, - Volume = {79}, - Year = {1997}} + Volume = 79, + Year = 1997} @article{Kol1997, Abstract = {Rigid-body molecular dynamics simulations typically are performed @@ -4778,14 +5061,14 @@ Annote = {Xq332 Times Cited:11 Cited References Count:18}, Author = {A. Kol and B. B. Laird and B. J. Leimkuhler}, Issn = {0021-9606}, - Journal = {Journal of Chemical Physics}, + Journal = jcp, Month = {Aug 15}, - Number = {7}, + Number = 7, Pages = {2580-2588}, Title = {A symplectic method for rigid-body molecular simulation}, Uri = {://A1997XQ33200046}, - Volume = {107}, - Year = {1997}} + Volume = 107, + Year = 1997} @article{Lansac2001, Abstract = {Cyanobiphenyls (nCB's) represent a useful and intensively studied @@ -4814,12 +5097,12 @@ Issn = {1063-651X}, Journal = {Physical Review E}, Month = {Nov}, - Number = {5}, + Number = 5, Pages = {-}, Title = {Microscopic structure and dynamics of a partial bilayer smectic liquid crystal}, Uri = {://000172406900063}, - Volume = {6405}, - Year = {2001}} + Volume = 6405, + Year = 2001} @article{Lansac2003, Abstract = {Recently, a new class of smectic liquid crystal phases characterized @@ -4842,12 +5125,12 @@ Issn = {1063-651X}, Journal = {Physical Review E}, Month = {Jan}, - Number = {1}, + Number = 1, Pages = {-}, Title = {Phase behavior of bent-core molecules}, Uri = {://000181017300042}, - Volume = {67}, - Year = {2003}} + Volume = 67, + Year = 2003} @book{Leach2001, Address = {Harlow, England}, @@ -4855,7 +5138,7 @@ Edition = {2nd}, Publisher = {Pearson Educated Limited}, Title = {Molecular Modeling: Principles and Applications}, - Year = {2001}} + Year = 2001} @article{Leimkuhler1999, Abstract = {Reversible and adaptive integration methods based on Kustaanheimo-Stiefel @@ -4875,43 +5158,43 @@ Issn = {1364-503X}, Journal = {Philosophical Transactions of the Royal Society of London Series a-Mathematical Physical and Engineering Sciences}, Month = {Apr 15}, - Number = {1754}, + Number = 1754, Pages = {1101-1133}, Title = {Reversible adaptive regularization: perturbed Kepler motion and classical atomic trajectories}, Uri = {://000080466800007}, - Volume = {357}, - Year = {1999}} + Volume = 357, + Year = 1999} @book{Leimkuhler2004, Address = {Cambridge}, Author = {B. Leimkuhler and S. Reich}, Publisher = {Cambridge University Press}, Title = {Simulating Hamiltonian Dynamics}, - Year = {2004}} + Year = 2004} @article{Levelut1981, Annote = {Ml751 Times Cited:96 Cited References Count:16}, Author = {A. M. Levelut and R. J. Tarento and F. Hardouin and M. F. Achard and G. Sigaud}, Issn = {1050-2947}, Journal = {Physical Review A}, - Number = {4}, + Number = 4, Pages = {2180-2186}, Title = {Number of Sa Phases}, Uri = {://A1981ML75100057}, - Volume = {24}, - Year = {1981}} + Volume = 24, + Year = 1981} @article{Lieb1982, Annote = {Nu461 Times Cited:40 Cited References Count:28}, Author = {W. R. Lieb and M. Kovalycsik and R. Mendelsohn}, Issn = {0006-3002}, Journal = {Biochimica Et Biophysica Acta}, - Number = {2}, + Number = 2, Pages = {388-398}, Title = {Do Clinical-Levels of General-Anesthetics Affect Lipid Bilayers - Evidence from Raman-Scattering}, Uri = {://A1982NU46100012}, - Volume = {688}, - Year = {1982}} + Volume = 688, + Year = 1982} @article{Link1997, Abstract = {A smectic liquid-crystal phase made from achiral molecules with bent @@ -4929,12 +5212,12 @@ Issn = {0036-8075}, Journal = {Science}, Month = {Dec 12}, - Number = {5345}, + Number = 5345, Pages = {1924-1927}, Title = {Spontaneous formation of macroscopic chiral domains in a fluid smectic phase of achiral molecules}, Uri = {://A1997YL00200028}, - Volume = {278}, - Year = {1997}} + Volume = 278, + Year = 1997} @article{Liwo2005, Annote = {Suppl. 1 005MG Times Cited:0 Cited References Count:0}, @@ -4945,8 +5228,8 @@ Pages = {359-360}, Title = {Ab initio simulations of protein folding pathways by molecular dynamics with the united-residue (UNRES) model of polypeptide chains}, Uri = {://000234826102043}, - Volume = {272}, - Year = {2005}} + Volume = 272, + Year = 2005} @article{Luty1994, Abstract = {We compare the Particle-Particle Particle-Mesh (PPPM) and Ewald methods @@ -4961,12 +5244,12 @@ Author = {B. A. Luty and M. E. Davis and I. G. Tironi and W. F. Vangunsteren}, Issn = {0892-7022}, Journal = {Molecular Simulation}, - Number = {1}, + Number = 1, Pages = {11-20}, Title = {A Comparison of Particle-Particle, Particle-Mesh and Ewald Methods for Calculating Electrostatic Interactions in Periodic Molecular-Systems}, Uri = {://A1994QF46400002}, - Volume = {14}, - Year = {1994}} + Volume = 14, + Year = 1994} @book{Marion1990, Address = {New York}, @@ -4974,7 +5257,7 @@ Edition = {2rd}, Publisher = {Academic Press}, Title = {Classical Dynamics of Particles and Systems}, - Year = {1990}} + Year = 1990} @article{Marrink1994, Abstract = {To obtain insight in the process of water permeation through a lipid @@ -5006,20 +5289,20 @@ Issn = {0022-3654}, Journal = {Journal of Physical Chemistry}, Month = {Apr 14}, - Number = {15}, + Number = 15, Pages = {4155-4168}, Title = {Simulation of Water Transport through a Lipid-Membrane}, Uri = {://A1994NG21900040}, - Volume = {98}, - Year = {1994}} + Volume = 98, + Year = 1994} @article{Marrink2004, Author = {S.~J. Marrink and A.~H. de~Vries and A.~E. Mark}, Journal = {J. Phys. Chem. B}, Pages = {750-760}, Title = {Coarse Grained Model for Semiquantitative Lipid Simulations}, - Volume = {108}, - Year = {2004}} + Volume = 108, + Year = 2004} @article{Marsden1998, Abstract = {This paper presents a geometric-variational approach to continuous @@ -5047,12 +5330,12 @@ Issn = {0010-3616}, Journal = {Communications in Mathematical Physics}, Month = {Dec}, - Number = {2}, + Number = 2, Pages = {351-395}, Title = {Multisymplectic geometry, variational integrators, and nonlinear PDEs}, Uri = {://000077902200006}, - Volume = {199}, - Year = {1998}} + Volume = 199, + Year = 1998} @article{Matthey2004, Abstract = {PROTOMOL is a high-performance framework in C++ for rapid prototyping @@ -5077,20 +5360,20 @@ Issn = {0098-3500}, Journal = {Acm Transactions on Mathematical Software}, Month = {Sep}, - Number = {3}, + Number = 3, Pages = {237-265}, Title = {ProtoMol, an object-oriented framework for prototyping novel algorithms for molecular dynamics}, Uri = {://000224325600001}, - Volume = {30}, - Year = {2004}} + Volume = 30, + Year = 2004} @article{McLachlan1993, Author = {R.~I McLachlan}, Journal = {prl}, Pages = {3043-3046}, Title = {Explicit Lie-Poisson integration and the Euler equations}, - Volume = {71}, - Year = {1993}} + Volume = 71, + Year = 1993} @article{McLachlan1998, Abstract = {We give a survey and some new examples of generating functions for @@ -5108,8 +5391,8 @@ Pages = {298-309}, Title = {Generating functions for dynamical systems with symmetries, integrals, and differential invariants}, Uri = {://000071558900021}, - Volume = {112}, - Year = {1998}} + Volume = 112, + Year = 1998} @article{McLachlan1998a, Abstract = {We consider properties of flows, the relationships between them, and @@ -5126,12 +5409,12 @@ Issn = {0036-1429}, Journal = {Siam Journal on Numerical Analysis}, Month = {Apr}, - Number = {2}, + Number = 2, Pages = {586-599}, Title = {Numerical integrators that preserve symmetries and reversing symmetries}, Uri = {://000072580500010}, - Volume = {35}, - Year = {1998}} + Volume = 35, + Year = 1998} @article{McLachlan2005, Abstract = {In this paper we revisit the Moser-Veselov description of the free @@ -5152,12 +5435,12 @@ Issn = {1615-3375}, Journal = {Foundations of Computational Mathematics}, Month = {Feb}, - Number = {1}, + Number = 1, Pages = {87-123}, Title = {The discrete Moser-Veselov algorithm for the free rigid body, revisited}, Uri = {://000228011900003}, - Volume = {5}, - Year = {2005}} + Volume = 5, + Year = 2005} @article{Meineke2005, Abstract = {OOPSE is a new molecular dynamics simulation program that is capable @@ -5173,14 +5456,14 @@ Annote = {891CF Times Cited:1 Cited References Count:56}, Author = {M. A. Meineke and C. F. Vardeman and T. Lin and C. J. Fennell and J. D. Gezelter}, Issn = {0192-8651}, - Journal = {Journal of Computational Chemistry}, + Journal = jcc, Month = {Feb}, - Number = {3}, + Number = 3, Pages = {252-271}, Title = {OOPSE: An object-oriented parallel simulation engine for molecular dynamics}, Uri = {://000226558200006}, - Volume = {26}, - Year = {2005}} + Volume = 26, + Year = 2005} @article{Melchionna1993, Abstract = {In this paper we write down equations of motion (following the approach @@ -5192,14 +5475,14 @@ Annote = {Kq355 Times Cited:172 Cited References Count:17}, Author = {S. Melchionna and G. Ciccotti and B. L. Holian}, Issn = {0026-8976}, - Journal = {Molecular Physics}, + Journal = mp, Month = {Feb 20}, - Number = {3}, + Number = 3, Pages = {533-544}, Title = {Hoover Npt Dynamics for Systems Varying in Shape and Size}, Uri = {://A1993KQ35500002}, - Volume = {78}, - Year = {1993}} + Volume = 78, + Year = 1993} @article{Memmer2002, Abstract = {The phase behaviour of achiral banana-shaped molecules was studied @@ -5232,20 +5515,20 @@ Issn = {0267-8292}, Journal = {Liquid Crystals}, Month = {Apr}, - Number = {4}, + Number = 4, Pages = {483-496}, Title = {Liquid crystal phases of achiral banana-shaped molecules: a computer simulation study}, Uri = {://000174410500001}, - Volume = {29}, - Year = {2002}} + Volume = 29, + Year = 2002} @article{Metropolis1949, Author = {N. Metropolis and S. Ulam}, Journal = {J. Am. Stat. Ass.}, Pages = {335-341}, Title = {The $\mbox{Monte Carlo}$ Method}, - Volume = {44}, - Year = {1949}} + Volume = 44, + Year = 1949} @article{Mielke2004, Abstract = {The torque generated by RNA polymerase as it tracks along double-stranded @@ -5276,14 +5559,14 @@ Annote = {861ZF Times Cited:3 Cited References Count:34}, Author = {S. P. Mielke and W. H. Fink and V. V. Krishnan and N. Gronbech-Jensen and C. J. Benham}, Issn = {0021-9606}, - Journal = {Journal of Chemical Physics}, + Journal = jcp, Month = {Oct 22}, - Number = {16}, + Number = 16, Pages = {8104-8112}, Title = {Transcription-driven twin supercoiling of a DNA loop: A Brownian dynamics study}, Uri = {://000224456500064}, - Volume = {121}, - Year = {2004}} + Volume = 121, + Year = 2004} @article{Naess2001, Abstract = {The three Eulerian angles constitute the classical choice of generalized @@ -5308,8 +5591,8 @@ Pages = {323-339}, Title = {Brownian dynamics simulation of rigid bodies and segmented polymer chains. Use of Cartesian rotation vectors as the generalized coordinates describing angular orientations}, Uri = {://000168774800005}, - Volume = {294}, - Year = {2001}} + Volume = 294, + Year = 2001} @article{Niori1996, Abstract = {The synthesis of a banana-shaped molecule is reported and it is found @@ -5324,12 +5607,12 @@ Issn = {0959-9428}, Journal = {Journal of Materials Chemistry}, Month = {Jul}, - Number = {7}, + Number = 7, Pages = {1231-1233}, Title = {Distinct ferroelectric smectic liquid crystals consisting of banana shaped achiral molecules}, Uri = {://A1996UX85500025}, - Volume = {6}, - Year = {1996}} + Volume = 6, + Year = 1996} @article{Noguchi2002, Abstract = {We Studied the structural changes of bilayer vesicles induced by mechanical @@ -5349,12 +5632,12 @@ Issn = {1063-651X}, Journal = {Physical Review E}, Month = {may}, - Number = {5}, + Number = 5, Pages = {-}, Title = {Structural changes of pulled vesicles: A Brownian dynamics simulation}, Uri = {://000176552300084}, - Volume = {65}, - Year = {2002}} + Volume = 65, + Year = 2002} @article{Noguchi2001, Abstract = {We studied the fusion dynamics of vesicles using a Brownian dynamics @@ -5371,21 +5654,21 @@ Annote = {491UW Times Cited:48 Cited References Count:25}, Author = {H. Noguchi and M. Takasu}, Issn = {0021-9606}, - Journal = {Journal of Chemical Physics}, + Journal = jcp, Month = {Nov 22}, - Number = {20}, + Number = 20, Pages = {9547-9551}, Title = {Fusion pathways of vesicles: A Brownian dynamics simulation}, Uri = {://000172129300049}, - Volume = {115}, - Year = {2001}} + Volume = 115, + Year = 2001} @book{Olver1986, Address = {New York}, Author = {P.J. Olver}, Publisher = {Springer}, Title = {Applications of Lie groups to differential equatitons}, - Year = {1986}} + Year = 1986} @article{Omelyan1998, Abstract = {A revised version of the quaternion approach for numerical integration @@ -5404,12 +5687,12 @@ Issn = {0894-1866}, Journal = {Computers in Physics}, Month = {Jan-Feb}, - Number = {1}, + Number = 1, Pages = {97-103}, Title = {On the numerical integration of motion for rigid polyatomics: The modified quaternion approach}, Uri = {://000072024300025}, - Volume = {12}, - Year = {1998}} + Volume = 12, + Year = 1998} @article{Omelyan1998a, Abstract = {An algorithm for numerical integration of the rigid-body equations @@ -5426,12 +5709,12 @@ Issn = {1063-651X}, Journal = {Physical Review E}, Month = {Jul}, - Number = {1}, + Number = 1, Pages = {1169-1172}, Title = {Algorithm for numerical integration of the rigid-body equations of motion}, Uri = {://000074893400151}, - Volume = {58}, - Year = {1998}} + Volume = 58, + Year = 1998} @article{Owren1992, Abstract = {Continuous, explicit Runge-Kutta methods with the minimal number of @@ -5452,12 +5735,12 @@ Issn = {0196-5204}, Journal = {Siam Journal on Scientific and Statistical Computing}, Month = {Nov}, - Number = {6}, + Number = 6, Pages = {1488-1501}, Title = {Derivation of Efficient, Continuous, Explicit Runge-Kutta Methods}, Uri = {://A1992JU93600013}, - Volume = {13}, - Year = {1992}} + Volume = 13, + Year = 1992} @article{Palacios1998, Abstract = {The stochastic Landau-Lifshitz-Gilbert equation of motion for a classical @@ -5495,12 +5778,12 @@ Issn = {0163-1829}, Journal = {Physical Review B}, Month = {Dec 1}, - Number = {22}, + Number = 22, Pages = {14937-14958}, Title = {Langevin-dynamics study of the dynamical properties of small magnetic particles}, Uri = {://000077460000052}, - Volume = {58}, - Year = {1998}} + Volume = 58, + Year = 1998} @article{Parr1995, Abstract = {Despite the parsing power of LR/LALR algorithms, e.g. YACC, programmers @@ -5527,25 +5810,25 @@ Issn = {0038-0644}, Journal = {Software-Practice \& Experience}, Month = {Jul}, - Number = {7}, + Number = 7, Pages = {789-810}, Title = {Antlr - a Predicated-Ll(K) Parser Generator}, Uri = {://A1995RK10400004}, - Volume = {25}, - Year = {1995}} + Volume = 25, + Year = 1995} @article{Pastor1988, Annote = {T1302 Times Cited:61 Cited References Count:26}, Author = {R. W. Pastor and B. R. Brooks and A. Szabo}, Issn = {0026-8976}, - Journal = {Molecular Physics}, + Journal = mp, Month = {Dec 20}, - Number = {6}, + Number = 6, Pages = {1409-1419}, Title = {An Analysis of the Accuracy of Langevin and Molecular-Dynamics Algorithms}, Uri = {://A1988T130200011}, - Volume = {65}, - Year = {1988}} + Volume = 65, + Year = 1988} @article{Pelzl1999, Annote = {220RC Times Cited:313 Cited References Count:49}, @@ -5553,56 +5836,56 @@ Issn = {0935-9648}, Journal = {Advanced Materials}, Month = {Jul 5}, - Number = {9}, + Number = 9, Pages = {707-724}, Title = {Banana-shaped compounds - A new field of liquid crystals}, Uri = {://000081680400007}, - Volume = {11}, - Year = {1999}} + Volume = 11, + Year = 1999} @article{Perram1985, Annote = {Akb93 Times Cited:71 Cited References Count:12}, Author = {J. W. Perram and M. S. Wertheim}, Issn = {0021-9991}, - Journal = {Journal of Computational Physics}, - Number = {3}, + Journal = jcop, + Number = 3, Pages = {409-416}, Title = {Statistical-Mechanics of Hard Ellipsoids .1. Overlap Algorithm and the Contact Function}, Uri = {://A1985AKB9300008}, - Volume = {58}, - Year = {1985}} + Volume = 58, + Year = 1985} @article{Rotne1969, Author = {F. Perrin}, Journal = {J. Chem. Phys.}, Pages = {4831-4837}, Title = {Variational treatment of hydrodynamic interaction in polymers}, - Volume = {50}, - Year = {1969}} + Volume = 50, + Year = 1969} @article{Perrin1936, Author = {F. Perrin}, Journal = {J. Phys. Radium}, Pages = {1-11}, Title = {Mouvement brownien d'un ellipsoid(II). Rotation libre et depolarisation des fluorescences. Translation et diffusion de moleculese ellipsoidales}, - Volume = {7}, - Year = {1936}} + Volume = 7, + Year = 1936} @article{Perrin1934, Author = {F. Perrin}, Journal = {J. Phys. Radium}, Pages = {497-511}, Title = {Mouvement brownien d'un ellipsoid(I). Dispersion dielectrique pour des molecules ellipsoidales}, - Volume = {5}, - Year = {1934}} + Volume = 5, + Year = 1934} @article{Petrache2000, Author = {H.~I. Petrache and S.~W. Dodd and M.~F. Brown}, - Journal = {Biophysical Journal}, + Journal = bj, Pages = {3172-3192}, Title = {Area per Lipid and Acyl Length Distributions in Fluid Phosphatidylcholines Determined by $^2\text{H}$ {\sc nmr} Spectroscopy}, - Volume = {79}, - Year = {2000}} + Volume = 79, + Year = 2000} @article{Petrache1998, Abstract = {X-ray diffraction data taken at high instrumental resolution were @@ -5627,20 +5910,20 @@ Issn = {0009-3084}, Journal = {Chemistry and Physics of Lipids}, Month = {Sep}, - Number = {1}, + Number = 1, Pages = {83-94}, Title = {Fluid phase structure of EPC and DMPC bilayers}, Uri = {://000076497600007}, - Volume = {95}, - Year = {1998}} + Volume = 95, + Year = 1998} @article{Powles1973, Author = {J.~G. Powles}, Journal = {Advan. Phys.}, Pages = {1-56}, Title = {A general ellipsoid can not always serve as a modle for the rotational diffusion properties of arbitrary shaped rigid molecules}, - Volume = {22}, - Year = {1973}} + Volume = 22, + Year = 1973} @article{Recio2004, Abstract = {Protein recognition is one of the most challenging and intriguing @@ -5669,14 +5952,14 @@ Annote = {763GQ Times Cited:21 Cited References Count:59}, Author = {J. Fernandez-Recio and M. Totrov and R. Abagyan}, Issn = {0022-2836}, - Journal = {Journal of Molecular Biology}, + Journal = jmb, Month = {Jan 16}, - Number = {3}, + Number = 3, Pages = {843-865}, Title = {Identification of protein-protein interaction sites from docking energy landscapes}, Uri = {://000188066900016}, - Volume = {335}, - Year = {2004}} + Volume = 335, + Year = 2004} @article{Reddy2006, Abstract = {An overview on the recent developments in the field of liquid crystalline @@ -5694,12 +5977,12 @@ Author = {R. A. Reddy and C. Tschierske}, Issn = {0959-9428}, Journal = {Journal of Materials Chemistry}, - Number = {10}, + Number = 10, Pages = {907-961}, Title = {Bent-core liquid crystals: polar order, superstructural chirality and spontaneous desymmetrisation in soft matter systems}, Uri = {://000235990500001}, - Volume = {16}, - Year = {2006}} + Volume = 16, + Year = 2006} @article{Reich1999, Abstract = {Backward error analysis has become an important tool for understanding @@ -5729,12 +6012,12 @@ Issn = {0036-1429}, Journal = {Siam Journal on Numerical Analysis}, Month = {Sep 8}, - Number = {5}, + Number = 5, Pages = {1549-1570}, Title = {Backward error analysis for numerical integrators}, Uri = {://000082650600010}, - Volume = {36}, - Year = {1999}} + Volume = 36, + Year = 1999} @article{Ros2005, Abstract = {The recent literature in the field of liquid crystals shows that banana-shaped @@ -5749,12 +6032,12 @@ Author = {M. B. Ros and J. L. Serrano and M. R. {de la Fuente} and C. L. Folcia}, Issn = {0959-9428}, Journal = {Journal of Materials Chemistry}, - Number = {48}, + Number = 48, Pages = {5093-5098}, Title = {Banana-shaped liquid crystals: a new field to explore}, Uri = {://000233775500001}, - Volume = {15}, - Year = {2005}} + Volume = 15, + Year = 2005} @article{Roux1991, Abstract = {The mobility of water, Na+. and K+ has been calculated inside a periodic @@ -5782,12 +6065,12 @@ Issn = {0022-3654}, Journal = {Journal of Physical Chemistry}, Month = {Jun 13}, - Number = {12}, + Number = 12, Pages = {4856-4868}, Title = {Ion-Transport in a Gramicidin-Like Channel - Dynamics and Mobility}, Uri = {://A1991FR75600049}, - Volume = {95}, - Year = {1991}} + Volume = 95, + Year = 1991} @article{Roy2005, Abstract = {A vast majority of compounds with bent core or banana shaped molecules @@ -5806,24 +6089,24 @@ Issn = {1292-8941}, Journal = {European Physical Journal E}, Month = {Nov}, - Number = {3}, + Number = 3, Pages = {253-258}, Title = {A frustrated packing model for the B-6-B-1-SmAP(A) sequence of phases in banana shaped molecules}, Uri = {://000233363300002}, - Volume = {18}, - Year = {2005}} + Volume = 18, + Year = 2005} @article{Ryckaert1977, Annote = {Cz253 Times Cited:3680 Cited References Count:7}, Author = {J. P. Ryckaert and G. Ciccotti and H. J. C. Berendsen}, Issn = {0021-9991}, - Journal = {Journal of Computational Physics}, - Number = {3}, + Journal = jcop, + Number = 3, Pages = {327-341}, Title = {Numerical-Integration of Cartesian Equations of Motion of a System with Constraints - Molecular-Dynamics of N-Alkanes}, Uri = {://A1977CZ25300007}, - Volume = {23}, - Year = {1977}} + Volume = 23, + Year = 1977} @article{Sagui1999, Abstract = {Current computer simulations of biomolecules typically make use of @@ -5848,8 +6131,8 @@ Pages = {155-179}, Title = {Molecular dynamics simulations of biomolecules: Long-range electrostatic effects}, Uri = {://000081271400008}, - Volume = {28}, - Year = {1999}} + Volume = 28, + Year = 1999} @article{Sandu1999, Abstract = {Numerical resonance artifacts have become recognized recently as a @@ -5892,14 +6175,14 @@ Annote = {194FM Times Cited:14 Cited References Count:32}, Author = {A. Sandu and T. Schlick}, Issn = {0021-9991}, - Journal = {Journal of Computational Physics}, + Journal = jcop, Month = {May 1}, - Number = {1}, + Number = 1, Pages = {74-113}, Title = {Masking resonance artifacts in force-splitting methods for biomolecular simulations by extrapolative Langevin dynamics}, Uri = {://000080181500004}, - Volume = {151}, - Year = {1999}} + Volume = 151, + Year = 1999} @article{Sasaki2004, Abstract = {Tris(2-aminoethyl) amine derivatives with appended urea and sulfonamide @@ -5913,12 +6196,12 @@ Author = {Y. Sasaki and R. Shukla and B. D. Smith}, Issn = {1477-0520}, Journal = {Organic \& Biomolecular Chemistry}, - Number = {2}, + Number = 2, Pages = {214-219}, Title = {Facilitated phosphatidylserine flip-flop across vesicle and cell membranes using urea-derived synthetic translocases}, Uri = {://000187843800012}, - Volume = {2}, - Year = {2004}} + Volume = 2, + Year = 2004} @article{Satoh1996, Abstract = {The effects of dipole-dipole interaction on mesophase formation are @@ -5937,8 +6220,8 @@ Pages = {99-104}, Title = {Monte Carlo simulations using the dipolar Gay-Berne model: Effect of terminal dipole moment on mesophase formation}, Uri = {://A1996UQ97500017}, - Volume = {255}, - Year = {1996}} + Volume = 255, + Year = 1996} @article{Schaps1999, Annote = {163EC Times Cited:0 Cited References Count:0}, @@ -5946,12 +6229,12 @@ Issn = {1044-789X}, Journal = {Dr Dobbs Journal}, Month = {Mar}, - Number = {3}, + Number = 3, Pages = {84-+}, Title = {Compiler construction with ANTLR and Java - Tools for building tools}, Uri = {://000078389200023}, - Volume = {24}, - Year = {1999}} + Volume = 24, + Year = 1999} @article{Shen2002, Abstract = {Met-enkephalin is one of the smallest opiate peptides. Yet, its dynamical @@ -5976,14 +6259,14 @@ Annote = {540MH Times Cited:36 Cited References Count:45}, Author = {M. Y. Shen and K. F. Freed}, Issn = {0006-3495}, - Journal = {Biophysical Journal}, + Journal = bj, Month = {Apr}, - Number = {4}, + Number = 4, Pages = {1791-1808}, Title = {Long time dynamics of met-enkephalin: Comparison of explicit and implicit solvent models}, Uri = {://000174932400010}, - Volume = {82}, - Year = {2002}} + Volume = 82, + Year = 2002} @article{Shillcock2005, Annote = {901QJ Times Cited:9 Cited References Count:23}, @@ -5991,12 +6274,12 @@ Issn = {1476-1122}, Journal = {Nature Materials}, Month = {Mar}, - Number = {3}, + Number = 3, Pages = {225-228}, Title = {Tension-induced fusion of bilayer membranes and vesicles}, Uri = {://000227296700019}, - Volume = {4}, - Year = {2005}} + Volume = 4, + Year = 2005} @article{Shimada1993, Abstract = {To make improved treatments of electrostatic interactions in biomacromolecular @@ -6019,14 +6302,14 @@ Annote = {Lh164 Times Cited:27 Cited References Count:47}, Author = {J. Shimada and H. Kaneko and T. Takada}, Issn = {0192-8651}, - Journal = {Journal of Computational Chemistry}, + Journal = jcc, Month = {Jul}, - Number = {7}, + Number = 7, Pages = {867-878}, Title = {Efficient Calculations of Coulombic Interactions in Biomolecular Simulations with Periodic Boundary-Conditions}, Uri = {://A1993LH16400011}, - Volume = {14}, - Year = {1993}} + Volume = 14, + Year = 1993} @article{Skeel2002, Abstract = {The best simple method for Newtonian molecular dynamics is indisputably @@ -6042,14 +6325,14 @@ Annote = {633RX Times Cited:8 Cited References Count:22}, Author = {R. D. Skeel and J. A. Izaguirre}, Issn = {0026-8976}, - Journal = {Molecular Physics}, + Journal = mp, Month = {Dec 20}, - Number = {24}, + Number = 24, Pages = {3885-3891}, Title = {An impulse integrator for Langevin dynamics}, Uri = {://000180297200014}, - Volume = {100}, - Year = {2002}} + Volume = 100, + Year = 2002} @article{Skeel1997, Abstract = {The following integration methods for special second-order ordinary @@ -6070,12 +6353,12 @@ Issn = {1064-8275}, Journal = {Siam Journal on Scientific Computing}, Month = {Jan}, - Number = {1}, + Number = 1, Pages = {203-222}, Title = {A family of symplectic integrators: Stability, accuracy, and molecular dynamics applications}, Uri = {://A1997WE98100012}, - Volume = {18}, - Year = {1997}} + Volume = 18, + Year = 1997} @article{Tao2005, Abstract = {Recently a microscopic theory for the dynamics of suspensions of long @@ -6101,23 +6384,23 @@ Annote = {943DN Times Cited:3 Cited References Count:26}, Author = {Y. G. Tao and W. K. {den Otter} and J. T. Padding and J. K. G. Dhont and W. J. Briels}, Issn = {0021-9606}, - Journal = {Journal of Chemical Physics}, + Journal = jcp, Month = {Jun 22}, - Number = {24}, + Number = 24, Pages = {-}, Title = {Brownian dynamics simulations of the self- and collective rotational diffusion coefficients of rigid long thin rods}, Uri = {://000230332400077}, - Volume = {122}, - Year = {2005}} + Volume = 122, + Year = 2005} @book{Tolman1979, Address = {New York}, Author = {R.~C. Tolman}, - Chapter = {2}, + Chapter = 2, Pages = {19-22}, Publisher = {Dover Publications, Inc.}, Title = {The Principles of Statistical Mechanics}, - Year = {1979}} + Year = 1979} @article{Tu1995, Abstract = {We report a constant pressure and temperature molecular dynamics simulation @@ -6142,14 +6425,14 @@ Annote = {Tv018 Times Cited:108 Cited References Count:34}, Author = {K. Tu and D. J. Tobias and M. L. Klein}, Issn = {0006-3495}, - Journal = {Biophysical Journal}, + Journal = bj, Month = {Dec}, - Number = {6}, + Number = 6, Pages = {2558-2562}, Title = {Constant pressure and temperature molecular dynamics simulation of a fully hydrated liquid crystal phase dipalmitoylphosphatidylcholine bilayer}, Uri = {://A1995TV01800037}, - Volume = {69}, - Year = {1995}} + Volume = 69, + Year = 1995} @article{Tuckerman1992, Abstract = {The Trotter factorization of the Liouville propagator is used to generate @@ -6167,21 +6450,21 @@ Annote = {Je891 Times Cited:680 Cited References Count:19}, Author = {M. Tuckerman and B. J. Berne and G. J. Martyna}, Issn = {0021-9606}, - Journal = {Journal of Chemical Physics}, + Journal = jcp, Month = {Aug 1}, - Number = {3}, + Number = 3, Pages = {1990-2001}, Title = {Reversible Multiple Time Scale Molecular-Dynamics}, Uri = {://A1992JE89100044}, - Volume = {97}, - Year = {1992}} + Volume = 97, + Year = 1992} @book{Varadarajan1974, Address = {New York}, Author = {V.S. Varadarajan}, Publisher = {Prentice-Hall}, Title = {Lie groups, Lie algebras, and their representations}, - Year = {1974}} + Year = 1974} @article{Vincent1995, Abstract = {We have implemented a portable parallel version of the macromolecular @@ -6201,30 +6484,30 @@ Annote = {Ta403 Times Cited:16 Cited References Count:23}, Author = {J. J. Vincent and K. M. Merz}, Issn = {0192-8651}, - Journal = {Journal of Computational Chemistry}, + Journal = jcc, Month = {Nov}, - Number = {11}, + Number = 11, Pages = {1420-1427}, Title = {A Highly Portable Parallel Implementation of Amber4 Using the Message-Passing Interface Standard}, Uri = {://A1995TA40300009}, - Volume = {16}, - Year = {1995}} + Volume = 16, + Year = 1995} @article{Wegener1979, Author = {W.~A. Wegener, V.~J. Koester and R.~M. Dowben}, Journal = {Proc. Natl. Acad. Sci.}, - Number = {12}, + Number = 12, Pages = {6356-6360}, Title = {A general ellipsoid can not always serve as a modle for the rotational diffusion properties of arbitrary shaped rigid molecules}, - Volume = {76}, - Year = {1979}} + Volume = 76, + Year = 1979} @article{Wilson2006, Author = {G.~V. Wilson}, Journal = {American Scientist}, Title = {Where's the Real Bottleneck in Scientific Computing?}, - Volume = {94}, - Year = {2006}} + Volume = 94, + Year = 2006} @article{Withers2003, Abstract = {The effects of longitudinal quadrupole moments on the formation of @@ -6257,14 +6540,14 @@ Annote = {738EF Times Cited:3 Cited References Count:43}, Author = {I. M. Withers}, Issn = {0021-9606}, - Journal = {Journal of Chemical Physics}, + Journal = jcp, Month = {Nov 15}, - Number = {19}, + Number = 19, Pages = {10209-10223}, Title = {Effects of longitudinal quadrupoles on the phase behavior of a Gay-Berne fluid}, Uri = {://000186273200027}, - Volume = {119}, - Year = {2003}} + Volume = 119, + Year = 2003} @article{Wolf1999, Abstract = {Based on a recent result showing that the net Coulomb potential in @@ -6291,14 +6574,14 @@ Annote = {189PD Times Cited:70 Cited References Count:34}, Author = {D. Wolf and P. Keblinski and S. R. Phillpot and J. Eggebrecht}, Issn = {0021-9606}, - Journal = {Journal of Chemical Physics}, + Journal = jcp, Month = {May 1}, - Number = {17}, + Number = 17, Pages = {8254-8282}, Title = {Exact method for the simulation of Coulombic systems by spherically truncated, pairwise r(-1) summation}, Uri = {://000079913000008}, - Volume = {110}, - Year = {1999}} + Volume = 110, + Year = 1999} @article{Yoshida1990, Annote = {Ej798 Times Cited:492 Cited References Count:9}, @@ -6310,12 +6593,12 @@ Pages = {262-268}, Title = {Construction of Higher-Order Symplectic Integrators}, Uri = {://A1990EJ79800009}, - Volume = {150}, - Year = {1990}} + Volume = 150, + Year = 1990} @article{Blum1972, Author = {L. Blum and A.~J. Torruella}, - Journal = {Journal of Chemical Physics}, + Journal = jcp, Number = 1, Pages = {303-309}, Title = {Computer simulations of bilayer membranes: Self-assembly and interfacial tension}, @@ -6324,7 +6607,7 @@ @article{Stone1978, Author = {A.~J. Stone}, - Journal = {Molecular Physics}, + Journal = mp, Number = 1, Pages = {241-256}, Title = {The description of bimolecular potentials, forces and torques: the S and V function expansions}, @@ -6333,7 +6616,7 @@ @article{Berardi2003, Author = {R. Berardi, M. Cecchini and C. Zannoni}, - Journal = {Journal of Chemical Physics}, + Journal = jcp, Number = 18, Pages = {9933-9946}, Title = {A Monte Carlo study of the chiral columnar organizations of dissymmetric discotic mesogens}, @@ -6342,7 +6625,7 @@ @article{Beard2000, Author = {D. A. Beard and T. Schlick}, - Journal = {Journal of Chemical Physics}, + Journal = jcp, Number = 17, Pages = {7313-7322}, Title = {Inertial Stochastic Dynamics. I. Long-time-step Methods for Langevin Dynamics}, @@ -6354,25 +6637,25 @@ Author = {M.W. Hirsch}, Publisher = {Springer}, Title = {Differential Topology}, - Year = {1997}} + Year = 1997} @book{Jost2002, Address = {Berlin}, Author = {J. Jost}, Publisher = {Springer-Verlag}, Title = {Riemannian Geometry and Geometric Analysis}, - Year = {2002}} + Year = 2002} @book{McDuff1998, Address = {Oxford}, Author = {D. McDuff and D. Salamon}, Publisher = {Oxford Mathematical Monographs}, Title = {Introduction to Symplectic Topology}, - Year = {1998}} + Year = 1998} @article{Matubayasi1999, Author = {N. Matubayasi and M. Nakahara}, - Journal = {Journal of Chemical Physics}, + Journal = jcp, Number = 7, Pages = {3291-3301}, Title = {Reversible molecular dynamics for rigid bodies and hybrid Monte Carlo}, @@ -6381,7 +6664,7 @@ @article{Miller2002, Author = {T.F. Miller III, M. Eleftheriou}, - Journal = {Journal of Chemical Physics}, + Journal = jcp, Number = 20, Pages = {8649-8659}, Title = {Symplectic quaternion scheme for biophysical molecular dynamics}, @@ -6390,7 +6673,7 @@ @article{McMillan1971, Author = {W.L. McMillan}, - Journal = {Journal of Chemical Physics}, + Journal = jcp, Number = 3, Pages = {1238-1246}, Title = {Simple Molecular Model for the Smectic A Phase of Liquid Crystals}, @@ -6432,3 +6715,42 @@ Title = {The Dynamics of Runge-Kutta Methods}, Volume = 2, Year = 1992} + +@article{HuseyinKaya07012005, + 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. +}, + Author = {Kaya, Huseyin and Liu, Zhirong and Chan, Hue Sun}, + Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/89/1/520}, + Bdsk-Url-2 = {http://dx.doi.org/10.1529/biophysj.104.057471}, + Doi = {10.1529/biophysj.104.057471}, + Eprint = {http://www.biophysj.org/cgi/reprint/89/1/520.pdf}, + Journal = {Biophys. J.}, + Number = 1, + Pages = {520-535}, + Title = {{Chevron Behavior and Isostable Enthalpic Barriers in Protein Folding: Successes and Limitations of Simple Go-like Modeling}}, + Url = {http://www.biophysj.org/cgi/content/abstract/89/1/520}, + Volume = 89, + Year = 2005} + +@article{JoseGarciadelaTorre02012000, + 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. +}, + Author = {{Garc\'{i}a de la Torre}, Jose and Huertas, Maria L. and Carrasco, Beatriz}, + Eprint = {http://www.biophysj.org/cgi/reprint/78/2/719.pdf}, + Journal = bj, + Number = {2}, + Pages = {719-730}, + Title = {{Calculation of Hydrodynamic Properties of Globular Proteins from Their Atomic-Level Structure}}, + Url = {http://www.biophysj.org/cgi/content/abstract/78/2/719}, + Volume = {78}, + Year = {2000}} + +@article{GarciadelaTorreJ2002, + Affiliation = {Departamento de Qu{\'\i}mica F{\'\i}sica, Facultad de Qu{\'\i}mica, Universidad de Murcia, 30071 Murcia, Spain}, + Author = {{Garc\'{i}a de la Torre}, Jose and Carrasco, B.}, + Journal = {Biopolymers}, + Number = {3}, + Pages = {163-167}, + Title = {Hydrodynamic Properties of Rigid Macromolecules Composed of Ellipsoidal and Cylindrical Subunits}, + Volume = {63}, + Year = {2002}}