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Revision 3344 by xsun, Tue Feb 12 21:57:10 2008 UTC vs.
Revision 3367 by gezelter, Thu Mar 13 22:16:01 2008 UTC

# Line 2 | Line 2
2   %% http://bibdesk.sourceforge.net/
3  
4  
5 < %% Created for Xiuquan Sun at 2008-02-12 16:53:41 -0500
5 > %% Created for Dan Gezelter at 2008-03-13 17:04:26 -0400
6  
7  
8   %% Saved with string encoding Western (ASCII)
# Line 10 | Line 10
10  
11   @string{acp = {Adv. Chem. Phys.}}
12  
13 + @string{bj = {Biophys. J.}}
14 +
15   @string{ccp5 = {CCP5 Information Quarterly}}
16  
17   @string{cp = {Chem. Phys.}}
# Line 26 | Line 28
28  
29   @string{jml = {J. Mol. Liq.}}
30  
31 + @string{jmb = {J. Mol. Bio.}}
32 +
33   @string{jpc = {J. Phys. Chem.}}
34  
35   @string{jpca = {J. Phys. Chem. A}}
# Line 53 | Line 57
57   @string{rmp = {Rev. Mod. Phys.}}
58  
59  
60 + @article{Peters:1999uq,
61 +        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.},
62 +        Author = {Peters, MH},
63 +        Date-Added = {2008-03-13 16:54:59 -0400},
64 +        Date-Modified = {2008-03-13 16:56:54 -0400},
65 +        Journal = {Journal of Statistical Physics},
66 +        Keywords = {Brownian particle; Fokker Planck equation; adsorption; molecular friction; force autocorrelation function; molecular dynamics},
67 +        Pages = {557-586},
68 +        Timescited = {0},
69 +        Title = {Fokker-Planck equation, molecular friction, and molecular dynamics for Brownian particle transport near external solid surfaces},
70 +        Volume = {94},
71 +        Year = {1999}}
72 +
73 + @article{Peters:1999qy,
74 +        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].},
75 +        Author = {Peters, MH},
76 +        Date-Added = {2008-03-13 16:54:59 -0400},
77 +        Date-Modified = {2008-03-13 16:56:44 -0400},
78 +        Journal = jcp,
79 +        Pages = {528-538},
80 +        Timescited = {0},
81 +        Title = {Fokker-Planck equation and the grand molecular friction tensor for coupled rotational and translational motions of structured Brownian particles near structured surfaces},
82 +        Volume = {110},
83 +        Year = {1999}}
84 +
85 + @article{Peters:2000fk,
86 +        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].},
87 +        Author = {Peters, MH},
88 +        Date-Added = {2008-03-13 16:54:59 -0400},
89 +        Date-Modified = {2008-03-13 16:56:20 -0400},
90 +        Journal = jcp,
91 +        Pages = {5488-5498},
92 +        Timescited = {0},
93 +        Title = {The Smoluchowski diffusion equation for structured macromolecules near structured surfaces},
94 +        Volume = {112},
95 +        Year = {2000}}
96 +
97 + @article{Nienhuis:1970lr,
98 +        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.},
99 +        Author = {Nienhuis, G. },
100 +        Date-Added = {2008-03-13 16:53:44 -0400},
101 +        Date-Modified = {2008-03-13 16:53:44 -0400},
102 +        Journal = {Physica},
103 +        Number = {1},
104 +        Pages = {26--48},
105 +        Title = {On the microscopic theory of Brownian motion with a rotational degree of freedom},
106 +        Ty = {JOUR},
107 +        Url = {http://www.sciencedirect.com/science/article/B6X42-46D224N-BW/2/0e1b39b5a20e979c5fa5e1f560de6413},
108 +        Volume = {49},
109 +        Year = {1970},
110 +        Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B6X42-46D224N-BW/2/0e1b39b5a20e979c5fa5e1f560de6413}}
111 +
112 + @article{SunX._jp0762020,
113 +        Affiliation = {Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556},
114 +        Author = {Sun, X. and Gezelter, J.D.},
115 +        Date-Added = {2008-02-15 13:48:18 -0500},
116 +        Date-Modified = {2008-02-15 13:48:18 -0500},
117 +        Issn = {1520-6106},
118 +        Journal = jpcb,
119 +        Number = {7},
120 +        Pages = {1968-1975},
121 +        Title = {Dipolar Ordering in the Ripple Phases of Molecular-Scale Models of Lipid Membranes},
122 +        Url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp0762020},
123 +        Volume = {112},
124 +        Year = {2008},
125 +        Bdsk-Url-1 = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp0762020}}
126 +
127   @book{Schlick2002,
128          Address = {Secaucus, NJ, USA},
129          Author = {Tamar Schlick},
# Line 63 | Line 134
134          Title = {Molecular Modeling and Simulation: An Interdisciplinary Guide},
135          Year = {2002}}
136  
137 < @misc{Chun:2000fj,
137 > @article{Chun:2000fj,
138          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.},
139          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},
140          Date-Added = {2008-01-22 10:38:33 -0500},
141          Date-Modified = {2008-01-22 10:38:49 -0500},
142          Keywords = {molecular dynamics; normal modes; anharmonicity; macromolecules; numerical integrators},
143 <        Note = {Journal of Computational Chemistry},
144 <        Pages = {159-184},
145 <        Timescited = {0},
146 <        Title = {MBO(N)D: A multibody method for long-time molecular dynamics simulations},
147 <        Volume = {21},
148 <        Year = {2000}}
143 >        Journal = jcc,
144 >        Pages = {159--184},
145 >        Timescited = 0,
146 >        Title = {{MBO(N)D:} A multibody method for long-time molecular dynamics simulations},
147 >        Volume = 21,
148 >        Year = 2000}
149  
150   @article{Fogolari:1996lr,
151          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.},
# Line 112 | Line 183
183  
184   @inbook{Ramachandran1996,
185          Address = {Providence, Rhode Island},
186 <        Author = {GOMATHI RAMACHANDRAN AND TAMAR SCHLICK},
186 >        author = {Gomathi Ramachandran and Tamar Schlick},
187          Chapter = {Beyond optimization: Simulating the dynamics of supercoiled DNA by a macroscopic model},
188          Date-Added = {2008-01-22 10:03:42 -0500},
189          Date-Modified = {2008-01-22 10:06:57 -0500},
# Line 125 | Line 196
196          Year = {1996}}
197  
198   @article{FIXMAN:1986lr,
199 <        Author = {FIXMAN, M},
199 >        Author = {Fixman, M},
200          Date-Added = {2008-01-22 09:59:29 -0500},
201          Date-Modified = {2008-01-22 09:59:35 -0500},
202          Journal = {Macromolecules},
# Line 172 | Line 243
243          Author = {{Garc\'{i}a de la Torre}, Jose and Rodes, Vicente},
244          Date-Added = {2008-01-11 16:16:43 -0500},
245          Date-Modified = {2008-01-11 16:16:43 -0500},
246 <        Journal = {The Journal of Chemical Physics},
246 >        Journal = jcp,
247          Journal1 = {The Journal of Chemical Physics},
248          Journal2 = {J. Chem. Phys.},
249          Keywords = {polymers; molecular models; hydrodynamics; rotation; interactions; macromolecules},
# Line 207 | Line 278
278          Date-Added = {2008-01-08 16:41:06 -0500},
279          Date-Modified = {2008-01-08 16:41:06 -0500},
280          Doi = {10.1063/1.1421362},
281 <        Journal = {The Journal of Chemical Physics},
281 >        Journal = jcp,
282          Keywords = {viscosity; molecular dynamics method; liquid theory; shear flow},
283          Number = 1,
284          Pages = {209-217},
# Line 258 | Line 329
329          Author = {Ravichandran, S and Bagchi, B},
330          Date-Added = {2008-01-08 15:24:48 -0500},
331          Date-Modified = {2008-01-08 15:25:41 -0500},
332 <        Journal = {Journal of Chemical Physics},
332 >        Journal = jcp,
333          Pages = {7505-7511},
334          Title = {Anisotropic diffusion of nonspherical molecules in dense liquids: A molecular dynamics simulation of isolated ellipsoids in the sea of spheres},
335          Volume = 111,
# Line 269 | Line 340
340          Author = {TANG, SA and EVANS, GT},
341          Date-Added = {2008-01-08 15:23:42 -0500},
342          Date-Modified = {2008-01-08 15:24:09 -0500},
343 <        Journal = {Molecular Physics},
343 >        Journal = mp,
344          Pages = {1443-1457},
345          Title = {A CRITIQUE OF SLIP AND STICK HYDRODYNAMICS FOR ELLIPSOIDAL BODIES},
346          Volume = 80,
# Line 281 | Line 352
352          Date-Added = {2008-01-08 15:12:53 -0500},
353          Date-Modified = {2008-01-08 15:13:21 -0500},
354          Doi = {DOI 10.1063/1.1610442},
355 <        Journal = {Journal of Chemical Physics},
355 >        Journal = jcp,
356          Pages = {8062-8068},
357          Title = {Hydrodynamic boundary conditions, the Stokes-Einstein law, and long-time tails in the Brownian limit},
358          Volume = 119,
# Line 294 | Line 365
365          Date-Added = {2008-01-08 15:12:53 -0500},
366          Date-Modified = {2008-01-08 15:13:20 -0500},
367          Doi = {DOI 10.1021/jp037185r},
368 <        Journal = {Journal of Physical Chemistry B},
368 >        Journal = jpcb,
369          Pages = {6767-6771},
370          Title = {Brownian motion of a rough sphere and the Stokes-Einstein Law},
371          Volume = 108,
# Line 1122 | Line 1193
1193          Author = {S.~J. Marrink and A.~E. Mark},
1194          Date-Added = {2008-01-08 14:58:56 -0500},
1195          Date-Modified = {2008-01-08 14:58:58 -0500},
1196 <        Journal = {Journal of Physical Chemistry B},
1196 >        Journal = jpcb,
1197          Pages = {6122-6127},
1198          Title = {Effect of undulations on surface tension in simulated bilayers},
1199          Volume = 105,
# Line 1492 | Line 1563
1563          Author = {Benninger, Richard K. P. and Onfelt, Bjorn and Neil, Mark A. A. and Davis, Daniel M. and French, Paul M. W.},
1564          Date-Added = {2008-01-08 14:58:56 -0500},
1565          Date-Modified = {2008-01-08 14:58:59 -0500},
1566 <        Journal = {Biophysical Journal},
1566 >        Journal = bj,
1567          Journal1 = {Biophys. J.},
1568          Number = 1,
1569          Pages = {609--622},
# Line 1552 | Line 1623
1623          Date-Added = {2008-01-08 14:58:56 -0500},
1624          Date-Modified = {2008-01-08 14:58:59 -0500},
1625          Eid = 157802,
1626 <        Journal = {Physical Review Letters},
1626 >        Journal = prl,
1627          Number = 15,
1628          Numpages = 4,
1629          Pages = 157802,
# Line 1744 | Line 1815
1815          Author = {E. Lindahl and O. Edholm},
1816          Date-Added = {2008-01-08 14:58:56 -0500},
1817          Date-Modified = {2008-01-08 14:58:59 -0500},
1818 <        Journal = {Biophysical Journal},
1818 >        Journal = bj,
1819          Month = {July},
1820          Pages = {426-433},
1821          Title = {Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations},
# Line 1836 | Line 1907
1907          Author = {A.~M. Smondyrev and M.~L. Berkowitz},
1908          Date-Added = {2008-01-08 14:58:56 -0500},
1909          Date-Modified = {2008-01-08 14:59:00 -0500},
1910 <        Journal = {Biophysical Journal},
1910 >        Journal = bj,
1911          Pages = {2472-2478},
1912          Title = {Molecular Dynamics Simulation of {\sc dppc} Bilayer in {\sc dmso}},
1913          Volume = 76,
# Line 1846 | Line 1917
1917          Author = {S.~J. Marrink and D.~P. Teileman},
1918          Date-Added = {2008-01-08 14:58:56 -0500},
1919          Date-Modified = {2008-01-08 14:59:00 -0500},
1920 <        Journal = {Biophysical Journal},
1920 >        Journal = bj,
1921          Pages = {2386-2392},
1922          Title = {Molecular Dynamics Simulation of Spontaneous Membrane Fusion during a Cubic-Hexagonal Phase Transition},
1923          Volume = 83,
# Line 1912 | Line 1983
1983          Author = {M. Patra and M. Karttunen and M.~T. Hyv\"{o}nen and E. Falk and P. Lindqvist and I. Vattulainen},
1984          Date-Added = {2008-01-08 14:58:56 -0500},
1985          Date-Modified = {2008-01-08 14:59:00 -0500},
1986 <        Journal = {Biophysical Journal},
1986 >        Journal = bj,
1987          Pages = {3636-3645},
1988          Title = {Molecular Dynamics Simulations of Lipid Bilayers: Major Artifacts Due to Truncating Electrostatic Interactions},
1989          Volume = 84,
# Line 1945 | Line 2016
2016          Author = {A.~K. Sum and J.~J. de~Pablo},
2017          Date-Added = {2008-01-08 14:58:56 -0500},
2018          Date-Modified = {2008-01-08 14:59:00 -0500},
2019 <        Journal = {Biophysical Journal},
2019 >        Journal = bj,
2020          Pages = {3636-3645},
2021          Title = {Molecular Simulation Study on the influence of Dimethylsulfoxide on the structure of Phospholipid Bilayers},
2022          Volume = 85,
# Line 2134 | Line 2205
2205          Author = {J. Norberg and L. Nilsson},
2206          Date-Added = {2008-01-08 14:58:56 -0500},
2207          Date-Modified = {2008-01-08 14:59:00 -0500},
2208 <        Journal = {Biophysical Journal},
2208 >        Journal = bj,
2209          Pages = {1537-1553},
2210          Title = {On the truncation of Long-Range Electrostatic Interactions in {\sc dna}},
2211          Volume = 79,
# Line 3447 | Line 3518
3518          Annote = {973OH Times Cited:1 Cited References Count:33},
3519          Author = {B. Alakent and M. C. Camurdan and P. Doruker},
3520          Issn = {0021-9606},
3521 <        Journal = {Journal of Chemical Physics},
3521 >        Journal = jcp,
3522          Month = {Oct 8},
3523          Number = 14,
3524          Pages = {-},
# Line 3501 | Line 3572
3572          Annote = {Rq238 Times Cited:559 Cited References Count:14},
3573          Author = {H. C. Andersen},
3574          Issn = {0021-9991},
3575 <        Journal = {Journal of Computational Physics},
3575 >        Journal = jcop,
3576          Number = 1,
3577          Pages = {24-34},
3578          Title = {Rattle - a Velocity Version of the Shake Algorithm for Molecular-Dynamics Calculations},
# Line 3532 | Line 3603
3603          Annote = {895QF Times Cited:9 Cited References Count:33},
3604          Author = {A. Auerbach},
3605          Issn = {0027-8424},
3606 <        Journal = {Proceedings of the National Academy of Sciences of the United States of America},
3606 >        Journal = pnas,
3607          Month = {Feb 1},
3608          Number = 5,
3609          Pages = {1408-1412},
# Line 3593 | Line 3664
3664          Annote = {816YY Times Cited:8 Cited References Count:35},
3665          Author = {D. Banerjee and B. C. Bag and S. K. Banik and D. S. Ray},
3666          Issn = {0021-9606},
3667 <        Journal = {Journal of Chemical Physics},
3667 >        Journal = jcp,
3668          Month = {May 15},
3669          Number = 19,
3670          Pages = {8960-8972},
# Line 3640 | Line 3711
3711          Annote = {105HH Times Cited:29 Cited References Count:49},
3712          Author = {E. Barth and T. Schlick},
3713          Issn = {0021-9606},
3714 <        Journal = {Journal of Chemical Physics},
3714 >        Journal = jcp,
3715          Month = {Aug 1},
3716          Number = 5,
3717          Pages = {1617-1632},
# Line 3664 | Line 3735
3735          Annote = {469KV Times Cited:6 Cited References Count:30},
3736          Author = {P. F. Batcho and T. Schlick},
3737          Issn = {0021-9606},
3738 <        Journal = {Journal of Chemical Physics},
3738 >        Journal = jcp,
3739          Month = {Sep 1},
3740          Number = 9,
3741          Pages = {4019-4029},
# Line 3717 | Line 3788
3788          Annote = {736UA Times Cited:0 Cited References Count:11},
3789          Author = {D. A. Beard and T. Schlick},
3790          Issn = {0006-3495},
3791 <        Journal = {Biophysical Journal},
3791 >        Journal = bj,
3792          Month = {Nov 1},
3793          Number = 5,
3794          Pages = {2973-2976},
# Line 3874 | Line 3945
3945          Annote = {Qp423 Times Cited:6414 Cited References Count:96},
3946          Author = {B. R. Brooks and R. E. Bruccoleri and B. D. Olafson and D. J. States and S. Swaminathan and M. Karplus},
3947          Issn = {0192-8651},
3948 <        Journal = {Journal of Computational Chemistry},
3948 >        Journal = jcc,
3949          Number = 2,
3950          Pages = {187-217},
3951          Title = {Charmm - a Program for Macromolecular Energy, Minimization, and Dynamics Calculations},
# Line 3947 | Line 4018
4018          Annote = {255TC Times Cited:24 Cited References Count:38},
4019          Author = {P. J. Camp and M. P. Allen and A. J. Masters},
4020          Issn = {0021-9606},
4021 <        Journal = {Journal of Chemical Physics},
4021 >        Journal = jcp,
4022          Month = {Dec 1},
4023          Number = 21,
4024          Pages = {9871-9881},
# Line 3998 | Line 4069
4069          Annote = {200TT Times Cited:46 Cited References Count:57},
4070          Author = {B. Carrasco and {Garc\'{i}a de la Torre}, Jose},
4071          Issn = {0006-3495},
4072 <        Journal = {Biophysical Journal},
4072 >        Journal = bj,
4073          Month = {Jun},
4074          Number = 6,
4075          Pages = {3044-3057},
# Line 4029 | Line 4100
4100          Annote = {221EN Times Cited:14 Cited References Count:66},
4101          Author = {A. Chandra and T. Ichiye},
4102          Issn = {0021-9606},
4103 <        Journal = {Journal of Chemical Physics},
4103 >        Journal = jcp,
4104          Month = {Aug 8},
4105          Number = 6,
4106          Pages = {2701-2709},
# Line 4089 | Line 4160
4160          Annote = {866UM Times Cited:4 Cited References Count:61},
4161          Author = {D. L. Cheung and S. J. Clark and M. R. Wilson},
4162          Issn = {0021-9606},
4163 <        Journal = {Journal of Chemical Physics},
4163 >        Journal = jcp,
4164          Month = {Nov 8},
4165          Number = 18,
4166          Pages = {9131-9139},
# Line 4140 | Line 4211
4211          Annote = {757TK Times Cited:1 Cited References Count:22},
4212          Author = {S. A. Chin},
4213          Issn = {0021-9606},
4214 <        Journal = {Journal of Chemical Physics},
4214 >        Journal = jcp,
4215          Month = {Jan 1},
4216          Number = 1,
4217          Pages = {8-13},
# Line 4199 | Line 4270
4270          Annote = {689LC Times Cited:3 Cited References Count:48},
4271          Author = {B. X. Cui and M. Y. Shen and K. F. Freed},
4272          Issn = {0027-8424},
4273 <        Journal = {Proceedings of the National Academy of Sciences of the United States of America},
4273 >        Journal = pnas,
4274          Month = {Jun 10},
4275          Number = 12,
4276          Pages = {7087-7092},
# Line 4259 | Line 4330
4330          Annote = {Zl046 Times Cited:30 Cited References Count:29},
4331          Author = {P. Derreumaux and T. Schlick},
4332          Issn = {0006-3495},
4333 <        Journal = {Biophysical Journal},
4333 >        Journal = bj,
4334          Month = {Jan},
4335          Number = 1,
4336          Pages = {72-81},
# Line 4291 | Line 4362
4362          Annote = {Ya587 Times Cited:35 Cited References Count:32},
4363          Author = {A. Dullweber and B. Leimkuhler and R. McLachlan},
4364          Issn = {0021-9606},
4365 <        Journal = {Journal of Chemical Physics},
4365 >        Journal = jcp,
4366          Month = {Oct 15},
4367          Number = 15,
4368          Pages = {5840-5851},
# Line 4335 | Line 4406
4406          Annote = {Q0188 Times Cited:219 Cited References Count:43},
4407          Author = {E. Egberts and H. J. C. Berendsen},
4408          Issn = {0021-9606},
4409 <        Journal = {Journal of Chemical Physics},
4409 >        Journal = jcp,
4410          Month = {Sep 15},
4411          Number = 6,
4412          Pages = {3718-3732},
# Line 4348 | Line 4419
4419          Annote = {Fp216 Times Cited:785 Cited References Count:42},
4420          Author = {D. L. Ermak and J. A. Mccammon},
4421          Issn = {0021-9606},
4422 <        Journal = {Journal of Chemical Physics},
4422 >        Journal = jcp,
4423          Number = 4,
4424          Pages = {1352-1360},
4425          Title = {Brownian Dynamics with Hydrodynamic Interactions},
# Line 4360 | Line 4431
4431          Annote = {Ds757 Times Cited:271 Cited References Count:18},
4432          Author = {D. J. Evans},
4433          Issn = {0026-8976},
4434 <        Journal = {Molecular Physics},
4434 >        Journal = mp,
4435          Number = 2,
4436          Pages = {317-325},
4437          Title = {Representation of Orientation Space},
# Line 4395 | Line 4466
4466          Annote = {816YY Times Cited:5 Cited References Count:39},
4467          Author = {C. J. Fennell and J. D. Gezelter},
4468          Issn = {0021-9606},
4469 <        Journal = {Journal of Chemical Physics},
4469 >        Journal = jcp,
4470          Month = {May 15},
4471          Number = 19,
4472          Pages = {9175-9184},
# Line 4419 | Line 4490
4490          Annote = {633AD Times Cited:2 Cited References Count:43},
4491          Author = {M. X. Fernandes and {Garc\'{i}a de la Torre}, Jose},
4492          Issn = {0006-3495},
4493 <        Journal = {Biophysical Journal},
4493 >        Journal = bj,
4494          Month = {Dec},
4495          Number = 6,
4496          Pages = {3039-3048},
# Line 4439 | Line 4510
4510          Annote = {Lj347 Times Cited:482 Cited References Count:13},
4511          Author = {J. G. Gay and B. J. Berne},
4512          Issn = {0021-9606},
4513 <        Journal = {Journal of Chemical Physics},
4513 >        Journal = jcp,
4514          Number = 6,
4515          Pages = {3316-3319},
4516          Title = {Modification of the Overlap Potential to Mimic a Linear Site-Site Potential},
# Line 4480 | Line 4551
4551  
4552   @article{Goetz1998,
4553          Author = {R. Goetz and R. Lipowsky},
4554 <        Journal = {Journal of Chemical Physics},
4554 >        Journal = jcp,
4555          Number = 17,
4556          Pages = 7397,
4557          Title = {Computer simulations of bilayer membranes: Self-assembly and interfacial tension},
# Line 4523 | Line 4594
4594          Annote = {704QL Times Cited:48 Cited References Count:60},
4595          Author = {J. J. Gray and S. Moughon and C. Wang and O. Schueler-Furman and B. Kuhlman and C. A. Rohl and D. Baker},
4596          Issn = {0022-2836},
4597 <        Journal = {Journal of Molecular Biology},
4597 >        Journal = jmb,
4598          Month = {Aug 1},
4599          Number = 1,
4600          Pages = {281-299},
# Line 4558 | Line 4629
4629          Annote = {L0498 Times Cited:899 Cited References Count:7},
4630          Author = {L. Greengard and V. Rokhlin},
4631          Issn = {0021-9991},
4632 <        Journal = {Journal of Computational Physics},
4632 >        Journal = jcop,
4633          Month = {Dec},
4634          Number = 2,
4635          Pages = {325-348},
# Line 4711 | Line 4782
4782          Annote = {Ju251 Times Cited:55 Cited References Count:44},
4783          Author = {C. Ho and C. D. Stubbs},
4784          Issn = {0006-3495},
4785 <        Journal = {Biophysical Journal},
4785 >        Journal = bj,
4786          Month = {Oct},
4787          Number = 4,
4788          Pages = {897-902},
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4824          Annote = {870FJ Times Cited:0 Cited References Count:63},
4825          Author = {Y. Huh and N. M. Cann},
4826          Issn = {0021-9606},
4827 <        Journal = {Journal of Chemical Physics},
4827 >        Journal = jcp,
4828          Month = {Nov 22},
4829          Number = 20,
4830          Pages = {10299-10308},
# Line 4832 | Line 4903
4903          Annote = {397CQ Times Cited:14 Cited References Count:36},
4904          Author = {J. A. Izaguirre and D. P. Catarello and J. M. Wozniak and R. D. Skeel},
4905          Issn = {0021-9606},
4906 <        Journal = {Journal of Chemical Physics},
4906 >        Journal = jcp,
4907          Month = {Feb 1},
4908          Number = 5,
4909          Pages = {2090-2098},
# Line 4875 | Line 4946
4946          Annote = {194FM Times Cited:373 Cited References Count:51},
4947          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},
4948          Issn = {0021-9991},
4949 <        Journal = {Journal of Computational Physics},
4949 >        Journal = jcop,
4950          Month = {May 1},
4951          Number = 1,
4952          Pages = {283-312},
# Line 4928 | Line 4999
4999          Annote = {Xk293 Times Cited:77 Cited References Count:17},
5000          Author = {D. K. Klimov and D. Thirumalai},
5001          Issn = {0031-9007},
5002 <        Journal = {Physical Review Letters},
5002 >        Journal = prl,
5003          Month = {Jul 14},
5004          Number = 2,
5005          Pages = {317-320},
# Line 4961 | Line 5032
5032          Annote = {Xq332 Times Cited:11 Cited References Count:18},
5033          Author = {A. Kol and B. B. Laird and B. J. Leimkuhler},
5034          Issn = {0021-9606},
5035 <        Journal = {Journal of Chemical Physics},
5035 >        Journal = jcp,
5036          Month = {Aug 15},
5037          Number = 7,
5038          Pages = {2580-2588},
# Line 5356 | Line 5427
5427          Annote = {891CF Times Cited:1 Cited References Count:56},
5428          Author = {M. A. Meineke and C. F. Vardeman and T. Lin and C. J. Fennell and J. D. Gezelter},
5429          Issn = {0192-8651},
5430 <        Journal = {Journal of Computational Chemistry},
5430 >        Journal = jcc,
5431          Month = {Feb},
5432          Number = 3,
5433          Pages = {252-271},
# Line 5375 | Line 5446
5446          Annote = {Kq355 Times Cited:172 Cited References Count:17},
5447          Author = {S. Melchionna and G. Ciccotti and B. L. Holian},
5448          Issn = {0026-8976},
5449 <        Journal = {Molecular Physics},
5449 >        Journal = mp,
5450          Month = {Feb 20},
5451          Number = 3,
5452          Pages = {533-544},
# Line 5459 | Line 5530
5530          Annote = {861ZF Times Cited:3 Cited References Count:34},
5531          Author = {S. P. Mielke and W. H. Fink and V. V. Krishnan and N. Gronbech-Jensen and C. J. Benham},
5532          Issn = {0021-9606},
5533 <        Journal = {Journal of Chemical Physics},
5533 >        Journal = jcp,
5534          Month = {Oct 22},
5535          Number = 16,
5536          Pages = {8104-8112},
# Line 5554 | Line 5625
5625          Annote = {491UW Times Cited:48 Cited References Count:25},
5626          Author = {H. Noguchi and M. Takasu},
5627          Issn = {0021-9606},
5628 <        Journal = {Journal of Chemical Physics},
5628 >        Journal = jcp,
5629          Month = {Nov 22},
5630          Number = 20,
5631          Pages = {9547-9551},
# Line 5721 | Line 5792
5792          Annote = {T1302 Times Cited:61 Cited References Count:26},
5793          Author = {R. W. Pastor and B. R. Brooks and A. Szabo},
5794          Issn = {0026-8976},
5795 <        Journal = {Molecular Physics},
5795 >        Journal = mp,
5796          Month = {Dec 20},
5797          Number = 6,
5798          Pages = {1409-1419},
# Line 5747 | Line 5818
5818          Annote = {Akb93 Times Cited:71 Cited References Count:12},
5819          Author = {J. W. Perram and M. S. Wertheim},
5820          Issn = {0021-9991},
5821 <        Journal = {Journal of Computational Physics},
5821 >        Journal = jcop,
5822          Number = 3,
5823          Pages = {409-416},
5824          Title = {Statistical-Mechanics of Hard Ellipsoids .1. Overlap Algorithm and the Contact Function},
# Line 5781 | Line 5852
5852  
5853   @article{Petrache2000,
5854          Author = {H.~I. Petrache and S.~W. Dodd and M.~F. Brown},
5855 <        Journal = {Biophysical Journal},
5855 >        Journal = bj,
5856          Pages = {3172-3192},
5857          Title = {Area per Lipid and Acyl Length Distributions in Fluid Phosphatidylcholines Determined by $^2\text{H}$ {\sc nmr} Spectroscopy},
5858          Volume = 79,
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5923          Annote = {763GQ Times Cited:21 Cited References Count:59},
5924          Author = {J. Fernandez-Recio and M. Totrov and R. Abagyan},
5925          Issn = {0022-2836},
5926 <        Journal = {Journal of Molecular Biology},
5926 >        Journal = jmb,
5927          Month = {Jan 16},
5928          Number = 3,
5929          Pages = {843-865},
# Line 6000 | Line 6071
6071          Annote = {Cz253 Times Cited:3680 Cited References Count:7},
6072          Author = {J. P. Ryckaert and G. Ciccotti and H. J. C. Berendsen},
6073          Issn = {0021-9991},
6074 <        Journal = {Journal of Computational Physics},
6074 >        Journal = jcop,
6075          Number = 3,
6076          Pages = {327-341},
6077          Title = {Numerical-Integration of Cartesian Equations of Motion of a System with Constraints - Molecular-Dynamics of N-Alkanes},
# Line 6075 | Line 6146
6146          Annote = {194FM Times Cited:14 Cited References Count:32},
6147          Author = {A. Sandu and T. Schlick},
6148          Issn = {0021-9991},
6149 <        Journal = {Journal of Computational Physics},
6149 >        Journal = jcop,
6150          Month = {May 1},
6151          Number = 1,
6152          Pages = {74-113},
# Line 6159 | Line 6230
6230          Annote = {540MH Times Cited:36 Cited References Count:45},
6231          Author = {M. Y. Shen and K. F. Freed},
6232          Issn = {0006-3495},
6233 <        Journal = {Biophysical Journal},
6233 >        Journal = bj,
6234          Month = {Apr},
6235          Number = 4,
6236          Pages = {1791-1808},
# Line 6202 | Line 6273
6273          Annote = {Lh164 Times Cited:27 Cited References Count:47},
6274          Author = {J. Shimada and H. Kaneko and T. Takada},
6275          Issn = {0192-8651},
6276 <        Journal = {Journal of Computational Chemistry},
6276 >        Journal = jcc,
6277          Month = {Jul},
6278          Number = 7,
6279          Pages = {867-878},
# Line 6225 | Line 6296
6296          Annote = {633RX Times Cited:8 Cited References Count:22},
6297          Author = {R. D. Skeel and J. A. Izaguirre},
6298          Issn = {0026-8976},
6299 <        Journal = {Molecular Physics},
6299 >        Journal = mp,
6300          Month = {Dec 20},
6301          Number = 24,
6302          Pages = {3885-3891},
# Line 6284 | Line 6355
6355          Annote = {943DN Times Cited:3 Cited References Count:26},
6356          Author = {Y. G. Tao and W. K. {den Otter} and J. T. Padding and J. K. G. Dhont and W. J. Briels},
6357          Issn = {0021-9606},
6358 <        Journal = {Journal of Chemical Physics},
6358 >        Journal = jcp,
6359          Month = {Jun 22},
6360          Number = 24,
6361          Pages = {-},
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6396          Annote = {Tv018 Times Cited:108 Cited References Count:34},
6397          Author = {K. Tu and D. J. Tobias and M. L. Klein},
6398          Issn = {0006-3495},
6399 <        Journal = {Biophysical Journal},
6399 >        Journal = bj,
6400          Month = {Dec},
6401          Number = 6,
6402          Pages = {2558-2562},
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6421          Annote = {Je891 Times Cited:680 Cited References Count:19},
6422          Author = {M. Tuckerman and B. J. Berne and G. J. Martyna},
6423          Issn = {0021-9606},
6424 <        Journal = {Journal of Chemical Physics},
6424 >        Journal = jcp,
6425          Month = {Aug 1},
6426          Number = 3,
6427          Pages = {1990-2001},
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6455          Annote = {Ta403 Times Cited:16 Cited References Count:23},
6456          Author = {J. J. Vincent and K. M. Merz},
6457          Issn = {0192-8651},
6458 <        Journal = {Journal of Computational Chemistry},
6458 >        Journal = jcc,
6459          Month = {Nov},
6460          Number = 11,
6461          Pages = {1420-1427},
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6511          Annote = {738EF Times Cited:3 Cited References Count:43},
6512          Author = {I. M. Withers},
6513          Issn = {0021-9606},
6514 <        Journal = {Journal of Chemical Physics},
6514 >        Journal = jcp,
6515          Month = {Nov 15},
6516          Number = 19,
6517          Pages = {10209-10223},
# Line 6474 | Line 6545
6545          Annote = {189PD Times Cited:70 Cited References Count:34},
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6547          Issn = {0021-9606},
6548 <        Journal = {Journal of Chemical Physics},
6548 >        Journal = jcp,
6549          Month = {May 1},
6550          Number = 17,
6551          Pages = {8254-8282},
# Line 6498 | Line 6569
6569  
6570   @article{Blum1972,
6571          Author = {L. Blum and A.~J. Torruella},
6572 <        Journal = {Journal of Chemical Physics},
6572 >        Journal = jcp,
6573          Number = 1,
6574          Pages = {303-309},
6575          Title = {Computer simulations of bilayer membranes: Self-assembly and interfacial tension},
# Line 6507 | Line 6578
6578  
6579   @article{Stone1978,
6580          Author = {A.~J. Stone},
6581 <        Journal = {Molecular Physics},
6581 >        Journal = mp,
6582          Number = 1,
6583          Pages = {241-256},
6584          Title = {The description of bimolecular potentials, forces and torques: the S and V function expansions},
# Line 6516 | Line 6587
6587  
6588   @article{Berardi2003,
6589          Author = {R. Berardi, M. Cecchini and C. Zannoni},
6590 <        Journal = {Journal of Chemical Physics},
6590 >        Journal = jcp,
6591          Number = 18,
6592          Pages = {9933-9946},
6593          Title = {A Monte Carlo study of the chiral columnar organizations of dissymmetric discotic mesogens},
# Line 6525 | Line 6596
6596  
6597   @article{Beard2000,
6598          Author = {D. A. Beard and T. Schlick},
6599 <        Journal = {Journal of Chemical Physics},
6599 >        Journal = jcp,
6600          Number = 17,
6601          Pages = {7313-7322},
6602          Title = {Inertial Stochastic Dynamics. I. Long-time-step Methods for Langevin Dynamics},
# Line 6555 | Line 6626
6626  
6627   @article{Matubayasi1999,
6628          Author = {N. Matubayasi and M. Nakahara},
6629 <        Journal = {Journal of Chemical Physics},
6629 >        Journal = jcp,
6630          Number = 7,
6631          Pages = {3291-3301},
6632          Title = {Reversible molecular dynamics for rigid bodies and hybrid Monte Carlo},
# Line 6564 | Line 6635
6635  
6636   @article{Miller2002,
6637          Author = {T.F. Miller III, M. Eleftheriou},
6638 <        Journal = {Journal of Chemical Physics},
6638 >        Journal = jcp,
6639          Number = 20,
6640          Pages = {8649-8659},
6641          Title = {Symplectic quaternion scheme for biophysical molecular dynamics},
# Line 6573 | Line 6644
6644  
6645   @article{McMillan1971,
6646          Author = {W.L. McMillan},
6647 <        Journal = {Journal of Chemical Physics},
6647 >        Journal = jcp,
6648          Number = 3,
6649          Pages = {1238-1246},
6650          Title = {Simple Molecular Model for the Smectic A Phase of Liquid Crystals},

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