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2   %% http://bibdesk.sourceforge.net/
3  
4  
5 < %% Created for Dan Gezelter at 2008-01-22 11:01:35 -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 52 | Line 56
56  
57   @string{rmp = {Rev. Mod. Phys.}}
58  
55 – @string{bj = {Biophys. J.}}
56 –
59   @string{cpc = "Comp. Phys. Comm."}
60  
61 < @misc{Chun:2000fj,
61 > @article{Peters:1999uq,
62 >        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.},
63 >        Author = {Peters, MH},
64 >        Date-Added = {2008-03-13 16:54:59 -0400},
65 >        Date-Modified = {2008-03-13 16:56:54 -0400},
66 >        Journal = {Journal of Statistical Physics},
67 >        Keywords = {Brownian particle; Fokker Planck equation; adsorption; molecular friction; force autocorrelation function; molecular dynamics},
68 >        Pages = {557-586},
69 >        Timescited = {0},
70 >        Title = {Fokker-Planck equation, molecular friction, and molecular dynamics for Brownian particle transport near external solid surfaces},
71 >        Volume = {94},
72 >        Year = {1999}}
73 >
74 > @article{Peters:1999qy,
75 >        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].},
76 >        Author = {Peters, MH},
77 >        Date-Added = {2008-03-13 16:54:59 -0400},
78 >        Date-Modified = {2008-03-13 16:56:44 -0400},
79 >        Journal = jcp,
80 >        Pages = {528-538},
81 >        Timescited = {0},
82 >        Title = {Fokker-Planck equation and the grand molecular friction tensor for coupled rotational and translational motions of structured Brownian particles near structured surfaces},
83 >        Volume = {110},
84 >        Year = {1999}}
85 >
86 > @article{Peters:2000fk,
87 >        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].},
88 >        Author = {Peters, MH},
89 >        Date-Added = {2008-03-13 16:54:59 -0400},
90 >        Date-Modified = {2008-03-13 16:56:20 -0400},
91 >        Journal = jcp,
92 >        Pages = {5488-5498},
93 >        Timescited = {0},
94 >        Title = {The Smoluchowski diffusion equation for structured macromolecules near structured surfaces},
95 >        Volume = {112},
96 >        Year = {2000}}
97 >
98 > @article{Nienhuis:1970lr,
99 >        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.},
100 >        Author = {Nienhuis, G. },
101 >        Date-Added = {2008-03-13 16:53:44 -0400},
102 >        Date-Modified = {2008-03-13 16:53:44 -0400},
103 >        Journal = {Physica},
104 >        Number = {1},
105 >        Pages = {26--48},
106 >        Title = {On the microscopic theory of Brownian motion with a rotational degree of freedom},
107 >        Ty = {JOUR},
108 >        Url = {http://www.sciencedirect.com/science/article/B6X42-46D224N-BW/2/0e1b39b5a20e979c5fa5e1f560de6413},
109 >        Volume = {49},
110 >        Year = {1970},
111 >        Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B6X42-46D224N-BW/2/0e1b39b5a20e979c5fa5e1f560de6413}}
112 >
113 > @article{SunX._jp0762020,
114 >        Affiliation = {Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556},
115 >        Author = {Sun, X. and Gezelter, J.D.},
116 >        Date-Added = {2008-02-15 13:48:18 -0500},
117 >        Date-Modified = {2008-02-15 13:48:18 -0500},
118 >        Issn = {1520-6106},
119 >        Journal = jpcb,
120 >        Number = {7},
121 >        Pages = {1968-1975},
122 >        Title = {Dipolar Ordering in the Ripple Phases of Molecular-Scale Models of Lipid Membranes},
123 >        Url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp0762020},
124 >        Volume = {112},
125 >        Year = {2008},
126 >        Bdsk-Url-1 = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp0762020}}
127 >
128 > @book{Schlick2002,
129 >        Address = {Secaucus, NJ, USA},
130 >        Author = {Tamar Schlick},
131 >        Date-Added = {2008-02-12 16:52:19 -0500},
132 >        Date-Modified = {2008-02-12 16:53:15 -0500},
133 >        Isbn = {038795404X},
134 >        Publisher = {Springer-Verlag New York, Inc.},
135 >        Title = {Molecular Modeling and Simulation: An Interdisciplinary Guide},
136 >        Year = {2002}}
137 >
138 > @article{Chun:2000fj,
139          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.},
140          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},
141          Date-Added = {2008-01-22 10:38:33 -0500},
142          Date-Modified = {2008-01-22 10:38:49 -0500},
143          Keywords = {molecular dynamics; normal modes; anharmonicity; macromolecules; numerical integrators},
144 <        Note = {Journal of Computational Chemistry},
145 <        Pages = {159-184},
146 <        Timescited = {0},
147 <        Title = {MBO(N)D: A multibody method for long-time molecular dynamics simulations},
148 <        Volume = {21},
149 <        Year = {2000}}
144 >        Journal = jcc,
145 >        Pages = {159--184},
146 >        Timescited = 0,
147 >        Title = {{MBO(N)D:} A multibody method for long-time molecular dynamics simulations},
148 >        Volume = 21,
149 >        Year = 2000}
150  
151   @article{Fogolari:1996lr,
152          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 105 | Line 184
184  
185   @inbook{Ramachandran1996,
186          Address = {Providence, Rhode Island},
187 <        Author = {GOMATHI RAMACHANDRAN AND TAMAR SCHLICK},
187 >        author = {Gomathi Ramachandran and Tamar Schlick},
188          Chapter = {Beyond optimization: Simulating the dynamics of supercoiled DNA by a macroscopic model},
189          Date-Added = {2008-01-22 10:03:42 -0500},
190          Date-Modified = {2008-01-22 10:06:57 -0500},
# Line 118 | Line 197
197          Year = {1996}}
198  
199   @article{FIXMAN:1986lr,
200 <        Author = {FIXMAN, M},
200 >        Author = {Fixman, M},
201          Date-Added = {2008-01-22 09:59:29 -0500},
202          Date-Modified = {2008-01-22 09:59:35 -0500},
203          Journal = {Macromolecules},
# Line 165 | Line 244
244          Author = {{Garc\'{i}a de la Torre}, Jose and Rodes, Vicente},
245          Date-Added = {2008-01-11 16:16:43 -0500},
246          Date-Modified = {2008-01-11 16:16:43 -0500},
247 <        Journal = {The Journal of Chemical Physics},
247 >        Journal = jcp,
248          Journal1 = {The Journal of Chemical Physics},
249          Journal2 = {J. Chem. Phys.},
250          Keywords = {polymers; molecular models; hydrodynamics; rotation; interactions; macromolecules},
# Line 200 | Line 279
279          Date-Added = {2008-01-08 16:41:06 -0500},
280          Date-Modified = {2008-01-08 16:41:06 -0500},
281          Doi = {10.1063/1.1421362},
282 <        Journal = {The Journal of Chemical Physics},
282 >        Journal = jcp,
283          Keywords = {viscosity; molecular dynamics method; liquid theory; shear flow},
284          Number = 1,
285          Pages = {209-217},
# Line 251 | Line 330
330          Author = {Ravichandran, S and Bagchi, B},
331          Date-Added = {2008-01-08 15:24:48 -0500},
332          Date-Modified = {2008-01-08 15:25:41 -0500},
333 <        Journal = {Journal of Chemical Physics},
333 >        Journal = jcp,
334          Pages = {7505-7511},
335          Title = {Anisotropic diffusion of nonspherical molecules in dense liquids: A molecular dynamics simulation of isolated ellipsoids in the sea of spheres},
336          Volume = 111,
# Line 262 | Line 341
341          Author = {TANG, SA and EVANS, GT},
342          Date-Added = {2008-01-08 15:23:42 -0500},
343          Date-Modified = {2008-01-08 15:24:09 -0500},
344 <        Journal = {Molecular Physics},
344 >        Journal = mp,
345          Pages = {1443-1457},
346          Title = {A CRITIQUE OF SLIP AND STICK HYDRODYNAMICS FOR ELLIPSOIDAL BODIES},
347          Volume = 80,
# Line 274 | Line 353
353          Date-Added = {2008-01-08 15:12:53 -0500},
354          Date-Modified = {2008-01-08 15:13:21 -0500},
355          Doi = {DOI 10.1063/1.1610442},
356 <        Journal = {Journal of Chemical Physics},
356 >        Journal = jcp,
357          Pages = {8062-8068},
358          Title = {Hydrodynamic boundary conditions, the Stokes-Einstein law, and long-time tails in the Brownian limit},
359          Volume = 119,
# Line 287 | Line 366
366          Date-Added = {2008-01-08 15:12:53 -0500},
367          Date-Modified = {2008-01-08 15:13:20 -0500},
368          Doi = {DOI 10.1021/jp037185r},
369 <        Journal = {Journal of Physical Chemistry B},
369 >        Journal = jpcb,
370          Pages = {6767-6771},
371          Title = {Brownian motion of a rough sphere and the Stokes-Einstein Law},
372          Volume = 108,
# Line 1115 | Line 1194
1194          Author = {S.~J. Marrink and A.~E. Mark},
1195          Date-Added = {2008-01-08 14:58:56 -0500},
1196          Date-Modified = {2008-01-08 14:58:58 -0500},
1197 <        Journal = {Journal of Physical Chemistry B},
1197 >        Journal = jpcb,
1198          Pages = {6122-6127},
1199          Title = {Effect of undulations on surface tension in simulated bilayers},
1200          Volume = 105,
# Line 1485 | Line 1564
1564          Author = {Benninger, Richard K. P. and Onfelt, Bjorn and Neil, Mark A. A. and Davis, Daniel M. and French, Paul M. W.},
1565          Date-Added = {2008-01-08 14:58:56 -0500},
1566          Date-Modified = {2008-01-08 14:58:59 -0500},
1567 <        Journal = {Biophysical Journal},
1567 >        Journal = bj,
1568          Journal1 = {Biophys. J.},
1569          Number = 1,
1570          Pages = {609--622},
# Line 1545 | Line 1624
1624          Date-Added = {2008-01-08 14:58:56 -0500},
1625          Date-Modified = {2008-01-08 14:58:59 -0500},
1626          Eid = 157802,
1627 <        Journal = {Physical Review Letters},
1627 >        Journal = prl,
1628          Number = 15,
1629          Numpages = 4,
1630          Pages = 157802,
# Line 1737 | Line 1816
1816          Author = {E. Lindahl and O. Edholm},
1817          Date-Added = {2008-01-08 14:58:56 -0500},
1818          Date-Modified = {2008-01-08 14:58:59 -0500},
1819 <        Journal = {Biophysical Journal},
1819 >        Journal = bj,
1820          Month = {July},
1821          Pages = {426-433},
1822          Title = {Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations},
# Line 1829 | Line 1908
1908          Author = {A.~M. Smondyrev and M.~L. Berkowitz},
1909          Date-Added = {2008-01-08 14:58:56 -0500},
1910          Date-Modified = {2008-01-08 14:59:00 -0500},
1911 <        Journal = {Biophysical Journal},
1911 >        Journal = bj,
1912          Pages = {2472-2478},
1913          Title = {Molecular Dynamics Simulation of {\sc dppc} Bilayer in {\sc dmso}},
1914          Volume = 76,
# Line 1839 | Line 1918
1918          Author = {S.~J. Marrink and D.~P. Teileman},
1919          Date-Added = {2008-01-08 14:58:56 -0500},
1920          Date-Modified = {2008-01-08 14:59:00 -0500},
1921 <        Journal = {Biophysical Journal},
1921 >        Journal = bj,
1922          Pages = {2386-2392},
1923          Title = {Molecular Dynamics Simulation of Spontaneous Membrane Fusion during a Cubic-Hexagonal Phase Transition},
1924          Volume = 83,
# Line 1905 | Line 1984
1984          Author = {M. Patra and M. Karttunen and M.~T. Hyv\"{o}nen and E. Falk and P. Lindqvist and I. Vattulainen},
1985          Date-Added = {2008-01-08 14:58:56 -0500},
1986          Date-Modified = {2008-01-08 14:59:00 -0500},
1987 <        Journal = {Biophysical Journal},
1987 >        Journal = bj,
1988          Pages = {3636-3645},
1989          Title = {Molecular Dynamics Simulations of Lipid Bilayers: Major Artifacts Due to Truncating Electrostatic Interactions},
1990          Volume = 84,
# Line 1938 | Line 2017
2017          Author = {A.~K. Sum and J.~J. de~Pablo},
2018          Date-Added = {2008-01-08 14:58:56 -0500},
2019          Date-Modified = {2008-01-08 14:59:00 -0500},
2020 <        Journal = {Biophysical Journal},
2020 >        Journal = bj,
2021          Pages = {3636-3645},
2022          Title = {Molecular Simulation Study on the influence of Dimethylsulfoxide on the structure of Phospholipid Bilayers},
2023          Volume = 85,
# Line 2127 | Line 2206
2206          Author = {J. Norberg and L. Nilsson},
2207          Date-Added = {2008-01-08 14:58:56 -0500},
2208          Date-Modified = {2008-01-08 14:59:00 -0500},
2209 <        Journal = {Biophysical Journal},
2209 >        Journal = bj,
2210          Pages = {1537-1553},
2211          Title = {On the truncation of Long-Range Electrostatic Interactions in {\sc dna}},
2212          Volume = 79,
# Line 3440 | Line 3519
3519          Annote = {973OH Times Cited:1 Cited References Count:33},
3520          Author = {B. Alakent and M. C. Camurdan and P. Doruker},
3521          Issn = {0021-9606},
3522 <        Journal = {Journal of Chemical Physics},
3522 >        Journal = jcp,
3523          Month = {Oct 8},
3524          Number = 14,
3525          Pages = {-},
# Line 3494 | Line 3573
3573          Annote = {Rq238 Times Cited:559 Cited References Count:14},
3574          Author = {H. C. Andersen},
3575          Issn = {0021-9991},
3576 <        Journal = {Journal of Computational Physics},
3576 >        Journal = jcop,
3577          Number = 1,
3578          Pages = {24-34},
3579          Title = {Rattle - a Velocity Version of the Shake Algorithm for Molecular-Dynamics Calculations},
# Line 3525 | Line 3604
3604          Annote = {895QF Times Cited:9 Cited References Count:33},
3605          Author = {A. Auerbach},
3606          Issn = {0027-8424},
3607 <        Journal = {Proceedings of the National Academy of Sciences of the United States of America},
3607 >        Journal = pnas,
3608          Month = {Feb 1},
3609          Number = 5,
3610          Pages = {1408-1412},
# Line 3586 | Line 3665
3665          Annote = {816YY Times Cited:8 Cited References Count:35},
3666          Author = {D. Banerjee and B. C. Bag and S. K. Banik and D. S. Ray},
3667          Issn = {0021-9606},
3668 <        Journal = {Journal of Chemical Physics},
3668 >        Journal = jcp,
3669          Month = {May 15},
3670          Number = 19,
3671          Pages = {8960-8972},
# Line 3633 | Line 3712
3712          Annote = {105HH Times Cited:29 Cited References Count:49},
3713          Author = {E. Barth and T. Schlick},
3714          Issn = {0021-9606},
3715 <        Journal = {Journal of Chemical Physics},
3715 >        Journal = jcp,
3716          Month = {Aug 1},
3717          Number = 5,
3718          Pages = {1617-1632},
# Line 3657 | Line 3736
3736          Annote = {469KV Times Cited:6 Cited References Count:30},
3737          Author = {P. F. Batcho and T. Schlick},
3738          Issn = {0021-9606},
3739 <        Journal = {Journal of Chemical Physics},
3739 >        Journal = jcp,
3740          Month = {Sep 1},
3741          Number = 9,
3742          Pages = {4019-4029},
# Line 3710 | Line 3789
3789          Annote = {736UA Times Cited:0 Cited References Count:11},
3790          Author = {D. A. Beard and T. Schlick},
3791          Issn = {0006-3495},
3792 <        Journal = {Biophysical Journal},
3792 >        Journal = bj,
3793          Month = {Nov 1},
3794          Number = 5,
3795          Pages = {2973-2976},
# Line 3867 | Line 3946
3946          Annote = {Qp423 Times Cited:6414 Cited References Count:96},
3947          Author = {B. R. Brooks and R. E. Bruccoleri and B. D. Olafson and D. J. States and S. Swaminathan and M. Karplus},
3948          Issn = {0192-8651},
3949 <        Journal = {Journal of Computational Chemistry},
3949 >        Journal = jcc,
3950          Number = 2,
3951          Pages = {187-217},
3952          Title = {Charmm - a Program for Macromolecular Energy, Minimization, and Dynamics Calculations},
# Line 3940 | Line 4019
4019          Annote = {255TC Times Cited:24 Cited References Count:38},
4020          Author = {P. J. Camp and M. P. Allen and A. J. Masters},
4021          Issn = {0021-9606},
4022 <        Journal = {Journal of Chemical Physics},
4022 >        Journal = jcp,
4023          Month = {Dec 1},
4024          Number = 21,
4025          Pages = {9871-9881},
# Line 3991 | Line 4070
4070          Annote = {200TT Times Cited:46 Cited References Count:57},
4071          Author = {B. Carrasco and {Garc\'{i}a de la Torre}, Jose},
4072          Issn = {0006-3495},
4073 <        Journal = {Biophysical Journal},
4073 >        Journal = bj,
4074          Month = {Jun},
4075          Number = 6,
4076          Pages = {3044-3057},
# Line 4022 | Line 4101
4101          Annote = {221EN Times Cited:14 Cited References Count:66},
4102          Author = {A. Chandra and T. Ichiye},
4103          Issn = {0021-9606},
4104 <        Journal = {Journal of Chemical Physics},
4104 >        Journal = jcp,
4105          Month = {Aug 8},
4106          Number = 6,
4107          Pages = {2701-2709},
# Line 4082 | Line 4161
4161          Annote = {866UM Times Cited:4 Cited References Count:61},
4162          Author = {D. L. Cheung and S. J. Clark and M. R. Wilson},
4163          Issn = {0021-9606},
4164 <        Journal = {Journal of Chemical Physics},
4164 >        Journal = jcp,
4165          Month = {Nov 8},
4166          Number = 18,
4167          Pages = {9131-9139},
# Line 4133 | Line 4212
4212          Annote = {757TK Times Cited:1 Cited References Count:22},
4213          Author = {S. A. Chin},
4214          Issn = {0021-9606},
4215 <        Journal = {Journal of Chemical Physics},
4215 >        Journal = jcp,
4216          Month = {Jan 1},
4217          Number = 1,
4218          Pages = {8-13},
# Line 4192 | Line 4271
4271          Annote = {689LC Times Cited:3 Cited References Count:48},
4272          Author = {B. X. Cui and M. Y. Shen and K. F. Freed},
4273          Issn = {0027-8424},
4274 <        Journal = {Proceedings of the National Academy of Sciences of the United States of America},
4274 >        Journal = pnas,
4275          Month = {Jun 10},
4276          Number = 12,
4277          Pages = {7087-7092},
# Line 4252 | Line 4331
4331          Annote = {Zl046 Times Cited:30 Cited References Count:29},
4332          Author = {P. Derreumaux and T. Schlick},
4333          Issn = {0006-3495},
4334 <        Journal = {Biophysical Journal},
4334 >        Journal = bj,
4335          Month = {Jan},
4336          Number = 1,
4337          Pages = {72-81},
# Line 4284 | Line 4363
4363          Annote = {Ya587 Times Cited:35 Cited References Count:32},
4364          Author = {A. Dullweber and B. Leimkuhler and R. McLachlan},
4365          Issn = {0021-9606},
4366 <        Journal = {Journal of Chemical Physics},
4366 >        Journal = jcp,
4367          Month = {Oct 15},
4368          Number = 15,
4369          Pages = {5840-5851},
# Line 4328 | Line 4407
4407          Annote = {Q0188 Times Cited:219 Cited References Count:43},
4408          Author = {E. Egberts and H. J. C. Berendsen},
4409          Issn = {0021-9606},
4410 <        Journal = {Journal of Chemical Physics},
4410 >        Journal = jcp,
4411          Month = {Sep 15},
4412          Number = 6,
4413          Pages = {3718-3732},
# Line 4341 | Line 4420
4420          Annote = {Fp216 Times Cited:785 Cited References Count:42},
4421          Author = {D. L. Ermak and J. A. Mccammon},
4422          Issn = {0021-9606},
4423 <        Journal = {Journal of Chemical Physics},
4423 >        Journal = jcp,
4424          Number = 4,
4425          Pages = {1352-1360},
4426          Title = {Brownian Dynamics with Hydrodynamic Interactions},
# Line 4353 | Line 4432
4432          Annote = {Ds757 Times Cited:271 Cited References Count:18},
4433          Author = {D. J. Evans},
4434          Issn = {0026-8976},
4435 <        Journal = {Molecular Physics},
4435 >        Journal = mp,
4436          Number = 2,
4437          Pages = {317-325},
4438          Title = {Representation of Orientation Space},
# Line 4388 | Line 4467
4467          Annote = {816YY Times Cited:5 Cited References Count:39},
4468          Author = {C. J. Fennell and J. D. Gezelter},
4469          Issn = {0021-9606},
4470 <        Journal = {Journal of Chemical Physics},
4470 >        Journal = jcp,
4471          Month = {May 15},
4472          Number = 19,
4473          Pages = {9175-9184},
# Line 4412 | Line 4491
4491          Annote = {633AD Times Cited:2 Cited References Count:43},
4492          Author = {M. X. Fernandes and {Garc\'{i}a de la Torre}, Jose},
4493          Issn = {0006-3495},
4494 <        Journal = {Biophysical Journal},
4494 >        Journal = bj,
4495          Month = {Dec},
4496          Number = 6,
4497          Pages = {3039-3048},
# Line 4432 | Line 4511
4511          Annote = {Lj347 Times Cited:482 Cited References Count:13},
4512          Author = {J. G. Gay and B. J. Berne},
4513          Issn = {0021-9606},
4514 <        Journal = {Journal of Chemical Physics},
4514 >        Journal = jcp,
4515          Number = 6,
4516          Pages = {3316-3319},
4517          Title = {Modification of the Overlap Potential to Mimic a Linear Site-Site Potential},
# Line 4473 | Line 4552
4552  
4553   @article{Goetz1998,
4554          Author = {R. Goetz and R. Lipowsky},
4555 <        Journal = {Journal of Chemical Physics},
4555 >        Journal = jcp,
4556          Number = 17,
4557          Pages = 7397,
4558          Title = {Computer simulations of bilayer membranes: Self-assembly and interfacial tension},
# Line 4516 | Line 4595
4595          Annote = {704QL Times Cited:48 Cited References Count:60},
4596          Author = {J. J. Gray and S. Moughon and C. Wang and O. Schueler-Furman and B. Kuhlman and C. A. Rohl and D. Baker},
4597          Issn = {0022-2836},
4598 <        Journal = {Journal of Molecular Biology},
4598 >        Journal = jmb,
4599          Month = {Aug 1},
4600          Number = 1,
4601          Pages = {281-299},
# Line 4551 | Line 4630
4630          Annote = {L0498 Times Cited:899 Cited References Count:7},
4631          Author = {L. Greengard and V. Rokhlin},
4632          Issn = {0021-9991},
4633 <        Journal = {Journal of Computational Physics},
4633 >        Journal = jcop,
4634          Month = {Dec},
4635          Number = 2,
4636          Pages = {325-348},
# Line 4704 | Line 4783
4783          Annote = {Ju251 Times Cited:55 Cited References Count:44},
4784          Author = {C. Ho and C. D. Stubbs},
4785          Issn = {0006-3495},
4786 <        Journal = {Biophysical Journal},
4786 >        Journal = bj,
4787          Month = {Oct},
4788          Number = 4,
4789          Pages = {897-902},
# Line 4746 | Line 4825
4825          Annote = {870FJ Times Cited:0 Cited References Count:63},
4826          Author = {Y. Huh and N. M. Cann},
4827          Issn = {0021-9606},
4828 <        Journal = {Journal of Chemical Physics},
4828 >        Journal = jcp,
4829          Month = {Nov 22},
4830          Number = 20,
4831          Pages = {10299-10308},
# Line 4825 | Line 4904
4904          Annote = {397CQ Times Cited:14 Cited References Count:36},
4905          Author = {J. A. Izaguirre and D. P. Catarello and J. M. Wozniak and R. D. Skeel},
4906          Issn = {0021-9606},
4907 <        Journal = {Journal of Chemical Physics},
4907 >        Journal = jcp,
4908          Month = {Feb 1},
4909          Number = 5,
4910          Pages = {2090-2098},
# Line 4868 | Line 4947
4947          Annote = {194FM Times Cited:373 Cited References Count:51},
4948          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},
4949          Issn = {0021-9991},
4950 <        Journal = {Journal of Computational Physics},
4950 >        Journal = jcop,
4951          Month = {May 1},
4952          Number = 1,
4953          Pages = {283-312},
# Line 4921 | Line 5000
5000          Annote = {Xk293 Times Cited:77 Cited References Count:17},
5001          Author = {D. K. Klimov and D. Thirumalai},
5002          Issn = {0031-9007},
5003 <        Journal = {Physical Review Letters},
5003 >        Journal = prl,
5004          Month = {Jul 14},
5005          Number = 2,
5006          Pages = {317-320},
# Line 4954 | Line 5033
5033          Annote = {Xq332 Times Cited:11 Cited References Count:18},
5034          Author = {A. Kol and B. B. Laird and B. J. Leimkuhler},
5035          Issn = {0021-9606},
5036 <        Journal = {Journal of Chemical Physics},
5036 >        Journal = jcp,
5037          Month = {Aug 15},
5038          Number = 7,
5039          Pages = {2580-2588},
# Line 5349 | Line 5428
5428          Annote = {891CF Times Cited:1 Cited References Count:56},
5429          Author = {M. A. Meineke and C. F. Vardeman and T. Lin and C. J. Fennell and J. D. Gezelter},
5430          Issn = {0192-8651},
5431 <        Journal = {Journal of Computational Chemistry},
5431 >        Journal = jcc,
5432          Month = {Feb},
5433          Number = 3,
5434          Pages = {252-271},
# Line 5368 | Line 5447
5447          Annote = {Kq355 Times Cited:172 Cited References Count:17},
5448          Author = {S. Melchionna and G. Ciccotti and B. L. Holian},
5449          Issn = {0026-8976},
5450 <        Journal = {Molecular Physics},
5450 >        Journal = mp,
5451          Month = {Feb 20},
5452          Number = 3,
5453          Pages = {533-544},
# Line 5452 | Line 5531
5531          Annote = {861ZF Times Cited:3 Cited References Count:34},
5532          Author = {S. P. Mielke and W. H. Fink and V. V. Krishnan and N. Gronbech-Jensen and C. J. Benham},
5533          Issn = {0021-9606},
5534 <        Journal = {Journal of Chemical Physics},
5534 >        Journal = jcp,
5535          Month = {Oct 22},
5536          Number = 16,
5537          Pages = {8104-8112},
# Line 5547 | Line 5626
5626          Annote = {491UW Times Cited:48 Cited References Count:25},
5627          Author = {H. Noguchi and M. Takasu},
5628          Issn = {0021-9606},
5629 <        Journal = {Journal of Chemical Physics},
5629 >        Journal = jcp,
5630          Month = {Nov 22},
5631          Number = 20,
5632          Pages = {9547-9551},
# Line 5714 | Line 5793
5793          Annote = {T1302 Times Cited:61 Cited References Count:26},
5794          Author = {R. W. Pastor and B. R. Brooks and A. Szabo},
5795          Issn = {0026-8976},
5796 <        Journal = {Molecular Physics},
5796 >        Journal = mp,
5797          Month = {Dec 20},
5798          Number = 6,
5799          Pages = {1409-1419},
# Line 5740 | Line 5819
5819          Annote = {Akb93 Times Cited:71 Cited References Count:12},
5820          Author = {J. W. Perram and M. S. Wertheim},
5821          Issn = {0021-9991},
5822 <        Journal = {Journal of Computational Physics},
5822 >        Journal = jcop,
5823          Number = 3,
5824          Pages = {409-416},
5825          Title = {Statistical-Mechanics of Hard Ellipsoids .1. Overlap Algorithm and the Contact Function},
# Line 5774 | Line 5853
5853  
5854   @article{Petrache2000,
5855          Author = {H.~I. Petrache and S.~W. Dodd and M.~F. Brown},
5856 <        Journal = {Biophysical Journal},
5856 >        Journal = bj,
5857          Pages = {3172-3192},
5858          Title = {Area per Lipid and Acyl Length Distributions in Fluid Phosphatidylcholines Determined by $^2\text{H}$ {\sc nmr} Spectroscopy},
5859          Volume = 79,
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5924          Annote = {763GQ Times Cited:21 Cited References Count:59},
5925          Author = {J. Fernandez-Recio and M. Totrov and R. Abagyan},
5926          Issn = {0022-2836},
5927 <        Journal = {Journal of Molecular Biology},
5927 >        Journal = jmb,
5928          Month = {Jan 16},
5929          Number = 3,
5930          Pages = {843-865},
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6072          Annote = {Cz253 Times Cited:3680 Cited References Count:7},
6073          Author = {J. P. Ryckaert and G. Ciccotti and H. J. C. Berendsen},
6074          Issn = {0021-9991},
6075 <        Journal = {Journal of Computational Physics},
6075 >        Journal = jcop,
6076          Number = 3,
6077          Pages = {327-341},
6078          Title = {Numerical-Integration of Cartesian Equations of Motion of a System with Constraints - Molecular-Dynamics of N-Alkanes},
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6147          Annote = {194FM Times Cited:14 Cited References Count:32},
6148          Author = {A. Sandu and T. Schlick},
6149          Issn = {0021-9991},
6150 <        Journal = {Journal of Computational Physics},
6150 >        Journal = jcop,
6151          Month = {May 1},
6152          Number = 1,
6153          Pages = {74-113},
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6231          Annote = {540MH Times Cited:36 Cited References Count:45},
6232          Author = {M. Y. Shen and K. F. Freed},
6233          Issn = {0006-3495},
6234 <        Journal = {Biophysical Journal},
6234 >        Journal = bj,
6235          Month = {Apr},
6236          Number = 4,
6237          Pages = {1791-1808},
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6274          Annote = {Lh164 Times Cited:27 Cited References Count:47},
6275          Author = {J. Shimada and H. Kaneko and T. Takada},
6276          Issn = {0192-8651},
6277 <        Journal = {Journal of Computational Chemistry},
6277 >        Journal = jcc,
6278          Month = {Jul},
6279          Number = 7,
6280          Pages = {867-878},
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6297          Annote = {633RX Times Cited:8 Cited References Count:22},
6298          Author = {R. D. Skeel and J. A. Izaguirre},
6299          Issn = {0026-8976},
6300 <        Journal = {Molecular Physics},
6300 >        Journal = mp,
6301          Month = {Dec 20},
6302          Number = 24,
6303          Pages = {3885-3891},
# Line 6277 | Line 6356
6356          Annote = {943DN Times Cited:3 Cited References Count:26},
6357          Author = {Y. G. Tao and W. K. {den Otter} and J. T. Padding and J. K. G. Dhont and W. J. Briels},
6358          Issn = {0021-9606},
6359 <        Journal = {Journal of Chemical Physics},
6359 >        Journal = jcp,
6360          Month = {Jun 22},
6361          Number = 24,
6362          Pages = {-},
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6397          Annote = {Tv018 Times Cited:108 Cited References Count:34},
6398          Author = {K. Tu and D. J. Tobias and M. L. Klein},
6399          Issn = {0006-3495},
6400 <        Journal = {Biophysical Journal},
6400 >        Journal = bj,
6401          Month = {Dec},
6402          Number = 6,
6403          Pages = {2558-2562},
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6422          Annote = {Je891 Times Cited:680 Cited References Count:19},
6423          Author = {M. Tuckerman and B. J. Berne and G. J. Martyna},
6424          Issn = {0021-9606},
6425 <        Journal = {Journal of Chemical Physics},
6425 >        Journal = jcp,
6426          Month = {Aug 1},
6427          Number = 3,
6428          Pages = {1990-2001},
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6456          Annote = {Ta403 Times Cited:16 Cited References Count:23},
6457          Author = {J. J. Vincent and K. M. Merz},
6458          Issn = {0192-8651},
6459 <        Journal = {Journal of Computational Chemistry},
6459 >        Journal = jcc,
6460          Month = {Nov},
6461          Number = 11,
6462          Pages = {1420-1427},
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6512          Annote = {738EF Times Cited:3 Cited References Count:43},
6513          Author = {I. M. Withers},
6514          Issn = {0021-9606},
6515 <        Journal = {Journal of Chemical Physics},
6515 >        Journal = jcp,
6516          Month = {Nov 15},
6517          Number = 19,
6518          Pages = {10209-10223},
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6546          Annote = {189PD Times Cited:70 Cited References Count:34},
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6548          Issn = {0021-9606},
6549 <        Journal = {Journal of Chemical Physics},
6549 >        Journal = jcp,
6550          Month = {May 1},
6551          Number = 17,
6552          Pages = {8254-8282},
# Line 6491 | Line 6570
6570  
6571   @article{Blum1972,
6572          Author = {L. Blum and A.~J. Torruella},
6573 <        Journal = {Journal of Chemical Physics},
6573 >        Journal = jcp,
6574          Number = 1,
6575          Pages = {303-309},
6576          Title = {Computer simulations of bilayer membranes: Self-assembly and interfacial tension},
# Line 6500 | Line 6579
6579  
6580   @article{Stone1978,
6581          Author = {A.~J. Stone},
6582 <        Journal = {Molecular Physics},
6582 >        Journal = mp,
6583          Number = 1,
6584          Pages = {241-256},
6585          Title = {The description of bimolecular potentials, forces and torques: the S and V function expansions},
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6588  
6589   @article{Berardi2003,
6590          Author = {R. Berardi, M. Cecchini and C. Zannoni},
6591 <        Journal = {Journal of Chemical Physics},
6591 >        Journal = jcp,
6592          Number = 18,
6593          Pages = {9933-9946},
6594          Title = {A Monte Carlo study of the chiral columnar organizations of dissymmetric discotic mesogens},
# Line 6518 | Line 6597
6597  
6598   @article{Beard2000,
6599          Author = {D. A. Beard and T. Schlick},
6600 <        Journal = {Journal of Chemical Physics},
6600 >        Journal = jcp,
6601          Number = 17,
6602          Pages = {7313-7322},
6603          Title = {Inertial Stochastic Dynamics. I. Long-time-step Methods for Langevin Dynamics},
# Line 6548 | Line 6627
6627  
6628   @article{Matubayasi1999,
6629          Author = {N. Matubayasi and M. Nakahara},
6630 <        Journal = {Journal of Chemical Physics},
6630 >        Journal = jcp,
6631          Number = 7,
6632          Pages = {3291-3301},
6633          Title = {Reversible molecular dynamics for rigid bodies and hybrid Monte Carlo},
# Line 6557 | Line 6636
6636  
6637   @article{Miller2002,
6638          Author = {T.F. Miller III, M. Eleftheriou},
6639 <        Journal = {Journal of Chemical Physics},
6639 >        Journal = jcp,
6640          Number = 20,
6641          Pages = {8649-8659},
6642          Title = {Symplectic quaternion scheme for biophysical molecular dynamics},
# Line 6566 | Line 6645
6645  
6646   @article{McMillan1971,
6647          Author = {W.L. McMillan},
6648 <        Journal = {Journal of Chemical Physics},
6648 >        Journal = jcp,
6649          Number = 3,
6650          Pages = {1238-1246},
6651          Title = {Simple Molecular Model for the Smectic A Phase of Liquid Crystals},

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