--- trunk/langevin/langevin.bib 2008/02/29 22:02:46 3352 +++ trunk/langevin/langevin.bib 2008/04/30 16:16:25 3391 @@ -2,7 +2,7 @@ %% http://bibdesk.sourceforge.net/ -%% Created for Dan Gezelter at 2008-02-15 13:48:27 -0500 +%% Created for Dan Gezelter at 2008-04-30 12:15:56 -0400 %% Saved with string encoding Western (ASCII) @@ -10,6 +10,8 @@ @string{acp = {Adv. Chem. Phys.}} +@string{bj = {Biophys. J.}} + @string{ccp5 = {CCP5 Information Quarterly}} @string{cp = {Chem. Phys.}} @@ -24,6 +26,8 @@ @string{jcp = {J. Chem. Phys.}} +@string{jmb = {J. Mol. Bio.}} + @string{jml = {J. Mol. Liq.}} @string{jpc = {J. Phys. Chem.}} @@ -51,7 +55,133 @@ @string{prl = {Phys. Rev. Lett.}} @string{rmp = {Rev. Mod. Phys.}} + + +@article{Jeffrey:2006dk, + Author = {Jeffrey,D. J. and Onishi,Y.}, + Date-Added = {2008-04-30 12:15:31 -0400}, + Date-Modified = {2008-04-30 12:15:31 -0400}, + Journal = {Journal of Fluid Mechanics Digital Archive}, + M3 = {10.1017/S0022112084000355}, + Number = {-1}, + Pages = {261--290}, + Title = {Calculation of the resistance and mobility functions for two unequal rigid spheres in low-Reynolds-number flow}, + Ty = {JOUR}, + Volume = {139}, + Year = {2006}} + +@article{Goldman:1966ph, + Abstract = { Bipolar coordinates are employed to determine the terminal settling motion of two, identical, homogeneous, unconstrained spheres in an unbounded fluid at small Reynolds numbers. Exact numerical values are obtained for the linear and angular velocities of the spheres as a function of their relative separation and of the orientation of their line-of-centers relative to the direction of gravity. Comparison with published experimental data indicates good agreement, especially when wall effects are taken into account.}, + Author = {Goldman, A. J. and Cox, R. G. and Brenner, H.}, + Date-Added = {2008-04-30 12:12:54 -0400}, + Date-Modified = {2008-04-30 12:12:54 -0400}, + Journal = {Chemical Engineering Science}, + Number = {12}, + Pages = {1151--1170}, + Title = {The slow motion of two identical arbitrarily oriented spheres through a viscous fluid}, + Ty = {JOUR}, + Url = {http://www.sciencedirect.com/science/article/B6TFK-44360XJ-D0/1/c14cf5c48fab65f0aaa096e60d15fa87}, + Volume = {21}, + Year = {1966}, + Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B6TFK-44360XJ-D0/1/c14cf5c48fab65f0aaa096e60d15fa87}} + +@article{Brenner:1972th, + Abstract = { A general theory is presented for determining the quasistatic Stokes resistance of a particle or an aggregate of particles of arbitrary shape which move with arbitrary translational and rotational velocities in an infinite viscous fluid subjected to a general linear shear flow in the absence of the particles. It is shown that the hydrodynamic resistance of the particles may be characterized by two intrinsic matrices-the grand resistance matrix and the shear resistance matrix, the elements of each matrix being dependent only upon the instantaneous geometrical configuration of the multiparticle system. Explicit expressions for these matrix elements are given for a single ellipsoidal particle and for two spheres. Analytical, closed-form expressions are given for the case where the spheres are widely spaced compared with their radii. When the separation between the spheres is arbitrary, the matrix elements are only determinate numerically for specified ratios of sphere radii and center-to-center separation distances. These numerical values are derived from available bipolar-coordinate system solutions for two spheres. Besides providing a compact and systematic representation of the intrinsic Stokes resistance of multiparticle systems subjected to shear, which does not depend upon the precise velocities of the particles or on the nature of the shear flow, it is demonstrated (by way of example) that the matrix representation permits an immediate determination of the translational and rotational velocities of the individual particles in a neutrally buoyant multiparticle system.}, + Author = {Brenner, Howard and O'Neill, Michael E.}, + Date-Added = {2008-04-30 12:12:49 -0400}, + Date-Modified = {2008-04-30 12:12:49 -0400}, + Journal = {Chemical Engineering Science}, + Number = {7}, + Pages = {1421--1439}, + Title = {On the Stokes resistance of multiparticle systems in a linear shear field}, + Ty = {JOUR}, + Url = {http://www.sciencedirect.com/science/article/B6TFK-444GW12-16J/1/ba6bda9d1e50c88fea6cd92aac2f6bd7}, + Volume = {27}, + Year = {1972}, + Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B6TFK-444GW12-16J/1/ba6bda9d1e50c88fea6cd92aac2f6bd7}} + +@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}, + Bdsk-Url-1 = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp0647941}} + +@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}, + Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B6TFB-44XJKW6-8/1/376af59f3b89aecd8486b1c6186b0953}} + +@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. }, + 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}, + Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B6X42-46D224N-BW/2/0e1b39b5a20e979c5fa5e1f560de6413}} @article{SunX._jp0762020, Affiliation = {Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556}, @@ -59,7 +189,7 @@ Date-Added = {2008-02-15 13:48:18 -0500}, Date-Modified = {2008-02-15 13:48:18 -0500}, Issn = {1520-6106}, - Journal = {Journal of Physical Chemistry B}, + Journal = jpcb, Number = {7}, Pages = {1968-1975}, Title = {Dipolar Ordering in the Ripple Phases of Molecular-Scale Models of Lipid Membranes}, @@ -78,18 +208,18 @@ Title = {Molecular Modeling and Simulation: An Interdisciplinary Guide}, Year = {2002}} -@misc{Chun:2000fj, +@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}, - Note = {Journal of Computational Chemistry}, - Pages = {159-184}, - Timescited = {0}, - Title = {MBO(N)D: A multibody method for long-time molecular dynamics simulations}, - Volume = {21}, - Year = {2000}} + 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.}, @@ -127,7 +257,7 @@ @inbook{Ramachandran1996, Address = {Providence, Rhode Island}, - Author = {GOMATHI RAMACHANDRAN AND TAMAR SCHLICK}, + 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}, @@ -140,7 +270,7 @@ Year = {1996}} @article{FIXMAN:1986lr, - Author = {FIXMAN, M}, + Author = {Fixman, M}, Date-Added = {2008-01-22 09:59:29 -0500}, Date-Modified = {2008-01-22 09:59:35 -0500}, Journal = {Macromolecules}, @@ -187,7 +317,7 @@ Author = {{Garc\'{i}a de la Torre}, Jose and Rodes, Vicente}, 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}, @@ -222,7 +352,7 @@ 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, Pages = {209-217}, @@ -273,7 +403,7 @@ 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, @@ -284,7 +414,7 @@ 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, @@ -296,7 +426,7 @@ 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, @@ -309,7 +439,7 @@ 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, @@ -1137,7 +1267,7 @@ 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, @@ -1507,7 +1637,7 @@ Author = {Benninger, Richard K. P. and Onfelt, Bjorn and Neil, Mark A. A. and Davis, Daniel M. and French, Paul M. W.}, 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, Pages = {609--622}, @@ -1567,7 +1697,7 @@ 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, @@ -1759,7 +1889,7 @@ 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}, @@ -1851,7 +1981,7 @@ 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, @@ -1861,7 +1991,7 @@ 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, @@ -1927,7 +2057,7 @@ 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, @@ -1960,7 +2090,7 @@ 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, @@ -2149,7 +2279,7 @@ 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, @@ -2326,11 +2456,11 @@ 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} @@ -3462,7 +3592,7 @@ 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, Pages = {-}, @@ -3516,7 +3646,7 @@ Annote = {Rq238 Times Cited:559 Cited References Count:14}, Author = {H. C. Andersen}, Issn = {0021-9991}, - Journal = {Journal of Computational Physics}, + Journal = jcop, Number = 1, Pages = {24-34}, Title = {Rattle - a Velocity Version of the Shake Algorithm for Molecular-Dynamics Calculations}, @@ -3547,7 +3677,7 @@ 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, Pages = {1408-1412}, @@ -3608,7 +3738,7 @@ 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, Pages = {8960-8972}, @@ -3655,7 +3785,7 @@ 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, Pages = {1617-1632}, @@ -3679,7 +3809,7 @@ 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, Pages = {4019-4029}, @@ -3732,7 +3862,7 @@ 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, Pages = {2973-2976}, @@ -3889,7 +4019,7 @@ 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}, + Journal = jcc, Number = 2, Pages = {187-217}, Title = {Charmm - a Program for Macromolecular Energy, Minimization, and Dynamics Calculations}, @@ -3962,7 +4092,7 @@ 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, Pages = {9871-9881}, @@ -4013,7 +4143,7 @@ Annote = {200TT Times Cited:46 Cited References Count:57}, Author = {B. Carrasco and {Garc\'{i}a de la Torre}, Jose}, Issn = {0006-3495}, - Journal = {Biophysical Journal}, + Journal = bj, Month = {Jun}, Number = 6, Pages = {3044-3057}, @@ -4044,7 +4174,7 @@ 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, Pages = {2701-2709}, @@ -4104,7 +4234,7 @@ 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, Pages = {9131-9139}, @@ -4155,7 +4285,7 @@ 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, Pages = {8-13}, @@ -4214,7 +4344,7 @@ 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, Pages = {7087-7092}, @@ -4274,7 +4404,7 @@ 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, Pages = {72-81}, @@ -4306,7 +4436,7 @@ 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, Pages = {5840-5851}, @@ -4350,7 +4480,7 @@ 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, Pages = {3718-3732}, @@ -4363,7 +4493,7 @@ 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}, + Journal = jcp, Number = 4, Pages = {1352-1360}, Title = {Brownian Dynamics with Hydrodynamic Interactions}, @@ -4375,7 +4505,7 @@ Annote = {Ds757 Times Cited:271 Cited References Count:18}, Author = {D. J. Evans}, Issn = {0026-8976}, - Journal = {Molecular Physics}, + Journal = mp, Number = 2, Pages = {317-325}, Title = {Representation of Orientation Space}, @@ -4410,7 +4540,7 @@ 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, Pages = {9175-9184}, @@ -4434,7 +4564,7 @@ Annote = {633AD Times Cited:2 Cited References Count:43}, Author = {M. X. Fernandes and {Garc\'{i}a de la Torre}, Jose}, Issn = {0006-3495}, - Journal = {Biophysical Journal}, + Journal = bj, Month = {Dec}, Number = 6, Pages = {3039-3048}, @@ -4454,7 +4584,7 @@ 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}, + Journal = jcp, Number = 6, Pages = {3316-3319}, Title = {Modification of the Overlap Potential to Mimic a Linear Site-Site Potential}, @@ -4495,7 +4625,7 @@ @article{Goetz1998, Author = {R. Goetz and R. Lipowsky}, - Journal = {Journal of Chemical Physics}, + Journal = jcp, Number = 17, Pages = 7397, Title = {Computer simulations of bilayer membranes: Self-assembly and interfacial tension}, @@ -4538,7 +4668,7 @@ 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, Pages = {281-299}, @@ -4573,7 +4703,7 @@ 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, Pages = {325-348}, @@ -4726,7 +4856,7 @@ 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, Pages = {897-902}, @@ -4768,7 +4898,7 @@ 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, Pages = {10299-10308}, @@ -4847,7 +4977,7 @@ 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, Pages = {2090-2098}, @@ -4890,7 +5020,7 @@ 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, Pages = {283-312}, @@ -4943,7 +5073,7 @@ 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, Pages = {317-320}, @@ -4976,7 +5106,7 @@ 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, Pages = {2580-2588}, @@ -5371,7 +5501,7 @@ 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, Pages = {252-271}, @@ -5390,7 +5520,7 @@ 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, Pages = {533-544}, @@ -5474,7 +5604,7 @@ 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, Pages = {8104-8112}, @@ -5569,7 +5699,7 @@ 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, Pages = {9547-9551}, @@ -5736,7 +5866,7 @@ 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, Pages = {1409-1419}, @@ -5762,7 +5892,7 @@ 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}, + Journal = jcop, Number = 3, Pages = {409-416}, Title = {Statistical-Mechanics of Hard Ellipsoids .1. Overlap Algorithm and the Contact Function}, @@ -5796,7 +5926,7 @@ @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, @@ -5867,7 +5997,7 @@ 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, Pages = {843-865}, @@ -6015,7 +6145,7 @@ 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}, + 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}, @@ -6090,7 +6220,7 @@ 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, Pages = {74-113}, @@ -6174,7 +6304,7 @@ 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, Pages = {1791-1808}, @@ -6217,7 +6347,7 @@ 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, Pages = {867-878}, @@ -6240,7 +6370,7 @@ 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, Pages = {3885-3891}, @@ -6299,7 +6429,7 @@ 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, Pages = {-}, @@ -6340,7 +6470,7 @@ 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, Pages = {2558-2562}, @@ -6365,7 +6495,7 @@ 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, Pages = {1990-2001}, @@ -6399,7 +6529,7 @@ 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, Pages = {1420-1427}, @@ -6455,7 +6585,7 @@ 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, Pages = {10209-10223}, @@ -6489,7 +6619,7 @@ 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, Pages = {8254-8282}, @@ -6513,7 +6643,7 @@ @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}, @@ -6522,7 +6652,7 @@ @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}, @@ -6531,7 +6661,7 @@ @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}, @@ -6540,7 +6670,7 @@ @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}, @@ -6570,7 +6700,7 @@ @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}, @@ -6579,7 +6709,7 @@ @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}, @@ -6588,7 +6718,7 @@ @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}, @@ -6646,3 +6776,27 @@ Year = 2005, 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}} + +@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}, + Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/78/2/719}} + +@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}}