--- trunk/tengDissertation/dissertation.bib 2006/06/06 02:05:07 2796 +++ trunk/tengDissertation/dissertation.bib 2006/06/06 02:12:34 2797 @@ -3,9 +3,9 @@ Encoding: GBK @ARTICLE{Torre2003, author = {J. G. {de la Torre} and H. E. Sanchez and A. Ortega and J. G. Hernandez - and M. X. Fernandes and F. G. Diaz and M. C. L. Martinez}, + and M. X. Fernandes and F. G. Diaz and M. C. L. Martinez}, title = {Calculation of the solution properties of flexible macromolecules: - methods and applications}, + methods and applications}, journal = {European Biophysics Journal with Biophysics Letters}, year = {2003}, volume = {32}, @@ -13,27 +13,27 @@ Encoding: GBK number = {5}, month = {Aug}, abstract = {While the prediction of hydrodynamic properties of rigid particles - is nowadays feasible using simple and efficient computer programs, - the calculation of such properties and, in general, the dynamic - behavior of flexible macromolecules has not reached a similar situation. - Although the theories are available, usually the computational work - is done using solutions specific for each problem. We intend to - develop computer programs that would greatly facilitate the task - of predicting solution behavior of flexible macromolecules. In this - paper, we first present an overview of the two approaches that are - most practical: the Monte Carlo rigid-body treatment, and the Brownian - dynamics simulation technique. The Monte Carlo procedure is based - on the calculation of properties for instantaneous conformations - of the macromolecule that are regarded as if they were instantaneously - rigid. We describe how a Monte Carlo program can be interfaced to - the programs in the HYDRO suite for rigid particles, and provide - an example of such calculation, for a hypothetical particle: a protein - with two domains connected by a flexible linker. We also describe - briefly the essentials of Brownian dynamics, and propose a general - mechanical model that includes several kinds of intramolecular interactions, - such as bending, internal rotation, excluded volume effects, etc. - We provide an example of the application of this methodology to - the dynamics of a semiflexible, wormlike DNA.}, + is nowadays feasible using simple and efficient computer programs, + the calculation of such properties and, in general, the dynamic + behavior of flexible macromolecules has not reached a similar situation. + Although the theories are available, usually the computational work + is done using solutions specific for each problem. We intend to + develop computer programs that would greatly facilitate the task + of predicting solution behavior of flexible macromolecules. In this + paper, we first present an overview of the two approaches that are + most practical: the Monte Carlo rigid-body treatment, and the Brownian + dynamics simulation technique. The Monte Carlo procedure is based + on the calculation of properties for instantaneous conformations + of the macromolecule that are regarded as if they were instantaneously + rigid. We describe how a Monte Carlo program can be interfaced to + the programs in the HYDRO suite for rigid particles, and provide + an example of such calculation, for a hypothetical particle: a protein + with two domains connected by a flexible linker. We also describe + briefly the essentials of Brownian dynamics, and propose a general + mechanical model that includes several kinds of intramolecular interactions, + such as bending, internal rotation, excluded volume effects, etc. + We provide an example of the application of this methodology to + the dynamics of a semiflexible, wormlike DNA.}, annote = {724XK Times Cited:6 Cited References Count:64}, issn = {0175-7571}, uri = {://000185513400011}, @@ -42,7 +42,7 @@ Encoding: GBK @ARTICLE{Alakent2005, author = {B. Alakent and M. C. Camurdan and P. Doruker}, title = {Hierarchical structure of the energy landscape of proteins revisited - by time series analysis. II. Investigation of explicit solvent effects}, + by time series analysis. II. Investigation of explicit solvent effects}, journal = {Journal of Chemical Physics}, year = {2005}, volume = {123}, @@ -50,39 +50,39 @@ Encoding: GBK number = {14}, month = {Oct 8}, abstract = {Time series analysis tools are employed on the principal modes obtained - from the C-alpha trajectories from two independent molecular-dynamics - simulations of alpha-amylase inhibitor (tendamistat). Fluctuations - inside an energy minimum (intraminimum motions), transitions between - minima (interminimum motions), and relaxations in different hierarchical - energy levels are investigated and compared with those encountered - in vacuum by using different sampling window sizes and intervals. - The low-frequency low-indexed mode relationship, established in - vacuum, is also encountered in water, which shows the reliability - of the important dynamics information offered by principal components - analysis in water. It has been shown that examining a short data - collection period (100 ps) may result in a high population of overdamped - modes, while some of the low-frequency oscillations (< 10 cm(-1)) - can be captured in water by using a longer data collection period - (1200 ps). Simultaneous analysis of short and long sampling window - sizes gives the following picture of the effect of water on protein - dynamics. Water makes the protein lose its memory: future conformations - are less dependent on previous conformations due to the lowering - of energy barriers in hierarchical levels of the energy landscape. - In short-time dynamics (< 10 ps), damping factors extracted from - time series model parameters are lowered. For tendamistat, the friction - coefficient in the Langevin equation is found to be around 40-60 - cm(-1) for the low-indexed modes, compatible with literature. The - fact that water has increased the friction and that on the other - hand has lubrication effect at first sight contradicts. However, - this comes about because water enhances the transitions between - minima and forces the protein to reduce its already inherent inability - to maintain oscillations observed in vacuum. Some of the frequencies - lower than 10 cm(-1) are found to be overdamped, while those higher - than 20 cm(-1) are slightly increased. As for the long-time dynamics - in water, it is found that random-walk motion is maintained for - approximately 200 ps (about five times of that in vacuum) in the - low-indexed modes, showing the lowering of energy barriers between - the higher-level minima.}, + from the C-alpha trajectories from two independent molecular-dynamics + simulations of alpha-amylase inhibitor (tendamistat). Fluctuations + inside an energy minimum (intraminimum motions), transitions between + minima (interminimum motions), and relaxations in different hierarchical + energy levels are investigated and compared with those encountered + in vacuum by using different sampling window sizes and intervals. + The low-frequency low-indexed mode relationship, established in + vacuum, is also encountered in water, which shows the reliability + of the important dynamics information offered by principal components + analysis in water. It has been shown that examining a short data + collection period (100 ps) may result in a high population of overdamped + modes, while some of the low-frequency oscillations (< 10 cm(-1)) + can be captured in water by using a longer data collection period + (1200 ps). Simultaneous analysis of short and long sampling window + sizes gives the following picture of the effect of water on protein + dynamics. Water makes the protein lose its memory: future conformations + are less dependent on previous conformations due to the lowering + of energy barriers in hierarchical levels of the energy landscape. + In short-time dynamics (< 10 ps), damping factors extracted from + time series model parameters are lowered. For tendamistat, the friction + coefficient in the Langevin equation is found to be around 40-60 + cm(-1) for the low-indexed modes, compatible with literature. The + fact that water has increased the friction and that on the other + hand has lubrication effect at first sight contradicts. However, + this comes about because water enhances the transitions between + minima and forces the protein to reduce its already inherent inability + to maintain oscillations observed in vacuum. Some of the frequencies + lower than 10 cm(-1) are found to be overdamped, while those higher + than 20 cm(-1) are slightly increased. As for the long-time dynamics + in water, it is found that random-walk motion is maintained for + approximately 200 ps (about five times of that in vacuum) in the + low-indexed modes, showing the lowering of energy barriers between + the higher-level minima.}, annote = {973OH Times Cited:1 Cited References Count:33}, issn = {0021-9606}, uri = {://000232532000064}, @@ -99,7 +99,7 @@ Encoding: GBK @ARTICLE{Allison1991, author = {S. A. Allison}, title = {A Brownian Dynamics Algorithm for Arbitrary Rigid Bodies - Application - to Polarized Dynamic Light-Scattering}, + to Polarized Dynamic Light-Scattering}, journal = {Macromolecules}, year = {1991}, volume = {24}, @@ -107,19 +107,19 @@ Encoding: GBK number = {2}, month = {Jan 21}, abstract = {A Brownian dynamics algorithm is developed to simulate dynamics experiments - of rigid macromolecules. It is applied to polarized dynamic light - scattering from rodlike sturctures and from a model of a DNA fragment - (762 base pairs). A number of rod cases are examined in which the - translational anisotropy is increased form zero to a large value. - Simulated first cumulants as well as amplitudes and lifetimes of - the dynamic form factor are compared with predictions of analytic - theories and found to be in very good agreement with them. For DNA - fragments 762 base pairs in length or longer, translational anisotropy - does not contribute significantly to dynamic light scattering. In - a comparison of rigid and flexible simulations on semistiff models - of this fragment, it is shown directly that flexing contributes - to the faster decay processes probed by light scattering and that - the flexible model studies are in good agreement with experiment.}, + of rigid macromolecules. It is applied to polarized dynamic light + scattering from rodlike sturctures and from a model of a DNA fragment + (762 base pairs). A number of rod cases are examined in which the + translational anisotropy is increased form zero to a large value. + Simulated first cumulants as well as amplitudes and lifetimes of + the dynamic form factor are compared with predictions of analytic + theories and found to be in very good agreement with them. For DNA + fragments 762 base pairs in length or longer, translational anisotropy + does not contribute significantly to dynamic light scattering. In + a comparison of rigid and flexible simulations on semistiff models + of this fragment, it is shown directly that flexing contributes + to the faster decay processes probed by light scattering and that + the flexible model studies are in good agreement with experiment.}, annote = {Eu814 Times Cited:8 Cited References Count:32}, issn = {0024-9297}, uri = {://A1991EU81400029}, @@ -128,7 +128,7 @@ Encoding: GBK @ARTICLE{Andersen1983, author = {H. C. Andersen}, title = {Rattle - a Velocity Version of the Shake Algorithm for Molecular-Dynamics - Calculations}, + Calculations}, journal = {Journal of Computational Physics}, year = {1983}, volume = {52}, @@ -142,33 +142,33 @@ Encoding: GBK @ARTICLE{Auerbach2005, author = {A. Auerbach}, title = {Gating of acetylcholine receptor channels: Brownian motion across - a broad transition state}, + a broad transition state}, journal = {Proceedings of the National Academy of Sciences of the United States - of America}, + of America}, year = {2005}, volume = {102}, pages = {1408-1412}, number = {5}, month = {Feb 1}, abstract = {Acetylcholine receptor channels (AChRs) are proteins that switch between - stable #closed# and #open# conformations. In patch clamp recordings, - diliganded AChR gating appears to be a simple, two-state reaction. - However, mutagenesis studies indicate that during gating dozens - of residues across the protein move asynchronously and are organized - into rigid body gating domains (#blocks#). Moreover, there is an - upper limit to the apparent channel opening rate constant. These - observations suggest that the gating reaction has a broad, corrugated - transition state region, with the maximum opening rate reflecting, - in part, the mean first-passage time across this ensemble. Simulations - reveal that a flat, isotropic energy profile for the transition - state can account for many of the essential features of AChR gating. - With this mechanism, concerted, local structural transitions that - occur on the broad transition state ensemble give rise to fractional - measures of reaction progress (Phi values) determined by rate-equilibrium - free energy relationship analysis. The results suggest that the - coarse-grained AChR gating conformational change propagates through - the protein with dynamics that are governed by the Brownian motion - of individual gating blocks.}, + stable #closed# and #open# conformations. In patch clamp recordings, + diliganded AChR gating appears to be a simple, two-state reaction. + However, mutagenesis studies indicate that during gating dozens + of residues across the protein move asynchronously and are organized + into rigid body gating domains (#blocks#). Moreover, there is an + upper limit to the apparent channel opening rate constant. These + observations suggest that the gating reaction has a broad, corrugated + transition state region, with the maximum opening rate reflecting, + in part, the mean first-passage time across this ensemble. Simulations + reveal that a flat, isotropic energy profile for the transition + state can account for many of the essential features of AChR gating. + With this mechanism, concerted, local structural transitions that + occur on the broad transition state ensemble give rise to fractional + measures of reaction progress (Phi values) determined by rate-equilibrium + free energy relationship analysis. The results suggest that the + coarse-grained AChR gating conformational change propagates through + the protein with dynamics that are governed by the Brownian motion + of individual gating blocks.}, annote = {895QF Times Cited:9 Cited References Count:33}, issn = {0027-8424}, uri = {://000226877300030}, @@ -177,7 +177,7 @@ Encoding: GBK @ARTICLE{Baber1995, author = {J. Baber and J. F. Ellena and D. S. Cafiso}, title = {Distribution of General-Anesthetics in Phospholipid-Bilayers Determined - Using H-2 Nmr and H-1-H-1 Noe Spectroscopy}, + Using H-2 Nmr and H-1-H-1 Noe Spectroscopy}, journal = {Biochemistry}, year = {1995}, volume = {34}, @@ -185,26 +185,26 @@ Encoding: GBK number = {19}, month = {May 16}, abstract = {The effect of the general anesthetics halothane, enflurane, and isoflurane - on hydrocarbon chain packing in palmitoyl(d(31))oleoylphosphatidylcholine - membranes in the liquid crystalline phase was investigated using - H-2 NMR. Upon the addition of the anesthetics, the first five methylene - units near the interface generally show a very small increase in - segmental order, while segments deeper within the bilayer show a - small decrease in segmental order. From the H-2 NMR results, the - chain length for the perdeuterated palmitoyl chain in the absence - of anesthetic was found to be 12.35 Angstrom. Upon the addition - of halothane enflurane, or isoflurane, the acyl chain undergoes - slight contractions of 0.11, 0.20, or 0.16 Angstrom, respectively, - at 50 mol % anesthetic. A simple model was used to estimate the - relative amounts of anesthetic located near the interface and deeper - in the bilayer hydrocarbon region, and only a slight preference - for an interfacial location was observed. Intermolecular H-1-H-1 - nuclear Overhauser effects (NOEs) were measured between phospholipid - and halothane protons. These NOEs are consistent with the intramembrane - location of the anesthetics suggested by the H-2 NMR data. In addition, - the NOE data indicate that anesthetics prefer the interfacial and - hydrocarbon regions of the membrane and are not found in high concentrations - in the phospholipid headgroup.}, + on hydrocarbon chain packing in palmitoyl(d(31))oleoylphosphatidylcholine + membranes in the liquid crystalline phase was investigated using + H-2 NMR. Upon the addition of the anesthetics, the first five methylene + units near the interface generally show a very small increase in + segmental order, while segments deeper within the bilayer show a + small decrease in segmental order. From the H-2 NMR results, the + chain length for the perdeuterated palmitoyl chain in the absence + of anesthetic was found to be 12.35 Angstrom. Upon the addition + of halothane enflurane, or isoflurane, the acyl chain undergoes + slight contractions of 0.11, 0.20, or 0.16 Angstrom, respectively, + at 50 mol % anesthetic. A simple model was used to estimate the + relative amounts of anesthetic located near the interface and deeper + in the bilayer hydrocarbon region, and only a slight preference + for an interfacial location was observed. Intermolecular H-1-H-1 + nuclear Overhauser effects (NOEs) were measured between phospholipid + and halothane protons. These NOEs are consistent with the intramembrane + location of the anesthetics suggested by the H-2 NMR data. In addition, + the NOE data indicate that anesthetics prefer the interfacial and + hydrocarbon regions of the membrane and are not found in high concentrations + in the phospholipid headgroup.}, annote = {Qz716 Times Cited:38 Cited References Count:37}, issn = {0006-2960}, uri = {://A1995QZ71600035}, @@ -213,7 +213,7 @@ Encoding: GBK @ARTICLE{Banerjee2004, author = {D. Banerjee and B. C. Bag and S. K. Banik and D. S. Ray}, title = {Solution of quantum Langevin equation: Approximations, theoretical - and numerical aspects}, + and numerical aspects}, journal = {Journal of Chemical Physics}, year = {2004}, volume = {120}, @@ -221,19 +221,19 @@ Encoding: GBK number = {19}, month = {May 15}, abstract = {Based on a coherent state representation of noise operator and an - ensemble averaging procedure using Wigner canonical thermal distribution - for harmonic oscillators, a generalized quantum Langevin equation - has been recently developed [Phys. Rev. E 65, 021109 (2002); 66, - 051106 (2002)] to derive the equations of motion for probability - distribution functions in c-number phase-space. We extend the treatment - to explore several systematic approximation schemes for the solutions - of the Langevin equation for nonlinear potentials for a wide range - of noise correlation, strength and temperature down to the vacuum - limit. The method is exemplified by an analytic application to harmonic - oscillator for arbitrary memory kernel and with the help of a numerical - calculation of barrier crossing, in a cubic potential to demonstrate - the quantum Kramers' turnover and the quantum Arrhenius plot. (C) - 2004 American Institute of Physics.}, + ensemble averaging procedure using Wigner canonical thermal distribution + for harmonic oscillators, a generalized quantum Langevin equation + has been recently developed [Phys. Rev. E 65, 021109 (2002); 66, + 051106 (2002)] to derive the equations of motion for probability + distribution functions in c-number phase-space. We extend the treatment + to explore several systematic approximation schemes for the solutions + of the Langevin equation for nonlinear potentials for a wide range + of noise correlation, strength and temperature down to the vacuum + limit. The method is exemplified by an analytic application to harmonic + oscillator for arbitrary memory kernel and with the help of a numerical + calculation of barrier crossing, in a cubic potential to demonstrate + the quantum Kramers' turnover and the quantum Arrhenius plot. (C) + 2004 American Institute of Physics.}, annote = {816YY Times Cited:8 Cited References Count:35}, issn = {0021-9606}, uri = {://000221146400009}, @@ -251,7 +251,7 @@ Encoding: GBK @ARTICLE{Barth1998, author = {E. Barth and T. Schlick}, title = {Overcoming stability limitations in biomolecular dynamics. I. Combining - force splitting via extrapolation with Langevin dynamics in LN}, + force splitting via extrapolation with Langevin dynamics in LN}, journal = {Journal of Chemical Physics}, year = {1998}, volume = {109}, @@ -259,31 +259,31 @@ Encoding: GBK number = {5}, month = {Aug 1}, abstract = {We present an efficient new method termed LN for propagating biomolecular - dynamics according to the Langevin equation that arose fortuitously - upon analysis of the range of harmonic validity of our normal-mode - scheme LIN. LN combines force linearization with force splitting - techniques and disposes of LIN'S computationally intensive minimization - (anharmonic correction) component. Unlike the competitive multiple-timestepping - (MTS) schemes today-formulated to be symplectic and time-reversible-LN - merges the slow and fast forces via extrapolation rather than impulses; - the Langevin heat bath prevents systematic energy drifts. This combination - succeeds in achieving more significant speedups than these MTS methods - which are Limited by resonance artifacts to an outer timestep less - than some integer multiple of half the period of the fastest motion - (around 4-5 fs for biomolecules). We show that LN achieves very - good agreement with small-timestep solutions of the Langevin equation - in terms of thermodynamics (energy means and variances), geometry, - and dynamics (spectral densities) for two proteins in vacuum and - a large water system. Significantly, the frequency of updating the - slow forces extends to 48 fs or more, resulting in speedup factors - exceeding 10. The implementation of LN in any program that employs - force-splitting computations is straightforward, with only partial - second-derivative information required, as well as sparse Hessian/vector - multiplication routines. The linearization part of LN could even - be replaced by direct evaluation of the fast components. The application - of LN to biomolecular dynamics is well suited for configurational - sampling, thermodynamic, and structural questions. (C) 1998 American - Institute of Physics.}, + dynamics according to the Langevin equation that arose fortuitously + upon analysis of the range of harmonic validity of our normal-mode + scheme LIN. LN combines force linearization with force splitting + techniques and disposes of LIN'S computationally intensive minimization + (anharmonic correction) component. Unlike the competitive multiple-timestepping + (MTS) schemes today-formulated to be symplectic and time-reversible-LN + merges the slow and fast forces via extrapolation rather than impulses; + the Langevin heat bath prevents systematic energy drifts. This combination + succeeds in achieving more significant speedups than these MTS methods + which are Limited by resonance artifacts to an outer timestep less + than some integer multiple of half the period of the fastest motion + (around 4-5 fs for biomolecules). We show that LN achieves very + good agreement with small-timestep solutions of the Langevin equation + in terms of thermodynamics (energy means and variances), geometry, + and dynamics (spectral densities) for two proteins in vacuum and + a large water system. Significantly, the frequency of updating the + slow forces extends to 48 fs or more, resulting in speedup factors + exceeding 10. The implementation of LN in any program that employs + force-splitting computations is straightforward, with only partial + second-derivative information required, as well as sparse Hessian/vector + multiplication routines. The linearization part of LN could even + be replaced by direct evaluation of the fast components. The application + of LN to biomolecular dynamics is well suited for configurational + sampling, thermodynamic, and structural questions. (C) 1998 American + Institute of Physics.}, annote = {105HH Times Cited:29 Cited References Count:49}, issn = {0021-9606}, uri = {://000075066300006}, @@ -292,7 +292,7 @@ Encoding: GBK @ARTICLE{Batcho2001, author = {P. F. Batcho and T. Schlick}, title = {Special stability advantages of position-Verlet over velocity-Verlet - in multiple-time step integration}, + in multiple-time step integration}, journal = {Journal of Chemical Physics}, year = {2001}, volume = {115}, @@ -300,16 +300,16 @@ Encoding: GBK number = {9}, month = {Sep 1}, abstract = {We present an analysis for a simple two-component harmonic oscillator - that compares the use of position-Verlet to velocity-Verlet for - multiple-time step integration. The numerical stability analysis - based on the impulse-Verlet splitting shows that position-Verlet - has enhanced stability, in terms of the largest allowable time step, - for cases where an ample separation of time scales exists. Numerical - investigations confirm the advantages of the position-Verlet scheme - when used for the fastest time scales of the system. Applications - to a biomolecule. a solvated protein, for both Newtonian and Langevin - dynamics echo these trends over large outer time-step regimes. (C) - 2001 American Institute of Physics.}, + that compares the use of position-Verlet to velocity-Verlet for + multiple-time step integration. The numerical stability analysis + based on the impulse-Verlet splitting shows that position-Verlet + has enhanced stability, in terms of the largest allowable time step, + for cases where an ample separation of time scales exists. Numerical + investigations confirm the advantages of the position-Verlet scheme + when used for the fastest time scales of the system. Applications + to a biomolecule. a solvated protein, for both Newtonian and Langevin + dynamics echo these trends over large outer time-step regimes. (C) + 2001 American Institute of Physics.}, annote = {469KV Times Cited:6 Cited References Count:30}, issn = {0021-9606}, uri = {://000170813800005}, @@ -318,7 +318,7 @@ Encoding: GBK @ARTICLE{Bates2005, author = {M. A. Bates and G. R. Luckhurst}, title = {Biaxial nematic phases and V-shaped molecules: A Monte Carlo simulation - study}, + study}, journal = {Physical Review E}, year = {2005}, volume = {72}, @@ -326,23 +326,23 @@ Encoding: GBK number = {5}, month = {Nov}, abstract = {Inspired by recent claims that compounds composed of V-shaped molecules - can exhibit the elusive biaxial nematic phase, we have developed - a generic simulation model for such systems. This contains the features - of the molecule that are essential to its liquid crystal behavior, - namely the anisotropies of the two arms and the angle between them. - The behavior of the model has been investigated using Monte Carlo - simulations for a wide range of these structural parameters. This - allows us to establish the relationship between the V-shaped molecule - and its ability to form a biaxial nematic phase. Of particular importance - are the criteria of geometry and the relative anisotropy necessary - for the system to exhibit a Landau point, at which the biaxial nematic - is formed directly from the isotropic phase. The simulations have - also been used to determine the orientational order parameters for - a selection of molecular axes. These are especially important because - they reveal the phase symmetry and are connected to the experimental - determination of this. The simulation results show that, whereas - some positions are extremely sensitive to the phase biaxiality, - others are totally blind to this.}, + can exhibit the elusive biaxial nematic phase, we have developed + a generic simulation model for such systems. This contains the features + of the molecule that are essential to its liquid crystal behavior, + namely the anisotropies of the two arms and the angle between them. + The behavior of the model has been investigated using Monte Carlo + simulations for a wide range of these structural parameters. This + allows us to establish the relationship between the V-shaped molecule + and its ability to form a biaxial nematic phase. Of particular importance + are the criteria of geometry and the relative anisotropy necessary + for the system to exhibit a Landau point, at which the biaxial nematic + is formed directly from the isotropic phase. The simulations have + also been used to determine the orientational order parameters for + a selection of molecular axes. These are especially important because + they reveal the phase symmetry and are connected to the experimental + determination of this. The simulation results show that, whereas + some positions are extremely sensitive to the phase biaxiality, + others are totally blind to this.}, annote = {Part 1 988LQ Times Cited:0 Cited References Count:38}, issn = {1539-3755}, uri = {://000233603100030}, @@ -358,14 +358,14 @@ Encoding: GBK number = {5}, month = {Nov 1}, abstract = {We introduce an unbiased protocol for performing rotational moves - in rigid-body dynamics simulations. This approach - based on the - analytic solution for the rotational equations of motion for an - orthogonal coordinate system at constant angular velocity - removes - deficiencies that have been largely ignored in Brownian dynamics - simulations, namely errors for finite rotations that result from - applying the noncommuting rotational matrices in an arbitrary order. - Our algorithm should thus replace standard approaches to rotate - local coordinate frames in Langevin and Brownian dynamics simulations.}, + in rigid-body dynamics simulations. This approach - based on the + analytic solution for the rotational equations of motion for an + orthogonal coordinate system at constant angular velocity - removes + deficiencies that have been largely ignored in Brownian dynamics + simulations, namely errors for finite rotations that result from + applying the noncommuting rotational matrices in an arbitrary order. + Our algorithm should thus replace standard approaches to rotate + local coordinate frames in Langevin and Brownian dynamics simulations.}, annote = {736UA Times Cited:0 Cited References Count:11}, issn = {0006-3495}, uri = {://000186190500018}, @@ -374,8 +374,8 @@ Encoding: GBK @ARTICLE{Beloborodov1998, author = {I. S. Beloborodov and V. Y. Orekhov and A. S. Arseniev}, title = {Effect of coupling between rotational and translational Brownian - motions on NMR spin relaxation: Consideration using green function - of rigid body diffusion}, + motions on NMR spin relaxation: Consideration using green function + of rigid body diffusion}, journal = {Journal of Magnetic Resonance}, year = {1998}, volume = {132}, @@ -383,14 +383,14 @@ Encoding: GBK number = {2}, month = {Jun}, abstract = {Using the Green function of arbitrary rigid Brownian diffusion (Goldstein, - Biopolymers 33, 409-436, 1993), it was analytically shown that coupling - between translation and rotation diffusion degrees of freedom does - not affect the correlation functions relevant to the NMR intramolecular - relaxation. It follows that spectral densities usually used for - the anisotropic rotation diffusion (Woessner, J. Chem. Phys. 37, - 647-654, 1962) can be regarded as exact in respect to the rotation-translation - coupling for the spin system connected with a rigid body. (C) 1998 - Academic Press.}, + Biopolymers 33, 409-436, 1993), it was analytically shown that coupling + between translation and rotation diffusion degrees of freedom does + not affect the correlation functions relevant to the NMR intramolecular + relaxation. It follows that spectral densities usually used for + the anisotropic rotation diffusion (Woessner, J. Chem. Phys. 37, + 647-654, 1962) can be regarded as exact in respect to the rotation-translation + coupling for the spin system connected with a rigid body. (C) 1998 + Academic Press.}, annote = {Zu605 Times Cited:2 Cited References Count:6}, issn = {1090-7807}, uri = {://000074214800017}, @@ -399,7 +399,7 @@ Encoding: GBK @ARTICLE{Berardi1996, author = {R. Berardi and S. Orlandi and C. Zannoni}, title = {Antiphase structures in polar smectic liquid crystals and their molecular - origin}, + origin}, journal = {Chemical Physics Letters}, year = {1996}, volume = {261}, @@ -407,14 +407,14 @@ Encoding: GBK number = {3}, month = {Oct 18}, abstract = {We demonstrate that the overall molecular dipole organization in a - smectic liquid crystal formed of polar molecules can be strongly - influenced by the position of the dipole in the molecule. We study - by large scale Monte Carlo simulations systems of attractive-repulsive - ''Gay-Berne'' elongated ellipsoids with an axial dipole at the center - or near the end of the molecule and we show that monolayer smectic - liquid crystals and modulated antiferroelectric bilayer stripe domains - similar to the experimentally observed ''antiphase'' structures - are obtained in the two cases.}, + smectic liquid crystal formed of polar molecules can be strongly + influenced by the position of the dipole in the molecule. We study + by large scale Monte Carlo simulations systems of attractive-repulsive + ''Gay-Berne'' elongated ellipsoids with an axial dipole at the center + or near the end of the molecule and we show that monolayer smectic + liquid crystals and modulated antiferroelectric bilayer stripe domains + similar to the experimentally observed ''antiphase'' structures + are obtained in the two cases.}, annote = {Vn637 Times Cited:49 Cited References Count:26}, issn = {0009-2614}, uri = {://A1996VN63700023}, @@ -423,7 +423,7 @@ Encoding: GBK @ARTICLE{Berkov2005, author = {D. V. Berkov and N. L. Gorn}, title = {Magnetization precession due to a spin-polarized current in a thin - nanoelement: Numerical simulation study}, + nanoelement: Numerical simulation study}, journal = {Physical Review B}, year = {2005}, volume = {72}, @@ -431,22 +431,22 @@ Encoding: GBK number = {9}, month = {Sep}, abstract = {In this paper a detailed numerical study (in frames of the Slonczewski - formalism) of magnetization oscillations driven by a spin-polarized - current through a thin elliptical nanoelement is presented. We show - that a sophisticated micromagnetic model, where a polycrystalline - structure of a nanoelement is taken into account, can explain qualitatively - all most important features of the magnetization oscillation spectra - recently observed experimentally [S. I. Kiselev , Nature 425, 380 - (2003)], namely, existence of several equidistant spectral bands, - sharp onset and abrupt disappearance of magnetization oscillations - with increasing current, absence of the out-of-plane regime predicted - by a macrospin model, and the relation between frequencies of so-called - small-angle and quasichaotic oscillations. However, a quantitative - agreement with experimental results (especially concerning the frequency - of quasichaotic oscillations) could not be achieved in the region - of reasonable parameter values, indicating that further model refinement - is necessary for a complete understanding of the spin-driven magnetization - precession even in this relatively simple experimental situation.}, + formalism) of magnetization oscillations driven by a spin-polarized + current through a thin elliptical nanoelement is presented. We show + that a sophisticated micromagnetic model, where a polycrystalline + structure of a nanoelement is taken into account, can explain qualitatively + all most important features of the magnetization oscillation spectra + recently observed experimentally [S. I. Kiselev , Nature 425, 380 + (2003)], namely, existence of several equidistant spectral bands, + sharp onset and abrupt disappearance of magnetization oscillations + with increasing current, absence of the out-of-plane regime predicted + by a macrospin model, and the relation between frequencies of so-called + small-angle and quasichaotic oscillations. However, a quantitative + agreement with experimental results (especially concerning the frequency + of quasichaotic oscillations) could not be achieved in the region + of reasonable parameter values, indicating that further model refinement + is necessary for a complete understanding of the spin-driven magnetization + precession even in this relatively simple experimental situation.}, annote = {969IT Times Cited:2 Cited References Count:55}, issn = {1098-0121}, uri = {://000232228500058}, @@ -455,27 +455,27 @@ Encoding: GBK @ARTICLE{Berkov2005a, author = {D. V. Berkov and N. L. Gorn}, title = {Stochastic dynamic simulations of fast remagnetization processes: - recent advances and applications}, + recent advances and applications}, journal = {Journal of Magnetism and Magnetic Materials}, year = {2005}, volume = {290}, pages = {442-448}, month = {Apr}, abstract = {Numerical simulations of fast remagnetization processes using stochastic - dynamics are widely used to study various magnetic systems. In this - paper, we first address several crucial methodological problems - of such simulations: (i) the influence of finite-element discretization - on simulated dynamics, (ii) choice between Ito and Stratonovich - stochastic calculi by the solution of micromagnetic stochastic equations - of motion and (iii) non-trivial correlation properties of the random - (thermal) field. Next, we discuss several examples to demonstrate - the great potential of the Langevin dynamics for studying fast remagnetization - processes in technically relevant applications: we present numerical - analysis of equilibrium magnon spectra in patterned structures, - study thermal noise effects on the magnetization dynamics of nanoelements - in pulsed fields and show some results for a remagnetization dynamics - induced by a spin-polarized current. (c) 2004 Elsevier B.V. All - rights reserved.}, + dynamics are widely used to study various magnetic systems. In this + paper, we first address several crucial methodological problems + of such simulations: (i) the influence of finite-element discretization + on simulated dynamics, (ii) choice between Ito and Stratonovich + stochastic calculi by the solution of micromagnetic stochastic equations + of motion and (iii) non-trivial correlation properties of the random + (thermal) field. Next, we discuss several examples to demonstrate + the great potential of the Langevin dynamics for studying fast remagnetization + processes in technically relevant applications: we present numerical + analysis of equilibrium magnon spectra in patterned structures, + study thermal noise effects on the magnetization dynamics of nanoelements + in pulsed fields and show some results for a remagnetization dynamics + induced by a spin-polarized current. (c) 2004 Elsevier B.V. All + rights reserved.}, annote = {Part 1 Sp. Iss. SI 922KU Times Cited:2 Cited References Count:25}, issn = {0304-8853}, uri = {://000228837600109}, @@ -484,7 +484,7 @@ Encoding: GBK @ARTICLE{Berkov2002, author = {D. V. Berkov and N. L. Gorn and P. Gornert}, title = {Magnetization dynamics in nanoparticle systems: Numerical simulation - using Langevin dynamics}, + using Langevin dynamics}, journal = {Physica Status Solidi a-Applied Research}, year = {2002}, volume = {189}, @@ -492,19 +492,19 @@ Encoding: GBK number = {2}, month = {Feb 16}, abstract = {We report on recent progress achieved by the development of numerical - methods based on the stochastic (Langevin) dynamics applied to systems - of interacting magnetic nanoparticles. The method enables direct - simulations of the trajectories of magnetic moments taking into - account (i) all relevant interactions, (ii) precession dynamics, - and (iii) temperature fluctuations included via the random (thermal) - field. We present several novel results obtained using new methods - developed for the solution of the Langevin equations. In particular, - we have investigated magnetic nanodots and disordered granular systems - of single-domain magnetic particles. For the first case we have - calculated the spectrum and the spatial distribution of spin excitations. - For the second system the complex ac susceptibility chi(omega, T) - for various particle concentrations and particle anisotropies were - computed and compared with numerous experimental results.}, + methods based on the stochastic (Langevin) dynamics applied to systems + of interacting magnetic nanoparticles. The method enables direct + simulations of the trajectories of magnetic moments taking into + account (i) all relevant interactions, (ii) precession dynamics, + and (iii) temperature fluctuations included via the random (thermal) + field. We present several novel results obtained using new methods + developed for the solution of the Langevin equations. In particular, + we have investigated magnetic nanodots and disordered granular systems + of single-domain magnetic particles. For the first case we have + calculated the spectrum and the spatial distribution of spin excitations. + For the second system the complex ac susceptibility chi(omega, T) + for various particle concentrations and particle anisotropies were + computed and compared with numerous experimental results.}, annote = {526TF Times Cited:4 Cited References Count:37}, issn = {0031-8965}, uri = {://000174145200026}, @@ -513,7 +513,7 @@ Encoding: GBK @ARTICLE{Bernal1980, author = {J.M. Bernal and J. G. {de la Torre}}, title = {Transport Properties and Hydrodynamic Centers of Rigid Macromolecules - with Arbitrary Shape}, + with Arbitrary Shape}, journal = {Biopolymers}, year = {1980}, volume = {19}, @@ -523,7 +523,7 @@ Encoding: GBK @ARTICLE{Brunger1984, author = {A. Brunger and C. L. Brooks and M. Karplus}, title = {Stochastic Boundary-Conditions for Molecular-Dynamics Simulations - of St2 Water}, + of St2 Water}, journal = {Chemical Physics Letters}, year = {1984}, volume = {105}, @@ -537,20 +537,20 @@ Encoding: GBK @ARTICLE{Budd1999, author = {C. J. Budd and G. J. Collins and W. Z. Huang and R. D. Russell}, title = {Self-similar numerical solutions of the porous-medium equation using - moving mesh methods}, + moving mesh methods}, journal = {Philosophical Transactions of the Royal Society of London Series - a-Mathematical Physical and Engineering Sciences}, + a-Mathematical Physical and Engineering Sciences}, year = {1999}, volume = {357}, pages = {1047-1077}, number = {1754}, month = {Apr 15}, abstract = {This paper examines a synthesis of adaptive mesh methods with the - use of symmetry to study a partial differential equation. In particular, - it considers methods which admit discrete self-similar solutions, - examining the convergence of these to the true self-similar solution - as well as their stability. Special attention is given to the nonlinear - diffusion equation describing flow in a porous medium.}, + use of symmetry to study a partial differential equation. In particular, + it considers methods which admit discrete self-similar solutions, + examining the convergence of these to the true self-similar solution + as well as their stability. Special attention is given to the nonlinear + diffusion equation describing flow in a porous medium.}, annote = {199EE Times Cited:4 Cited References Count:14}, issn = {1364-503X}, uri = {://000080466800005}, @@ -566,35 +566,35 @@ Encoding: GBK number = {21}, month = {Dec 1}, abstract = {Fluids of hard bent-core molecules have been studied using theory - and computer simulation. The molecules are composed of two hard - spherocylinders, with length-to-breadth ratio L/D, joined by their - ends at an angle 180 degrees - gamma. For L/D = 2 and gamma = 0,10,20 - degrees, the simulations show isotropic, nematic, smectic, and solid - phases. For L/D = 2 and gamma = 30 degrees, only isotropic, nematic, - and solid phases are in evidence, which suggests that there is a - nematic-smectic-solid triple point at an angle in the range 20 degrees - < gamma < 30 degrees. In all of the orientationally ordered fluid - phases the order is purely uniaxial. For gamma = 10 degrees and - 20 degrees, at the studied densities, the solid is also uniaxially - ordered, whilst for gamma = 30 degrees the solid layers are biaxially - ordered. For L/D = 2 and gamma = 60 degrees and 90 degrees we find - no spontaneous orientational ordering. This is shown to be due to - the interlocking of dimer pairs which precludes alignment. We find - similar results for L/D = 9.5 and gamma = 72 degrees, where an isotropic-biaxial - nematic transition is predicted by Onsager theory. Simulations in - the biaxial nematic phase show it to be at least mechanically stable - with respect to the isotropic phase, however. We have compared the - quasi-exact simulation results in the isotropic phase with the predicted - equations of state from three theories: the virial expansion containing - the second and third virial coefficients; the Parsons-Lee equation - of state; an application of Wertheim's theory of associating fluids - in the limit of infinite attractive association energy. For all - of the molecule elongations and geometries we have simulated, the - Wertheim theory proved to be the most accurate. Interestingly, the - isotropic equation of state is virtually independent of the dimer - bond angle-a feature that is also reflected in the lack of variation - with angle of the calculated second and third virial coefficients. - (C) 1999 American Institute of Physics. [S0021-9606(99)50445-5].}, + and computer simulation. The molecules are composed of two hard + spherocylinders, with length-to-breadth ratio L/D, joined by their + ends at an angle 180 degrees - gamma. For L/D = 2 and gamma = 0,10,20 + degrees, the simulations show isotropic, nematic, smectic, and solid + phases. For L/D = 2 and gamma = 30 degrees, only isotropic, nematic, + and solid phases are in evidence, which suggests that there is a + nematic-smectic-solid triple point at an angle in the range 20 degrees + < gamma < 30 degrees. In all of the orientationally ordered fluid + phases the order is purely uniaxial. For gamma = 10 degrees and + 20 degrees, at the studied densities, the solid is also uniaxially + ordered, whilst for gamma = 30 degrees the solid layers are biaxially + ordered. For L/D = 2 and gamma = 60 degrees and 90 degrees we find + no spontaneous orientational ordering. This is shown to be due to + the interlocking of dimer pairs which precludes alignment. We find + similar results for L/D = 9.5 and gamma = 72 degrees, where an isotropic-biaxial + nematic transition is predicted by Onsager theory. Simulations in + the biaxial nematic phase show it to be at least mechanically stable + with respect to the isotropic phase, however. We have compared the + quasi-exact simulation results in the isotropic phase with the predicted + equations of state from three theories: the virial expansion containing + the second and third virial coefficients; the Parsons-Lee equation + of state; an application of Wertheim's theory of associating fluids + in the limit of infinite attractive association energy. For all + of the molecule elongations and geometries we have simulated, the + Wertheim theory proved to be the most accurate. Interestingly, the + isotropic equation of state is virtually independent of the dimer + bond angle-a feature that is also reflected in the lack of variation + with angle of the calculated second and third virial coefficients. + (C) 1999 American Institute of Physics. [S0021-9606(99)50445-5].}, annote = {255TC Times Cited:24 Cited References Count:38}, issn = {0021-9606}, uri = {://000083685400056}, @@ -610,12 +610,12 @@ Encoding: GBK number = {11}, month = {Nov}, abstract = {A review is presented of molecular and mesoscopic computer simulations - of liquid crystalline systems. Molecular simulation approaches applied - to such systems are described, and the key findings for bulk phase - behaviour are reported. Following this, recently developed lattice - Boltzmann approaches to the mesoscale modelling of nemato-dynanics - are reviewed. This paper concludes with a discussion of possible - areas for future development in this field.}, + of liquid crystalline systems. Molecular simulation approaches applied + to such systems are described, and the key findings for bulk phase + behaviour are reported. Following this, recently developed lattice + Boltzmann approaches to the mesoscale modelling of nemato-dynanics + are reviewed. This paper concludes with a discussion of possible + areas for future development in this field.}, annote = {989TU Times Cited:2 Cited References Count:258}, issn = {0034-4885}, uri = {://000233697600004}, @@ -624,7 +624,7 @@ Encoding: GBK @ARTICLE{Carrasco1999, author = {B. Carrasco and J. G. {de la Torre}}, title = {Hydrodynamic properties of rigid particles: Comparison of different - modeling and computational procedures}, + modeling and computational procedures}, journal = {Biophysical Journal}, year = {1999}, volume = {76}, @@ -632,23 +632,23 @@ Encoding: GBK number = {6}, month = {Jun}, abstract = {The hydrodynamic properties of rigid particles are calculated from - models composed of spherical elements (beads) using theories developed - by Kirkwood, Bloomfield, and their coworkers. Bead models have usually - been built in such a way that the beads fill the volume occupied - by the particles. Sometimes the beads are few and of varying sizes - (bead models in the strict sense), and other times there are many - small beads (filling models). Because hydrodynamic friction takes - place at the molecular surface, another possibility is to use shell - models, as originally proposed by Bloomfield. In this work, we have - developed procedures to build models of the various kinds, and we - describe the theory and methods for calculating their hydrodynamic - properties, including approximate methods that may be needed to - treat models with a very large number of elements. By combining - the various possibilities of model building and hydrodynamic calculation, - several strategies can be designed. We have made a quantitative - comparison of the performance of the various strategies by applying - them to some test cases, for which the properties are known a priori. - We provide guidelines and computational tools for bead modeling.}, + models composed of spherical elements (beads) using theories developed + by Kirkwood, Bloomfield, and their coworkers. Bead models have usually + been built in such a way that the beads fill the volume occupied + by the particles. Sometimes the beads are few and of varying sizes + (bead models in the strict sense), and other times there are many + small beads (filling models). Because hydrodynamic friction takes + place at the molecular surface, another possibility is to use shell + models, as originally proposed by Bloomfield. In this work, we have + developed procedures to build models of the various kinds, and we + describe the theory and methods for calculating their hydrodynamic + properties, including approximate methods that may be needed to + treat models with a very large number of elements. By combining + the various possibilities of model building and hydrodynamic calculation, + several strategies can be designed. We have made a quantitative + comparison of the performance of the various strategies by applying + them to some test cases, for which the properties are known a priori. + We provide guidelines and computational tools for bead modeling.}, annote = {200TT Times Cited:46 Cited References Count:57}, issn = {0006-3495}, uri = {://000080556700016}, @@ -657,7 +657,7 @@ Encoding: GBK @ARTICLE{Chandra1999, author = {A. Chandra and T. Ichiye}, title = {Dynamical properties of the soft sticky dipole model of water: Molecular - dynamics simulations}, + dynamics simulations}, journal = {Journal of Chemical Physics}, year = {1999}, volume = {111}, @@ -665,23 +665,23 @@ Encoding: GBK number = {6}, month = {Aug 8}, abstract = {Dynamical properties of the soft sticky dipole (SSD) model of water - are calculated by means of molecular dynamics simulations. Since - this is not a simple point model, the forces and torques arising - from the SSD potential are derived here. Simulations are carried - out in the microcanonical ensemble employing the Ewald method for - the electrostatic interactions. Various time correlation functions - and dynamical quantities associated with the translational and rotational - motion of water molecules are evaluated and compared with those - of two other commonly used models of liquid water, namely the transferable - intermolecular potential-three points (TIP3P) and simple point charge/extended - (SPC/E) models, and also with experiments. The dynamical properties - of the SSD water model are found to be in good agreement with the - experimental results and appear to be better than the TIP3P and - SPC/E models in most cases, as has been previously shown for its - thermodynamic, structural, and dielectric properties. Also, molecular - dynamics simulations of the SSD model are found to run much faster - than TIP3P, SPC/E, and other multisite models. (C) 1999 American - Institute of Physics. [S0021-9606(99)51430-X].}, + are calculated by means of molecular dynamics simulations. Since + this is not a simple point model, the forces and torques arising + from the SSD potential are derived here. Simulations are carried + out in the microcanonical ensemble employing the Ewald method for + the electrostatic interactions. Various time correlation functions + and dynamical quantities associated with the translational and rotational + motion of water molecules are evaluated and compared with those + of two other commonly used models of liquid water, namely the transferable + intermolecular potential-three points (TIP3P) and simple point charge/extended + (SPC/E) models, and also with experiments. The dynamical properties + of the SSD water model are found to be in good agreement with the + experimental results and appear to be better than the TIP3P and + SPC/E models in most cases, as has been previously shown for its + thermodynamic, structural, and dielectric properties. Also, molecular + dynamics simulations of the SSD model are found to run much faster + than TIP3P, SPC/E, and other multisite models. (C) 1999 American + Institute of Physics. [S0021-9606(99)51430-X].}, annote = {221EN Times Cited:14 Cited References Count:66}, issn = {0021-9606}, uri = {://000081711200038}, @@ -711,14 +711,14 @@ Encoding: GBK number = {1-2}, month = {Jan}, abstract = {We investigate the asymptotic behavior of systems of nonlinear differential - equations and introduce a family of mixed methods from combinations - of explicit Runge-Kutta methods. These methods have better stability - behavior than traditional Runge-Kutta methods and generally extend - the range of validity of the calculated solutions. These methods - also give a way of determining if the numerical solutions are real - or spurious. Emphasis is put on examples coming from mathematical - models in ecology. (C) 2002 IMACS. Published by Elsevier Science - B.V. All rights reserved.}, + equations and introduce a family of mixed methods from combinations + of explicit Runge-Kutta methods. These methods have better stability + behavior than traditional Runge-Kutta methods and generally extend + the range of validity of the calculated solutions. These methods + also give a way of determining if the numerical solutions are real + or spurious. Emphasis is put on examples coming from mathematical + models in ecology. (C) 2002 IMACS. Published by Elsevier Science + B.V. All rights reserved.}, annote = {633ZD Times Cited:0 Cited References Count:9}, issn = {0168-9274}, uri = {://000180314200002}, @@ -727,7 +727,7 @@ Encoding: GBK @ARTICLE{Cheung2004, author = {D. L. Cheung and S. J. Clark and M. R. Wilson}, title = {Calculation of flexoelectric coefficients for a nematic liquid crystal - by atomistic simulation}, + by atomistic simulation}, journal = {Journal of Chemical Physics}, year = {2004}, volume = {121}, @@ -735,17 +735,17 @@ Encoding: GBK number = {18}, month = {Nov 8}, abstract = {Equilibrium molecular dynamics calculations have been performed for - the liquid crystal molecule n-4-(trans-4-n-pentylcyclohexyl)benzonitrile - (PCH5) using a fully atomistic model. Simulation data have been - obtained for a series of temperatures in the nematic phase. The - simulation data have been used to calculate the flexoelectric coefficients - e(s) and e(b) using the linear response formalism of Osipov and - Nemtsov [M. A. Osipov and V. B. Nemtsov, Sov. Phys. Crstallogr. - 31, 125 (1986)]. The temperature and order parameter dependence - of e(s) and e(b) are examined, as are separate contributions from - different intermolecular interactions. Values of e(s) and e(b) calculated - from simulation are consistent with those found from experiment. - (C) 2004 American Institute of Physics.}, + the liquid crystal molecule n-4-(trans-4-n-pentylcyclohexyl)benzonitrile + (PCH5) using a fully atomistic model. Simulation data have been + obtained for a series of temperatures in the nematic phase. The + simulation data have been used to calculate the flexoelectric coefficients + e(s) and e(b) using the linear response formalism of Osipov and + Nemtsov [M. A. Osipov and V. B. Nemtsov, Sov. Phys. Crstallogr. + 31, 125 (1986)]. The temperature and order parameter dependence + of e(s) and e(b) are examined, as are separate contributions from + different intermolecular interactions. Values of e(s) and e(b) calculated + from simulation are consistent with those found from experiment. + (C) 2004 American Institute of Physics.}, annote = {866UM Times Cited:4 Cited References Count:61}, issn = {0021-9606}, uri = {://000224798900053}, @@ -761,15 +761,15 @@ Encoding: GBK number = {1-2}, month = {Apr 15}, abstract = {Equilibrium molecular dynamics calculations have been performed for - the liquid crystal molecule n-4-(trans-4-npentylcyclohexyl)benzonitrile - (PCH5) using a fully atomistic model. Simulation data has been obtained - for a series of temperatures in the nematic phase. The rotational - viscosity co-efficient gamma(1), has been calculated using the angular - velocity correlation function of the nematic director, n, the mean - squared diffusion of n and statistical mechanical methods based - on the rotational diffusion co-efficient. We find good agreement - between the first two methods and experimental values. (C) 2002 - Published by Elsevier Science B.V.}, + the liquid crystal molecule n-4-(trans-4-npentylcyclohexyl)benzonitrile + (PCH5) using a fully atomistic model. Simulation data has been obtained + for a series of temperatures in the nematic phase. The rotational + viscosity co-efficient gamma(1), has been calculated using the angular + velocity correlation function of the nematic director, n, the mean + squared diffusion of n and statistical mechanical methods based + on the rotational diffusion co-efficient. We find good agreement + between the first two methods and experimental values. (C) 2002 + Published by Elsevier Science B.V.}, annote = {547KF Times Cited:8 Cited References Count:31}, issn = {0009-2614}, uri = {://000175331000020}, @@ -778,7 +778,7 @@ Encoding: GBK @ARTICLE{Chin2004, author = {S. A. Chin}, title = {Dynamical multiple-time stepping methods for overcoming resonance - instabilities}, + instabilities}, journal = {Journal of Chemical Physics}, year = {2004}, volume = {120}, @@ -786,20 +786,20 @@ Encoding: GBK number = {1}, month = {Jan 1}, abstract = {Current molecular dynamics simulations of biomolecules using multiple - time steps to update the slowly changing force are hampered by instabilities - beginning at time steps near the half period of the fastest vibrating - mode. These #resonance# instabilities have became a critical barrier - preventing the long time simulation of biomolecular dynamics. Attempts - to tame these instabilities by altering the slowly changing force - and efforts to damp them out by Langevin dynamics do not address - the fundamental cause of these instabilities. In this work, we trace - the instability to the nonanalytic character of the underlying spectrum - and show that a correct splitting of the Hamiltonian, which renders - the spectrum analytic, restores stability. The resulting Hamiltonian - dictates that in addition to updating the momentum due to the slowly - changing force, one must also update the position with a modified - mass. Thus multiple-time stepping must be done dynamically. (C) - 2004 American Institute of Physics.}, + time steps to update the slowly changing force are hampered by instabilities + beginning at time steps near the half period of the fastest vibrating + mode. These #resonance# instabilities have became a critical barrier + preventing the long time simulation of biomolecular dynamics. Attempts + to tame these instabilities by altering the slowly changing force + and efforts to damp them out by Langevin dynamics do not address + the fundamental cause of these instabilities. In this work, we trace + the instability to the nonanalytic character of the underlying spectrum + and show that a correct splitting of the Hamiltonian, which renders + the spectrum analytic, restores stability. The resulting Hamiltonian + dictates that in addition to updating the momentum due to the slowly + changing force, one must also update the position with a modified + mass. Thus multiple-time stepping must be done dynamically. (C) + 2004 American Institute of Physics.}, annote = {757TK Times Cited:1 Cited References Count:22}, issn = {0021-9606}, uri = {://000187577400003}, @@ -808,7 +808,7 @@ Encoding: GBK @ARTICLE{Cook2000, author = {M. J. Cook and M. R. Wilson}, title = {Simulation studies of dipole correlation in the isotropic liquid - phase}, + phase}, journal = {Liquid Crystals}, year = {2000}, volume = {27}, @@ -816,21 +816,21 @@ Encoding: GBK number = {12}, month = {Dec}, abstract = {The Kirkwood correlation factor g(1) determines the preference for - local parallel or antiparallel dipole association in the isotropic - phase. Calamitic mesogens with longitudinal dipole moments and Kirkwood - factors greater than 1 have an enhanced effective dipole moment - along the molecular long axis. This leads to higher values of Delta - epsilon in the nematic phase. This paper describes state-of-the-art - molecular dynamics simulations of two calamitic mesogens 4-(trans-4-n-pentylcyclohexyl)benzonitrile - (PCH5) and 4-(trans-4-n-pentylcyclohexyl) chlorobenzene (PCH5-Cl) - in the isotropic liquid phase using an all-atom force field and - taking long range electrostatics into account using an Ewald summation. - Using this methodology, PCH5 is seen to prefer antiparallel dipole - alignment with a negative g(1) and PCH5-Cl is seen to prefer parallel - dipole alignment with a positive g(1); this is in accordance with - experimental dielectric measurements. Analysis of the molecular - dynamics trajectories allows an assessment of why these molecules - behave differently.}, + local parallel or antiparallel dipole association in the isotropic + phase. Calamitic mesogens with longitudinal dipole moments and Kirkwood + factors greater than 1 have an enhanced effective dipole moment + along the molecular long axis. This leads to higher values of Delta + epsilon in the nematic phase. This paper describes state-of-the-art + molecular dynamics simulations of two calamitic mesogens 4-(trans-4-n-pentylcyclohexyl)benzonitrile + (PCH5) and 4-(trans-4-n-pentylcyclohexyl) chlorobenzene (PCH5-Cl) + in the isotropic liquid phase using an all-atom force field and + taking long range electrostatics into account using an Ewald summation. + Using this methodology, PCH5 is seen to prefer antiparallel dipole + alignment with a negative g(1) and PCH5-Cl is seen to prefer parallel + dipole alignment with a positive g(1); this is in accordance with + experimental dielectric measurements. Analysis of the molecular + dynamics trajectories allows an assessment of why these molecules + behave differently.}, annote = {376BF Times Cited:10 Cited References Count:16}, issn = {0267-8292}, uri = {://000165437800002}, @@ -839,31 +839,31 @@ Encoding: GBK @ARTICLE{Cui2003, author = {B. X. Cui and M. Y. Shen and K. F. Freed}, title = {Folding and misfolding of the papillomavirus E6 interacting peptide - E6ap}, + E6ap}, journal = {Proceedings of the National Academy of Sciences of the United States - of America}, + of America}, year = {2003}, volume = {100}, pages = {7087-7092}, number = {12}, month = {Jun 10}, abstract = {All-atom Langevin dynamics simulations have been performed to study - the folding pathways of the 18-residue binding domain fragment E6ap - of the human papillomavirus E6 interacting peptide. Six independent - folding trajectories, with a total duration of nearly 2 mus, all - lead to the same native state in which the E6ap adopts a fluctuating - a-helix structure in the central portion (Ser-4-Leu-13) but with - very flexible N and C termini. Simulations starting from different - core configurations exhibit the E6ap folding dynamics as either - a two- or three-state folder with an intermediate misfolded state. - The essential leucine hydrophobic core (Leu-9, Leu-12, and Leu-13) - is well conserved in the native-state structure but absent in the - intermediate structure, suggesting that the leucine core is not - only essential for the binding activity of E6ap but also important - for the stability of the native structure. The free energy landscape - reveals a significant barrier between the basins separating the - native and misfolded states. We also discuss the various underlying - forces that drive the peptide into its native state.}, + the folding pathways of the 18-residue binding domain fragment E6ap + of the human papillomavirus E6 interacting peptide. Six independent + folding trajectories, with a total duration of nearly 2 mus, all + lead to the same native state in which the E6ap adopts a fluctuating + a-helix structure in the central portion (Ser-4-Leu-13) but with + very flexible N and C termini. Simulations starting from different + core configurations exhibit the E6ap folding dynamics as either + a two- or three-state folder with an intermediate misfolded state. + The essential leucine hydrophobic core (Leu-9, Leu-12, and Leu-13) + is well conserved in the native-state structure but absent in the + intermediate structure, suggesting that the leucine core is not + only essential for the binding activity of E6ap but also important + for the stability of the native structure. The free energy landscape + reveals a significant barrier between the basins separating the + native and misfolded states. We also discuss the various underlying + forces that drive the peptide into its native state.}, annote = {689LC Times Cited:3 Cited References Count:48}, issn = {0027-8424}, uri = {://000183493500037}, @@ -879,15 +879,15 @@ Encoding: GBK number = {1}, month = {Jan 1}, abstract = {We study the slow phase of thermally activated magnetic relaxation - in finite two-dimensional ensembles of dipolar interacting ferromagnetic - nanoparticles whose easy axes of magnetization are perpendicular - to the distribution plane. We develop a method to numerically simulate - the magnetic relaxation for the case that the smallest heights of - the potential barriers between the equilibrium directions of the - nanoparticle magnetic moments are much larger than the thermal energy. - Within this framework, we analyze in detail the role that the correlations - of the nanoparticle magnetic moments and the finite size of the - nanoparticle ensemble play in magnetic relaxation.}, + in finite two-dimensional ensembles of dipolar interacting ferromagnetic + nanoparticles whose easy axes of magnetization are perpendicular + to the distribution plane. We develop a method to numerically simulate + the magnetic relaxation for the case that the smallest heights of + the potential barriers between the equilibrium directions of the + nanoparticle magnetic moments are much larger than the thermal energy. + Within this framework, we analyze in detail the role that the correlations + of the nanoparticle magnetic moments and the finite size of the + nanoparticle ensemble play in magnetic relaxation.}, annote = {642XH Times Cited:11 Cited References Count:31}, issn = {1098-0121}, uri = {://000180830400056}, @@ -903,29 +903,29 @@ Encoding: GBK number = {1}, month = {Jan}, abstract = {To explore the origin of the large-scale motion of triosephosphate - isomerase's flexible loop (residues 166 to 176) at the active site, - several simulation protocols are employed both for the free enzyme - in vacuo and for the free enzyme with some solvent modeling: high-temperature - Langevin dynamics simulations, sampling by a #dynamics##driver# - approach, and potential-energy surface calculations. Our focus is - on obtaining the energy barrier to the enzyme's motion and establishing - the nature of the loop movement. Previous calculations did not determine - this energy barrier and the effect of solvent on the barrier. High-temperature - molecular dynamics simulations and crystallographic studies have - suggested a rigid-body motion with two hinges located at both ends - of the loop; Brownian dynamics simulations at room temperature pointed - to a very flexible behavior. The present simulations and analyses - reveal that although solute/solvent hydrogen bonds play a crucial - role in lowering the energy along the pathway, there still remains - a high activation barrier, This finding clearly indicates that, - if the loop opens and closes in the absence of a substrate at standard - conditions (e.g., room temperature, appropriate concentration of - isomerase), the time scale for transition is not in the nanosecond - but rather the microsecond range. Our results also indicate that - in the context of spontaneous opening in the free enzyme, the motion - is of rigid-body type and that the specific interaction between - residues Ala(176) and Tyr(208) plays a crucial role in the loop - opening/closing mechanism.}, + isomerase's flexible loop (residues 166 to 176) at the active site, + several simulation protocols are employed both for the free enzyme + in vacuo and for the free enzyme with some solvent modeling: high-temperature + Langevin dynamics simulations, sampling by a #dynamics##driver# + approach, and potential-energy surface calculations. Our focus is + on obtaining the energy barrier to the enzyme's motion and establishing + the nature of the loop movement. Previous calculations did not determine + this energy barrier and the effect of solvent on the barrier. High-temperature + molecular dynamics simulations and crystallographic studies have + suggested a rigid-body motion with two hinges located at both ends + of the loop; Brownian dynamics simulations at room temperature pointed + to a very flexible behavior. The present simulations and analyses + reveal that although solute/solvent hydrogen bonds play a crucial + role in lowering the energy along the pathway, there still remains + a high activation barrier, This finding clearly indicates that, + if the loop opens and closes in the absence of a substrate at standard + conditions (e.g., room temperature, appropriate concentration of + isomerase), the time scale for transition is not in the nanosecond + but rather the microsecond range. Our results also indicate that + in the context of spontaneous opening in the free enzyme, the motion + is of rigid-body type and that the specific interaction between + residues Ala(176) and Tyr(208) plays a crucial role in the loop + opening/closing mechanism.}, annote = {Zl046 Times Cited:30 Cited References Count:29}, issn = {0006-3495}, uri = {://000073393400009}, @@ -941,24 +941,24 @@ Encoding: GBK number = {15}, month = {Oct 15}, abstract = {Rigid body molecular models possess symplectic structure and time-reversal - symmetry. Standard numerical integration methods destroy both properties, - introducing nonphysical dynamical behavior such as numerically induced - dissipative states and drift in the energy during long term simulations. - This article describes the construction, implementation, and practical - application of fast explicit symplectic-reversible integrators for - multiple rigid body molecular simulations, These methods use a reduction - to Euler equations for the free rigid body, together with a symplectic - splitting technique. In every time step, the orientational dynamics - of each rigid body is integrated by a sequence of planar rotations. - Besides preserving the symplectic and reversible structures of the - flow, this scheme accurately conserves the total angular momentum - of a system of interacting rigid bodies. Excellent energy conservation - fan be obtained relative to traditional methods, especially in long-time - simulations. The method is implemented in a research code, ORIENT - and compared with a quaternion/extrapolation scheme for the TIP4P - model of water. Our experiments show that the symplectic-reversible - scheme is far superior to the more traditional quaternion method. - (C) 1997 American Institute of Physics.}, + symmetry. Standard numerical integration methods destroy both properties, + introducing nonphysical dynamical behavior such as numerically induced + dissipative states and drift in the energy during long term simulations. + This article describes the construction, implementation, and practical + application of fast explicit symplectic-reversible integrators for + multiple rigid body molecular simulations, These methods use a reduction + to Euler equations for the free rigid body, together with a symplectic + splitting technique. In every time step, the orientational dynamics + of each rigid body is integrated by a sequence of planar rotations. + Besides preserving the symplectic and reversible structures of the + flow, this scheme accurately conserves the total angular momentum + of a system of interacting rigid bodies. Excellent energy conservation + fan be obtained relative to traditional methods, especially in long-time + simulations. The method is implemented in a research code, ORIENT + and compared with a quaternion/extrapolation scheme for the TIP4P + model of water. Our experiments show that the symplectic-reversible + scheme is far superior to the more traditional quaternion method. + (C) 1997 American Institute of Physics.}, annote = {Ya587 Times Cited:35 Cited References Count:32}, issn = {0021-9606}, uri = {://A1997YA58700024}, @@ -967,7 +967,7 @@ Encoding: GBK @ARTICLE{Edwards2005, author = {S. A. Edwards and D. R. M. Williams}, title = {Stretching a single diblock copolymer in a selective solvent: Langevin - dynamics simulations}, + dynamics simulations}, journal = {Macromolecules}, year = {2005}, volume = {38}, @@ -975,15 +975,15 @@ Encoding: GBK number = {25}, month = {Dec 13}, abstract = {Using the Langevin dynamics technique, we have carried out simulations - of a single-chain flexible diblock copolymer. The polymer consists - of two blocks of equal length, one very poorly solvated and the - other close to theta-conditions. We study what happens when such - a polymer is stretched, for a range of different stretching speeds, - and correlate our observations with features in the plot of force - vs extension. We find that at slow speeds this force profile does - not increase monotonically, in disagreement with earlier predictions, - and that at high speeds there is a strong dependence on which end - of the polymer is pulled, as well as a high level of hysteresis.}, + of a single-chain flexible diblock copolymer. The polymer consists + of two blocks of equal length, one very poorly solvated and the + other close to theta-conditions. We study what happens when such + a polymer is stretched, for a range of different stretching speeds, + and correlate our observations with features in the plot of force + vs extension. We find that at slow speeds this force profile does + not increase monotonically, in disagreement with earlier predictions, + and that at high speeds there is a strong dependence on which end + of the polymer is pulled, as well as a high level of hysteresis.}, annote = {992EC Times Cited:0 Cited References Count:13}, issn = {0024-9297}, uri = {://000233866200035}, @@ -992,7 +992,7 @@ Encoding: GBK @ARTICLE{Egberts1988, author = {E. Egberts and H. J. C. Berendsen}, title = {Molecular-Dynamics Simulation of a Smectic Liquid-Crystal with Atomic - Detail}, + Detail}, journal = {Journal of Chemical Physics}, year = {1988}, volume = {89}, @@ -1020,7 +1020,7 @@ Encoding: GBK @ARTICLE{Fennell2004, author = {C. J. Fennell and J. D. Gezelter}, title = {On the structural and transport properties of the soft sticky dipole - and related single-point water models}, + and related single-point water models}, journal = {Journal of Chemical Physics}, year = {2004}, volume = {120}, @@ -1028,28 +1028,28 @@ Encoding: GBK number = {19}, month = {May 15}, abstract = {The density maximum and temperature dependence of the self-diffusion - constant were investigated for the soft sticky dipole (SSD) water - model and two related reparametrizations of this single-point model. - A combination of microcanonical and isobaric-isothermal molecular - dynamics simulations was used to calculate these properties, both - with and without the use of reaction field to handle long-range - electrostatics. The isobaric-isothermal simulations of the melting - of both ice-I-h and ice-I-c showed a density maximum near 260 K. - In most cases, the use of the reaction field resulted in calculated - densities which were significantly lower than experimental densities. - Analysis of self-diffusion constants shows that the original SSD - model captures the transport properties of experimental water very - well in both the normal and supercooled liquid regimes. We also - present our reparametrized versions of SSD for use both with the - reaction field or without any long-range electrostatic corrections. - These are called the SSD/RF and SSD/E models, respectively. These - modified models were shown to maintain or improve upon the experimental - agreement with the structural and transport properties that can - be obtained with either the original SSD or the density-corrected - version of the original model (SSD1). Additionally, a novel low-density - ice structure is presented which appears to be the most stable ice - structure for the entire SSD family. (C) 2004 American Institute - of Physics.}, + constant were investigated for the soft sticky dipole (SSD) water + model and two related reparametrizations of this single-point model. + A combination of microcanonical and isobaric-isothermal molecular + dynamics simulations was used to calculate these properties, both + with and without the use of reaction field to handle long-range + electrostatics. The isobaric-isothermal simulations of the melting + of both ice-I-h and ice-I-c showed a density maximum near 260 K. + In most cases, the use of the reaction field resulted in calculated + densities which were significantly lower than experimental densities. + Analysis of self-diffusion constants shows that the original SSD + model captures the transport properties of experimental water very + well in both the normal and supercooled liquid regimes. We also + present our reparametrized versions of SSD for use both with the + reaction field or without any long-range electrostatic corrections. + These are called the SSD/RF and SSD/E models, respectively. These + modified models were shown to maintain or improve upon the experimental + agreement with the structural and transport properties that can + be obtained with either the original SSD or the density-corrected + version of the original model (SSD1). Additionally, a novel low-density + ice structure is presented which appears to be the most stable ice + structure for the entire SSD family. (C) 2004 American Institute + of Physics.}, annote = {816YY Times Cited:5 Cited References Count:39}, issn = {0021-9606}, uri = {://000221146400032}, @@ -1058,7 +1058,7 @@ Encoding: GBK @ARTICLE{Fernandes2002, author = {M. X. Fernandes and J. G. {de la Torre}}, title = {Brownian dynamics simulation of rigid particles of arbitrary shape - in external fields}, + in external fields}, journal = {Biophysical Journal}, year = {2002}, volume = {83}, @@ -1066,16 +1066,16 @@ Encoding: GBK number = {6}, month = {Dec}, abstract = {We have developed a Brownian dynamics simulation algorithm to generate - Brownian trajectories of an isolated, rigid particle of arbitrary - shape in the presence of electric fields or any other external agents. - Starting from the generalized diffusion tensor, which can be calculated - with the existing HYDRO software, the new program BROWNRIG (including - a case-specific subprogram for the external agent) carries out a - simulation that is analyzed later to extract the observable dynamic - properties. We provide a variety of examples of utilization of this - method, which serve as tests of its performance, and also illustrate - its applicability. Examples include free diffusion, transport in - an electric field, and diffusion in a restricting environment.}, + Brownian trajectories of an isolated, rigid particle of arbitrary + shape in the presence of electric fields or any other external agents. + Starting from the generalized diffusion tensor, which can be calculated + with the existing HYDRO software, the new program BROWNRIG (including + a case-specific subprogram for the external agent) carries out a + simulation that is analyzed later to extract the observable dynamic + properties. We provide a variety of examples of utilization of this + method, which serve as tests of its performance, and also illustrate + its applicability. Examples include free diffusion, transport in + an electric field, and diffusion in a restricting environment.}, annote = {633AD Times Cited:2 Cited References Count:43}, issn = {0006-3495}, uri = {://000180256300012}, @@ -1084,7 +1084,7 @@ Encoding: GBK @ARTICLE{Gay1981, author = {J. G. Gay and B. J. Berne}, title = {Modification of the Overlap Potential to Mimic a Linear Site-Site - Potential}, + Potential}, journal = {Journal of Chemical Physics}, year = {1981}, volume = {74}, @@ -1105,23 +1105,23 @@ Encoding: GBK number = {6}, month = {Nov}, abstract = {To investigate the influence of inertial effects on the dynamics of - an assembly of beads subjected to rigid constraints and placed in - a buffer medium, a convenient method to introduce suitable generalized - coordinates is presented. Without any restriction on the nature - of the soft forces involved (both stochastic and deterministic), - pertinent Langevin equations are derived. Provided that the Brownian - forces are Gaussian and Markovian, the corresponding Fokker-Planck - equation (FPE) is obtained in the complete phase space of generalized - coordinates and momenta. The correct short time behavior for correlation - functions (CFs) of generalized coordinates is established, and the - diffusion equation with memory (DEM) is deduced from the FPE in - the high friction Limit. The DEM is invoked to perform illustrative - calculations in two dimensions of the orientational CFs for once - broken nonrigid rods immobilized on a surface. These calculations - reveal that the CFs under certain conditions exhibit an oscillatory - behavior, which is irreproducible within the standard diffusion - equation. Several methods are considered for the approximate solution - of the DEM, and their application to three dimensional DEMs is discussed.}, + an assembly of beads subjected to rigid constraints and placed in + a buffer medium, a convenient method to introduce suitable generalized + coordinates is presented. Without any restriction on the nature + of the soft forces involved (both stochastic and deterministic), + pertinent Langevin equations are derived. Provided that the Brownian + forces are Gaussian and Markovian, the corresponding Fokker-Planck + equation (FPE) is obtained in the complete phase space of generalized + coordinates and momenta. The correct short time behavior for correlation + functions (CFs) of generalized coordinates is established, and the + diffusion equation with memory (DEM) is deduced from the FPE in + the high friction Limit. The DEM is invoked to perform illustrative + calculations in two dimensions of the orientational CFs for once + broken nonrigid rods immobilized on a surface. These calculations + reveal that the CFs under certain conditions exhibit an oscillatory + behavior, which is irreproducible within the standard diffusion + equation. Several methods are considered for the approximate solution + of the DEM, and their application to three dimensional DEMs is discussed.}, annote = {257MM Times Cited:2 Cited References Count:82}, issn = {1022-1344}, uri = {://000083785700002}, @@ -1138,9 +1138,9 @@ Encoding: GBK @ARTICLE{Gray2003, author = {J. J. Gray and S. Moughon and C. Wang and O. Schueler-Furman and - B. Kuhlman and C. A. Rohl and D. Baker}, + B. Kuhlman and C. A. Rohl and D. Baker}, title = {Protein-protein docking with simultaneous optimization of rigid-body - displacement and side-chain conformations}, + displacement and side-chain conformations}, journal = {Journal of Molecular Biology}, year = {2003}, volume = {331}, @@ -1148,29 +1148,29 @@ Encoding: GBK number = {1}, month = {Aug 1}, abstract = {Protein-protein docking algorithms provide a means to elucidate structural - details for presently unknown complexes. Here, we present and evaluate - a new method to predict protein-protein complexes from the coordinates - of the unbound monomer components. The method employs a low-resolution, - rigid-body, Monte Carlo search followed by simultaneous optimization - of backbone displacement and side-chain conformations using Monte - Carlo minimization. Up to 10(5) independent simulations are carried - out, and the resulting #decoys# are ranked using an energy function - dominated by van der Waals interactions, an implicit solvation model, - and an orientation-dependent hydrogen bonding potential. Top-ranking - decoys are clustered to select the final predictions. Small-perturbation - studies reveal the formation of binding funnels in 42 of 54 cases - using coordinates derived from the bound complexes and in 32 of - 54 cases using independently determined coordinates of one or both - monomers. Experimental binding affinities correlate with the calculated - score function and explain the predictive success or failure of - many targets. Global searches using one or both unbound components - predict at least 25% of the native residue-residue contacts in 28 - of the 32 cases where binding funnels exist. The results suggest - that the method may soon be useful for generating models of biologically - important complexes from the structures of the isolated components, - but they also highlight the challenges that must be met to achieve - consistent and accurate prediction of protein-protein interactions. - (C) 2003 Elsevier Ltd. All rights reserved.}, + details for presently unknown complexes. Here, we present and evaluate + a new method to predict protein-protein complexes from the coordinates + of the unbound monomer components. The method employs a low-resolution, + rigid-body, Monte Carlo search followed by simultaneous optimization + of backbone displacement and side-chain conformations using Monte + Carlo minimization. Up to 10(5) independent simulations are carried + out, and the resulting #decoys# are ranked using an energy function + dominated by van der Waals interactions, an implicit solvation model, + and an orientation-dependent hydrogen bonding potential. Top-ranking + decoys are clustered to select the final predictions. Small-perturbation + studies reveal the formation of binding funnels in 42 of 54 cases + using coordinates derived from the bound complexes and in 32 of + 54 cases using independently determined coordinates of one or both + monomers. Experimental binding affinities correlate with the calculated + score function and explain the predictive success or failure of + many targets. Global searches using one or both unbound components + predict at least 25% of the native residue-residue contacts in 28 + of the 32 cases where binding funnels exist. The results suggest + that the method may soon be useful for generating models of biologically + important complexes from the structures of the isolated components, + but they also highlight the challenges that must be met to achieve + consistent and accurate prediction of protein-protein interactions. + (C) 2003 Elsevier Ltd. All rights reserved.}, annote = {704QL Times Cited:48 Cited References Count:60}, issn = {0022-2836}, uri = {://000184351300022}, @@ -1186,14 +1186,14 @@ Encoding: GBK number = {5174}, month = {Aug 12}, abstract = {Some of the recently developed fast summation methods that have arisen - in scientific computing are described. These methods require an - amount of work proportional to N or N log N to evaluate all pairwise - interactions in an ensemble of N particles. Traditional methods, - by contrast, require an amount of work proportional to N-2. AS a - result, large-scale simulations can be carried out using only modest - computer resources. In combination with supercomputers, it is possible - to address questions that were previously out of reach. Problems - from diffusion, gravitation, and wave propagation are considered.}, + in scientific computing are described. These methods require an + amount of work proportional to N or N log N to evaluate all pairwise + interactions in an ensemble of N particles. Traditional methods, + by contrast, require an amount of work proportional to N-2. AS a + result, large-scale simulations can be carried out using only modest + computer resources. In combination with supercomputers, it is possible + to address questions that were previously out of reach. Problems + from diffusion, gravitation, and wave propagation are considered.}, annote = {Pb499 Times Cited:99 Cited References Count:44}, issn = {0036-8075}, uri = {://A1994PB49900031}, @@ -1223,18 +1223,18 @@ Encoding: GBK number = {4}, month = {Jun}, abstract = {Backward error analysis is a useful tool for the study of numerical - approximations to ordinary differential equations. The numerical - solution is formally interpreted as the exact solution of a perturbed - differential equation, given as a formal and usually divergent series - in powers of the step size. For a rigorous analysis, this series - has to be truncated. In this article we study the influence of this - truncation to the difference between the numerical solution and - the exact solution of the perturbed differential equation. Results - on the long-time behaviour of numerical solutions are obtained in - this way. We present applications to the numerical phase portrait - near hyperbolic equilibrium points, to asymptotically stable periodic - orbits and Hopf bifurcation, and to energy conservation and approximation - of invariant tori in Hamiltonian systems.}, + approximations to ordinary differential equations. The numerical + solution is formally interpreted as the exact solution of a perturbed + differential equation, given as a formal and usually divergent series + in powers of the step size. For a rigorous analysis, this series + has to be truncated. In this article we study the influence of this + truncation to the difference between the numerical solution and + the exact solution of the perturbed differential equation. Results + on the long-time behaviour of numerical solutions are obtained in + this way. We present applications to the numerical phase portrait + near hyperbolic equilibrium points, to asymptotically stable periodic + orbits and Hopf bifurcation, and to energy conservation and approximation + of invariant tori in Hamiltonian systems.}, annote = {Xj488 Times Cited:50 Cited References Count:19}, issn = {0029-599X}, uri = {://A1997XJ48800002}, @@ -1243,7 +1243,7 @@ Encoding: GBK @ARTICLE{Hao1993, author = {M. H. Hao and M. R. Pincus and S. Rackovsky and H. A. Scheraga}, title = {Unfolding and Refolding of the Native Structure of Bovine Pancreatic - Trypsin-Inhibitor Studied by Computer-Simulations}, + Trypsin-Inhibitor Studied by Computer-Simulations}, journal = {Biochemistry}, year = {1993}, volume = {32}, @@ -1251,39 +1251,39 @@ Encoding: GBK number = {37}, month = {Sep 21}, abstract = {A new procedure for studying the folding and unfolding of proteins, - with an application to bovine pancreatic trypsin inhibitor (BPTI), - is reported. The unfolding and refolding of the native structure - of the protein are characterized by the dimensions of the protein, - expressed in terms of the three principal radii of the structure - considered as an ellipsoid. A dynamic equation, describing the variations - of the principal radii on the unfolding path, and a numerical procedure - to solve this equation are proposed. Expanded and distorted conformations - are refolded to the native structure by a dimensional-constraint - energy minimization procedure. A unique and reproducible unfolding - pathway for an intermediate of BPTI lacking the [30,51] disulfide - bond is obtained. The resulting unfolded conformations are extended; - they contain near-native local structure, but their longest principal - radii are more than 2.5 times greater than that of the native structure. - The most interesting finding is that the majority of expanded conformations, - generated under various conditions, can be refolded closely to the - native structure, as measured by the correct overall chain fold, - by the rms deviations from the native structure of only 1.9-3.1 - angstrom, and by the energy differences of about 10 kcal/mol from - the native structure. Introduction of the [30,51] disulfide bond - at this stage, followed by minimization, improves the closeness - of the refolded structures to the native structure, reducing the - rms deviations to 0.9-2.0 angstrom. The unique refolding of these - expanded structures over such a large conformational space implies - that the folding is strongly dictated by the interactions in the - amino acid sequence of BPTI. The simulations indicate that, under - conditions that favor a compact structure as mimicked by the volume - constraints in our algorithm; the expanded conformations have a - strong tendency to move toward the native structure; therefore, - they probably would be favorable folding intermediates. The results - presented here support a general model for protein folding, i.e., - progressive formation of partially folded structural units, followed - by collapse to the compact native structure. The general applicability - of the procedure is also discussed.}, + with an application to bovine pancreatic trypsin inhibitor (BPTI), + is reported. The unfolding and refolding of the native structure + of the protein are characterized by the dimensions of the protein, + expressed in terms of the three principal radii of the structure + considered as an ellipsoid. A dynamic equation, describing the variations + of the principal radii on the unfolding path, and a numerical procedure + to solve this equation are proposed. Expanded and distorted conformations + are refolded to the native structure by a dimensional-constraint + energy minimization procedure. A unique and reproducible unfolding + pathway for an intermediate of BPTI lacking the [30,51] disulfide + bond is obtained. The resulting unfolded conformations are extended; + they contain near-native local structure, but their longest principal + radii are more than 2.5 times greater than that of the native structure. + The most interesting finding is that the majority of expanded conformations, + generated under various conditions, can be refolded closely to the + native structure, as measured by the correct overall chain fold, + by the rms deviations from the native structure of only 1.9-3.1 + angstrom, and by the energy differences of about 10 kcal/mol from + the native structure. Introduction of the [30,51] disulfide bond + at this stage, followed by minimization, improves the closeness + of the refolded structures to the native structure, reducing the + rms deviations to 0.9-2.0 angstrom. The unique refolding of these + expanded structures over such a large conformational space implies + that the folding is strongly dictated by the interactions in the + amino acid sequence of BPTI. The simulations indicate that, under + conditions that favor a compact structure as mimicked by the volume + constraints in our algorithm; the expanded conformations have a + strong tendency to move toward the native structure; therefore, + they probably would be favorable folding intermediates. The results + presented here support a general model for protein folding, i.e., + progressive formation of partially folded structural units, followed + by collapse to the compact native structure. The general applicability + of the procedure is also discussed.}, annote = {Ly294 Times Cited:27 Cited References Count:57}, issn = {0006-2960}, uri = {://A1993LY29400014}, @@ -1291,7 +1291,7 @@ Encoding: GBK @ARTICLE{Hinsen2000, author = {K. Hinsen and A. J. Petrescu and S. Dellerue and M. C. Bellissent-Funel - and G. R. Kneller}, + and G. R. Kneller}, title = {Harmonicity in slow protein dynamics}, journal = {Chemical Physics}, year = {2000}, @@ -1300,32 +1300,32 @@ Encoding: GBK number = {1-2}, month = {Nov 1}, abstract = {The slow dynamics of proteins around its native folded state is usually - described by diffusion in a strongly anharmonic potential. In this - paper, we try to understand the form and origin of the anharmonicities, - with the principal aim of gaining a better understanding of the - principal motion types, but also in order to develop more efficient - numerical methods for simulating neutron scattering spectra of large - proteins. First, we decompose a molecular dynamics (MD) trajectory - of 1.5 ns for a C-phycocyanin dimer surrounded by a layer of water - into three contributions that we expect to be independent: the global - motion of the residues, the rigid-body motion of the sidechains - relative to the backbone, and the internal deformations of the sidechains. - We show that they are indeed almost independent by verifying the - factorization of the incoherent intermediate scattering function. - Then, we show that the global residue motions, which include all - large-scale backbone motions, can be reproduced by a simple harmonic - model which contains two contributions: a short-time vibrational - term, described by a standard normal mode calculation in a local - minimum, and a long-time diffusive term, described by Brownian motion - in an effective harmonic potential. The potential and the friction - constants were fitted to the MD data. The major anharmonic contribution - to the incoherent intermediate scattering function comes from the - rigid-body diffusion of the sidechains. This model can be used to - calculate scattering functions for large proteins and for long-time - scales very efficiently, and thus provides a useful complement to - MD simulations, which are best suited for detailed studies on smaller - systems or for shorter time scales. (C) 2000 Elsevier Science B.V. - All rights reserved.}, + described by diffusion in a strongly anharmonic potential. In this + paper, we try to understand the form and origin of the anharmonicities, + with the principal aim of gaining a better understanding of the + principal motion types, but also in order to develop more efficient + numerical methods for simulating neutron scattering spectra of large + proteins. First, we decompose a molecular dynamics (MD) trajectory + of 1.5 ns for a C-phycocyanin dimer surrounded by a layer of water + into three contributions that we expect to be independent: the global + motion of the residues, the rigid-body motion of the sidechains + relative to the backbone, and the internal deformations of the sidechains. + We show that they are indeed almost independent by verifying the + factorization of the incoherent intermediate scattering function. + Then, we show that the global residue motions, which include all + large-scale backbone motions, can be reproduced by a simple harmonic + model which contains two contributions: a short-time vibrational + term, described by a standard normal mode calculation in a local + minimum, and a long-time diffusive term, described by Brownian motion + in an effective harmonic potential. The potential and the friction + constants were fitted to the MD data. The major anharmonic contribution + to the incoherent intermediate scattering function comes from the + rigid-body diffusion of the sidechains. This model can be used to + calculate scattering functions for large proteins and for long-time + scales very efficiently, and thus provides a useful complement to + MD simulations, which are best suited for detailed studies on smaller + systems or for shorter time scales. (C) 2000 Elsevier Science B.V. + All rights reserved.}, annote = {Sp. Iss. SI 368MT Times Cited:16 Cited References Count:31}, issn = {0301-0104}, uri = {://000090121700003}, @@ -1341,32 +1341,32 @@ Encoding: GBK number = {4}, month = {Oct}, abstract = {Evidence has been found for the existence water at the protein-lipid - hydrophobic interface ot the membrane proteins, gramicidin and apocytochrome - C, using two related fluorescence spectroscopic approaches. The - first approach exploited the fact that the presence of water in - the excited state solvent cage of a fluorophore increases the rate - of decay. For 1,6-diphenyl-1,3,5-hexatriene (DPH) and 1-palmitoyl-2-[[2-[4-(6-phenyl-trans-1,3,5-hexatrienyl) - phenyl]ethyl]carbonyl]-3-sn-PC (DPH-PC), where the fluorophores - are located in the hydrophobic core of the lipid bilayer, the introduction - of gramicidin reduced the fluorescence lifetime, indicative of an - increased presence of water in the bilayer. Since a high protein:lipid - ratio was used, the fluorophores were forced to be adjacent to the - protein hydrophobic surface, hence the presence of water in this - region could be inferred. Cholesterol is known to reduce the water - content of lipid bilayers and this effect was maintained at the - protein-lipid interface with both gramicidin and apocytochrome C, - again suggesting hydration in this region. The second approach was - to use the fluorescence enhancement induced by exchanging deuterium - oxide (D2O) for H2O. Both the fluorescence intensities of trimethylammonium-DPH, - located in the lipid head group region, and of the gramicidin intrinsic - tryptophans were greater in a D2O buffer compared with H2O, showing - that the fluorophores were exposed to water in the bilayer at the - protein-lipid interface. In the presence of cholesterol the fluorescence - intensity ratio of D2O to H2O decreased, indicating a removal of - water by the cholesterol, in keeping with the lifetime data. Altered - hydration at the protein-lipid interface could affect conformation, - thereby offering a new route by which membrane protein functioning - may be modified.}, + hydrophobic interface ot the membrane proteins, gramicidin and apocytochrome + C, using two related fluorescence spectroscopic approaches. The + first approach exploited the fact that the presence of water in + the excited state solvent cage of a fluorophore increases the rate + of decay. For 1,6-diphenyl-1,3,5-hexatriene (DPH) and 1-palmitoyl-2-[[2-[4-(6-phenyl-trans-1,3,5-hexatrienyl) + phenyl]ethyl]carbonyl]-3-sn-PC (DPH-PC), where the fluorophores + are located in the hydrophobic core of the lipid bilayer, the introduction + of gramicidin reduced the fluorescence lifetime, indicative of an + increased presence of water in the bilayer. Since a high protein:lipid + ratio was used, the fluorophores were forced to be adjacent to the + protein hydrophobic surface, hence the presence of water in this + region could be inferred. Cholesterol is known to reduce the water + content of lipid bilayers and this effect was maintained at the + protein-lipid interface with both gramicidin and apocytochrome C, + again suggesting hydration in this region. The second approach was + to use the fluorescence enhancement induced by exchanging deuterium + oxide (D2O) for H2O. Both the fluorescence intensities of trimethylammonium-DPH, + located in the lipid head group region, and of the gramicidin intrinsic + tryptophans were greater in a D2O buffer compared with H2O, showing + that the fluorophores were exposed to water in the bilayer at the + protein-lipid interface. In the presence of cholesterol the fluorescence + intensity ratio of D2O to H2O decreased, indicating a removal of + water by the cholesterol, in keeping with the lifetime data. Altered + hydration at the protein-lipid interface could affect conformation, + thereby offering a new route by which membrane protein functioning + may be modified.}, annote = {Ju251 Times Cited:55 Cited References Count:44}, issn = {0006-3495}, uri = {://A1992JU25100002}, @@ -1383,7 +1383,7 @@ Encoding: GBK @ARTICLE{Huh2004, author = {Y. Huh and N. M. Cann}, title = {Discrimination in isotropic, nematic, and smectic phases of chiral - calamitic molecules: A computer simulation study}, + calamitic molecules: A computer simulation study}, journal = {Journal of Chemical Physics}, year = {2004}, volume = {121}, @@ -1391,15 +1391,15 @@ Encoding: GBK number = {20}, month = {Nov 22}, abstract = {Racemic fluids of chiral calamitic molecules are investigated with - molecular dynamics simulations. In particular, the phase behavior - as a function of density is examined for eight racemates. The relationship - between chiral discrimination and orientational order in the phase - is explored. We find that the transition from the isotropic phase - to a liquid crystal phase is accompanied by an increase in chiral - discrimination, as measured by differences in radial distributions. - Among ordered phases, discrimination is largest for smectic phases - with a significant preference for heterochiral contact within the - layers. (C) 2004 American Institute of Physics.}, + molecular dynamics simulations. In particular, the phase behavior + as a function of density is examined for eight racemates. The relationship + between chiral discrimination and orientational order in the phase + is explored. We find that the transition from the isotropic phase + to a liquid crystal phase is accompanied by an increase in chiral + discrimination, as measured by differences in radial distributions. + Among ordered phases, discrimination is largest for smectic phases + with a significant preference for heterochiral contact within the + layers. (C) 2004 American Institute of Physics.}, annote = {870FJ Times Cited:0 Cited References Count:63}, issn = {0021-9606}, uri = {://000225042700059}, @@ -1415,47 +1415,37 @@ Encoding: GBK number = {5}, month = {Feb 1}, abstract = {In this paper we show the possibility of using very mild stochastic - damping to stabilize long time step integrators for Newtonian molecular - dynamics. More specifically, stable and accurate integrations are - obtained for damping coefficients that are only a few percent of - the natural decay rate of processes of interest, such as the velocity - autocorrelation function. Two new multiple time stepping integrators, - Langevin Molly (LM) and Brunger-Brooks-Karplus-Molly (BBK-M), are - introduced in this paper. Both use the mollified impulse method - for the Newtonian term. LM uses a discretization of the Langevin - equation that is exact for the constant force, and BBK-M uses the - popular Brunger-Brooks-Karplus integrator (BBK). These integrators, - along with an extrapolative method called LN, are evaluated across - a wide range of damping coefficient values. When large damping coefficients - are used, as one would for the implicit modeling of solvent molecules, - the method LN is superior, with LM closely following. However, with - mild damping of 0.2 ps(-1), LM produces the best results, allowing - long time steps of 14 fs in simulations containing explicitly modeled - flexible water. With BBK-M and the same damping coefficient, time - steps of 12 fs are possible for the same system. Similar results - are obtained for a solvated protein-DNA simulation of estrogen receptor - ER with estrogen response element ERE. A parallel version of BBK-M - runs nearly three times faster than the Verlet-I/r-RESPA (reversible - reference system propagator algorithm) when using the largest stable - time step on each one, and it also parallelizes well. The computation - of diffusion coefficients for flexible water and ER/ERE shows that - when mild damping of up to 0.2 ps-1 is used the dynamics are not - significantly distorted. (C) 2001 American Institute of Physics.}, + damping to stabilize long time step integrators for Newtonian molecular + dynamics. More specifically, stable and accurate integrations are + obtained for damping coefficients that are only a few percent of + the natural decay rate of processes of interest, such as the velocity + autocorrelation function. Two new multiple time stepping integrators, + Langevin Molly (LM) and Brunger-Brooks-Karplus-Molly (BBK-M), are + introduced in this paper. Both use the mollified impulse method + for the Newtonian term. LM uses a discretization of the Langevin + equation that is exact for the constant force, and BBK-M uses the + popular Brunger-Brooks-Karplus integrator (BBK). These integrators, + along with an extrapolative method called LN, are evaluated across + a wide range of damping coefficient values. When large damping coefficients + are used, as one would for the implicit modeling of solvent molecules, + the method LN is superior, with LM closely following. However, with + mild damping of 0.2 ps(-1), LM produces the best results, allowing + long time steps of 14 fs in simulations containing explicitly modeled + flexible water. With BBK-M and the same damping coefficient, time + steps of 12 fs are possible for the same system. Similar results + are obtained for a solvated protein-DNA simulation of estrogen receptor + ER with estrogen response element ERE. A parallel version of BBK-M + runs nearly three times faster than the Verlet-I/r-RESPA (reversible + reference system propagator algorithm) when using the largest stable + time step on each one, and it also parallelizes well. The computation + of diffusion coefficients for flexible water and ER/ERE shows that + when mild damping of up to 0.2 ps-1 is used the dynamics are not + significantly distorted. (C) 2001 American Institute of Physics.}, annote = {397CQ Times Cited:14 Cited References Count:36}, issn = {0021-9606}, uri = {://000166676100020}, } -@ARTICLE{Gray2003, - author = {J.~J Gray,S. Moughon, C. Wang }, - title = {Protein-protein docking with simultaneous optimization of rigid-body - displacement and side-chain conformations}, - journal = {jmb}, - year = {2003}, - volume = {331}, - pages = {281-299}, -} - @ARTICLE{Torre1977, author = {Jose Garcia De La Torre, V.A. Bloomfield}, title = {Hydrodynamic properties of macromolecular complexes. I. Translation}, @@ -1468,7 +1458,7 @@ Encoding: GBK @ARTICLE{Kane2000, author = {C. Kane and J. E. Marsden and M. Ortiz and M. West}, title = {Variational integrators and the Newmark algorithm for conservative - and dissipative mechanical systems}, + and dissipative mechanical systems}, journal = {International Journal for Numerical Methods in Engineering}, year = {2000}, volume = {49}, @@ -1476,21 +1466,21 @@ Encoding: GBK number = {10}, month = {Dec 10}, abstract = {The purpose of this work is twofold. First, we demonstrate analytically - that the classical Newmark family as well as related integration - algorithms are variational in the sense of the Veselov formulation - of discrete mechanics. Such variational algorithms are well known - to be symplectic and momentum preserving and to often have excellent - global energy behaviour. This analytical result is verified through - numerical examples and is believed to be one of the primary reasons - that this class of algorithms performs so well. Second, we develop - algorithms for mechanical systems with forcing, and in particular, - for dissipative systems. In this case, we develop integrators that - are based on a discretization of the Lagrange d'Alembert principle - as well as on a variational formulation of dissipation. It is demonstrated - that these types of structured integrators have good numerical behaviour - in terms of obtaining the correct amounts by which the energy changes - over the integration run. Copyright (C) 2000 John Wiley & Sons, - Ltd.}, + that the classical Newmark family as well as related integration + algorithms are variational in the sense of the Veselov formulation + of discrete mechanics. Such variational algorithms are well known + to be symplectic and momentum preserving and to often have excellent + global energy behaviour. This analytical result is verified through + numerical examples and is believed to be one of the primary reasons + that this class of algorithms performs so well. Second, we develop + algorithms for mechanical systems with forcing, and in particular, + for dissipative systems. In this case, we develop integrators that + are based on a discretization of the Lagrange d'Alembert principle + as well as on a variational formulation of dissipation. It is demonstrated + that these types of structured integrators have good numerical behaviour + in terms of obtaining the correct amounts by which the energy changes + over the integration run. Copyright (C) 2000 John Wiley & Sons, + Ltd.}, annote = {373CJ Times Cited:30 Cited References Count:41}, issn = {0029-5981}, uri = {://000165270600004}, @@ -1506,16 +1496,16 @@ Encoding: GBK number = {2}, month = {Jul 14}, abstract = {The viscosity (eta) dependence of the folding rates for four sequences - (the native state of three sequences is a beta sheet, while the - fourth forms an alpha helix) is calculated for off-lattice models - of proteins. Assuming that the dynamics is given by the Langevin - equation, we show that the folding rates increase linearly at low - viscosities eta, decrease as 1/eta at large eta, and have a maximum - at intermediate values. The Kramers' theory of barrier crossing - provides a quantitative fit of the numerical results. By mapping - the simulation results to real proteins we estimate that for optimized - sequences the time scale for forming a four turn alpha-helix topology - is about 500 ns, whereas for beta sheet it is about 10 mu s.}, + (the native state of three sequences is a beta sheet, while the + fourth forms an alpha helix) is calculated for off-lattice models + of proteins. Assuming that the dynamics is given by the Langevin + equation, we show that the folding rates increase linearly at low + viscosities eta, decrease as 1/eta at large eta, and have a maximum + at intermediate values. The Kramers' theory of barrier crossing + provides a quantitative fit of the numerical results. By mapping + the simulation results to real proteins we estimate that for optimized + sequences the time scale for forming a four turn alpha-helix topology + is about 500 ns, whereas for beta sheet it is about 10 mu s.}, annote = {Xk293 Times Cited:77 Cited References Count:17}, issn = {0031-9007}, uri = {://A1997XK29300035}, @@ -1531,25 +1521,25 @@ Encoding: GBK number = {7}, month = {Aug 15}, abstract = {Rigid-body molecular dynamics simulations typically are performed - in a quaternion representation. The nonseparable form of the Hamiltonian - in quaternions prevents the use of a standard leapfrog (Verlet) - integrator, so nonsymplectic Runge-Kutta, multistep, or extrapolation - methods are generally used, This is unfortunate since symplectic - methods like Verlet exhibit superior energy conservation in long-time - integrations. In this article, we describe an alternative method, - which we call RSHAKE (for rotation-SHAKE), in which the entire rotation - matrix is evolved (using the scheme of McLachlan and Scovel [J. - Nonlin. Sci, 16 233 (1995)]) in tandem with the particle positions. - We employ a fast approximate Newton solver to preserve the orthogonality - of the rotation matrix. We test our method on a system of soft-sphere - dipoles and compare with quaternion evolution using a 4th-order - predictor-corrector integrator, Although the short-time error of - the quaternion algorithm is smaller for fixed time step than that - for RSHAKE, the quaternion scheme exhibits an energy drift which - is not observed in simulations with RSHAKE, hence a fixed energy - tolerance can be achieved by using a larger time step, The superiority - of RSHAKE increases with system size. (C) 1997 American Institute - of Physics.}, + in a quaternion representation. The nonseparable form of the Hamiltonian + in quaternions prevents the use of a standard leapfrog (Verlet) + integrator, so nonsymplectic Runge-Kutta, multistep, or extrapolation + methods are generally used, This is unfortunate since symplectic + methods like Verlet exhibit superior energy conservation in long-time + integrations. In this article, we describe an alternative method, + which we call RSHAKE (for rotation-SHAKE), in which the entire rotation + matrix is evolved (using the scheme of McLachlan and Scovel [J. + Nonlin. Sci, 16 233 (1995)]) in tandem with the particle positions. + We employ a fast approximate Newton solver to preserve the orthogonality + of the rotation matrix. We test our method on a system of soft-sphere + dipoles and compare with quaternion evolution using a 4th-order + predictor-corrector integrator, Although the short-time error of + the quaternion algorithm is smaller for fixed time step than that + for RSHAKE, the quaternion scheme exhibits an energy drift which + is not observed in simulations with RSHAKE, hence a fixed energy + tolerance can be achieved by using a larger time step, The superiority + of RSHAKE increases with system size. (C) 1997 American Institute + of Physics.}, annote = {Xq332 Times Cited:11 Cited References Count:18}, issn = {0021-9606}, uri = {://A1997XQ33200046}, @@ -1558,7 +1548,7 @@ Encoding: GBK @ARTICLE{Lansac2001, author = {Y. Lansac and M. A. Glaser and N. A. Clark}, title = {Microscopic structure and dynamics of a partial bilayer smectic liquid - crystal}, + crystal}, journal = {Physical Review E}, year = {2001}, volume = {6405}, @@ -1566,26 +1556,26 @@ Encoding: GBK number = {5}, month = {Nov}, abstract = {Cyanobiphenyls (nCB's) represent a useful and intensively studied - class of mesogens. Many of the peculiar properties of nCB's (e.g., - the occurence of the partial bilayer smectic-A(d) phase) are thought - to be a manifestation of short-range antiparallel association of - neighboring molecules, resulting from strong dipole-dipole interactions - between cyano groups. To test and extend existing models of microscopic - ordering in nCB's, we carry out large-scale atomistic simulation - studies of the microscopic structure and dynamics of the Sm-A(d) - phase of 4-octyl-4'-cyanobiphenyl (8CB). We compute a variety of - thermodynamic, structural, and dynamical properties for this material, - and make a detailed comparison of our results with experimental - measurements in order to validate our molecular model. Semiquantitative - agreement with experiment is found: the smectic layer spacing and - mass density are well reproduced, translational diffusion constants - are similar to experiment, but the orientational ordering of alkyl - chains is overestimated. This simulation provides a detailed picture - of molecular conformation, smectic layer structure, and intermolecular - correlations in Sm-A(d) 8CB, and demonstrates that pronounced short-range - antiparallel association of molecules arising from dipole-dipole - interactions plays a dominant role in determining the molecular-scale - structure of 8CB.}, + class of mesogens. Many of the peculiar properties of nCB's (e.g., + the occurence of the partial bilayer smectic-A(d) phase) are thought + to be a manifestation of short-range antiparallel association of + neighboring molecules, resulting from strong dipole-dipole interactions + between cyano groups. To test and extend existing models of microscopic + ordering in nCB's, we carry out large-scale atomistic simulation + studies of the microscopic structure and dynamics of the Sm-A(d) + phase of 4-octyl-4'-cyanobiphenyl (8CB). We compute a variety of + thermodynamic, structural, and dynamical properties for this material, + and make a detailed comparison of our results with experimental + measurements in order to validate our molecular model. Semiquantitative + agreement with experiment is found: the smectic layer spacing and + mass density are well reproduced, translational diffusion constants + are similar to experiment, but the orientational ordering of alkyl + chains is overestimated. This simulation provides a detailed picture + of molecular conformation, smectic layer structure, and intermolecular + correlations in Sm-A(d) 8CB, and demonstrates that pronounced short-range + antiparallel association of molecules arising from dipole-dipole + interactions plays a dominant role in determining the molecular-scale + structure of 8CB.}, annote = {Part 1 496QF Times Cited:10 Cited References Count:60}, issn = {1063-651X}, uri = {://000172406900063}, @@ -1601,20 +1591,20 @@ Encoding: GBK number = {1}, month = {Jan}, abstract = {Recently, a new class of smectic liquid crystal phases characterized - by the spontaneous formation of macroscopic chiral domains from - achiral bent-core molecules has been discovered. We have carried - out Monte Carlo simulations of a minimal hard spherocylinder dimer - model to investigate the role of excluded volume interactions in - determining the phase behavior of bent-core materials and to probe - the molecular origins of polar and chiral symmetry breaking. We - present the phase diagram of hard spherocylinder dimers of length-diameter - ratio of 5 as a function of pressure or density and dimer opening - angle psi. With decreasing psi, a transition from a nonpolar to - a polar smectic A phase is observed near psi=167degrees, and the - nematic phase becomes thermodynamically unstable for psi<135degrees. - Free energy calculations indicate that the antipolar smectic A (SmAP(A)) - phase is more stable than the polar smectic A phase (SmAP(F)). No - chiral smectic or biaxial nematic phases were found.}, + by the spontaneous formation of macroscopic chiral domains from + achiral bent-core molecules has been discovered. We have carried + out Monte Carlo simulations of a minimal hard spherocylinder dimer + model to investigate the role of excluded volume interactions in + determining the phase behavior of bent-core materials and to probe + the molecular origins of polar and chiral symmetry breaking. We + present the phase diagram of hard spherocylinder dimers of length-diameter + ratio of 5 as a function of pressure or density and dimer opening + angle psi. With decreasing psi, a transition from a nonpolar to + a polar smectic A phase is observed near psi=167degrees, and the + nematic phase becomes thermodynamically unstable for psi<135degrees. + Free energy calculations indicate that the antipolar smectic A (SmAP(A)) + phase is more stable than the polar smectic A phase (SmAP(F)). No + chiral smectic or biaxial nematic phases were found.}, annote = {Part 1 646CM Times Cited:15 Cited References Count:38}, issn = {1063-651X}, uri = {://000181017300042}, @@ -1632,26 +1622,26 @@ Encoding: GBK @ARTICLE{Leimkuhler1999, author = {B. Leimkuhler}, title = {Reversible adaptive regularization: perturbed Kepler motion and classical - atomic trajectories}, + atomic trajectories}, journal = {Philosophical Transactions of the Royal Society of London Series - a-Mathematical Physical and Engineering Sciences}, + a-Mathematical Physical and Engineering Sciences}, year = {1999}, volume = {357}, pages = {1101-1133}, number = {1754}, month = {Apr 15}, abstract = {Reversible and adaptive integration methods based on Kustaanheimo-Stiefel - regularization and modified Sundman transformations are applied - to simulate general perturbed Kepler motion and to compute classical - trajectories of atomic systems (e.g. Rydberg atoms). The new family - of reversible adaptive regularization methods also conserves angular - momentum and exhibits superior energy conservation and numerical - stability in long-time integrations. The schemes are appropriate - for scattering, for astronomical calculations of escape time and - long-term stability, and for classical and semiclassical studies - of atomic dynamics. The components of an algorithm for trajectory - calculations are described. Numerical experiments illustrate the - effectiveness of the reversible approach.}, + regularization and modified Sundman transformations are applied + to simulate general perturbed Kepler motion and to compute classical + trajectories of atomic systems (e.g. Rydberg atoms). The new family + of reversible adaptive regularization methods also conserves angular + momentum and exhibits superior energy conservation and numerical + stability in long-time integrations. The schemes are appropriate + for scattering, for astronomical calculations of escape time and + long-term stability, and for classical and semiclassical studies + of atomic dynamics. The components of an algorithm for trajectory + calculations are described. Numerical experiments illustrate the + effectiveness of the reversible approach.}, annote = {199EE Times Cited:11 Cited References Count:48}, issn = {1364-503X}, uri = {://000080466800007}, @@ -1667,7 +1657,7 @@ Encoding: GBK @ARTICLE{Levelut1981, author = {A. M. Levelut and R. J. Tarento and F. Hardouin and M. F. Achard - and G. Sigaud}, + and G. Sigaud}, title = {Number of Sa Phases}, journal = {Physical Review A}, year = {1981}, @@ -1682,7 +1672,7 @@ Encoding: GBK @ARTICLE{Lieb1982, author = {W. R. Lieb and M. Kovalycsik and R. Mendelsohn}, title = {Do Clinical-Levels of General-Anesthetics Affect Lipid Bilayers - - Evidence from Raman-Scattering}, + Evidence from Raman-Scattering}, journal = {Biochimica Et Biophysica Acta}, year = {1982}, volume = {688}, @@ -1695,9 +1685,9 @@ Encoding: GBK @ARTICLE{Link1997, author = {D. R. Link and G. Natale and R. Shao and J. E. Maclennan and N. A. - Clark and E. Korblova and D. M. Walba}, + Clark and E. Korblova and D. M. Walba}, title = {Spontaneous formation of macroscopic chiral domains in a fluid smectic - phase of achiral molecules}, + phase of achiral molecules}, journal = {Science}, year = {1997}, volume = {278}, @@ -1705,15 +1695,15 @@ Encoding: GBK number = {5345}, month = {Dec 12}, abstract = {A smectic liquid-crystal phase made from achiral molecules with bent - cores was found to have fluid layers that exhibit two spontaneous - symmetry-breaking instabilities: polar molecular orientational ordering - about the layer normal and molecular tilt. These instabilities combine - to form a chiral layer structure with a handedness that depends - on the sign of the tilt. The bulk states are either antiferroelectric-racemic, - with the layer polar direction and handedness alternating in sign - from layer to layer, or antiferroelectric-chiral, which is of uniform - layer handedness. Both states exhibit an electric field-induced - transition from antiferroelectric to ferroelectric.}, + cores was found to have fluid layers that exhibit two spontaneous + symmetry-breaking instabilities: polar molecular orientational ordering + about the layer normal and molecular tilt. These instabilities combine + to form a chiral layer structure with a handedness that depends + on the sign of the tilt. The bulk states are either antiferroelectric-racemic, + with the layer polar direction and handedness alternating in sign + from layer to layer, or antiferroelectric-chiral, which is of uniform + layer handedness. Both states exhibit an electric field-induced + transition from antiferroelectric to ferroelectric.}, annote = {Yl002 Times Cited:407 Cited References Count:25}, issn = {0036-8075}, uri = {://A1997YL00200028}, @@ -1722,7 +1712,7 @@ Encoding: GBK @ARTICLE{Liwo2005, author = {A. Liwo and M. Khalili and H. A. Scheraga}, title = {Ab initio simulations of protein folding pathways by molecular dynamics - with the united-residue (UNRES) model of polypeptide chains}, + with the united-residue (UNRES) model of polypeptide chains}, journal = {Febs Journal}, year = {2005}, volume = {272}, @@ -1736,20 +1726,20 @@ Encoding: GBK @ARTICLE{Luty1994, author = {B. A. Luty and M. E. Davis and I. G. Tironi and W. F. Vangunsteren}, title = {A Comparison of Particle-Particle, Particle-Mesh and Ewald Methods - for Calculating Electrostatic Interactions in Periodic Molecular-Systems}, + for Calculating Electrostatic Interactions in Periodic Molecular-Systems}, journal = {Molecular Simulation}, year = {1994}, volume = {14}, pages = {11-20}, number = {1}, abstract = {We compare the Particle-Particle Particle-Mesh (PPPM) and Ewald methods - for calculating electrostatic interactions in periodic molecular - systems. A brief comparison of the theories shows that the methods - are very similar differing mainly in the technique which is used - to perform the ''k-space'' or mesh calculation. Because the PPPM - utilizes the highly efficient numerical Fast Fourier Transform (FFT) - method it requires significantly less computational effort than - the Ewald method and scale's almost linearly with system size.}, + for calculating electrostatic interactions in periodic molecular + systems. A brief comparison of the theories shows that the methods + are very similar differing mainly in the technique which is used + to perform the ''k-space'' or mesh calculation. Because the PPPM + utilizes the highly efficient numerical Fast Fourier Transform (FFT) + method it requires significantly less computational effort than + the Ewald method and scale's almost linearly with system size.}, annote = {Qf464 Times Cited:50 Cited References Count:20}, issn = {0892-7022}, uri = {://A1994QF46400002}, @@ -1767,7 +1757,7 @@ Encoding: GBK @ARTICLE{Marsden1998, author = {J. E. Marsden and G. W. Patrick and S. Shkoller}, title = {Multisymplectic geometry, variational integrators, and nonlinear - PDEs}, + PDEs}, journal = {Communications in Mathematical Physics}, year = {1998}, volume = {199}, @@ -1775,25 +1765,25 @@ Encoding: GBK number = {2}, month = {Dec}, abstract = {This paper presents a geometric-variational approach to continuous - and discrete mechanics and field theories. Using multisymplectic - geometry, we show that the existence of the fundamental geometric - structures as well as their preservation along solutions can be - obtained directly from the variational principle. In particular, - we prove that a unique multisymplectic structure is obtained by - taking the derivative of an action function, and use this structure - to prove covariant generalizations of conservation of symplecticity - and Noether's theorem. Natural discretization schemes for PDEs, - which have these important preservation properties, then follow - by choosing a discrete action functional. In the case of mechanics, - we recover the variational symplectic integrators of Veselov type, - while for PDEs we obtain covariant spacetime integrators which conserve - the corresponding discrete multisymplectic form as well as the discrete - momentum mappings corresponding to symmetries. We show that the - usual notion of symplecticity along an infinite-dimensional space - of fields can be naturally obtained by making a spacetime split. - All of the aspects of our method are demonstrated with a nonlinear - sine-Gordon equation, including computational results and a comparison - with other discretization schemes.}, + and discrete mechanics and field theories. Using multisymplectic + geometry, we show that the existence of the fundamental geometric + structures as well as their preservation along solutions can be + obtained directly from the variational principle. In particular, + we prove that a unique multisymplectic structure is obtained by + taking the derivative of an action function, and use this structure + to prove covariant generalizations of conservation of symplecticity + and Noether's theorem. Natural discretization schemes for PDEs, + which have these important preservation properties, then follow + by choosing a discrete action functional. In the case of mechanics, + we recover the variational symplectic integrators of Veselov type, + while for PDEs we obtain covariant spacetime integrators which conserve + the corresponding discrete multisymplectic form as well as the discrete + momentum mappings corresponding to symmetries. We show that the + usual notion of symplecticity along an infinite-dimensional space + of fields can be naturally obtained by making a spacetime split. + All of the aspects of our method are demonstrated with a nonlinear + sine-Gordon equation, including computational results and a comparison + with other discretization schemes.}, annote = {154RH Times Cited:88 Cited References Count:36}, issn = {0010-3616}, uri = {://000077902200006}, @@ -1811,7 +1801,7 @@ Encoding: GBK @ARTICLE{McLachlan1998a, author = {R. I. McLachlan and G. R. W. Quispel}, title = {Generating functions for dynamical systems with symmetries, integrals, - and differential invariants}, + and differential invariants}, journal = {Physica D}, year = {1998}, volume = {112}, @@ -1819,11 +1809,11 @@ Encoding: GBK number = {1-2}, month = {Jan 15}, abstract = {We give a survey and some new examples of generating functions for - systems with symplectic structure, systems with a first integral, - systems that preserve volume, and systems with symmetries and/or - time-reversing symmetries. Both ODEs and maps are treated, and we - discuss how generating functions may be used in the structure-preserving - numerical integration of ODEs with the above properties.}, + systems with symplectic structure, systems with a first integral, + systems that preserve volume, and systems with symmetries and/or + time-reversing symmetries. Both ODEs and maps are treated, and we + discuss how generating functions may be used in the structure-preserving + numerical integration of ODEs with the above properties.}, annote = {Yt049 Times Cited:7 Cited References Count:26}, issn = {0167-2789}, uri = {://000071558900021}, @@ -1839,14 +1829,14 @@ Encoding: GBK number = {2}, month = {Apr}, abstract = {We consider properties of flows, the relationships between them, and - whether numerical integrators can be made to preserve these properties. - This is done in the context of automorphisms and antiautomorphisms - of a certain group generated by maps associated to vector fields. - This new framework unifies several known constructions. We also - use the concept of #covariance# of a numerical method with respect - to a group of coordinate transformations. The main application is - to explore the relationship between spatial symmetries, reversing - symmetries, and time symmetry of flows and numerical integrators.}, + whether numerical integrators can be made to preserve these properties. + This is done in the context of automorphisms and antiautomorphisms + of a certain group generated by maps associated to vector fields. + This new framework unifies several known constructions. We also + use the concept of #covariance# of a numerical method with respect + to a group of coordinate transformations. The main application is + to explore the relationship between spatial symmetries, reversing + symmetries, and time symmetry of flows and numerical integrators.}, annote = {Zc449 Times Cited:14 Cited References Count:33}, issn = {0036-1429}, uri = {://000072580500010}, @@ -1862,18 +1852,18 @@ Encoding: GBK number = {1}, month = {Feb}, abstract = {In this paper we revisit the Moser-Veselov description of the free - rigid body in body coordinates, which, in the 3 x 3 case, can be - implemented as an explicit, second-order, integrable approximation - of the continuous solution. By backward error analysis, we study - the modified vector field which is integrated exactly by the discrete - algorithm. We deduce that the discrete Moser-Veselov (DMV) is well - approximated to higher order by time reparametrizations of the continuous - equations (modified vector field). We use the modified vector field - to scale the initial data of the DMV to improve the order of the - approximation and show the equivalence of the DMV and the RATTLE - algorithm. Numerical integration with these preprocessed initial - data is several orders of magnitude more accurate than the original - DMV and RATTLE approach.}, + rigid body in body coordinates, which, in the 3 x 3 case, can be + implemented as an explicit, second-order, integrable approximation + of the continuous solution. By backward error analysis, we study + the modified vector field which is integrated exactly by the discrete + algorithm. We deduce that the discrete Moser-Veselov (DMV) is well + approximated to higher order by time reparametrizations of the continuous + equations (modified vector field). We use the modified vector field + to scale the initial data of the DMV to improve the order of the + approximation and show the equivalence of the DMV and the RATTLE + algorithm. Numerical integration with these preprocessed initial + data is several orders of magnitude more accurate than the original + DMV and RATTLE approach.}, annote = {911NS Times Cited:0 Cited References Count:14}, issn = {1615-3375}, uri = {://000228011900003}, @@ -1882,7 +1872,7 @@ Encoding: GBK @ARTICLE{Memmer2002, author = {R. Memmer}, title = {Liquid crystal phases of achiral banana-shaped molecules: a computer - simulation study}, + simulation study}, journal = {Liquid Crystals}, year = {2002}, volume = {29}, @@ -1890,30 +1880,30 @@ Encoding: GBK number = {4}, month = {Apr}, abstract = {The phase behaviour of achiral banana-shaped molecules was studied - by computer simulation. The banana-shaped molecules were described - by model intermolecular interactions based on the Gay-Berne potential. - The characteristic molecular structure was considered by joining - two calamitic Gay-Berne particles through a bond to form a biaxial - molecule of point symmetry group C-2v with a suitable bending angle. - The dependence on temperature of systems of N=1024 rigid banana-shaped - molecules with bending angle phi=140degrees has been studied by - means of Monte Carlo simulations in the isobaric-isothermal ensemble - (NpT). On cooling an isotropic system, two phase transitions characterized - by phase transition enthalpy, entropy and relative volume change - have been observed. For the first time by computer simulation of - a many-particle system of banana-shaped molecules, at low temperature - an untilted smectic phase showing a global phase biaxiality and - a spontaneous local polarization in the layers, i.e. a local polar - arrangement of the steric dipoles, with an antiferroelectric-like - superstructure could be proven, a phase structure which recently - has been discovered experimentally. Additionally, at intermediate - temperature a nematic-like phase has been proved, whereas close - to the transition to the smectic phase hints of a spontaneous achiral - symmetry breaking have been determined. Here, in the absence of - a layered structure a helical superstructure has been formed. All - phases have been characterized by visual representations of selected - configurations, scalar and pseudoscalar correlation functions, and - order parameters.}, + by computer simulation. The banana-shaped molecules were described + by model intermolecular interactions based on the Gay-Berne potential. + The characteristic molecular structure was considered by joining + two calamitic Gay-Berne particles through a bond to form a biaxial + molecule of point symmetry group C-2v with a suitable bending angle. + The dependence on temperature of systems of N=1024 rigid banana-shaped + molecules with bending angle phi=140degrees has been studied by + means of Monte Carlo simulations in the isobaric-isothermal ensemble + (NpT). On cooling an isotropic system, two phase transitions characterized + by phase transition enthalpy, entropy and relative volume change + have been observed. For the first time by computer simulation of + a many-particle system of banana-shaped molecules, at low temperature + an untilted smectic phase showing a global phase biaxiality and + a spontaneous local polarization in the layers, i.e. a local polar + arrangement of the steric dipoles, with an antiferroelectric-like + superstructure could be proven, a phase structure which recently + has been discovered experimentally. Additionally, at intermediate + temperature a nematic-like phase has been proved, whereas close + to the transition to the smectic phase hints of a spontaneous achiral + symmetry breaking have been determined. Here, in the absence of + a layered structure a helical superstructure has been formed. All + phases have been characterized by visual representations of selected + configurations, scalar and pseudoscalar correlation functions, and + order parameters.}, annote = {531HT Times Cited:12 Cited References Count:37}, issn = {0267-8292}, uri = {://000174410500001}, @@ -1930,9 +1920,9 @@ Encoding: GBK @ARTICLE{Mielke2004, author = {S. P. Mielke and W. H. Fink and V. V. Krishnan and N. Gronbech-Jensen - and C. J. Benham}, + and C. J. Benham}, title = {Transcription-driven twin supercoiling of a DNA loop: A Brownian - dynamics study}, + dynamics study}, journal = {Journal of Chemical Physics}, year = {2004}, volume = {121}, @@ -1940,30 +1930,30 @@ Encoding: GBK number = {16}, month = {Oct 22}, abstract = {The torque generated by RNA polymerase as it tracks along double-stranded - DNA can potentially induce long-range structural deformations integral - to mechanisms of biological significance in both prokaryotes and - eukaryotes. In this paper, we introduce a dynamic computer model - for investigating this phenomenon. Duplex DNA is represented as - a chain of hydrodynamic beads interacting through potentials of - linearly elastic stretching, bending, and twisting, as well as excluded - volume. The chain, linear when relaxed, is looped to form two open - but topologically constrained subdomains. This permits the dynamic - introduction of torsional stress via a centrally applied torque. - We simulate by Brownian dynamics the 100 mus response of a 477-base - pair B-DNA template to the localized torque generated by the prokaryotic - transcription ensemble. Following a sharp rise at early times, the - distributed twist assumes a nearly constant value in both subdomains, - and a succession of supercoiling deformations occurs as superhelical - stress is increasingly partitioned to writhe. The magnitude of writhe - surpasses that of twist before also leveling off when the structure - reaches mechanical equilibrium with the torsional load. Superhelicity - is simultaneously right handed in one subdomain and left handed - in the other, as predicted by the #transcription-induced##twin-supercoiled-domain# - model [L. F. Liu and J. C. Wang, Proc. Natl. Acad. Sci. U.S.A. 84, - 7024 (1987)]. The properties of the chain at the onset of writhing - agree well with predictions from theory, and the generated stress - is ample for driving secondary structural transitions in physiological - DNA. (C) 2004 American Institute of Physics.}, + DNA can potentially induce long-range structural deformations integral + to mechanisms of biological significance in both prokaryotes and + eukaryotes. In this paper, we introduce a dynamic computer model + for investigating this phenomenon. Duplex DNA is represented as + a chain of hydrodynamic beads interacting through potentials of + linearly elastic stretching, bending, and twisting, as well as excluded + volume. The chain, linear when relaxed, is looped to form two open + but topologically constrained subdomains. This permits the dynamic + introduction of torsional stress via a centrally applied torque. + We simulate by Brownian dynamics the 100 mus response of a 477-base + pair B-DNA template to the localized torque generated by the prokaryotic + transcription ensemble. Following a sharp rise at early times, the + distributed twist assumes a nearly constant value in both subdomains, + and a succession of supercoiling deformations occurs as superhelical + stress is increasingly partitioned to writhe. The magnitude of writhe + surpasses that of twist before also leveling off when the structure + reaches mechanical equilibrium with the torsional load. Superhelicity + is simultaneously right handed in one subdomain and left handed + in the other, as predicted by the #transcription-induced##twin-supercoiled-domain# + model [L. F. Liu and J. C. Wang, Proc. Natl. Acad. Sci. U.S.A. 84, + 7024 (1987)]. The properties of the chain at the onset of writhing + agree well with predictions from theory, and the generated stress + is ample for driving secondary structural transitions in physiological + DNA. (C) 2004 American Institute of Physics.}, annote = {861ZF Times Cited:3 Cited References Count:34}, issn = {0021-9606}, uri = {://000224456500064}, @@ -1972,8 +1962,8 @@ Encoding: GBK @ARTICLE{Naess2001, author = {S. N. Naess and H. M. Adland and A. Mikkelsen and A. Elgsaeter}, title = {Brownian dynamics simulation of rigid bodies and segmented polymer - chains. Use of Cartesian rotation vectors as the generalized coordinates - describing angular orientations}, + chains. Use of Cartesian rotation vectors as the generalized coordinates + describing angular orientations}, journal = {Physica A}, year = {2001}, volume = {294}, @@ -1981,18 +1971,18 @@ Encoding: GBK number = {3-4}, month = {May 15}, abstract = {The three Eulerian angles constitute the classical choice of generalized - coordinates used to describe the three degrees of rotational freedom - of a rigid body, but it has long been known that this choice yields - singular equations of motion. The latter is also true when Eulerian - angles are used in Brownian dynamics analyses of the angular orientation - of single rigid bodies and segmented polymer chains. Starting from - kinetic theory we here show that by instead employing the three - components of Cartesian rotation vectors as the generalized coordinates - describing angular orientation, no singularity appears in the configuration - space diffusion equation and the associated Brownian dynamics algorithm. - The suitability of Cartesian rotation vectors in Brownian dynamics - simulations of segmented polymer chains with spring-like or ball-socket - joints is discussed. (C) 2001 Elsevier Science B.V. All rights reserved.}, + coordinates used to describe the three degrees of rotational freedom + of a rigid body, but it has long been known that this choice yields + singular equations of motion. The latter is also true when Eulerian + angles are used in Brownian dynamics analyses of the angular orientation + of single rigid bodies and segmented polymer chains. Starting from + kinetic theory we here show that by instead employing the three + components of Cartesian rotation vectors as the generalized coordinates + describing angular orientation, no singularity appears in the configuration + space diffusion equation and the associated Brownian dynamics algorithm. + The suitability of Cartesian rotation vectors in Brownian dynamics + simulations of segmented polymer chains with spring-like or ball-socket + joints is discussed. (C) 2001 Elsevier Science B.V. All rights reserved.}, annote = {433TA Times Cited:7 Cited References Count:19}, issn = {0378-4371}, uri = {://000168774800005}, @@ -2001,7 +1991,7 @@ Encoding: GBK @ARTICLE{Niori1996, author = {T. Niori and T. Sekine and J. Watanabe and T. Furukawa and H. Takezoe}, title = {Distinct ferroelectric smectic liquid crystals consisting of banana - shaped achiral molecules}, + shaped achiral molecules}, journal = {Journal of Materials Chemistry}, year = {1996}, volume = {6}, @@ -2009,12 +1999,12 @@ Encoding: GBK number = {7}, month = {Jul}, abstract = {The synthesis of a banana-shaped molecule is reported and it is found - that the smectic phase which it forms is biaxial with the molecules - packed in the best,direction into a layer. Because of this characteristic - packing, spontaneous polarization appears parallel to the layer - and switches on reversal of an applied electric field. This is the - first obvious example of ferroelectricity in an achiral smectic - phase and is ascribed to the C-2v symmetry of the molecular packing.}, + that the smectic phase which it forms is biaxial with the molecules + packed in the best,direction into a layer. Because of this characteristic + packing, spontaneous polarization appears parallel to the layer + and switches on reversal of an applied electric field. This is the + first obvious example of ferroelectricity in an achiral smectic + phase and is ascribed to the C-2v symmetry of the molecular packing.}, annote = {Ux855 Times Cited:447 Cited References Count:18}, issn = {0959-9428}, uri = {://A1996UX85500025}, @@ -2030,17 +2020,17 @@ Encoding: GBK number = {5}, month = {may}, abstract = {We Studied the structural changes of bilayer vesicles induced by mechanical - forces using a Brownian dynamics simulation. Two nanoparticles, - which interact repulsively with amphiphilic molecules, are put inside - a vesicle. The position of one nanoparticle is fixed, and the other - is moved by a constant force as in optical-trapping experiments. - First, the pulled vesicle stretches into a pear or tube shape. Then - the inner monolayer in the tube-shaped region is deformed, and a - cylindrical structure is formed between two vesicles. After stretching - the cylindrical region, fission occurs near the moved vesicle. Soon - after this the cylindrical region shrinks. The trapping force similar - to 100 pN is needed to induce the formation of the cylindrical structure - and fission.}, + forces using a Brownian dynamics simulation. Two nanoparticles, + which interact repulsively with amphiphilic molecules, are put inside + a vesicle. The position of one nanoparticle is fixed, and the other + is moved by a constant force as in optical-trapping experiments. + First, the pulled vesicle stretches into a pear or tube shape. Then + the inner monolayer in the tube-shaped region is deformed, and a + cylindrical structure is formed between two vesicles. After stretching + the cylindrical region, fission occurs near the moved vesicle. Soon + after this the cylindrical region shrinks. The trapping force similar + to 100 pN is needed to induce the formation of the cylindrical structure + and fission.}, annote = {Part 1 568PX Times Cited:5 Cited References Count:39}, issn = {1063-651X}, uri = {://000176552300084}, @@ -2056,16 +2046,16 @@ Encoding: GBK number = {20}, month = {Nov 22}, abstract = {We studied the fusion dynamics of vesicles using a Brownian dynamics - simulation. Amphiphilic molecules spontaneously form vesicles with - a bilayer structure. Two vesicles come into contact and form a stalk - intermediate, in which a necklike structure only connects the outer - monolayers, as predicted by the stalk hypothesis. We have found - a new pathway of pore opening from stalks at high temperature: the - elliptic stalk bends and contact between the ends of the arc-shaped - stalk leads to pore opening. On the other hand, we have clarified - that the pore-opening process at low temperature agrees with the - modified stalk model: a pore is induced by contact between the inner - monolayers inside the stalk. (C) 2001 American Institute of Physics.}, + simulation. Amphiphilic molecules spontaneously form vesicles with + a bilayer structure. Two vesicles come into contact and form a stalk + intermediate, in which a necklike structure only connects the outer + monolayers, as predicted by the stalk hypothesis. We have found + a new pathway of pore opening from stalks at high temperature: the + elliptic stalk bends and contact between the ends of the arc-shaped + stalk leads to pore opening. On the other hand, we have clarified + that the pore-opening process at low temperature agrees with the + modified stalk model: a pore is induced by contact between the inner + monolayers inside the stalk. (C) 2001 American Institute of Physics.}, annote = {491UW Times Cited:48 Cited References Count:25}, issn = {0021-9606}, uri = {://000172129300049}, @@ -2082,7 +2072,7 @@ Encoding: GBK @ARTICLE{Omelyan1998, author = {I. P. Omelyan}, title = {On the numerical integration of motion for rigid polyatomics: The - modified quaternion approach}, + modified quaternion approach}, journal = {Computers in Physics}, year = {1998}, volume = {12}, @@ -2090,16 +2080,16 @@ Encoding: GBK number = {1}, month = {Jan-Feb}, abstract = {A revised version of the quaternion approach for numerical integration - of the equations of motion for rigid polyatomic molecules is proposed. - The modified approach is based on a formulation of the quaternion - dynamics with constraints. This allows one to resolve the rigidity - problem rigorously using constraint forces. It is shown that the - procedure for preservation of molecular rigidity can be realized - particularly simply within the Verlet algorithm in velocity form. - We demonstrate that the method presented leads to an improved numerical - stability with respect to the usual quaternion rescaling scheme - and it is roughly as good as the cumbersome atomic-constraint technique. - (C) 1998 American Institute of Physics.}, + of the equations of motion for rigid polyatomic molecules is proposed. + The modified approach is based on a formulation of the quaternion + dynamics with constraints. This allows one to resolve the rigidity + problem rigorously using constraint forces. It is shown that the + procedure for preservation of molecular rigidity can be realized + particularly simply within the Verlet algorithm in velocity form. + We demonstrate that the method presented leads to an improved numerical + stability with respect to the usual quaternion rescaling scheme + and it is roughly as good as the cumbersome atomic-constraint technique. + (C) 1998 American Institute of Physics.}, annote = {Yx279 Times Cited:12 Cited References Count:28}, issn = {0894-1866}, uri = {://000072024300025}, @@ -2108,7 +2098,7 @@ Encoding: GBK @ARTICLE{Omelyan1998a, author = {I. P. Omelyan}, title = {Algorithm for numerical integration of the rigid-body equations of - motion}, + motion}, journal = {Physical Review E}, year = {1998}, volume = {58}, @@ -2116,14 +2106,14 @@ Encoding: GBK number = {1}, month = {Jul}, abstract = {An algorithm for numerical integration of the rigid-body equations - of motion is proposed. The algorithm uses the leapfrog scheme and - the quantities involved are angular velocities and orientational - variables that can be expressed in terms of either principal axes - or quaternions. Due to specific features of the algorithm, orthonormality - and unit norms of the orientational variables are integrals of motion, - despite an approximate character of the produced trajectories. It - is shown that the method presented appears to be the most efficient - among all such algorithms known.}, + of motion is proposed. The algorithm uses the leapfrog scheme and + the quantities involved are angular velocities and orientational + variables that can be expressed in terms of either principal axes + or quaternions. Due to specific features of the algorithm, orthonormality + and unit norms of the orientational variables are integrals of motion, + despite an approximate character of the produced trajectories. It + is shown that the method presented appears to be the most efficient + among all such algorithms known.}, annote = {101XL Times Cited:8 Cited References Count:22}, issn = {1063-651X}, uri = {://000074893400151}, @@ -2132,7 +2122,7 @@ Encoding: GBK @ARTICLE{Orlandi2006, author = {S. Orlandi and R. Berardi and J. Steltzer and C. Zannoni}, title = {A Monte Carlo study of the mesophases formed by polar bent-shaped - molecules}, + molecules}, journal = {Journal of Chemical Physics}, year = {2006}, volume = {124}, @@ -2140,15 +2130,15 @@ Encoding: GBK number = {12}, month = {Mar 28}, abstract = {Liquid crystal phases formed by bent-shaped (or #banana#) molecules - are currently of great interest. Here we investigate by Monte Carlo - computer simulations the phases formed by rigid banana molecules - modeled combining three Gay-Berne sites and containing either one - central or two lateral and transversal dipoles. We show that changing - the dipole position and orientation has a profound effect on the - mesophase stability and molecular organization. In particular, we - find a uniaxial nematic phase only for off-center dipolar models - and tilted phases only for the one with terminal dipoles. (c) 2006 - American Institute of Physics.}, + are currently of great interest. Here we investigate by Monte Carlo + computer simulations the phases formed by rigid banana molecules + modeled combining three Gay-Berne sites and containing either one + central or two lateral and transversal dipoles. We show that changing + the dipole position and orientation has a profound effect on the + mesophase stability and molecular organization. In particular, we + find a uniaxial nematic phase only for off-center dipolar models + and tilted phases only for the one with terminal dipoles. (c) 2006 + American Institute of Physics.}, annote = {028CP Times Cited:0 Cited References Count:42}, issn = {0021-9606}, uri = {://000236464000072}, @@ -2164,18 +2154,18 @@ Encoding: GBK number = {6}, month = {Nov}, abstract = {Continuous, explicit Runge-Kutta methods with the minimal number of - stages are considered. These methods are continuously differentiable - if and only if one of the stages is the FSAL evaluation. A characterization - of a subclass of these methods is developed for orders 3, 4, and - 5. It is shown how the free parameters of these methods can be used - either to minimize the continuous truncation error coefficients - or to maximize the stability region. As a representative for these - methods the fifth-order method with minimized error coefficients - is chosen, supplied with an error estimation method, and analysed - by using the DETEST software. The results are compared with a similar - implementation of the Dormand-Prince 5(4) pair with interpolant, - showing a significant advantage in the new method for the chosen - problems.}, + stages are considered. These methods are continuously differentiable + if and only if one of the stages is the FSAL evaluation. A characterization + of a subclass of these methods is developed for orders 3, 4, and + 5. It is shown how the free parameters of these methods can be used + either to minimize the continuous truncation error coefficients + or to maximize the stability region. As a representative for these + methods the fifth-order method with minimized error coefficients + is chosen, supplied with an error estimation method, and analysed + by using the DETEST software. The results are compared with a similar + implementation of the Dormand-Prince 5(4) pair with interpolant, + showing a significant advantage in the new method for the chosen + problems.}, annote = {Ju936 Times Cited:25 Cited References Count:20}, issn = {0196-5204}, uri = {://A1992JU93600013}, @@ -2184,7 +2174,7 @@ Encoding: GBK @ARTICLE{Palacios1998, author = {J. L. Garcia-Palacios and F. J. Lazaro}, title = {Langevin-dynamics study of the dynamical properties of small magnetic - particles}, + particles}, journal = {Physical Review B}, year = {1998}, volume = {58}, @@ -2192,35 +2182,35 @@ Encoding: GBK number = {22}, month = {Dec 1}, abstract = {The stochastic Landau-Lifshitz-Gilbert equation of motion for a classical - magnetic moment is numerically solved (properly observing the customary - interpretation of it as a Stratonovich stochastic differential equation), - in order to study the dynamics of magnetic nanoparticles. The corresponding - Langevin-dynamics approach allows for the study of the fluctuating - trajectories of individual magnetic moments, where we have encountered - remarkable phenomena in the overbarrier rotation process, such as - crossing-back or multiple crossing of the potential barrier, rooted - in the gyromagnetic nature of the system. Concerning averaged quantities, - we study the linear dynamic response of the archetypal ensemble - of noninteracting classical magnetic moments with axially symmetric - magnetic anisotropy. The results are compared with different analytical - expressions used to model the relaxation of nanoparticle ensembles, - assessing their accuracy. It has been found that, among a number - of heuristic expressions for the linear dynamic susceptibility, - only the simple formula proposed by Shliomis and Stepanov matches - the coarse features of the susceptibility reasonably. By comparing - the numerical results with the asymptotic formula of Storonkin {Sov. - Phys. Crystallogr. 30, 489 (1985) [Kristallografiya 30, 841 (1985)]}, - the effects of the intra-potential-well relaxation modes on the - low-temperature longitudinal dynamic response have been assessed, - showing their relatively small reflection in the susceptibility - curves but their dramatic influence on the phase shifts. Comparison - of the numerical results with the exact zero-damping expression - for the transverse susceptibility by Garanin, Ishchenko, and Panina - {Theor. Math. Phys. (USSR) 82, 169 (1990) [Teor. Mat. Fit. 82, 242 - (1990)]}, reveals a sizable contribution of the spread of the precession - frequencies of the magnetic moment in the anisotropy field to the - dynamic response at intermediate-to-high temperatures. [S0163-1829 - (98)00446-9].}, + magnetic moment is numerically solved (properly observing the customary + interpretation of it as a Stratonovich stochastic differential equation), + in order to study the dynamics of magnetic nanoparticles. The corresponding + Langevin-dynamics approach allows for the study of the fluctuating + trajectories of individual magnetic moments, where we have encountered + remarkable phenomena in the overbarrier rotation process, such as + crossing-back or multiple crossing of the potential barrier, rooted + in the gyromagnetic nature of the system. Concerning averaged quantities, + we study the linear dynamic response of the archetypal ensemble + of noninteracting classical magnetic moments with axially symmetric + magnetic anisotropy. The results are compared with different analytical + expressions used to model the relaxation of nanoparticle ensembles, + assessing their accuracy. It has been found that, among a number + of heuristic expressions for the linear dynamic susceptibility, + only the simple formula proposed by Shliomis and Stepanov matches + the coarse features of the susceptibility reasonably. By comparing + the numerical results with the asymptotic formula of Storonkin {Sov. + Phys. Crystallogr. 30, 489 (1985) [Kristallografiya 30, 841 (1985)]}, + the effects of the intra-potential-well relaxation modes on the + low-temperature longitudinal dynamic response have been assessed, + showing their relatively small reflection in the susceptibility + curves but their dramatic influence on the phase shifts. Comparison + of the numerical results with the exact zero-damping expression + for the transverse susceptibility by Garanin, Ishchenko, and Panina + {Theor. Math. Phys. (USSR) 82, 169 (1990) [Teor. Mat. Fit. 82, 242 + (1990)]}, reveals a sizable contribution of the spread of the precession + frequencies of the magnetic moment in the anisotropy field to the + dynamic response at intermediate-to-high temperatures. [S0163-1829 + (98)00446-9].}, annote = {146XW Times Cited:66 Cited References Count:45}, issn = {0163-1829}, uri = {://000077460000052}, @@ -2257,7 +2247,7 @@ Encoding: GBK @ARTICLE{Perram1985, author = {J. W. Perram and M. S. Wertheim}, title = {Statistical-Mechanics of Hard Ellipsoids .1. Overlap Algorithm and - the Contact Function}, + the Contact Function}, journal = {Journal of Computational Physics}, year = {1985}, volume = {58}, @@ -2280,7 +2270,7 @@ Encoding: GBK @ARTICLE{Perrin1936, author = {F. Perrin}, title = {Mouvement brownien d'un ellipsoid(II). Rotation libre et depolarisation - des fluorescences. Translation et diffusion de moleculese ellipsoidales}, + des fluorescences. Translation et diffusion de moleculese ellipsoidales}, journal = {J. Phys. Radium}, year = {1936}, volume = {7}, @@ -2290,7 +2280,7 @@ Encoding: GBK @ARTICLE{Perrin1934, author = {F. Perrin}, title = {Mouvement brownien d'un ellipsoid(I). Dispersion dielectrique pour - des molecules ellipsoidales}, + des molecules ellipsoidales}, journal = {J. Phys. Radium}, year = {1934}, volume = {5}, @@ -2307,22 +2297,22 @@ Encoding: GBK number = {1}, month = {Sep}, abstract = {X-ray diffraction data taken at high instrumental resolution were - obtained for EPC and DMPC under various osmotic pressures, primarily - at T = 30 degrees C. The headgroup thickness D-HH was obtained from - relative electron density profiles. By using volumetric results - and by comparing to gel phase DPPC we obtain areas A(EPC)(F) = 69.4 - +/- 1.1 Angstrom(2) and A(DMPC)(F) = 59.7 +/- 0.2 Angstrom(2). The - analysis also gives estimates for the areal compressibility K-A. - The A(F) results lead to other structural results regarding membrane - thickness and associated waters. Using the recently determined absolute - electrons density profile of DPPC, the AF results also lead to absolute - electron density profiles and absolute continuous transforms \F(q)\ - for EPC and DMPC, Limited measurements of temperature dependence - show directly that fluctuations increase with increasing temperature - and that a small decrease in bending modulus K-c accounts for the - increased water spacing reported by Simon et al. (1995) Biophys. - J. 69, 1473-1483. (C) 1998 Elsevier Science Ireland Ltd. All rights - reserved.}, + obtained for EPC and DMPC under various osmotic pressures, primarily + at T = 30 degrees C. The headgroup thickness D-HH was obtained from + relative electron density profiles. By using volumetric results + and by comparing to gel phase DPPC we obtain areas A(EPC)(F) = 69.4 + +/- 1.1 Angstrom(2) and A(DMPC)(F) = 59.7 +/- 0.2 Angstrom(2). The + analysis also gives estimates for the areal compressibility K-A. + The A(F) results lead to other structural results regarding membrane + thickness and associated waters. Using the recently determined absolute + electrons density profile of DPPC, the AF results also lead to absolute + electron density profiles and absolute continuous transforms \F(q)\ + for EPC and DMPC, Limited measurements of temperature dependence + show directly that fluctuations increase with increasing temperature + and that a small decrease in bending modulus K-c accounts for the + increased water spacing reported by Simon et al. (1995) Biophys. + J. 69, 1473-1483. (C) 1998 Elsevier Science Ireland Ltd. All rights + reserved.}, annote = {130AT Times Cited:98 Cited References Count:39}, issn = {0009-3084}, uri = {://000076497600007}, @@ -2331,7 +2321,7 @@ Encoding: GBK @ARTICLE{Powles1973, author = {J.~G. Powles}, title = {A general ellipsoid can not always serve as a modle for the rotational - diffusion properties of arbitrary shaped rigid molecules}, + diffusion properties of arbitrary shaped rigid molecules}, journal = {Advan. Phys.}, year = {1973}, volume = {22}, @@ -2341,7 +2331,7 @@ Encoding: GBK @ARTICLE{Recio2004, author = {J. Fernandez-Recio and M. Totrov and R. Abagyan}, title = {Identification of protein-protein interaction sites from docking - energy landscapes}, + energy landscapes}, journal = {Journal of Molecular Biology}, year = {2004}, volume = {335}, @@ -2349,28 +2339,28 @@ Encoding: GBK number = {3}, month = {Jan 16}, abstract = {Protein recognition is one of the most challenging and intriguing - problems in structural biology. Despite all the available structural, - sequence and biophysical information about protein-protein complexes, - the physico-chemical patterns, if any, that make a protein surface - likely to be involved in protein-protein interactions, remain elusive. - Here, we apply protein docking simulations and analysis of the interaction - energy landscapes to identify protein-protein interaction sites. - The new protocol for global docking based on multi-start global - energy optimization of an allatom model of the ligand, with detailed - receptor potentials and atomic solvation parameters optimized in - a training set of 24 complexes, explores the conformational space - around the whole receptor without restrictions. The ensembles of - the rigid-body docking solutions generated by the simulations were - subsequently used to project the docking energy landscapes onto - the protein surfaces. We found that highly populated low-energy - regions consistently corresponded to actual binding sites. The procedure - was validated on a test set of 21 known protein-protein complexes - not used in the training set. As much as 81% of the predicted high-propensity - patch residues were located correctly in the native interfaces. - This approach can guide the design of mutations on the surfaces - of proteins, provide geometrical details of a possible interaction, - and help to annotate protein surfaces in structural proteomics. - (C) 2003 Elsevier Ltd. All rights reserved.}, + problems in structural biology. Despite all the available structural, + sequence and biophysical information about protein-protein complexes, + the physico-chemical patterns, if any, that make a protein surface + likely to be involved in protein-protein interactions, remain elusive. + Here, we apply protein docking simulations and analysis of the interaction + energy landscapes to identify protein-protein interaction sites. + The new protocol for global docking based on multi-start global + energy optimization of an allatom model of the ligand, with detailed + receptor potentials and atomic solvation parameters optimized in + a training set of 24 complexes, explores the conformational space + around the whole receptor without restrictions. The ensembles of + the rigid-body docking solutions generated by the simulations were + subsequently used to project the docking energy landscapes onto + the protein surfaces. We found that highly populated low-energy + regions consistently corresponded to actual binding sites. The procedure + was validated on a test set of 21 known protein-protein complexes + not used in the training set. As much as 81% of the predicted high-propensity + patch residues were located correctly in the native interfaces. + This approach can guide the design of mutations on the surfaces + of proteins, provide geometrical details of a possible interaction, + and help to annotate protein surfaces in structural proteomics. + (C) 2003 Elsevier Ltd. All rights reserved.}, annote = {763GQ Times Cited:21 Cited References Count:59}, issn = {0022-2836}, uri = {://000188066900016}, @@ -2379,23 +2369,23 @@ Encoding: GBK @ARTICLE{Reddy2006, author = {R. A. Reddy and C. Tschierske}, title = {Bent-core liquid crystals: polar order, superstructural chirality - and spontaneous desymmetrisation in soft matter systems}, + and spontaneous desymmetrisation in soft matter systems}, journal = {Journal of Materials Chemistry}, year = {2006}, volume = {16}, pages = {907-961}, number = {10}, abstract = {An overview on the recent developments in the field of liquid crystalline - bent-core molecules (so-called banana liquid crystals) is given. - After some basic issues, dealing with general aspects of the systematisation - of the mesophases, development of polar order and chirality in this - class of LC systems and explaining some general structure-property - relationships, we focus on fascinating new developments in this - field, such as modulated, undulated and columnar phases, so-called - B7 phases, phase biaxiality, ferroelectric and antiferroelectric - polar order in smectic and columnar phases, amplification and switching - of chirality and the spontaneous formation of superstructural and - supramolecular chirality.}, + bent-core molecules (so-called banana liquid crystals) is given. + After some basic issues, dealing with general aspects of the systematisation + of the mesophases, development of polar order and chirality in this + class of LC systems and explaining some general structure-property + relationships, we focus on fascinating new developments in this + field, such as modulated, undulated and columnar phases, so-called + B7 phases, phase biaxiality, ferroelectric and antiferroelectric + polar order in smectic and columnar phases, amplification and switching + of chirality and the spontaneous formation of superstructural and + supramolecular chirality.}, annote = {021NS Times Cited:2 Cited References Count:316}, issn = {0959-9428}, uri = {://000235990500001}, @@ -2411,27 +2401,27 @@ Encoding: GBK number = {5}, month = {Sep 8}, abstract = {Backward error analysis has become an important tool for understanding - the long time behavior of numerical integration methods. This is - true in particular for the integration of Hamiltonian systems where - backward error analysis can be used to show that a symplectic method - will conserve energy over exponentially long periods of time. Such - results are typically based on two aspects of backward error analysis: - (i) It can be shown that the modified vector fields have some qualitative - properties which they share with the given problem and (ii) an estimate - is given for the difference between the best interpolating vector - field and the numerical method. These aspects have been investigated - recently, for example, by Benettin and Giorgilli in [J. Statist. - Phys., 74 (1994), pp. 1117-1143], by Hairer in [Ann. Numer. Math., - 1 (1994), pp. 107-132], and by Hairer and Lubich in [Numer. Math., - 76 (1997), pp. 441-462]. In this paper we aim at providing a unifying - framework and a simplification of the existing results and corresponding - proofs. Our approach to backward error analysis is based on a simple - recursive definition of the modified vector fields that does not - require explicit Taylor series expansion of the numerical method - and the corresponding flow maps as in the above-cited works. As - an application we discuss the long time integration of chaotic Hamiltonian - systems and the approximation of time averages along numerically - computed trajectories.}, + the long time behavior of numerical integration methods. This is + true in particular for the integration of Hamiltonian systems where + backward error analysis can be used to show that a symplectic method + will conserve energy over exponentially long periods of time. Such + results are typically based on two aspects of backward error analysis: + (i) It can be shown that the modified vector fields have some qualitative + properties which they share with the given problem and (ii) an estimate + is given for the difference between the best interpolating vector + field and the numerical method. These aspects have been investigated + recently, for example, by Benettin and Giorgilli in [J. Statist. + Phys., 74 (1994), pp. 1117-1143], by Hairer in [Ann. Numer. Math., + 1 (1994), pp. 107-132], and by Hairer and Lubich in [Numer. Math., + 76 (1997), pp. 441-462]. In this paper we aim at providing a unifying + framework and a simplification of the existing results and corresponding + proofs. Our approach to backward error analysis is based on a simple + recursive definition of the modified vector fields that does not + require explicit Taylor series expansion of the numerical method + and the corresponding flow maps as in the above-cited works. As + an application we discuss the long time integration of chaotic Hamiltonian + systems and the approximation of time averages along numerically + computed trajectories.}, annote = {237HV Times Cited:43 Cited References Count:41}, issn = {0036-1429}, uri = {://000082650600010}, @@ -2446,13 +2436,13 @@ Encoding: GBK pages = {5093-5098}, number = {48}, abstract = {The recent literature in the field of liquid crystals shows that banana-shaped - mesogenic materials represent a bewitching and stimulating field - of research that is interesting both academically and in terms of - applications. Numerous topics are open to investigation in this - area because of the rich phenomenology and new possibilities that - these materials offer. The principal concepts in this area are reviewed - along with recent results. In addition, new directions to stimulate - further research activities are highlighted.}, + mesogenic materials represent a bewitching and stimulating field + of research that is interesting both academically and in terms of + applications. Numerous topics are open to investigation in this + area because of the rich phenomenology and new possibilities that + these materials offer. The principal concepts in this area are reviewed + along with recent results. In addition, new directions to stimulate + further research activities are highlighted.}, annote = {990XA Times Cited:3 Cited References Count:72}, issn = {0959-9428}, uri = {://000233775500001}, @@ -2461,7 +2451,7 @@ Encoding: GBK @ARTICLE{Roy2005, author = {A. Roy and N. V. Madhusudana}, title = {A frustrated packing model for the B-6-B-1-SmAP(A) sequence of phases - in banana shaped molecules}, + in banana shaped molecules}, journal = {European Physical Journal E}, year = {2005}, volume = {18}, @@ -2469,16 +2459,16 @@ Encoding: GBK number = {3}, month = {Nov}, abstract = {A vast majority of compounds with bent core or banana shaped molecules - exhibit the phase sequence B-6-B-1-B-2 as the chain length is increased - in a homologous series. The B-6 phase has an intercalated fluid - lamellar structure with a layer spacing of half the molecular length. - The B-1 phase has a two dimensionally periodic rectangular columnar - structure. The B-2 phase has a monolayer fluid lamellar structure - with molecules tilted with respect to the layer normal. Neglecting - the tilt order of the molecules in the B-2 phase, we have developed - a frustrated packing model to describe this phase sequence qualitatively. - The model has some analogy with that of the frustrated smectics - exhibited by highly polar rod like molecules.}, + exhibit the phase sequence B-6-B-1-B-2 as the chain length is increased + in a homologous series. The B-6 phase has an intercalated fluid + lamellar structure with a layer spacing of half the molecular length. + The B-1 phase has a two dimensionally periodic rectangular columnar + structure. The B-2 phase has a monolayer fluid lamellar structure + with molecules tilted with respect to the layer normal. Neglecting + the tilt order of the molecules in the B-2 phase, we have developed + a frustrated packing model to describe this phase sequence qualitatively. + The model has some analogy with that of the frustrated smectics + exhibited by highly polar rod like molecules.}, annote = {985FW Times Cited:0 Cited References Count:30}, issn = {1292-8941}, uri = {://000233363300002}, @@ -2487,7 +2477,7 @@ Encoding: GBK @ARTICLE{Ryckaert1977, author = {J. P. Ryckaert and G. Ciccotti and H. J. C. Berendsen}, title = {Numerical-Integration of Cartesian Equations of Motion of a System - with Constraints - Molecular-Dynamics of N-Alkanes}, + with Constraints - Molecular-Dynamics of N-Alkanes}, journal = {Journal of Computational Physics}, year = {1977}, volume = {23}, @@ -2501,26 +2491,26 @@ Encoding: GBK @ARTICLE{Sagui1999, author = {C. Sagui and T. A. Darden}, title = {Molecular dynamics simulations of biomolecules: Long-range electrostatic - effects}, + effects}, journal = {Annual Review of Biophysics and Biomolecular Structure}, year = {1999}, volume = {28}, pages = {155-179}, abstract = {Current computer simulations of biomolecules typically make use of - classical molecular dynamics methods, as a very large number (tens - to hundreds of thousands) of atoms are involved over timescales - of many nanoseconds. The methodology for treating short-range bonded - and van der Waals interactions has matured. However, long-range - electrostatic interactions still represent a bottleneck in simulations. - In this article, we introduce the basic issues for an accurate representation - of the relevant electrostatic interactions. In spite of the huge - computational time demanded by most biomolecular systems, it is - no longer necessary to resort to uncontrolled approximations such - as the use of cutoffs. In particular, we discuss the Ewald summation - methods, the fast particle mesh methods, and the fast multipole - methods. We also review recent efforts to understand the role of - boundary conditions in systems with long-range interactions, and - conclude with a short perspective on future trends.}, + classical molecular dynamics methods, as a very large number (tens + to hundreds of thousands) of atoms are involved over timescales + of many nanoseconds. The methodology for treating short-range bonded + and van der Waals interactions has matured. However, long-range + electrostatic interactions still represent a bottleneck in simulations. + In this article, we introduce the basic issues for an accurate representation + of the relevant electrostatic interactions. In spite of the huge + computational time demanded by most biomolecular systems, it is + no longer necessary to resort to uncontrolled approximations such + as the use of cutoffs. In particular, we discuss the Ewald summation + methods, the fast particle mesh methods, and the fast multipole + methods. We also review recent efforts to understand the role of + boundary conditions in systems with long-range interactions, and + conclude with a short perspective on future trends.}, annote = {213KJ Times Cited:126 Cited References Count:73}, issn = {1056-8700}, uri = {://000081271400008}, @@ -2529,7 +2519,7 @@ Encoding: GBK @ARTICLE{Sandu1999, author = {A. Sandu and T. Schlick}, title = {Masking resonance artifacts in force-splitting methods for biomolecular - simulations by extrapolative Langevin dynamics}, + simulations by extrapolative Langevin dynamics}, journal = {Journal of Computational Physics}, year = {1999}, volume = {151}, @@ -2537,42 +2527,42 @@ Encoding: GBK number = {1}, month = {May 1}, abstract = {Numerical resonance artifacts have become recognized recently as a - limiting factor to increasing the timestep in multiple-timestep - (MTS) biomolecular dynamics simulations. At certain timesteps correlated - to internal motions (e.g., 5 fs, around half the period of the fastest - bond stretch, T-min), visible inaccuracies or instabilities can - occur. Impulse-MTS schemes are vulnerable to these resonance errors - since large energy pulses are introduced to the governing dynamics - equations when the slow forces are evaluated. We recently showed - that such resonance artifacts can be masked significantly by applying - extrapolative splitting to stochastic dynamics. Theoretical and - numerical analyses of force-splitting integrators based on the Verlet - discretization are reported here for linear models to explain these - observations and to suggest how to construct effective integrators - for biomolecular dynamics that balance stability with accuracy. - Analyses for Newtonian dynamics demonstrate the severe resonance - patterns of the Impulse splitting, with this severity worsening - with the outer timestep. Delta t: Constant Extrapolation is generally - unstable, but the disturbances do not grow with Delta t. Thus. the - stochastic extrapolative combination can counteract generic instabilities - and largely alleviate resonances with a sufficiently strong Langevin - heat-bath coupling (gamma), estimates for which are derived here - based on the fastest and slowest motion periods. These resonance - results generally hold for nonlinear test systems: a water tetramer - and solvated protein. Proposed related approaches such as Extrapolation/Correction - and Midpoint Extrapolation work better than Constant Extrapolation - only for timesteps less than T-min/2. An effective extrapolative - stochastic approach for biomolecules that balances long-timestep - stability with good accuracy for the fast subsystem is then applied - to a biomolecule using a three-class partitioning: the medium forces - are treated by Midpoint Extrapolation via position Verlet, and the - slow forces are incorporated by Constant Extrapolation. The resulting - algorithm (LN) performs well on a solvated protein system in terms - of thermodynamic properties and yields an order of magnitude speedup - with respect to single-timestep Langevin trajectories. Computed - spectral density functions also show how the Newtonian modes can - be approximated by using a small gamma in the range Of 5-20 ps(-1). - (C) 1999 Academic Press.}, + limiting factor to increasing the timestep in multiple-timestep + (MTS) biomolecular dynamics simulations. At certain timesteps correlated + to internal motions (e.g., 5 fs, around half the period of the fastest + bond stretch, T-min), visible inaccuracies or instabilities can + occur. Impulse-MTS schemes are vulnerable to these resonance errors + since large energy pulses are introduced to the governing dynamics + equations when the slow forces are evaluated. We recently showed + that such resonance artifacts can be masked significantly by applying + extrapolative splitting to stochastic dynamics. Theoretical and + numerical analyses of force-splitting integrators based on the Verlet + discretization are reported here for linear models to explain these + observations and to suggest how to construct effective integrators + for biomolecular dynamics that balance stability with accuracy. + Analyses for Newtonian dynamics demonstrate the severe resonance + patterns of the Impulse splitting, with this severity worsening + with the outer timestep. Delta t: Constant Extrapolation is generally + unstable, but the disturbances do not grow with Delta t. Thus. the + stochastic extrapolative combination can counteract generic instabilities + and largely alleviate resonances with a sufficiently strong Langevin + heat-bath coupling (gamma), estimates for which are derived here + based on the fastest and slowest motion periods. These resonance + results generally hold for nonlinear test systems: a water tetramer + and solvated protein. Proposed related approaches such as Extrapolation/Correction + and Midpoint Extrapolation work better than Constant Extrapolation + only for timesteps less than T-min/2. An effective extrapolative + stochastic approach for biomolecules that balances long-timestep + stability with good accuracy for the fast subsystem is then applied + to a biomolecule using a three-class partitioning: the medium forces + are treated by Midpoint Extrapolation via position Verlet, and the + slow forces are incorporated by Constant Extrapolation. The resulting + algorithm (LN) performs well on a solvated protein system in terms + of thermodynamic properties and yields an order of magnitude speedup + with respect to single-timestep Langevin trajectories. Computed + spectral density functions also show how the Newtonian modes can + be approximated by using a small gamma in the range Of 5-20 ps(-1). + (C) 1999 Academic Press.}, annote = {194FM Times Cited:14 Cited References Count:32}, issn = {0021-9991}, uri = {://000080181500004}, @@ -2581,7 +2571,7 @@ Encoding: GBK @ARTICLE{Satoh1996, author = {K. Satoh and S. Mita and S. Kondo}, title = {Monte Carlo simulations using the dipolar Gay-Berne model: Effect - of terminal dipole moment on mesophase formation}, + of terminal dipole moment on mesophase formation}, journal = {Chemical Physics Letters}, year = {1996}, volume = {255}, @@ -2589,12 +2579,12 @@ Encoding: GBK number = {1-3}, month = {Jun 7}, abstract = {The effects of dipole-dipole interaction on mesophase formation are - investigated with a Monte Carlo simulation using the dipolar Gay-Berne - potential. It is shown that the dipole moment at the end of a molecule - causes a shift in the nematic-isotropic transition toward higher - temperature and a spread of the temperature range of the nematic - phase and that layer structures with various interdigitations are - formed in the smectic phase.}, + investigated with a Monte Carlo simulation using the dipolar Gay-Berne + potential. It is shown that the dipole moment at the end of a molecule + causes a shift in the nematic-isotropic transition toward higher + temperature and a spread of the temperature range of the nematic + phase and that layer structures with various interdigitations are + formed in the smectic phase.}, annote = {Uq975 Times Cited:32 Cited References Count:33}, issn = {0009-2614}, uri = {://A1996UQ97500017}, @@ -2603,7 +2593,7 @@ Encoding: GBK @ARTICLE{Shen2002, author = {M. Y. Shen and K. F. Freed}, title = {Long time dynamics of met-enkephalin: Comparison of explicit and - implicit solvent models}, + implicit solvent models}, journal = {Biophysical Journal}, year = {2002}, volume = {82}, @@ -2611,24 +2601,24 @@ Encoding: GBK number = {4}, month = {Apr}, abstract = {Met-enkephalin is one of the smallest opiate peptides. Yet, its dynamical - structure and receptor docking mechanism are still not well understood. - The conformational dynamics of this neuron peptide in liquid water - are studied here by using all-atom molecular dynamics (MID) and - implicit water Langevin dynamics (LD) simulations with AMBER potential - functions and the three-site transferable intermolecular potential - (TIP3P) model for water. To achieve the same simulation length in - physical time, the full MID simulations require 200 times as much - CPU time as the implicit water LID simulations. The solvent hydrophobicity - and dielectric behavior are treated in the implicit solvent LD simulations - by using a macroscopic solvation potential, a single dielectric - constant, and atomic friction coefficients computed using the accessible - surface area method with the TIP3P model water viscosity as determined - here from MID simulations for pure TIP3P water. Both the local and - the global dynamics obtained from the implicit solvent LD simulations - agree very well with those from the explicit solvent MD simulations. - The simulations provide insights into the conformational restrictions - that are associated with the bioactivity of the opiate peptide dermorphin - for the delta-receptor.}, + structure and receptor docking mechanism are still not well understood. + The conformational dynamics of this neuron peptide in liquid water + are studied here by using all-atom molecular dynamics (MID) and + implicit water Langevin dynamics (LD) simulations with AMBER potential + functions and the three-site transferable intermolecular potential + (TIP3P) model for water. To achieve the same simulation length in + physical time, the full MID simulations require 200 times as much + CPU time as the implicit water LID simulations. The solvent hydrophobicity + and dielectric behavior are treated in the implicit solvent LD simulations + by using a macroscopic solvation potential, a single dielectric + constant, and atomic friction coefficients computed using the accessible + surface area method with the TIP3P model water viscosity as determined + here from MID simulations for pure TIP3P water. Both the local and + the global dynamics obtained from the implicit solvent LD simulations + agree very well with those from the explicit solvent MD simulations. + The simulations provide insights into the conformational restrictions + that are associated with the bioactivity of the opiate peptide dermorphin + for the delta-receptor.}, annote = {540MH Times Cited:36 Cited References Count:45}, issn = {0006-3495}, uri = {://000174932400010}, @@ -2651,7 +2641,7 @@ Encoding: GBK @ARTICLE{Shimada1993, author = {J. Shimada and H. Kaneko and T. Takada}, title = {Efficient Calculations of Coulombic Interactions in Biomolecular - Simulations with Periodic Boundary-Conditions}, + Simulations with Periodic Boundary-Conditions}, journal = {Journal of Computational Chemistry}, year = {1993}, volume = {14}, @@ -2659,22 +2649,22 @@ Encoding: GBK number = {7}, month = {Jul}, abstract = {To make improved treatments of electrostatic interactions in biomacromolecular - simulations, two possibilities are considered. The first is the - famous particle-particle and particle-mesh (PPPM) method developed - by Hockney and Eastwood, and the second is a new one developed here - in their spirit but by the use of the multipole expansion technique - suggested by Ladd. It is then numerically found that the new PPPM - method gives more accurate results for a two-particle system at - small separation of particles. Preliminary numerical examination - of the various computational methods for a single configuration - of a model BPTI-water system containing about 24,000 particles indicates - that both of the PPPM methods give far more accurate values with - reasonable computational cost than do the conventional truncation - methods. It is concluded the two PPPM methods are nearly comparable - in overall performance for the many-particle systems, although the - first method has the drawback that the accuracy in the total electrostatic - energy is not high for configurations of charged particles randomly - generated.}, + simulations, two possibilities are considered. The first is the + famous particle-particle and particle-mesh (PPPM) method developed + by Hockney and Eastwood, and the second is a new one developed here + in their spirit but by the use of the multipole expansion technique + suggested by Ladd. It is then numerically found that the new PPPM + method gives more accurate results for a two-particle system at + small separation of particles. Preliminary numerical examination + of the various computational methods for a single configuration + of a model BPTI-water system containing about 24,000 particles indicates + that both of the PPPM methods give far more accurate values with + reasonable computational cost than do the conventional truncation + methods. It is concluded the two PPPM methods are nearly comparable + in overall performance for the many-particle systems, although the + first method has the drawback that the accuracy in the total electrostatic + energy is not high for configurations of charged particles randomly + generated.}, annote = {Lh164 Times Cited:27 Cited References Count:47}, issn = {0192-8651}, uri = {://A1993LH16400011}, @@ -2690,15 +2680,15 @@ Encoding: GBK number = {24}, month = {Dec 20}, abstract = {The best simple method for Newtonian molecular dynamics is indisputably - the leapfrog Stormer-Verlet method. The appropriate generalization - to simple Langevin dynamics is unclear. An analysis is presented - comparing an 'impulse method' (kick; fluctuate; kick), the 1982 - method of van Gunsteren and Berendsen, and the Brunger-Brooks-Karplus - (BBK) method. It is shown how the impulse method and the van Gunsteren-Berendsen - methods can be implemented as efficiently as the BBK method. Other - considerations suggest that the impulse method is the best basic - method for simple Langevin dynamics, with the van Gunsteren-Berendsen - method a close contender.}, + the leapfrog Stormer-Verlet method. The appropriate generalization + to simple Langevin dynamics is unclear. An analysis is presented + comparing an 'impulse method' (kick; fluctuate; kick), the 1982 + method of van Gunsteren and Berendsen, and the Brunger-Brooks-Karplus + (BBK) method. It is shown how the impulse method and the van Gunsteren-Berendsen + methods can be implemented as efficiently as the BBK method. Other + considerations suggest that the impulse method is the best basic + method for simple Langevin dynamics, with the van Gunsteren-Berendsen + method a close contender.}, annote = {633RX Times Cited:8 Cited References Count:22}, issn = {0026-8976}, uri = {://000180297200014}, @@ -2707,7 +2697,7 @@ Encoding: GBK @ARTICLE{Skeel1997, author = {R. D. Skeel and G. H. Zhang and T. Schlick}, title = {A family of symplectic integrators: Stability, accuracy, and molecular - dynamics applications}, + dynamics applications}, journal = {Siam Journal on Scientific Computing}, year = {1997}, volume = {18}, @@ -2715,18 +2705,18 @@ Encoding: GBK number = {1}, month = {Jan}, abstract = {The following integration methods for special second-order ordinary - differential equations are studied: leapfrog, implicit midpoint, - trapezoid, Stormer-Verlet, and Cowell-Numerov. We show that all - are members, or equivalent to members, of a one-parameter family - of schemes. Some methods have more than one common form, and we - discuss a systematic enumeration of these forms. We also present - a stability and accuracy analysis based on the idea of ''modified - equations'' and a proof of symplecticness. It follows that Cowell-Numerov - and ''LIM2'' (a method proposed by Zhang and Schlick) are symplectic. - A different interpretation of the values used by these integrators - leads to higher accuracy and better energy conservation. Hence, - we suggest that the straightforward analysis of energy conservation - is misleading.}, + differential equations are studied: leapfrog, implicit midpoint, + trapezoid, Stormer-Verlet, and Cowell-Numerov. We show that all + are members, or equivalent to members, of a one-parameter family + of schemes. Some methods have more than one common form, and we + discuss a systematic enumeration of these forms. We also present + a stability and accuracy analysis based on the idea of ''modified + equations'' and a proof of symplecticness. It follows that Cowell-Numerov + and ''LIM2'' (a method proposed by Zhang and Schlick) are symplectic. + A different interpretation of the values used by these integrators + leads to higher accuracy and better energy conservation. Hence, + we suggest that the straightforward analysis of energy conservation + is misleading.}, annote = {We981 Times Cited:30 Cited References Count:35}, issn = {1064-8275}, uri = {://A1997WE98100012}, @@ -2734,9 +2724,9 @@ Encoding: GBK @ARTICLE{Tao2005, author = {Y. G. Tao and W. K. {den Otter} and J. T. Padding and J. K. G. Dhont - and W. J. Briels}, + and W. J. Briels}, title = {Brownian dynamics simulations of the self- and collective rotational - diffusion coefficients of rigid long thin rods}, + diffusion coefficients of rigid long thin rods}, journal = {Journal of Chemical Physics}, year = {2005}, volume = {122}, @@ -2744,25 +2734,25 @@ Encoding: GBK number = {24}, month = {Jun 22}, abstract = {Recently a microscopic theory for the dynamics of suspensions of long - thin rigid rods was presented, confirming and expanding the well-known - theory by Doi and Edwards [The Theory of Polymer Dynamics (Clarendon, - Oxford, 1986)] and Kuzuu [J. Phys. Soc. Jpn. 52, 3486 (1983)]. Here - this theory is put to the test by comparing it against computer - simulations. A Brownian dynamics simulation program was developed - to follow the dynamics of the rods, with a length over a diameter - ratio of 60, on the Smoluchowski time scale. The model accounts - for excluded volume interactions between rods, but neglects hydrodynamic - interactions. The self-rotational diffusion coefficients D-r(phi) - of the rods were calculated by standard methods and by a new, more - efficient method based on calculating average restoring torques. - Collective decay of orientational order was calculated by means - of equilibrium and nonequilibrium simulations. Our results show - that, for the currently accessible volume fractions, the decay times - in both cases are virtually identical. Moreover, the observed decay - of diffusion coefficients with volume fraction is much quicker than - predicted by the theory, which is attributed to an oversimplification - of dynamic correlations in the theory. (c) 2005 American Institute - of Physics.}, + thin rigid rods was presented, confirming and expanding the well-known + theory by Doi and Edwards [The Theory of Polymer Dynamics (Clarendon, + Oxford, 1986)] and Kuzuu [J. Phys. Soc. Jpn. 52, 3486 (1983)]. Here + this theory is put to the test by comparing it against computer + simulations. A Brownian dynamics simulation program was developed + to follow the dynamics of the rods, with a length over a diameter + ratio of 60, on the Smoluchowski time scale. The model accounts + for excluded volume interactions between rods, but neglects hydrodynamic + interactions. The self-rotational diffusion coefficients D-r(phi) + of the rods were calculated by standard methods and by a new, more + efficient method based on calculating average restoring torques. + Collective decay of orientational order was calculated by means + of equilibrium and nonequilibrium simulations. Our results show + that, for the currently accessible volume fractions, the decay times + in both cases are virtually identical. Moreover, the observed decay + of diffusion coefficients with volume fraction is much quicker than + predicted by the theory, which is attributed to an oversimplification + of dynamic correlations in the theory. (c) 2005 American Institute + of Physics.}, annote = {943DN Times Cited:3 Cited References Count:26}, issn = {0021-9606}, uri = {://000230332400077}, @@ -2781,8 +2771,8 @@ Encoding: GBK @ARTICLE{Tu1995, author = {K. Tu and D. J. Tobias and M. L. Klein}, title = {Constant pressure and temperature molecular dynamics simulation of - a fully hydrated liquid crystal phase dipalmitoylphosphatidylcholine - bilayer}, + a fully hydrated liquid crystal phase dipalmitoylphosphatidylcholine + bilayer}, journal = {Biophysical Journal}, year = {1995}, volume = {69}, @@ -2790,24 +2780,24 @@ Encoding: GBK number = {6}, month = {Dec}, abstract = {We report a constant pressure and temperature molecular dynamics simulation - of a fully hydrated liquid crystal (L(alpha) phase bilayer of dipalmitoylphosphatidylcholine - at 50 degrees C and 28 water molecules/lipid. We have shown that - the bilayer is stable throughout the 1550-ps simulation and have - demonstrated convergence of the system dimensions. Several important - aspects of the bilayer structure have been investigated and compared - favorably with experimental results. For example, the average positions - of specific carbon atoms along the bilayer normal agree well with - neutron diffraction data, and the electron density profile is in - accord with x-ray diffraction results. The hydrocarbon chain deuterium - order parameters agree reasonably well with NMR results for the - middles of the chains, but the simulation predicts too much order - at the chain ends. In spite of the deviations in the order parameters, - the hydrocarbon chain packing density appears to be essentially - correct, inasmuch as the area/lipid and bilayer thickness are in - agreement with the most refined experimental estimates. The deuterium - order parameters for the glycerol and choline groups, as well as - the phosphorus chemical shift anisotropy, are in qualitative agreement - with those extracted from NMR measurements.}, + of a fully hydrated liquid crystal (L(alpha) phase bilayer of dipalmitoylphosphatidylcholine + at 50 degrees C and 28 water molecules/lipid. We have shown that + the bilayer is stable throughout the 1550-ps simulation and have + demonstrated convergence of the system dimensions. Several important + aspects of the bilayer structure have been investigated and compared + favorably with experimental results. For example, the average positions + of specific carbon atoms along the bilayer normal agree well with + neutron diffraction data, and the electron density profile is in + accord with x-ray diffraction results. The hydrocarbon chain deuterium + order parameters agree reasonably well with NMR results for the + middles of the chains, but the simulation predicts too much order + at the chain ends. In spite of the deviations in the order parameters, + the hydrocarbon chain packing density appears to be essentially + correct, inasmuch as the area/lipid and bilayer thickness are in + agreement with the most refined experimental estimates. The deuterium + order parameters for the glycerol and choline groups, as well as + the phosphorus chemical shift anisotropy, are in qualitative agreement + with those extracted from NMR measurements.}, annote = {Tv018 Times Cited:108 Cited References Count:34}, issn = {0006-3495}, uri = {://A1995TV01800037}, @@ -2823,17 +2813,17 @@ Encoding: GBK number = {3}, month = {Aug 1}, abstract = {The Trotter factorization of the Liouville propagator is used to generate - new reversible molecular dynamics integrators. This strategy is - applied to derive reversible reference system propagator algorithms - (RESPA) that greatly accelerate simulations of systems with a separation - of time scales or with long range forces. The new algorithms have - all of the advantages of previous RESPA integrators but are reversible, - and more stable than those methods. These methods are applied to - a set of paradigmatic systems and are shown to be superior to earlier - methods. It is shown how the new RESPA methods are related to predictor-corrector - integrators. Finally, we show how these methods can be used to accelerate - the integration of the equations of motion of systems with Nose - thermostats.}, + new reversible molecular dynamics integrators. This strategy is + applied to derive reversible reference system propagator algorithms + (RESPA) that greatly accelerate simulations of systems with a separation + of time scales or with long range forces. The new algorithms have + all of the advantages of previous RESPA integrators but are reversible, + and more stable than those methods. These methods are applied to + a set of paradigmatic systems and are shown to be superior to earlier + methods. It is shown how the new RESPA methods are related to predictor-corrector + integrators. Finally, we show how these methods can be used to accelerate + the integration of the equations of motion of systems with Nose + thermostats.}, annote = {Je891 Times Cited:680 Cited References Count:19}, issn = {0021-9606}, uri = {://A1992JE89100044}, @@ -2850,7 +2840,7 @@ Encoding: GBK @ARTICLE{Wegener1979, author = {W.~A. Wegener, V.~J. Koester and R.~M. Dowben}, title = {A general ellipsoid can not always serve as a modle for the rotational - diffusion properties of arbitrary shaped rigid molecules}, + diffusion properties of arbitrary shaped rigid molecules}, journal = {Proc. Natl. Acad. Sci.}, year = {1979}, volume = {76}, @@ -2861,7 +2851,7 @@ Encoding: GBK @ARTICLE{Withers2003, author = {I. M. Withers}, title = {Effects of longitudinal quadrupoles on the phase behavior of a Gay-Berne - fluid}, + fluid}, journal = {Journal of Chemical Physics}, year = {2003}, volume = {119}, @@ -2869,32 +2859,32 @@ Encoding: GBK number = {19}, month = {Nov 15}, abstract = {The effects of longitudinal quadrupole moments on the formation of - liquid crystalline phases are studied by means of constant NPT Monte - Carlo simulation methods. The popular Gay-Berne model mesogen is - used as the reference fluid, which displays the phase sequences - isotropic-smectic A-smectic B and isotropic-smectic B at high (T*=2.0) - and low (T*=1.5) temperatures, respectively. With increasing quadrupole - magnitude the smectic phases are observed to be stabilized with - respect to the isotropic liquid, while the smectic B is destabilized - with respect to the smectic A. At the lower temperature, a sufficiently - large quadrupole magnitude results in the injection of the smectic - A phase into the phase sequence and the replacement of the smectic - B phase by the tilted smectic J phase. The nematic phase is also - injected into the phase sequence at both temperatures considered, - and ultimately for sufficiently large quadrupole magnitudes no coherent - layered structures were observed. The stabilization of the smectic - A phase supports the commonly held belief that, while the inclusion - of polar groups is not a prerequisite for the formation of the smectic - A phase, quadrupolar interactions help to increase the temperature - and pressure range for which the smectic A phase is observed. The - quality of the layered structure is worsened with increasing quadrupole - magnitude. This behavior, along with the injection of the nematic - phase into the phase sequence, indicate that the general tendency - of the quadrupolar interactions is to destabilize the layered structure. - A pressure dependence upon the smectic layer spacing is observed. - This behavior is in much closer agreement with experimental findings - than has been observed previously for nonpolar Gay-Berne and hard - spherocylinder models. (C) 2003 American Institute of Physics.}, + liquid crystalline phases are studied by means of constant NPT Monte + Carlo simulation methods. The popular Gay-Berne model mesogen is + used as the reference fluid, which displays the phase sequences + isotropic-smectic A-smectic B and isotropic-smectic B at high (T*=2.0) + and low (T*=1.5) temperatures, respectively. With increasing quadrupole + magnitude the smectic phases are observed to be stabilized with + respect to the isotropic liquid, while the smectic B is destabilized + with respect to the smectic A. At the lower temperature, a sufficiently + large quadrupole magnitude results in the injection of the smectic + A phase into the phase sequence and the replacement of the smectic + B phase by the tilted smectic J phase. The nematic phase is also + injected into the phase sequence at both temperatures considered, + and ultimately for sufficiently large quadrupole magnitudes no coherent + layered structures were observed. The stabilization of the smectic + A phase supports the commonly held belief that, while the inclusion + of polar groups is not a prerequisite for the formation of the smectic + A phase, quadrupolar interactions help to increase the temperature + and pressure range for which the smectic A phase is observed. The + quality of the layered structure is worsened with increasing quadrupole + magnitude. This behavior, along with the injection of the nematic + phase into the phase sequence, indicate that the general tendency + of the quadrupolar interactions is to destabilize the layered structure. + A pressure dependence upon the smectic layer spacing is observed. + This behavior is in much closer agreement with experimental findings + than has been observed previously for nonpolar Gay-Berne and hard + spherocylinder models. (C) 2003 American Institute of Physics.}, annote = {738EF Times Cited:3 Cited References Count:43}, issn = {0021-9606}, uri = {://000186273200027}, @@ -2903,7 +2893,7 @@ Encoding: GBK @ARTICLE{Wolf1999, author = {D. Wolf and P. Keblinski and S. R. Phillpot and J. Eggebrecht}, title = {Exact method for the simulation of Coulombic systems by spherically - truncated, pairwise r(-1) summation}, + truncated, pairwise r(-1) summation}, journal = {Journal of Chemical Physics}, year = {1999}, volume = {110}, @@ -2911,26 +2901,26 @@ Encoding: GBK number = {17}, month = {May 1}, abstract = {Based on a recent result showing that the net Coulomb potential in - condensed ionic systems is rather short ranged, an exact and physically - transparent method permitting the evaluation of the Coulomb potential - by direct summation over the r(-1) Coulomb pair potential is presented. - The key observation is that the problems encountered in determining - the Coulomb energy by pairwise, spherically truncated r(-1) summation - are a direct consequence of the fact that the system summed over - is practically never neutral. A simple method is developed that - achieves charge neutralization wherever the r(-1) pair potential - is truncated. This enables the extraction of the Coulomb energy, - forces, and stresses from a spherically truncated, usually charged - environment in a manner that is independent of the grouping of the - pair terms. The close connection of our approach with the Ewald - method is demonstrated and exploited, providing an efficient method - for the simulation of even highly disordered ionic systems by direct, - pairwise r(-1) summation with spherical truncation at rather short - range, i.e., a method which fully exploits the short-ranged nature - of the interactions in ionic systems. The method is validated by - simulations of crystals, liquids, and interfacial systems, such - as free surfaces and grain boundaries. (C) 1999 American Institute - of Physics. [S0021-9606(99)51517-1].}, + condensed ionic systems is rather short ranged, an exact and physically + transparent method permitting the evaluation of the Coulomb potential + by direct summation over the r(-1) Coulomb pair potential is presented. + The key observation is that the problems encountered in determining + the Coulomb energy by pairwise, spherically truncated r(-1) summation + are a direct consequence of the fact that the system summed over + is practically never neutral. A simple method is developed that + achieves charge neutralization wherever the r(-1) pair potential + is truncated. This enables the extraction of the Coulomb energy, + forces, and stresses from a spherically truncated, usually charged + environment in a manner that is independent of the grouping of the + pair terms. The close connection of our approach with the Ewald + method is demonstrated and exploited, providing an efficient method + for the simulation of even highly disordered ionic systems by direct, + pairwise r(-1) summation with spherical truncation at rather short + range, i.e., a method which fully exploits the short-ranged nature + of the interactions in ionic systems. The method is validated by + simulations of crystals, liquids, and interfacial systems, such + as free surfaces and grain boundaries. (C) 1999 American Institute + of Physics. [S0021-9606(99)51517-1].}, annote = {189PD Times Cited:70 Cited References Count:34}, issn = {0021-9606}, uri = {://000079913000008}, @@ -2949,4 +2939,3 @@ Encoding: GBK issn = {0375-9601}, uri = {://A1990EJ79800009}, } -