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@ARTICLE{2003, |
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author = {J. G. {de la Torre} and H. E. Sanchez and A. Ortega and J. G. Hernandez |
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and M. X. Fernandes and F. G. Diaz and M. C. L. Martinez}, |
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title = {Calculation of the solution properties of flexible macromolecules: |
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methods and applications}, |
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journal = {European Biophysics Journal with Biophysics Letters}, |
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year = {2003}, |
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volume = {32}, |
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pages = {477-486}, |
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number = {5}, |
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month = {Aug}, |
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abstract = {While the prediction of hydrodynamic properties of rigid particles |
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is nowadays feasible using simple and efficient computer programs, |
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the calculation of such properties and, in general, the dynamic |
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behavior of flexible macromolecules has not reached a similar situation. |
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Although the theories are available, usually the computational work |
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is done using solutions specific for each problem. We intend to |
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develop computer programs that would greatly facilitate the task |
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of predicting solution behavior of flexible macromolecules. In this |
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paper, we first present an overview of the two approaches that are |
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most practical: the Monte Carlo rigid-body treatment, and the Brownian |
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dynamics simulation technique. The Monte Carlo procedure is based |
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on the calculation of properties for instantaneous conformations |
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of the macromolecule that are regarded as if they were instantaneously |
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rigid. We describe how a Monte Carlo program can be interfaced to |
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the programs in the HYDRO suite for rigid particles, and provide |
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an example of such calculation, for a hypothetical particle: a protein |
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with two domains connected by a flexible linker. We also describe |
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briefly the essentials of Brownian dynamics, and propose a general |
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mechanical model that includes several kinds of intramolecular interactions, |
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such as bending, internal rotation, excluded volume effects, etc. |
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We provide an example of the application of this methodology to |
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the dynamics of a semiflexible, wormlike DNA.}, |
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annote = {724XK Times Cited:6 Cited References Count:64}, |
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issn = {0175-7571}, |
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uri = {<Go to ISI>://000185513400011}, |
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} |
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@ARTICLE{Alakent2005, |
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author = {B. Alakent and M. C. Camurdan and P. Doruker}, |
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title = {Hierarchical structure of the energy landscape of proteins revisited |
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by time series analysis. II. Investigation of explicit solvent effects}, |
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journal = {Journal of Chemical Physics}, |
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year = {2005}, |
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volume = {123}, |
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pages = {-}, |
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number = {14}, |
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month = {Oct 8}, |
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abstract = {Time series analysis tools are employed on the principal modes obtained |
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from the C-alpha trajectories from two independent molecular-dynamics |
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simulations of alpha-amylase inhibitor (tendamistat). Fluctuations |
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inside an energy minimum (intraminimum motions), transitions between |
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minima (interminimum motions), and relaxations in different hierarchical |
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energy levels are investigated and compared with those encountered |
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in vacuum by using different sampling window sizes and intervals. |
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The low-frequency low-indexed mode relationship, established in |
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vacuum, is also encountered in water, which shows the reliability |
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of the important dynamics information offered by principal components |
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analysis in water. It has been shown that examining a short data |
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collection period (100 ps) may result in a high population of overdamped |
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modes, while some of the low-frequency oscillations (< 10 cm(-1)) |
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can be captured in water by using a longer data collection period |
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(1200 ps). Simultaneous analysis of short and long sampling window |
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sizes gives the following picture of the effect of water on protein |
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dynamics. Water makes the protein lose its memory: future conformations |
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are less dependent on previous conformations due to the lowering |
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of energy barriers in hierarchical levels of the energy landscape. |
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In short-time dynamics (< 10 ps), damping factors extracted from |
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time series model parameters are lowered. For tendamistat, the friction |
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coefficient in the Langevin equation is found to be around 40-60 |
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cm(-1) for the low-indexed modes, compatible with literature. The |
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fact that water has increased the friction and that on the other |
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hand has lubrication effect at first sight contradicts. However, |
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this comes about because water enhances the transitions between |
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minima and forces the protein to reduce its already inherent inability |
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to maintain oscillations observed in vacuum. Some of the frequencies |
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lower than 10 cm(-1) are found to be overdamped, while those higher |
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than 20 cm(-1) are slightly increased. As for the long-time dynamics |
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in water, it is found that random-walk motion is maintained for |
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approximately 200 ps (about five times of that in vacuum) in the |
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low-indexed modes, showing the lowering of energy barriers between |
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the higher-level minima.}, |
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annote = {973OH Times Cited:1 Cited References Count:33}, |
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issn = {0021-9606}, |
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uri = {<Go to ISI>://000232532000064}, |
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} |
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@ARTICLE{Allison1991, |
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author = {S. A. Allison}, |
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title = {A Brownian Dynamics Algorithm for Arbitrary Rigid Bodies - Application |
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to Polarized Dynamic Light-Scattering}, |
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journal = {Macromolecules}, |
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year = {1991}, |
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volume = {24}, |
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pages = {530-536}, |
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number = {2}, |
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month = {Jan 21}, |
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abstract = {A Brownian dynamics algorithm is developed to simulate dynamics experiments |
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of rigid macromolecules. It is applied to polarized dynamic light |
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scattering from rodlike sturctures and from a model of a DNA fragment |
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(762 base pairs). A number of rod cases are examined in which the |
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translational anisotropy is increased form zero to a large value. |
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Simulated first cumulants as well as amplitudes and lifetimes of |
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the dynamic form factor are compared with predictions of analytic |
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theories and found to be in very good agreement with them. For DNA |
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fragments 762 base pairs in length or longer, translational anisotropy |
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does not contribute significantly to dynamic light scattering. In |
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a comparison of rigid and flexible simulations on semistiff models |
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of this fragment, it is shown directly that flexing contributes |
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to the faster decay processes probed by light scattering and that |
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the flexible model studies are in good agreement with experiment.}, |
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annote = {Eu814 Times Cited:8 Cited References Count:32}, |
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issn = {0024-9297}, |
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uri = {<Go to ISI>://A1991EU81400029}, |
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} |
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@ARTICLE{Auerbach2005, |
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author = {A. Auerbach}, |
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title = {Gating of acetylcholine receptor channels: Brownian motion across |
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a broad transition state}, |
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journal = {Proceedings of the National Academy of Sciences of the United States |
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of America}, |
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year = {2005}, |
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volume = {102}, |
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pages = {1408-1412}, |
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number = {5}, |
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month = {Feb 1}, |
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abstract = {Acetylcholine receptor channels (AChRs) are proteins that switch between |
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stable #closed# and #open# conformations. In patch clamp recordings, |
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diliganded AChR gating appears to be a simple, two-state reaction. |
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However, mutagenesis studies indicate that during gating dozens |
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of residues across the protein move asynchronously and are organized |
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into rigid body gating domains (#blocks#). Moreover, there is an |
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upper limit to the apparent channel opening rate constant. These |
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observations suggest that the gating reaction has a broad, corrugated |
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transition state region, with the maximum opening rate reflecting, |
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in part, the mean first-passage time across this ensemble. Simulations |
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reveal that a flat, isotropic energy profile for the transition |
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state can account for many of the essential features of AChR gating. |
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With this mechanism, concerted, local structural transitions that |
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occur on the broad transition state ensemble give rise to fractional |
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measures of reaction progress (Phi values) determined by rate-equilibrium |
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free energy relationship analysis. The results suggest that the |
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coarse-grained AChR gating conformational change propagates through |
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the protein with dynamics that are governed by the Brownian motion |
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of individual gating blocks.}, |
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annote = {895QF Times Cited:9 Cited References Count:33}, |
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issn = {0027-8424}, |
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uri = {<Go to ISI>://000226877300030}, |
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} |
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@ARTICLE{Banerjee2004, |
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author = {D. Banerjee and B. C. Bag and S. K. Banik and D. S. Ray}, |
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title = {Solution of quantum Langevin equation: Approximations, theoretical |
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and numerical aspects}, |
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journal = {Journal of Chemical Physics}, |
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year = {2004}, |
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volume = {120}, |
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pages = {8960-8972}, |
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number = {19}, |
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month = {May 15}, |
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abstract = {Based on a coherent state representation of noise operator and an |
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ensemble averaging procedure using Wigner canonical thermal distribution |
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for harmonic oscillators, a generalized quantum Langevin equation |
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has been recently developed [Phys. Rev. E 65, 021109 (2002); 66, |
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051106 (2002)] to derive the equations of motion for probability |
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distribution functions in c-number phase-space. We extend the treatment |
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to explore several systematic approximation schemes for the solutions |
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of the Langevin equation for nonlinear potentials for a wide range |
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of noise correlation, strength and temperature down to the vacuum |
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limit. The method is exemplified by an analytic application to harmonic |
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oscillator for arbitrary memory kernel and with the help of a numerical |
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calculation of barrier crossing, in a cubic potential to demonstrate |
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the quantum Kramers' turnover and the quantum Arrhenius plot. (C) |
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2004 American Institute of Physics.}, |
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annote = {816YY Times Cited:8 Cited References Count:35}, |
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issn = {0021-9606}, |
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uri = {<Go to ISI>://000221146400009}, |
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} |
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@ARTICLE{Barth1998, |
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author = {E. Barth and T. Schlick}, |
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title = {Overcoming stability limitations in biomolecular dynamics. I. Combining |
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force splitting via extrapolation with Langevin dynamics in LN}, |
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journal = {Journal of Chemical Physics}, |
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year = {1998}, |
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volume = {109}, |
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pages = {1617-1632}, |
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number = {5}, |
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month = {Aug 1}, |
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abstract = {We present an efficient new method termed LN for propagating biomolecular |
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dynamics according to the Langevin equation that arose fortuitously |
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upon analysis of the range of harmonic validity of our normal-mode |
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scheme LIN. LN combines force linearization with force splitting |
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techniques and disposes of LIN'S computationally intensive minimization |
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(anharmonic correction) component. Unlike the competitive multiple-timestepping |
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(MTS) schemes today-formulated to be symplectic and time-reversible-LN |
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merges the slow and fast forces via extrapolation rather than impulses; |
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the Langevin heat bath prevents systematic energy drifts. This combination |
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succeeds in achieving more significant speedups than these MTS methods |
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which are Limited by resonance artifacts to an outer timestep less |
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than some integer multiple of half the period of the fastest motion |
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(around 4-5 fs for biomolecules). We show that LN achieves very |
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good agreement with small-timestep solutions of the Langevin equation |
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in terms of thermodynamics (energy means and variances), geometry, |
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and dynamics (spectral densities) for two proteins in vacuum and |
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a large water system. Significantly, the frequency of updating the |
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slow forces extends to 48 fs or more, resulting in speedup factors |
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exceeding 10. The implementation of LN in any program that employs |
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force-splitting computations is straightforward, with only partial |
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second-derivative information required, as well as sparse Hessian/vector |
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multiplication routines. The linearization part of LN could even |
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be replaced by direct evaluation of the fast components. The application |
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of LN to biomolecular dynamics is well suited for configurational |
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sampling, thermodynamic, and structural questions. (C) 1998 American |
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Institute of Physics.}, |
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annote = {105HH Times Cited:29 Cited References Count:49}, |
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issn = {0021-9606}, |
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uri = {<Go to ISI>://000075066300006}, |
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} |
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@ARTICLE{Batcho2001, |
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author = {P. F. Batcho and T. Schlick}, |
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title = {Special stability advantages of position-Verlet over velocity-Verlet |
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in multiple-time step integration}, |
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journal = {Journal of Chemical Physics}, |
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year = {2001}, |
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volume = {115}, |
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pages = {4019-4029}, |
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number = {9}, |
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month = {Sep 1}, |
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abstract = {We present an analysis for a simple two-component harmonic oscillator |
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that compares the use of position-Verlet to velocity-Verlet for |
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multiple-time step integration. The numerical stability analysis |
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based on the impulse-Verlet splitting shows that position-Verlet |
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has enhanced stability, in terms of the largest allowable time step, |
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for cases where an ample separation of time scales exists. Numerical |
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investigations confirm the advantages of the position-Verlet scheme |
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when used for the fastest time scales of the system. Applications |
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to a biomolecule. a solvated protein, for both Newtonian and Langevin |
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dynamics echo these trends over large outer time-step regimes. (C) |
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2001 American Institute of Physics.}, |
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annote = {469KV Times Cited:6 Cited References Count:30}, |
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issn = {0021-9606}, |
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uri = {<Go to ISI>://000170813800005}, |
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} |
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@ARTICLE{Beard2003, |
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author = {D. A. Beard and T. Schlick}, |
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title = {Unbiased rotational moves for rigid-body dynamics}, |
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journal = {Biophysical Journal}, |
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year = {2003}, |
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volume = {85}, |
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pages = {2973-2976}, |
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number = {5}, |
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month = {Nov 1}, |
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abstract = {We introduce an unbiased protocol for performing rotational moves |
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in rigid-body dynamics simulations. This approach - based on the |
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analytic solution for the rotational equations of motion for an |
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orthogonal coordinate system at constant angular velocity - removes |
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deficiencies that have been largely ignored in Brownian dynamics |
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simulations, namely errors for finite rotations that result from |
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applying the noncommuting rotational matrices in an arbitrary order. |
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Our algorithm should thus replace standard approaches to rotate |
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local coordinate frames in Langevin and Brownian dynamics simulations.}, |
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annote = {736UA Times Cited:0 Cited References Count:11}, |
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issn = {0006-3495}, |
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uri = {<Go to ISI>://000186190500018}, |
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} |
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@ARTICLE{Beloborodov1998, |
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author = {I. S. Beloborodov and V. Y. Orekhov and A. S. Arseniev}, |
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title = {Effect of coupling between rotational and translational Brownian |
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motions on NMR spin relaxation: Consideration using green function |
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of rigid body diffusion}, |
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journal = {Journal of Magnetic Resonance}, |
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year = {1998}, |
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volume = {132}, |
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pages = {328-329}, |
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number = {2}, |
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month = {Jun}, |
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abstract = {Using the Green function of arbitrary rigid Brownian diffusion (Goldstein, |
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Biopolymers 33, 409-436, 1993), it was analytically shown that coupling |
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between translation and rotation diffusion degrees of freedom does |
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not affect the correlation functions relevant to the NMR intramolecular |
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relaxation. It follows that spectral densities usually used for |
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the anisotropic rotation diffusion (Woessner, J. Chem. Phys. 37, |
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647-654, 1962) can be regarded as exact in respect to the rotation-translation |
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coupling for the spin system connected with a rigid body. (C) 1998 |
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Academic Press.}, |
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annote = {Zu605 Times Cited:2 Cited References Count:6}, |
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issn = {1090-7807}, |
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uri = {<Go to ISI>://000074214800017}, |
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} |
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@ARTICLE{Berkov2005, |
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author = {D. V. Berkov and N. L. Gorn}, |
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title = {Stochastic dynamic simulations of fast remagnetization processes: |
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recent advances and applications}, |
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journal = {Journal of Magnetism and Magnetic Materials}, |
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year = {2005}, |
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volume = {290}, |
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pages = {442-448}, |
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month = {Apr}, |
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abstract = {Numerical simulations of fast remagnetization processes using stochastic |
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dynamics are widely used to study various magnetic systems. In this |
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paper, we first address several crucial methodological problems |
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of such simulations: (i) the influence of finite-element discretization |
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on simulated dynamics, (ii) choice between Ito and Stratonovich |
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stochastic calculi by the solution of micromagnetic stochastic equations |
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of motion and (iii) non-trivial correlation properties of the random |
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(thermal) field. Next, we discuss several examples to demonstrate |
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the great potential of the Langevin dynamics for studying fast remagnetization |
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processes in technically relevant applications: we present numerical |
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analysis of equilibrium magnon spectra in patterned structures, |
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study thermal noise effects on the magnetization dynamics of nanoelements |
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in pulsed fields and show some results for a remagnetization dynamics |
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induced by a spin-polarized current. (c) 2004 Elsevier B.V. All |
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rights reserved.}, |
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annote = {Part 1 Sp. Iss. SI 922KU Times Cited:2 Cited References Count:25}, |
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issn = {0304-8853}, |
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uri = {<Go to ISI>://000228837600109}, |
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} |
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@ARTICLE{Berkov2005a, |
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author = {D. V. Berkov and N. L. Gorn}, |
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title = {Magnetization precession due to a spin-polarized current in a thin |
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nanoelement: Numerical simulation study}, |
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journal = {Physical Review B}, |
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year = {2005}, |
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volume = {72}, |
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pages = {-}, |
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number = {9}, |
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month = {Sep}, |
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abstract = {In this paper a detailed numerical study (in frames of the Slonczewski |
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formalism) of magnetization oscillations driven by a spin-polarized |
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current through a thin elliptical nanoelement is presented. We show |
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that a sophisticated micromagnetic model, where a polycrystalline |
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|
|
structure of a nanoelement is taken into account, can explain qualitatively |
343 |
|
|
all most important features of the magnetization oscillation spectra |
344 |
|
|
recently observed experimentally [S. I. Kiselev , Nature 425, 380 |
345 |
|
|
(2003)], namely, existence of several equidistant spectral bands, |
346 |
|
|
sharp onset and abrupt disappearance of magnetization oscillations |
347 |
|
|
with increasing current, absence of the out-of-plane regime predicted |
348 |
|
|
by a macrospin model, and the relation between frequencies of so-called |
349 |
|
|
small-angle and quasichaotic oscillations. However, a quantitative |
350 |
|
|
agreement with experimental results (especially concerning the frequency |
351 |
|
|
of quasichaotic oscillations) could not be achieved in the region |
352 |
|
|
of reasonable parameter values, indicating that further model refinement |
353 |
|
|
is necessary for a complete understanding of the spin-driven magnetization |
354 |
|
|
precession even in this relatively simple experimental situation.}, |
355 |
|
|
annote = {969IT Times Cited:2 Cited References Count:55}, |
356 |
|
|
issn = {1098-0121}, |
357 |
|
|
uri = {<Go to ISI>://000232228500058}, |
358 |
|
|
} |
359 |
|
|
|
360 |
|
|
@ARTICLE{Berkov2002, |
361 |
|
|
author = {D. V. Berkov and N. L. Gorn and P. Gornert}, |
362 |
|
|
title = {Magnetization dynamics in nanoparticle systems: Numerical simulation |
363 |
|
|
using Langevin dynamics}, |
364 |
|
|
journal = {Physica Status Solidi a-Applied Research}, |
365 |
|
|
year = {2002}, |
366 |
|
|
volume = {189}, |
367 |
|
|
pages = {409-421}, |
368 |
|
|
number = {2}, |
369 |
|
|
month = {Feb 16}, |
370 |
|
|
abstract = {We report on recent progress achieved by the development of numerical |
371 |
|
|
methods based on the stochastic (Langevin) dynamics applied to systems |
372 |
|
|
of interacting magnetic nanoparticles. The method enables direct |
373 |
|
|
simulations of the trajectories of magnetic moments taking into |
374 |
|
|
account (i) all relevant interactions, (ii) precession dynamics, |
375 |
|
|
and (iii) temperature fluctuations included via the random (thermal) |
376 |
|
|
field. We present several novel results obtained using new methods |
377 |
|
|
developed for the solution of the Langevin equations. In particular, |
378 |
|
|
we have investigated magnetic nanodots and disordered granular systems |
379 |
|
|
of single-domain magnetic particles. For the first case we have |
380 |
|
|
calculated the spectrum and the spatial distribution of spin excitations. |
381 |
|
|
For the second system the complex ac susceptibility chi(omega, T) |
382 |
|
|
for various particle concentrations and particle anisotropies were |
383 |
|
|
computed and compared with numerous experimental results.}, |
384 |
|
|
annote = {526TF Times Cited:4 Cited References Count:37}, |
385 |
|
|
issn = {0031-8965}, |
386 |
|
|
uri = {<Go to ISI>://000174145200026}, |
387 |
|
|
} |
388 |
|
|
|
389 |
|
|
@ARTICLE{Bernal1980, |
390 |
|
|
author = {J.M. Bernal and J. G. {de la Torre}}, |
391 |
|
|
title = {Transport Properties and Hydrodynamic Centers of Rigid Macromolecules |
392 |
|
|
with Arbitrary Shape}, |
393 |
|
|
journal = {Biopolymers}, |
394 |
|
|
year = {1980}, |
395 |
|
|
volume = {19}, |
396 |
|
|
pages = {751-766}, |
397 |
|
|
} |
398 |
|
|
|
399 |
|
|
@ARTICLE{Brunger1984, |
400 |
|
|
author = {A. Brunger and C. L. Brooks and M. Karplus}, |
401 |
|
|
title = {Stochastic Boundary-Conditions for Molecular-Dynamics Simulations |
402 |
|
|
of St2 Water}, |
403 |
|
|
journal = {Chemical Physics Letters}, |
404 |
|
|
year = {1984}, |
405 |
|
|
volume = {105}, |
406 |
|
|
pages = {495-500}, |
407 |
|
|
number = {5}, |
408 |
|
|
annote = {Sm173 Times Cited:143 Cited References Count:22}, |
409 |
|
|
issn = {0009-2614}, |
410 |
|
|
uri = {<Go to ISI>://A1984SM17300007}, |
411 |
|
|
} |
412 |
|
|
|
413 |
|
|
@ARTICLE{Chin2004, |
414 |
|
|
author = {S. A. Chin}, |
415 |
|
|
title = {Dynamical multiple-time stepping methods for overcoming resonance |
416 |
|
|
instabilities}, |
417 |
|
|
journal = {Journal of Chemical Physics}, |
418 |
|
|
year = {2004}, |
419 |
|
|
volume = {120}, |
420 |
|
|
pages = {8-13}, |
421 |
|
|
number = {1}, |
422 |
|
|
month = {Jan 1}, |
423 |
|
|
abstract = {Current molecular dynamics simulations of biomolecules using multiple |
424 |
|
|
time steps to update the slowly changing force are hampered by instabilities |
425 |
|
|
beginning at time steps near the half period of the fastest vibrating |
426 |
|
|
mode. These #resonance# instabilities have became a critical barrier |
427 |
|
|
preventing the long time simulation of biomolecular dynamics. Attempts |
428 |
|
|
to tame these instabilities by altering the slowly changing force |
429 |
|
|
and efforts to damp them out by Langevin dynamics do not address |
430 |
|
|
the fundamental cause of these instabilities. In this work, we trace |
431 |
|
|
the instability to the nonanalytic character of the underlying spectrum |
432 |
|
|
and show that a correct splitting of the Hamiltonian, which renders |
433 |
|
|
the spectrum analytic, restores stability. The resulting Hamiltonian |
434 |
|
|
dictates that in addition to updating the momentum due to the slowly |
435 |
|
|
changing force, one must also update the position with a modified |
436 |
|
|
mass. Thus multiple-time stepping must be done dynamically. (C) |
437 |
|
|
2004 American Institute of Physics.}, |
438 |
|
|
annote = {757TK Times Cited:1 Cited References Count:22}, |
439 |
|
|
issn = {0021-9606}, |
440 |
|
|
uri = {<Go to ISI>://000187577400003}, |
441 |
|
|
} |
442 |
|
|
|
443 |
|
|
@ARTICLE{Cui2003, |
444 |
|
|
author = {B. X. Cui and M. Y. Shen and K. F. Freed}, |
445 |
|
|
title = {Folding and misfolding of the papillomavirus E6 interacting peptide |
446 |
|
|
E6ap}, |
447 |
|
|
journal = {Proceedings of the National Academy of Sciences of the United States |
448 |
|
|
of America}, |
449 |
|
|
year = {2003}, |
450 |
|
|
volume = {100}, |
451 |
|
|
pages = {7087-7092}, |
452 |
|
|
number = {12}, |
453 |
|
|
month = {Jun 10}, |
454 |
|
|
abstract = {All-atom Langevin dynamics simulations have been performed to study |
455 |
|
|
the folding pathways of the 18-residue binding domain fragment E6ap |
456 |
|
|
of the human papillomavirus E6 interacting peptide. Six independent |
457 |
|
|
folding trajectories, with a total duration of nearly 2 mus, all |
458 |
|
|
lead to the same native state in which the E6ap adopts a fluctuating |
459 |
|
|
a-helix structure in the central portion (Ser-4-Leu-13) but with |
460 |
|
|
very flexible N and C termini. Simulations starting from different |
461 |
|
|
core configurations exhibit the E6ap folding dynamics as either |
462 |
|
|
a two- or three-state folder with an intermediate misfolded state. |
463 |
|
|
The essential leucine hydrophobic core (Leu-9, Leu-12, and Leu-13) |
464 |
|
|
is well conserved in the native-state structure but absent in the |
465 |
|
|
intermediate structure, suggesting that the leucine core is not |
466 |
|
|
only essential for the binding activity of E6ap but also important |
467 |
|
|
for the stability of the native structure. The free energy landscape |
468 |
|
|
reveals a significant barrier between the basins separating the |
469 |
|
|
native and misfolded states. We also discuss the various underlying |
470 |
|
|
forces that drive the peptide into its native state.}, |
471 |
|
|
annote = {689LC Times Cited:3 Cited References Count:48}, |
472 |
|
|
issn = {0027-8424}, |
473 |
|
|
uri = {<Go to ISI>://000183493500037}, |
474 |
|
|
} |
475 |
|
|
|
476 |
|
|
@ARTICLE{Denisov2003, |
477 |
|
|
author = {S. I. Denisov and T. V. Lyutyy and K. N. Trohidou}, |
478 |
|
|
title = {Magnetic relaxation in finite two-dimensional nanoparticle ensembles}, |
479 |
|
|
journal = {Physical Review B}, |
480 |
|
|
year = {2003}, |
481 |
|
|
volume = {67}, |
482 |
|
|
pages = {-}, |
483 |
|
|
number = {1}, |
484 |
|
|
month = {Jan 1}, |
485 |
|
|
abstract = {We study the slow phase of thermally activated magnetic relaxation |
486 |
|
|
in finite two-dimensional ensembles of dipolar interacting ferromagnetic |
487 |
|
|
nanoparticles whose easy axes of magnetization are perpendicular |
488 |
|
|
to the distribution plane. We develop a method to numerically simulate |
489 |
|
|
the magnetic relaxation for the case that the smallest heights of |
490 |
|
|
the potential barriers between the equilibrium directions of the |
491 |
|
|
nanoparticle magnetic moments are much larger than the thermal energy. |
492 |
|
|
Within this framework, we analyze in detail the role that the correlations |
493 |
|
|
of the nanoparticle magnetic moments and the finite size of the |
494 |
|
|
nanoparticle ensemble play in magnetic relaxation.}, |
495 |
|
|
annote = {642XH Times Cited:11 Cited References Count:31}, |
496 |
|
|
issn = {1098-0121}, |
497 |
|
|
uri = {<Go to ISI>://000180830400056}, |
498 |
|
|
} |
499 |
|
|
|
500 |
|
|
@ARTICLE{Derreumaux1998, |
501 |
|
|
author = {P. Derreumaux and T. Schlick}, |
502 |
|
|
title = {The loop opening/closing motion of the enzyme triosephosphate isomerase}, |
503 |
|
|
journal = {Biophysical Journal}, |
504 |
|
|
year = {1998}, |
505 |
|
|
volume = {74}, |
506 |
|
|
pages = {72-81}, |
507 |
|
|
number = {1}, |
508 |
|
|
month = {Jan}, |
509 |
|
|
abstract = {To explore the origin of the large-scale motion of triosephosphate |
510 |
|
|
isomerase's flexible loop (residues 166 to 176) at the active site, |
511 |
|
|
several simulation protocols are employed both for the free enzyme |
512 |
|
|
in vacuo and for the free enzyme with some solvent modeling: high-temperature |
513 |
|
|
Langevin dynamics simulations, sampling by a #dynamics##driver# |
514 |
|
|
approach, and potential-energy surface calculations. Our focus is |
515 |
|
|
on obtaining the energy barrier to the enzyme's motion and establishing |
516 |
|
|
the nature of the loop movement. Previous calculations did not determine |
517 |
|
|
this energy barrier and the effect of solvent on the barrier. High-temperature |
518 |
|
|
molecular dynamics simulations and crystallographic studies have |
519 |
|
|
suggested a rigid-body motion with two hinges located at both ends |
520 |
|
|
of the loop; Brownian dynamics simulations at room temperature pointed |
521 |
|
|
to a very flexible behavior. The present simulations and analyses |
522 |
|
|
reveal that although solute/solvent hydrogen bonds play a crucial |
523 |
|
|
role in lowering the energy along the pathway, there still remains |
524 |
|
|
a high activation barrier, This finding clearly indicates that, |
525 |
|
|
if the loop opens and closes in the absence of a substrate at standard |
526 |
|
|
conditions (e.g., room temperature, appropriate concentration of |
527 |
|
|
isomerase), the time scale for transition is not in the nanosecond |
528 |
|
|
but rather the microsecond range. Our results also indicate that |
529 |
|
|
in the context of spontaneous opening in the free enzyme, the motion |
530 |
|
|
is of rigid-body type and that the specific interaction between |
531 |
|
|
residues Ala(176) and Tyr(208) plays a crucial role in the loop |
532 |
|
|
opening/closing mechanism.}, |
533 |
|
|
annote = {Zl046 Times Cited:30 Cited References Count:29}, |
534 |
|
|
issn = {0006-3495}, |
535 |
|
|
uri = {<Go to ISI>://000073393400009}, |
536 |
|
|
} |
537 |
|
|
|
538 |
|
|
@ARTICLE{Edwards2005, |
539 |
|
|
author = {S. A. Edwards and D. R. M. Williams}, |
540 |
|
|
title = {Stretching a single diblock copolymer in a selective solvent: Langevin |
541 |
|
|
dynamics simulations}, |
542 |
|
|
journal = {Macromolecules}, |
543 |
|
|
year = {2005}, |
544 |
|
|
volume = {38}, |
545 |
|
|
pages = {10590-10595}, |
546 |
|
|
number = {25}, |
547 |
|
|
month = {Dec 13}, |
548 |
|
|
abstract = {Using the Langevin dynamics technique, we have carried out simulations |
549 |
|
|
of a single-chain flexible diblock copolymer. The polymer consists |
550 |
|
|
of two blocks of equal length, one very poorly solvated and the |
551 |
|
|
other close to theta-conditions. We study what happens when such |
552 |
|
|
a polymer is stretched, for a range of different stretching speeds, |
553 |
|
|
and correlate our observations with features in the plot of force |
554 |
|
|
vs extension. We find that at slow speeds this force profile does |
555 |
|
|
not increase monotonically, in disagreement with earlier predictions, |
556 |
|
|
and that at high speeds there is a strong dependence on which end |
557 |
|
|
of the polymer is pulled, as well as a high level of hysteresis.}, |
558 |
|
|
annote = {992EC Times Cited:0 Cited References Count:13}, |
559 |
|
|
issn = {0024-9297}, |
560 |
|
|
uri = {<Go to ISI>://000233866200035}, |
561 |
|
|
} |
562 |
|
|
|
563 |
|
|
@ARTICLE{Ermak1978, |
564 |
|
|
author = {D. L. Ermak and J. A. Mccammon}, |
565 |
|
|
title = {Brownian Dynamics with Hydrodynamic Interactions}, |
566 |
|
|
journal = {Journal of Chemical Physics}, |
567 |
|
|
year = {1978}, |
568 |
|
|
volume = {69}, |
569 |
|
|
pages = {1352-1360}, |
570 |
|
|
number = {4}, |
571 |
|
|
annote = {Fp216 Times Cited:785 Cited References Count:42}, |
572 |
|
|
issn = {0021-9606}, |
573 |
|
|
uri = {<Go to ISI>://A1978FP21600004}, |
574 |
|
|
} |
575 |
|
|
|
576 |
|
|
@ARTICLE{Fernandes2002, |
577 |
|
|
author = {M. X. Fernandes and J. G. {de la Torre}}, |
578 |
|
|
title = {Brownian dynamics simulation of rigid particles of arbitrary shape |
579 |
|
|
in external fields}, |
580 |
|
|
journal = {Biophysical Journal}, |
581 |
|
|
year = {2002}, |
582 |
|
|
volume = {83}, |
583 |
|
|
pages = {3039-3048}, |
584 |
|
|
number = {6}, |
585 |
|
|
month = {Dec}, |
586 |
|
|
abstract = {We have developed a Brownian dynamics simulation algorithm to generate |
587 |
|
|
Brownian trajectories of an isolated, rigid particle of arbitrary |
588 |
|
|
shape in the presence of electric fields or any other external agents. |
589 |
|
|
Starting from the generalized diffusion tensor, which can be calculated |
590 |
|
|
with the existing HYDRO software, the new program BROWNRIG (including |
591 |
|
|
a case-specific subprogram for the external agent) carries out a |
592 |
|
|
simulation that is analyzed later to extract the observable dynamic |
593 |
|
|
properties. We provide a variety of examples of utilization of this |
594 |
|
|
method, which serve as tests of its performance, and also illustrate |
595 |
|
|
its applicability. Examples include free diffusion, transport in |
596 |
|
|
an electric field, and diffusion in a restricting environment.}, |
597 |
|
|
annote = {633AD Times Cited:2 Cited References Count:43}, |
598 |
|
|
issn = {0006-3495}, |
599 |
|
|
uri = {<Go to ISI>://000180256300012}, |
600 |
|
|
} |
601 |
|
|
|
602 |
|
|
@ARTICLE{Gelin1999, |
603 |
|
|
author = {M. F. Gelin}, |
604 |
|
|
title = {Inertial effects in the Brownian dynamics with rigid constraints}, |
605 |
|
|
journal = {Macromolecular Theory and Simulations}, |
606 |
|
|
year = {1999}, |
607 |
|
|
volume = {8}, |
608 |
|
|
pages = {529-543}, |
609 |
|
|
number = {6}, |
610 |
|
|
month = {Nov}, |
611 |
|
|
abstract = {To investigate the influence of inertial effects on the dynamics of |
612 |
|
|
an assembly of beads subjected to rigid constraints and placed in |
613 |
|
|
a buffer medium, a convenient method to introduce suitable generalized |
614 |
|
|
coordinates is presented. Without any restriction on the nature |
615 |
|
|
of the soft forces involved (both stochastic and deterministic), |
616 |
|
|
pertinent Langevin equations are derived. Provided that the Brownian |
617 |
|
|
forces are Gaussian and Markovian, the corresponding Fokker-Planck |
618 |
|
|
equation (FPE) is obtained in the complete phase space of generalized |
619 |
|
|
coordinates and momenta. The correct short time behavior for correlation |
620 |
|
|
functions (CFs) of generalized coordinates is established, and the |
621 |
|
|
diffusion equation with memory (DEM) is deduced from the FPE in |
622 |
|
|
the high friction Limit. The DEM is invoked to perform illustrative |
623 |
|
|
calculations in two dimensions of the orientational CFs for once |
624 |
|
|
broken nonrigid rods immobilized on a surface. These calculations |
625 |
|
|
reveal that the CFs under certain conditions exhibit an oscillatory |
626 |
|
|
behavior, which is irreproducible within the standard diffusion |
627 |
|
|
equation. Several methods are considered for the approximate solution |
628 |
|
|
of the DEM, and their application to three dimensional DEMs is discussed.}, |
629 |
|
|
annote = {257MM Times Cited:2 Cited References Count:82}, |
630 |
|
|
issn = {1022-1344}, |
631 |
|
|
uri = {<Go to ISI>://000083785700002}, |
632 |
|
|
} |
633 |
|
|
|
634 |
|
|
@ARTICLE{Gray2003, |
635 |
|
|
author = {J. J. Gray and S. Moughon and C. Wang and O. Schueler-Furman and |
636 |
|
|
B. Kuhlman and C. A. Rohl and D. Baker}, |
637 |
|
|
title = {Protein-protein docking with simultaneous optimization of rigid-body |
638 |
|
|
displacement and side-chain conformations}, |
639 |
|
|
journal = {Journal of Molecular Biology}, |
640 |
|
|
year = {2003}, |
641 |
|
|
volume = {331}, |
642 |
|
|
pages = {281-299}, |
643 |
|
|
number = {1}, |
644 |
|
|
month = {Aug 1}, |
645 |
|
|
abstract = {Protein-protein docking algorithms provide a means to elucidate structural |
646 |
|
|
details for presently unknown complexes. Here, we present and evaluate |
647 |
|
|
a new method to predict protein-protein complexes from the coordinates |
648 |
|
|
of the unbound monomer components. The method employs a low-resolution, |
649 |
|
|
rigid-body, Monte Carlo search followed by simultaneous optimization |
650 |
|
|
of backbone displacement and side-chain conformations using Monte |
651 |
|
|
Carlo minimization. Up to 10(5) independent simulations are carried |
652 |
|
|
out, and the resulting #decoys# are ranked using an energy function |
653 |
|
|
dominated by van der Waals interactions, an implicit solvation model, |
654 |
|
|
and an orientation-dependent hydrogen bonding potential. Top-ranking |
655 |
|
|
decoys are clustered to select the final predictions. Small-perturbation |
656 |
|
|
studies reveal the formation of binding funnels in 42 of 54 cases |
657 |
|
|
using coordinates derived from the bound complexes and in 32 of |
658 |
|
|
54 cases using independently determined coordinates of one or both |
659 |
|
|
monomers. Experimental binding affinities correlate with the calculated |
660 |
|
|
score function and explain the predictive success or failure of |
661 |
|
|
many targets. Global searches using one or both unbound components |
662 |
|
|
predict at least 25% of the native residue-residue contacts in 28 |
663 |
|
|
of the 32 cases where binding funnels exist. The results suggest |
664 |
|
|
that the method may soon be useful for generating models of biologically |
665 |
|
|
important complexes from the structures of the isolated components, |
666 |
|
|
but they also highlight the challenges that must be met to achieve |
667 |
|
|
consistent and accurate prediction of protein-protein interactions. |
668 |
|
|
(C) 2003 Elsevier Ltd. All rights reserved.}, |
669 |
|
|
annote = {704QL Times Cited:48 Cited References Count:60}, |
670 |
|
|
issn = {0022-2836}, |
671 |
|
|
uri = {<Go to ISI>://000184351300022}, |
672 |
|
|
} |
673 |
|
|
|
674 |
|
|
@ARTICLE{Hao1993, |
675 |
|
|
author = {M. H. Hao and M. R. Pincus and S. Rackovsky and H. A. Scheraga}, |
676 |
|
|
title = {Unfolding and Refolding of the Native Structure of Bovine Pancreatic |
677 |
|
|
Trypsin-Inhibitor Studied by Computer-Simulations}, |
678 |
|
|
journal = {Biochemistry}, |
679 |
|
|
year = {1993}, |
680 |
|
|
volume = {32}, |
681 |
|
|
pages = {9614-9631}, |
682 |
|
|
number = {37}, |
683 |
|
|
month = {Sep 21}, |
684 |
|
|
abstract = {A new procedure for studying the folding and unfolding of proteins, |
685 |
|
|
with an application to bovine pancreatic trypsin inhibitor (BPTI), |
686 |
|
|
is reported. The unfolding and refolding of the native structure |
687 |
|
|
of the protein are characterized by the dimensions of the protein, |
688 |
|
|
expressed in terms of the three principal radii of the structure |
689 |
|
|
considered as an ellipsoid. A dynamic equation, describing the variations |
690 |
|
|
of the principal radii on the unfolding path, and a numerical procedure |
691 |
|
|
to solve this equation are proposed. Expanded and distorted conformations |
692 |
|
|
are refolded to the native structure by a dimensional-constraint |
693 |
|
|
energy minimization procedure. A unique and reproducible unfolding |
694 |
|
|
pathway for an intermediate of BPTI lacking the [30,51] disulfide |
695 |
|
|
bond is obtained. The resulting unfolded conformations are extended; |
696 |
|
|
they contain near-native local structure, but their longest principal |
697 |
|
|
radii are more than 2.5 times greater than that of the native structure. |
698 |
|
|
The most interesting finding is that the majority of expanded conformations, |
699 |
|
|
generated under various conditions, can be refolded closely to the |
700 |
|
|
native structure, as measured by the correct overall chain fold, |
701 |
|
|
by the rms deviations from the native structure of only 1.9-3.1 |
702 |
|
|
angstrom, and by the energy differences of about 10 kcal/mol from |
703 |
|
|
the native structure. Introduction of the [30,51] disulfide bond |
704 |
|
|
at this stage, followed by minimization, improves the closeness |
705 |
|
|
of the refolded structures to the native structure, reducing the |
706 |
|
|
rms deviations to 0.9-2.0 angstrom. The unique refolding of these |
707 |
|
|
expanded structures over such a large conformational space implies |
708 |
|
|
that the folding is strongly dictated by the interactions in the |
709 |
|
|
amino acid sequence of BPTI. The simulations indicate that, under |
710 |
|
|
conditions that favor a compact structure as mimicked by the volume |
711 |
|
|
constraints in our algorithm; the expanded conformations have a |
712 |
|
|
strong tendency to move toward the native structure; therefore, |
713 |
|
|
they probably would be favorable folding intermediates. The results |
714 |
|
|
presented here support a general model for protein folding, i.e., |
715 |
|
|
progressive formation of partially folded structural units, followed |
716 |
|
|
by collapse to the compact native structure. The general applicability |
717 |
|
|
of the procedure is also discussed.}, |
718 |
|
|
annote = {Ly294 Times Cited:27 Cited References Count:57}, |
719 |
|
|
issn = {0006-2960}, |
720 |
|
|
uri = {<Go to ISI>://A1993LY29400014}, |
721 |
|
|
} |
722 |
|
|
|
723 |
|
|
@ARTICLE{Hinsen2000, |
724 |
|
|
author = {K. Hinsen and A. J. Petrescu and S. Dellerue and M. C. Bellissent-Funel |
725 |
|
|
and G. R. Kneller}, |
726 |
|
|
title = {Harmonicity in slow protein dynamics}, |
727 |
|
|
journal = {Chemical Physics}, |
728 |
|
|
year = {2000}, |
729 |
|
|
volume = {261}, |
730 |
|
|
pages = {25-37}, |
731 |
|
|
number = {1-2}, |
732 |
|
|
month = {Nov 1}, |
733 |
|
|
abstract = {The slow dynamics of proteins around its native folded state is usually |
734 |
|
|
described by diffusion in a strongly anharmonic potential. In this |
735 |
|
|
paper, we try to understand the form and origin of the anharmonicities, |
736 |
|
|
with the principal aim of gaining a better understanding of the |
737 |
|
|
principal motion types, but also in order to develop more efficient |
738 |
|
|
numerical methods for simulating neutron scattering spectra of large |
739 |
|
|
proteins. First, we decompose a molecular dynamics (MD) trajectory |
740 |
|
|
of 1.5 ns for a C-phycocyanin dimer surrounded by a layer of water |
741 |
|
|
into three contributions that we expect to be independent: the global |
742 |
|
|
motion of the residues, the rigid-body motion of the sidechains |
743 |
|
|
relative to the backbone, and the internal deformations of the sidechains. |
744 |
|
|
We show that they are indeed almost independent by verifying the |
745 |
|
|
factorization of the incoherent intermediate scattering function. |
746 |
|
|
Then, we show that the global residue motions, which include all |
747 |
|
|
large-scale backbone motions, can be reproduced by a simple harmonic |
748 |
|
|
model which contains two contributions: a short-time vibrational |
749 |
|
|
term, described by a standard normal mode calculation in a local |
750 |
|
|
minimum, and a long-time diffusive term, described by Brownian motion |
751 |
|
|
in an effective harmonic potential. The potential and the friction |
752 |
|
|
constants were fitted to the MD data. The major anharmonic contribution |
753 |
|
|
to the incoherent intermediate scattering function comes from the |
754 |
|
|
rigid-body diffusion of the sidechains. This model can be used to |
755 |
|
|
calculate scattering functions for large proteins and for long-time |
756 |
|
|
scales very efficiently, and thus provides a useful complement to |
757 |
|
|
MD simulations, which are best suited for detailed studies on smaller |
758 |
|
|
systems or for shorter time scales. (C) 2000 Elsevier Science B.V. |
759 |
|
|
All rights reserved.}, |
760 |
|
|
annote = {Sp. Iss. SI 368MT Times Cited:16 Cited References Count:31}, |
761 |
|
|
issn = {0301-0104}, |
762 |
|
|
uri = {<Go to ISI>://000090121700003}, |
763 |
|
|
} |
764 |
|
|
|
765 |
|
|
@ARTICLE{Izaguirre2001, |
766 |
|
|
author = {J. A. Izaguirre and D. P. Catarello and J. M. Wozniak and R. D. Skeel}, |
767 |
|
|
title = {Langevin stabilization of molecular dynamics}, |
768 |
|
|
journal = {Journal of Chemical Physics}, |
769 |
|
|
year = {2001}, |
770 |
|
|
volume = {114}, |
771 |
|
|
pages = {2090-2098}, |
772 |
|
|
number = {5}, |
773 |
|
|
month = {Feb 1}, |
774 |
|
|
abstract = {In this paper we show the possibility of using very mild stochastic |
775 |
|
|
damping to stabilize long time step integrators for Newtonian molecular |
776 |
|
|
dynamics. More specifically, stable and accurate integrations are |
777 |
|
|
obtained for damping coefficients that are only a few percent of |
778 |
|
|
the natural decay rate of processes of interest, such as the velocity |
779 |
|
|
autocorrelation function. Two new multiple time stepping integrators, |
780 |
|
|
Langevin Molly (LM) and Brunger-Brooks-Karplus-Molly (BBK-M), are |
781 |
|
|
introduced in this paper. Both use the mollified impulse method |
782 |
|
|
for the Newtonian term. LM uses a discretization of the Langevin |
783 |
|
|
equation that is exact for the constant force, and BBK-M uses the |
784 |
|
|
popular Brunger-Brooks-Karplus integrator (BBK). These integrators, |
785 |
|
|
along with an extrapolative method called LN, are evaluated across |
786 |
|
|
a wide range of damping coefficient values. When large damping coefficients |
787 |
|
|
are used, as one would for the implicit modeling of solvent molecules, |
788 |
|
|
the method LN is superior, with LM closely following. However, with |
789 |
|
|
mild damping of 0.2 ps(-1), LM produces the best results, allowing |
790 |
|
|
long time steps of 14 fs in simulations containing explicitly modeled |
791 |
|
|
flexible water. With BBK-M and the same damping coefficient, time |
792 |
|
|
steps of 12 fs are possible for the same system. Similar results |
793 |
|
|
are obtained for a solvated protein-DNA simulation of estrogen receptor |
794 |
|
|
ER with estrogen response element ERE. A parallel version of BBK-M |
795 |
|
|
runs nearly three times faster than the Verlet-I/r-RESPA (reversible |
796 |
|
|
reference system propagator algorithm) when using the largest stable |
797 |
|
|
time step on each one, and it also parallelizes well. The computation |
798 |
|
|
of diffusion coefficients for flexible water and ER/ERE shows that |
799 |
|
|
when mild damping of up to 0.2 ps-1 is used the dynamics are not |
800 |
|
|
significantly distorted. (C) 2001 American Institute of Physics.}, |
801 |
|
|
annote = {397CQ Times Cited:14 Cited References Count:36}, |
802 |
|
|
issn = {0021-9606}, |
803 |
|
|
uri = {<Go to ISI>://000166676100020}, |
804 |
|
|
} |
805 |
|
|
|
806 |
|
|
@ARTICLE{Klimov1997, |
807 |
|
|
author = {D. K. Klimov and D. Thirumalai}, |
808 |
|
|
title = {Viscosity dependence of the folding rates of proteins}, |
809 |
|
|
journal = {Physical Review Letters}, |
810 |
|
|
year = {1997}, |
811 |
|
|
volume = {79}, |
812 |
|
|
pages = {317-320}, |
813 |
|
|
number = {2}, |
814 |
|
|
month = {Jul 14}, |
815 |
|
|
abstract = {The viscosity (eta) dependence of the folding rates for four sequences |
816 |
|
|
(the native state of three sequences is a beta sheet, while the |
817 |
|
|
fourth forms an alpha helix) is calculated for off-lattice models |
818 |
|
|
of proteins. Assuming that the dynamics is given by the Langevin |
819 |
|
|
equation, we show that the folding rates increase linearly at low |
820 |
|
|
viscosities eta, decrease as 1/eta at large eta, and have a maximum |
821 |
|
|
at intermediate values. The Kramers' theory of barrier crossing |
822 |
|
|
provides a quantitative fit of the numerical results. By mapping |
823 |
|
|
the simulation results to real proteins we estimate that for optimized |
824 |
|
|
sequences the time scale for forming a four turn alpha-helix topology |
825 |
|
|
is about 500 ns, whereas for beta sheet it is about 10 mu s.}, |
826 |
|
|
annote = {Xk293 Times Cited:77 Cited References Count:17}, |
827 |
|
|
issn = {0031-9007}, |
828 |
|
|
uri = {<Go to ISI>://A1997XK29300035}, |
829 |
|
|
} |
830 |
|
|
|
831 |
|
|
@ARTICLE{Liwo2005, |
832 |
|
|
author = {A. Liwo and M. Khalili and H. A. Scheraga}, |
833 |
|
|
title = {Ab initio simulations of protein folding pathways by molecular dynamics |
834 |
|
|
with the united-residue (UNRES) model of polypeptide chains}, |
835 |
|
|
journal = {Febs Journal}, |
836 |
|
|
year = {2005}, |
837 |
|
|
volume = {272}, |
838 |
|
|
pages = {359-360}, |
839 |
|
|
month = {Jul}, |
840 |
|
|
annote = {Suppl. 1 005MG Times Cited:0 Cited References Count:0}, |
841 |
|
|
issn = {1742-464X}, |
842 |
|
|
uri = {<Go to ISI>://000234826102043}, |
843 |
|
|
} |
844 |
|
|
|
845 |
|
|
@ARTICLE{Mielke2004, |
846 |
|
|
author = {S. P. Mielke and W. H. Fink and V. V. Krishnan and N. Gronbech-Jensen |
847 |
|
|
and C. J. Benham}, |
848 |
|
|
title = {Transcription-driven twin supercoiling of a DNA loop: A Brownian |
849 |
|
|
dynamics study}, |
850 |
|
|
journal = {Journal of Chemical Physics}, |
851 |
|
|
year = {2004}, |
852 |
|
|
volume = {121}, |
853 |
|
|
pages = {8104-8112}, |
854 |
|
|
number = {16}, |
855 |
|
|
month = {Oct 22}, |
856 |
|
|
abstract = {The torque generated by RNA polymerase as it tracks along double-stranded |
857 |
|
|
DNA can potentially induce long-range structural deformations integral |
858 |
|
|
to mechanisms of biological significance in both prokaryotes and |
859 |
|
|
eukaryotes. In this paper, we introduce a dynamic computer model |
860 |
|
|
for investigating this phenomenon. Duplex DNA is represented as |
861 |
|
|
a chain of hydrodynamic beads interacting through potentials of |
862 |
|
|
linearly elastic stretching, bending, and twisting, as well as excluded |
863 |
|
|
volume. The chain, linear when relaxed, is looped to form two open |
864 |
|
|
but topologically constrained subdomains. This permits the dynamic |
865 |
|
|
introduction of torsional stress via a centrally applied torque. |
866 |
|
|
We simulate by Brownian dynamics the 100 mus response of a 477-base |
867 |
|
|
pair B-DNA template to the localized torque generated by the prokaryotic |
868 |
|
|
transcription ensemble. Following a sharp rise at early times, the |
869 |
|
|
distributed twist assumes a nearly constant value in both subdomains, |
870 |
|
|
and a succession of supercoiling deformations occurs as superhelical |
871 |
|
|
stress is increasingly partitioned to writhe. The magnitude of writhe |
872 |
|
|
surpasses that of twist before also leveling off when the structure |
873 |
|
|
reaches mechanical equilibrium with the torsional load. Superhelicity |
874 |
|
|
is simultaneously right handed in one subdomain and left handed |
875 |
|
|
in the other, as predicted by the #transcription-induced##twin-supercoiled-domain# |
876 |
|
|
model [L. F. Liu and J. C. Wang, Proc. Natl. Acad. Sci. U.S.A. 84, |
877 |
|
|
7024 (1987)]. The properties of the chain at the onset of writhing |
878 |
|
|
agree well with predictions from theory, and the generated stress |
879 |
|
|
is ample for driving secondary structural transitions in physiological |
880 |
|
|
DNA. (C) 2004 American Institute of Physics.}, |
881 |
|
|
annote = {861ZF Times Cited:3 Cited References Count:34}, |
882 |
|
|
issn = {0021-9606}, |
883 |
|
|
uri = {<Go to ISI>://000224456500064}, |
884 |
|
|
} |
885 |
|
|
|
886 |
|
|
@ARTICLE{Naess2001, |
887 |
|
|
author = {S. N. Naess and H. M. Adland and A. Mikkelsen and A. Elgsaeter}, |
888 |
|
|
title = {Brownian dynamics simulation of rigid bodies and segmented polymer |
889 |
|
|
chains. Use of Cartesian rotation vectors as the generalized coordinates |
890 |
|
|
describing angular orientations}, |
891 |
|
|
journal = {Physica A}, |
892 |
|
|
year = {2001}, |
893 |
|
|
volume = {294}, |
894 |
|
|
pages = {323-339}, |
895 |
|
|
number = {3-4}, |
896 |
|
|
month = {May 15}, |
897 |
|
|
abstract = {The three Eulerian angles constitute the classical choice of generalized |
898 |
|
|
coordinates used to describe the three degrees of rotational freedom |
899 |
|
|
of a rigid body, but it has long been known that this choice yields |
900 |
|
|
singular equations of motion. The latter is also true when Eulerian |
901 |
|
|
angles are used in Brownian dynamics analyses of the angular orientation |
902 |
|
|
of single rigid bodies and segmented polymer chains. Starting from |
903 |
|
|
kinetic theory we here show that by instead employing the three |
904 |
|
|
components of Cartesian rotation vectors as the generalized coordinates |
905 |
|
|
describing angular orientation, no singularity appears in the configuration |
906 |
|
|
space diffusion equation and the associated Brownian dynamics algorithm. |
907 |
|
|
The suitability of Cartesian rotation vectors in Brownian dynamics |
908 |
|
|
simulations of segmented polymer chains with spring-like or ball-socket |
909 |
|
|
joints is discussed. (C) 2001 Elsevier Science B.V. All rights reserved.}, |
910 |
|
|
annote = {433TA Times Cited:7 Cited References Count:19}, |
911 |
|
|
issn = {0378-4371}, |
912 |
|
|
uri = {<Go to ISI>://000168774800005}, |
913 |
|
|
} |
914 |
|
|
|
915 |
|
|
@ARTICLE{Noguchi2002, |
916 |
|
|
author = {H. Noguchi and M. Takasu}, |
917 |
|
|
title = {Structural changes of pulled vesicles: A Brownian dynamics simulation}, |
918 |
|
|
journal = {Physical Review E}, |
919 |
|
|
year = {2002}, |
920 |
|
|
volume = {65}, |
921 |
|
|
pages = {-}, |
922 |
|
|
number = {5}, |
923 |
|
|
month = {may}, |
924 |
|
|
abstract = {We Studied the structural changes of bilayer vesicles induced by mechanical |
925 |
|
|
forces using a Brownian dynamics simulation. Two nanoparticles, |
926 |
|
|
which interact repulsively with amphiphilic molecules, are put inside |
927 |
|
|
a vesicle. The position of one nanoparticle is fixed, and the other |
928 |
|
|
is moved by a constant force as in optical-trapping experiments. |
929 |
|
|
First, the pulled vesicle stretches into a pear or tube shape. Then |
930 |
|
|
the inner monolayer in the tube-shaped region is deformed, and a |
931 |
|
|
cylindrical structure is formed between two vesicles. After stretching |
932 |
|
|
the cylindrical region, fission occurs near the moved vesicle. Soon |
933 |
|
|
after this the cylindrical region shrinks. The trapping force similar |
934 |
|
|
to 100 pN is needed to induce the formation of the cylindrical structure |
935 |
|
|
and fission.}, |
936 |
|
|
annote = {Part 1 568PX Times Cited:5 Cited References Count:39}, |
937 |
|
|
issn = {1063-651X}, |
938 |
|
|
uri = {<Go to ISI>://000176552300084}, |
939 |
|
|
} |
940 |
|
|
|
941 |
|
|
@ARTICLE{Noguchi2001, |
942 |
|
|
author = {H. Noguchi and M. Takasu}, |
943 |
|
|
title = {Fusion pathways of vesicles: A Brownian dynamics simulation}, |
944 |
|
|
journal = {Journal of Chemical Physics}, |
945 |
|
|
year = {2001}, |
946 |
|
|
volume = {115}, |
947 |
|
|
pages = {9547-9551}, |
948 |
|
|
number = {20}, |
949 |
|
|
month = {Nov 22}, |
950 |
|
|
abstract = {We studied the fusion dynamics of vesicles using a Brownian dynamics |
951 |
|
|
simulation. Amphiphilic molecules spontaneously form vesicles with |
952 |
|
|
a bilayer structure. Two vesicles come into contact and form a stalk |
953 |
|
|
intermediate, in which a necklike structure only connects the outer |
954 |
|
|
monolayers, as predicted by the stalk hypothesis. We have found |
955 |
|
|
a new pathway of pore opening from stalks at high temperature: the |
956 |
|
|
elliptic stalk bends and contact between the ends of the arc-shaped |
957 |
|
|
stalk leads to pore opening. On the other hand, we have clarified |
958 |
|
|
that the pore-opening process at low temperature agrees with the |
959 |
|
|
modified stalk model: a pore is induced by contact between the inner |
960 |
|
|
monolayers inside the stalk. (C) 2001 American Institute of Physics.}, |
961 |
|
|
annote = {491UW Times Cited:48 Cited References Count:25}, |
962 |
|
|
issn = {0021-9606}, |
963 |
|
|
uri = {<Go to ISI>://000172129300049}, |
964 |
|
|
} |
965 |
|
|
|
966 |
|
|
@ARTICLE{Palacios1998, |
967 |
|
|
author = {J. L. Garcia-Palacios and F. J. Lazaro}, |
968 |
|
|
title = {Langevin-dynamics study of the dynamical properties of small magnetic |
969 |
|
|
particles}, |
970 |
|
|
journal = {Physical Review B}, |
971 |
|
|
year = {1998}, |
972 |
|
|
volume = {58}, |
973 |
|
|
pages = {14937-14958}, |
974 |
|
|
number = {22}, |
975 |
|
|
month = {Dec 1}, |
976 |
|
|
abstract = {The stochastic Landau-Lifshitz-Gilbert equation of motion for a classical |
977 |
|
|
magnetic moment is numerically solved (properly observing the customary |
978 |
|
|
interpretation of it as a Stratonovich stochastic differential equation), |
979 |
|
|
in order to study the dynamics of magnetic nanoparticles. The corresponding |
980 |
|
|
Langevin-dynamics approach allows for the study of the fluctuating |
981 |
|
|
trajectories of individual magnetic moments, where we have encountered |
982 |
|
|
remarkable phenomena in the overbarrier rotation process, such as |
983 |
|
|
crossing-back or multiple crossing of the potential barrier, rooted |
984 |
|
|
in the gyromagnetic nature of the system. Concerning averaged quantities, |
985 |
|
|
we study the linear dynamic response of the archetypal ensemble |
986 |
|
|
of noninteracting classical magnetic moments with axially symmetric |
987 |
|
|
magnetic anisotropy. The results are compared with different analytical |
988 |
|
|
expressions used to model the relaxation of nanoparticle ensembles, |
989 |
|
|
assessing their accuracy. It has been found that, among a number |
990 |
|
|
of heuristic expressions for the linear dynamic susceptibility, |
991 |
|
|
only the simple formula proposed by Shliomis and Stepanov matches |
992 |
|
|
the coarse features of the susceptibility reasonably. By comparing |
993 |
|
|
the numerical results with the asymptotic formula of Storonkin {Sov. |
994 |
|
|
Phys. Crystallogr. 30, 489 (1985) [Kristallografiya 30, 841 (1985)]}, |
995 |
|
|
the effects of the intra-potential-well relaxation modes on the |
996 |
|
|
low-temperature longitudinal dynamic response have been assessed, |
997 |
|
|
showing their relatively small reflection in the susceptibility |
998 |
|
|
curves but their dramatic influence on the phase shifts. Comparison |
999 |
|
|
of the numerical results with the exact zero-damping expression |
1000 |
|
|
for the transverse susceptibility by Garanin, Ishchenko, and Panina |
1001 |
|
|
{Theor. Math. Phys. (USSR) 82, 169 (1990) [Teor. Mat. Fit. 82, 242 |
1002 |
|
|
(1990)]}, reveals a sizable contribution of the spread of the precession |
1003 |
|
|
frequencies of the magnetic moment in the anisotropy field to the |
1004 |
|
|
dynamic response at intermediate-to-high temperatures. [S0163-1829 |
1005 |
|
|
(98)00446-9].}, |
1006 |
|
|
annote = {146XW Times Cited:66 Cited References Count:45}, |
1007 |
|
|
issn = {0163-1829}, |
1008 |
|
|
uri = {<Go to ISI>://000077460000052}, |
1009 |
|
|
} |
1010 |
|
|
|
1011 |
|
|
@ARTICLE{Pastor1988, |
1012 |
|
|
author = {R. W. Pastor and B. R. Brooks and A. Szabo}, |
1013 |
|
|
title = {An Analysis of the Accuracy of Langevin and Molecular-Dynamics Algorithms}, |
1014 |
|
|
journal = {Molecular Physics}, |
1015 |
|
|
year = {1988}, |
1016 |
|
|
volume = {65}, |
1017 |
|
|
pages = {1409-1419}, |
1018 |
|
|
number = {6}, |
1019 |
|
|
month = {Dec 20}, |
1020 |
|
|
annote = {T1302 Times Cited:61 Cited References Count:26}, |
1021 |
|
|
issn = {0026-8976}, |
1022 |
|
|
uri = {<Go to ISI>://A1988T130200011}, |
1023 |
|
|
} |
1024 |
|
|
|
1025 |
|
|
@ARTICLE{Recio2004, |
1026 |
|
|
author = {J. Fernandez-Recio and M. Totrov and R. Abagyan}, |
1027 |
|
|
title = {Identification of protein-protein interaction sites from docking |
1028 |
|
|
energy landscapes}, |
1029 |
|
|
journal = {Journal of Molecular Biology}, |
1030 |
|
|
year = {2004}, |
1031 |
|
|
volume = {335}, |
1032 |
|
|
pages = {843-865}, |
1033 |
|
|
number = {3}, |
1034 |
|
|
month = {Jan 16}, |
1035 |
|
|
abstract = {Protein recognition is one of the most challenging and intriguing |
1036 |
|
|
problems in structural biology. Despite all the available structural, |
1037 |
|
|
sequence and biophysical information about protein-protein complexes, |
1038 |
|
|
the physico-chemical patterns, if any, that make a protein surface |
1039 |
|
|
likely to be involved in protein-protein interactions, remain elusive. |
1040 |
|
|
Here, we apply protein docking simulations and analysis of the interaction |
1041 |
|
|
energy landscapes to identify protein-protein interaction sites. |
1042 |
|
|
The new protocol for global docking based on multi-start global |
1043 |
|
|
energy optimization of an allatom model of the ligand, with detailed |
1044 |
|
|
receptor potentials and atomic solvation parameters optimized in |
1045 |
|
|
a training set of 24 complexes, explores the conformational space |
1046 |
|
|
around the whole receptor without restrictions. The ensembles of |
1047 |
|
|
the rigid-body docking solutions generated by the simulations were |
1048 |
|
|
subsequently used to project the docking energy landscapes onto |
1049 |
|
|
the protein surfaces. We found that highly populated low-energy |
1050 |
|
|
regions consistently corresponded to actual binding sites. The procedure |
1051 |
|
|
was validated on a test set of 21 known protein-protein complexes |
1052 |
|
|
not used in the training set. As much as 81% of the predicted high-propensity |
1053 |
|
|
patch residues were located correctly in the native interfaces. |
1054 |
|
|
This approach can guide the design of mutations on the surfaces |
1055 |
|
|
of proteins, provide geometrical details of a possible interaction, |
1056 |
|
|
and help to annotate protein surfaces in structural proteomics. |
1057 |
|
|
(C) 2003 Elsevier Ltd. All rights reserved.}, |
1058 |
|
|
annote = {763GQ Times Cited:21 Cited References Count:59}, |
1059 |
|
|
issn = {0022-2836}, |
1060 |
|
|
uri = {<Go to ISI>://000188066900016}, |
1061 |
|
|
} |
1062 |
|
|
|
1063 |
|
|
@ARTICLE{Sandu1999, |
1064 |
|
|
author = {A. Sandu and T. Schlick}, |
1065 |
|
|
title = {Masking resonance artifacts in force-splitting methods for biomolecular |
1066 |
|
|
simulations by extrapolative Langevin dynamics}, |
1067 |
|
|
journal = {Journal of Computational Physics}, |
1068 |
|
|
year = {1999}, |
1069 |
|
|
volume = {151}, |
1070 |
|
|
pages = {74-113}, |
1071 |
|
|
number = {1}, |
1072 |
|
|
month = {May 1}, |
1073 |
|
|
abstract = {Numerical resonance artifacts have become recognized recently as a |
1074 |
|
|
limiting factor to increasing the timestep in multiple-timestep |
1075 |
|
|
(MTS) biomolecular dynamics simulations. At certain timesteps correlated |
1076 |
|
|
to internal motions (e.g., 5 fs, around half the period of the fastest |
1077 |
|
|
bond stretch, T-min), visible inaccuracies or instabilities can |
1078 |
|
|
occur. Impulse-MTS schemes are vulnerable to these resonance errors |
1079 |
|
|
since large energy pulses are introduced to the governing dynamics |
1080 |
|
|
equations when the slow forces are evaluated. We recently showed |
1081 |
|
|
that such resonance artifacts can be masked significantly by applying |
1082 |
|
|
extrapolative splitting to stochastic dynamics. Theoretical and |
1083 |
|
|
numerical analyses of force-splitting integrators based on the Verlet |
1084 |
|
|
discretization are reported here for linear models to explain these |
1085 |
|
|
observations and to suggest how to construct effective integrators |
1086 |
|
|
for biomolecular dynamics that balance stability with accuracy. |
1087 |
|
|
Analyses for Newtonian dynamics demonstrate the severe resonance |
1088 |
|
|
patterns of the Impulse splitting, with this severity worsening |
1089 |
|
|
with the outer timestep. Delta t: Constant Extrapolation is generally |
1090 |
|
|
unstable, but the disturbances do not grow with Delta t. Thus. the |
1091 |
|
|
stochastic extrapolative combination can counteract generic instabilities |
1092 |
|
|
and largely alleviate resonances with a sufficiently strong Langevin |
1093 |
|
|
heat-bath coupling (gamma), estimates for which are derived here |
1094 |
|
|
based on the fastest and slowest motion periods. These resonance |
1095 |
|
|
results generally hold for nonlinear test systems: a water tetramer |
1096 |
|
|
and solvated protein. Proposed related approaches such as Extrapolation/Correction |
1097 |
|
|
and Midpoint Extrapolation work better than Constant Extrapolation |
1098 |
|
|
only for timesteps less than T-min/2. An effective extrapolative |
1099 |
|
|
stochastic approach for biomolecules that balances long-timestep |
1100 |
|
|
stability with good accuracy for the fast subsystem is then applied |
1101 |
|
|
to a biomolecule using a three-class partitioning: the medium forces |
1102 |
|
|
are treated by Midpoint Extrapolation via position Verlet, and the |
1103 |
|
|
slow forces are incorporated by Constant Extrapolation. The resulting |
1104 |
|
|
algorithm (LN) performs well on a solvated protein system in terms |
1105 |
|
|
of thermodynamic properties and yields an order of magnitude speedup |
1106 |
|
|
with respect to single-timestep Langevin trajectories. Computed |
1107 |
|
|
spectral density functions also show how the Newtonian modes can |
1108 |
|
|
be approximated by using a small gamma in the range Of 5-20 ps(-1). |
1109 |
|
|
(C) 1999 Academic Press.}, |
1110 |
|
|
annote = {194FM Times Cited:14 Cited References Count:32}, |
1111 |
|
|
issn = {0021-9991}, |
1112 |
|
|
uri = {<Go to ISI>://000080181500004}, |
1113 |
|
|
} |
1114 |
|
|
|
1115 |
|
|
@ARTICLE{Shen2002, |
1116 |
|
|
author = {M. Y. Shen and K. F. Freed}, |
1117 |
|
|
title = {Long time dynamics of met-enkephalin: Comparison of explicit and |
1118 |
|
|
implicit solvent models}, |
1119 |
|
|
journal = {Biophysical Journal}, |
1120 |
|
|
year = {2002}, |
1121 |
|
|
volume = {82}, |
1122 |
|
|
pages = {1791-1808}, |
1123 |
|
|
number = {4}, |
1124 |
|
|
month = {Apr}, |
1125 |
|
|
abstract = {Met-enkephalin is one of the smallest opiate peptides. Yet, its dynamical |
1126 |
|
|
structure and receptor docking mechanism are still not well understood. |
1127 |
|
|
The conformational dynamics of this neuron peptide in liquid water |
1128 |
|
|
are studied here by using all-atom molecular dynamics (MID) and |
1129 |
|
|
implicit water Langevin dynamics (LD) simulations with AMBER potential |
1130 |
|
|
functions and the three-site transferable intermolecular potential |
1131 |
|
|
(TIP3P) model for water. To achieve the same simulation length in |
1132 |
|
|
physical time, the full MID simulations require 200 times as much |
1133 |
|
|
CPU time as the implicit water LID simulations. The solvent hydrophobicity |
1134 |
|
|
and dielectric behavior are treated in the implicit solvent LD simulations |
1135 |
|
|
by using a macroscopic solvation potential, a single dielectric |
1136 |
|
|
constant, and atomic friction coefficients computed using the accessible |
1137 |
|
|
surface area method with the TIP3P model water viscosity as determined |
1138 |
|
|
here from MID simulations for pure TIP3P water. Both the local and |
1139 |
|
|
the global dynamics obtained from the implicit solvent LD simulations |
1140 |
|
|
agree very well with those from the explicit solvent MD simulations. |
1141 |
|
|
The simulations provide insights into the conformational restrictions |
1142 |
|
|
that are associated with the bioactivity of the opiate peptide dermorphin |
1143 |
|
|
for the delta-receptor.}, |
1144 |
|
|
annote = {540MH Times Cited:36 Cited References Count:45}, |
1145 |
|
|
issn = {0006-3495}, |
1146 |
|
|
uri = {<Go to ISI>://000174932400010}, |
1147 |
|
|
} |
1148 |
|
|
|
1149 |
|
|
@ARTICLE{Shillcock2005, |
1150 |
|
|
author = {J. C. Shillcock and R. Lipowsky}, |
1151 |
|
|
title = {Tension-induced fusion of bilayer membranes and vesicles}, |
1152 |
|
|
journal = {Nature Materials}, |
1153 |
|
|
year = {2005}, |
1154 |
|
|
volume = {4}, |
1155 |
|
|
pages = {225-228}, |
1156 |
|
|
number = {3}, |
1157 |
|
|
month = {Mar}, |
1158 |
|
|
annote = {901QJ Times Cited:9 Cited References Count:23}, |
1159 |
|
|
issn = {1476-1122}, |
1160 |
|
|
uri = {<Go to ISI>://000227296700019}, |
1161 |
|
|
} |
1162 |
|
|
|
1163 |
|
|
@ARTICLE{Skeel2002, |
1164 |
|
|
author = {R. D. Skeel and J. A. Izaguirre}, |
1165 |
|
|
title = {An impulse integrator for Langevin dynamics}, |
1166 |
|
|
journal = {Molecular Physics}, |
1167 |
|
|
year = {2002}, |
1168 |
|
|
volume = {100}, |
1169 |
|
|
pages = {3885-3891}, |
1170 |
|
|
number = {24}, |
1171 |
|
|
month = {Dec 20}, |
1172 |
|
|
abstract = {The best simple method for Newtonian molecular dynamics is indisputably |
1173 |
|
|
the leapfrog Stormer-Verlet method. The appropriate generalization |
1174 |
|
|
to simple Langevin dynamics is unclear. An analysis is presented |
1175 |
|
|
comparing an 'impulse method' (kick; fluctuate; kick), the 1982 |
1176 |
|
|
method of van Gunsteren and Berendsen, and the Brunger-Brooks-Karplus |
1177 |
|
|
(BBK) method. It is shown how the impulse method and the van Gunsteren-Berendsen |
1178 |
|
|
methods can be implemented as efficiently as the BBK method. Other |
1179 |
|
|
considerations suggest that the impulse method is the best basic |
1180 |
|
|
method for simple Langevin dynamics, with the van Gunsteren-Berendsen |
1181 |
|
|
method a close contender.}, |
1182 |
|
|
annote = {633RX Times Cited:8 Cited References Count:22}, |
1183 |
|
|
issn = {0026-8976}, |
1184 |
|
|
uri = {<Go to ISI>://000180297200014}, |
1185 |
|
|
} |
1186 |
|
|
|
1187 |
|
|
@ARTICLE{Skeel1997, |
1188 |
|
|
author = {R. D. Skeel and G. H. Zhang and T. Schlick}, |
1189 |
|
|
title = {A family of symplectic integrators: Stability, accuracy, and molecular |
1190 |
|
|
dynamics applications}, |
1191 |
|
|
journal = {Siam Journal on Scientific Computing}, |
1192 |
|
|
year = {1997}, |
1193 |
|
|
volume = {18}, |
1194 |
|
|
pages = {203-222}, |
1195 |
|
|
number = {1}, |
1196 |
|
|
month = {Jan}, |
1197 |
|
|
abstract = {The following integration methods for special second-order ordinary |
1198 |
|
|
differential equations are studied: leapfrog, implicit midpoint, |
1199 |
|
|
trapezoid, Stormer-Verlet, and Cowell-Numerov. We show that all |
1200 |
|
|
are members, or equivalent to members, of a one-parameter family |
1201 |
|
|
of schemes. Some methods have more than one common form, and we |
1202 |
|
|
discuss a systematic enumeration of these forms. We also present |
1203 |
|
|
a stability and accuracy analysis based on the idea of ''modified |
1204 |
|
|
equations'' and a proof of symplecticness. It follows that Cowell-Numerov |
1205 |
|
|
and ''LIM2'' (a method proposed by Zhang and Schlick) are symplectic. |
1206 |
|
|
A different interpretation of the values used by these integrators |
1207 |
|
|
leads to higher accuracy and better energy conservation. Hence, |
1208 |
|
|
we suggest that the straightforward analysis of energy conservation |
1209 |
|
|
is misleading.}, |
1210 |
|
|
annote = {We981 Times Cited:30 Cited References Count:35}, |
1211 |
|
|
issn = {1064-8275}, |
1212 |
|
|
uri = {<Go to ISI>://A1997WE98100012}, |
1213 |
|
|
} |
1214 |
|
|
|
1215 |
|
|
@ARTICLE{Tao2005, |
1216 |
|
|
author = {Y. G. Tao and W. K. {den Otter} and J. T. Padding and J. K. G. Dhont |
1217 |
|
|
and W. J. Briels}, |
1218 |
|
|
title = {Brownian dynamics simulations of the self- and collective rotational |
1219 |
|
|
diffusion coefficients of rigid long thin rods}, |
1220 |
|
|
journal = {Journal of Chemical Physics}, |
1221 |
|
|
year = {2005}, |
1222 |
|
|
volume = {122}, |
1223 |
|
|
pages = {-}, |
1224 |
|
|
number = {24}, |
1225 |
|
|
month = {Jun 22}, |
1226 |
|
|
abstract = {Recently a microscopic theory for the dynamics of suspensions of long |
1227 |
|
|
thin rigid rods was presented, confirming and expanding the well-known |
1228 |
|
|
theory by Doi and Edwards [The Theory of Polymer Dynamics (Clarendon, |
1229 |
|
|
Oxford, 1986)] and Kuzuu [J. Phys. Soc. Jpn. 52, 3486 (1983)]. Here |
1230 |
|
|
this theory is put to the test by comparing it against computer |
1231 |
|
|
simulations. A Brownian dynamics simulation program was developed |
1232 |
|
|
to follow the dynamics of the rods, with a length over a diameter |
1233 |
|
|
ratio of 60, on the Smoluchowski time scale. The model accounts |
1234 |
|
|
for excluded volume interactions between rods, but neglects hydrodynamic |
1235 |
|
|
interactions. The self-rotational diffusion coefficients D-r(phi) |
1236 |
|
|
of the rods were calculated by standard methods and by a new, more |
1237 |
|
|
efficient method based on calculating average restoring torques. |
1238 |
|
|
Collective decay of orientational order was calculated by means |
1239 |
|
|
of equilibrium and nonequilibrium simulations. Our results show |
1240 |
|
|
that, for the currently accessible volume fractions, the decay times |
1241 |
|
|
in both cases are virtually identical. Moreover, the observed decay |
1242 |
|
|
of diffusion coefficients with volume fraction is much quicker than |
1243 |
|
|
predicted by the theory, which is attributed to an oversimplification |
1244 |
|
|
of dynamic correlations in the theory. (c) 2005 American Institute |
1245 |
|
|
of Physics.}, |
1246 |
|
|
annote = {943DN Times Cited:3 Cited References Count:26}, |
1247 |
|
|
issn = {0021-9606}, |
1248 |
|
|
uri = {<Go to ISI>://000230332400077}, |
1249 |
|
|
} |
1250 |
|
|
|
1251 |
|
|
@ARTICLE{Tuckerman1992, |
1252 |
|
|
author = {M. Tuckerman and B. J. Berne and G. J. Martyna}, |
1253 |
|
|
title = {Reversible Multiple Time Scale Molecular-Dynamics}, |
1254 |
|
|
journal = {Journal of Chemical Physics}, |
1255 |
|
|
year = {1992}, |
1256 |
|
|
volume = {97}, |
1257 |
|
|
pages = {1990-2001}, |
1258 |
|
|
number = {3}, |
1259 |
|
|
month = {Aug 1}, |
1260 |
|
|
abstract = {The Trotter factorization of the Liouville propagator is used to generate |
1261 |
|
|
new reversible molecular dynamics integrators. This strategy is |
1262 |
|
|
applied to derive reversible reference system propagator algorithms |
1263 |
|
|
(RESPA) that greatly accelerate simulations of systems with a separation |
1264 |
|
|
of time scales or with long range forces. The new algorithms have |
1265 |
|
|
all of the advantages of previous RESPA integrators but are reversible, |
1266 |
|
|
and more stable than those methods. These methods are applied to |
1267 |
|
|
a set of paradigmatic systems and are shown to be superior to earlier |
1268 |
|
|
methods. It is shown how the new RESPA methods are related to predictor-corrector |
1269 |
|
|
integrators. Finally, we show how these methods can be used to accelerate |
1270 |
|
|
the integration of the equations of motion of systems with Nose |
1271 |
|
|
thermostats.}, |
1272 |
|
|
annote = {Je891 Times Cited:680 Cited References Count:19}, |
1273 |
|
|
issn = {0021-9606}, |
1274 |
|
|
uri = {<Go to ISI>://A1992JE89100044}, |
1275 |
|
|
} |
1276 |
|
|
|