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@ARTICLE{Torre2003, |
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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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@BOOK{Allen1987, |
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title = {Computer Simulations of Liquids}, |
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publisher = {Oxford University Press}, |
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year = {1987}, |
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author = {M.~P. Allen and D.~J. Tildesley}, |
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address = {New York}, |
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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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|
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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{Baber1995, |
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author = {J. Baber and J. F. Ellena and D. S. Cafiso}, |
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title = {Distribution of General-Anesthetics in Phospholipid-Bilayers Determined |
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Using H-2 Nmr and H-1-H-1 Noe Spectroscopy}, |
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journal = {Biochemistry}, |
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year = {1995}, |
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volume = {34}, |
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pages = {6533-6539}, |
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number = {19}, |
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month = {May 16}, |
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abstract = {The effect of the general anesthetics halothane, enflurane, and isoflurane |
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on hydrocarbon chain packing in palmitoyl(d(31))oleoylphosphatidylcholine |
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membranes in the liquid crystalline phase was investigated using |
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H-2 NMR. Upon the addition of the anesthetics, the first five methylene |
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units near the interface generally show a very small increase in |
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segmental order, while segments deeper within the bilayer show a |
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small decrease in segmental order. From the H-2 NMR results, the |
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chain length for the perdeuterated palmitoyl chain in the absence |
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of anesthetic was found to be 12.35 Angstrom. Upon the addition |
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of halothane enflurane, or isoflurane, the acyl chain undergoes |
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slight contractions of 0.11, 0.20, or 0.16 Angstrom, respectively, |
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at 50 mol % anesthetic. A simple model was used to estimate the |
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relative amounts of anesthetic located near the interface and deeper |
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in the bilayer hydrocarbon region, and only a slight preference |
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for an interfacial location was observed. Intermolecular H-1-H-1 |
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nuclear Overhauser effects (NOEs) were measured between phospholipid |
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and halothane protons. These NOEs are consistent with the intramembrane |
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location of the anesthetics suggested by the H-2 NMR data. In addition, |
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the NOE data indicate that anesthetics prefer the interfacial and |
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hydrocarbon regions of the membrane and are not found in high concentrations |
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in the phospholipid headgroup.}, |
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annote = {Qz716 Times Cited:38 Cited References Count:37}, |
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issn = {0006-2960}, |
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uri = {<Go to ISI>://A1995QZ71600035}, |
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} |
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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}, |
276 |
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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 |
282 |
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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 |
285 |
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investigations confirm the advantages of the position-Verlet scheme |
286 |
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when used for the fastest time scales of the system. Applications |
287 |
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to a biomolecule. a solvated protein, for both Newtonian and Langevin |
288 |
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dynamics echo these trends over large outer time-step regimes. (C) |
289 |
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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{Bates2005, |
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author = {M. A. Bates and G. R. Luckhurst}, |
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title = {Biaxial nematic phases and V-shaped molecules: A Monte Carlo simulation |
298 |
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study}, |
299 |
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journal = {Physical Review E}, |
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year = {2005}, |
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volume = {72}, |
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pages = {-}, |
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number = {5}, |
304 |
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month = {Nov}, |
305 |
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abstract = {Inspired by recent claims that compounds composed of V-shaped molecules |
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can exhibit the elusive biaxial nematic phase, we have developed |
307 |
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a generic simulation model for such systems. This contains the features |
308 |
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of the molecule that are essential to its liquid crystal behavior, |
309 |
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namely the anisotropies of the two arms and the angle between them. |
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The behavior of the model has been investigated using Monte Carlo |
311 |
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simulations for a wide range of these structural parameters. This |
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allows us to establish the relationship between the V-shaped molecule |
313 |
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and its ability to form a biaxial nematic phase. Of particular importance |
314 |
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are the criteria of geometry and the relative anisotropy necessary |
315 |
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for the system to exhibit a Landau point, at which the biaxial nematic |
316 |
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is formed directly from the isotropic phase. The simulations have |
317 |
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also been used to determine the orientational order parameters for |
318 |
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a selection of molecular axes. These are especially important because |
319 |
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they reveal the phase symmetry and are connected to the experimental |
320 |
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determination of this. The simulation results show that, whereas |
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some positions are extremely sensitive to the phase biaxiality, |
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others are totally blind to this.}, |
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annote = {Part 1 988LQ Times Cited:0 Cited References Count:38}, |
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issn = {1539-3755}, |
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uri = {<Go to ISI>://000233603100030}, |
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} |
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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}, |
331 |
|
|
journal = {Biophysical Journal}, |
332 |
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year = {2003}, |
333 |
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volume = {85}, |
334 |
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pages = {2973-2976}, |
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number = {5}, |
336 |
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month = {Nov 1}, |
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|
|
abstract = {We introduce an unbiased protocol for performing rotational moves |
338 |
|
|
in rigid-body dynamics simulations. This approach - based on the |
339 |
|
|
analytic solution for the rotational equations of motion for an |
340 |
|
|
orthogonal coordinate system at constant angular velocity - removes |
341 |
|
|
deficiencies that have been largely ignored in Brownian dynamics |
342 |
|
|
simulations, namely errors for finite rotations that result from |
343 |
|
|
applying the noncommuting rotational matrices in an arbitrary order. |
344 |
|
|
Our algorithm should thus replace standard approaches to rotate |
345 |
|
|
local coordinate frames in Langevin and Brownian dynamics simulations.}, |
346 |
|
|
annote = {736UA Times Cited:0 Cited References Count:11}, |
347 |
|
|
issn = {0006-3495}, |
348 |
|
|
uri = {<Go to ISI>://000186190500018}, |
349 |
tim |
2685 |
} |
350 |
|
|
|
351 |
tim |
2786 |
@ARTICLE{Beloborodov1998, |
352 |
|
|
author = {I. S. Beloborodov and V. Y. Orekhov and A. S. Arseniev}, |
353 |
|
|
title = {Effect of coupling between rotational and translational Brownian |
354 |
|
|
motions on NMR spin relaxation: Consideration using green function |
355 |
|
|
of rigid body diffusion}, |
356 |
|
|
journal = {Journal of Magnetic Resonance}, |
357 |
|
|
year = {1998}, |
358 |
|
|
volume = {132}, |
359 |
|
|
pages = {328-329}, |
360 |
|
|
number = {2}, |
361 |
|
|
month = {Jun}, |
362 |
|
|
abstract = {Using the Green function of arbitrary rigid Brownian diffusion (Goldstein, |
363 |
|
|
Biopolymers 33, 409-436, 1993), it was analytically shown that coupling |
364 |
|
|
between translation and rotation diffusion degrees of freedom does |
365 |
|
|
not affect the correlation functions relevant to the NMR intramolecular |
366 |
|
|
relaxation. It follows that spectral densities usually used for |
367 |
|
|
the anisotropic rotation diffusion (Woessner, J. Chem. Phys. 37, |
368 |
|
|
647-654, 1962) can be regarded as exact in respect to the rotation-translation |
369 |
|
|
coupling for the spin system connected with a rigid body. (C) 1998 |
370 |
|
|
Academic Press.}, |
371 |
|
|
annote = {Zu605 Times Cited:2 Cited References Count:6}, |
372 |
|
|
issn = {1090-7807}, |
373 |
|
|
uri = {<Go to ISI>://000074214800017}, |
374 |
tim |
2685 |
} |
375 |
|
|
|
376 |
tim |
2786 |
@ARTICLE{Berardi1996, |
377 |
|
|
author = {R. Berardi and S. Orlandi and C. Zannoni}, |
378 |
|
|
title = {Antiphase structures in polar smectic liquid crystals and their molecular |
379 |
|
|
origin}, |
380 |
|
|
journal = {Chemical Physics Letters}, |
381 |
|
|
year = {1996}, |
382 |
|
|
volume = {261}, |
383 |
|
|
pages = {357-362}, |
384 |
|
|
number = {3}, |
385 |
|
|
month = {Oct 18}, |
386 |
|
|
abstract = {We demonstrate that the overall molecular dipole organization in a |
387 |
|
|
smectic liquid crystal formed of polar molecules can be strongly |
388 |
|
|
influenced by the position of the dipole in the molecule. We study |
389 |
|
|
by large scale Monte Carlo simulations systems of attractive-repulsive |
390 |
|
|
''Gay-Berne'' elongated ellipsoids with an axial dipole at the center |
391 |
|
|
or near the end of the molecule and we show that monolayer smectic |
392 |
|
|
liquid crystals and modulated antiferroelectric bilayer stripe domains |
393 |
|
|
similar to the experimentally observed ''antiphase'' structures |
394 |
|
|
are obtained in the two cases.}, |
395 |
|
|
annote = {Vn637 Times Cited:49 Cited References Count:26}, |
396 |
|
|
issn = {0009-2614}, |
397 |
|
|
uri = {<Go to ISI>://A1996VN63700023}, |
398 |
tim |
2685 |
} |
399 |
|
|
|
400 |
tim |
2786 |
@ARTICLE{Berkov2005, |
401 |
|
|
author = {D. V. Berkov and N. L. Gorn}, |
402 |
|
|
title = {Stochastic dynamic simulations of fast remagnetization processes: |
403 |
|
|
recent advances and applications}, |
404 |
|
|
journal = {Journal of Magnetism and Magnetic Materials}, |
405 |
|
|
year = {2005}, |
406 |
|
|
volume = {290}, |
407 |
|
|
pages = {442-448}, |
408 |
|
|
month = {Apr}, |
409 |
|
|
abstract = {Numerical simulations of fast remagnetization processes using stochastic |
410 |
|
|
dynamics are widely used to study various magnetic systems. In this |
411 |
|
|
paper, we first address several crucial methodological problems |
412 |
|
|
of such simulations: (i) the influence of finite-element discretization |
413 |
|
|
on simulated dynamics, (ii) choice between Ito and Stratonovich |
414 |
|
|
stochastic calculi by the solution of micromagnetic stochastic equations |
415 |
|
|
of motion and (iii) non-trivial correlation properties of the random |
416 |
|
|
(thermal) field. Next, we discuss several examples to demonstrate |
417 |
|
|
the great potential of the Langevin dynamics for studying fast remagnetization |
418 |
|
|
processes in technically relevant applications: we present numerical |
419 |
|
|
analysis of equilibrium magnon spectra in patterned structures, |
420 |
|
|
study thermal noise effects on the magnetization dynamics of nanoelements |
421 |
|
|
in pulsed fields and show some results for a remagnetization dynamics |
422 |
|
|
induced by a spin-polarized current. (c) 2004 Elsevier B.V. All |
423 |
|
|
rights reserved.}, |
424 |
|
|
annote = {Part 1 Sp. Iss. SI 922KU Times Cited:2 Cited References Count:25}, |
425 |
|
|
issn = {0304-8853}, |
426 |
|
|
uri = {<Go to ISI>://000228837600109}, |
427 |
tim |
2685 |
} |
428 |
|
|
|
429 |
tim |
2786 |
@ARTICLE{Berkov2005a, |
430 |
|
|
author = {D. V. Berkov and N. L. Gorn}, |
431 |
|
|
title = {Magnetization precession due to a spin-polarized current in a thin |
432 |
|
|
nanoelement: Numerical simulation study}, |
433 |
|
|
journal = {Physical Review B}, |
434 |
|
|
year = {2005}, |
435 |
|
|
volume = {72}, |
436 |
|
|
pages = {-}, |
437 |
|
|
number = {9}, |
438 |
|
|
month = {Sep}, |
439 |
|
|
abstract = {In this paper a detailed numerical study (in frames of the Slonczewski |
440 |
|
|
formalism) of magnetization oscillations driven by a spin-polarized |
441 |
|
|
current through a thin elliptical nanoelement is presented. We show |
442 |
|
|
that a sophisticated micromagnetic model, where a polycrystalline |
443 |
|
|
structure of a nanoelement is taken into account, can explain qualitatively |
444 |
|
|
all most important features of the magnetization oscillation spectra |
445 |
|
|
recently observed experimentally [S. I. Kiselev , Nature 425, 380 |
446 |
|
|
(2003)], namely, existence of several equidistant spectral bands, |
447 |
|
|
sharp onset and abrupt disappearance of magnetization oscillations |
448 |
|
|
with increasing current, absence of the out-of-plane regime predicted |
449 |
|
|
by a macrospin model, and the relation between frequencies of so-called |
450 |
|
|
small-angle and quasichaotic oscillations. However, a quantitative |
451 |
|
|
agreement with experimental results (especially concerning the frequency |
452 |
|
|
of quasichaotic oscillations) could not be achieved in the region |
453 |
|
|
of reasonable parameter values, indicating that further model refinement |
454 |
|
|
is necessary for a complete understanding of the spin-driven magnetization |
455 |
|
|
precession even in this relatively simple experimental situation.}, |
456 |
|
|
annote = {969IT Times Cited:2 Cited References Count:55}, |
457 |
|
|
issn = {1098-0121}, |
458 |
|
|
uri = {<Go to ISI>://000232228500058}, |
459 |
tim |
2685 |
} |
460 |
|
|
|
461 |
tim |
2786 |
@ARTICLE{Berkov2002, |
462 |
|
|
author = {D. V. Berkov and N. L. Gorn and P. Gornert}, |
463 |
|
|
title = {Magnetization dynamics in nanoparticle systems: Numerical simulation |
464 |
|
|
using Langevin dynamics}, |
465 |
|
|
journal = {Physica Status Solidi a-Applied Research}, |
466 |
|
|
year = {2002}, |
467 |
|
|
volume = {189}, |
468 |
|
|
pages = {409-421}, |
469 |
|
|
number = {2}, |
470 |
|
|
month = {Feb 16}, |
471 |
|
|
abstract = {We report on recent progress achieved by the development of numerical |
472 |
|
|
methods based on the stochastic (Langevin) dynamics applied to systems |
473 |
|
|
of interacting magnetic nanoparticles. The method enables direct |
474 |
|
|
simulations of the trajectories of magnetic moments taking into |
475 |
|
|
account (i) all relevant interactions, (ii) precession dynamics, |
476 |
|
|
and (iii) temperature fluctuations included via the random (thermal) |
477 |
|
|
field. We present several novel results obtained using new methods |
478 |
|
|
developed for the solution of the Langevin equations. In particular, |
479 |
|
|
we have investigated magnetic nanodots and disordered granular systems |
480 |
|
|
of single-domain magnetic particles. For the first case we have |
481 |
|
|
calculated the spectrum and the spatial distribution of spin excitations. |
482 |
|
|
For the second system the complex ac susceptibility chi(omega, T) |
483 |
|
|
for various particle concentrations and particle anisotropies were |
484 |
|
|
computed and compared with numerous experimental results.}, |
485 |
|
|
annote = {526TF Times Cited:4 Cited References Count:37}, |
486 |
|
|
issn = {0031-8965}, |
487 |
|
|
uri = {<Go to ISI>://000174145200026}, |
488 |
tim |
2685 |
} |
489 |
|
|
|
490 |
tim |
2786 |
@ARTICLE{Bernal1980, |
491 |
|
|
author = {J.M. Bernal and J. G. {de la Torre}}, |
492 |
|
|
title = {Transport Properties and Hydrodynamic Centers of Rigid Macromolecules |
493 |
|
|
with Arbitrary Shape}, |
494 |
|
|
journal = {Biopolymers}, |
495 |
|
|
year = {1980}, |
496 |
|
|
volume = {19}, |
497 |
|
|
pages = {751-766}, |
498 |
tim |
2685 |
} |
499 |
|
|
|
500 |
tim |
2786 |
@ARTICLE{Brunger1984, |
501 |
|
|
author = {A. Brunger and C. L. Brooks and M. Karplus}, |
502 |
|
|
title = {Stochastic Boundary-Conditions for Molecular-Dynamics Simulations |
503 |
|
|
of St2 Water}, |
504 |
|
|
journal = {Chemical Physics Letters}, |
505 |
|
|
year = {1984}, |
506 |
|
|
volume = {105}, |
507 |
|
|
pages = {495-500}, |
508 |
|
|
number = {5}, |
509 |
|
|
annote = {Sm173 Times Cited:143 Cited References Count:22}, |
510 |
|
|
issn = {0009-2614}, |
511 |
|
|
uri = {<Go to ISI>://A1984SM17300007}, |
512 |
tim |
2685 |
} |
513 |
|
|
|
514 |
tim |
2786 |
@ARTICLE{Camp1999, |
515 |
|
|
author = {P. J. Camp and M. P. Allen and A. J. Masters}, |
516 |
|
|
title = {Theory and computer simulation of bent-core molecules}, |
517 |
|
|
journal = {Journal of Chemical Physics}, |
518 |
|
|
year = {1999}, |
519 |
|
|
volume = {111}, |
520 |
|
|
pages = {9871-9881}, |
521 |
|
|
number = {21}, |
522 |
|
|
month = {Dec 1}, |
523 |
|
|
abstract = {Fluids of hard bent-core molecules have been studied using theory |
524 |
|
|
and computer simulation. The molecules are composed of two hard |
525 |
|
|
spherocylinders, with length-to-breadth ratio L/D, joined by their |
526 |
|
|
ends at an angle 180 degrees - gamma. For L/D = 2 and gamma = 0,10,20 |
527 |
|
|
degrees, the simulations show isotropic, nematic, smectic, and solid |
528 |
|
|
phases. For L/D = 2 and gamma = 30 degrees, only isotropic, nematic, |
529 |
|
|
and solid phases are in evidence, which suggests that there is a |
530 |
|
|
nematic-smectic-solid triple point at an angle in the range 20 degrees |
531 |
|
|
< gamma < 30 degrees. In all of the orientationally ordered fluid |
532 |
|
|
phases the order is purely uniaxial. For gamma = 10 degrees and |
533 |
|
|
20 degrees, at the studied densities, the solid is also uniaxially |
534 |
|
|
ordered, whilst for gamma = 30 degrees the solid layers are biaxially |
535 |
|
|
ordered. For L/D = 2 and gamma = 60 degrees and 90 degrees we find |
536 |
|
|
no spontaneous orientational ordering. This is shown to be due to |
537 |
|
|
the interlocking of dimer pairs which precludes alignment. We find |
538 |
|
|
similar results for L/D = 9.5 and gamma = 72 degrees, where an isotropic-biaxial |
539 |
|
|
nematic transition is predicted by Onsager theory. Simulations in |
540 |
|
|
the biaxial nematic phase show it to be at least mechanically stable |
541 |
|
|
with respect to the isotropic phase, however. We have compared the |
542 |
|
|
quasi-exact simulation results in the isotropic phase with the predicted |
543 |
|
|
equations of state from three theories: the virial expansion containing |
544 |
|
|
the second and third virial coefficients; the Parsons-Lee equation |
545 |
|
|
of state; an application of Wertheim's theory of associating fluids |
546 |
|
|
in the limit of infinite attractive association energy. For all |
547 |
|
|
of the molecule elongations and geometries we have simulated, the |
548 |
|
|
Wertheim theory proved to be the most accurate. Interestingly, the |
549 |
|
|
isotropic equation of state is virtually independent of the dimer |
550 |
|
|
bond angle-a feature that is also reflected in the lack of variation |
551 |
|
|
with angle of the calculated second and third virial coefficients. |
552 |
|
|
(C) 1999 American Institute of Physics. [S0021-9606(99)50445-5].}, |
553 |
|
|
annote = {255TC Times Cited:24 Cited References Count:38}, |
554 |
|
|
issn = {0021-9606}, |
555 |
|
|
uri = {<Go to ISI>://000083685400056}, |
556 |
tim |
2685 |
} |
557 |
|
|
|
558 |
tim |
2786 |
@ARTICLE{Care2005, |
559 |
|
|
author = {C. M. Care and D. J. Cleaver}, |
560 |
|
|
title = {Computer simulation of liquid crystals}, |
561 |
|
|
journal = {Reports on Progress in Physics}, |
562 |
|
|
year = {2005}, |
563 |
|
|
volume = {68}, |
564 |
|
|
pages = {2665-2700}, |
565 |
|
|
number = {11}, |
566 |
|
|
month = {Nov}, |
567 |
|
|
abstract = {A review is presented of molecular and mesoscopic computer simulations |
568 |
|
|
of liquid crystalline systems. Molecular simulation approaches applied |
569 |
|
|
to such systems are described, and the key findings for bulk phase |
570 |
|
|
behaviour are reported. Following this, recently developed lattice |
571 |
|
|
Boltzmann approaches to the mesoscale modelling of nemato-dynanics |
572 |
|
|
are reviewed. This paper concludes with a discussion of possible |
573 |
|
|
areas for future development in this field.}, |
574 |
|
|
annote = {989TU Times Cited:2 Cited References Count:258}, |
575 |
|
|
issn = {0034-4885}, |
576 |
|
|
uri = {<Go to ISI>://000233697600004}, |
577 |
tim |
2685 |
} |
578 |
|
|
|
579 |
tim |
2786 |
@ARTICLE{Carrasco1999, |
580 |
|
|
author = {B. Carrasco and J. G. {de la Torre}}, |
581 |
|
|
title = {Hydrodynamic properties of rigid particles: Comparison of different |
582 |
|
|
modeling and computational procedures}, |
583 |
|
|
journal = {Biophysical Journal}, |
584 |
|
|
year = {1999}, |
585 |
|
|
volume = {76}, |
586 |
|
|
pages = {3044-3057}, |
587 |
|
|
number = {6}, |
588 |
|
|
month = {Jun}, |
589 |
|
|
abstract = {The hydrodynamic properties of rigid particles are calculated from |
590 |
|
|
models composed of spherical elements (beads) using theories developed |
591 |
|
|
by Kirkwood, Bloomfield, and their coworkers. Bead models have usually |
592 |
|
|
been built in such a way that the beads fill the volume occupied |
593 |
|
|
by the particles. Sometimes the beads are few and of varying sizes |
594 |
|
|
(bead models in the strict sense), and other times there are many |
595 |
|
|
small beads (filling models). Because hydrodynamic friction takes |
596 |
|
|
place at the molecular surface, another possibility is to use shell |
597 |
|
|
models, as originally proposed by Bloomfield. In this work, we have |
598 |
|
|
developed procedures to build models of the various kinds, and we |
599 |
|
|
describe the theory and methods for calculating their hydrodynamic |
600 |
|
|
properties, including approximate methods that may be needed to |
601 |
|
|
treat models with a very large number of elements. By combining |
602 |
|
|
the various possibilities of model building and hydrodynamic calculation, |
603 |
|
|
several strategies can be designed. We have made a quantitative |
604 |
|
|
comparison of the performance of the various strategies by applying |
605 |
|
|
them to some test cases, for which the properties are known a priori. |
606 |
|
|
We provide guidelines and computational tools for bead modeling.}, |
607 |
|
|
annote = {200TT Times Cited:46 Cited References Count:57}, |
608 |
|
|
issn = {0006-3495}, |
609 |
|
|
uri = {<Go to ISI>://000080556700016}, |
610 |
tim |
2685 |
} |
611 |
|
|
|
612 |
tim |
2786 |
@ARTICLE{Chandra1999, |
613 |
|
|
author = {A. Chandra and T. Ichiye}, |
614 |
|
|
title = {Dynamical properties of the soft sticky dipole model of water: Molecular |
615 |
|
|
dynamics simulations}, |
616 |
|
|
journal = {Journal of Chemical Physics}, |
617 |
|
|
year = {1999}, |
618 |
|
|
volume = {111}, |
619 |
|
|
pages = {2701-2709}, |
620 |
|
|
number = {6}, |
621 |
|
|
month = {Aug 8}, |
622 |
|
|
abstract = {Dynamical properties of the soft sticky dipole (SSD) model of water |
623 |
|
|
are calculated by means of molecular dynamics simulations. Since |
624 |
|
|
this is not a simple point model, the forces and torques arising |
625 |
|
|
from the SSD potential are derived here. Simulations are carried |
626 |
|
|
out in the microcanonical ensemble employing the Ewald method for |
627 |
|
|
the electrostatic interactions. Various time correlation functions |
628 |
|
|
and dynamical quantities associated with the translational and rotational |
629 |
|
|
motion of water molecules are evaluated and compared with those |
630 |
|
|
of two other commonly used models of liquid water, namely the transferable |
631 |
|
|
intermolecular potential-three points (TIP3P) and simple point charge/extended |
632 |
|
|
(SPC/E) models, and also with experiments. The dynamical properties |
633 |
|
|
of the SSD water model are found to be in good agreement with the |
634 |
|
|
experimental results and appear to be better than the TIP3P and |
635 |
|
|
SPC/E models in most cases, as has been previously shown for its |
636 |
|
|
thermodynamic, structural, and dielectric properties. Also, molecular |
637 |
|
|
dynamics simulations of the SSD model are found to run much faster |
638 |
|
|
than TIP3P, SPC/E, and other multisite models. (C) 1999 American |
639 |
|
|
Institute of Physics. [S0021-9606(99)51430-X].}, |
640 |
|
|
annote = {221EN Times Cited:14 Cited References Count:66}, |
641 |
|
|
issn = {0021-9606}, |
642 |
|
|
uri = {<Go to ISI>://000081711200038}, |
643 |
tim |
2685 |
} |
644 |
|
|
|
645 |
tim |
2786 |
@ARTICLE{Cheung2004, |
646 |
|
|
author = {D. L. Cheung and S. J. Clark and M. R. Wilson}, |
647 |
|
|
title = {Calculation of flexoelectric coefficients for a nematic liquid crystal |
648 |
|
|
by atomistic simulation}, |
649 |
|
|
journal = {Journal of Chemical Physics}, |
650 |
|
|
year = {2004}, |
651 |
|
|
volume = {121}, |
652 |
|
|
pages = {9131-9139}, |
653 |
|
|
number = {18}, |
654 |
|
|
month = {Nov 8}, |
655 |
|
|
abstract = {Equilibrium molecular dynamics calculations have been performed for |
656 |
|
|
the liquid crystal molecule n-4-(trans-4-n-pentylcyclohexyl)benzonitrile |
657 |
|
|
(PCH5) using a fully atomistic model. Simulation data have been |
658 |
|
|
obtained for a series of temperatures in the nematic phase. The |
659 |
|
|
simulation data have been used to calculate the flexoelectric coefficients |
660 |
|
|
e(s) and e(b) using the linear response formalism of Osipov and |
661 |
|
|
Nemtsov [M. A. Osipov and V. B. Nemtsov, Sov. Phys. Crstallogr. |
662 |
|
|
31, 125 (1986)]. The temperature and order parameter dependence |
663 |
|
|
of e(s) and e(b) are examined, as are separate contributions from |
664 |
|
|
different intermolecular interactions. Values of e(s) and e(b) calculated |
665 |
|
|
from simulation are consistent with those found from experiment. |
666 |
|
|
(C) 2004 American Institute of Physics.}, |
667 |
|
|
annote = {866UM Times Cited:4 Cited References Count:61}, |
668 |
|
|
issn = {0021-9606}, |
669 |
|
|
uri = {<Go to ISI>://000224798900053}, |
670 |
tim |
2685 |
} |
671 |
|
|
|
672 |
tim |
2786 |
@ARTICLE{Cheung2002, |
673 |
|
|
author = {D. L. Cheung and S. J. Clark and M. R. Wilson}, |
674 |
|
|
title = {Calculation of the rotational viscosity of a nematic liquid crystal}, |
675 |
|
|
journal = {Chemical Physics Letters}, |
676 |
|
|
year = {2002}, |
677 |
|
|
volume = {356}, |
678 |
|
|
pages = {140-146}, |
679 |
|
|
number = {1-2}, |
680 |
|
|
month = {Apr 15}, |
681 |
|
|
abstract = {Equilibrium molecular dynamics calculations have been performed for |
682 |
|
|
the liquid crystal molecule n-4-(trans-4-npentylcyclohexyl)benzonitrile |
683 |
|
|
(PCH5) using a fully atomistic model. Simulation data has been obtained |
684 |
|
|
for a series of temperatures in the nematic phase. The rotational |
685 |
|
|
viscosity co-efficient gamma(1), has been calculated using the angular |
686 |
|
|
velocity correlation function of the nematic director, n, the mean |
687 |
|
|
squared diffusion of n and statistical mechanical methods based |
688 |
|
|
on the rotational diffusion co-efficient. We find good agreement |
689 |
|
|
between the first two methods and experimental values. (C) 2002 |
690 |
|
|
Published by Elsevier Science B.V.}, |
691 |
|
|
annote = {547KF Times Cited:8 Cited References Count:31}, |
692 |
|
|
issn = {0009-2614}, |
693 |
|
|
uri = {<Go to ISI>://000175331000020}, |
694 |
tim |
2685 |
} |
695 |
|
|
|
696 |
tim |
2786 |
@ARTICLE{Chin2004, |
697 |
|
|
author = {S. A. Chin}, |
698 |
|
|
title = {Dynamical multiple-time stepping methods for overcoming resonance |
699 |
|
|
instabilities}, |
700 |
|
|
journal = {Journal of Chemical Physics}, |
701 |
|
|
year = {2004}, |
702 |
|
|
volume = {120}, |
703 |
|
|
pages = {8-13}, |
704 |
|
|
number = {1}, |
705 |
|
|
month = {Jan 1}, |
706 |
|
|
abstract = {Current molecular dynamics simulations of biomolecules using multiple |
707 |
|
|
time steps to update the slowly changing force are hampered by instabilities |
708 |
|
|
beginning at time steps near the half period of the fastest vibrating |
709 |
|
|
mode. These #resonance# instabilities have became a critical barrier |
710 |
|
|
preventing the long time simulation of biomolecular dynamics. Attempts |
711 |
|
|
to tame these instabilities by altering the slowly changing force |
712 |
|
|
and efforts to damp them out by Langevin dynamics do not address |
713 |
|
|
the fundamental cause of these instabilities. In this work, we trace |
714 |
|
|
the instability to the nonanalytic character of the underlying spectrum |
715 |
|
|
and show that a correct splitting of the Hamiltonian, which renders |
716 |
|
|
the spectrum analytic, restores stability. The resulting Hamiltonian |
717 |
|
|
dictates that in addition to updating the momentum due to the slowly |
718 |
|
|
changing force, one must also update the position with a modified |
719 |
|
|
mass. Thus multiple-time stepping must be done dynamically. (C) |
720 |
|
|
2004 American Institute of Physics.}, |
721 |
|
|
annote = {757TK Times Cited:1 Cited References Count:22}, |
722 |
|
|
issn = {0021-9606}, |
723 |
|
|
uri = {<Go to ISI>://000187577400003}, |
724 |
tim |
2685 |
} |
725 |
|
|
|
726 |
tim |
2786 |
@ARTICLE{Cook2000, |
727 |
|
|
author = {M. J. Cook and M. R. Wilson}, |
728 |
|
|
title = {Simulation studies of dipole correlation in the isotropic liquid |
729 |
|
|
phase}, |
730 |
|
|
journal = {Liquid Crystals}, |
731 |
|
|
year = {2000}, |
732 |
|
|
volume = {27}, |
733 |
|
|
pages = {1573-1583}, |
734 |
|
|
number = {12}, |
735 |
|
|
month = {Dec}, |
736 |
|
|
abstract = {The Kirkwood correlation factor g(1) determines the preference for |
737 |
|
|
local parallel or antiparallel dipole association in the isotropic |
738 |
|
|
phase. Calamitic mesogens with longitudinal dipole moments and Kirkwood |
739 |
|
|
factors greater than 1 have an enhanced effective dipole moment |
740 |
|
|
along the molecular long axis. This leads to higher values of Delta |
741 |
|
|
epsilon in the nematic phase. This paper describes state-of-the-art |
742 |
|
|
molecular dynamics simulations of two calamitic mesogens 4-(trans-4-n-pentylcyclohexyl)benzonitrile |
743 |
|
|
(PCH5) and 4-(trans-4-n-pentylcyclohexyl) chlorobenzene (PCH5-Cl) |
744 |
|
|
in the isotropic liquid phase using an all-atom force field and |
745 |
|
|
taking long range electrostatics into account using an Ewald summation. |
746 |
|
|
Using this methodology, PCH5 is seen to prefer antiparallel dipole |
747 |
|
|
alignment with a negative g(1) and PCH5-Cl is seen to prefer parallel |
748 |
|
|
dipole alignment with a positive g(1); this is in accordance with |
749 |
|
|
experimental dielectric measurements. Analysis of the molecular |
750 |
|
|
dynamics trajectories allows an assessment of why these molecules |
751 |
|
|
behave differently.}, |
752 |
|
|
annote = {376BF Times Cited:10 Cited References Count:16}, |
753 |
|
|
issn = {0267-8292}, |
754 |
|
|
uri = {<Go to ISI>://000165437800002}, |
755 |
tim |
2685 |
} |
756 |
|
|
|
757 |
tim |
2786 |
@ARTICLE{Cui2003, |
758 |
|
|
author = {B. X. Cui and M. Y. Shen and K. F. Freed}, |
759 |
|
|
title = {Folding and misfolding of the papillomavirus E6 interacting peptide |
760 |
|
|
E6ap}, |
761 |
|
|
journal = {Proceedings of the National Academy of Sciences of the United States |
762 |
|
|
of America}, |
763 |
|
|
year = {2003}, |
764 |
|
|
volume = {100}, |
765 |
|
|
pages = {7087-7092}, |
766 |
|
|
number = {12}, |
767 |
|
|
month = {Jun 10}, |
768 |
|
|
abstract = {All-atom Langevin dynamics simulations have been performed to study |
769 |
|
|
the folding pathways of the 18-residue binding domain fragment E6ap |
770 |
|
|
of the human papillomavirus E6 interacting peptide. Six independent |
771 |
|
|
folding trajectories, with a total duration of nearly 2 mus, all |
772 |
|
|
lead to the same native state in which the E6ap adopts a fluctuating |
773 |
|
|
a-helix structure in the central portion (Ser-4-Leu-13) but with |
774 |
|
|
very flexible N and C termini. Simulations starting from different |
775 |
|
|
core configurations exhibit the E6ap folding dynamics as either |
776 |
|
|
a two- or three-state folder with an intermediate misfolded state. |
777 |
|
|
The essential leucine hydrophobic core (Leu-9, Leu-12, and Leu-13) |
778 |
|
|
is well conserved in the native-state structure but absent in the |
779 |
|
|
intermediate structure, suggesting that the leucine core is not |
780 |
|
|
only essential for the binding activity of E6ap but also important |
781 |
|
|
for the stability of the native structure. The free energy landscape |
782 |
|
|
reveals a significant barrier between the basins separating the |
783 |
|
|
native and misfolded states. We also discuss the various underlying |
784 |
|
|
forces that drive the peptide into its native state.}, |
785 |
|
|
annote = {689LC Times Cited:3 Cited References Count:48}, |
786 |
|
|
issn = {0027-8424}, |
787 |
|
|
uri = {<Go to ISI>://000183493500037}, |
788 |
tim |
2685 |
} |
789 |
|
|
|
790 |
tim |
2786 |
@ARTICLE{Denisov2003, |
791 |
|
|
author = {S. I. Denisov and T. V. Lyutyy and K. N. Trohidou}, |
792 |
|
|
title = {Magnetic relaxation in finite two-dimensional nanoparticle ensembles}, |
793 |
|
|
journal = {Physical Review B}, |
794 |
|
|
year = {2003}, |
795 |
|
|
volume = {67}, |
796 |
|
|
pages = {-}, |
797 |
|
|
number = {1}, |
798 |
|
|
month = {Jan 1}, |
799 |
|
|
abstract = {We study the slow phase of thermally activated magnetic relaxation |
800 |
|
|
in finite two-dimensional ensembles of dipolar interacting ferromagnetic |
801 |
|
|
nanoparticles whose easy axes of magnetization are perpendicular |
802 |
|
|
to the distribution plane. We develop a method to numerically simulate |
803 |
|
|
the magnetic relaxation for the case that the smallest heights of |
804 |
|
|
the potential barriers between the equilibrium directions of the |
805 |
|
|
nanoparticle magnetic moments are much larger than the thermal energy. |
806 |
|
|
Within this framework, we analyze in detail the role that the correlations |
807 |
|
|
of the nanoparticle magnetic moments and the finite size of the |
808 |
|
|
nanoparticle ensemble play in magnetic relaxation.}, |
809 |
|
|
annote = {642XH Times Cited:11 Cited References Count:31}, |
810 |
|
|
issn = {1098-0121}, |
811 |
|
|
uri = {<Go to ISI>://000180830400056}, |
812 |
tim |
2685 |
} |
813 |
|
|
|
814 |
tim |
2786 |
@ARTICLE{Derreumaux1998, |
815 |
|
|
author = {P. Derreumaux and T. Schlick}, |
816 |
|
|
title = {The loop opening/closing motion of the enzyme triosephosphate isomerase}, |
817 |
|
|
journal = {Biophysical Journal}, |
818 |
|
|
year = {1998}, |
819 |
|
|
volume = {74}, |
820 |
|
|
pages = {72-81}, |
821 |
|
|
number = {1}, |
822 |
|
|
month = {Jan}, |
823 |
|
|
abstract = {To explore the origin of the large-scale motion of triosephosphate |
824 |
|
|
isomerase's flexible loop (residues 166 to 176) at the active site, |
825 |
|
|
several simulation protocols are employed both for the free enzyme |
826 |
|
|
in vacuo and for the free enzyme with some solvent modeling: high-temperature |
827 |
|
|
Langevin dynamics simulations, sampling by a #dynamics##driver# |
828 |
|
|
approach, and potential-energy surface calculations. Our focus is |
829 |
|
|
on obtaining the energy barrier to the enzyme's motion and establishing |
830 |
|
|
the nature of the loop movement. Previous calculations did not determine |
831 |
|
|
this energy barrier and the effect of solvent on the barrier. High-temperature |
832 |
|
|
molecular dynamics simulations and crystallographic studies have |
833 |
|
|
suggested a rigid-body motion with two hinges located at both ends |
834 |
|
|
of the loop; Brownian dynamics simulations at room temperature pointed |
835 |
|
|
to a very flexible behavior. The present simulations and analyses |
836 |
|
|
reveal that although solute/solvent hydrogen bonds play a crucial |
837 |
|
|
role in lowering the energy along the pathway, there still remains |
838 |
|
|
a high activation barrier, This finding clearly indicates that, |
839 |
|
|
if the loop opens and closes in the absence of a substrate at standard |
840 |
|
|
conditions (e.g., room temperature, appropriate concentration of |
841 |
|
|
isomerase), the time scale for transition is not in the nanosecond |
842 |
|
|
but rather the microsecond range. Our results also indicate that |
843 |
|
|
in the context of spontaneous opening in the free enzyme, the motion |
844 |
|
|
is of rigid-body type and that the specific interaction between |
845 |
|
|
residues Ala(176) and Tyr(208) plays a crucial role in the loop |
846 |
|
|
opening/closing mechanism.}, |
847 |
|
|
annote = {Zl046 Times Cited:30 Cited References Count:29}, |
848 |
|
|
issn = {0006-3495}, |
849 |
|
|
uri = {<Go to ISI>://000073393400009}, |
850 |
tim |
2685 |
} |
851 |
|
|
|
852 |
tim |
2786 |
@ARTICLE{Dullweber1997, |
853 |
|
|
author = {A. Dullweber and B. Leimkuhler and R. McLachlan}, |
854 |
|
|
title = {Symplectic splitting methods for rigid body molecular dynamics}, |
855 |
|
|
journal = {Journal of Chemical Physics}, |
856 |
|
|
year = {1997}, |
857 |
|
|
volume = {107}, |
858 |
|
|
pages = {5840-5851}, |
859 |
|
|
number = {15}, |
860 |
|
|
month = {Oct 15}, |
861 |
|
|
abstract = {Rigid body molecular models possess symplectic structure and time-reversal |
862 |
|
|
symmetry. Standard numerical integration methods destroy both properties, |
863 |
|
|
introducing nonphysical dynamical behavior such as numerically induced |
864 |
|
|
dissipative states and drift in the energy during long term simulations. |
865 |
|
|
This article describes the construction, implementation, and practical |
866 |
|
|
application of fast explicit symplectic-reversible integrators for |
867 |
|
|
multiple rigid body molecular simulations, These methods use a reduction |
868 |
|
|
to Euler equations for the free rigid body, together with a symplectic |
869 |
|
|
splitting technique. In every time step, the orientational dynamics |
870 |
|
|
of each rigid body is integrated by a sequence of planar rotations. |
871 |
|
|
Besides preserving the symplectic and reversible structures of the |
872 |
|
|
flow, this scheme accurately conserves the total angular momentum |
873 |
|
|
of a system of interacting rigid bodies. Excellent energy conservation |
874 |
|
|
fan be obtained relative to traditional methods, especially in long-time |
875 |
|
|
simulations. The method is implemented in a research code, ORIENT |
876 |
|
|
and compared with a quaternion/extrapolation scheme for the TIP4P |
877 |
|
|
model of water. Our experiments show that the symplectic-reversible |
878 |
|
|
scheme is far superior to the more traditional quaternion method. |
879 |
|
|
(C) 1997 American Institute of Physics.}, |
880 |
|
|
annote = {Ya587 Times Cited:35 Cited References Count:32}, |
881 |
|
|
issn = {0021-9606}, |
882 |
|
|
uri = {<Go to ISI>://A1997YA58700024}, |
883 |
tim |
2685 |
} |
884 |
|
|
|
885 |
tim |
2786 |
@ARTICLE{Edwards2005, |
886 |
|
|
author = {S. A. Edwards and D. R. M. Williams}, |
887 |
|
|
title = {Stretching a single diblock copolymer in a selective solvent: Langevin |
888 |
|
|
dynamics simulations}, |
889 |
|
|
journal = {Macromolecules}, |
890 |
|
|
year = {2005}, |
891 |
|
|
volume = {38}, |
892 |
|
|
pages = {10590-10595}, |
893 |
|
|
number = {25}, |
894 |
|
|
month = {Dec 13}, |
895 |
|
|
abstract = {Using the Langevin dynamics technique, we have carried out simulations |
896 |
|
|
of a single-chain flexible diblock copolymer. The polymer consists |
897 |
|
|
of two blocks of equal length, one very poorly solvated and the |
898 |
|
|
other close to theta-conditions. We study what happens when such |
899 |
|
|
a polymer is stretched, for a range of different stretching speeds, |
900 |
|
|
and correlate our observations with features in the plot of force |
901 |
|
|
vs extension. We find that at slow speeds this force profile does |
902 |
|
|
not increase monotonically, in disagreement with earlier predictions, |
903 |
|
|
and that at high speeds there is a strong dependence on which end |
904 |
|
|
of the polymer is pulled, as well as a high level of hysteresis.}, |
905 |
|
|
annote = {992EC Times Cited:0 Cited References Count:13}, |
906 |
|
|
issn = {0024-9297}, |
907 |
|
|
uri = {<Go to ISI>://000233866200035}, |
908 |
tim |
2685 |
} |
909 |
|
|
|
910 |
tim |
2786 |
@ARTICLE{Egberts1988, |
911 |
|
|
author = {E. Egberts and H. J. C. Berendsen}, |
912 |
|
|
title = {Molecular-Dynamics Simulation of a Smectic Liquid-Crystal with Atomic |
913 |
|
|
Detail}, |
914 |
|
|
journal = {Journal of Chemical Physics}, |
915 |
|
|
year = {1988}, |
916 |
|
|
volume = {89}, |
917 |
|
|
pages = {3718-3732}, |
918 |
|
|
number = {6}, |
919 |
|
|
month = {Sep 15}, |
920 |
|
|
annote = {Q0188 Times Cited:219 Cited References Count:43}, |
921 |
|
|
issn = {0021-9606}, |
922 |
|
|
uri = {<Go to ISI>://A1988Q018800036}, |
923 |
tim |
2685 |
} |
924 |
|
|
|
925 |
tim |
2786 |
@ARTICLE{Ermak1978, |
926 |
|
|
author = {D. L. Ermak and J. A. Mccammon}, |
927 |
|
|
title = {Brownian Dynamics with Hydrodynamic Interactions}, |
928 |
|
|
journal = {Journal of Chemical Physics}, |
929 |
|
|
year = {1978}, |
930 |
|
|
volume = {69}, |
931 |
|
|
pages = {1352-1360}, |
932 |
|
|
number = {4}, |
933 |
|
|
annote = {Fp216 Times Cited:785 Cited References Count:42}, |
934 |
|
|
issn = {0021-9606}, |
935 |
|
|
uri = {<Go to ISI>://A1978FP21600004}, |
936 |
tim |
2685 |
} |
937 |
|
|
|
938 |
tim |
2786 |
@ARTICLE{Fennell2004, |
939 |
|
|
author = {C. J. Fennell and J. D. Gezelter}, |
940 |
|
|
title = {On the structural and transport properties of the soft sticky dipole |
941 |
|
|
and related single-point water models}, |
942 |
|
|
journal = {Journal of Chemical Physics}, |
943 |
|
|
year = {2004}, |
944 |
|
|
volume = {120}, |
945 |
|
|
pages = {9175-9184}, |
946 |
|
|
number = {19}, |
947 |
|
|
month = {May 15}, |
948 |
|
|
abstract = {The density maximum and temperature dependence of the self-diffusion |
949 |
|
|
constant were investigated for the soft sticky dipole (SSD) water |
950 |
|
|
model and two related reparametrizations of this single-point model. |
951 |
|
|
A combination of microcanonical and isobaric-isothermal molecular |
952 |
|
|
dynamics simulations was used to calculate these properties, both |
953 |
|
|
with and without the use of reaction field to handle long-range |
954 |
|
|
electrostatics. The isobaric-isothermal simulations of the melting |
955 |
|
|
of both ice-I-h and ice-I-c showed a density maximum near 260 K. |
956 |
|
|
In most cases, the use of the reaction field resulted in calculated |
957 |
|
|
densities which were significantly lower than experimental densities. |
958 |
|
|
Analysis of self-diffusion constants shows that the original SSD |
959 |
|
|
model captures the transport properties of experimental water very |
960 |
|
|
well in both the normal and supercooled liquid regimes. We also |
961 |
|
|
present our reparametrized versions of SSD for use both with the |
962 |
|
|
reaction field or without any long-range electrostatic corrections. |
963 |
|
|
These are called the SSD/RF and SSD/E models, respectively. These |
964 |
|
|
modified models were shown to maintain or improve upon the experimental |
965 |
|
|
agreement with the structural and transport properties that can |
966 |
|
|
be obtained with either the original SSD or the density-corrected |
967 |
|
|
version of the original model (SSD1). Additionally, a novel low-density |
968 |
|
|
ice structure is presented which appears to be the most stable ice |
969 |
|
|
structure for the entire SSD family. (C) 2004 American Institute |
970 |
|
|
of Physics.}, |
971 |
|
|
annote = {816YY Times Cited:5 Cited References Count:39}, |
972 |
|
|
issn = {0021-9606}, |
973 |
|
|
uri = {<Go to ISI>://000221146400032}, |
974 |
tim |
2685 |
} |
975 |
|
|
|
976 |
tim |
2786 |
@ARTICLE{Fernandes2002, |
977 |
|
|
author = {M. X. Fernandes and J. G. {de la Torre}}, |
978 |
|
|
title = {Brownian dynamics simulation of rigid particles of arbitrary shape |
979 |
|
|
in external fields}, |
980 |
|
|
journal = {Biophysical Journal}, |
981 |
|
|
year = {2002}, |
982 |
|
|
volume = {83}, |
983 |
|
|
pages = {3039-3048}, |
984 |
|
|
number = {6}, |
985 |
|
|
month = {Dec}, |
986 |
|
|
abstract = {We have developed a Brownian dynamics simulation algorithm to generate |
987 |
|
|
Brownian trajectories of an isolated, rigid particle of arbitrary |
988 |
|
|
shape in the presence of electric fields or any other external agents. |
989 |
|
|
Starting from the generalized diffusion tensor, which can be calculated |
990 |
|
|
with the existing HYDRO software, the new program BROWNRIG (including |
991 |
|
|
a case-specific subprogram for the external agent) carries out a |
992 |
|
|
simulation that is analyzed later to extract the observable dynamic |
993 |
|
|
properties. We provide a variety of examples of utilization of this |
994 |
|
|
method, which serve as tests of its performance, and also illustrate |
995 |
|
|
its applicability. Examples include free diffusion, transport in |
996 |
|
|
an electric field, and diffusion in a restricting environment.}, |
997 |
|
|
annote = {633AD Times Cited:2 Cited References Count:43}, |
998 |
|
|
issn = {0006-3495}, |
999 |
|
|
uri = {<Go to ISI>://000180256300012}, |
1000 |
tim |
2685 |
} |
1001 |
|
|
|
1002 |
tim |
2786 |
@ARTICLE{Gay1981, |
1003 |
|
|
author = {J. G. Gay and B. J. Berne}, |
1004 |
|
|
title = {Modification of the Overlap Potential to Mimic a Linear Site-Site |
1005 |
|
|
Potential}, |
1006 |
|
|
journal = {Journal of Chemical Physics}, |
1007 |
|
|
year = {1981}, |
1008 |
|
|
volume = {74}, |
1009 |
|
|
pages = {3316-3319}, |
1010 |
|
|
number = {6}, |
1011 |
|
|
annote = {Lj347 Times Cited:482 Cited References Count:13}, |
1012 |
|
|
issn = {0021-9606}, |
1013 |
|
|
uri = {<Go to ISI>://A1981LJ34700029}, |
1014 |
tim |
2685 |
} |
1015 |
|
|
|
1016 |
tim |
2786 |
@ARTICLE{Gelin1999, |
1017 |
|
|
author = {M. F. Gelin}, |
1018 |
|
|
title = {Inertial effects in the Brownian dynamics with rigid constraints}, |
1019 |
|
|
journal = {Macromolecular Theory and Simulations}, |
1020 |
|
|
year = {1999}, |
1021 |
|
|
volume = {8}, |
1022 |
|
|
pages = {529-543}, |
1023 |
|
|
number = {6}, |
1024 |
|
|
month = {Nov}, |
1025 |
|
|
abstract = {To investigate the influence of inertial effects on the dynamics of |
1026 |
|
|
an assembly of beads subjected to rigid constraints and placed in |
1027 |
|
|
a buffer medium, a convenient method to introduce suitable generalized |
1028 |
|
|
coordinates is presented. Without any restriction on the nature |
1029 |
|
|
of the soft forces involved (both stochastic and deterministic), |
1030 |
|
|
pertinent Langevin equations are derived. Provided that the Brownian |
1031 |
|
|
forces are Gaussian and Markovian, the corresponding Fokker-Planck |
1032 |
|
|
equation (FPE) is obtained in the complete phase space of generalized |
1033 |
|
|
coordinates and momenta. The correct short time behavior for correlation |
1034 |
|
|
functions (CFs) of generalized coordinates is established, and the |
1035 |
|
|
diffusion equation with memory (DEM) is deduced from the FPE in |
1036 |
|
|
the high friction Limit. The DEM is invoked to perform illustrative |
1037 |
|
|
calculations in two dimensions of the orientational CFs for once |
1038 |
|
|
broken nonrigid rods immobilized on a surface. These calculations |
1039 |
|
|
reveal that the CFs under certain conditions exhibit an oscillatory |
1040 |
|
|
behavior, which is irreproducible within the standard diffusion |
1041 |
|
|
equation. Several methods are considered for the approximate solution |
1042 |
|
|
of the DEM, and their application to three dimensional DEMs is discussed.}, |
1043 |
|
|
annote = {257MM Times Cited:2 Cited References Count:82}, |
1044 |
|
|
issn = {1022-1344}, |
1045 |
|
|
uri = {<Go to ISI>://000083785700002}, |
1046 |
tim |
2685 |
} |
1047 |
|
|
|
1048 |
tim |
2786 |
@BOOK{Goldstein2001, |
1049 |
|
|
title = {Classical Mechanics}, |
1050 |
|
|
publisher = {Addison Wesley}, |
1051 |
|
|
year = {2001}, |
1052 |
|
|
author = {H. Goldstein and C. Poole and J. Safko}, |
1053 |
|
|
address = {San Francisco}, |
1054 |
|
|
edition = {3rd}, |
1055 |
tim |
2685 |
} |
1056 |
|
|
|
1057 |
tim |
2786 |
@ARTICLE{Gray2003, |
1058 |
|
|
author = {J. J. Gray and S. Moughon and C. Wang and O. Schueler-Furman and |
1059 |
|
|
B. Kuhlman and C. A. Rohl and D. Baker}, |
1060 |
|
|
title = {Protein-protein docking with simultaneous optimization of rigid-body |
1061 |
|
|
displacement and side-chain conformations}, |
1062 |
|
|
journal = {Journal of Molecular Biology}, |
1063 |
|
|
year = {2003}, |
1064 |
|
|
volume = {331}, |
1065 |
|
|
pages = {281-299}, |
1066 |
|
|
number = {1}, |
1067 |
|
|
month = {Aug 1}, |
1068 |
|
|
abstract = {Protein-protein docking algorithms provide a means to elucidate structural |
1069 |
|
|
details for presently unknown complexes. Here, we present and evaluate |
1070 |
|
|
a new method to predict protein-protein complexes from the coordinates |
1071 |
|
|
of the unbound monomer components. The method employs a low-resolution, |
1072 |
|
|
rigid-body, Monte Carlo search followed by simultaneous optimization |
1073 |
|
|
of backbone displacement and side-chain conformations using Monte |
1074 |
|
|
Carlo minimization. Up to 10(5) independent simulations are carried |
1075 |
|
|
out, and the resulting #decoys# are ranked using an energy function |
1076 |
|
|
dominated by van der Waals interactions, an implicit solvation model, |
1077 |
|
|
and an orientation-dependent hydrogen bonding potential. Top-ranking |
1078 |
|
|
decoys are clustered to select the final predictions. Small-perturbation |
1079 |
|
|
studies reveal the formation of binding funnels in 42 of 54 cases |
1080 |
|
|
using coordinates derived from the bound complexes and in 32 of |
1081 |
|
|
54 cases using independently determined coordinates of one or both |
1082 |
|
|
monomers. Experimental binding affinities correlate with the calculated |
1083 |
|
|
score function and explain the predictive success or failure of |
1084 |
|
|
many targets. Global searches using one or both unbound components |
1085 |
|
|
predict at least 25% of the native residue-residue contacts in 28 |
1086 |
|
|
of the 32 cases where binding funnels exist. The results suggest |
1087 |
|
|
that the method may soon be useful for generating models of biologically |
1088 |
|
|
important complexes from the structures of the isolated components, |
1089 |
|
|
but they also highlight the challenges that must be met to achieve |
1090 |
|
|
consistent and accurate prediction of protein-protein interactions. |
1091 |
|
|
(C) 2003 Elsevier Ltd. All rights reserved.}, |
1092 |
|
|
annote = {704QL Times Cited:48 Cited References Count:60}, |
1093 |
|
|
issn = {0022-2836}, |
1094 |
|
|
uri = {<Go to ISI>://000184351300022}, |
1095 |
tim |
2685 |
} |
1096 |
|
|
|
1097 |
tim |
2786 |
@ARTICLE{Hao1993, |
1098 |
|
|
author = {M. H. Hao and M. R. Pincus and S. Rackovsky and H. A. Scheraga}, |
1099 |
|
|
title = {Unfolding and Refolding of the Native Structure of Bovine Pancreatic |
1100 |
|
|
Trypsin-Inhibitor Studied by Computer-Simulations}, |
1101 |
|
|
journal = {Biochemistry}, |
1102 |
|
|
year = {1993}, |
1103 |
|
|
volume = {32}, |
1104 |
|
|
pages = {9614-9631}, |
1105 |
|
|
number = {37}, |
1106 |
|
|
month = {Sep 21}, |
1107 |
|
|
abstract = {A new procedure for studying the folding and unfolding of proteins, |
1108 |
|
|
with an application to bovine pancreatic trypsin inhibitor (BPTI), |
1109 |
|
|
is reported. The unfolding and refolding of the native structure |
1110 |
|
|
of the protein are characterized by the dimensions of the protein, |
1111 |
|
|
expressed in terms of the three principal radii of the structure |
1112 |
|
|
considered as an ellipsoid. A dynamic equation, describing the variations |
1113 |
|
|
of the principal radii on the unfolding path, and a numerical procedure |
1114 |
|
|
to solve this equation are proposed. Expanded and distorted conformations |
1115 |
|
|
are refolded to the native structure by a dimensional-constraint |
1116 |
|
|
energy minimization procedure. A unique and reproducible unfolding |
1117 |
|
|
pathway for an intermediate of BPTI lacking the [30,51] disulfide |
1118 |
|
|
bond is obtained. The resulting unfolded conformations are extended; |
1119 |
|
|
they contain near-native local structure, but their longest principal |
1120 |
|
|
radii are more than 2.5 times greater than that of the native structure. |
1121 |
|
|
The most interesting finding is that the majority of expanded conformations, |
1122 |
|
|
generated under various conditions, can be refolded closely to the |
1123 |
|
|
native structure, as measured by the correct overall chain fold, |
1124 |
|
|
by the rms deviations from the native structure of only 1.9-3.1 |
1125 |
|
|
angstrom, and by the energy differences of about 10 kcal/mol from |
1126 |
|
|
the native structure. Introduction of the [30,51] disulfide bond |
1127 |
|
|
at this stage, followed by minimization, improves the closeness |
1128 |
|
|
of the refolded structures to the native structure, reducing the |
1129 |
|
|
rms deviations to 0.9-2.0 angstrom. The unique refolding of these |
1130 |
|
|
expanded structures over such a large conformational space implies |
1131 |
|
|
that the folding is strongly dictated by the interactions in the |
1132 |
|
|
amino acid sequence of BPTI. The simulations indicate that, under |
1133 |
|
|
conditions that favor a compact structure as mimicked by the volume |
1134 |
|
|
constraints in our algorithm; the expanded conformations have a |
1135 |
|
|
strong tendency to move toward the native structure; therefore, |
1136 |
|
|
they probably would be favorable folding intermediates. The results |
1137 |
|
|
presented here support a general model for protein folding, i.e., |
1138 |
|
|
progressive formation of partially folded structural units, followed |
1139 |
|
|
by collapse to the compact native structure. The general applicability |
1140 |
|
|
of the procedure is also discussed.}, |
1141 |
|
|
annote = {Ly294 Times Cited:27 Cited References Count:57}, |
1142 |
|
|
issn = {0006-2960}, |
1143 |
|
|
uri = {<Go to ISI>://A1993LY29400014}, |
1144 |
tim |
2685 |
} |
1145 |
|
|
|
1146 |
tim |
2786 |
@ARTICLE{Hinsen2000, |
1147 |
|
|
author = {K. Hinsen and A. J. Petrescu and S. Dellerue and M. C. Bellissent-Funel |
1148 |
|
|
and G. R. Kneller}, |
1149 |
|
|
title = {Harmonicity in slow protein dynamics}, |
1150 |
|
|
journal = {Chemical Physics}, |
1151 |
|
|
year = {2000}, |
1152 |
|
|
volume = {261}, |
1153 |
|
|
pages = {25-37}, |
1154 |
|
|
number = {1-2}, |
1155 |
|
|
month = {Nov 1}, |
1156 |
|
|
abstract = {The slow dynamics of proteins around its native folded state is usually |
1157 |
|
|
described by diffusion in a strongly anharmonic potential. In this |
1158 |
|
|
paper, we try to understand the form and origin of the anharmonicities, |
1159 |
|
|
with the principal aim of gaining a better understanding of the |
1160 |
|
|
principal motion types, but also in order to develop more efficient |
1161 |
|
|
numerical methods for simulating neutron scattering spectra of large |
1162 |
|
|
proteins. First, we decompose a molecular dynamics (MD) trajectory |
1163 |
|
|
of 1.5 ns for a C-phycocyanin dimer surrounded by a layer of water |
1164 |
|
|
into three contributions that we expect to be independent: the global |
1165 |
|
|
motion of the residues, the rigid-body motion of the sidechains |
1166 |
|
|
relative to the backbone, and the internal deformations of the sidechains. |
1167 |
|
|
We show that they are indeed almost independent by verifying the |
1168 |
|
|
factorization of the incoherent intermediate scattering function. |
1169 |
|
|
Then, we show that the global residue motions, which include all |
1170 |
|
|
large-scale backbone motions, can be reproduced by a simple harmonic |
1171 |
|
|
model which contains two contributions: a short-time vibrational |
1172 |
|
|
term, described by a standard normal mode calculation in a local |
1173 |
|
|
minimum, and a long-time diffusive term, described by Brownian motion |
1174 |
|
|
in an effective harmonic potential. The potential and the friction |
1175 |
|
|
constants were fitted to the MD data. The major anharmonic contribution |
1176 |
|
|
to the incoherent intermediate scattering function comes from the |
1177 |
|
|
rigid-body diffusion of the sidechains. This model can be used to |
1178 |
|
|
calculate scattering functions for large proteins and for long-time |
1179 |
|
|
scales very efficiently, and thus provides a useful complement to |
1180 |
|
|
MD simulations, which are best suited for detailed studies on smaller |
1181 |
|
|
systems or for shorter time scales. (C) 2000 Elsevier Science B.V. |
1182 |
|
|
All rights reserved.}, |
1183 |
|
|
annote = {Sp. Iss. SI 368MT Times Cited:16 Cited References Count:31}, |
1184 |
|
|
issn = {0301-0104}, |
1185 |
|
|
uri = {<Go to ISI>://000090121700003}, |
1186 |
tim |
2685 |
} |
1187 |
|
|
|
1188 |
tim |
2786 |
@ARTICLE{Ho1992, |
1189 |
|
|
author = {C. Ho and C. D. Stubbs}, |
1190 |
|
|
title = {Hydration at the Membrane Protein-Lipid Interface}, |
1191 |
|
|
journal = {Biophysical Journal}, |
1192 |
|
|
year = {1992}, |
1193 |
|
|
volume = {63}, |
1194 |
|
|
pages = {897-902}, |
1195 |
|
|
number = {4}, |
1196 |
|
|
month = {Oct}, |
1197 |
|
|
abstract = {Evidence has been found for the existence water at the protein-lipid |
1198 |
|
|
hydrophobic interface ot the membrane proteins, gramicidin and apocytochrome |
1199 |
|
|
C, using two related fluorescence spectroscopic approaches. The |
1200 |
|
|
first approach exploited the fact that the presence of water in |
1201 |
|
|
the excited state solvent cage of a fluorophore increases the rate |
1202 |
|
|
of decay. For 1,6-diphenyl-1,3,5-hexatriene (DPH) and 1-palmitoyl-2-[[2-[4-(6-phenyl-trans-1,3,5-hexatrienyl) |
1203 |
|
|
phenyl]ethyl]carbonyl]-3-sn-PC (DPH-PC), where the fluorophores |
1204 |
|
|
are located in the hydrophobic core of the lipid bilayer, the introduction |
1205 |
|
|
of gramicidin reduced the fluorescence lifetime, indicative of an |
1206 |
|
|
increased presence of water in the bilayer. Since a high protein:lipid |
1207 |
|
|
ratio was used, the fluorophores were forced to be adjacent to the |
1208 |
|
|
protein hydrophobic surface, hence the presence of water in this |
1209 |
|
|
region could be inferred. Cholesterol is known to reduce the water |
1210 |
|
|
content of lipid bilayers and this effect was maintained at the |
1211 |
|
|
protein-lipid interface with both gramicidin and apocytochrome C, |
1212 |
|
|
again suggesting hydration in this region. The second approach was |
1213 |
|
|
to use the fluorescence enhancement induced by exchanging deuterium |
1214 |
|
|
oxide (D2O) for H2O. Both the fluorescence intensities of trimethylammonium-DPH, |
1215 |
|
|
located in the lipid head group region, and of the gramicidin intrinsic |
1216 |
|
|
tryptophans were greater in a D2O buffer compared with H2O, showing |
1217 |
|
|
that the fluorophores were exposed to water in the bilayer at the |
1218 |
|
|
protein-lipid interface. In the presence of cholesterol the fluorescence |
1219 |
|
|
intensity ratio of D2O to H2O decreased, indicating a removal of |
1220 |
|
|
water by the cholesterol, in keeping with the lifetime data. Altered |
1221 |
|
|
hydration at the protein-lipid interface could affect conformation, |
1222 |
|
|
thereby offering a new route by which membrane protein functioning |
1223 |
|
|
may be modified.}, |
1224 |
|
|
annote = {Ju251 Times Cited:55 Cited References Count:44}, |
1225 |
|
|
issn = {0006-3495}, |
1226 |
|
|
uri = {<Go to ISI>://A1992JU25100002}, |
1227 |
tim |
2685 |
} |
1228 |
|
|
|
1229 |
tim |
2786 |
@ARTICLE{Huh2004, |
1230 |
|
|
author = {Y. Huh and N. M. Cann}, |
1231 |
|
|
title = {Discrimination in isotropic, nematic, and smectic phases of chiral |
1232 |
|
|
calamitic molecules: A computer simulation study}, |
1233 |
|
|
journal = {Journal of Chemical Physics}, |
1234 |
|
|
year = {2004}, |
1235 |
|
|
volume = {121}, |
1236 |
|
|
pages = {10299-10308}, |
1237 |
|
|
number = {20}, |
1238 |
|
|
month = {Nov 22}, |
1239 |
|
|
abstract = {Racemic fluids of chiral calamitic molecules are investigated with |
1240 |
|
|
molecular dynamics simulations. In particular, the phase behavior |
1241 |
|
|
as a function of density is examined for eight racemates. The relationship |
1242 |
|
|
between chiral discrimination and orientational order in the phase |
1243 |
|
|
is explored. We find that the transition from the isotropic phase |
1244 |
|
|
to a liquid crystal phase is accompanied by an increase in chiral |
1245 |
|
|
discrimination, as measured by differences in radial distributions. |
1246 |
|
|
Among ordered phases, discrimination is largest for smectic phases |
1247 |
|
|
with a significant preference for heterochiral contact within the |
1248 |
|
|
layers. (C) 2004 American Institute of Physics.}, |
1249 |
|
|
annote = {870FJ Times Cited:0 Cited References Count:63}, |
1250 |
|
|
issn = {0021-9606}, |
1251 |
|
|
uri = {<Go to ISI>://000225042700059}, |
1252 |
tim |
2685 |
} |
1253 |
|
|
|
1254 |
tim |
2786 |
@ARTICLE{Izaguirre2001, |
1255 |
|
|
author = {J. A. Izaguirre and D. P. Catarello and J. M. Wozniak and R. D. Skeel}, |
1256 |
|
|
title = {Langevin stabilization of molecular dynamics}, |
1257 |
|
|
journal = {Journal of Chemical Physics}, |
1258 |
|
|
year = {2001}, |
1259 |
|
|
volume = {114}, |
1260 |
|
|
pages = {2090-2098}, |
1261 |
|
|
number = {5}, |
1262 |
|
|
month = {Feb 1}, |
1263 |
|
|
abstract = {In this paper we show the possibility of using very mild stochastic |
1264 |
|
|
damping to stabilize long time step integrators for Newtonian molecular |
1265 |
|
|
dynamics. More specifically, stable and accurate integrations are |
1266 |
|
|
obtained for damping coefficients that are only a few percent of |
1267 |
|
|
the natural decay rate of processes of interest, such as the velocity |
1268 |
|
|
autocorrelation function. Two new multiple time stepping integrators, |
1269 |
|
|
Langevin Molly (LM) and Brunger-Brooks-Karplus-Molly (BBK-M), are |
1270 |
|
|
introduced in this paper. Both use the mollified impulse method |
1271 |
|
|
for the Newtonian term. LM uses a discretization of the Langevin |
1272 |
|
|
equation that is exact for the constant force, and BBK-M uses the |
1273 |
|
|
popular Brunger-Brooks-Karplus integrator (BBK). These integrators, |
1274 |
|
|
along with an extrapolative method called LN, are evaluated across |
1275 |
|
|
a wide range of damping coefficient values. When large damping coefficients |
1276 |
|
|
are used, as one would for the implicit modeling of solvent molecules, |
1277 |
|
|
the method LN is superior, with LM closely following. However, with |
1278 |
|
|
mild damping of 0.2 ps(-1), LM produces the best results, allowing |
1279 |
|
|
long time steps of 14 fs in simulations containing explicitly modeled |
1280 |
|
|
flexible water. With BBK-M and the same damping coefficient, time |
1281 |
|
|
steps of 12 fs are possible for the same system. Similar results |
1282 |
|
|
are obtained for a solvated protein-DNA simulation of estrogen receptor |
1283 |
|
|
ER with estrogen response element ERE. A parallel version of BBK-M |
1284 |
|
|
runs nearly three times faster than the Verlet-I/r-RESPA (reversible |
1285 |
|
|
reference system propagator algorithm) when using the largest stable |
1286 |
|
|
time step on each one, and it also parallelizes well. The computation |
1287 |
|
|
of diffusion coefficients for flexible water and ER/ERE shows that |
1288 |
|
|
when mild damping of up to 0.2 ps-1 is used the dynamics are not |
1289 |
|
|
significantly distorted. (C) 2001 American Institute of Physics.}, |
1290 |
|
|
annote = {397CQ Times Cited:14 Cited References Count:36}, |
1291 |
|
|
issn = {0021-9606}, |
1292 |
|
|
uri = {<Go to ISI>://000166676100020}, |
1293 |
tim |
2685 |
} |
1294 |
|
|
|
1295 |
tim |
2786 |
@ARTICLE{Gray2003, |
1296 |
|
|
author = {J.~J Gray,S. Moughon, C. Wang }, |
1297 |
|
|
title = {Protein-protein docking with simultaneous optimization of rigid-body |
1298 |
|
|
displacement and side-chain conformations}, |
1299 |
|
|
journal = {jmb}, |
1300 |
|
|
year = {2003}, |
1301 |
|
|
volume = {331}, |
1302 |
|
|
pages = {281-299}, |
1303 |
tim |
2685 |
} |
1304 |
|
|
|
1305 |
tim |
2786 |
@ARTICLE{Klimov1997, |
1306 |
|
|
author = {D. K. Klimov and D. Thirumalai}, |
1307 |
|
|
title = {Viscosity dependence of the folding rates of proteins}, |
1308 |
|
|
journal = {Physical Review Letters}, |
1309 |
|
|
year = {1997}, |
1310 |
|
|
volume = {79}, |
1311 |
|
|
pages = {317-320}, |
1312 |
|
|
number = {2}, |
1313 |
|
|
month = {Jul 14}, |
1314 |
|
|
abstract = {The viscosity (eta) dependence of the folding rates for four sequences |
1315 |
|
|
(the native state of three sequences is a beta sheet, while the |
1316 |
|
|
fourth forms an alpha helix) is calculated for off-lattice models |
1317 |
|
|
of proteins. Assuming that the dynamics is given by the Langevin |
1318 |
|
|
equation, we show that the folding rates increase linearly at low |
1319 |
|
|
viscosities eta, decrease as 1/eta at large eta, and have a maximum |
1320 |
|
|
at intermediate values. The Kramers' theory of barrier crossing |
1321 |
|
|
provides a quantitative fit of the numerical results. By mapping |
1322 |
|
|
the simulation results to real proteins we estimate that for optimized |
1323 |
|
|
sequences the time scale for forming a four turn alpha-helix topology |
1324 |
|
|
is about 500 ns, whereas for beta sheet it is about 10 mu s.}, |
1325 |
|
|
annote = {Xk293 Times Cited:77 Cited References Count:17}, |
1326 |
|
|
issn = {0031-9007}, |
1327 |
|
|
uri = {<Go to ISI>://A1997XK29300035}, |
1328 |
tim |
2685 |
} |
1329 |
|
|
|
1330 |
tim |
2786 |
@ARTICLE{Lansac2001, |
1331 |
|
|
author = {Y. Lansac and M. A. Glaser and N. A. Clark}, |
1332 |
|
|
title = {Microscopic structure and dynamics of a partial bilayer smectic liquid |
1333 |
|
|
crystal}, |
1334 |
|
|
journal = {Physical Review E}, |
1335 |
|
|
year = {2001}, |
1336 |
|
|
volume = {6405}, |
1337 |
|
|
pages = {-}, |
1338 |
|
|
number = {5}, |
1339 |
|
|
month = {Nov}, |
1340 |
|
|
abstract = {Cyanobiphenyls (nCB's) represent a useful and intensively studied |
1341 |
|
|
class of mesogens. Many of the peculiar properties of nCB's (e.g., |
1342 |
|
|
the occurence of the partial bilayer smectic-A(d) phase) are thought |
1343 |
|
|
to be a manifestation of short-range antiparallel association of |
1344 |
|
|
neighboring molecules, resulting from strong dipole-dipole interactions |
1345 |
|
|
between cyano groups. To test and extend existing models of microscopic |
1346 |
|
|
ordering in nCB's, we carry out large-scale atomistic simulation |
1347 |
|
|
studies of the microscopic structure and dynamics of the Sm-A(d) |
1348 |
|
|
phase of 4-octyl-4'-cyanobiphenyl (8CB). We compute a variety of |
1349 |
|
|
thermodynamic, structural, and dynamical properties for this material, |
1350 |
|
|
and make a detailed comparison of our results with experimental |
1351 |
|
|
measurements in order to validate our molecular model. Semiquantitative |
1352 |
|
|
agreement with experiment is found: the smectic layer spacing and |
1353 |
|
|
mass density are well reproduced, translational diffusion constants |
1354 |
|
|
are similar to experiment, but the orientational ordering of alkyl |
1355 |
|
|
chains is overestimated. This simulation provides a detailed picture |
1356 |
|
|
of molecular conformation, smectic layer structure, and intermolecular |
1357 |
|
|
correlations in Sm-A(d) 8CB, and demonstrates that pronounced short-range |
1358 |
|
|
antiparallel association of molecules arising from dipole-dipole |
1359 |
|
|
interactions plays a dominant role in determining the molecular-scale |
1360 |
|
|
structure of 8CB.}, |
1361 |
|
|
annote = {Part 1 496QF Times Cited:10 Cited References Count:60}, |
1362 |
|
|
issn = {1063-651X}, |
1363 |
|
|
uri = {<Go to ISI>://000172406900063}, |
1364 |
tim |
2685 |
} |
1365 |
|
|
|
1366 |
tim |
2786 |
@ARTICLE{Lansac2003, |
1367 |
|
|
author = {Y. Lansac and P. K. Maiti and N. A. Clark and M. A. Glaser}, |
1368 |
|
|
title = {Phase behavior of bent-core molecules}, |
1369 |
|
|
journal = {Physical Review E}, |
1370 |
|
|
year = {2003}, |
1371 |
|
|
volume = {67}, |
1372 |
|
|
pages = {-}, |
1373 |
|
|
number = {1}, |
1374 |
|
|
month = {Jan}, |
1375 |
|
|
abstract = {Recently, a new class of smectic liquid crystal phases characterized |
1376 |
|
|
by the spontaneous formation of macroscopic chiral domains from |
1377 |
|
|
achiral bent-core molecules has been discovered. We have carried |
1378 |
|
|
out Monte Carlo simulations of a minimal hard spherocylinder dimer |
1379 |
|
|
model to investigate the role of excluded volume interactions in |
1380 |
|
|
determining the phase behavior of bent-core materials and to probe |
1381 |
|
|
the molecular origins of polar and chiral symmetry breaking. We |
1382 |
|
|
present the phase diagram of hard spherocylinder dimers of length-diameter |
1383 |
|
|
ratio of 5 as a function of pressure or density and dimer opening |
1384 |
|
|
angle psi. With decreasing psi, a transition from a nonpolar to |
1385 |
|
|
a polar smectic A phase is observed near psi=167degrees, and the |
1386 |
|
|
nematic phase becomes thermodynamically unstable for psi<135degrees. |
1387 |
|
|
Free energy calculations indicate that the antipolar smectic A (SmAP(A)) |
1388 |
|
|
phase is more stable than the polar smectic A phase (SmAP(F)). No |
1389 |
|
|
chiral smectic or biaxial nematic phases were found.}, |
1390 |
|
|
annote = {Part 1 646CM Times Cited:15 Cited References Count:38}, |
1391 |
|
|
issn = {1063-651X}, |
1392 |
|
|
uri = {<Go to ISI>://000181017300042}, |
1393 |
tim |
2685 |
} |
1394 |
|
|
|
1395 |
tim |
2786 |
@BOOK{Leach2001, |
1396 |
|
|
title = {Molecular Modeling: Principles and Applications}, |
1397 |
|
|
publisher = {Pearson Educated Limited}, |
1398 |
|
|
year = {2001}, |
1399 |
|
|
author = {A. Leach}, |
1400 |
|
|
address = {Harlow, England}, |
1401 |
|
|
edition = {2nd}, |
1402 |
tim |
2685 |
} |
1403 |
|
|
|
1404 |
tim |
2786 |
@BOOK{Leimkuhler2004, |
1405 |
|
|
title = {Simulating Hamiltonian Dynamics}, |
1406 |
|
|
publisher = {Cambridge University Press}, |
1407 |
|
|
year = {2004}, |
1408 |
|
|
author = {B. Leimkuhler and S. Reich}, |
1409 |
|
|
address = {Cambridge}, |
1410 |
tim |
2685 |
} |
1411 |
|
|
|
1412 |
tim |
2786 |
@ARTICLE{Levelut1981, |
1413 |
|
|
author = {A. M. Levelut and R. J. Tarento and F. Hardouin and M. F. Achard |
1414 |
|
|
and G. Sigaud}, |
1415 |
|
|
title = {Number of Sa Phases}, |
1416 |
|
|
journal = {Physical Review A}, |
1417 |
|
|
year = {1981}, |
1418 |
|
|
volume = {24}, |
1419 |
|
|
pages = {2180-2186}, |
1420 |
|
|
number = {4}, |
1421 |
|
|
annote = {Ml751 Times Cited:96 Cited References Count:16}, |
1422 |
|
|
issn = {1050-2947}, |
1423 |
|
|
uri = {<Go to ISI>://A1981ML75100057}, |
1424 |
tim |
2685 |
} |
1425 |
|
|
|
1426 |
tim |
2786 |
@ARTICLE{Lieb1982, |
1427 |
|
|
author = {W. R. Lieb and M. Kovalycsik and R. Mendelsohn}, |
1428 |
|
|
title = {Do Clinical-Levels of General-Anesthetics Affect Lipid Bilayers - |
1429 |
|
|
Evidence from Raman-Scattering}, |
1430 |
|
|
journal = {Biochimica Et Biophysica Acta}, |
1431 |
|
|
year = {1982}, |
1432 |
|
|
volume = {688}, |
1433 |
|
|
pages = {388-398}, |
1434 |
|
|
number = {2}, |
1435 |
|
|
annote = {Nu461 Times Cited:40 Cited References Count:28}, |
1436 |
|
|
issn = {0006-3002}, |
1437 |
|
|
uri = {<Go to ISI>://A1982NU46100012}, |
1438 |
tim |
2685 |
} |
1439 |
|
|
|
1440 |
tim |
2786 |
@ARTICLE{Link1997, |
1441 |
|
|
author = {D. R. Link and G. Natale and R. Shao and J. E. Maclennan and N. A. |
1442 |
|
|
Clark and E. Korblova and D. M. Walba}, |
1443 |
|
|
title = {Spontaneous formation of macroscopic chiral domains in a fluid smectic |
1444 |
|
|
phase of achiral molecules}, |
1445 |
|
|
journal = {Science}, |
1446 |
|
|
year = {1997}, |
1447 |
|
|
volume = {278}, |
1448 |
|
|
pages = {1924-1927}, |
1449 |
|
|
number = {5345}, |
1450 |
|
|
month = {Dec 12}, |
1451 |
|
|
abstract = {A smectic liquid-crystal phase made from achiral molecules with bent |
1452 |
|
|
cores was found to have fluid layers that exhibit two spontaneous |
1453 |
|
|
symmetry-breaking instabilities: polar molecular orientational ordering |
1454 |
|
|
about the layer normal and molecular tilt. These instabilities combine |
1455 |
|
|
to form a chiral layer structure with a handedness that depends |
1456 |
|
|
on the sign of the tilt. The bulk states are either antiferroelectric-racemic, |
1457 |
|
|
with the layer polar direction and handedness alternating in sign |
1458 |
|
|
from layer to layer, or antiferroelectric-chiral, which is of uniform |
1459 |
|
|
layer handedness. Both states exhibit an electric field-induced |
1460 |
|
|
transition from antiferroelectric to ferroelectric.}, |
1461 |
|
|
annote = {Yl002 Times Cited:407 Cited References Count:25}, |
1462 |
|
|
issn = {0036-8075}, |
1463 |
|
|
uri = {<Go to ISI>://A1997YL00200028}, |
1464 |
tim |
2685 |
} |
1465 |
|
|
|
1466 |
tim |
2786 |
@ARTICLE{Liwo2005, |
1467 |
|
|
author = {A. Liwo and M. Khalili and H. A. Scheraga}, |
1468 |
|
|
title = {Ab initio simulations of protein folding pathways by molecular dynamics |
1469 |
|
|
with the united-residue (UNRES) model of polypeptide chains}, |
1470 |
|
|
journal = {Febs Journal}, |
1471 |
|
|
year = {2005}, |
1472 |
|
|
volume = {272}, |
1473 |
|
|
pages = {359-360}, |
1474 |
|
|
month = {Jul}, |
1475 |
|
|
annote = {Suppl. 1 005MG Times Cited:0 Cited References Count:0}, |
1476 |
|
|
issn = {1742-464X}, |
1477 |
|
|
uri = {<Go to ISI>://000234826102043}, |
1478 |
tim |
2685 |
} |
1479 |
|
|
|
1480 |
tim |
2786 |
@BOOK{Marion1990, |
1481 |
|
|
title = {Classical Dynamics of Particles and Systems}, |
1482 |
|
|
publisher = {Academic Press}, |
1483 |
|
|
year = {1990}, |
1484 |
|
|
author = {J.~B. Marion}, |
1485 |
|
|
address = {New York}, |
1486 |
|
|
edition = {2rd}, |
1487 |
tim |
2685 |
} |
1488 |
|
|
|
1489 |
tim |
2786 |
@ARTICLE{McLachlan1993, |
1490 |
|
|
author = {R.~I McLachlan}, |
1491 |
|
|
title = {Explicit Lie-Poisson integration and the Euler equations}, |
1492 |
|
|
journal = {prl}, |
1493 |
|
|
year = {1993}, |
1494 |
|
|
volume = {71}, |
1495 |
|
|
pages = {3043-3046}, |
1496 |
tim |
2685 |
} |
1497 |
|
|
|
1498 |
tim |
2786 |
@ARTICLE{McLachlan2005, |
1499 |
|
|
author = {R. I. McLachlan and A. Zanna}, |
1500 |
|
|
title = {The discrete Moser-Veselov algorithm for the free rigid body, revisited}, |
1501 |
|
|
journal = {Foundations of Computational Mathematics}, |
1502 |
|
|
year = {2005}, |
1503 |
|
|
volume = {5}, |
1504 |
|
|
pages = {87-123}, |
1505 |
|
|
number = {1}, |
1506 |
|
|
month = {Feb}, |
1507 |
|
|
abstract = {In this paper we revisit the Moser-Veselov description of the free |
1508 |
|
|
rigid body in body coordinates, which, in the 3 x 3 case, can be |
1509 |
|
|
implemented as an explicit, second-order, integrable approximation |
1510 |
|
|
of the continuous solution. By backward error analysis, we study |
1511 |
|
|
the modified vector field which is integrated exactly by the discrete |
1512 |
|
|
algorithm. We deduce that the discrete Moser-Veselov (DMV) is well |
1513 |
|
|
approximated to higher order by time reparametrizations of the continuous |
1514 |
|
|
equations (modified vector field). We use the modified vector field |
1515 |
|
|
to scale the initial data of the DMV to improve the order of the |
1516 |
|
|
approximation and show the equivalence of the DMV and the RATTLE |
1517 |
|
|
algorithm. Numerical integration with these preprocessed initial |
1518 |
|
|
data is several orders of magnitude more accurate than the original |
1519 |
|
|
DMV and RATTLE approach.}, |
1520 |
|
|
annote = {911NS Times Cited:0 Cited References Count:14}, |
1521 |
|
|
issn = {1615-3375}, |
1522 |
|
|
uri = {<Go to ISI>://000228011900003}, |
1523 |
tim |
2685 |
} |
1524 |
|
|
|
1525 |
tim |
2786 |
@ARTICLE{Memmer2002, |
1526 |
|
|
author = {R. Memmer}, |
1527 |
|
|
title = {Liquid crystal phases of achiral banana-shaped molecules: a computer |
1528 |
|
|
simulation study}, |
1529 |
|
|
journal = {Liquid Crystals}, |
1530 |
|
|
year = {2002}, |
1531 |
|
|
volume = {29}, |
1532 |
|
|
pages = {483-496}, |
1533 |
|
|
number = {4}, |
1534 |
|
|
month = {Apr}, |
1535 |
|
|
abstract = {The phase behaviour of achiral banana-shaped molecules was studied |
1536 |
|
|
by computer simulation. The banana-shaped molecules were described |
1537 |
|
|
by model intermolecular interactions based on the Gay-Berne potential. |
1538 |
|
|
The characteristic molecular structure was considered by joining |
1539 |
|
|
two calamitic Gay-Berne particles through a bond to form a biaxial |
1540 |
|
|
molecule of point symmetry group C-2v with a suitable bending angle. |
1541 |
|
|
The dependence on temperature of systems of N=1024 rigid banana-shaped |
1542 |
|
|
molecules with bending angle phi=140degrees has been studied by |
1543 |
|
|
means of Monte Carlo simulations in the isobaric-isothermal ensemble |
1544 |
|
|
(NpT). On cooling an isotropic system, two phase transitions characterized |
1545 |
|
|
by phase transition enthalpy, entropy and relative volume change |
1546 |
|
|
have been observed. For the first time by computer simulation of |
1547 |
|
|
a many-particle system of banana-shaped molecules, at low temperature |
1548 |
|
|
an untilted smectic phase showing a global phase biaxiality and |
1549 |
|
|
a spontaneous local polarization in the layers, i.e. a local polar |
1550 |
|
|
arrangement of the steric dipoles, with an antiferroelectric-like |
1551 |
|
|
superstructure could be proven, a phase structure which recently |
1552 |
|
|
has been discovered experimentally. Additionally, at intermediate |
1553 |
|
|
temperature a nematic-like phase has been proved, whereas close |
1554 |
|
|
to the transition to the smectic phase hints of a spontaneous achiral |
1555 |
|
|
symmetry breaking have been determined. Here, in the absence of |
1556 |
|
|
a layered structure a helical superstructure has been formed. All |
1557 |
|
|
phases have been characterized by visual representations of selected |
1558 |
|
|
configurations, scalar and pseudoscalar correlation functions, and |
1559 |
|
|
order parameters.}, |
1560 |
|
|
annote = {531HT Times Cited:12 Cited References Count:37}, |
1561 |
|
|
issn = {0267-8292}, |
1562 |
|
|
uri = {<Go to ISI>://000174410500001}, |
1563 |
tim |
2685 |
} |
1564 |
|
|
|
1565 |
tim |
2786 |
@ARTICLE{Metropolis1949, |
1566 |
|
|
author = {N. Metropolis and S. Ulam}, |
1567 |
|
|
title = {The $\mbox{Monte Carlo}$ Method}, |
1568 |
|
|
journal = {J. Am. Stat. Ass.}, |
1569 |
|
|
year = {1949}, |
1570 |
|
|
volume = {44}, |
1571 |
|
|
pages = {335-341}, |
1572 |
tim |
2685 |
} |
1573 |
|
|
|
1574 |
tim |
2786 |
@ARTICLE{Mielke2004, |
1575 |
|
|
author = {S. P. Mielke and W. H. Fink and V. V. Krishnan and N. Gronbech-Jensen |
1576 |
|
|
and C. J. Benham}, |
1577 |
|
|
title = {Transcription-driven twin supercoiling of a DNA loop: A Brownian |
1578 |
|
|
dynamics study}, |
1579 |
|
|
journal = {Journal of Chemical Physics}, |
1580 |
|
|
year = {2004}, |
1581 |
|
|
volume = {121}, |
1582 |
|
|
pages = {8104-8112}, |
1583 |
|
|
number = {16}, |
1584 |
|
|
month = {Oct 22}, |
1585 |
|
|
abstract = {The torque generated by RNA polymerase as it tracks along double-stranded |
1586 |
|
|
DNA can potentially induce long-range structural deformations integral |
1587 |
|
|
to mechanisms of biological significance in both prokaryotes and |
1588 |
|
|
eukaryotes. In this paper, we introduce a dynamic computer model |
1589 |
|
|
for investigating this phenomenon. Duplex DNA is represented as |
1590 |
|
|
a chain of hydrodynamic beads interacting through potentials of |
1591 |
|
|
linearly elastic stretching, bending, and twisting, as well as excluded |
1592 |
|
|
volume. The chain, linear when relaxed, is looped to form two open |
1593 |
|
|
but topologically constrained subdomains. This permits the dynamic |
1594 |
|
|
introduction of torsional stress via a centrally applied torque. |
1595 |
|
|
We simulate by Brownian dynamics the 100 mus response of a 477-base |
1596 |
|
|
pair B-DNA template to the localized torque generated by the prokaryotic |
1597 |
|
|
transcription ensemble. Following a sharp rise at early times, the |
1598 |
|
|
distributed twist assumes a nearly constant value in both subdomains, |
1599 |
|
|
and a succession of supercoiling deformations occurs as superhelical |
1600 |
|
|
stress is increasingly partitioned to writhe. The magnitude of writhe |
1601 |
|
|
surpasses that of twist before also leveling off when the structure |
1602 |
|
|
reaches mechanical equilibrium with the torsional load. Superhelicity |
1603 |
|
|
is simultaneously right handed in one subdomain and left handed |
1604 |
|
|
in the other, as predicted by the #transcription-induced##twin-supercoiled-domain# |
1605 |
|
|
model [L. F. Liu and J. C. Wang, Proc. Natl. Acad. Sci. U.S.A. 84, |
1606 |
|
|
7024 (1987)]. The properties of the chain at the onset of writhing |
1607 |
|
|
agree well with predictions from theory, and the generated stress |
1608 |
|
|
is ample for driving secondary structural transitions in physiological |
1609 |
|
|
DNA. (C) 2004 American Institute of Physics.}, |
1610 |
|
|
annote = {861ZF Times Cited:3 Cited References Count:34}, |
1611 |
|
|
issn = {0021-9606}, |
1612 |
|
|
uri = {<Go to ISI>://000224456500064}, |
1613 |
tim |
2685 |
} |
1614 |
|
|
|
1615 |
tim |
2786 |
@ARTICLE{Naess2001, |
1616 |
|
|
author = {S. N. Naess and H. M. Adland and A. Mikkelsen and A. Elgsaeter}, |
1617 |
|
|
title = {Brownian dynamics simulation of rigid bodies and segmented polymer |
1618 |
|
|
chains. Use of Cartesian rotation vectors as the generalized coordinates |
1619 |
|
|
describing angular orientations}, |
1620 |
|
|
journal = {Physica A}, |
1621 |
|
|
year = {2001}, |
1622 |
|
|
volume = {294}, |
1623 |
|
|
pages = {323-339}, |
1624 |
|
|
number = {3-4}, |
1625 |
|
|
month = {May 15}, |
1626 |
|
|
abstract = {The three Eulerian angles constitute the classical choice of generalized |
1627 |
|
|
coordinates used to describe the three degrees of rotational freedom |
1628 |
|
|
of a rigid body, but it has long been known that this choice yields |
1629 |
|
|
singular equations of motion. The latter is also true when Eulerian |
1630 |
|
|
angles are used in Brownian dynamics analyses of the angular orientation |
1631 |
|
|
of single rigid bodies and segmented polymer chains. Starting from |
1632 |
|
|
kinetic theory we here show that by instead employing the three |
1633 |
|
|
components of Cartesian rotation vectors as the generalized coordinates |
1634 |
|
|
describing angular orientation, no singularity appears in the configuration |
1635 |
|
|
space diffusion equation and the associated Brownian dynamics algorithm. |
1636 |
|
|
The suitability of Cartesian rotation vectors in Brownian dynamics |
1637 |
|
|
simulations of segmented polymer chains with spring-like or ball-socket |
1638 |
|
|
joints is discussed. (C) 2001 Elsevier Science B.V. All rights reserved.}, |
1639 |
|
|
annote = {433TA Times Cited:7 Cited References Count:19}, |
1640 |
|
|
issn = {0378-4371}, |
1641 |
|
|
uri = {<Go to ISI>://000168774800005}, |
1642 |
tim |
2685 |
} |
1643 |
|
|
|
1644 |
tim |
2786 |
@ARTICLE{Niori1996, |
1645 |
|
|
author = {T. Niori and T. Sekine and J. Watanabe and T. Furukawa and H. Takezoe}, |
1646 |
|
|
title = {Distinct ferroelectric smectic liquid crystals consisting of banana |
1647 |
|
|
shaped achiral molecules}, |
1648 |
|
|
journal = {Journal of Materials Chemistry}, |
1649 |
|
|
year = {1996}, |
1650 |
|
|
volume = {6}, |
1651 |
|
|
pages = {1231-1233}, |
1652 |
|
|
number = {7}, |
1653 |
|
|
month = {Jul}, |
1654 |
|
|
abstract = {The synthesis of a banana-shaped molecule is reported and it is found |
1655 |
|
|
that the smectic phase which it forms is biaxial with the molecules |
1656 |
|
|
packed in the best,direction into a layer. Because of this characteristic |
1657 |
|
|
packing, spontaneous polarization appears parallel to the layer |
1658 |
|
|
and switches on reversal of an applied electric field. This is the |
1659 |
|
|
first obvious example of ferroelectricity in an achiral smectic |
1660 |
|
|
phase and is ascribed to the C-2v symmetry of the molecular packing.}, |
1661 |
|
|
annote = {Ux855 Times Cited:447 Cited References Count:18}, |
1662 |
|
|
issn = {0959-9428}, |
1663 |
|
|
uri = {<Go to ISI>://A1996UX85500025}, |
1664 |
tim |
2685 |
} |
1665 |
|
|
|
1666 |
tim |
2786 |
@ARTICLE{Noguchi2002, |
1667 |
|
|
author = {H. Noguchi and M. Takasu}, |
1668 |
|
|
title = {Structural changes of pulled vesicles: A Brownian dynamics simulation}, |
1669 |
|
|
journal = {Physical Review E}, |
1670 |
|
|
year = {2002}, |
1671 |
|
|
volume = {65}, |
1672 |
|
|
pages = {-}, |
1673 |
|
|
number = {5}, |
1674 |
|
|
month = {may}, |
1675 |
|
|
abstract = {We Studied the structural changes of bilayer vesicles induced by mechanical |
1676 |
|
|
forces using a Brownian dynamics simulation. Two nanoparticles, |
1677 |
|
|
which interact repulsively with amphiphilic molecules, are put inside |
1678 |
|
|
a vesicle. The position of one nanoparticle is fixed, and the other |
1679 |
|
|
is moved by a constant force as in optical-trapping experiments. |
1680 |
|
|
First, the pulled vesicle stretches into a pear or tube shape. Then |
1681 |
|
|
the inner monolayer in the tube-shaped region is deformed, and a |
1682 |
|
|
cylindrical structure is formed between two vesicles. After stretching |
1683 |
|
|
the cylindrical region, fission occurs near the moved vesicle. Soon |
1684 |
|
|
after this the cylindrical region shrinks. The trapping force similar |
1685 |
|
|
to 100 pN is needed to induce the formation of the cylindrical structure |
1686 |
|
|
and fission.}, |
1687 |
|
|
annote = {Part 1 568PX Times Cited:5 Cited References Count:39}, |
1688 |
|
|
issn = {1063-651X}, |
1689 |
|
|
uri = {<Go to ISI>://000176552300084}, |
1690 |
tim |
2685 |
} |
1691 |
|
|
|
1692 |
tim |
2786 |
@ARTICLE{Noguchi2001, |
1693 |
|
|
author = {H. Noguchi and M. Takasu}, |
1694 |
|
|
title = {Fusion pathways of vesicles: A Brownian dynamics simulation}, |
1695 |
|
|
journal = {Journal of Chemical Physics}, |
1696 |
|
|
year = {2001}, |
1697 |
|
|
volume = {115}, |
1698 |
|
|
pages = {9547-9551}, |
1699 |
|
|
number = {20}, |
1700 |
|
|
month = {Nov 22}, |
1701 |
|
|
abstract = {We studied the fusion dynamics of vesicles using a Brownian dynamics |
1702 |
|
|
simulation. Amphiphilic molecules spontaneously form vesicles with |
1703 |
|
|
a bilayer structure. Two vesicles come into contact and form a stalk |
1704 |
|
|
intermediate, in which a necklike structure only connects the outer |
1705 |
|
|
monolayers, as predicted by the stalk hypothesis. We have found |
1706 |
|
|
a new pathway of pore opening from stalks at high temperature: the |
1707 |
|
|
elliptic stalk bends and contact between the ends of the arc-shaped |
1708 |
|
|
stalk leads to pore opening. On the other hand, we have clarified |
1709 |
|
|
that the pore-opening process at low temperature agrees with the |
1710 |
|
|
modified stalk model: a pore is induced by contact between the inner |
1711 |
|
|
monolayers inside the stalk. (C) 2001 American Institute of Physics.}, |
1712 |
|
|
annote = {491UW Times Cited:48 Cited References Count:25}, |
1713 |
|
|
issn = {0021-9606}, |
1714 |
|
|
uri = {<Go to ISI>://000172129300049}, |
1715 |
tim |
2685 |
} |
1716 |
|
|
|
1717 |
tim |
2786 |
@ARTICLE{Orlandi2006, |
1718 |
|
|
author = {S. Orlandi and R. Berardi and J. Steltzer and C. Zannoni}, |
1719 |
|
|
title = {A Monte Carlo study of the mesophases formed by polar bent-shaped |
1720 |
|
|
molecules}, |
1721 |
|
|
journal = {Journal of Chemical Physics}, |
1722 |
|
|
year = {2006}, |
1723 |
|
|
volume = {124}, |
1724 |
|
|
pages = {-}, |
1725 |
|
|
number = {12}, |
1726 |
|
|
month = {Mar 28}, |
1727 |
|
|
abstract = {Liquid crystal phases formed by bent-shaped (or #banana#) molecules |
1728 |
|
|
are currently of great interest. Here we investigate by Monte Carlo |
1729 |
|
|
computer simulations the phases formed by rigid banana molecules |
1730 |
|
|
modeled combining three Gay-Berne sites and containing either one |
1731 |
|
|
central or two lateral and transversal dipoles. We show that changing |
1732 |
|
|
the dipole position and orientation has a profound effect on the |
1733 |
|
|
mesophase stability and molecular organization. In particular, we |
1734 |
|
|
find a uniaxial nematic phase only for off-center dipolar models |
1735 |
|
|
and tilted phases only for the one with terminal dipoles. (c) 2006 |
1736 |
|
|
American Institute of Physics.}, |
1737 |
|
|
annote = {028CP Times Cited:0 Cited References Count:42}, |
1738 |
|
|
issn = {0021-9606}, |
1739 |
|
|
uri = {<Go to ISI>://000236464000072}, |
1740 |
tim |
2685 |
} |
1741 |
|
|
|
1742 |
tim |
2786 |
@ARTICLE{Palacios1998, |
1743 |
|
|
author = {J. L. Garcia-Palacios and F. J. Lazaro}, |
1744 |
|
|
title = {Langevin-dynamics study of the dynamical properties of small magnetic |
1745 |
|
|
particles}, |
1746 |
|
|
journal = {Physical Review B}, |
1747 |
|
|
year = {1998}, |
1748 |
|
|
volume = {58}, |
1749 |
|
|
pages = {14937-14958}, |
1750 |
|
|
number = {22}, |
1751 |
|
|
month = {Dec 1}, |
1752 |
|
|
abstract = {The stochastic Landau-Lifshitz-Gilbert equation of motion for a classical |
1753 |
|
|
magnetic moment is numerically solved (properly observing the customary |
1754 |
|
|
interpretation of it as a Stratonovich stochastic differential equation), |
1755 |
|
|
in order to study the dynamics of magnetic nanoparticles. The corresponding |
1756 |
|
|
Langevin-dynamics approach allows for the study of the fluctuating |
1757 |
|
|
trajectories of individual magnetic moments, where we have encountered |
1758 |
|
|
remarkable phenomena in the overbarrier rotation process, such as |
1759 |
|
|
crossing-back or multiple crossing of the potential barrier, rooted |
1760 |
|
|
in the gyromagnetic nature of the system. Concerning averaged quantities, |
1761 |
|
|
we study the linear dynamic response of the archetypal ensemble |
1762 |
|
|
of noninteracting classical magnetic moments with axially symmetric |
1763 |
|
|
magnetic anisotropy. The results are compared with different analytical |
1764 |
|
|
expressions used to model the relaxation of nanoparticle ensembles, |
1765 |
|
|
assessing their accuracy. It has been found that, among a number |
1766 |
|
|
of heuristic expressions for the linear dynamic susceptibility, |
1767 |
|
|
only the simple formula proposed by Shliomis and Stepanov matches |
1768 |
|
|
the coarse features of the susceptibility reasonably. By comparing |
1769 |
|
|
the numerical results with the asymptotic formula of Storonkin {Sov. |
1770 |
|
|
Phys. Crystallogr. 30, 489 (1985) [Kristallografiya 30, 841 (1985)]}, |
1771 |
|
|
the effects of the intra-potential-well relaxation modes on the |
1772 |
|
|
low-temperature longitudinal dynamic response have been assessed, |
1773 |
|
|
showing their relatively small reflection in the susceptibility |
1774 |
|
|
curves but their dramatic influence on the phase shifts. Comparison |
1775 |
|
|
of the numerical results with the exact zero-damping expression |
1776 |
|
|
for the transverse susceptibility by Garanin, Ishchenko, and Panina |
1777 |
|
|
{Theor. Math. Phys. (USSR) 82, 169 (1990) [Teor. Mat. Fit. 82, 242 |
1778 |
|
|
(1990)]}, reveals a sizable contribution of the spread of the precession |
1779 |
|
|
frequencies of the magnetic moment in the anisotropy field to the |
1780 |
|
|
dynamic response at intermediate-to-high temperatures. [S0163-1829 |
1781 |
|
|
(98)00446-9].}, |
1782 |
|
|
annote = {146XW Times Cited:66 Cited References Count:45}, |
1783 |
|
|
issn = {0163-1829}, |
1784 |
|
|
uri = {<Go to ISI>://000077460000052}, |
1785 |
tim |
2685 |
} |
1786 |
|
|
|
1787 |
tim |
2786 |
@ARTICLE{Pastor1988, |
1788 |
|
|
author = {R. W. Pastor and B. R. Brooks and A. Szabo}, |
1789 |
|
|
title = {An Analysis of the Accuracy of Langevin and Molecular-Dynamics Algorithms}, |
1790 |
|
|
journal = {Molecular Physics}, |
1791 |
|
|
year = {1988}, |
1792 |
|
|
volume = {65}, |
1793 |
|
|
pages = {1409-1419}, |
1794 |
|
|
number = {6}, |
1795 |
|
|
month = {Dec 20}, |
1796 |
|
|
annote = {T1302 Times Cited:61 Cited References Count:26}, |
1797 |
|
|
issn = {0026-8976}, |
1798 |
|
|
uri = {<Go to ISI>://A1988T130200011}, |
1799 |
tim |
2685 |
} |
1800 |
|
|
|
1801 |
tim |
2786 |
@ARTICLE{Pelzl1999, |
1802 |
|
|
author = {G. Pelzl and S. Diele and W. Weissflog}, |
1803 |
|
|
title = {Banana-shaped compounds - A new field of liquid crystals}, |
1804 |
|
|
journal = {Advanced Materials}, |
1805 |
|
|
year = {1999}, |
1806 |
|
|
volume = {11}, |
1807 |
|
|
pages = {707-724}, |
1808 |
|
|
number = {9}, |
1809 |
|
|
month = {Jul 5}, |
1810 |
|
|
annote = {220RC Times Cited:313 Cited References Count:49}, |
1811 |
|
|
issn = {0935-9648}, |
1812 |
|
|
uri = {<Go to ISI>://000081680400007}, |
1813 |
tim |
2685 |
} |
1814 |
|
|
|
1815 |
tim |
2786 |
@ARTICLE{Perram1985, |
1816 |
|
|
author = {J. W. Perram and M. S. Wertheim}, |
1817 |
|
|
title = {Statistical-Mechanics of Hard Ellipsoids .1. Overlap Algorithm and |
1818 |
|
|
the Contact Function}, |
1819 |
|
|
journal = {Journal of Computational Physics}, |
1820 |
|
|
year = {1985}, |
1821 |
|
|
volume = {58}, |
1822 |
|
|
pages = {409-416}, |
1823 |
|
|
number = {3}, |
1824 |
|
|
annote = {Akb93 Times Cited:71 Cited References Count:12}, |
1825 |
|
|
issn = {0021-9991}, |
1826 |
|
|
uri = {<Go to ISI>://A1985AKB9300008}, |
1827 |
tim |
2685 |
} |
1828 |
|
|
|
1829 |
tim |
2786 |
@ARTICLE{Petrache1998, |
1830 |
|
|
author = {H. I. Petrache and S. Tristram-Nagle and J. F. Nagle}, |
1831 |
|
|
title = {Fluid phase structure of EPC and DMPC bilayers}, |
1832 |
|
|
journal = {Chemistry and Physics of Lipids}, |
1833 |
|
|
year = {1998}, |
1834 |
|
|
volume = {95}, |
1835 |
|
|
pages = {83-94}, |
1836 |
|
|
number = {1}, |
1837 |
|
|
month = {Sep}, |
1838 |
|
|
abstract = {X-ray diffraction data taken at high instrumental resolution were |
1839 |
|
|
obtained for EPC and DMPC under various osmotic pressures, primarily |
1840 |
|
|
at T = 30 degrees C. The headgroup thickness D-HH was obtained from |
1841 |
|
|
relative electron density profiles. By using volumetric results |
1842 |
|
|
and by comparing to gel phase DPPC we obtain areas A(EPC)(F) = 69.4 |
1843 |
|
|
+/- 1.1 Angstrom(2) and A(DMPC)(F) = 59.7 +/- 0.2 Angstrom(2). The |
1844 |
|
|
analysis also gives estimates for the areal compressibility K-A. |
1845 |
|
|
The A(F) results lead to other structural results regarding membrane |
1846 |
|
|
thickness and associated waters. Using the recently determined absolute |
1847 |
|
|
electrons density profile of DPPC, the AF results also lead to absolute |
1848 |
|
|
electron density profiles and absolute continuous transforms \F(q)\ |
1849 |
|
|
for EPC and DMPC, Limited measurements of temperature dependence |
1850 |
|
|
show directly that fluctuations increase with increasing temperature |
1851 |
|
|
and that a small decrease in bending modulus K-c accounts for the |
1852 |
|
|
increased water spacing reported by Simon et al. (1995) Biophys. |
1853 |
|
|
J. 69, 1473-1483. (C) 1998 Elsevier Science Ireland Ltd. All rights |
1854 |
|
|
reserved.}, |
1855 |
|
|
annote = {130AT Times Cited:98 Cited References Count:39}, |
1856 |
|
|
issn = {0009-3084}, |
1857 |
|
|
uri = {<Go to ISI>://000076497600007}, |
1858 |
tim |
2685 |
} |
1859 |
|
|
|
1860 |
tim |
2786 |
@ARTICLE{Powles1973, |
1861 |
|
|
author = {J.~G. Powles}, |
1862 |
|
|
title = {A general ellipsoid can not always serve as a modle for the rotational |
1863 |
|
|
diffusion properties of arbitrary shaped rigid molecules}, |
1864 |
|
|
journal = {Advan. Phys.}, |
1865 |
|
|
year = {1973}, |
1866 |
|
|
volume = {22}, |
1867 |
|
|
pages = {1-56}, |
1868 |
tim |
2685 |
} |
1869 |
|
|
|
1870 |
tim |
2786 |
@ARTICLE{Recio2004, |
1871 |
|
|
author = {J. Fernandez-Recio and M. Totrov and R. Abagyan}, |
1872 |
|
|
title = {Identification of protein-protein interaction sites from docking |
1873 |
|
|
energy landscapes}, |
1874 |
|
|
journal = {Journal of Molecular Biology}, |
1875 |
|
|
year = {2004}, |
1876 |
|
|
volume = {335}, |
1877 |
|
|
pages = {843-865}, |
1878 |
|
|
number = {3}, |
1879 |
|
|
month = {Jan 16}, |
1880 |
|
|
abstract = {Protein recognition is one of the most challenging and intriguing |
1881 |
|
|
problems in structural biology. Despite all the available structural, |
1882 |
|
|
sequence and biophysical information about protein-protein complexes, |
1883 |
|
|
the physico-chemical patterns, if any, that make a protein surface |
1884 |
|
|
likely to be involved in protein-protein interactions, remain elusive. |
1885 |
|
|
Here, we apply protein docking simulations and analysis of the interaction |
1886 |
|
|
energy landscapes to identify protein-protein interaction sites. |
1887 |
|
|
The new protocol for global docking based on multi-start global |
1888 |
|
|
energy optimization of an allatom model of the ligand, with detailed |
1889 |
|
|
receptor potentials and atomic solvation parameters optimized in |
1890 |
|
|
a training set of 24 complexes, explores the conformational space |
1891 |
|
|
around the whole receptor without restrictions. The ensembles of |
1892 |
|
|
the rigid-body docking solutions generated by the simulations were |
1893 |
|
|
subsequently used to project the docking energy landscapes onto |
1894 |
|
|
the protein surfaces. We found that highly populated low-energy |
1895 |
|
|
regions consistently corresponded to actual binding sites. The procedure |
1896 |
|
|
was validated on a test set of 21 known protein-protein complexes |
1897 |
|
|
not used in the training set. As much as 81% of the predicted high-propensity |
1898 |
|
|
patch residues were located correctly in the native interfaces. |
1899 |
|
|
This approach can guide the design of mutations on the surfaces |
1900 |
|
|
of proteins, provide geometrical details of a possible interaction, |
1901 |
|
|
and help to annotate protein surfaces in structural proteomics. |
1902 |
|
|
(C) 2003 Elsevier Ltd. All rights reserved.}, |
1903 |
|
|
annote = {763GQ Times Cited:21 Cited References Count:59}, |
1904 |
|
|
issn = {0022-2836}, |
1905 |
|
|
uri = {<Go to ISI>://000188066900016}, |
1906 |
tim |
2685 |
} |
1907 |
|
|
|
1908 |
tim |
2786 |
@ARTICLE{Reddy2006, |
1909 |
|
|
author = {R. A. Reddy and C. Tschierske}, |
1910 |
|
|
title = {Bent-core liquid crystals: polar order, superstructural chirality |
1911 |
|
|
and spontaneous desymmetrisation in soft matter systems}, |
1912 |
|
|
journal = {Journal of Materials Chemistry}, |
1913 |
|
|
year = {2006}, |
1914 |
|
|
volume = {16}, |
1915 |
|
|
pages = {907-961}, |
1916 |
|
|
number = {10}, |
1917 |
|
|
abstract = {An overview on the recent developments in the field of liquid crystalline |
1918 |
|
|
bent-core molecules (so-called banana liquid crystals) is given. |
1919 |
|
|
After some basic issues, dealing with general aspects of the systematisation |
1920 |
|
|
of the mesophases, development of polar order and chirality in this |
1921 |
|
|
class of LC systems and explaining some general structure-property |
1922 |
|
|
relationships, we focus on fascinating new developments in this |
1923 |
|
|
field, such as modulated, undulated and columnar phases, so-called |
1924 |
|
|
B7 phases, phase biaxiality, ferroelectric and antiferroelectric |
1925 |
|
|
polar order in smectic and columnar phases, amplification and switching |
1926 |
|
|
of chirality and the spontaneous formation of superstructural and |
1927 |
|
|
supramolecular chirality.}, |
1928 |
|
|
annote = {021NS Times Cited:2 Cited References Count:316}, |
1929 |
|
|
issn = {0959-9428}, |
1930 |
|
|
uri = {<Go to ISI>://000235990500001}, |
1931 |
tim |
2685 |
} |
1932 |
|
|
|
1933 |
tim |
2786 |
@ARTICLE{Ros2005, |
1934 |
|
|
author = {M. B. Ros and J. L. Serrano and M. R. {de la Fuente} and C. L. Folcia}, |
1935 |
|
|
title = {Banana-shaped liquid crystals: a new field to explore}, |
1936 |
|
|
journal = {Journal of Materials Chemistry}, |
1937 |
|
|
year = {2005}, |
1938 |
|
|
volume = {15}, |
1939 |
|
|
pages = {5093-5098}, |
1940 |
|
|
number = {48}, |
1941 |
|
|
abstract = {The recent literature in the field of liquid crystals shows that banana-shaped |
1942 |
|
|
mesogenic materials represent a bewitching and stimulating field |
1943 |
|
|
of research that is interesting both academically and in terms of |
1944 |
|
|
applications. Numerous topics are open to investigation in this |
1945 |
|
|
area because of the rich phenomenology and new possibilities that |
1946 |
|
|
these materials offer. The principal concepts in this area are reviewed |
1947 |
|
|
along with recent results. In addition, new directions to stimulate |
1948 |
|
|
further research activities are highlighted.}, |
1949 |
|
|
annote = {990XA Times Cited:3 Cited References Count:72}, |
1950 |
|
|
issn = {0959-9428}, |
1951 |
|
|
uri = {<Go to ISI>://000233775500001}, |
1952 |
tim |
2685 |
} |
1953 |
|
|
|
1954 |
tim |
2786 |
@ARTICLE{Roy2005, |
1955 |
|
|
author = {A. Roy and N. V. Madhusudana}, |
1956 |
|
|
title = {A frustrated packing model for the B-6-B-1-SmAP(A) sequence of phases |
1957 |
|
|
in banana shaped molecules}, |
1958 |
|
|
journal = {European Physical Journal E}, |
1959 |
|
|
year = {2005}, |
1960 |
|
|
volume = {18}, |
1961 |
|
|
pages = {253-258}, |
1962 |
|
|
number = {3}, |
1963 |
|
|
month = {Nov}, |
1964 |
|
|
abstract = {A vast majority of compounds with bent core or banana shaped molecules |
1965 |
|
|
exhibit the phase sequence B-6-B-1-B-2 as the chain length is increased |
1966 |
|
|
in a homologous series. The B-6 phase has an intercalated fluid |
1967 |
|
|
lamellar structure with a layer spacing of half the molecular length. |
1968 |
|
|
The B-1 phase has a two dimensionally periodic rectangular columnar |
1969 |
|
|
structure. The B-2 phase has a monolayer fluid lamellar structure |
1970 |
|
|
with molecules tilted with respect to the layer normal. Neglecting |
1971 |
|
|
the tilt order of the molecules in the B-2 phase, we have developed |
1972 |
|
|
a frustrated packing model to describe this phase sequence qualitatively. |
1973 |
|
|
The model has some analogy with that of the frustrated smectics |
1974 |
|
|
exhibited by highly polar rod like molecules.}, |
1975 |
|
|
annote = {985FW Times Cited:0 Cited References Count:30}, |
1976 |
|
|
issn = {1292-8941}, |
1977 |
|
|
uri = {<Go to ISI>://000233363300002}, |
1978 |
tim |
2685 |
} |
1979 |
|
|
|
1980 |
tim |
2786 |
@ARTICLE{Sandu1999, |
1981 |
|
|
author = {A. Sandu and T. Schlick}, |
1982 |
|
|
title = {Masking resonance artifacts in force-splitting methods for biomolecular |
1983 |
|
|
simulations by extrapolative Langevin dynamics}, |
1984 |
|
|
journal = {Journal of Computational Physics}, |
1985 |
|
|
year = {1999}, |
1986 |
|
|
volume = {151}, |
1987 |
|
|
pages = {74-113}, |
1988 |
|
|
number = {1}, |
1989 |
|
|
month = {May 1}, |
1990 |
|
|
abstract = {Numerical resonance artifacts have become recognized recently as a |
1991 |
|
|
limiting factor to increasing the timestep in multiple-timestep |
1992 |
|
|
(MTS) biomolecular dynamics simulations. At certain timesteps correlated |
1993 |
|
|
to internal motions (e.g., 5 fs, around half the period of the fastest |
1994 |
|
|
bond stretch, T-min), visible inaccuracies or instabilities can |
1995 |
|
|
occur. Impulse-MTS schemes are vulnerable to these resonance errors |
1996 |
|
|
since large energy pulses are introduced to the governing dynamics |
1997 |
|
|
equations when the slow forces are evaluated. We recently showed |
1998 |
|
|
that such resonance artifacts can be masked significantly by applying |
1999 |
|
|
extrapolative splitting to stochastic dynamics. Theoretical and |
2000 |
|
|
numerical analyses of force-splitting integrators based on the Verlet |
2001 |
|
|
discretization are reported here for linear models to explain these |
2002 |
|
|
observations and to suggest how to construct effective integrators |
2003 |
|
|
for biomolecular dynamics that balance stability with accuracy. |
2004 |
|
|
Analyses for Newtonian dynamics demonstrate the severe resonance |
2005 |
|
|
patterns of the Impulse splitting, with this severity worsening |
2006 |
|
|
with the outer timestep. Delta t: Constant Extrapolation is generally |
2007 |
|
|
unstable, but the disturbances do not grow with Delta t. Thus. the |
2008 |
|
|
stochastic extrapolative combination can counteract generic instabilities |
2009 |
|
|
and largely alleviate resonances with a sufficiently strong Langevin |
2010 |
|
|
heat-bath coupling (gamma), estimates for which are derived here |
2011 |
|
|
based on the fastest and slowest motion periods. These resonance |
2012 |
|
|
results generally hold for nonlinear test systems: a water tetramer |
2013 |
|
|
and solvated protein. Proposed related approaches such as Extrapolation/Correction |
2014 |
|
|
and Midpoint Extrapolation work better than Constant Extrapolation |
2015 |
|
|
only for timesteps less than T-min/2. An effective extrapolative |
2016 |
|
|
stochastic approach for biomolecules that balances long-timestep |
2017 |
|
|
stability with good accuracy for the fast subsystem is then applied |
2018 |
|
|
to a biomolecule using a three-class partitioning: the medium forces |
2019 |
|
|
are treated by Midpoint Extrapolation via position Verlet, and the |
2020 |
|
|
slow forces are incorporated by Constant Extrapolation. The resulting |
2021 |
|
|
algorithm (LN) performs well on a solvated protein system in terms |
2022 |
|
|
of thermodynamic properties and yields an order of magnitude speedup |
2023 |
|
|
with respect to single-timestep Langevin trajectories. Computed |
2024 |
|
|
spectral density functions also show how the Newtonian modes can |
2025 |
|
|
be approximated by using a small gamma in the range Of 5-20 ps(-1). |
2026 |
|
|
(C) 1999 Academic Press.}, |
2027 |
|
|
annote = {194FM Times Cited:14 Cited References Count:32}, |
2028 |
|
|
issn = {0021-9991}, |
2029 |
|
|
uri = {<Go to ISI>://000080181500004}, |
2030 |
tim |
2685 |
} |
2031 |
|
|
|
2032 |
tim |
2786 |
@ARTICLE{Satoh1996, |
2033 |
|
|
author = {K. Satoh and S. Mita and S. Kondo}, |
2034 |
|
|
title = {Monte Carlo simulations using the dipolar Gay-Berne model: Effect |
2035 |
|
|
of terminal dipole moment on mesophase formation}, |
2036 |
|
|
journal = {Chemical Physics Letters}, |
2037 |
|
|
year = {1996}, |
2038 |
|
|
volume = {255}, |
2039 |
|
|
pages = {99-104}, |
2040 |
|
|
number = {1-3}, |
2041 |
|
|
month = {Jun 7}, |
2042 |
|
|
abstract = {The effects of dipole-dipole interaction on mesophase formation are |
2043 |
|
|
investigated with a Monte Carlo simulation using the dipolar Gay-Berne |
2044 |
|
|
potential. It is shown that the dipole moment at the end of a molecule |
2045 |
|
|
causes a shift in the nematic-isotropic transition toward higher |
2046 |
|
|
temperature and a spread of the temperature range of the nematic |
2047 |
|
|
phase and that layer structures with various interdigitations are |
2048 |
|
|
formed in the smectic phase.}, |
2049 |
|
|
annote = {Uq975 Times Cited:32 Cited References Count:33}, |
2050 |
|
|
issn = {0009-2614}, |
2051 |
|
|
uri = {<Go to ISI>://A1996UQ97500017}, |
2052 |
tim |
2685 |
} |
2053 |
|
|
|
2054 |
tim |
2786 |
@ARTICLE{Shen2002, |
2055 |
|
|
author = {M. Y. Shen and K. F. Freed}, |
2056 |
|
|
title = {Long time dynamics of met-enkephalin: Comparison of explicit and |
2057 |
|
|
implicit solvent models}, |
2058 |
|
|
journal = {Biophysical Journal}, |
2059 |
|
|
year = {2002}, |
2060 |
|
|
volume = {82}, |
2061 |
|
|
pages = {1791-1808}, |
2062 |
|
|
number = {4}, |
2063 |
|
|
month = {Apr}, |
2064 |
|
|
abstract = {Met-enkephalin is one of the smallest opiate peptides. Yet, its dynamical |
2065 |
|
|
structure and receptor docking mechanism are still not well understood. |
2066 |
|
|
The conformational dynamics of this neuron peptide in liquid water |
2067 |
|
|
are studied here by using all-atom molecular dynamics (MID) and |
2068 |
|
|
implicit water Langevin dynamics (LD) simulations with AMBER potential |
2069 |
|
|
functions and the three-site transferable intermolecular potential |
2070 |
|
|
(TIP3P) model for water. To achieve the same simulation length in |
2071 |
|
|
physical time, the full MID simulations require 200 times as much |
2072 |
|
|
CPU time as the implicit water LID simulations. The solvent hydrophobicity |
2073 |
|
|
and dielectric behavior are treated in the implicit solvent LD simulations |
2074 |
|
|
by using a macroscopic solvation potential, a single dielectric |
2075 |
|
|
constant, and atomic friction coefficients computed using the accessible |
2076 |
|
|
surface area method with the TIP3P model water viscosity as determined |
2077 |
|
|
here from MID simulations for pure TIP3P water. Both the local and |
2078 |
|
|
the global dynamics obtained from the implicit solvent LD simulations |
2079 |
|
|
agree very well with those from the explicit solvent MD simulations. |
2080 |
|
|
The simulations provide insights into the conformational restrictions |
2081 |
|
|
that are associated with the bioactivity of the opiate peptide dermorphin |
2082 |
|
|
for the delta-receptor.}, |
2083 |
|
|
annote = {540MH Times Cited:36 Cited References Count:45}, |
2084 |
|
|
issn = {0006-3495}, |
2085 |
|
|
uri = {<Go to ISI>://000174932400010}, |
2086 |
tim |
2685 |
} |
2087 |
|
|
|
2088 |
tim |
2786 |
@ARTICLE{Shillcock2005, |
2089 |
|
|
author = {J. C. Shillcock and R. Lipowsky}, |
2090 |
|
|
title = {Tension-induced fusion of bilayer membranes and vesicles}, |
2091 |
|
|
journal = {Nature Materials}, |
2092 |
|
|
year = {2005}, |
2093 |
|
|
volume = {4}, |
2094 |
|
|
pages = {225-228}, |
2095 |
|
|
number = {3}, |
2096 |
|
|
month = {Mar}, |
2097 |
|
|
annote = {901QJ Times Cited:9 Cited References Count:23}, |
2098 |
|
|
issn = {1476-1122}, |
2099 |
|
|
uri = {<Go to ISI>://000227296700019}, |
2100 |
tim |
2685 |
} |
2101 |
|
|
|
2102 |
tim |
2786 |
@ARTICLE{Skeel2002, |
2103 |
|
|
author = {R. D. Skeel and J. A. Izaguirre}, |
2104 |
|
|
title = {An impulse integrator for Langevin dynamics}, |
2105 |
|
|
journal = {Molecular Physics}, |
2106 |
|
|
year = {2002}, |
2107 |
|
|
volume = {100}, |
2108 |
|
|
pages = {3885-3891}, |
2109 |
|
|
number = {24}, |
2110 |
|
|
month = {Dec 20}, |
2111 |
|
|
abstract = {The best simple method for Newtonian molecular dynamics is indisputably |
2112 |
|
|
the leapfrog Stormer-Verlet method. The appropriate generalization |
2113 |
|
|
to simple Langevin dynamics is unclear. An analysis is presented |
2114 |
|
|
comparing an 'impulse method' (kick; fluctuate; kick), the 1982 |
2115 |
|
|
method of van Gunsteren and Berendsen, and the Brunger-Brooks-Karplus |
2116 |
|
|
(BBK) method. It is shown how the impulse method and the van Gunsteren-Berendsen |
2117 |
|
|
methods can be implemented as efficiently as the BBK method. Other |
2118 |
|
|
considerations suggest that the impulse method is the best basic |
2119 |
|
|
method for simple Langevin dynamics, with the van Gunsteren-Berendsen |
2120 |
|
|
method a close contender.}, |
2121 |
|
|
annote = {633RX Times Cited:8 Cited References Count:22}, |
2122 |
|
|
issn = {0026-8976}, |
2123 |
|
|
uri = {<Go to ISI>://000180297200014}, |
2124 |
tim |
2685 |
} |
2125 |
|
|
|
2126 |
tim |
2786 |
@ARTICLE{Skeel1997, |
2127 |
|
|
author = {R. D. Skeel and G. H. Zhang and T. Schlick}, |
2128 |
|
|
title = {A family of symplectic integrators: Stability, accuracy, and molecular |
2129 |
|
|
dynamics applications}, |
2130 |
|
|
journal = {Siam Journal on Scientific Computing}, |
2131 |
|
|
year = {1997}, |
2132 |
|
|
volume = {18}, |
2133 |
|
|
pages = {203-222}, |
2134 |
|
|
number = {1}, |
2135 |
|
|
month = {Jan}, |
2136 |
|
|
abstract = {The following integration methods for special second-order ordinary |
2137 |
|
|
differential equations are studied: leapfrog, implicit midpoint, |
2138 |
|
|
trapezoid, Stormer-Verlet, and Cowell-Numerov. We show that all |
2139 |
|
|
are members, or equivalent to members, of a one-parameter family |
2140 |
|
|
of schemes. Some methods have more than one common form, and we |
2141 |
|
|
discuss a systematic enumeration of these forms. We also present |
2142 |
|
|
a stability and accuracy analysis based on the idea of ''modified |
2143 |
|
|
equations'' and a proof of symplecticness. It follows that Cowell-Numerov |
2144 |
|
|
and ''LIM2'' (a method proposed by Zhang and Schlick) are symplectic. |
2145 |
|
|
A different interpretation of the values used by these integrators |
2146 |
|
|
leads to higher accuracy and better energy conservation. Hence, |
2147 |
|
|
we suggest that the straightforward analysis of energy conservation |
2148 |
|
|
is misleading.}, |
2149 |
|
|
annote = {We981 Times Cited:30 Cited References Count:35}, |
2150 |
|
|
issn = {1064-8275}, |
2151 |
|
|
uri = {<Go to ISI>://A1997WE98100012}, |
2152 |
tim |
2685 |
} |
2153 |
|
|
|
2154 |
tim |
2786 |
@ARTICLE{Tao2005, |
2155 |
|
|
author = {Y. G. Tao and W. K. {den Otter} and J. T. Padding and J. K. G. Dhont |
2156 |
|
|
and W. J. Briels}, |
2157 |
|
|
title = {Brownian dynamics simulations of the self- and collective rotational |
2158 |
|
|
diffusion coefficients of rigid long thin rods}, |
2159 |
|
|
journal = {Journal of Chemical Physics}, |
2160 |
|
|
year = {2005}, |
2161 |
|
|
volume = {122}, |
2162 |
|
|
pages = {-}, |
2163 |
|
|
number = {24}, |
2164 |
|
|
month = {Jun 22}, |
2165 |
|
|
abstract = {Recently a microscopic theory for the dynamics of suspensions of long |
2166 |
|
|
thin rigid rods was presented, confirming and expanding the well-known |
2167 |
|
|
theory by Doi and Edwards [The Theory of Polymer Dynamics (Clarendon, |
2168 |
|
|
Oxford, 1986)] and Kuzuu [J. Phys. Soc. Jpn. 52, 3486 (1983)]. Here |
2169 |
|
|
this theory is put to the test by comparing it against computer |
2170 |
|
|
simulations. A Brownian dynamics simulation program was developed |
2171 |
|
|
to follow the dynamics of the rods, with a length over a diameter |
2172 |
|
|
ratio of 60, on the Smoluchowski time scale. The model accounts |
2173 |
|
|
for excluded volume interactions between rods, but neglects hydrodynamic |
2174 |
|
|
interactions. The self-rotational diffusion coefficients D-r(phi) |
2175 |
|
|
of the rods were calculated by standard methods and by a new, more |
2176 |
|
|
efficient method based on calculating average restoring torques. |
2177 |
|
|
Collective decay of orientational order was calculated by means |
2178 |
|
|
of equilibrium and nonequilibrium simulations. Our results show |
2179 |
|
|
that, for the currently accessible volume fractions, the decay times |
2180 |
|
|
in both cases are virtually identical. Moreover, the observed decay |
2181 |
|
|
of diffusion coefficients with volume fraction is much quicker than |
2182 |
|
|
predicted by the theory, which is attributed to an oversimplification |
2183 |
|
|
of dynamic correlations in the theory. (c) 2005 American Institute |
2184 |
|
|
of Physics.}, |
2185 |
|
|
annote = {943DN Times Cited:3 Cited References Count:26}, |
2186 |
|
|
issn = {0021-9606}, |
2187 |
|
|
uri = {<Go to ISI>://000230332400077}, |
2188 |
tim |
2685 |
} |
2189 |
|
|
|
2190 |
tim |
2786 |
@BOOK{Tolman1979, |
2191 |
|
|
title = {The Principles of Statistical Mechanics}, |
2192 |
|
|
publisher = {Dover Publications, Inc.}, |
2193 |
|
|
year = {1979}, |
2194 |
|
|
author = {R.~C. Tolman}, |
2195 |
|
|
address = {New York}, |
2196 |
|
|
chapter = {2}, |
2197 |
|
|
pages = {19-22}, |
2198 |
tim |
2685 |
} |
2199 |
|
|
|
2200 |
tim |
2786 |
@ARTICLE{Tu1995, |
2201 |
|
|
author = {K. Tu and D. J. Tobias and M. L. Klein}, |
2202 |
|
|
title = {Constant pressure and temperature molecular dynamics simulation of |
2203 |
|
|
a fully hydrated liquid crystal phase dipalmitoylphosphatidylcholine |
2204 |
|
|
bilayer}, |
2205 |
|
|
journal = {Biophysical Journal}, |
2206 |
|
|
year = {1995}, |
2207 |
|
|
volume = {69}, |
2208 |
|
|
pages = {2558-2562}, |
2209 |
|
|
number = {6}, |
2210 |
|
|
month = {Dec}, |
2211 |
|
|
abstract = {We report a constant pressure and temperature molecular dynamics simulation |
2212 |
|
|
of a fully hydrated liquid crystal (L(alpha) phase bilayer of dipalmitoylphosphatidylcholine |
2213 |
|
|
at 50 degrees C and 28 water molecules/lipid. We have shown that |
2214 |
|
|
the bilayer is stable throughout the 1550-ps simulation and have |
2215 |
|
|
demonstrated convergence of the system dimensions. Several important |
2216 |
|
|
aspects of the bilayer structure have been investigated and compared |
2217 |
|
|
favorably with experimental results. For example, the average positions |
2218 |
|
|
of specific carbon atoms along the bilayer normal agree well with |
2219 |
|
|
neutron diffraction data, and the electron density profile is in |
2220 |
|
|
accord with x-ray diffraction results. The hydrocarbon chain deuterium |
2221 |
|
|
order parameters agree reasonably well with NMR results for the |
2222 |
|
|
middles of the chains, but the simulation predicts too much order |
2223 |
|
|
at the chain ends. In spite of the deviations in the order parameters, |
2224 |
|
|
the hydrocarbon chain packing density appears to be essentially |
2225 |
|
|
correct, inasmuch as the area/lipid and bilayer thickness are in |
2226 |
|
|
agreement with the most refined experimental estimates. The deuterium |
2227 |
|
|
order parameters for the glycerol and choline groups, as well as |
2228 |
|
|
the phosphorus chemical shift anisotropy, are in qualitative agreement |
2229 |
|
|
with those extracted from NMR measurements.}, |
2230 |
|
|
annote = {Tv018 Times Cited:108 Cited References Count:34}, |
2231 |
|
|
issn = {0006-3495}, |
2232 |
|
|
uri = {<Go to ISI>://A1995TV01800037}, |
2233 |
tim |
2685 |
} |
2234 |
|
|
|
2235 |
tim |
2786 |
@ARTICLE{Tuckerman1992, |
2236 |
|
|
author = {M. Tuckerman and B. J. Berne and G. J. Martyna}, |
2237 |
|
|
title = {Reversible Multiple Time Scale Molecular-Dynamics}, |
2238 |
|
|
journal = {Journal of Chemical Physics}, |
2239 |
|
|
year = {1992}, |
2240 |
|
|
volume = {97}, |
2241 |
|
|
pages = {1990-2001}, |
2242 |
|
|
number = {3}, |
2243 |
|
|
month = {Aug 1}, |
2244 |
|
|
abstract = {The Trotter factorization of the Liouville propagator is used to generate |
2245 |
|
|
new reversible molecular dynamics integrators. This strategy is |
2246 |
|
|
applied to derive reversible reference system propagator algorithms |
2247 |
|
|
(RESPA) that greatly accelerate simulations of systems with a separation |
2248 |
|
|
of time scales or with long range forces. The new algorithms have |
2249 |
|
|
all of the advantages of previous RESPA integrators but are reversible, |
2250 |
|
|
and more stable than those methods. These methods are applied to |
2251 |
|
|
a set of paradigmatic systems and are shown to be superior to earlier |
2252 |
|
|
methods. It is shown how the new RESPA methods are related to predictor-corrector |
2253 |
|
|
integrators. Finally, we show how these methods can be used to accelerate |
2254 |
|
|
the integration of the equations of motion of systems with Nose |
2255 |
|
|
thermostats.}, |
2256 |
|
|
annote = {Je891 Times Cited:680 Cited References Count:19}, |
2257 |
|
|
issn = {0021-9606}, |
2258 |
|
|
uri = {<Go to ISI>://A1992JE89100044}, |
2259 |
tim |
2685 |
} |
2260 |
|
|
|
2261 |
tim |
2786 |
@ARTICLE{Wegener1979, |
2262 |
|
|
author = {W.~A. Wegener, V.~J. Koester and R.~M. Dowben}, |
2263 |
|
|
title = {A general ellipsoid can not always serve as a modle for the rotational |
2264 |
|
|
diffusion properties of arbitrary shaped rigid molecules}, |
2265 |
|
|
journal = {Proc. Natl. Acad. Sci.}, |
2266 |
|
|
year = {1979}, |
2267 |
|
|
volume = {76}, |
2268 |
|
|
pages = {6356-6360}, |
2269 |
|
|
number = {12}, |
2270 |
tim |
2685 |
} |
2271 |
|
|
|
2272 |
tim |
2786 |
@ARTICLE{Withers2003, |
2273 |
|
|
author = {I. M. Withers}, |
2274 |
|
|
title = {Effects of longitudinal quadrupoles on the phase behavior of a Gay-Berne |
2275 |
|
|
fluid}, |
2276 |
|
|
journal = {Journal of Chemical Physics}, |
2277 |
|
|
year = {2003}, |
2278 |
|
|
volume = {119}, |
2279 |
|
|
pages = {10209-10223}, |
2280 |
|
|
number = {19}, |
2281 |
|
|
month = {Nov 15}, |
2282 |
|
|
abstract = {The effects of longitudinal quadrupole moments on the formation of |
2283 |
|
|
liquid crystalline phases are studied by means of constant NPT Monte |
2284 |
|
|
Carlo simulation methods. The popular Gay-Berne model mesogen is |
2285 |
|
|
used as the reference fluid, which displays the phase sequences |
2286 |
|
|
isotropic-smectic A-smectic B and isotropic-smectic B at high (T*=2.0) |
2287 |
|
|
and low (T*=1.5) temperatures, respectively. With increasing quadrupole |
2288 |
|
|
magnitude the smectic phases are observed to be stabilized with |
2289 |
|
|
respect to the isotropic liquid, while the smectic B is destabilized |
2290 |
|
|
with respect to the smectic A. At the lower temperature, a sufficiently |
2291 |
|
|
large quadrupole magnitude results in the injection of the smectic |
2292 |
|
|
A phase into the phase sequence and the replacement of the smectic |
2293 |
|
|
B phase by the tilted smectic J phase. The nematic phase is also |
2294 |
|
|
injected into the phase sequence at both temperatures considered, |
2295 |
|
|
and ultimately for sufficiently large quadrupole magnitudes no coherent |
2296 |
|
|
layered structures were observed. The stabilization of the smectic |
2297 |
|
|
A phase supports the commonly held belief that, while the inclusion |
2298 |
|
|
of polar groups is not a prerequisite for the formation of the smectic |
2299 |
|
|
A phase, quadrupolar interactions help to increase the temperature |
2300 |
|
|
and pressure range for which the smectic A phase is observed. The |
2301 |
|
|
quality of the layered structure is worsened with increasing quadrupole |
2302 |
|
|
magnitude. This behavior, along with the injection of the nematic |
2303 |
|
|
phase into the phase sequence, indicate that the general tendency |
2304 |
|
|
of the quadrupolar interactions is to destabilize the layered structure. |
2305 |
|
|
A pressure dependence upon the smectic layer spacing is observed. |
2306 |
|
|
This behavior is in much closer agreement with experimental findings |
2307 |
|
|
than has been observed previously for nonpolar Gay-Berne and hard |
2308 |
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spherocylinder models. (C) 2003 American Institute of Physics.}, |
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annote = {738EF Times Cited:3 Cited References Count:43}, |
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issn = {0021-9606}, |
2311 |
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uri = {<Go to ISI>://000186273200027}, |
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tim |
2685 |
} |
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