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At least 145 records · Page 8Linked to original sources
PubMed2005

Diffusion coefficients of small gas molecules in amorphous cis-1,4-polybutadiene estimated by molecular dynamics simulations.

Molecular dynamics (MD) simulations were employed to estimate the diffusion coefficients of small gas molecules (Ar, O2, N2, CO2, and CH4) in amorphous cis-1,4-polybutadiene in the temperature range of 250-400 K. The VT diagram and solubility parameter of the amorphous polymer have been successfully reproduced using a full atomistic potential. Diffusion coefficients were calculated from long NPT MD runs (up to 3 ns) at temperature ranging from 250 up to 400 K. Calculated diffusion coefficients compare well with experimental data as well as previous published work, though a systematic overestimation is found due to the finite-size effect of the model. The influence of various physical and computational parameters on the results is discussed. The diffusion mechanism is examined at the different temperatures of study.

Journal Article↗
PubMed2006

Evaluation of intrinsic compressibility of proteins by molecular dynamics simulation.

Molecular dynamics simulation has been performed on five native proteins in water to evaluate their intrinsic isothermal compressibilities beta(T,int). To identify physical factors contributing to protein compressibility, a general method is presented for analyzing the compressibility of mechanically inhomogeneous systems. The value of beta(T,int) varies with protein species considerably: beta-lactoglobulin (14.15 x 10(-2) GPa(-1)) is more than twice as compressible as ribonuclease A (6.77 x 10(-2) GPa(-1)). Beta-lactoglobulin and myoglobin (13.95 x 10(-2) GPa(-1)) have similar values of beta(T,int), but the mechanisms responsible for them are significantly different. The volume fluctuations of internal cavities and the magnitudes of the crosscorrelation between them are the key factors determining beta(T,int) of proteins. Though the volume fractions of internal cavity for the five studied proteins are nearly equal to one another, the mean cavity compressibilities beta(T,cav) vary considerably with protein species and range from 0.35 to 0.69 GPa(-1), which are much smaller than those of normal organic liquids such as methanol, ethanol, and benzene and close to that of glycerol (0.55 GPa(-1)), a strongly associated liquid.

Animals↗
PubMed2006

General continuum boundary conditions for miscible binary fluids from molecular dynamics simulations.

Molecular dynamics simulations are used to explore the flow behavior and diffusion of miscible fluids near solid surfaces. The solid produces deviations from bulk fluid behavior that decay over a distance of the order of the fluid correlation length. Atomistic results are mapped onto two types of continuum model: Mesoscopic models that follow this decay and conventional sharp interface boundary conditions for the stress and velocity. The atomistic results, and mesoscopic models derived from them, are consistent with the conventional Marangoni stress boundary condition. However, there are deviations from the conventional Navier boundary condition that states that the slip velocity between wall and fluid is proportional to the strain rate. A general slip boundary condition is derived from the mesoscopic model that contains additional terms associated with the Marangoni stress and diffusion, and is shown to describe the atomistic simulations. The additional terms lead to strong flows when there is a concentration gradient. The potential for using this effect to make a nanomotor or pump is evaluated.

Journal Article↗
PubMed1993

Nonexponential relaxation after ligand dissociation from myoglobin: a molecular dynamics simulation.

Molecular dynamics simulations of myoglobin after ligand photodissociation show that the out-of-plane motion of the heme iron has a rapid subpicosecond phase followed by a slower nonexponential process involving more global protein relaxation. Individual trajectories show rather different behavior, suggesting there is an inhomogeneous component to the relaxation. The calculated time dependence of the iron motion over 100 ps is in excellent agreement with the frequency shift of band III of the heme group [see Lim, M., Jackson, T. A. & Anfinrud, P. A. (1993) Proc. Natl. Acad. Sci. USA 90, 5801-5804]. If that the barrier to rebinding depends on the out-of-plane iron position, the time dependence obtained from the simulation can explain the nonexponential room-temperature geminate recombination of NO.

Kinetics↗
PubMed1996

Glass transition in DNA from molecular dynamics simulations.

Molecular dynamics simulations of the oligonucleotide duplex d(CGCGCG)2 in aqueous solution are used to investigate the glass transition phenomenon. The simulations were performed at temperatures in the 20 K to 340 K range. The mean square atomic fluctuations showed that the behavior of the oligonucleotide duplex was harmonic at low temperatures. A glass transition temperature at 223 K to 234 K was inferred for the oligonucleotide duplex, which is in agreement with experimental observations. The largest number of hydrogen bounds between the polar atoms of the oligonucleotide duplex and the water molecules was obtained at the glass transition temperature. With increasing temperature we observed a decrease in the average lifetime of the hydrogen bonds to water molecules.

Base Sequence↗
PubMed2000

Growth of taylor vortices: A molecular dynamics study

Molecular dynamics methods have been used in a quantitative study of the growth and decay of Taylor vortices in a fluid confined between concentric cylinders when the rotation of the inner cylinder is instantaneously started or stopped. Analysis of the temporal evolution of the vortex flow fields shows that the behavior of this microscopic system agrees with experiment. In order to make the analysis entirely self-contained, torque measurements have been used to determine the effective viscosity of the fluid.

Journal Article↗
PubMed2002

Bridge function and other structural properties of core-softened model fluids from molecular dynamics simulations.

Molecular dynamics (MD) simulations in three dimensions have been performed for a fluid with particles interacting with a continuous version of the Stell-Hemmer core-softened potential that in two dimensions has been known to reproduce most of the static and dynamic anomalies of liquid water. The pair distribution function obtained from the MD simulation is extrapolated with the help of integral equation theory with a suitable closure relation and the bridge function is extracted. A strong dependence of the bridge function on the system size, i.e., the total number of particles (N) used in the simulation box is observed, which leads to spurious values of the structure factor at long wavelengths. A simple self-consistent correction scheme for the finite size effect has been adopted to correct the bridge function and this scheme produces the correct bridge function even for a small system size. The effects of temperature, number density, and potential parameters on the pair distribution functions and extracted bridge functions are extensively studied.

Journal Article↗
PubMed2004

Surface structure of liquid Li and Na: an ab initio molecular dynamics study.

Molecular dynamics simulations of the liquid-vapor interfaces of liquid metals have been performed using first principles methods. Results are presented for liquid lithium and sodium near their respective triple points, for samples of 2000 particles in a slab geometry. The atomic density profiles show a pronounced stratification extending several atomic diameters into the bulk, which is similar to that already experimentally observed in liquid K, Ga, In, and Hg.

Journal Article↗
PubMed2005

Simulation of screw dislocation motion in iron by molecular dynamics simulations.

Molecular dynamics (MD) simulations are used to investigate the response of a/2<111> screw dislocation in iron submitted to pure shear strain. The dislocation glides and remains in a (110) plane; the motion occurs exclusively through the nucleation and propagation of double kinks. The critical stress is calculated as a function of the temperature. A new method is developed and used to determine the activation energy of the double kink mechanism from MD simulations. It is shown that the differences between experimental and simulation conditions lead to a significant difference in activation energy. These differences are explained, and the method developed provides the link between MD and mesoscopic simulations.

Journal Article↗
PubMed1992

Conformation and fluctuations of free stefin B: a molecular dynamics study.

Molecular dynamics study was performed on the cysteine proteinase inhibitor stefin B. Structure of inhibitor from the complex with papain was used as a starting point. Amino terminal "trunk" of the inhibitor which lies extended along the cleft of the enzyme in the complex, folded onto the body of inhibitor during MD simulation, thereby reducing the total and particularly hydrophobic surface exposed to the solvent. This effect counterbalances hydrophobic contribution of the "trunk" and explains why its deletion in stefin B and related inhibitors doesn't reduce the dissociation constant. The rest of stefin B conformation is conserved together with main chain hydrogen bonds. Fluctuations of C alpha atoms resembles crystallographic B factors with exception of residues in contact with enzyme.

Chemical Phenomena↗
PubMed2005

Effects of solute-solvent proton exchange on polypeptide chain dynamics: a constant-pH molecular dynamics study.

A method for performing implicit-solvent molecular dynamics simulations at constant pH was applied to a pentapeptide acetyl-Ala-Asp-Ala-Lys-Ala-amide at pH 4. As a reference, molecular dynamics simulations were done for the same peptide with two variants of its fixed protonation patterns expected to dominate at pH 4, i.e., with a protonated and a deprotonated side chain of the Asp residue and the protonated Lys residue in both cases. The dynamic trajectories of the peptide were used to discuss the problem of the significance of the solute-solvent proton exchange phenomena for the dynamics and structural distributions of the polypeptide chain. The Asp-Lys distance was used as a probe of the overall molecular structure of the investigated pentapeptide. To characterize the dynamics, distributions of the "waiting" times for a transition from a "short" distance conformation to a "long" distance conformation were constructed, based on the generated molecular dynamics trajectories. We show that the relaxation time for the transitions, derived from the constant-pH simulations, is very close to the relaxation time characterizing a permanently protonated molecule, although the average protonation probability of the short-distance conformation is close to zero. However, the distribution of the Asp-Lys distances obtained from constant-pH simulations cannot be reproduced as a linear combination of the distributions resulting from the simulations with fixed protonation states.

Aspartic Acid↗
PubMed2005

Pressure-dependent transition in protein dynamics at about revealed by molecular dynamics simulation.

Molecular dynamics simulations of a crystalline protein, Staphylococcal nuclease, over the pressure range 1 bar to 15 kbar reveal a qualitative change in the internal protein motions at approximately 4 kbar. This change involves the existence of two linear regimes in the mean-square displacement for internal protein motion, (P) with a twofold decrease in the slope for P>4 kbar. The major effect of pressure on the dynamics is a loss, with increasing pressure of large amplitude, collective protein modes below 2 THz effective frequency, accompanied by restriction of large-scale solvent translational motion.

Computer Simulation↗
PubMed2006

Phenol-benzene complexation dynamics: quantum chemistry calculation, molecular dynamics simulations, and two dimensional IR spectroscopy.

Molecular dynamics (MD) simulations and quantum mechanical electronic structure calculations are used to investigate the nature and dynamics of the phenol-benzene complex in the mixed solvent, benzene/CCl4. Under thermal equilibrium conditions, the complexes are continuously dissociating and forming. The MD simulations are used to calculate the experimental observables related to the phenol hydroxyl stretching mode, i.e., the two dimensional infrared vibrational echo spectrum as a function of time, which directly displays the formation and dissociation of the complex through the growth of off-diagonal peaks, and the linear absorption spectrum, which displays two hydroxyl stretch peaks, one for the complex and one for the free phenol. The results of the simulations are compared to previously reported experimental data and are found to be in quite reasonable agreement. The electronic structure calculations show that the complex is T shaped. The classical potential used for the phenol-benzene interaction in the MD simulations is in good accord with the highest level of the electronic structure calculations. A variety of other features is extracted from the simulations including the relationship between the structure and the projection of the electric field on the hydroxyl group. The fluctuating electric field is used to determine the hydroxyl stretch frequency-frequency correlation function (FFCF). The simulations are also used to examine the number distribution of benzene and CCl4 molecules in the first solvent shell around the phenol. It is found that the distribution is not that of the solvent mole fraction of benzene. There are substantial probabilities of finding a phenol in either a pure benzene environment or a pure CCl4 environment. A conjecture is made that relates the FFCF to the local number of benzene molecules in phenol's first solvent shell.

Benzene↗
PubMed1996

NMR-based, molecular dynamics- and random walk molecular mechanics-supported study of conformational aspects of a carbohydrate ligand (Gal beta 1-2Gal beta 1-R) for an animal galectin in the free and in the bound state.

The binding of a carbohydrate to a lectin may affect the conformation of the ligand. To address this question for the galectin from chicken liver, the conformation of Gal beta 1-2Gal beta 1-R was analyzed in the free and in the galectin-bound state with 2D-ROESY- and 1D- as well as 2D-transferred NOE-experiments. A computer-assisted analysis of spatial parameters of the ligand by molecular dynamics (MD) and random walk molecular mechanics (RAMM) calculations, taking different dielectric constraints from epsilon = 1 to epsilon = 80 and various force fields into account, were instrumental to define the energetic minima of the free state. NMR-derived interresidual distance constraints enabled a conformational mapping. The two overlapping interresidual distance constraints obtained from transferred-NOE experiments of the galectin-ligand complex clearly support the notion that the conformation of the disaccharide in the bound state is at least very close to its global energy minimum state in solution.

Animals↗
PubMed1999

On the convergence of the conformational coordinates basis set obtained by the essential dynamics analysis of proteins' molecular dynamics simulations.

In this article we present a quantitative evaluation of the convergence of the conformational coordinates of proteins, obtained by the Essential Dynamics method. Using a detailed analysis of long molecular dynamics trajectories in combination with a statistical assessment of the significance of the measured convergence, we obtained that simulations of a few hundreds of picoseconds are in general sufficient to provide a stable and statistically reliable definition of the essential and near constraints subspaces, at least within the nanoseconds time range. Proteins 1999;36:419-424.

Algorithms↗
PubMed1996

H-bond stability in the tRNA(Asp) anticodon hairpin: 3 ns of multiple molecular dynamics simulations.

Multiple molecular dynamics trajectories of the solvated and neutralized 17-residue tRNA(Asp) anticodon hairpin were generated for a total of 3 ns. Explicit treatment of all long-ranged electrostatic interactions by the particle mesh Ewald algorithm, as implemented in the AMBER MD software package, effected a degree of structural stabilization not previously achieved by use of a long 16-A solvent interaction truncation scheme. The increased stability of this multiple molecular dynamics set was appropriate for an in-depth analysis of the six 500-ps-long trajectories and allowed the characterization of a number of key structural interactions. The dynamical behavior of the standard Watson-Crick base pairs, the noncanonical G30-U40 "wobble" base pair, and the psi 32-C38 pseudo-base pair is presented as well as that of two C--H... O hydrogen bonds found to contribute to the array of tertiary interactions that stabilize the seven-nucleotide native loop conformation. The least mobile residue in the loop is U33, which forms the U-turn motif and which participates in several hydrogen-bonding interactions, whereas the most mobile residue is the apical residue G34 at the wobble position, a factor undoubtedly important in its biological function. The set of multiple molecular dynamics trajectories obtained does not converge on a 500-ps time scale to a unique dynamical model but instead describes an ensemble of structural microstates accessible to the system under the present simulation protocol, which is the result of local structural heterogeneity rather than of global conformational changes.

Anticodon↗
PubMed1999

Comparison of the dynamics of bovine and human angiogenin: a molecular dynamics study.

Molecular dynamics simulations have been carried out for 1 ns on human and bovine angiogenin systems in an effort to compare and contrast their dynamics. An analysis of their dynamics is done by examining the rms deviations, following hydrogen-bonding interactions and looking at the role of water in and around the protein. The C-terminus of bovine angiogenin moves appreciably during dynamics suggesting a better structure for ligand binding. However, we do not find any evidence of a conformation where the glutamate residue that obstructs the active site takes on a different conformation. We observe a differential hydrogen-bonding pattern in the active site regions of bovine and human angiogenins, which could have a bearing on the different catalytic activities of the proteins. We also propose that the differential binding of the monoclonal antibody toward the two proteins might be due sequential and not conformational differences. Water molecules might play an important functional role in both proteins given their subtle functional differences. A simple computation on the molecular dynamics data has been carried out to identify locations in and around the protein that are invariably occupied by water. The locations of nearly half the waters we have identified from the simulation as being invariant in bovine angiogenin occupy similar locations in the bovine angiogenin crystal structure. The positions of the waters identified in human angiogenin differ considerably from that of bovine angiogenin.

Animals↗
PubMed2003

Interdomain dynamics and ligand binding: molecular dynamics simulations of glutamine binding protein.

Periplasmic binding proteins from Gram-negative bacteria possess a common architecture, comprised of two domains linked by a hinge region, a fold which they share with the neurotransmitter-binding domains of ionotropic glutamate receptors (GluRs). Glutamine-binding protein (GlnBP) is one such protein, whose crystal structure has been solved in both open and closed forms. Multi-nanosecond molecular dynamics simulations have been used to explore motions about the hinge region and how they are altered by ligand binding. Glutamine binding is seen to significantly reduce inter-domain motions about the hinge region. Essential dynamics analysis of inter-domain motion revealed the presence of both hinge-bending and twisting motions, as has been reported for a related sugar-binding protein. Significantly, the influence of the ligand on GlnBP dynamics is similar to that previously observed in simulations of rat glutamate receptor (GluR2) ligand-binding domain. The essential dynamics analysis of GlnBP also revealed a third class of motion which suggests a mechanism for signal transmission in GluRs.

Binding Sites↗