Molecular dynamics

About: Molecular dynamics is a research topic. Over the lifetime, 22482 publications have been published within this topic receiving 800625 citations. The topic is also known as: molecular dynamics.

Molecular-dynamics simulation of structural and conformational properties of poly(propylene oxide)

Abstract: Molecular-dynamics simulations of poly(propylene oxide) (PPO) have been performed in the temperature range 300 K⩽T⩽450 K using a newly developed atomistic force field. Chains with 1, 11 and 45 repeat units have been considered. We find excellent agreement for the short and intermediate range order as deduced from x-ray and neutron diffraction measurements with deviations (excluding quantum mechanical effects for the nuclear motion) lying within experimental uncertainties. The static structure factor S(q) shows a first sharp diffraction peak due to interchain correlations which is shifted to smaller wave vectors with increasing temperature. The molecular weight dependence of the short and intermediate range order is found to be weak and the obtained density and thermal expansivity compare favorably with experimental data. The backbone dihedral angle distributions are essentially identical for PO11 and PO45, but deviate slightly from those for PO1, and the probability for gauche conformations is quite large resulting in a small characteristic ratio. The dihedral and bond angle distributions obtained from the present MD study are more closely related to experiments than those that have been achieved previously by combining experimental data with reverse Monte Carlo modeling.

Molecular insights into the differential dynamics of SARS-CoV-2 variants of concern

Abstract: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has affected the lives and livelihood of millions of individuals around the world. It has mutated several times after its first inception, with an estimated two mutations occurring every month. Although we have been successful in developing vaccines against the virus, the emergence of variants has enabled it to escape therapy. Few of the generated variants are also reported to be more infectious than the wild-type (WT). In this study, we analyze the attributes of all RBD/ACE2 complexes for the reported VOCs, namely, Alpha, Beta, Gamma, and Delta through computer simulations. Results indicate differences in orientation and binding energies of the VOCs from the WT. Overall, it was observed that electrostatic interactions play a major role in the binding of the complexes. Detailed residue level energetics revealed that the most prominent changes in interaction energies were seen particularly at the mutated residues which were present at RBD/ACE2 interface. We found that the Delta variant is one of the most tightly bound variants of SARS-CoV-2 with dynamics similar to WT. The high binding affinity of RBD towards ACE2 is indicative of an increase in viral transmission and infectivity. The details presented in our study provide additional information for the design and development of effective therapeutic strategies for the emerging variants of the virus in the future.

Time resolved stimulated light scattering from a solvated chromophore : a molecular dynamics study

Abstract: We calculate the signal in a time‐resolved, coherent light scattering experiment on a dilute solution of a nonpolar solute dissolved in a nonpolar solvent. We model the solute and solvent molecules as electronic two level systems, and assume that only the solute interacts with radiation. The electronic degree of freedom is treated perturbatively within the Born–Oppenheimer approximation. The nuclear degrees of freedom are treated classically, and their effects are modeled by a molecular dynamics simulation. We assume the electronic absorption spectrum is dominated by inhomogeneous broadening. The validity of this assumption for our model is verified through the calculation of the absorption line shape with and without the inhomogeneous broadening assumption. A quantitative measure of the homogeneous dephasing time is obtained from a calculation of the photon echo signal for our model. The time dependence of the light scattering signal is shown to reflect both dynamics of the fluid in its electronic ground...

Motion and Conformation of Side Chains in Peptides. A Comparison of 2D Umbrella-Sampling Molecular Dynamics and NMR Results

Abstract: An extension of the technique of umbrella sampling to two dimensions is presented and applied to the study of the kinetic and thermodynamic properties of side chains in peptides. Four two-dimensional potential-of-mean-force surfaces for the two degrees of freedom χ1 and χ2 of the four phenylalanine residues in antamanide at 300 K are calculated using the stochastic dynamics simulation method with the molecular force field GROMOS. From these surfaces, time constants for the transitions between the favored conformations along χ1 and χ2 are calculated using transition state theory. The results are compared with experimental values determined by NMR. In addition, motionally averaged 3J-coupling constants are calculated from the rotamer probability distributions derived from the χ1, χ2 potential-of-mean-force surfaces using the generalized Karplus equations. The average values are compared to the experimental NMR results. It is shown that the two-dimensional umbrella-sampling approach is capable of providing d...