Scaling and universality of critical fluctuations in granular gases

The global energy fluctuations of a low density gas granular gas in the homogeneous cooling state near its clustering instability are studied by means of molecular dynamics simulations. The relative dispersion of the fluctuations is shown to exhibit a power-law divergent behavior. Moreover, the probability distribution of the fluctuations presents data collapse as the system approaches the instability, for different values of the inelasticity. The function describing the collapse turns out to be the same as the one found in several molecular equilibrium and non-equilibrium systems, except for the change in the sign of the fluctuations

Fluctuations of water near extended hydrophobic and hydrophilic surfaces

We use molecular dynamics simulations of the SPC-E model of liquid water to derive probability distributions for water density fluctuations in probe volumes of different shapes and sizes, both in the bulk as well as near hydrophobic and hydrophilic surfaces. To obtain our results, we introduce a biased sampling of coarse-grained densities, which in turn biases the actual solvent density. The technique is easily combined with molecular dynamics integration algorithms. Our principal result is that the probability for density fluctuations of water near a hydrophobic surface, with or without surface-water attractions, is akin to density fluctuations at the water-vapor interface. Specifically, the probability of density depletion near the surface is significantly larger than that in bulk. In contrast, we find that the statistics of water density fluctuations near a model hydrophilic surface are similar to that in the bulk

Investigation of Structural Dynamics of Enzymes and Protonation States of Substrates Using Computational Tools.

This review discusses the use of molecular modeling tools, together with existing experimental findings, to provide a complete atomic-level description of enzyme dynamics and function. We focus on functionally relevant conformational dynamics of enzymes and the protonation states of substrates. The conformational fluctuations of enzymes usually play a crucial role in substrate recognition and catalysis. Protein dynamics can be altered by a tiny change in a molecular system such as different protonation states of various intermediates or by a significant perturbation such as a ligand association. Here we review recent advances in applying atomistic molecular dynamics (MD) simulations to investigate allosteric and network regulation of tryptophan synthase (TRPS) and protonation states of its intermediates and catalysis. In addition, we review studies using quantum mechanics/molecular mechanics (QM/MM) methods to investigate the protonation states of catalytic residues of β-Ketoacyl ACP synthase I (KasA). We also discuss modeling of large-scale protein motions for HIV-1 protease with coarse-grained Brownian dynamics (BD) simulations

Simulation of quantum zero-point effects in water using a frequency-dependent thermostat

Molecules like water have vibrational modes with a zero-point energy well above room temperature. As a consequence, classical molecular dynamics simulations of their liquids largely underestimate the energy of modes with a higher zero-point temperature, which translates into an underestimation of covalent interatomic distances due to anharmonic effects. Zero-point effects can be recovered using path integral molecular dynamics simulations, but these are computationally expensive, making their combination with ab initio molecular dynamics simulations a challenge. As an alternative to path integral methods, from a computationally simple perspective, one would envision the design of a thermostat capable of equilibrating and maintaining the different vibrational modes at their corresponding zero-point temperatures. Recently, Ceriotti et al. (Phys. Rev. Lett. 102 020601 (2009)) introduced a framework to use a custom-tailored Langevin equation with correlated noise that can be used to include quantum fluctuations in classical molecular dynamics simulations. Here we show that it is possible to use the generalized Langevin equation with suppressed noise in combination with Nose-Hoover thermostats to efficiently impose a zero-point temperature on independent modes in liquid water. Using our simple and inexpensive method, we achieve excellent agreement for all atomic pair correlation functions compared to the path integral molecular dynamics simulation.Comment: 27 pages, 12 figs, Published versio

Neutrino Scattering in Heterogeneous Supernova Plasmas

Neutrinos in core collapse supernovae are likely trapped by neutrino-nucleus elastic scattering. Using molecular dynamics simulations, we calculate neutrino mean free paths and ion-ion correlation functions for heterogeneous plasmas. Mean free paths are systematically shorter in plasmas containing a mixture of ions compared to a plasma composed of a single ion species. This is because neutrinos can scatter from concentration fluctuations. The dynamical response function of a heterogeneous plasma is found to have an extra peak at low energies describing the diffusion of concentration fluctuations. Our exact molecular dynamics results for the static structure factor reduce to the Debye Huckel approximation, but only in the limit of very low momentum transfers.Comment: 11 pages, 13 figure

Maintaining the equipartition theorem in small heterogeneous molecular dynamics ensembles

It has been reported recently that the equipartition theorem is violated in molecular dynamics simulations with periodic boundary condition [Shirts et al, J. Chem. Phys. 125, 164102 (2006)]. This effect is associated with the conservation of the center of mass momentum. Here, we propose a fluctuating center of mass molecular dynamics approach (FCMMD) to solve this problem. Using the analogy to a system exchanging momentum with its surroundings, we work out --and validate via simulations-- an expression for the rate at which fluctuations shall be added to the system. The restoration of equipartition within the FCMMD is then shown both at equilibrium as well as beyond equilibrium in the linear response regime