相关论文: Long-Time Mean Square Displacements in Proteins

We describe a new technique to estimate the mean square velocity of a Brownian particle from time series of the position of the particle sampled at frequencies several orders of magnitude smaller than the momentum relaxation frequency. We…

Diffusion at solid-liquid interfaces is crucial in many technological and biophysical processes. Although its behavior seems deceivingly simple, recent studies showing passive superdiffusive transport suggest diffusion on surfaces may hide…

Many real objects are modeled as discrete sets of points, such as corners or other salient features. For our main applications in chemistry, points represent atomic centers in a molecule or a solid material. We study the problem of…

We study the dynamics of hydration water/protein association in folded proteins, using lysozyme and myoglobin as examples. Extensive molecular dynamics simulations are performed to identify underlying mechanisms of the dynamical transition…

Because diffusion models have shown impressive performances in a number of tasks, such as image synthesis, there is a trend in recent works to prove (with certain assumptions) that these models have strong approximation capabilities. In…

Coarse-graining of fully atomistic molecular dynamics simulations is a long-standing goal in order to allow the description of processes occurring on biologically relevant timescales. For example, the prediction of pathways, rates and…

Time-dependent partial differential equations (PDEs) often develop sharp fronts, localized peaks, and other moving structures that occupy only a small portion of the space--time domain but dominate the approximation error. This makes fixed…

A novel combination of discontinuous molecular dynamics and the Langevin equation, together with an intermediate-resolution model, are used to carry out long (several $\mu$s) simulation and study folding transition and transport of proteins…

A molecular dynamics (MD) simulation was performed to study the propagation of soundwaves in a fluid. Soundwaves are generated by a sinusoidally oscillating wall and annihilated by a locally applied Langevin thermostat near the opposite…

A tutorial introduction to the technique of Molecular Dynamics (MD) is given, and some characteristic examples of applications are described. The purpose and scope of these simulations and the relation to other simulation methods is…

Molecular dynamics (MD) is a widely-used tool for simulating the molecular and materials properties. It is a common wisdom that molecular dynamics simulations should obey physical laws and, hence, lots of effort is put into ensuring that…

We have extended the multilevel summation (MLS) method, originally developed to evaluate long-range Coulombic interactions in molecular dynamics (MD) simulations [Skeel et al., J. Comput. Chem., 23, 673 (2002)], to handle dispersion…

Recent advances in molecular biology and fluorescence microscopy imaging have made possible the inference of the dynamics of single molecules in living cells. Such inference allows to determine the organization and function of the cell. The…

The algebraic reformulation of molecular Quantum Electrodynamics (mQED) at finite temperatures is applied to Nuclear Magnetic Resonance (NMR) in order to provide a foundation for the reconstruction of much more detailed molecular…

Quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations have been developed to simulate molecular systems, where an explicit description of changes in the electronic structure is necessary. However, QM/MM MD…

We perform Discrete Element Method (DEM) simulations of granular particles (polystyrene spheres) vibrated inside a cubic container. The study investigates the evolution of the packing fraction with and without rotational friction at…

The length-scale dependence of the dynamic entropy is studied in a molecular dynamics simulation of a binary Lennard-Jones liquid above the mode-coupling critical temperature $T_c$. A number of methods exist for estimating the entropy of…

Several experiments on tagged molecules or particles in living systems suggest that they move anomalously slow - their mean squared displacement (MSD) increase slower than linearly with time. Leading models aimed at understanding these…

The general covariance of the diffusion equation is exploited in order to explore the curvature effects appearing on brownian motion over a d-dimensional curved manifold. We use the local frame defined by the so called Riemann normal…

Simulating the dynamics of ions near polarizable nanoparticles (NPs) using coarse-grained models is extremely challenging due to the need to solve the Poisson equation at every simulation timestep. Recently, a molecular dynamics (MD) method…