相关论文: Small ionic radii limit time step in Martini 3 mol…
Molecular dynamics simulations have been performed on pure liquid water, aqueous solutions of sodium chloride, and polymer solutions exposed to a strong external electric field with the goal to gain molecular insight into the structural…
Molecular dynamics (MD) simulation is a widely used technique to simulate molecular systems, most commonly at the all-atom resolution where equations of motion are integrated with timesteps on the order of femtoseconds…
The adoption of detailed mechanisms for chemical kinetics often poses two types of severe challenges: First, the number of degrees of freedom is large; and second, the dynamics is characterized by widely disparate time scales. As a result,…
We present a ``coarse molecular dynamics'' approach and apply it to studying the kinetics and thermodynamics of a peptide fragment dissolved in water. Short bursts of appropriately initialized simulations are used to infer the deterministic…
The computational difficulty of solving fully quantum many-body spin problems is a significant obstacle to understanding the behavior of strongly correlated quantum matter. Experimental ion-trap quantum simulation is a promising approach…
The numerical solutions of nonlocal and local Boltzmann kinetic equations for the simulation of central heavy ion reactions are parameterized in terms of time dependent thermodynamical variables in the Fermi liquid sense. This allows one to…
We develop a coarse grained (CG) approach for efficiently simulating calcium dynamics in the endoplasmic reticulum membrane based on a fine stochastic lattice gas model. By grouping neighboring microscopic sites together into CG cells and…
Significant progress in computer hardware and software have enabled molecular dynamics (MD) simulations to model complex biological phenomena such as protein folding. However, enabling MD simulations to access biologically relevant…
Pore forming toxins (PFTs) are virulent proteins released by several species, including many strains of bacteria, to attack and kill host cells. In this article, we focus on the utility of molecular dynamics (MD) simulations and the…
Protein folding produces characteristic and functional three-dimensional structures from unfolded polypeptides or disordered coils. The emergence of extraordinary complexity in the protein folding process poses astonishing challenges to…
Simulations have acted as a cornerstone to understand MOF/polymer interface structure, however, no molecular-level simulation has yet been performed at the nanoparticle scale. In this work, a hybrid MARTINI/Force Matching (FM) force field…
Microscopic dynamics of complex fluids in the early stage of spinodal decomposition (SD) is strongly intertwined with the kinetics of structural evolution, which makes a quantitative characterization challenging. In this work, we use x-ray…
Accurate modeling of aqueous monovalent ions is essential for understanding the function of biomolecules, such as nucleic acid stability and binding of charged drugs to protein targets. The 1D and 3D reference interaction site models (1D-…
Shock-boundary layer interactions (SBLI) on hypersonic cone step flows exhibit a range of intrinsic unsteady behaviors, from shear-layer oscillations to large-scale pulsations. This work investigates the unsteadiness in a cone-step geometry…
We propose a method for obtaining the intrinsic, long time mean square displacement (MSD) of atoms and molecules in proteins from finite time molecular dynamics (MD) simulations. Typical data from simulations are limited to times of 1 to 10…
We develop an algorithm suitable for parallel molecular dynamics simulations in $d$ spatial dimensions and describe its implementation in C++. All routines work in arbitrary $d$; the maximum simulated $d$ is limited only by available…
We examine the physical basis for algorithms to replace mixing-length theory (MLT) in stellar evolutionary computations. Our 321D procedure is based on numerical solutions of the Navier-Stokes equations. These implicit large eddy…
The time-dependent optical properties of molecular systems are investigated by step-scan Fourier-transform spectroscopy in order to explore the dynamics at phase transitions and molecular orientation in the milli- and microsecond range. The…
The folding of RNA and DNA strands plays crucial roles in biological systems and bionanotechnology. However, studying these processes with high-resolution numerical models is beyond current computational capabilities due to the timescales…
We have investigated the dynamics of Na ions in amorphous Na2Si2O5, a potential solid electrolyte material for Na-battery. We have employed quasielastic neutron scattering (QENS) technique in the amorphous Na2Si2O5 from 300 to 748 K to…