相关论文: How to remove the spurious resonances from ring po…

We develop a method for simulating colloidal suspensions using multiparticle collision dynamics (MPCD) with a discrete particle model represented as a rigid body. The key steps for incorporating the rigid-body constraints are to thermalize…

We investigate the motion of a colloidal particle driven out of equilibrium by an external torque. We use the molecular dynamics simulation that is alternative to the numerical integration approach based on the Langevin equation and is…

Spatial multiscale methods have established themselves as useful tools for extending the length scales accessible by conventional statics (i.e., zero temperature molecular dynamics). Recently, extensions of these methods, such as the…

Time domain simulations of electromagnetic problems are highly valuable in engineering applications, as they allow for the analysis of transient behavior and broadband responses. These simulations utilize time stepping schemes, where each…

We present an accelerated ``on-the-fly'' coupled-cluster path-integral molecular dynamics (PIMD) method for finite-temperature simulations in which electron correlation and nuclear quantum effects are treated simultaneously. The approach is…

We introduce a framework for model reduction of chain models for dissipative particle dynamics (DPD) simulations, where the characteristic size of the chain, pressure, density, and temperature are preserved. The proposed methodology reduces…

We present a new method for introducing stable non-equilibrium concentration gradients in molecular dynamics simulations of mixtures. This method extends earlier Reverse Non-Equilibrium Molecular Dynamics (RNEMD) methods which use kinetic…

Ring polymers are prevalent in natural and engineered systems, including circular bacterial DNA, crown ethers for cation chelation, and mechanical nanoswitches. The morphology and dynamics of ring polymers are governed by the chemistry and…

Direct simulation of the von Neumann dynamics for a general (pure or mixed) quantum state can often be expensive. One prominent example is the real-time time-dependent density functional theory (rt-TDDFT), a widely used framework for the…

A quantum simulation of vibrational strong coupling (VSC) in the collective regime via thermostatted ring-polymer molecular dynamics (TRPMD) is reported. For a collection of liquid-phase water molecules resonantly coupled to a single…

We model the flow behaviour of dense melts of flexible and semiflexible ring polymers in the presence of walls using a hybrid multiscale approach. Specifically, we perform molecular dynamics simulations and apply the Irving-Kirkwood formula…

The Lindblad equation determines the time evolution of the density operator of open quantum systems. While valid for any system size, its use is, in practice, restricted to prototype/surrogate models with the aim of tackling specific…

Replica exchange molecular dynamics (REMD) becomes more efficient as the frequency of swap between the temperatures is increased. Recently in [Plattner et al, J. Chem. Phys. 135, 134111 (2011)] a method was proposed to implement infinite…

The molecular dynamics simulations were used to obtain the radius of gyration of real ring polymer chains with different topological structures consisting of 360 monomers. We focus on the entropic force which is exerted by a dilute solution…

In applications of mechanics, including quantum mechanics, we often consider complex systems, where complete solutions of the underlying "fundamental" equations is both impractical and unnecessary to describe appropriate observations…

We study theoretically dynamics of a driven-dissipative qubit-resonator system. Specifically, a transmon qubit is coupled to a transmission-line resonator; this system is considered to be probed via a resonator, by means of either…

Based on the analysis of a large number of high-fidelity nonlinear gyrokinetic simulations, we propose a novel strategy to improve confinement in spherical tokamak plasmas by combining up-down asymmetric flux surface shaping with the Low…

Molecular simulations of the forced unfolding and refolding of biomolecules or molecular complexes allow to gain important kinetic, structural and thermodynamic information about the folding process and the underlying energy landscape. In…

Protein-ligand (un)binding simulations are a recent focus of biased molecular dynamics simulations. Such binding and unbinding can occur via different pathways in and out of a binding site. We here present a theoretical framework how to…

We demonstrate a new method of simulation of nonstationary quantum processes, considering the tunneling of two {\it interacting identical particles}, represented by wave packets. The used method of quantum molecular dynamics (WMD) is based…