Related papers: A molecular-dynamics algorithm for mixed hard-core…
We derive a master equation for the motion of a polarizable particle weakly interacting with one or several strongly pumped cavity modes. We focus here on massive particles with complex internal structure such as large molecules and…
Dynamics simulations of constrained particles can greatly aid in understanding the temporal and spatial evolution of biological processes such as lateral transport along membranes and self-assembly of viruses. Most theoretical efforts in…
Most computer simulations of molecular dynamics take place under equilibrium conditions--in a closed, isolated system, or perhaps one held at constant temperature or pressure. Sometimes, extra tensions, shears, or temperature gradients are…
Protein-peptide interactions play essential roles in many cellular processes and their structural characterization is the major focus of current experimental and theoretical research. Two decades ago, it was proposed to employ the steered…
Particle-in-cell methods couple mesh-based methods for the solution of continuum mechanics problems, with the ability to advect and evolve particles. They have a long history and many applications in scientific computing. However, they have…
Computational chemistry allows researchers to experiment in sillico: by running a computer simulations of a biological or chemical processes of interest. Molecular dynamics with molecular mechanics model of interactions simulates N-body…
The simulation of systems that act on multiple time scales is challenging. A stable integration of the fast dynamics requires a highly accurate approximation whereas for the simulation of the slow part, a coarser approximation is accurate…
A recently proposed method for computer simulations in the isothermal-isobaric (NPT) ensemble, based on Langevin-type equations of motion for the particle coordinates and the ``piston'' degree of freedom, is re-derived by straightforward…
The leapfrog integrator is widely used because of its excellent stability in molecular dynamics simulation. This is recognized as being due to the existence of a discrete variational structure of the equations. We introduce a modified…
In this paper, we present a new, optimization-based method to exhibit cyclic behavior in non-reversible stochastic processes. While our method is general, it is strongly motivated by discrete simulations of ordinary differential equations…
Several methods in nonadiabatic molecular dynamics are based on Madelung's hydrodynamic description of nuclear motion, while the electronic component is treated as a finite-dimensional quantum system. In this context, the quantum potential…
We present a concurrent Monte Carlo (MC) - molecular dynamics (MD) approach to modeling of matter response to excitation of its electronic system. The two methods are combined on-the-fly at each time step in one code, TREKIS-4. The MC model…
We formulate and analyze a hybrid system model that involves Volterra integral operators with multiple integrals and two types of impulsive terms. We give a constructive proof, via an iteration method, of existence and uniqueness of…
We present a highly efficient molecular dynamics scheme for calculating the concentration profile of dopants implanted in group-IV alloy, and III-V zinc blende structure materials. Our program incorporates methods for reducing computational…
We present a reversible and symplectic algorithm called ROLL, for integrating the equations of motion in molecular dynamics simulations of simple fluids on a hypersphere $\mathcal{S}^d$ of arbitrary dimension $d$. It is derived in the…
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…
A simple and efficient algorithm of the molecular-dynamics simulation of the hard disk system based on the Event-Driven method is developed. From the analysis of algorithm, the complexity is O(log N) per 1 event, and the constant…
Molecular dynamics is one of the most commonly used approaches for studying the dynamics and statistical distributions of many physical, chemical, and biological systems using atomistic or coarse-grained models. It is often the case,…
We introduce a Monte-Carlo algorithm for the simulation of charged particles moving in the continuum. Electrostatic interactions are not instantaneous as in conventional approaches, but are mediated by a constrained, diffusing electric…
We present a numerical model and a set of conservative algorithms for Non-Maxwellian plasma kinetics with inelastic collisions. These algorithms self-consistently solve for the time evolution of an isotropic electron energy distribution…