Related papers: Molecular dynamics simulations of complex shaped p…
Molecular dynamics simulations have a prominent role in biophysics and drug discovery due to the atomistic information they provide on the structure, energetics and dynamics of biomolecules. Specialized software packages are required to…
Three coarse-grained molecular dynamics (MD) models are investigated with the aim of developing and analyzing multiscale methods which use MD simulations in parts of the computational domain and (less detailed) Brownian dynamics (BD)…
Molecular Dynamics (MD) simulation is a powerful tool for understanding the dynamics and structure of matter. Since the resolution of MD is atomic-scale, achieving long time-scale simulations with femtosecond integration is very expensive.…
We present a review of recent developments of simulations of the Vlasov-Maxwell system of equations using a Fourier transform method in velocity space. In this method, the distribution functions for electrons and ions are Fourier…
Faceted shapes, such as polyhedra, are commonly found in systems of nanoscale, colloidal, and granular particles. Many interesting physical phenomena, like crystal nucleation and growth, vacancy motion, and glassy dynamics are challenging…
This letter casts the problem of optimum discrete beamforming as the computation of the Minkowski sum of convex polygons, which is itself a convex polygon. The number of vertices of the latter is at most the sum of the number of vertices of…
We propose a microscopic simulation for quark many-body system based on molecular dynamics. Using color confinement and one-gluon exchange potentials together with the meson exchange potentials between quarks, we construct nucleons and…
ParticLS (\emph{Partic}le \emph{L}evel \emph{S}ets) is a software library that implements the discrete element method (DEM) and meshfree methods. ParticLS tracks the interaction between individual particles whose geometries are defined by…
In what has been described as the fourth age of Quantum Chemistry, variational nuclear motion programs are now routinely being used to obtain the vibration-rotation levels and corresponding wavefunctions of small molecules to the sort of…
We present a matrix formalism, inspired by the Minkowski four-vectors of special relativity, useful to solve classical physics problems related to both mechanics and thermodynamics. The formalism turns out to be convenient to deal with…
The geometry of atomic arrangement underpins the structural understanding of molecules in many fields. However, no general framework of mathematical/computational theory for the geometry of atomic arrangement exists. Here we present…
Decades of hardware, methodological, and algorithmic development have propelled molecular dynamics (MD) simulations to the forefront of materials-modeling techniques, bridging the gap between electronic-structure theory and continuum…
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…
We show how to simulate numerically both the evolution of 1D quantum systems under dissipation as well as in thermal equilibrium. The method applies to both finite and inhomogeneous systems and it is based on two ideas: (a) a representation…
Atomistic simulations using accurate energy functions can provide molecular-level insight into functional motions of molecules in the gas- and in the condensed phase. Together with recently developed and currently pursued efforts in…
Molecular dynamics refers to the computer simulation of a material at the atomic level. An open problem in numerical analysis is to explain the apparent reliability of molecular dynamics simulations. The difficulty is that individual…
We point out that two of Milne's fourth-order integrators are well-suited to bit-reversible simulations. The fourth-order method improves on the accuracy of Levesque and Verlet's algorithm and simplifies the definition of the velocity $v$…
Molecular dynamics simulations use statistical mechanics at the atomistic scale to enable both the elucidation of fundamental mechanisms and the engineering of matter for desired tasks. The behavior of molecular systems at the microscale is…
Particle-based simulations of the Vlasov equation typically require a large number of particles, which leads to a high-dimensional system of ordinary differential equations. Solving such systems is computationally very expensive, especially…
Computer simulation of the time evolution in a classical system is a standard numerical method, used in numerous scientific articles in Natural Science. Almost all the simulations are performed by discrete Molecular Dynamics (MD). The…