Related papers: Mesodynamics with implicit degrees for freedom
We describe a recent multiscale approach based on the concurrent coupling of constrained molecular dynamics for long biomolecules with a mesoscopic lattice Boltzmann treatment of solvent hydrodynamics. The multiscale approach is based on a…
Neither of the two prevalent theories, namely thermodynamic stability and kinetic stability, provides a comprehensive understanding of protein folding. The thermodynamic theory is misleading because it assumes that free energy is the…
Rigid bodies, made of smaller composite beads, are commonly used to simulate anisotropic particles with molecular dynamics or Monte Carlo methods. To accurately represent the particle shape and to obtain smooth and realistic effective pair…
We study the non-equilibrium dissipative dynamics of the center of mass of a particle coupled to a field via its internal degrees of freedom. We model the internal and external degrees of freedom of the particle as quantum harmonic…
We provide a numerical study of the macroscopic model of [3] derived from an agent-based model for a system of particles interacting through a dynamical network of links. Assuming that the network remodelling process is very fast, the…
Particle methods are less computationally efficient than grid based numerical solution of the Navier Stokes equation. However, they have important advantages including rigorous mass conservation, momentum conservation and isotropy. In…
On the basis of information theory, a new formalism of classical non-relativistic mechanics of a mass point is proposed. The particle trajectories of a general dynamical system defined on an (1+n)-dimensional smooth manifold are treated…
In this review, we describe and analyze a mesoscale simulation method for fluid flow, which was introduced by Malevanets and Kapral in 1999, and is now called multi-particle collision dynamics (MPC) or stochastic rotation dynamics (SRD).…
We propose a way to simulate mesoscopic transport processes with counter-propagating wavepackets of ultracold atoms in quasi one-dimensional (1D) waveguides, and show quantitative agreement with analytical results. The method allows the…
Here we investigate how local properties of particles in a thermal bath influence the thermodynamics of the bath. We utilize nanothermodynamics, based on two postulates: that small systems can be treated self-consistently by coupling to an…
We study the formation of clusters consisting of several chains in dilute solutions of amphiphilic heteropolymers. By means of the Gaussian variational theory we show that in a region of the phase diagram within the conventional two-phase…
Results are presented from numerical experiments aiming at the computation of stochastic phase-field models for phase transformations by coarse-graining molecular dynamics. The studied phase transformations occur between a solid crystal and…
Using very general and well established ideas of the statistical physics of macroscopic bodies, that is, of those composed of many degrees of freedom, we show how classical behavior of the center of mass motion arises from a fully quantum…
Stochastic dynamical systems arise naturally across nearly all areas of science and engineering. Typically, a dynamical system model is based on some prior knowledge about the underlying dynamics of interest in which probabilistic features…
The rise of machine learning has greatly influenced the field of computational chemistry, and that of atomistic molecular dynamics simulations in particular. One of its most exciting prospects is the development of accurate,…
Molecular dynamics (MD) provides insights into atomic-scale processes by integrating over time the equations that describe the motion of atoms under the action of interatomic forces. Machine learning models have substantially accelerated MD…
Atomistic modeling of thin-film processes provides an avenue not only for discovering key chemical mechanisms of the processes but also to extract quantitative metrics on the events and reactions taking place at the gas-surface interface.…
Acid-base reactions are ubiquitous in nature. Understanding their mechanisms is crucial in many fields, from biochemistry to industrial catalysis. Unfortunately, experiments only give limited information without much insight into the…
Mesoscopic $N-$atom systems derive their structural and dynamical properties from processes coupled across multiple scales in space and time. An efficient method for understanding these systems in the friction dominated regime from the…
Time-resolved investigations of ultrafast electronic and molecular dynamics were not possible until recently. The typical time scale of these processes is in the picosecond to attosecond realm. The tremendous technological progress in…