Related papers: Optimizing Replica Exchange Moves For Molecular Dy…
Entropic dynamics is a framework for defining dynamical systems that is aligned with the principles of information theory. In an entropic dynamics model for motion on a statistical manifold, we find that the rate of changes for expected…
We present some applications of an Interacting Particle System (IPS) methodology to the field of Molecular Dynamics. This IPS method allows several simulations of a switched random process to keep closer to equilibrium at each time, thanks…
This short communication develops a new numerical procedure suitable for a large class of ordinary differential equation systems found in models in physics and engineering. The main numerical procedure is analogous to those concerning the…
This article covers few selected aspects of quantum theory of molecular rotations and vibrations. Triatomic molecules are the simplest systems, which show qualitative characteristics of larger polyatomic molecules. On the minimal example of…
The quantum normal form approach to quantum transition state theory is used to compute the cumulative reaction probability for collinear exchange reactions. It is shown that for heavy atom systems like the nitrogen exchange reaction the…
Large molecules have complex potential-energy surfaces with many local minima. They exhibit multiple stereo-isomers, even at very low temperatures. In this paper we discuss the different approaches for the manipulation of the motion of…
In particle-in-cell simulations, excessive or even unfeasible computational demands can be caused by the growth of the number of particles in the course of prolific ionization or cascaded pair production due to the effects of quantum…
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…
The powerful molecular dynamics (MD) simulation is basically based on a picture that the atoms experience classical-like trajectories under the exertion of classical force field determined by the quantum mechanically solved electronic…
Computer simulations that demonstrate the valueof novel approaches are crucial to developing more flexibleand robust power systems operations with high penetrations ofrenewable energy at multiple geographic and temporal scales.However,…
Metadynamics is a powerful method to accelerate molecular dynamics simulations, but its efficiency critically depends on the identification of collective variables that capture the slow modes of the process. Unfortunately, collective…
In many situations, one can approximate the behavior of a quantum system, i.e. a wave function subject to a partial differential equation, by effective classical equations which are ordinary differential equations. A general method and…
This review describes recent advances by the authors and others on the topic of incorporating experimental data into molecular simulations through maximum entropy methods. Methods which incorporate experimental data improve accuracy in…
Reaction-diffusion processes are the foundational model for a diverse range of complex systems, ranging from biochemical reactions to social agent-based phenomena. The underlying dynamics of these systems occur at the individual…
We propose a new method for molecular dynamics and Monte Carlo simulations, which is referred to as the replica-permutation method (RPM), to realize more efficient sampling than the replica-exchange method (REM).In RPM not only exchanges…
We review progress towards direct simulation of quantum dynamics in many-body systems, using recently developed stochastic gauge techniques. We consider master equations, canonical ensemble calculations and reversible quantum dynamics are…
We use molecular dynamic to simulate the directional growth of binary mixtures. our results compare very well with analitical and experimental results. This opens up the possibility to probe growth situations which are difficult to reach…
A new methodology is developed to integrate numerically the equations of motion for classical many-body systems in molecular dynamics simulations. Its distinguishable feature is the possibility to preserve, independently on the size of the…
We reconsider the immediate exchange model and define a more general class of models where mass is split, exchanged and merged. We relate the splitting process to the symmetric inclusion process via thermalization and from that obtain…
We consider complex dynamical systems showing metastable behavior but no local separation of fast and slow time scales. The article raises the question of whether such systems exhibit a low-dimensional manifold supporting its effective…