Related papers: Understanding Molecular Dynamics with Stochastic P…
When simulating molecular systems using deterministic equations of motion (e.g., Newtonian dynamics), such equations are generally numerically integrated according to a well-developed set of algorithms that share commonly agreed-upon…
Numerical simulations of fast remagnetization processes using the stochastic dynamics are widely used to study various magnetic systems. In this paper we first address several crucial methodological problems of such simulations: (i) the…
A model has two main aims: predicting the behavior of a physical system and understanding its nature, that is how it works, at some desired level of abstraction. A promising recent approach to model building consists in deriving a…
The dynamics of biological systems, from proteins to cells to organisms, is complex and stochastic. To decipher their physical laws, we need to bridge between experimental observations and theoretical modeling. Thanks to progress in…
The understanding of the statistical properties and of the dynamics of multistable systems is gaining more and more importance in a vast variety of scientific fields. This is especially relevant for the investigation of the tipping points…
Molecular dynamics simulation is used to investigate the crystallization of a classical two-dimensional electron system, in which electrons interact with the Coulomb repulsion. From the positional and the orientational correlation…
Molecular dynamics (MD) simulations are used in biochemistry, physics, and other fields to study the motions, thermodynamic properties, and the interactions between molecules. Computational limitations and the complexity of these problems,…
We study heat exchange in temperature-biased metal-molecule-metal molecular junctions by employing the LAMMPS atomic molecular dynamics simulator. Generating the nonequilibrium steady state with Langevin thermostats at the boundaries of the…
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…
We discuss the use of a Langevin equation with a colored (correlated) noise to perform constant-temperature molecular dynamics simulations. Since the equations of motion are linear in nature, it is easy to predict the response of a…
We propose a very accurate computational scheme for the dynamics of a classical oscillator coupled to a molecular junction driven by a finite bias, including the finite mass effect. We focus on two minimal models for the molecular junction:…
We present a new method of conducting molecular dynamics simulation in isothermal-isobaric ensemble based on Langevin equations of motion. The stochastic coupling to all particle and cell degrees of freedoms is introduced in a correct way,…
Allosteric regulation is often viewed as thermodynamic in nature. However protein internal motions during an enzymatic reaction cycle can be slow hopping processes over numerous potential barriers. We propose that regulating molecules may…
The physical behavior of glass-forming liquids presents complex features of both dynamic and thermodynamic nature. Some studies indicate the presence of thermodynamic anomalies and of crossovers in the dynamic properties, but their origin…
Dynamical equations describing physical systems at statistical equilibrium are commonly extended by mathematical tools called "thermostats". These tools are designed for sampling ensembles of statistical mechanics. We propose a dynamic…
Chemical signaling is one of the ubiquitous mechanisms by which inter-cellular communication takes place at the microscopic level, particularly via chemotaxis. Such multi-cellular systems are popularly studied using continuum, mean-field…
Stochastic systems often exhibit multiple viable metastable states that are long-lived. Over very long timescales, fluctuations may push the system to transition between them, drastically changing its macroscopic configuration. In realistic…
Numerical computations have become a pillar of all modern quantitative sciences. Any computation involves modeling--even if often this step is not made explicit--and any model has to neglect details while still being physically accurate.…
Microscopic thermal machines promise to play an important role in future quantum technologies. Making such devices widely applicable will require effective strategies to channel their output into easily accessible storage systems like…
The relationship between the thermodynamic and computational characteristics of dynamical physical systems has been a major theoretical interest since at least the 19th century, and has been of increasing practical importance as the…