Related papers: Coarse-Graining of Microscopic Dynamics into Mesos…
The combination of high-dimensionality and disparity of time scales encountered in many problems in computational physics has motivated the development of coarse-grained (CG) models. In this paper, we advocate the paradigm of data-driven…
Stochastic thermodynamics provides the framework to analyze thermodynamic laws and quantities along individual trajectories of small but fully observable systems. If the observable level fails to capture all relevant degrees of freedom,…
Dissipative particle dynamics (DPD) is now a well-established method for simulating soft matter systems. However, its applicability was recently questioned because some investigations showed an upper coarse-graining limit that would prevent…
This paper considers the reduction of the Langevin equation arising from bio-molecular models. To facilitate the construction and implementation of the reduced models, the problem is formulated as a reduced-order modeling problem. The…
One of the ultimate goals of computational modeling in condensed matter is to be able to accurately compute materials properties with minimal empirical information. First-principles approaches such as the density functional theory (DFT)…
The data-based discovery of effective, coarse-grained (CG) models of high-dimensional dynamical systems presents a unique challenge in computational physics and particularly in the context of multiscale problems. The present paper offers a…
Complex physical dynamics can often be modeled as a Markov jump process between mesoscopic configurations. When jumps between mesoscopic states are mediated by thermodynamic reservoirs, the time-irreversibility of the jump process is a…
Efficient sampling of the Boltzmann distribution of molecular systems is a long-standing challenge. Recently, instead of generating long molecular dynamics simulations, generative machine learning methods such as normalizing flows have been…
Coarse-graining (CG) enables molecular dynamics (MD) simulations of larger systems and longer timescales that are otherwise infeasible with atomistic models. Machine learning potentials (MLPs), with their capacity to capture many-body…
While existing mathematical descriptions can accurately account for phenomena at microscopic scales (e.g. molecular dynamics), these are often high-dimensional, stochastic and their applicability over macroscopic time scales of physical…
We present an approximate and heuristic scheme for the derivation of continuum kinetic equations from microscopic dynamics for stochastic, interacting systems. The method consists of a mean-field type, decoupled approximation of the master…
Systems out of equilibrium exhibit a net production of entropy. We study the dynamics of a stochastic system represented by a Master Equation that can be modeled by a Fokker-Planck equation in a coarse-grained, mesoscopic description. We…
We study the convergence to equilibrium of an underdamped Langevin equation that is controlled by a linear feedback force. Specifically, we are interested in sampling the possibly multimodal invariant probability distribution of a Langevin…
The available potential energy (APE) of a fluid can be defined locally in space, providing useful insights into both the energetics and dynamics of stratified flows ranging from three-dimensional turbulence to planetary scale circulations.…
Coarse-grained (CG) models provide an effective route to reducing the complexity of molecular simulations (MD), but conventional approaches depend heavily on long all-atom MD trajectories to adequately sample configurational space. This…
The individual motion of a colloidal particle is described by an overdamped Langevin equation. When rotational degrees of freedom are relevant, these are described by a corresponding Langevin process. Our purpose is to show that the…
We introduce a coarse-grained model for atomic glass formers. Its elements are physically motivated local microscopic dynamical rules parameterized by observables. Results of the model are established and used to interpret the measured…
We propose a general coarse-graining method to derive a continuity equation that describes any dissipative system of repulsive particles interacting through short-ranged potentials. In our approach, the effect of particle-particle…
A coarse-grained model is developed to allow large-scale molecular dynamics (MD) simulations of a branched polyetherimide derived from two backbone monomers [4,4'-bisphenol A dianhydride (BPADA) and m-phenylenediamine (MPD)], a chain…
Modelling micro- and meso-scopic scale thermodynamic and transport properties of soft condensed matter hinges upon its representation. This is especially relevant for polar solvents such as water, since these require effective…