Related papers: Iterative Reconstruction of Memory Kernels

Coarse-graining or model reduction is a term describing a range of approaches used to extend the time-scale of molecular simulations by reducing the number of degrees of freedom. In the context of molecular simulation, standard…

In many far-from-equilibrium biological systems, energy injected by irreversible processes at microscopic scales propagates to larger scales to fulfill important biological functions. But given dissipative dynamics at the microscale, how…

This work presents a systematic methodology for describing the transient dynamics of coarse-grained molecular systems inferred from all-atom simulated data. We suggest Langevin-type dynamics where the coarse-grained interaction potential…

Stochastic dynamics, such as molecular dynamics, are important in many scientific applications. However, summarizing and analyzing the results of such simulations is often challenging, due to the high dimension in which simulations are…

We introduce a novel approach for learning memory kernels in Generalized Langevin Equations. This approach initially utilizes a regularized Prony method to estimate correlation functions from trajectory data, followed by regression over a…

With the guidance offered by nonequilibrium statistical thermodynamics, simulation techniques are elevated from brute-force computer experiments to systematic tools for extracting complete, redundancy-free and consistent coarse grained…

The most popular and universally predictive protein simulation models employ all-atom molecular dynamics (MD), but they come at extreme computational cost. The development of a universal, computationally efficient coarse-grained (CG) model…

Coarse-grained models are a core computational tool in theoretical chemistry and biophysics. A judicious choice of a coarse-grained model can yield physical insight by isolating the essential degrees of freedom that dictate the…

We present a detailed derivation and testing of our approach to rescale the dynamics of mesoscale simulations of coarse-grained polymer melts (I. Y. Lyubimov et al. J. Chem. Phys. \textbf{132}, 11876, 2010). Starting from the…

Developing accurate and efficient coarse-grained representations of proteins is crucial for understanding their folding, function, and interactions over extended timescales. Our methodology involves simulating proteins with molecular…

A new approach to describing correlation properties of complex dynamic systems with long-range memory based on a concept of additive Markov chains (Phys. Rev. E 68, 061107 (2003)) is developed. An equation connecting a memory function of…

We utilize connections between molecular coarse-graining approaches and implicit generative models in machine learning to describe a new framework for systematic molecular coarse-graining (CG). Focus is placed on the formalism encompassing…

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…

We establish, through coarse-grained computation, a connection between traditional, continuum numerical algorithms (initial value problems as well as fixed point algorithms) and atomistic simulations of the Larson model of micelle…

Coarse-grained (CG) molecular dynamics (MD) simulations can simulate large molecular complexes over extended timescales by reducing degrees of freedom. A critical step in CG modeling is the selection of the CG mapping algorithm, which…

We introduce a machine-learning-based coarse-grained molecular dynamics (CGMD) model that faithfully retains the many-body nature of the inter-molecular dissipative interactions. Unlike common empirical CG models, the present model is…

-Molecular simulations allow the study of properties and interactions of molecular systems. This article presents an improved version of the Adaptive Resolution Scheme that links two systems having atomistic (also called fine-grained) and…

Memory effects are ubiquitous in a wide variety of complex physical phenomena, ranging from glassy dynamics and metamaterials to climate models. The Generalised Langevin Equation (GLE) provides a rigorous way to describe memory effects via…

Coarse-grained (CG) molecular dynamics simulations extend the length and time scale of atomistic simulations by replacing groups of correlated atoms with CG beads. Machine-learned coarse-graining (MLCG) has recently emerged as a promising…

The large time and length scales and, not least, the vast number of particles involved in industrial-scale simulations inflate the computational costs of the Discrete Element Method (DEM) excessively. Coarse grain models can help to lower…