Related papers: Kinetically Consistent Coarse Graining using Kerne…
We present a differentiable formalism for learning free energies that is capable of capturing arbitrarily complex model dependencies on coarse-grained coordinates and finite-temperature response to variation of general system parameters.…
Reduced modeling in high-dimensional reproducing kernel Hilbert spaces offers the opportunity to approximate efficiently non-linear dynamics. In this work, we devise an algorithm based on low rank constraint optimization and kernel-based…
Coarse-grained molecular dynamics often sacrifices accuracy and transferability for computational efficiency, but the use of machine learned potentials is helping coarse-grained models attain performance on par with atomistic molecular…
For optimal processing and design of entangled polymeric materials it is important to establish a rigorous link between the detailed molecular composition of the polymer and the viscoelastic properties of the macroscopic melt. We review…
Molecular dynamics (MD) is a crucial technique for simulating biological systems, enabling the exploration of their dynamic nature and fostering an understanding of their functions and properties. To address exploration inefficiency,…
Structural and thermodynamic consistency of coarse-graining models across multiple length scales is essential for the predictive role of multi-scale modeling and molecular dynamic simulations that use mesoscale descriptions. Our approach is…
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…
The present work concerns the transferability of coarse-grained (CG) modeling in reproducing the dynamic properties of the reference atomistic systems across a range of parameters. In particular, we focus on implicit-solvent CG modeling of…
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…
A dynamical atomistic chain to simulate mechanical properties of a one-dimensional material with zero temperature may be modelled by the molecular dynamics (MD) model. Because the number of particles (atoms) is huge for a MD model, in…
Diffusion-based generative models have demonstrated exceptional performance, yet their iterative sampling procedures remain computationally expensive. A prominent strategy to mitigate this cost is distillation, with offline distillation…
In this work, a coarse-graining method previously proposed by the authors in a companion paper based on solving diffusion equations is applied to CFD-DEM simulations, where coarse graining is used to obtain solid volume fraction, particle…
One essential goal of constructing coarse-grained molecular dynamics (CGMD) models is to accurately predict non-equilibrium processes beyond the atomistic scale. While a CG model can be constructed by projecting the full dynamics onto a set…
We develop a coarse grained (CG) approach for efficiently simulating calcium dynamics in the endoplasmic reticulum membrane based on a fine stochastic lattice gas model. By grouping neighboring microscopic sites together into CG cells and…
In molecular dynamics and sampling of high dimensional Gibbs measures coarse-graining is an important technique to reduce the dimensionality of the problem. We will study and quantify the coarse-graining error between the coarse-grained…
The estimation of equations from data is of interest in physics. One of the famous methods is the sparse identification of nonlinear dynamics (SINDy), which utilizes sparse estimation techniques to estimate equations from data. Recently, a…
Coarse-grained (CG) models play a crucial role in the study of protein structures, protein thermodynamic properties, and protein conformation dynamics. Due to the information loss in the coarse-graining process, backmapping from CG to…
Coarse-graining is a molecular modeling technique in which an atomistic system is represented in a simplified fashion that retains the most significant system features that contribute to a target output, while removing the degrees of…
Representing and predicting high-dimensional and spatiotemporally chaotic dynamical systems remains a fundamental challenge in dynamical systems and machine learning. Although data-driven models can achieve accurate short-term forecasts,…
We develop a novel EDMD-type algorithm that captures the spectrum of the Koopman operator defined on a reproducing kernel Hilbert space of analytic functions. This method, which we call analytic EDMD, relies on an orthogonal projection on…