Bottom-up coarse-graining: Principles and perspectives

J Jin, AJ Pak, AEP Durumeric, TD Loose… - Journal of chemical …, 2022 - ACS Publications
Large-scale computational molecular models provide scientists a means to investigate the
effect of microscopic details on emergent mesoscopic behavior. Elucidating the relationship …

Chemically specific coarse‐graining of polymers: Methods and prospects

S Dhamankar, MA Webb - Journal of Polymer Science, 2021 - Wiley Online Library
Coarse‐grained (CG) modeling is an invaluable tool for the study of polymers and other soft
matter systems due to the span of spatiotemporal scales that typify their physics and …

Introducing memory in coarse-grained molecular simulations

V Klippenstein, M Tripathy, G Jung… - The Journal of …, 2021 - ACS Publications
Preserving the correct dynamics at the coarse-grained (CG) level is a pressing problem in
the development of systematic CG models in soft matter simulation. Starting from the seminal …

111 years of Brownian motion

X Bian, C Kim, GE Karniadakis - Soft Matter, 2016 - pubs.rsc.org
We consider the Brownian motion of a particle and present a tutorial review over the last 111
years since Einstein's paper in 1905. We describe Einstein's model, Langevin's model and …

Understanding and modeling polymers: The challenge of multiple scales

F Schmid - ACS Polymers Au, 2022 - ACS Publications
Polymer materials are multiscale systems by definition. Already the description of a single
macromolecule involves a multitude of scales, and cooperative processes in polymer …

Stable a posteriori LES of 2D turbulence using convolutional neural networks: Backscattering analysis and generalization to higher Re via transfer learning

Y Guan, A Chattopadhyay, A Subel… - Journal of Computational …, 2022 - Elsevier
There is a growing interest in developing data-driven subgrid-scale (SGS) models for large-
eddy simulation (LES) using machine learning (ML). In a priori (offline) tests, some recent …

A physics-informed operator regression framework for extracting data-driven continuum models

RG Patel, NA Trask, MA Wood, EC Cyr - Computer Methods in Applied …, 2021 - Elsevier
The application of deep learning toward discovery of data-driven models requires careful
application of inductive biases to obtain a description of physics which is both accurate and …

Likelihood-based non-Markovian models from molecular dynamics

H Vroylandt, L Goudenège… - Proceedings of the …, 2022 - National Acad Sciences
We introduce a method to accurately and efficiently estimate the effective dynamics of
collective variables in molecular simulations. Such reduced dynamics play an essential role …

Data-driven parameterization of the generalized Langevin equation

H Lei, NA Baker, X Li - … of the National Academy of Sciences, 2016 - National Acad Sciences
We present a data-driven approach to determine the memory kernel and random noise in
generalized Langevin equations. To facilitate practical implementations, we parameterize …

Iterative reconstruction of memory kernels

G Jung, M Hanke, F Schmid - Journal of chemical theory and …, 2017 - ACS Publications
In recent years, it has become increasingly popular to construct coarse-grained models with
non-Markovian dynamics to account for an incomplete separation of time scales. One …