Machine learning-driven multiscale modeling: bridging the scales with a next-generation simulation infrastructure

HI Ingólfsson, H Bhatia, F Aydin… - Journal of Chemical …, 2023 - ACS Publications
Interdependence across time and length scales is common in biology, where atomic
interactions can impact larger-scale phenomenon. Such dependence is especially true for a …

MiMiC: a novel framework for multiscale modeling in computational chemistry

JMH Olsen, V Bolnykh, S Meloni, E Ippoliti… - Journal of chemical …, 2019 - ACS Publications
We present a flexible and efficient framework for multiscale modeling in computational
chemistry (MiMiC). It is based on a multiple-program multiple-data (MPMD) model with …

Equation-free multiscale computation: Algorithms and applications

IG Kevrekidis, G Samaey - Annual review of physical chemistry, 2009 - annualreviews.org
In traditional physicochemical modeling, one derives evolution equations at the
(macroscopic, coarse) scale of interest; these are used to perform a variety of tasks …

[HTML][HTML] Bridging scales through multiscale modeling: a case study on protein kinase A

BW Boras, SP Hirakis, LW Votapka… - Frontiers in …, 2015 - frontiersin.org
The goal of multiscale modeling in biology is to use structurally based physico-chemical
models to integrate across temporal and spatial scales of biology and thereby improve …

Asynchronous reciprocal coupling of Martini 2.2 coarse-grained and CHARMM36 all-atom simulations in an automated multiscale framework

CA López, X Zhang, F Aydin, R Shrestha… - Journal of Chemical …, 2022 - ACS Publications
The appeal of multiscale modeling approaches is predicated on the promise of
combinatorial synergy. However, this promise can only be realized when distinct scales are …

Harnessing the combined power of theoretical and experimental data through multiscale informatics

MP Burke - International Journal of Chemical Kinetics, 2016 - Wiley Online Library
Monumental, recent and rapidly continuing, improvements in the capabilities of ab initio
theoretical kinetics calculations provides reason to believe that progress in the field of …

Multiscale modeling of biomolecular systems: in serial and in parallel

GS Ayton, WG Noid, GA Voth - Current opinion in structural biology, 2007 - Elsevier
Considerable progress has been recently achieved in the multiscale modeling of complex
biological processes. Multiscale models have now investigated the structure and dynamics …

Software components for parallel multiscale simulation: an example with LAMMPS

B FrantzDale, SJ Plimpton, MS Shephard - Engineering with Computers, 2010 - Springer
Multiscale simulation is a promising approach for addressing a variety of real-world
engineering problems. Various mathematical approaches have been proposed to link single …

From coarse grained to atomistic: a serial multiscale approach to membrane protein simulations

PJ Stansfeld, MSP Sansom - Journal of chemical theory and …, 2011 - ACS Publications
Coarse-grained molecular dynamics provides a means for simulating the assembly and the
interactions of membrane protein/lipid complexes at a reduced level of representation …

Machine learning–driven multiscale modeling reveals lipid-dependent dynamics of RAS signaling proteins

HI Ingólfsson, C Neale, TS Carpenter… - Proceedings of the …, 2022 - National Acad Sciences
RAS is a signaling protein associated with the cell membrane that is mutated in up to 30% of
human cancers. RAS signaling has been proposed to be regulated by dynamic …