Accelerators for classical molecular dynamics simulations of biomolecules

D Jones, JE Allen, Y Yang… - Journal of chemical …, 2022‏ - ACS Publications
Atomistic Molecular Dynamics (MD) simulations provide researchers the ability to model
biomolecular structures such as proteins and their interactions with drug-like small …

preCICE v2: A sustainable and user-friendly coupling library

G Chourdakis, K Davis, B Rodenberg… - Open Research …, 2022‏ - pmc.ncbi.nlm.nih.gov
preCICE is a free/open-source coupling library. It enables creating partitioned multi-physics
simulations by gluing together separate software packages. This paper summarizes the …

AI-coupled HPC workflow applications, middleware and performance

W Brewer, A Gainaru, F Suter, F Wang… - ar** triangulated surfaces to coarse-grained membrane models
W Pezeshkian, M König, TA Wassenaar… - Nature …, 2020‏ - nature.com
Many biological processes involve large-scale changes in membrane shape. Computer
simulations of these processes are challenging since they occur across a wide range of …

Membrane lipids drive formation of KRAS4b-RAF1 RBDCRD nanoclusters on the membrane

R Shrestha, TS Carpenter, QN Van, C Agamasu… - Communications …, 2024‏ - nature.com
The oncogene RAS, extensively studied for decades, presents persistent gaps in
understanding, hindering the development of effective therapeutic strategies due to a lack of …

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 …

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

HI Ingólfsson, C Neale, TS Carpenter… - Proceedings of the …, 2022‏ - pnas.org
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 …

Flux: Overcoming scheduling challenges for exascale workflows

DH Ahn, N Bass, A Chu, J Garlick, M Grondona… - Future Generation …, 2020‏ - Elsevier
Many emerging scientific workflows that target high-end HPC systems require complex
interplay with the resource and job management software (RJMS). However, portable …

A population data-driven workflow for COVID-19 modeling and learning

J Ozik, JM Wozniak, N Collier… - … Journal of High …, 2021‏ - journals.sagepub.com
CityCOVID is a detailed agent-based model that represents the behaviors and social
interactions of 2.7 million residents of Chicago as they move between and colocate in 1.2 …

[HTML][HTML] Development of 6-way CFD-DEM-FEM momentum coupling interface using partitioned coupling approach

P Adhav, X Besseron, B Peters - Results in Engineering, 2024‏ - Elsevier
Fluid-particle-structure interactions (FPSI) govern a wide range of natural and engineering
phenomena, from landslides to erosion in abrasive water jet cutting nozzles. Despite the …