Two decades of Martini: Better beads, broader scope

SJ Marrink, L Monticelli, MN Melo… - Wiley …, 2023‏ - Wiley Online Library
The Martini model, a coarse‐grained force field for molecular dynamics simulations, has
been around for nearly two decades. Originally developed for lipid‐based systems by the …

Mesoscale simulations: an indispensable approach to understand biomembranes

AL Duncan, W Pezeshkian - Biophysical Journal, 2023‏ - cell.com
Computer simulation techniques form a versatile tool, a computational microscope, for
exploring biological processes. This tool has been particularly effective in exploring different …

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 …

Exaworks: Workflows for exascale

A Al-Saadi, DH Ahn, Y Babuji, K Chard… - … IEEE Workshop on …, 2021‏ - ieeexplore.ieee.org
Exascale computers will offer transformative capabilities to combine data-driven and
learning-based approaches with traditional simulation applications to accelerate scientific …

An empirical study of high performance computing (HPC) performance bugs

MAK Azad, N Iqbal, F Hassan… - 2023 IEEE/ACM 20th …, 2023‏ - ieeexplore.ieee.org
Performance efficiency and scalability are the major design goals for high performance
computing (HPC) applications. However, it is challenging to achieve high efficiency and …

The flux operator

V Sochat, A Culquicondor, A Ojea, D Milroy - F1000Research, 2024‏ - pmc.ncbi.nlm.nih.gov
Converged computing is an emerging area of computing that brings together the best of both
worlds for high performance computing (HPC) and cloud-native communities. The economic …

AI-coupled HPC workflows

S Jha, VR Pascuzzi, M Turilli - arxiv preprint arxiv:2208.11745, 2022‏ - arxiv.org
Increasingly, scientific discovery requires sophisticated and scalable workflows. Workflows
have become the``new applications,''wherein multi-scale computing campaigns comprise …

Exploring CRD mobility during RAS/RAF engagement at the membrane

K Nguyen, CA López, C Neale, QN Van, TS Carpenter… - Biophysical journal, 2022‏ - cell.com
During the activation of mitogen-activated protein kinase (MAPK) signaling, the RAS-binding
domain (RBD) and cysteine-rich domain (CRD) of RAF bind to active RAS at the plasma …

One step closer to converged computing: Achieving scalability with cloud-native hpc

DJ Milroy, C Misale, G Georgakoudis… - 2022 IEEE/ACM 4th …, 2022‏ - ieeexplore.ieee.org
As High Performance Computing (HPC) workflows increase in complexity, their designers
seek to enable automation and flexibility offered by cloud technologies. Container …

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 …