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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 …
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 …
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 …
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 …
learning-based approaches with traditional simulation applications to accelerate scientific …
Perspective: New directions in dynamical density functional theory
M Te Vrugt, R Wittkowski - Journal of Physics: Condensed Matter, 2022 - iopscience.iop.org
Classical dynamical density functional theory (DDFT) has become one of the central
modeling approaches in nonequilibrium soft matter physics. Recent years have seen the …
modeling approaches in nonequilibrium soft matter physics. Recent years have seen the …
An empirical study of high performance computing (HPC) performance bugs
Performance efficiency and scalability are the major design goals for high performance
computing (HPC) applications. However, it is challenging to achieve high efficiency and …
computing (HPC) applications. However, it is challenging to achieve high efficiency and …
The flux operator
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 …
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 …
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 …
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 …
seek to enable automation and flexibility offered by cloud technologies. Container …