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Two decades of Martini: Better beads, broader scope
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
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
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
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 …
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
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
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
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 …
Asynchronous reciprocal coupling of Martini 2.2 coarse-grained and CHARMM36 all-atom simulations in an automated multiscale framework
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 …
combinatorial synergy. However, this promise can only be realized when distinct scales are …