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 …

Emerging diversity in lipid–protein interactions

V Corradi, BI Sejdiu, H Mesa-Galloso… - Chemical …, 2019 - ACS Publications
Membrane lipids interact with proteins in a variety of ways, ranging from providing a stable
membrane environment for proteins to being embedded in to detailed roles in complicated …

Multiscale simulations of biological membranes: the challenge to understand biological phenomena in a living substance

G Enkavi, M Javanainen, W Kulig, T Róg… - Chemical …, 2019 - ACS Publications
Biological membranes are tricky to investigate. They are complex in terms of molecular
composition and structure, functional over a wide range of time scales, and characterized by …

Ceramides bind VDAC2 to trigger mitochondrial apoptosis

S Dadsena, S Bockelmann, JGM Mina… - Nature …, 2019 - nature.com
Ceramides draw wide attention as tumor suppressor lipids that act directly on mitochondria
to trigger apoptotic cell death. However, molecular details of the underlying mechanism are …

CHARMM‐GUI Martini Maker for modeling and simulation of complex bacterial membranes with lipopolysaccharides

PC Hsu, BMH Bruininks, D Jefferies… - 2017 - Wiley Online Library
A complex cell envelope, composed of a mixture of lipid types including
lipopolysaccharides, protects bacteria from the external environment. Clearly, the proteins …

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 …

A massively parallel infrastructure for adaptive multiscale simulations: modeling RAS initiation pathway for cancer

F Di Natale, H Bhatia, TS Carpenter, C Neale… - Proceedings of the …, 2019 - dl.acm.org
Computational models can define the functional dynamics of complex systems in
exceptional detail. However, many modeling studies face seemingly incommensurate …

Capturing biologically complex tissue-specific membranes at different levels of compositional complexity

HI Ingólfsson, H Bhatia, T Zeppelin… - The Journal of …, 2020 - ACS Publications
Plasma membranes (PMs) contain hundreds of different lipid species that contribute
differently to overall bilayer properties. By modulation of these properties, membrane protein …

Martini 3 coarse-grained model for type III deep eutectic solvents: Thermodynamic, structural, and extraction properties

P Vainikka, S Thallmair, PCT Souza… - ACS Sustainable …, 2021 - ACS Publications
Deep eutectic solvents (DESs) are a more environmentally friendly, cost-effective, and
recyclable alternative for ionic liquids. Since the number of possible deep eutectic solvents …

Generalizable coordination of large multiscale workflows: challenges and learnings at scale

H Bhatia, F Di Natale, JY Moon, X Zhang… - Proceedings of the …, 2021 - dl.acm.org
The advancement of machine learning techniques and the heterogeneous architectures of
most current supercomputers are propelling the demand for large multiscale simulations that …