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 …

Computational modeling of realistic cell membranes

SJ Marrink, V Corradi, PCT Souza, HI Ingolfsson… - Chemical …, 2019 - ACS Publications
Cell membranes contain a large variety of lipid types and are crowded with proteins,
endowing them with the plasticity needed to fulfill their key roles in cell functioning. The …

Martini 3: a general purpose force field for coarse-grained molecular dynamics

PCT Souza, R Alessandri, J Barnoud, S Thallmair… - Nature …, 2021 - nature.com
The coarse-grained Martini force field is widely used in biomolecular simulations. Here we
present the refined model, Martini 3 (http://cgmartini. nl), with an improved interaction …

Bioactive scaffolds with enhanced supramolecular motion promote recovery from spinal cord injury

Z Álvarez, AN Kolberg-Edelbrock, IR Sasselli… - Science, 2021 - science.org
The signaling of cells by scaffolds of synthetic molecules that mimic proteins is known to be
effective in the regeneration of tissues. Here, we describe peptide amphiphile …

Structural basis of NINJ1-mediated plasma membrane rupture in cell death

M Degen, JC Santos, K Pluhackova, G Cebrero… - Nature, 2023 - nature.com
Eukaryotic cells can undergo different forms of programmed cell death, many of which
culminate in plasma membrane rupture as the defining terminal event,,,,,–. Plasma …

Accelerating the prediction and discovery of peptide hydrogels with human-in-the-loop

T Xu, J Wang, S Zhao, D Chen, H Zhang… - Nature …, 2023 - nature.com
The amino acid sequences of peptides determine their self-assembling properties. Accurate
prediction of peptidic hydrogel formation, however, remains a challenging task. This work …

Machine-guided path sampling to discover mechanisms of molecular self-organization

H Jung, R Covino, A Arjun, C Leitold… - Nature Computational …, 2023 - nature.com
Molecular self-organization driven by concerted many-body interactions produces the
ordered structures that define both inanimate and living matter. Here we present an …

Reconstitution of autophagosome nucleation defines Atg9 vesicles as seeds for membrane formation

J Sawa-Makarska, V Baumann, N Coudevylle… - Science, 2020 - science.org
INTRODUCTION Macroautophagy (hereafter autophagy) is an evolutionarily conserved
lysosomal degradation pathway. It ensures cellular homeostasis and health by removing …

Structures of the TMC-1 complex illuminate mechanosensory transduction

H Jeong, S Clark, A Goehring… - Nature, 2022 - nature.com
The initial step in the sensory transduction pathway underpinning hearing and balance in
mammals involves the conversion of force into the gating of a mechanosensory transduction …

Modeling and simulations of polymers: a roadmap

TE Gartner III, A Jayaraman - Macromolecules, 2019 - ACS Publications
Molecular modeling and simulations are invaluable tools for the polymer science and
engineering community. These computational approaches enable predictions and provide …