[HTML][HTML] Simulating realistic membrane shapes

W Pezeshkian, SJ Marrink - Current opinion in cell biology, 2021‏ - Elsevier
Biological membranes exhibit diversity in their shapes and complexity in chemical
compositions that are linked to many cellular functions. These two central features of …

Structural and mechanical properties of the red blood cell's cytoplasmic membrane seen through the lens of biophysics

S Himbert, MC Rheinstädter - Frontiers in Physiology, 2022‏ - frontiersin.org
Red blood cells (RBCs) are the most abundant cell type in the human body and critical
suppliers of oxygen. The cells are characterized by a simple structure with no internal …

LiPyphilic: A Python toolkit for the analysis of lipid membrane simulations

P Smith, CD Lorenz - Journal of chemical theory and computation, 2021‏ - ACS Publications
Molecular dynamics simulations are now widely used to study emergent phenomena in lipid
membranes with complex compositions. Here, we present LiPyphilic—a fast, fully tested …

Comparative molecular dynamics simulation studies of realistic eukaryotic, prokaryotic, and archaeal membranes

ID Pogozheva, GA Armstrong, L Kong… - Journal of chemical …, 2022‏ - ACS Publications
We present a comparative all-atom molecular dynamics simulation study of 18
biomembrane systems with lipid compositions corresponding to eukaryotic, bacterial, and …

Membrane lipids drive formation of KRAS4b-RAF1 RBDCRD nanoclusters on the membrane

R Shrestha, TS Carpenter, QN Van, C Agamasu… - Communications …, 2024‏ - nature.com
The oncogene RAS, extensively studied for decades, presents persistent gaps in
understanding, hindering the development of effective therapeutic strategies due to a lack of …

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 …

Machine learning–driven multiscale modeling reveals lipid-dependent dynamics of RAS signaling proteins

HI Ingólfsson, C Neale, TS Carpenter… - Proceedings of the …, 2022‏ - pnas.org
RAS is a signaling protein associated with the cell membrane that is mutated in up to 30% of
human cancers. RAS signaling has been proposed to be regulated by dynamic …

Membrane-specific binding of 4 nm lipid nanoparticles mediated by an entropy-driven interaction mechanism

L Ou, H Chen, B Yuan, K Yang - ACS nano, 2022‏ - ACS Publications
Lipid nanoparticles (LNPs) are a leading biomimetic drug delivery platform due to their
distinctive advantages and highly tunable formulations. A mechanistic understanding of the …

Nonconverged constraints cause artificial temperature gradients in lipid bilayer simulations

S Thallmair, M Javanainen, B Fábián… - The Journal of …, 2021‏ - ACS Publications
Molecular dynamics (MD) simulations have become an indispensable tool to investigate
phase separation in model membrane systems. In particular, simulations based on coarse …

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 …