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 …

Characterization of lipid–protein interactions and lipid-mediated modulation of membrane protein function through molecular simulation

MP Muller, T Jiang, C Sun, M Lihan, S Pant… - Chemical …, 2019 - ACS Publications
The cellular membrane constitutes one of the most fundamental compartments of a living
cell, where key processes such as selective transport of material and exchange of …

Backmapping triangulated surfaces to coarse-grained membrane models

W Pezeshkian, M König, TA Wassenaar… - Nature …, 2020 - nature.com
Many biological processes involve large-scale changes in membrane shape. Computer
simulations of these processes are challenging since they occur across a wide range of …

Recent advances in coarse-grained models for biomolecules and their applications

N Singh, W Li - International journal of molecular sciences, 2019 - mdpi.com
Molecular dynamics simulations have emerged as a powerful tool to study biological
systems at varied length and timescales. The conventional all-atom molecular dynamics …

Mesoscale simulation of biomembranes with FreeDTS

W Pezeshkian, JH Ipsen - Nature Communications, 2024 - nature.com
We present FreeDTS software for performing computational research on biomembranes at
the mesoscale. In this software, a membrane is represented by a dynamically triangulated …

Large-scale simulation of biomembranes incorporating realistic kinetics into coarse-grained models

M Sadeghi, F Noé - Nature communications, 2020 - nature.com
Biomembranes are two-dimensional assemblies of phospholipids that are only a few
nanometres thick, but form micrometre-sized structures vital to cellular function. Explicit …

A review of mechanics-based mesoscopic membrane remodeling methods: capturing both the physics and the chemical diversity

G Kumar, SC Duggisetty, A Srivastava - The Journal of Membrane Biology, 2022 - Springer
Specialized classes of proteins, working together in a tightly orchestrated manner, induce
and maintain highly curved cellular and organelles membrane morphology. Due to the …

Computational and experimental approaches to investigate lipid nanoparticles as drug and gene delivery systems

C Chan, S Du, Y Dong, X Cheng - Current topics in medicinal …, 2021 - ingentaconnect.com
Lipid nanoparticles (LNPs) have been widely applied in drug and gene delivery. More than
twenty years ago, DoxilTM was the first LNPs-based drug approved by the US Food and …

Unusual organization of I-BAR proteins on tubular and vesicular membranes

Z Jarin, FC Tsai, A Davtyan, AJ Pak, P Bassereau… - Biophysical …, 2019 - cell.com
Protein-mediated membrane remodeling is a ubiquitous and critical process for proper
cellular function. Inverse Bin/Amphiphysin/Rvs (I-BAR) domains drive local membrane …

Biophysics of membrane curvature remodeling at molecular and mesoscopic lengthscales

N Ramakrishnan, RP Bradley… - Journal of Physics …, 2018 - iopscience.iop.org
At the micron scale, where cell organelles display an amazing complexity in their shape and
organization, the physical properties of a biological membrane can be better-understood …