Computational modeling of realistic cell membranes
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 …
endowing them with the plasticity needed to fulfill their key roles in cell functioning. The …
Molecular dynamics simulations of membrane permeability
This Review illustrates the evaluation of permeability of lipid membranes from molecular
dynamics (MD) simulation primarily using water and oxygen as examples. Membrane …
dynamics (MD) simulation primarily using water and oxygen as examples. Membrane …
Multiscale simulations of biological membranes: the challenge to understand biological phenomena in a living substance
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 …
composition and structure, functional over a wide range of time scales, and characterized by …
Best practices for computing transport properties 1. Self-diffusivity and viscosity from equilibrium molecular dynamics [article v1. 0]
EJ Maginn, RA Messerly, DJ Carlson… - Living Journal of …, 2019 - livecomsjournal.org
The ability to predict transport properties (eg, diffusivity, viscosity, and conductivity) is one of
the primary benefits of molecular simulation. Although most studies focus on the accuracy of …
the primary benefits of molecular simulation. Although most studies focus on the accuracy of …
Computational lipidomics of the neuronal plasma membrane
Membrane lipid composition varies greatly within submembrane compartments, different
organelle membranes, and also between cells of different cell stage, cell and tissue types …
organelle membranes, and also between cells of different cell stage, cell and tissue types …
Machine learning–driven multiscale modeling reveals lipid-dependent dynamics of RAS signaling proteins
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 …
human cancers. RAS signaling has been proposed to be regulated by dynamic …
Accelerating membrane simulations with hydrogen mass repartitioning
C Balusek, H Hwang, CH Lau… - Journal of chemical …, 2019 - ACS Publications
The time step of atomistic molecular dynamics (MD) simulations is determined by the fastest
motions in the system and is typically limited to 2 fs. An increasingly popular approach is to …
motions in the system and is typically limited to 2 fs. An increasingly popular approach is to …
CHARMM36 lipid force field with explicit treatment of long-range dispersion: parametrization and validation for phosphatidylethanolamine, phosphatidylglycerol, and …
Long-range Lennard-Jones (LJ) interactions have been incorporated into the CHARMM36
(C36) lipid force field (FF) using the LJ particle-mesh Ewald (LJ-PME) method in order to …
(C36) lipid force field (FF) using the LJ particle-mesh Ewald (LJ-PME) method in order to …
Optimization of slipids force field parameters describing headgroups of phospholipids
F Grote, AP Lyubartsev - The Journal of Physical Chemistry B, 2020 - ACS Publications
The molecular mechanics force field Slipids developed in a series of works by Jämbeck
and Lyubartsev (J. Phys. Chem. B 2012, 116, 3164–3179; J. Chem. Theory Comput. 2012 …
and Lyubartsev (J. Phys. Chem. B 2012, 116, 3164–3179; J. Chem. Theory Comput. 2012 …
Concepts and methods of solid-state NMR spectroscopy applied to biomembranes
TR Molugu, S Lee, MF Brown - Chemical reviews, 2017 - ACS Publications
Concepts of solid-state NMR spectroscopy and applications to fluid membranes are
reviewed in this paper. Membrane lipids with 2H-labeled acyl chains or polar head groups …
reviewed in this paper. Membrane lipids with 2H-labeled acyl chains or polar head groups …