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 …
Quantitative comparison against experiments reveals imperfections in force fields' descriptions of popc–cholesterol interactions
M Javanainen, P Heftberger, JJ Madsen… - Journal of Chemical …, 2023 - ACS Publications
Cholesterol is a central building block in biomembranes, where it induces orientational
order, slows diffusion, renders the membrane stiffer, and drives domain formation. Molecular …
order, slows diffusion, renders the membrane stiffer, and drives domain formation. Molecular …
Finite-size effects of binary mutual diffusion coefficients from molecular dynamics
Molecular dynamics simulations were performed for the prediction of the finite-size effects of
Maxwell-Stefan diffusion coefficients of molecular mixtures and a wide variety of binary …
Maxwell-Stefan diffusion coefficients of molecular mixtures and a wide variety of binary …
On the importance of statistics in molecular simulations for thermodynamics, kinetics and simulation box size
V Gapsys, BL de Groot - Elife, 2020 - elifesciences.org
Computational simulations, akin to wetlab experimentation, are subject to statistical
fluctuations. Assessing the magnitude of these fluctuations, that is, assigning uncertainties to …
fluctuations. Assessing the magnitude of these fluctuations, that is, assigning uncertainties to …
Lipid and Peptide Diffusion in Bilayers: The Saffman–Delbrück Model and Periodic Boundary Conditions
RM Venable, HI Ingólfsson, MG Lerner… - The Journal of …, 2017 - ACS Publications
The periodic Saffman–Delbrück (PSD) model, an extension of the Saffman–Delbrück
model developed to describe the effects of periodic boundary conditions on the diffusion …
model developed to describe the effects of periodic boundary conditions on the diffusion …
Diffusion under confinement: Hydrodynamic finite-size effects in simulation
We investigate finite-size effects on diffusion in confined fluids using molecular dynamics
simulations and hydrodynamic calculations. Specifically, we consider a Lennard-Jones fluid …
simulations and hydrodynamic calculations. Specifically, we consider a Lennard-Jones fluid …
Membrane fusion and drug delivery with carbon nanotube porins
Drug delivery mitigates toxic side effects and poor pharmacokinetics of life-saving
therapeutics and enhances treatment efficacy. However, direct cytoplasmic delivery of drugs …
therapeutics and enhances treatment efficacy. However, direct cytoplasmic delivery of drugs …
Generalized form for finite-size corrections in mutual diffusion coefficients of multicomponent mixtures obtained from equilibrium molecular dynamics simulation
The system-size dependence of computed mutual diffusion coefficients of multicomponent
mixtures is investigated, and a generalized correction term is derived. The generalized finite …
mixtures is investigated, and a generalized correction term is derived. The generalized finite …