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 …

[HTML][HTML] Programming assembly of biomimetic exosomes: an emerging theranostic nanomedicine platform

X Xu, L Xu, C Wen, J **a, Y Zhang, Y Liang - Materials Today Bio, 2023 - Elsevier
Exosomes have emerged as a promising cell-free therapeutic approach. However,
challenges in large-scale production, quality control, and heterogeneity must be overcome …

GROMACS: fast, flexible, and free

D Van Der Spoel, E Lindahl, B Hess… - Journal of …, 2005 - Wiley Online Library
This article describes the software suite GROMACS (Groningen MAchine for Chemical
Simulation) that was developed at the University of Groningen, The Netherlands, in the early …

Computational Lipidomics with insane: A Versatile Tool for Generating Custom Membranes for Molecular Simulations

TA Wassenaar, HI Ingólfsson… - Journal of chemical …, 2015 - ACS Publications
For simulations of membranes and membrane proteins, the generation of the lipid bilayer is
a critical step in the setup of the system. Membranes comprising multiple components pose …

Coarse grained model for semiquantitative lipid simulations

SJ Marrink, AH De Vries, AE Mark - The Journal of Physical …, 2004 - ACS Publications
This paper describes the parametrization of a new coarse grained (CG) model for lipid and
surfactant systems. Reduction of the number of degrees of freedom together with the use of …

[BOOK][B] Coarse-graining of condensed phase and biomolecular systems

GA Voth - 2008 - taylorfrancis.com
Exploring recent developments in the field, Coarse-Graining of Condensed Phase and
Biomolecular Systems examines systematic ways of constructing coarse-grained …

Dry Martini, a coarse-grained force field for lipid membrane simulations with implicit solvent

C Arnarez, JJ Uusitalo, MF Masman… - Journal of chemical …, 2015 - ACS Publications
Coarse-grained (CG) models allow simulation of larger systems for longer times by
decreasing the number of degrees of freedom compared with all-atom models. Here we …

Simulation of pore formation in lipid bilayers by mechanical stress and electric fields

DP Tieleman, H Leontiadou, AE Mark… - Journal of the …, 2003 - ACS Publications
We describe computer simulations of pore formation and membrane rupture of phospholipid
bilayers under mechanical and electrical stress. On the nanosecond simulation time scale …

Coarse grain models and the computer simulation of soft materials

SO Nielsen, CF Lopez, G Srinivas… - Journal of Physics …, 2004 - iopscience.iop.org
This article presents a topical review of coarse grain simulation techniques. First, we
motivate these techniques with illustrative examples from biology and materials science …

Multi-property fitting and parameterization of a coarse grained model for aqueous surfactants

W Shinoda, R DeVane, ML Klein - Molecular Simulation, 2007 - Taylor & Francis
A new systematic approach to build coarse-grained (CG) molecular models for
surfactants/water systems is proposed. A step-by-step approach using several molecular …