Mesoscopic Simulation of Cell Membrane Damage, Morphology Change and Rupture by Nonionic Surfactants
Robert D. Groot,K.L. Rabone +1 more
TLDR
Some simulations have been carried out to determine the rupture properties of mixed bilayers of phosphatidylethanolamine and C(12)E(6), and indicate that the area of a pure lipid bilayer can be increased by a factor 2, and why dividing cells are more at risk than static cells.About:
This article is published in Biophysical Journal.The article was published on 2001-08-01 and is currently open access. It has received 921 citations till now. The article focuses on the topics: Bilayer & Lipid bilayer phase behavior.read more
Citations
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The MARTINI force field : Coarse grained model for biomolecular simulations
TL;DR: An improved and extended version of the coarse grained lipid model is presented, coined the MARTINI force field, based on the reproduction of partitioning free energies between polar and apolar phases of a large number of chemical compounds to reproduce the free energies of these chemical building blocks.
Journal ArticleDOI
Coarse grained model for semiquantitative lipid simulations
TL;DR: In this article, a coarse-grained (CG) model for lipid and surfactant systems is presented, where only a small number of coarse grained atom types interact using a few discrete levels of interaction.
Journal ArticleDOI
Graphene microsheets enter cells through spontaneous membrane penetration at edge asperities and corner sites
Yinfeng Li,Hongyan Yuan,Annette von dem Bussche,Megan A. Creighton,Robert H. Hurt,Agnes B. Kane,Huajian Gao +6 more
TL;DR: This work investigates the interactions of graphene and few-layer graphene (FLG) microsheets with three cell types and with model lipid bilayers by combining coarse-grained molecular dynamics (MD), all-atom MD, analytical modeling, confocal fluorescence imaging, and electron microscopic imaging and proposed mechanism allows cellular uptake of even large multilayer sheets of micrometer-scale lateral dimension.
Journal ArticleDOI
Lipids on the move: simulations of membrane pores, domains, stalks and curves.
TL;DR: This review describes the state-of-the-art of computer simulation studies of lipid membranes, showing that many important biological processes including self-aggregation of membrane components into domains, the formation of non-lamellar phases, and membrane poration and curving, are now amenable to detailed simulation studies.
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Simulation of pore formation in lipid bilayers by mechanical stress and electric fields
TL;DR: Computer simulations of pore formation and membrane rupture of phospholipid bilayers under mechanical and electrical stress, on the nanosecond simulation time scale, are described.
References
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Book
Computer Simulation of Liquids
Michael P. Allen,D. J. Tildesley +1 more
TL;DR: In this paper, the gear predictor -corrector is used to calculate forces and torques in a non-equilibrium molecular dynamics simulation using Monte Carlo methods. But it is not suitable for the gear prediction problem.
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Dissipative particle dynamics : bridging the gap between atomistic and mesoscopic simulation
TL;DR: In this article, a review of dissipative particle dynamics (DPD) as a mesoscopic simulation method is presented, and a link between these parameters and χ-parameters in Flory-Huggins-type models is made.
Journal ArticleDOI
Molecular Transport in Liquids and Glasses
Morrel H. Cohen,David Turnbull +1 more
TL;DR: In this paper, the authors derived a relation between the diffusion constant D in a liquid of hard spheres and the free volume vf, which is based on the concept that statistical redistribution of free volume occasionally opens up voids large enough for diffusive displacement.
Journal ArticleDOI
Simulating microscopic hydrodynamic phenomena with dissipative particle dynamics
PJ Hoogerbrugge,J.M.V.A. Koelman +1 more
Abstract: We present a novel method for simulating hydrodynamic phenomena. This particle-based method combines features from molecular dynamics and lattice-gas automata. It is shown theoretically as well as in simulations that a quantitative description of isothermal Navier-Stokes flow is obtained with relatively few particles. Computationally, the method is much faster than molecular dynamics, and the at same time it is much more flexible than lattice-gas automata schemes.
Journal ArticleDOI
Statistical Mechanics of Dissipative Particle Dynamics.
Pep Español,Patrick B. Warren +1 more
TL;DR: In this paper, the authors derived the stochastic differential equations corresponding to the updating algorithm of Dissipative Particle Dynamics (DPD), and the corresponding Fokker-Planck equation.
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