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Open AccessJournal ArticleDOI

The MARTINI force field : Coarse grained model for biomolecular simulations

TLDR
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.
Abstract
We present an improved and extended version of our coarse grained lipid model. The new version, coined the MARTINI force field, is parametrized in a systematic way, 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, the number of possible interaction levels of the coarse-grained sites has increased compared to those of the previous model. Application of the new model to lipid bilayers shows an improved behavior in terms of the stress profile across the bilayer and the tendency to form pores. An extension of the force field now also allows the simulation of planar (ring) compounds, including sterols. Application to a bilayer/cholesterol system at various concentrations shows the typical cholesterol condensation effect similar to that observed in all atom representations.

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PEGylation on mixed monolayer gold nanoparticles: Effect of grafting density, chain length, and surface curvature.

TL;DR: Using molecular dynamics simulation to understand the structural and dynamic the PEG coating of mixed monolayer gold NPs, it is shown that moderate grafting density and short chain length are sufficient enough to prevent NPs from aggregating in an aqueous medium.
Journal ArticleDOI

Ribonuclease A adsorption onto charged self-assembled monolayers: A multiscale simulation study

TL;DR: The orientations and conformation of ribonuclease A (RNase A) adsorbed on oppositely charged self-assembled monolayers (SAM) have been studied by a multiscale approach, including parallel tempering Monte Carlo, all-atom molecular dynamics and coarse-grained molecular dynamics simulations.
Journal ArticleDOI

Dissipative Particle Dynamics Aided Design of Drug Delivery Systems: A Review.

TL;DR: This article reviews the application of DPD simulations in drug delivery systems and establishes the connection between existing studies and proposed some outlooks for the further combination between DPD simulation and the design of drug delivery system.
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Permeation of nanoparticles across the intestinal lipid membrane: dependence on shape and surface chemistry studied through molecular simulations.

TL;DR: The apical model lipid membrane and protocols used in this study can thus be utilized for the in silico design of nanoparticles for the oral delivery of therapeutics.
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Molecular Understanding of the Penetration of Functionalized Gold Nanoparticles into Asymmetric Membranes

TL;DR: It is demonstrated that the hydrophobic contact between protruding solvent-exposed lipid tails and theHydrophobic moieties of ligands can mediate the insertion of AuNPs with a low SCD into cell membranes, which will exhibit less cytotoxicity in most in vivo applications.
References
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Book

CRC Handbook of Chemistry and Physics

TL;DR: CRC handbook of chemistry and physics, CRC Handbook of Chemistry and Physics, CRC handbook as discussed by the authors, CRC Handbook for Chemistry and Physiology, CRC Handbook for Physics,
Journal ArticleDOI

VMD: Visual molecular dynamics

TL;DR: VMD is a molecular graphics program designed for the display and analysis of molecular assemblies, in particular biopolymers such as proteins and nucleic acids, which can simultaneously display any number of structures using a wide variety of rendering styles and coloring methods.
Book

Intermolecular and surface forces

TL;DR: The forces between atoms and molecules are discussed in detail in this article, including the van der Waals forces between surfaces, and the forces between particles and surfaces, as well as their interactions with other forces.
Journal ArticleDOI

GROMACS: Fast, flexible, and free

TL;DR: The software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s is described, which is a very fast program for molecular dynamics simulation.
Journal ArticleDOI

GROMACS 3.0: a package for molecular simulation and trajectory analysis

TL;DR: The design includes an extraction of virial and periodic boundary conditions from the loops over pairwise interactions, and special software routines to enable rapid calculation of x–1/2.
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