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.read more
Citations
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Enhancing doping efficiency by improving host-dopant miscibility for fullerene-based n-type thermoelectrics
Li Qiu,Jian Liu,Riccardo Alessandri,Xinkai Qiu,Marten Koopmans,Remco W. A. Havenith,Remco W. A. Havenith,Siewert J. Marrink,Ryan C. Chiechi,L. Jan Anton Koster,Jan C. Hummelen +10 more
TL;DR: In this paper, a promising n-type doping system with high performance for thermoelectric applications was described, where the polar triethylene glycol (TEG) side chain was introduced onto both fullerene host (PTEG-1) and dopant materials, leading to high doping efficiency up to 18% at 20 mol% doping concentration and thus high carrier density and mobility, which are critical to the electrical conductivity.
Posted Content
Many-Body Coarse-Grained Interactions using Gaussian Approximation Potentials
TL;DR: A computational framework that is able to describe general many-body coarse-grained interactions of molecules and use it to model the free energy surface of molecular liquids as a cluster expansion in terms of monomer, dimer, and trimer terms is introduced.
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Dynamic Cholesterol-Conditioned Dimerization of the G Protein Coupled Chemokine Receptor Type 4
Kristyna Pluhackova,Stefan Gahbauer,Franziska Kranz,Tsjerk A. Wassenaar,Tsjerk A. Wassenaar,Rainer A. Böckmann +5 more
TL;DR: Using ensembles of molecular dynamics simulations, it is shown that CXCR4 dimerizes promiscuously in phospholipid membranes and in cholesterol-rich membranes, providing a molecular basis for the modulation of GPCR activity by its lipid environment.
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Interactions of Pleckstrin Homology Domains with Membranes: Adding Back the Bilayer via High-Throughput Molecular Dynamics.
TL;DR: A molecular simulation pipeline for determining the mode of interaction of pleckstrin homology (PH) domains with phosphatidylinositol phosphate (PIP)-containing lipid bilayers with predictions of the membrane localization and interactions of 13 PH domains reveal canonical, non-canonical, and dual PIP-binding sites on the proteins.
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Application of mean field boundary potentials in simulations of lipid vesicles
TL;DR: A method is presented to enhance the efficiency of simulations of lipid vesicles by eliminating water molecules that either surround the vesicle or reside in the interior of thevesicle, without altering the properties of the water at the membrane interface.
References
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