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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Insights into Membrane Protein–Lipid Interactions from Free Energy Calculations
TL;DR: It is demonstrated that the energetics of protein–lipid interactions may be reliably and reproducibly calculated using three simulation-based approaches: potential of mean force calculations, alchemical free energy perturbation, and well-tempered metadynamics.
Journal ArticleDOI
The Flocculating Cationic Polypetide from Moringa oleifera Seeds Damages Bacterial Cell Membranes by Causing Membrane Fusion.
Kevin Shebek,Allen B. Schantz,Ian T. Sines,Kathleen Lauser,Stephanie Butler Velegol,Manish Kumar +5 more
TL;DR: It is demonstrated here that a dominant mechanism of MOCP antimicrobial activity is membrane fusion.
Journal ArticleDOI
Divergent Diffusion Coefficients in Simulations of Fluids and Lipid Membranes
Martin Vögele,Gerhard Hummer +1 more
TL;DR: The dependence of single-particle diffusion coefficients on the size and shape of the simulation box in molecular dynamics simulations of fluids and lipid membranes is investigated and it is found that the diffusion coefficients of lipids and a carbon nanotube embedded in a lipid membrane diverge with the logarithm of the box width.
Journal ArticleDOI
Cooperative Supramolecular Block Copolymerization for the Synthesis of Functional Axial Organic Heterostructures
Aritra Sarkar,Tejmani Behera,Ranjan Sasmal,Riccardo Capelli,Charly Empereur-Mot,Jaladhar Mahato,Sarit S. Agasti,Giovanni M. Pavan,Giovanni M. Pavan,Arindam Chowdhury,Subi J. George +10 more
TL;DR: This work reports the cooperative supramolecular block copolymerization of fluorescent monomers in solution under thermodynamic control, for the synthesis of axial organic heterostructures with light-harvesting property and is expected to pave the way forThe synthesis of multi-component organic heterstructures for various functions.
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Coarse-grained simulations of polyelectrolyte complexes: MARTINI models for poly(styrene sulfonate) and poly(diallyldimethylammonium).
TL;DR: The authors' coarse-grained models are able to quantitatively reproduce previous findings like the correct charge compensation mechanism and a reduced dielectric constant of water, which can be interpreted as the underlying reason for the stability of polyelectrolyte multilayers and complexes and validate the robustness of the proposed models.
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