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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Binary interactions and salt-induced coalescence of spherical micelles of cationic surfactants from molecular dynamics simulations.
TL;DR: A direct estimation of salt-mediated potential of mean force (PMF) between spherical micelles of cationic surfactants is obtained for the first time using molecular dynamics simulations and shows qualitative agreement and magnitude is significantly greater than that of the DLVO potentials.
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Characterization of Solubilizing Nanoaggregates Present in Different Versions of Simulated Intestinal Fluid.
Andrew J. Clulow,Albin Parrow,Adrian Hawley,Jamal Khan,Anna C. Pham,Per Larsson,Christel A. S. Bergström,Ben J. Boyd +7 more
TL;DR: The structural homogeneity of the NaTDC/DOPC micelles makes them ideal candidates for standardizing SIF formulations as the structures of the solubilizing nanoaggregates therein are not sensitive to the preparation method.
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Simulation and Theory of Antibody Binding to Crowded Antigen-Covered Surfaces.
TL;DR: A fully flexible coarse-grained model of immunoglobulin G (IgG) antibodies parametrized directly on cryo-EM data is introduced and it is proved that screening effects are concealed in relative measures, such as the fraction of bivalently bound antibodies.
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Towards a new class of stimuli-responsive polymer-based materials – Recent advances and challenges
TL;DR: The rapidly growing field of polymer stimuli-responsive materials (smart materials) resulted in many advances in designing and developing multi-functional systems, novel architectures, and new synthetic routes for many different applications as mentioned in this paper.
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Aggregation of amyloids in a cellular context: modelling and experiment.
TL;DR: In the present review, recent developments on modelling and experiments of amyloid aggregation are reviewed, and an integrative account on how isolated interactions (as observed in vitro and in silico) combine during the course ofAmyloid-related diseases is presented.
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