The Martini Model in Materials Science.
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In this article, the main applications to date of the Martini model in materials science are highlighted, and a perspective for the future developments in this field is given, particularly in light of recent developments such as the new version of the model, Martini 3.Abstract:
The Martini model, a coarse-grained force field initially developed with biomolecular simulations in mind, has found an increasing number of applications in the field of soft materials science. The model's underlying building block principle does not pose restrictions on its application beyond biomolecular systems. Here, the main applications to date of the Martini model in materials science are highlighted, and a perspective for the future developments in this field is given, particularly in light of recent developments such as the new version of the model, Martini 3.read more
Citations
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Chemically specific coarse-graining of polymers: Methods and prospects
Satyen Dhamankar,Michael A. Webb +1 more
Journal ArticleDOI
Two decades of Martini: Better beads, broader scope
Siewert J. Marrink,Luca Monticelli,Manuel N. Melo,Riccardo Alessandri,D. Peter Tieleman,Paulo C. T. Souza +5 more
TL;DR: The Martini model as mentioned in this paper is a coarse-grained force field for molecular dynamics simulations, originally developed for lipid-based systems by the groups of Marrink and Tieleman, has over the years been extended as a community effort to the current level of a general-purpose force field.
Journal ArticleDOI
Polyply; a python suite for facilitating simulations of macromolecules and nanomaterials
Fabian Grünewald,Riccardo Alessandri,Peter C. Kroon,Luca Monticelli,Paulo C. T. Souza,Siewert J. Marrink +5 more
TL;DR: The polyply software suite as mentioned in this paper leverages a multi-scale graph matching algorithm designed to generate parameters quickly and for arbitrarily complex polymeric topologies, and a generic multiscale random walk protocol capable of setting up complex systems efficiently and independent of the target force-field or model resolution.
Journal ArticleDOI
Theory and Practice of Coarse-Grained Molecular Dynamics of Biologically Important Systems
Adam Liwo,Cezary Czaplewski,Adam K. Sieradzan,Agnieszka G. Lipska,Sergey A. Samsonov,Rajesh K. Murarka +5 more
TL;DR: In this article, the physical basis of coarse-grained molecular dynamics, the coarsegrained force fields, the equations of motion and the respective numerical integration algorithms, and selected practical applications are discussed.
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Nonconverged Constraints Cause Artificial Temperature Gradients in Lipid Bilayer Simulations
Sebastian Thallmair,Sebastian Thallmair,Matti Javanainen,Balázs Fábián,Hector Martinez-Seara,Siewert J. Marrink +5 more
TL;DR: In this paper, the authors show that a significant temperature difference between molecule types can artificially arise in CG MD simulations with the standard Martini simulation parameters in GROMACS, and demonstrate that the underlying reason for this behavior is the presence of highly constrained moieties, such as cholesterol.
References
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Molecular Modeling for Nanomaterial-Biology Interactions: Opportunities, Challenges, and Perspectives.
Tommaso Casalini,Vittorio Limongelli,Vittorio Limongelli,Mélanie Schmutz,Claudia Som,Olivier Jordan,Peter Wick,Gerrit Borchard,Giuseppe Perale,Giuseppe Perale +9 more
TL;DR: This review aims at exploring and discussing the opportunities and perspectives offered by molecular modeling in this field through selected examples from literature at the nano–bio interface.
Journal ArticleDOI
Properties of Poloxamer Molecules and Poloxamer Micelles Dissolved in Water and Next to Lipid Bilayers: Results from Computer Simulations
TL;DR: Simulations of systems containing poloxamer molecules or mouselles solvated in bulk water showed that structural properties, such as radii of gyration of the molecules and micelles, agree with the ones inferred from experiments.
Journal ArticleDOI
Electronic structure at coarse-grained resolutions from supervised machine learning
Nicholas E. Jackson,Nicholas E. Jackson,Alec Bowen,Lucas Antony,Michael A. Webb,Venkatram Vishwanath,Juan J. de Pablo,Juan J. de Pablo +7 more
TL;DR: A machine learning approach, denoted as artificial neural network electronic coarse graining (ANN-ECG), is presented here in which the conformationally dependent electronic structure of a molecule is mapped directly to CG pseudo-atom configurations, which accelerates simulations by eliminating backmapping and repeated quantum-chemical calculations.
Journal ArticleDOI
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.
Journal ArticleDOI
The Supramolecular Organization of a Peptide-Based Nanocarrier at High Molecular Detail.
Mazda Rad-Malekshahi,Koen M. Visscher,João P. G. L. M. Rodrigues,Renko de Vries,Wim E. Hennink,Marc Baldus,Alexandre M. J. J. Bonvin,Enrico Mastrobattista,Markus Weingarth +8 more
TL;DR: The atomic level study allows analyzing the vesicle surface structure and dynamics as well as the intermolecular forces between peptides, providing a number of potential leads to improve and tune the biophysical properties of the nanocarrier.