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
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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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Properties of the polarizable MARTINI water model: A comparative study for aqueous electrolyte solutions
TL;DR: In this paper, the properties of the polarizable MARTINI water model in the presence of varying sodium chloride concentrations are compared to results obtained by a Kirkwood-Buff based atomistic force field in combination with the SPC/E water model.
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Dispersion of Nafion Ionomer Aggregates in 1-Propanol/Water Solutions: Effects of Ionomer Concentration, Alcohol Content, and Salt Addition
TL;DR: In this paper, coarse-grained molecular dynamics simulations using explicit solvent models were performed to understand Nafion ionomer morphology in 1-propanol (NPA)/water solutions under various conditions (iono...
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Molecular Simulations of the Synthesis of Periodic Mesoporous Silica Phases at High Surfactant Concentrations
Szu Chia Chien,Germán Pérez-Sánchez,Germán Pérez-Sánchez,José R. B. Gomes,M. Natália Sias Soeiro Cordeiro,Miguel Jorge,Scott M. Auerbach,Peter A. Monson +7 more
TL;DR: In this paper, the formation mechanism of periodic mesoporous silica over a wide range of cationic surfactant concentrations was studied and it was shown that the liquid-crystal templating mechanism is not viable because the preformed liquid crystal collapses as silica monomers are added into the solution.
Journal ArticleDOI
PEDOT:PSS nano-particles in aqueous media: A comparative experimental and molecular dynamics study of particle size, morphology and z-potential.
TL;DR: The results show that the molecular model developed in this work represents very well the PEDOT:PSS nano-particles in aqueous dispersion and the trend in change of particle size, charge density and z- potential with changing pH and ionic strength are in good agreement between the simulations and experiments.
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From Microscale to Macroscale: Nine Orders of Magnitude for a Comprehensive Modeling of Hydrogels for Controlled Drug Delivery.
Tommaso Casalini,Giuseppe Perale +1 more
TL;DR: This review aims at providing a summary of the most frequently used modeling approaches (molecular dynamics, coarse-grained models, Brownian dynamics, dissipative particle dynamics, Monte Carlo simulations, and mass conservation equations), which are here classified according to the characteristic length scale.