The Martini Model in Materials Science.
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TLDR
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.
Journal ArticleDOI
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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Multiscale modeling and simulations of responsive polymers
TL;DR: In this paper, the authors systematically review the computational progresses of stimuli-responsive polymers, including simulations of pH, temperature, solvent, salt ionic strength, photo field, electrical field, and so on.
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In silico design of anti-atherogenic biomaterials
Daniel R. Lewis,Vladyslav Kholodovych,Michael D. Tomasini,Michael D. Tomasini,Dalia Abdelhamid,Latrisha K. Petersen,William J. Welsh,Kathryn E. Uhrich,Prabhas V. Moghe +8 more
TL;DR: A new ligand-based drug design framework was successfully adapted to computationally screen and design biomaterials with cardiovascular therapeutic properties, and five key descriptors were identified to provide a strong linear correlation between the predicted and observed anti-atherogenic activity values.
Journal ArticleDOI
Promising Route for the Development of a Computational Framework for Self-Assembly and Phase Behavior Prediction of Ionic Surfactants Using MARTINI.
TL;DR: The MARTINI forcefield, with careful treatment of electrostatic interactions and appropriate modification of parameters for some key functional groups, can be a powerful ally in the quest for a universal computational framework for the design of new surfactants with improved properties.
Journal ArticleDOI
How the Dynamics of a Supramolecular Polymer Determines Its Dynamic Adaptivity and Stimuli-Responsiveness: Structure-Dynamics-Property Relationships From Coarse-Grained Simulations.
TL;DR: In this article, a water-soluble 1,3,5-benzenetricarboxamide (BTA) supramolecular polymer incorporating (charged) receptor monomers is shown to undergo dynamic clustering following the superselective binding to a multivalent recruiter.
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Size-Selective, Noncovalent Dispersion of Carbon Nanotubes by PEGylated Lipids: A Coarse-Grained Molecular Dynamics Study
TL;DR: In this article, a coarse-grained molecular dynamics simulation was conducted to explore the relation between micellar and CNT-assembled PEG structures, and the influence of PEG length on assembly and dispersion.