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.
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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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MARTINI Coarse-Grained Models of Polyethylene and Polypropylene
TL;DR: Two coarse-grained models of everyday use polymers, polyethylene (PE) and polypropylene (PP), aimed at the study of the interaction of hydrophobic plastics with lipid membranes are developed.
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Understanding the Interaction of Block Copolymers with DMPC Lipid Bilayer Using Coarse-Grained Molecular Dynamics Simulations
TL;DR: A computational model of the adsorption and percolation mechanism of poloxamers across a 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) lipid bilayer shows that polymer chains containing a PPO block with a length comparable to the DMPC bilayer thickness, such as P85, tends to percolate across the lipid bilayers.
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From Cooperative Self-Assembly to Water-Soluble Supramolecular Polymers Using Coarse-Grained Simulations.
TL;DR: This work has developed a transferable coarse-grained model that allows studying BTA supramolecular polymerization in water, while preserving remarkable consistency with the atomistic models in the description of the key interactions between the monomers, self-assembly cooperativity, and amplification of order into the growing fibers.
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Improving Internal Peptide Dynamics in the Coarse-Grained MARTINI Model: Toward Large-Scale Simulations of Amyloid- and Elastin-like Peptides.
TL;DR: The modified coarse-grained MARTINI model shows reasonable transferability of parameters for the amyloid- and elastin-like peptides and is applied to investigate the self-assembly of β-sheet forming peptides on the microsecond time scale.
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In vitro blood cell viability profiling of polymers used in molecular assembly
TL;DR: Researchers can produce nanofilms that are better suited for drug delivery and biomedical applications by reducing the possible cytotoxicity of polymers widely used for the layer-by-layer assembly technique using human blood cells.