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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A polarizable MARTINI model for monovalent ions in aqueous solution.
TL;DR: The introduction of a new polarizable coarse-grained martini force field for monovalent ions, called refIon, is developed mainly for the accurate reproduction of electrostatic properties in aqueous electrolyte solutions and provides a better agreement between simulation and experimental results.
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Free-Energy Landscape for Peptide Amphiphile Self-Assembly: Stepwise versus Continuous Assembly Mechanisms
Tao Yu,George C. Schatz +1 more
TL;DR: The mechanism of self-assembly of 140 peptide amphiphiles (PAs) to give nanofiber structures was investigated using a coarse-grained method to quantitatively determine whether the assembly process involves discrete intermediates or is a continuous process.
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MARTINI-Compatible Coarse-Grained Model for the Mesoscale Simulation of Peptoids.
Mingfei Zhao,Janani Sampath,Sarah Alamdari,Gillian Shen,Chun-Long Chen,Chun-Long Chen,Christopher J. Mundy,Christopher J. Mundy,Jim Pfaendtner,Jim Pfaendtner,Andrew L. Ferguson +10 more
TL;DR: This work establishes a new rigorously-parameterized coarse-grained peptoid force field for the understanding and design of peptoid nanomaterials at length and time scales inaccessible to all-atom calculations.
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Resolving Donor–Acceptor Interfaces and Charge Carrier Energy Levels of Organic Semiconductors with Polar Side Chains
Riccardo Alessandri,Selim Sami,Jonathan Barnoud,Alex H. de Vries,Siewert J. Marrink,Remco W. A. Havenith +5 more
TL;DR: In this article, the impact of polar side chains on bulk heterojunction overall morphology, molecular configurations at donor-acceptor (DA) interfaces, and charge carrier energy levels is investigated.
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From isodesmic to highly cooperative : Reverting the supramolecular polymerization mechanism in water by fine monomer design
Nicolás M. Casellas,Silvia Pujals,Davide Bochicchio,Giovanni M. Pavan,Tomás Torres,Tomás Torres,Lorenzo Albertazzi,Miguel García-Iglesias,Miguel García-Iglesias +8 more
TL;DR: Two structurally-similar discotic molecules able to self-assemble in water, forming supramolecular fibers, are reported and one shows one of the highest cooperativity values.