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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Self-Assembly of Charge-Containing Copolymers at the Liquid-Liquid Interface.
Felipe Jiménez-Ángeles,Ha-Kyung Kwon,Kazi Sadman,Thomas Wu,Kenneth R. Shull,Monica Olvera de la Cruz +5 more
TL;DR: The self-assembly of charge-containing copolymers is found to be driven by the association of the charged component in the hydrophilic block, with hydrophobic segments extending away from the hydphilic cores into the chloroform phase.
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Effect of side chain on the electrochemical performance of poly (ether ether ketone) based anion-exchange membrane: A molecular dynamics study
TL;DR: In this paper, the authors conduct coarse-grained molecular dynamics simulations to investigate two PEEK-based membranes, in which the side chains contain one (SQ) or two (GQ) quaternary ammonium groups.
Journal ArticleDOI
Mesoscale Simulation and Machine Learning of Asphaltene Aggregation Phase Behavior and Molecular Assembly Landscapes
TL;DR: A variant of diffusion maps designed to handle data sets with large local density variations, and the first application of many-body diffusion maps to molecular self-assembly to recover a pseudo-1D free energy landscape are introduced.
Journal ArticleDOI
Caught in the Act: Mechanistic Insight into Supramolecular Polymerization-Driven Self-Replication from Real-Time Visualization.
Sourav Maity,Jim Ottelé,Guillermo Monreal Santiago,Pim W. J. M. Frederix,Peter C. Kroon,Omer Markovitch,Marc C. A. Stuart,Siewert J. Marrink,Sijbren Otto,Wouter H. Roos +9 more
TL;DR: This mechanism of precursor reservoir formation, followed by one-dimensional diffusion, which guides the precursor molecules to the sites of growth, reduces the entropic penalty associated with colocalizing precursors and growth sites and constitutes a new mechanism for supramolecular polymerization.
Journal ArticleDOI
Characterization of Long Linear and Branched Alkanes and Alcohols for Temperatures up to 573.15 K by Surface Light Scattering and Molecular Dynamics Simulations
Tobias Klein,Frances D. Lenahan,Manuel Kerscher,Michael H. Rausch,Ioannis G. Economou,Thomas M. Koller,Andreas P. Fröba +6 more
TL;DR: To improve the simulation results for the best-performing all-atom L-OPLS FF at larger temperatures, a modified version was suggested that incorporates a temperature dependence for the energy parameters of the Lennard-Jones potential obtained by calibrating only against the experimental liquid density data of n-dodecane.