The Martini Model in Materials Science.
Reads0
Chats0
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
More filters
Journal ArticleDOI
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
More filters
Journal ArticleDOI
A Coarse-Grained MARTINI Model of Polyethylene Glycol and of Polyoxyethylene Alkyl Ether Surfactants
Giulia Rossi,Giulia Rossi,Patrick F.J. Fuchs,Patrick F.J. Fuchs,Jonathan Barnoud,Jonathan Barnoud,Luca Monticelli,Luca Monticelli +7 more
TL;DR: A new coarse-grained model of polyethylene glycol (PEG) and of the family of polyoxyethylene alkyl ether (C(i)E(j)) surfactants is presented and it is shown that the model reproduces the phase behavior of water-surfactant mixtures as a function of water concentration.
Journal ArticleDOI
Into the Dynamics of a Supramolecular Polymer at Submolecular Resolution.
TL;DR: In this paper, the molecular mechanisms and relative kinetics of monomer exchange in structural variants of a synthetic supramolecular polymer in different conditions are modeled using atomistic, coarse-grained modelling combined with advanced simulation approaches.
Journal ArticleDOI
Effects of PEGylation on the Size and Internal Structure of Dendrimers: Self-Penetration of Long PEG Chains into the Dendrimer Core
Hwankyu Lee,Ronald G. Larson +1 more
TL;DR: Simulations of G4 PAMAM dendrimers grafted with poly(ethylene glycol) (PEG) of different sizes and grafting densities were simulated using the coarse-grained force fields previously developed and reparametrized, showing a structural transition from dense-core to dense-shell structure and in agreement with recent scattering experiments and all-atom simulations.
Journal ArticleDOI
A Block Supramolecular Polymer and Its Kinetically Enhanced Stability
TL;DR: The synthesis of porphyrin-based supramolecular polymers in which two distinct block segments consisting of different metal porphyrs are connected is reported, in which monomer exchange occurs from the termini of the SP, which corroborated the enhanced stability of the BSP.
Journal ArticleDOI
The interaction of C60 and its derivatives with a lipid bilayer via molecular dynamics simulations.
TL;DR: Coarse-grained molecular dynamics simulations have been used to explore the interactions of C(60) and its derivatives with lipid bilayers, finding that entry into cells via bilayer permeation whilst maintaining solubility in water is promoted.