scholarly journals Coarse-Grained Model of Collagen Molecules Using an Extended MARTINI Force Field

2010 ◽  
Vol 6 (4) ◽  
pp. 1210-1218 ◽  
Author(s):  
Alfonso Gautieri ◽  
Antonio Russo ◽  
Simone Vesentini ◽  
Alberto Redaelli ◽  
Markus J. Buehler
Keyword(s):  
Force Field ◽  
Coarse Grained ◽  
Coarse Grained Model ◽  
Martini Force Field ◽  
Collagen Molecules

scholarly journals Coarse-grained Simulation of Anionic Surfactant Sodium Dodecyl Sulfate

2021 ◽  
Author(s):  
Xiang-feng Jia ◽  
Jing-fei Chen ◽  
Hui-xue Ren ◽  
Qi Wang ◽  
Wen Xu ◽  
...  
Keyword(s):  
Force Field ◽  
Sodium Dodecyl ◽  
Coarse Grained ◽  
Inversion Method ◽  
Ionic Surfactant ◽  
Coarse Grained Model ◽  
Piecewise Function ◽  
Martini Force Field ◽  
Improved Model ◽  
Vdw Interaction

Abstract Through analyzing the deficiency of the current coarse-grained (CG) model, a new CG model for the ionic surfactant was proposed based on the Martini force field and iterative Boltzmann inversion method. In this model, the electrostatic interaction can be tackled by using a self-defined piecewise function to avoid the disadvantage of using coarse-grained solvents, and the VDW interaction parameters were derived by iterative methods. Using the improved model, the radial distribution function of NaCl and SDS solution in all-atom OPLS can be completely reproduced. The successful setup of the new coarse-grained model provides a good example of the construction of a high-precision coarse-grained force field.

scholarly journals The MARTINI Force Field:  Coarse Grained Model for Biomolecular Simulations

2007 ◽  
Vol 111 (27) ◽  
pp. 7812-7824 ◽  
Author(s):  
Siewert J. Marrink ◽  
H. Jelger Risselada ◽  
Serge Yefimov ◽  
D. Peter Tieleman ◽  
Alex H. de Vries
Keyword(s):  
Force Field ◽  
Coarse Grained ◽  
Coarse Grained Model ◽  
Martini Force Field ◽  
Biomolecular Simulations

A refined polarizable water model for the coarse-grained MARTINI force field with long-range electrostatic interactions

2017 ◽  
Vol 146 (5) ◽  
pp. 054501 ◽  
Author(s):  
Julian Michalowsky ◽  
Lars V. Schäfer ◽  
Christian Holm ◽  
Jens Smiatek
Keyword(s):  
Force Field ◽  
Long Range ◽  
Electrostatic Interactions ◽  
Coarse Grained ◽  
Water Model ◽  
Martini Force Field

scholarly journals Structural-Kinetic-Thermodynamic Relationships Identified from Physics-based Molecular Simulation Models

2017 ◽  
Author(s):  
Joseph F. Rudzinski ◽  
Tristan Bereau
Keyword(s):  
Thermodynamic Properties ◽  
Force Field ◽  
Molecular Simulation ◽  
Simulation Models ◽  
Coarse Grained ◽  
Kinetic Properties ◽  
Coarse Grained Model ◽  
Forbidden Configurations ◽  
Force Field Parameters ◽  
Representative System

Coarse-grained molecular simulation models have provided immense, often general, insight into the complex behavior of condensed-phase systems, but suffer from a lost connection to the true dynamical properties of the underlying system. In general, the physics that is built into a model shapes the free-energy landscape, restricting the attainable static and kinetic properties. In this work, we perform a detailed investigation into the property interrelationships resulting from these restrictions, for a representative system of the helix-coil transition. Inspired by high-throughput studies, we systematically vary force-field parameters and monitor their structural, kinetic, and thermodynamic properties. The focus of our investigation is a simple coarse-grained model, which accurately represents the underlying structural ensemble, i.e., effectively avoids sterically-forbidden configurations. As a result of this built-in physics, we observe a rather large restriction in the topology of the networks characterizing the simulation kinetics. When screening across force-field parameters, we find that structurally-accurate models also best reproduce the kinetics, suggesting structural-kinetic relationships for these models. Additionally, an investigation into thermodynamic properties reveals a link between the cooperativity of the transition and the network topology at a single reference temperature.

scholarly journals Martini Coarse-Grained Models of Imidazolium-Based Ionic Liquids: From Nanostructural Organization to Liquid-Liquid Extraction

2020 ◽  
Author(s):  
Luis Itza Vazquez-Salazar ◽  
Michele Selle ◽  
Alex H. de Vries ◽  
Siewert-Jan Marrink ◽  
Paulo C. T. Souza
Keyword(s):  
Ionic Liquids ◽  
Force Field ◽  
Rational Design ◽  
Value Added ◽  
Liquid Extraction ◽  
Coarse Grained ◽  
Great Success ◽  
Liquid Liquid Extraction ◽  
Martini Force Field ◽  
Wide Range

<div> <div> <div> <p>Ionic liquids (IL) are remarkable green solvents, which find applications in many areas of nano- and biotechnology including extraction and purification of value-added compounds or fine chemicals. These liquid salts possess versatile solvation properties that can be tuned by modifications in the cation or anion structure. So far, in contrast to the great success of theoretical and computational methodologies applied to other fields, only a few IL models have been able to bring insights towards the rational design of such solvents. In this work, we develop coarse-grained (CG) models for imidazolium-based ILs using a new version of the Martini force field. The model is able to reproduce the main structural properties of pure ILs, including spatial heterogeneity and global densities over a wide range of temperatures. More importantly, given the high intermolecular compatibility of the Martini force field, this new IL CG model opens the possibility of large-scale simulations of liquid-liquid extraction experiments. As examples, we show two applications, namely the extraction of aromatic molecules from a petroleum oil model and the extraction of omega-3 polyunsaturated fatty acids from a fish oil model. In semi-quantitative agreement with the experiments, we show how the extraction capacity and selectivity of the IL could be affected by the cation chain length or addition of co-solvents. </p> </div> </div> </div>

CHARMM-GUI Martini Maker for Coarse-Grained Simulations with the Martini Force Field

2015 ◽  
Vol 11 (9) ◽  
pp. 4486-4494 ◽  
Author(s):  
Yifei Qi ◽  
Helgi I. Ingólfsson ◽  
Xi Cheng ◽  
Jumin Lee ◽  
Siewert J. Marrink ◽  
...  
Keyword(s):  
Force Field ◽  
Coarse Grained ◽  
Martini Force Field ◽  
Coarse Grained Simulations

scholarly journals SAFT-γ Force Field for the Simulation of Molecular Fluids. 1. A Single-Site Coarse Grained Model of Carbon Dioxide

2011 ◽  
Vol 115 (38) ◽  
pp. 11154-11169 ◽  
Author(s):  
Carlos Avendaño ◽  
Thomas Lafitte ◽  
Amparo Galindo ◽  
Claire S. Adjiman ◽  
George Jackson ◽  
...  
Keyword(s):  
Carbon Dioxide ◽  
Force Field ◽  
Single Site ◽  
Coarse Grained ◽  
Molecular Fluids ◽  
Coarse Grained Model

scholarly journals Coarse Grained Molecular Dynamic Simulations for the Study of TNF Receptor Family Members' Transmembrane Organization

2021 ◽  
Vol 8 ◽  
Author(s):  
Mauricio P. Sica ◽  
Cristian R. Smulski
Keyword(s):  
Force Field ◽  
Higher Order ◽  
Coarse Grained ◽  
Structural Basis ◽  
Tnf Receptor ◽  
Dynamic Simulations ◽  
Rich Domain ◽  
Martini Force Field ◽  
The Impact ◽  
Homotypic Interactions

The Tumor Necrosis Factor (TNF) and the TNF receptor (TNFR) superfamilies are composed of 19 ligands and 30 receptors, respectively. The oligomeric properties of ligands, both membrane bound and soluble, has been studied most. However, less is known about the oligomeric properties of TNFRs. Earlier reports identified the extracellular, membrane-distal, cysteine-rich domain as a pre-ligand assembly domain which stabilizes receptor dimers and/or trimers in the absence of ligand. Nevertheless, recent reports based on structural nuclear magnetic resonance (NMR) highlight the intrinsic role of the transmembrane domains to form dimers (p75NTR), trimers (Fas), or dimers of trimers (DR5). Thus, understanding the structural basis of transmembrane oligomerization may shed light on the mechanism for signal transduction and the impact of disease-associated mutations in this region. To this end, here we used an in silico coarse grained molecular dynamics approach with Martini force field to study TNFR transmembrane homotypic interactions. We have first validated this approach studying the three TNFR described by NMR (p75NTR, Fas, and DR5). We have simulated membrane patches composed of 36 helices of the same receptor equidistantly distributed in order to get unbiassed information on spontaneous proteins assemblies. Good agreement was found in the specific residues involved in homotypic interactions and we were able to observe dimers, trimers, and higher-order oligomers corresponding to those reported in NMR experiments. We have, applied this approach to study the assembly of disease-related mutations being able to assess their impact on oligomerization stability. In conclusion, our results showed the usefulness of coarse grained simulations with Martini force field to study in an unbiased manner higher order transmembrane oligomerization.

scholarly journals The Effect of Enzymatic Crosslink Degradation on the Mechanics of the Anterior Cruciate Ligament: A Hybrid Multi-Domain Model

2021 ◽  
Vol 11 (18) ◽  
pp. 8580
Author(s):  
Fadi Al Khatib ◽  
Afif Gouissem ◽  
Armin Eilaghi ◽  
Malek Adouni
Keyword(s):  
Cruciate Ligament ◽  
Three Dimensional ◽  
Domain Model ◽  
Coarse Grained ◽  
Elastic Response ◽  
Type I ◽  
Coarse Grained Model ◽  
Promising Tool ◽  
Collagen Molecules ◽  
Anterior Cruciate

The anterior cruciate ligament’s (ACL) mechanics is an important factor governing the ligament’s integrity and, hence, the knee joint’s response. Despite many investigations in this area, the cause and effect of injuries remain unclear or unknown. This may be due to the complexity of the direct link between macro- and micro-scale damage mechanisms. In the first part of this investigation, a three-dimensional coarse-grained model of collagen fibril (type I) was developed using a bottom-up approach to investigate deformation mechanisms under tensile testing. The output of this molecular level was used later to calibrate the parameters of a hierarchical multi-scale fibril-reinforced hyper-elastoplastic model of the ACL. Our model enabled us to determine the mechanical behavior of the ACL as a function of the basic response of the collagen molecules. Modeled elastic response and damage distribution were in good agreement with the reported measurements and computational investigations. Our results suggest that degradation of crosslink content dictates the loss of the stiffness of the fibrils and, hence, damage to the ACL. Therefore, the proposed computational frame is a promising tool that will allow new insights into the biomechanics of the ACL.

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