A simple, efficient polarizable coarse-grained water model for molecular dynamics simulations

2011 ◽  
Vol 134 (8) ◽  
pp. 084110 ◽  
Author(s):  
Sereina Riniker ◽  
Wilfred F. van Gunsteren
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Coarse Grained ◽  
Water Model ◽  
Dynamics Simulations

scholarly journals Abstract P-2: Multiscale Molecular Dynamics Simulations of the Skin Membranes as a Tool for the Interpretation of the Transmission Electron Microscopy Images

2021 ◽  
Vol 11 (Suppl_1) ◽  
pp. S11-S11
Author(s):  
Marine Bozdaganyan
Keyword(s):  
Electron Microscopy ◽  
Molecular Dynamics ◽  
Transmission Electron Microscopy ◽  
Linoleic Acid ◽  
Molecular Dynamics Simulations ◽  
Coarse Grained ◽  
Water Model ◽  
Active Ingredients ◽  
Transmission Electron ◽  
Dynamics Simulations

Background: Human skin can inhibit chemical penetration which limits the clinical applications of transdermal drug delivery. The stratum corneum (SC) is the primary barrier and organized in lamellar membranes containing the lipids of ceramides (CER), free fatty acids (FFA), and cholesterol (CHOL). One of the most widely used ways to overcome the SC is the addition of chemical penetration enhancers (CPEs) to active ingredients. There are various methods, which have been employed to explore the mechanisms by which CPEs with drugs can change the morphology of SC including transmission electron microscopy. Here, we propose to use multiscale coarse-grained (CG) molecular dynamics (MD) simulations for the interpretation of the images of the SC from the electron microscopy experiments. Methods: We utilized the MARTINI force field for the CG simulations. We employed the mixed-lipid bilayer model of SC consisting of CER, CHOL, and FFA in a 1:1:1 molar ratio assembled with CHARMM-GUI web-service. The systems of the SC model membrane and various enhancers were simulated in the NPT ensemble with the polarizable water model and the reaction field approach for the long-range electrostatics with the usage of Gromacs 2019.4 software. Results: The membrane model was validated with standard characteristics: thickness, diffusion of the lipids, order parameters, and density profiles. After, we have added CPEs and active ingredients to the systems: menthol and osthole as control simulations, ethanol with linoleic acid and lidocaine as test simulations. We have observed the membrane desegregation in the case of menthol and osthole formulations similar to the published results while the permeation of lidocaine with ethanol and linoleic acid did not cause the disruption of the membranes but increased its fluidity and permeability properties. Conclusion: The method of multiscale coarse-grained molecular dynamics simulations can be utilized for the prediction and interpretation of morphology change of SC in addition to various substances.

Parameterization of Divalent Cations for Coarse-Grained Simulations

2020 ◽  
Author(s):  
Florencia Klein ◽  
Daniela Cáceres-Rojas ◽  
Monica Carrasco ◽  
Juan Carlos Tapia ◽  
Julio Caballero ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Metal Ions ◽  
Molecular Dynamics Simulations ◽  
Divalent Cations ◽  
Computational Cost ◽  
Data Bank ◽  
Coarse Grained ◽  
Interaction Parameters ◽  
Dynamics Simulations ◽  
Dynamical Description

<p>Although molecular dynamics simulations allow for the study of interactions among virtually all biomolecular entities, metal ions still pose significant challenges to achieve an accurate structural and dynamical description of many biological assemblies. This is particularly the case for coarse-grained (CG) models. Although the reduced computational cost of CG methods often makes them the technique of choice for the study of large biomolecular systems, the parameterization of metal ions is still very crude or simply not available for the vast majority of CG- force fields. Here, we show that incorporating statistical data retrieved from the Protein Data Bank (PDB) to set specific Lennard-Jones interactions can produce structurally accurate CG molecular dynamics simulations. Using this simple approach, we provide a set of interaction parameters for Calcium, Magnesium, and Zinc ions, which cover more than 80% of the metal-bound structures reported on the PDB. Simulations performed using the SIRAH force field on several proteins and DNA systems show that using the present approach it is possible to obtain non-bonded interaction parameters that obviate the use of topological constraints. </p>

scholarly journals Variation of Interaction Zone Size For The Target Design of 2D Supramolecular Networks

2021 ◽  
Author(s):  
Łukasz Piotr Baran ◽  
Wojciech Rżysko ◽  
Dariusz Tarasewicz
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Self Assembly ◽  
The Self ◽  
Coarse Grained ◽  
Zone Size ◽  
Interaction Zone ◽  
Supramolecular Networks ◽  
Dynamics Simulations ◽  
Target Design

In this study we have performed extensive coarse-grained molecular dynamics simulations of the self-assembly of tetra-substituted molecules. We have found that such molecules are able to form a variety of...

Adsorption-induced co-assembly of hairy and isotropic particles

2020 ◽  
Vol 22 (16) ◽  
pp. 8757-8767
Author(s):  
Tomasz Staszewski ◽  
Małgorzata Borówko
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Coarse Grained ◽  
Dynamics Simulations ◽  
Coarse Grained Molecular Dynamics

We use coarse-grained molecular dynamics simulations to study the behavior of polymer-tethered particles immersed in fluids of isotropic particles.

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