A comparative computational study of coarse-grained and all-atom water models in shock Hugoniot states

2018 ◽  
Vol 148 (14) ◽  
pp. 144504 ◽  
Author(s):  
Sa Hoon Min ◽  
Max L. Berkowitz
Keyword(s):  
Computational Study ◽  
Coarse Grained ◽  
Shock Hugoniot ◽  
Water Models

Computational study of imperfect networks using a coarse-grained model

2013 ◽  
Vol 139 (19) ◽  
pp. 194904 ◽  
Author(s):  
Yelena R. Sliozberg ◽  
Tanya L. Chantawansri
Keyword(s):  
Computational Study ◽  
Coarse Grained ◽  
Coarse Grained Model

PSO-Assisted Development of New Transferable Coarse-Grained Water Models

2018 ◽  
Vol 122 (6) ◽  
pp. 1958-1971 ◽  
Author(s):  
Karteek K. Bejagam ◽  
Samrendra Singh ◽  
Yaxin An ◽  
Carter Berry ◽  
Sanket A. Deshmukh
Keyword(s):  
Coarse Grained ◽  
Water Models

Development of hybrid coarse-grained atomistic models for rapid assessment of local structuring of polymeric semiconductors

2022 ◽  
Author(s):  
Maryam Reisjalali ◽  
Rex Manurung ◽  
Paola Carbone ◽  
Alessandro Troisi
Keyword(s):  
Computational Study ◽  
Rapid Assessment ◽  
Semiconducting Polymers ◽  
Coarse Grained ◽  
Atomistic Models

Decades of work in the field of computational study of semiconducting polymers using atomistic models illustrate the challenges of generating equilibrated models for this class of materials. While adopting a...

scholarly journals Computational Study of C-X-C Chemokine Receptor (CXCR)3 Binding with Its Natural Agonists Chemokine (C-X-C Motif) Ligand (CXCL)9, 10 and 11 and with Synthetic Antagonists: Insights of Receptor Activation towards Drug Design for Vitiligo

Molecules ◽  
2020 ◽  
Vol 25 (19) ◽  
pp. 4413
Author(s):  
Giovanny Aguilera-Durán ◽  
Antonio Romo-Mancillas
Keyword(s):  
Molecular Dynamics ◽  
Computational Study ◽  
Md Simulations ◽  
Receptor Activation ◽  
Activation Mechanism ◽  
Coarse Grained ◽  
Dimensional Structure ◽  
Cytotoxic Lymphocytes ◽  
Ligand Interaction ◽  
Α Subunit

Vitiligo is a hypopigmentary skin pathology resulting from the death of melanocytes due to the activity of CD8+ cytotoxic lymphocytes and overexpression of chemokines. These include CXCL9, CXCL10, and CXCL11 and its receptor CXCR3, both in peripheral cells of the immune system and in the skin of patients diagnosed with vitiligo. The three-dimensional structure of CXCR3 and CXCL9 has not been reported experimentally; thus, homology modeling and molecular dynamics could be useful for the study of this chemotaxis-promoter axis. In this work, a homology model of CXCR3 and CXCL9 and the structure of the CXCR3/Gαi/0βγ complex with post-translational modifications of CXCR3 are reported for the study of the interaction of chemokines with CXCR3 through all-atom (AA-MD) and coarse-grained molecular dynamics (CG-MD) simulations. AA-MD and CG-MD simulations showed the first activation step of the CXCR3 receptor with all chemokines and the second activation step in the CXCR3-CXCL10 complex through a decrease in the distance between the chemokine and the transmembrane region of CXCR3 and the separation of the βγ complex from the α subunit in the G-protein. Additionally, a general protein–ligand interaction model was calculated, based on known antagonists binding to CXCR3. These results contribute to understanding the activation mechanism of CXCR3 and the design of new molecules that inhibit chemokine binding or antagonize the receptor, provoking a decrease of chemotaxis caused by the CXCR3/chemokines axis.

Exploring the utility of coarse-grained water models for computational studies of interfacial systems

2010 ◽  
Vol 108 (15) ◽  
pp. 2007-2020 ◽  
Author(s):  
Xibing He ◽  
Wataru Shinoda ◽  
Russell DeVane ◽  
Michael L. Klein
Keyword(s):  
Coarse Grained ◽  
Computational Studies ◽  
Water Models

scholarly journals Size-Independent Mechanical Response of Ultrathin Carbon Nanotube Films in Mesoscopic Distinct Element Method Simulations

2019 ◽  
Vol 86 (12) ◽  
Author(s):  
Igor Ostanin ◽  
Traian Dumitrică ◽  
Sebastian Eibl ◽  
Ulrich Rüde
Keyword(s):  
Carbon Nanotube ◽  
Load Transfer ◽  
Mechanical Response ◽  
Computational Study ◽  
Distinct Element ◽  
Small Strain ◽  
Distinct Element Method ◽  
Coarse Grained ◽  
Vector Model ◽  
Element Method

Abstract In this work, we present a computational study of the small strain mechanics of freestanding ultrathin carbon nanotube (CNT) films under in-plane loading. The numerical modeling of the mechanics of representatively large specimens with realistic micro- and nanostructure is presented. Our simulations utilize the scalable implementation of the mesoscopic distinct element method of the waLBerla multi-physics framework. Within our modeling approach, CNTs are represented as chains of interacting rigid segments. Neighboring segments in the chain are connected with elastic bonds, resolving tension, bending, shear, and torsional deformations. These bonds represent a covalent bonding within the CNT surface and utilize enhanced vector model (EVM) formalism. Segments of the neighboring CNTs interact with realistic coarse-grained anisotropic van der Waals potential, enabling a relative slip of CNTs in contact. The advanced simulation technique allowed us to gain useful insights on the behavior of CNT materials. It was established that the energy dissipation during CNT sliding leads to extended load transfer that conditions size-independent, material-like mechanical response of the weakly bonded assemblies of CNTs.

scholarly journals Mechanical anisotropy of two-dimensional metamaterials: a computational study

2019 ◽  
Vol 1 (8) ◽  
pp. 2891-2900 ◽  
Author(s):  
Ning Liu ◽  
Mathew Becton ◽  
Liuyang Zhang ◽  
Keke Tang ◽  
Xianqiao Wang
Keyword(s):  
Mechanical Properties ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Computational Study ◽  
2D Materials ◽  
Mechanical Anisotropy ◽  
Coarse Grained ◽  
Two Dimensional ◽  
Geometrical Factors ◽  
Dynamics Simulations

Mechanical properties, especially negative Poisson's, of 2D sinusoidal lattice metamaterials based on 2D materials depends highly on both geometrical factors and tuned mechanical anisotropy according to our generic coarse-grained molecular dynamics simulations.

Thermal conductivity of ice polymorphs: a computational study

2018 ◽  
Vol 20 (16) ◽  
pp. 11028-11036
Author(s):  
Irene Iriarte-Carretero ◽  
Miguel A. Gonzalez ◽  
Fernando Bresme
Keyword(s):  
Thermal Conductivity ◽  
State Of The Art ◽  
Computational Study ◽  
Water Models

Testing the accuracy of state of the art water models in predicting the thermal conductivity of ice polymorphs.

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