Geometrical Nonlinear Elasticity of Axon Under Tension: A Coarse-grained Computational Study

2021 ◽  
Author(s):  
Ning Liu ◽  
Poorya Chavoshnejad ◽  
Shaoheng Li ◽  
Mir Jalil Razavi ◽  
Tianming Liu ◽  
...  
Keyword(s):  
Nonlinear Elasticity ◽  
Computational Study ◽  
Coarse Grained ◽  
Geometrical Nonlinear

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

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.

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.

scholarly journals LES-BASED COMPUTATIONAL STUDY ON FRICTION FACTOR UNDER COARSE-GRAINED SHEET-FLOW

2015 ◽  
Vol 71 (2) ◽  
pp. I_493-I_498
Author(s):  
Eiji HARADA ◽  
Naoki TSURUTA ◽  
Hitoshi GOTOH
Keyword(s):  
Friction Factor ◽  
Computational Study ◽  
Coarse Grained ◽  
Sheet Flow

scholarly journals AN EQUATION-FREE APPROACH TO COUPLED OSCILLATOR DYNAMICS: THE KURAMOTO MODEL EXAMPLE

2006 ◽  
Vol 16 (07) ◽  
pp. 2043-2052 ◽  
Author(s):  
SUNG JOON MOON ◽  
IOANNIS G. KEVREKIDIS
Keyword(s):  
Computational Study ◽  
Kuramoto Model ◽  
Coarse Grained ◽  
Multiscale Approach ◽  
Angle Distribution ◽  
Dynamical Equations ◽  
Coupled Oscillator ◽  
The Kuramoto Model ◽  
Prototypical Model ◽  
Coupled Oscillator Model

We present an equation-free multiscale approach to the computational study of the collective dynamics of the Kuramoto model [Kuramoto, 1984], a prototypical model for coupled oscillator populations. Our study takes place in a reduced phase space of coarse-grained "observables" of the system: the first few moments of the oscillator phase angle distribution. We circumvent the derivation of explicit dynamical equations (approximately) governing the evolution of these coarse-grained macroscopic variables; instead we use the equation-free framework [Kevrekidis et al., 2003] to computationally solve these equations without obtaining them in closed form. In this approach, the numerical tasks for the conceptually existing but unavailable coarse-grained equations are implemented through short bursts of appropriately initialized simulations of the "fine-scale", detailed coupled oscillator model. Coarse projective integration and coarse fixed point computations are illustrated.

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

scholarly journals Development of Martini 2.2 parameters for N-glycans: A case study of the HIV-1 Env glycoprotein dynamics

Glycobiology ◽  
2021 ◽  
Author(s):  
Srirupa Chakraborty ◽  
Kshitij Wagh ◽  
S Gnanakaran ◽  
Cesar A López
Keyword(s):  
Force Field ◽  
Complex Dynamics ◽  
Computational Study ◽  
Fundamental Property ◽  
Coarse Grained ◽  
Chemical Variability ◽  
Experimental Approaches ◽  
Hiv 1 ◽  
Good Agreement

Abstract N-linked glycans are ubiquitous in nature and play key roles in biology. For example, glycosylation of pathogenic proteins is a common immune evasive mechanism, hampering the development of successful vaccines. Due to their chemical variability and complex dynamics, an accurate molecular understanding of glycans is still limited by the lack of effective resolution of current experimental approaches. Here, we have developed and implemented a reductive model based on the popular Martini 2.2 coarse grained force field for to the computational study of N-glycosylation. We used the HIV-1 Env as a direct applied example of a highly glycosylated protein. Our results indicate that the model not only reproduces many observables in very good agreement with a fully atomistic force field, but it can be extended to study large amount of glycosylation variants, a fundamental property which can aid in the development of drugs and vaccines.

scholarly journals Simulating the directional translocation of a substrate by the AAA+ motor in the 26S proteasome

2021 ◽  
Vol 118 (23) ◽  
pp. e2104245118
Author(s):  
Arjun Saha ◽  
Arieh Warshel
Keyword(s):  
Electrostatic Interactions ◽  
Atp Hydrolysis ◽  
Computational Study ◽  
26S Proteasome ◽  
Coarse Grained ◽  
Free Energies ◽  
Ongoing Research ◽  
Lysine Residues ◽  
Coarse Grained Simulations ◽  
Binding Free Energies

This work explored the molecular origin of substrate translocation by the AAA+ motor of the 26S proteasome. This exploration was performed by combining different simulation approaches including calculations of binding free energies, coarse-grained simulations, and considerations of the ATP hydrolysis energy. The simulations were used to construct the free energy landscape for the translocation process. This included the evaluation of the conformational barriers in different translocation steps. Our simulation reveals that the substrate translocation by the AAA+ motor is guided in part by electrostatic interactions. We also validated the experimental observation that bulkier residues in pore loop 1 are responsible for substrate translocation. However, our calculation also reveals that the lysine residues prior to the bulkier residues (conserved along pore loop 1) are also important for the translocation process. We believe that this computational study can help in guiding the ongoing research of the proteasome.

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