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

Author(s):  
Maryam Reisjalali ◽  
Rex Manurung ◽  
Paola Carbone ◽  
Alessandro Troisi

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...

2013 ◽  
Vol 139 (19) ◽  
pp. 194904 ◽  
Author(s):  
Yelena R. Sliozberg ◽  
Tanya L. Chantawansri

Molecules ◽  
2020 ◽  
Vol 25 (19) ◽  
pp. 4413
Author(s):  
Giovanny Aguilera-Durán ◽  
Antonio Romo-Mancillas

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.


2011 ◽  
Author(s):  
Helena M. G. Correia ◽  
Hélder M. C. Barbosa ◽  
Marta M. D. Ramos

2018 ◽  
Vol 149 (4) ◽  
pp. 044104 ◽  
Author(s):  
Yining Han ◽  
James F. Dama ◽  
Gregory A. Voth

2019 ◽  
Vol 86 (12) ◽  
Author(s):  
Igor Ostanin ◽  
Traian Dumitrică ◽  
Sebastian Eibl ◽  
Ulrich Rüde

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.


2019 ◽  
Vol 1 (8) ◽  
pp. 2891-2900 ◽  
Author(s):  
Ning Liu ◽  
Mathew Becton ◽  
Liuyang Zhang ◽  
Keke Tang ◽  
Xianqiao Wang

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.


2004 ◽  
Vol 844 ◽  
Author(s):  
Brendan O'Malley ◽  
David J. Moore ◽  
Massimo Noro ◽  
Jamshed Anwar ◽  
Becky Notman ◽  
...  

ABSTRACTThe stratum corneum (SC), the outermost layer of the skin, provides the body with a physiologically essential barrier to unregulated water loss and the influx of exogenous substances. Furthermore, the 10–20 micron thick SC, composed of overlapping protein-rich corneocytes surrounded by a heterogeneous multilamellar lipid matrix, displays tremendous mechanical cohesion and thermal integrity. To understand the contribution of these components to SC mechanical properties requires building a complete mechanical model of the skin. In this study we focus on modelling the hierarchical microstructure of the lipid phase and its relation to mechanical properties using a combination of atomistic and mesoscale simulations. The modelling approaches are parameterised with experimental data from FT-IR spectroscopy, X-ray scattering and, in the case of the mesoscale simulations, with detailed density profiles derived from atomic models. The atomistic models are used to probe the role of specific lipid species in maintaining the thermal and structural stability of the SC extracellular lipid matrix and to investigate the role of hydrogen bonding networks in SC lipid cohesion. Mesoscale models are used to investigate domain formation and lipid bilayer organisation on length and time scales inaccessible with atomistic models. These coarse grained models display transitions between ordered hexagonal gel phases and fluid phases, reproducing the experimentally observed ordering of the hydrophilic and hydrophobic regions.


2004 ◽  
Vol 859 ◽  
Author(s):  
Maozhi Li ◽  
Maria C. Bartelt ◽  
J. W. Evans

ABSTRACTKinetic Monte Carlo (KMC) simulation of atomistic models reveals the failure of mean-field treatments of the island size distribution (ISD) for islands formed by homogeneous nucleation during submonolayer deposition on perfect surfaces. KMC also facilitates analysis of scaling properties of the ISD, although here some misperceptions persist which we attempt to clarify. However, KMC becomes inefficient for highly reversible island formation (e.g., for large values of a critical size, i, above which islands are stable) due to the high density of diffusing adatoms on the surface. This reduced efficiency is quantified here with results for CPU time versus i. This feature has motivated development of alternative beyond-mean-field coarse-grained approaches which should be more efficient for large i. We provide results for the ISD for a range of i = 1, 2, 3, and 6 using one such approach, a stochastic geometry-based simulation (GBS) strategy.


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