scholarly journals Heterogeneous dynamics and its length scale in simple ionic liquid models: a computational study

2016 ◽  
Vol 18 (9) ◽  
pp. 6486-6497 ◽  
Author(s):  
Soree Kim ◽  
Sang-Won Park ◽  
YounJoon Jung
Keyword(s):  
Ionic Liquid ◽  
Computational Study ◽  
Model Systems ◽  
Coarse Grained ◽  
Length Scale ◽  
Dynamic Heterogeneity ◽  
Heterogeneous Dynamics ◽  
Liquid Model

We numerically investigate the dynamic heterogeneity and its length scale found in coarse-grained ionic liquid model systems.

Time scale of dynamic heterogeneity in model ionic liquids and its relation to static length scale and charge distribution

2015 ◽  
Vol 17 (43) ◽  
pp. 29281-29292 ◽  
Author(s):  
Sang-Won Park ◽  
Soree Kim ◽  
YounJoon Jung
Keyword(s):  
Ionic Liquid ◽  
Ionic Liquids ◽  
Charge Distribution ◽  
Power Law ◽  
Structural Relaxation ◽  
Time Scale ◽  
Length Scale ◽  
Dynamic Heterogeneity ◽  
General Power

We find a general power-law behavior: , where ζdh ≈ 1.2 for all the ionic liquid models, regardless of charges and the length scale of structural relaxation.

scholarly journals Unveiling the Dynamics of KRAS4b on Lipid Model Membranes

2021 ◽  
Author(s):  
Cesar A. López ◽  
Animesh Agarwal ◽  
Que N. Van ◽  
Andrew G. Stephen ◽  
S. Gnanakaran
Keyword(s):  
Molecular Mechanisms ◽  
Hypervariable Region ◽  
Small Gtpase ◽  
Model Systems ◽  
Coarse Grained ◽  
Regulatory Function ◽  
Limited Information ◽  
Long Time ◽  
Cell Growth And Differentiation ◽  
State Models

AbstractSmall GTPase proteins are ubiquitous and responsible for regulating several processes related to cell growth and differentiation. Mutations that stabilize their active state can lead to uncontrolled cell proliferation and cancer. Although these proteins are well characterized at the cellular scale, the molecular mechanisms governing their functions are still poorly understood. In addition, there is limited information about the regulatory function of the cell membrane which supports their activity. Thus, we have studied the dynamics and conformations of the farnesylated KRAS4b in various membrane model systems, ranging from binary fluid mixtures to heterogeneous raft mimics. Our approach combines long time-scale coarse-grained (CG) simulations and Markov state models to dissect the membrane-supported dynamics of KRAS4b. Our simulations reveal that protein dynamics is mainly modulated by the presence of anionic lipids and to some extent by the nucleotide state (activation) of the protein. In addition, our results suggest that both the farnesyl and the polybasic hypervariable region (HVR) are responsible for its preferential partitioning within the liquid-disordered (Ld) domains in membranes, potentially enhancing the formation of membrane-driven signaling platforms. Graphic Abstract

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

scholarly journals A computational study on how structure influences the optical properties in model crystal structures of amyloid fibrils

2017 ◽  
Vol 19 (5) ◽  
pp. 4030-4040 ◽  
Author(s):  
Luca Grisanti ◽  
Dorothea Pinotsi ◽  
Ralph Gebauer ◽  
Gabriele S. Kaminski Schierle ◽  
Ali A. Hassanali
Keyword(s):  
Optical Properties ◽  
Hydrogen Bonding ◽  
Proton Transfer ◽  
Crystal Structures ◽  
Amyloid Fibrils ◽  
Computational Study ◽  
Model Systems ◽  
Hydrogen Bonding Interactions ◽  
Model Crystal ◽  
Different Types

Different types of hydrogen bonding interactions that occur in amyloids model systems and molecular factors that control the susceptibility of the protons to undergo proton transfer and how this couples to the optical properties.

Impact of polydispersity and confinement on diffusion in hydrodynamically interacting colloidal suspensions

2021 ◽  
Vol 925 ◽  
Author(s):  
Emma Gonzalez ◽  
Christian Aponte-Rivera ◽  
Roseanna N. Zia
Keyword(s):  
Computational Study ◽  
Mean Square Displacement ◽  
Configurational Entropy ◽  
Colloidal Suspensions ◽  
Colloidal Dispersion ◽  
Length Scale ◽  
Many Body ◽  
Stokesian Dynamics ◽  
Time Dynamics ◽  
Long Time

We present a computational study of the equilibrium dynamics of a polydisperse hard-sphere colloidal dispersion confined in a spherical cavity. We account for many-body hydrodynamic and lubrication interactions between particles and with the confining cavity utilizing our confined Stokesian dynamics model, expanded here for size polydispersity. We find that, even though the tendency of polydispersity to homogenize structure in a suspension is still present in confinement, strong correlations induced by the cavity resist homogenization. Although seemingly opposite, these two effects have a common driver, which is to maximize configurational entropy of particles in the cavity interior. These structural effects couple with the hydrodynamics to change the particle dynamics: polydispersity weakens lubrication effects near the cavity wall, allowing small (large) particles to diffuse faster (slower) than in a monodisperse suspension. As a small (large) particle gets farther from the wall, polydispersity weakens many-body hydrodynamic couplings, driving diffusivity up (down). While the local cage dynamics dominates short-time self-diffusion, long-time dynamics is also affected. In the concentrated regime, polydispersity and confinement combine to induce radial de-mixing into size-segregated populations. The cavity becomes the most influential ‘nearest neighbour’, setting the length scale of and dynamics within these radial domains. This intermediate length-scale caging makes the angular dynamics insensitive to polydispersity but leads to radial long-time mean-square displacement that changes qualitatively with volume composition. These results hold promise for explaining colloidal-scale physics implicated in the functioning of biological cells, and the engineering of non-living confined colloids where size de-mixing could be useful in the design of encapsulated micro-reactors and therapeutic vesicles.

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 Structure and Electronic Properties of TiO2 Nanoclusters and Dye–Nanocluster Systems Appropriate to Model Hybrid Photovoltaic or Photocatalytic Applications

Nanomaterials ◽  
2019 ◽  
Vol 9 (3) ◽  
pp. 357 ◽  
Author(s):  
Corneliu Oprea ◽  
Mihai Gîrțu
Keyword(s):  
Complex Systems ◽  
Density Functional ◽  
Computational Study ◽  
Computational Cost ◽  
Adsorbed Molecule ◽  
Model Systems ◽  
Cyanine Dye ◽  
Practical Applications ◽  
Hybrid Photovoltaics ◽  
Photocatalytic Applications

We report the results of a computational study of TiO2 nanoclusters of various sizes as well as of complex systems with various molecules adsorbed onto the clusters to set the ground for the modeling of charge transfer processes in hybrid organic–inorganic photovoltaics or photocatalytic degradation of pollutants. Despite the large number of existing computational studies of TiO2 clusters and in spite of the higher computing power of the typical available hardware, allowing for calculations of larger systems, there are still studies that use cluster sizes that are too small and not appropriate to address particular problems or certain complex systems relevant in photovoltaic or photocatalytic applications. By means of density functional theory (DFT) calculations, we attempt to find acceptable minimal sizes of the TinO2n+2H4 (n = 14, 24, 34, 44, 54) nanoclusters in correlation with the size of the adsorbed molecule and the rigidity of the backbone of the molecule to model systems and interface processes that occur in hybrid photovoltaics and photocatalysis. We illustrate various adsorption cases with a small rigid molecule based on coumarin, a larger rigid oligomethine cyanine dye with indol groups, and the penicillin V antibiotic having a flexible backbone. We find that the use of the n = 14 cluster to describe adsorption leads to significant distortions of both the cluster and the molecule and to unusual tridentate binding configurations not seen for larger clusters. Moreover, the significantly weaker bonding as well as the differences in the density of states and in the optical spectra suggest that the n = 14 cluster is a poor choice for simulating the materials used in the practical applications envisaged here. As the n = 24 cluster has provided mixed results, we argue that cluster sizes larger than or equal to n = 34 are necessary to provide the reliability required by photovoltaic and photocatalytic applications. Furthermore, the tendency to saturate the key quantities of interest when moving from n = 44 to n = 54 suggests that the largest cluster may bring little improvement at a significantly higher computational cost.

Capillarity‐induced resonance of oil blobs in capillary tubes and porous media

Geophysics ◽  
2000 ◽  
Vol 65 (3) ◽  
pp. 874-883 ◽  
Author(s):  
Markus Hilpert ◽  
Gerhard H. Jirka ◽  
Erich J. Plate
Keyword(s):  
Porous Media ◽  
Model Systems ◽  
Coarse Grained ◽  
Sound Waves ◽  
Contact Lines ◽  
Phase Contact ◽  
Capillary Tubes ◽  
Fine Grained ◽  
Three Phase ◽  
Analytical Expressions

We investigate the excitation by sound waves of capillary trapped oil blobs. The three‐phase contact lines either remain pinned to the heterogeneities of the solid surface or slide if sound waves are applied. We derive approximate, analytical expressions for the resonance of oil blobs in capillary tubes for both types of contact line behavior. Based upon these simple model systems, we conclude that resonance of oil blobs is significant for coarse‐grained but not fine‐grained media.

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