Can Nematic Transitions Be Predicted By Atomistic Simulations? A Computational Study of The Odd–Even Effect

ChemPhysChem ◽  
2004 ◽  
Vol 5 (1) ◽  
pp. 104-111 ◽  
Author(s):  
Roberto Berardi ◽  
Luca Muccioli ◽  
Claudio Zannoni
Keyword(s):  
Computational Study ◽  
Atomistic Simulations

scholarly journals Allosteric Modulation of Conformational Dynamics in Human Hsp90α: A Computational Study

2017 ◽  
Author(s):  
David L. Penkler ◽  
Canan Atilgan ◽  
Özlem Tastan Bishop
Keyword(s):  
Binding Sites ◽  
Drug Targeting ◽  
Therapeutic Strategy ◽  
Computational Study ◽  
Conformational Dynamics ◽  
Atomistic Simulations ◽  
Functional Sites ◽  
Naturally Occurring ◽  
Open Conformation ◽  
Modeling Techniques

AbstractCentral to Hsp90’s biological function is its ability to interconvert between various conformational states. Drug targeting of Hsp90’s regulatory mechanisms, including its modulation by co-chaperone association, presents as an attractive therapeutic strategy for Hsp90 associated pathologies. Here, we utilize homology modeling techniques to calculate full-length structures of human Hsp90α in closed and partially-open conformations. Atomistic simulations of these structures demonstrated that bound ATP stabilizes the dimer by ‘tensing’ each protomer, while ADP and apo configurations ‘relax’ the complex by increasing global flexibility. Dynamic residue network analysis revealed regions of the protein involved in intra-protein communication, and identified several overlapping key communication hubs that correlate with known functional sites. Perturbation response scanning analysis identified several potential residue sites capable of modulating conformational change in favour of interstate conversion. For the ATP-bound open conformation, these sites were found to overlap with known Aha1 and client binding sites, demonstrating how naturally occurring forces associated with co-factor binding could allosterically modulate conformational dynamics.

scholarly journals Cyclic Photoisomerization of Azobenzene in Atomistic Simulations: Modeling the Effect of Light on Columnar Aggregates of Azo Stars

Molecules ◽  
2021 ◽  
Vol 26 (24) ◽  
pp. 7674
Author(s):  
Markus Koch ◽  
Marina Saphiannikova ◽  
Olga Guskova
Keyword(s):  
Molecular Mechanisms ◽  
Driving Forces ◽  
Computational Study ◽  
Morphological Changes ◽  
Md Simulations ◽  
Atomistic Simulations ◽  
Experimental Works ◽  
New Interpretation ◽  
Kinetics Of ◽  
Supramolecular Aggregates

This computational study investigates the influence of light on supramolecular aggregates of three-arm azobenzene stars. Every star contains three azobenzene (azo) moieties, each able to undergo reversible photoisomerization. In solution, the azo stars build column-shaped supramolecular aggregates. Previous experimental works report severe morphological changes of these aggregates under UV–Vis light. However, the underlying molecular mechanisms are still debated. Here we aim to elucidate how light affects the structure and stability of the columnar stacks on the molecular scale. The system is investigated using fully atomistic molecular dynamics (MD) simulations. To implement the effects of light, we first developed a stochastic model of the cyclic photoisomerization of azobenzene. This model reproduces the collective photoisomerization kinetics of the azo stars in good agreement with theory and previous experiments. We then apply light of various intensities and wavelengths on an equilibrated columnar stack of azo stars in water. The simulations indicate that the aggregate does not break into separate fragments upon light irradiation. Instead, the stack develops defects in the form of molecular shifts and reorientations and, as a result, it eventually loses its columnar shape. The mechanism and driving forces behind this order–disorder structural transition are clarified based on the simulations. In the end, we provide a new interpretation of the experimentally observed morphological changes.

scholarly journals A computational study of the interaction of organic surfactants with goethite α-FeO(OH) surfaces

RSC Advances ◽  
2016 ◽  
Vol 6 (94) ◽  
pp. 91893-91903 ◽  
Author(s):  
David Santos-Carballal ◽  
Zhimei Du ◽  
Helen E. King ◽  
Nora H. de Leeuw
Keyword(s):  
Carboxylic Acids ◽  
Computational Study ◽  
Atomistic Simulations ◽  
Interatomic Potentials

Atomistic simulations based on interatomic potentials show that a range of carboxylic acids adsorb to goethite surfaces.

Computational Study of Nanomaterials: From Large-Scale Atomistic Simulations to Mesoscopic Modeling

2012 ◽  
pp. 470-480 ◽  
Author(s):  
Dimitrios Peroulis ◽  
Prashant R. Waghmare ◽  
Sushanta K. Mitra ◽  
Supone Manakasettharn ◽  
J. Ashley Taylor ◽  
...  
Keyword(s):  
Large Scale ◽  
Computational Study ◽  
Atomistic Simulations ◽  
Mesoscopic Modeling
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