Bioinformatics Group

Our paper at Colloid and Polymer Science!

Simulation of AOT reverse micelles with polyethylenimine in hexane - Colloid and Polymer Science In this work, we used long (for a total of 2.5 µs) “all-atom” molecular dynamics (MD) simulations to investigate the adsorption behaviors of polyethylenimine (PEI) linear chains in Bis(2-ethylhexyl) sulfosuccinate sodium salt (or Aerosol-OT, AOT) reverse micelle (RM) in hexane with a water/AOT ...

Our new paper at Journal of Molecular Modeling.

Surface coverage and adsorption properties of 1-vinyl-1,2,4-triazole on Au(111) surface: a molecular dynamics study - Journal of Molecular Modeling Context The adsorption of 1-vinyl-1,2,4-triazole monomers on Au(111) surface was investigated via molecular dynamics method. Our results indicate that the surface coverage varied depending on the concentration of the monomers. Specifically, as the concentration of the monomers increased, the surface...

Our new joint paper published in "Journal of Molecular Liquids".

NSAID Solubilisation Promotes Morphological Transitions in Triton X-114 Surfactant Micelles The structural properties of micelles formed by the non-ionic surfactant, Triton X-114 (TX-114), were investigated using all-atom molecular dynamics (…

The Bioinformatics group of International Scientific-Educational Center of NAS RA, in collaboration with Russian-Armenian University - RAU (Dr. Yevgeni Mamasakhlisov), was published new joint paper in "Colloids and Surfaces A: Physicochemical and Engineering Aspects" Journal. We would like to thank the Institute for Informatics and Automation Problems of NAS RA (Ինֆորմատիկայի և ավտոմատացման պրոբլեմների ինստիտուտ / IIAP) team for providing us with huge computing resources to perform this large-scale computational project.

The mechanism of flip-flops in a AOT lamella: A Molecular Dynamics Study A long 5000ns run was conducted on sodium dioctyl sulfosuccinate (AOT)/water lamellar system to understand the unusual behavior. During the simulation…

Our new joint paper published in "Colloids and Surfaces A: Physicochemical and Engineering Aspects" Journal. We would also like to thank the Institute for Informatics and Automation Problems of NAS RA (Ինֆորմատիկայի և ավտոմատացման պրոբլեմների ինստիտուտ / IIAP) staff for providing us with the computational resources.

A protonated L-cysteine adsorption on gold surface: A Molecular Dynamics Study The adsorption of protonated L-cysteine onto Au(111) surface was studied via molecular dynamics method. The detailed examination of trajectories revea…

Our new paper at Journal of Molecular Modeling.

A molecular dynamics study of protein denaturation induced by sulfonate-based surfactants - Journal of Molecular Modeling Microsecond timescale explicit-solvent atomistic simulations were carried out to investigate how anionic surfactants modulate protein structure and dynamics. We found that lysozyme undergoes near-complete denaturation at the high concentration (> 0.1 M) of sodium pentadecyl sulfonate (SPDS), while...

Our new joint paper at Journal of Polymer Research.

Electrosynthesis of silver metal nanocomposites in a copolymer matrix of 1-vinyl-1,2,4-triazole and acrylic acid Nanocomposites and silver nanocomposite coatings based on a copolymer of 1-vinyl-1,2,4-triazole and acrylic acid were synthesized in an aqueous and aqueous-ethanol medium on pure iron and steel electrodes by the electrochemical method. The composition and structure of nanocomposites is confirmed by....

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Our new preprint at biorxiv.org
https://www.biorxiv.org/content/10.1101/2020.12.11.420968v1

Quantum Approximated Graph Cutting: A Rapid Replacement for T-REMD? Determining an optimal protein configuration for the employment of protein binding analysis as completed by Temperature based Replica Exchange Molecular Dynamics (T-REMD) is an important process in the accurate depiction of a protein’s behavior in different solvent environments, especially when de...

Our new article at RSC Advances (Royal Society of Chemistry) Journal.

Spiked gold nanotriangles: formation, characterization and applications in surface-enhanced Raman spectroscopy and plasmon-enhanced catalysis - RSC Advances (RSC Publishing) We show the formation of metallic spikes on the surface of gold nanotriangles (AuNTs) by using the same reduction process which has been used for the synthesis of gold nanostars. We confirm that silver nitrate operates as a shape-directing agent in combination with ascorbic acid as the reducing agen...

Our new paper at PEDS (Oxford Academic (Oxford University Press) Journal. We would like to thank the Institute for Informatics and Automation Problems of NAS RA ( Ինֆորմատիկայի և ավտոմատացման պրոբլեմների ինստիտուտ / IIAP team for providing us with the computing resources to perform this large-scale computational project.

Molecular dynamics study of ACBP denaturation in alkyl sulfates demonstrates possible pathways of unfolding through fused surfactant clusters Abstract. Anionic surfactants denature proteins at low millimolar concentrations, yet little is known about the underlying molecular mechanisms. Here, we under

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