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We develop methods and software for the computational simulation of biophysical, biochemical and condensed-phase systems.
QM/MM methods and simulations
QM/MM calculations allow the study of large systems to investigate complicated processes such as chemical reactions by simulating the reacting part of the system at the QM level while allowing the simulation of the rest of the system by a much faster classical method.
Advanced force field development
Conventional force fields (FFs) are parametric functions that calculate the energies and forces of the systems of interest. These functions use terms that reproduce bonded (bond length, angle, etc.) and non bonded (electrostatics, Van der Waals) properties using parameters obtained from experimental and theoretical determinations. We are developing new polarizable force fields like the Gaussian Electrostatic Model, and AMOEBA for ionic liquids using high accuracy quantum mechanical methods to parametrize these potentials.
Computational investigation of DNA and RNA transaction enzymes
DNA and RNA transaction enzymes are crucial for various cell processes. Errors in either of these processes can result in mutations, some of which can lead to disease or even death. The understanding of the mechanisms carried out by these proteins at the atomic level may provide insights into these processes.
Biomarker Determination
Our work on DNA and RNA transaction enzymes has resulted in our interest in bioinformatics. We have developed a new method called Hypothesis Driven-SNP-Search (HyDn-SNP-S), which allows the determination of disease related SNPs for any disease, followed by the use of computational simulations to determine the impact of the mutations arising from the disease-associated SNPs.
Publications
Current Status of AMOEBA–IL: A Multipolar/Polarizable Force Field for Ionic Liquids 2020 - Journal Article
Polarizable ab initio QM/MM Study of the Reaction Mechanism of N-tert-Butyloxycarbonylation of Aniline in [EMIm][BF4] 2018 - Journal Article
Mutations along a TET2 active site scaffold stall oxidation at 5-hydroxymethylcytosine 2017 - Journal Article
ALKBH7 Variant Related to Prostate Cancer Exhibits Altered Substrate Binding 2017 - Journal Article
Investigating carbohydrate based ligands for galectin-3 with docking and molecular dynamics studies 2017 - Journal Article
Simulations of the water exchange dynamics of lanthanide ions in 1-ethyl-3-methylimidazolium ethyl sulfate ([EMIm][EtSO4]) and water (vol 18, pg 30877, 2016) 2016 - Journal Article
Modeling Molecular Interactions in Water: From Pairwise to Many Body Potential Energy Functions 2016 - Journal Article
Simulations of the water exchange dynamics of lanthanide ions in 1-ethyl-3-methylimidazolium ethyl sulfate ([EMIm][EtSO4]) and water 2016 - Journal Article