A5053139524- DNA and Nucleic Acid Chemistry
- Advanced biosensing and bioanalysis techniques
- Metal complexes synthesis and properties
- Machine Learning in Materials Science
- Advanced NMR Techniques and Applications
- Theoretical and Computational Physics
- Organoboron and organosilicon chemistry
- Catalytic Cross-Coupling Reactions
- Synthesis and characterization of novel inorganic/organometallic compounds
- Parallel Computing and Optimization Techniques
- Physics of Superconductivity and Magnetism
- DNA Repair Mechanisms
- Photochemistry and Electron Transfer Studies
- Advanced Physical and Chemical Molecular Interactions
- Protein Structure and Dynamics
- Nanopore and Nanochannel Transport Studies
École Polytechnique Fédérale de Lausanne
2023-2024
University of Tennessee at Knoxville
2022
The University of Texas at Austin
2022
MiMiC is a framework for modeling large-scale chemical processes that require treatment at multiple resolutions. It does not aim to implement single-handedly all methods required treat individual subsystems, but instead, it relegates this task specialized computational chemistry software while serves as an intermediary between these external programs and computes the interactions subsystems. minimizes issues typically associated with molecular dynamics performed by adopting multiple-program...
MiMiC is a highly flexible, extremely scalable multiscale modeling framework. It couples the CPMD (quantum mechanics, QM) and GROMACS (molecular MM) codes. The code requires preparing separate input files for two programs with selection of QM region. This can be tedious procedure prone to human error, especially when dealing large regions. Here, we present MiMiCPy, user-friendly tool that automatizes preparation files. written in Python 3 an object-oriented approach. main subcommand PrepQM...
MiMiC is a framework for performing multiscale simulations in which loosely coupled external programs describe individual subsystems at different resolutions and levels of theory. To make it highly efficient flexible, we adopt an interoperable approach based on multiple-program multiple-data (MPMD) paradigm, serving as intermediary responsible fast data exchange interactions between the subsystems. The main goal to avoid interfering with underlying parallelization programs, including...
MiMiC is a framework for performing multiscale simulations in which loosely coupled external programs describe individual subsystems at different resolutions and levels of theory. To make it highly efficient flexible, we adopt an interoperable approach based on multiple-program multiple-data (MPMD) paradigm, serving as intermediary responsible fast data exchange interactions between the subsystems. The main goal to avoid interfering with underlying parallelization programs, including...
The impact of an 8-oxoguanine (8oxoG) defect on the redox properties DNA within nucleosome core particle (NCP) was investigated employing hybrid quantum mechanical/molecular mechanics (QM/MM) molecular dynamics simulations native and 8oxoG-containing NCP systems with explicit representation a biologically relevant environment. Two distinct positions varying solvent accessibility were considered for 8oxoG insertion. In both cases, it is found that presence drastically decreases free energy...
The impact of an 8-oxoguanine (8oxoG) defect on the redox properties DNA within Nucleosome Core Particle (NCP) was investigated employing hybrid Quantum Mechanical/Molecular Mechanics (QM/MM) molecular dynamics simulations native and 8oxoG-containing NCP systems with explicit representation a biologically relevant environment. Two distinct positions varying solvent accessibility were considered for 8oxoG insertion. In both cases, it is found that presence drastically decreases free energy...
Base excision repair enzymes (BERs) detect and oxidative DNA damage with efficacy despite the small size of defects their often only minor structural impact. A charge transfer (CT) model for rapid scanning stretches has been evoked to explain high detection rate in face numerous, lesions. The viability CT defect is explored via hybrid QM/MM computational studies that leverage accuracy quantum mechanics (QM) a region interest descriptive power molecularmechanics (MM) remainder system. We find...
Activation of the dinitrogen triple bond is a crucial step in overall fixation atmospheric nitrogen into usable forms for industrial and biological applications. Current synthetic catalysts incorporate metal ions to facilitate activation cleavage dinitrogen. The high price metal-based challenge catalyst recovery during catalytic processes has led increasing interest metal-free catalysts. One toward catalysis use frustrated Lewis pairs (FLPs). In this study, we have examined 18 functionalized...
The impact of an 8-oxoguanine (8oxoG) defect on the redox properties DNA within Nucleosome Core Particle (NCP) structure was investigated employing hybrid Quantum Mechanical/Molecular Mechanics (QM/MM) molecular dynamics simulations native and 8oxoG-containing NCP systems with explicit representation a biologically relevant environment. Two distinct positions were considered for 8oxoG insertion. In both cases, it is found that presence drastically decreases free energy oxidation, by roughly...