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Kavya K. M

Kavya K. M

Assistant Professor

About

Dr. Kavya K. M. is an Assistant Professor in the School of Pure and Applied Sciences. She obtained her Ph.D. in Physics from the University of Mysore, specializing in Computational Biophysics. Her Ph.D. research combined application of computational physics to investigate how the dynamic behavior of biological molecules contributes to their biological functions.

During her Ph.D., she received a research internship from the National Science and Technology Council (NSTC), Taiwan, and conducted research at Taipei Medical University. There, she applied quantum chemical calculations to investigate the fluorescence properties of molecular probes used in diagnostic applications. Following her Ph.D., she worked as a Research Associate under the RUSA project at the Institution of Excellence (IoE), University of Mysore.

Her research interests lie at the interface of physics, biology, and computation, where she uses physics-based computational approaches to investigate how molecular interactions govern protein function and how mutations can influence cellular processes associated with cancer.

Knowing yourself is the beginning of all wisdom -Aristotle

Insights from molecular dynamics and metadynamics simulations into nucleotide-regulated and species-specific conformational dynamics of Era GTPase.
This study employed molecular dynamics and metadynamics simulations to investigate the nucleotide-dependent conformational dynamics of Era GTPases from different bacterial species. The work revealed how nucleotide binding regulates domain motions and identified species-specific dynamic features that may influence biological function. The findings provide mechanistic insights into GTPase regulation and contribute to understanding the role of Era proteins in ribosome biogenesis and bacterial cell physiology.
Conformational dynamics and ribosomal interactions of Bacillus subtilis Obg in various nucleotide-bound states: Insights from molecular dynamics simulation.
This work investigated the conformational dynamics of Bacillus subtilis Obg in different nucleotide-bound states using molecular dynamics simulations. The study demonstrated how nucleotide-induced structural changes influence domain motions and interactions with the premature 50S ribosomal subunit. The results provided molecular-level insights into the mechanism by which Obg participates in ribosome maturation and highlighted the importance of nucleotide-dependent regulation in bacterial GTPases.
Nucleotide-dependent structural dynamics and domain motion in Coxiella burnetii EngA GTPases: Insights from molecular dynamics simulation.
This study explored the effect of different nucleotide-bound states on the structural dynamics of Coxiella burnetii EngA GTPase. Molecular dynamics simulations revealed significant changes in domain communication, flexibility, and conformational transitions associated with nucleotide binding. The findings improve our understanding of EngA-mediated ribosome biogenesis and the molecular basis of its functional regulation.
Molecular dynamics simulation studies on Bacillus subtilis RbgA: insights into the RbgA-ribosome association and GTPase activity.
Investigated structural dynamics associated with ribosome recognition and GTPase activity in RbgA. The study provided molecular insights into the role of RbgA during large ribosomal subunit biogenesis.
Molecular dynamics simulation study on Bacillus subtilis EngA: the presence of Mg2+ at the active-sites promotes the functionally important conformation.
Examined the influence of Mg²⁺ ions on EngA structure and function. The results demonstrated that Mg²⁺ stabilizes conformations important for nucleotide binding and biological activity.
DFT-Guided Design of Bioextract-Based Triboelectric Nanogenerators: A Green Pathway to Self-Powered Electronics.
Contributed computational investigations supporting the design of environmentally sustainable triboelectric nanogenerators. The study demonstrated the potential of bioextract-derived materials for self-powered electronic applications.
High-performance tribopositive PEG-PVA blends for smart energy harvesting: A pathway to self-powered security and healthcare monitoring.
Contributed computational analysis toward understanding material properties that enhance triboelectric performance. The work supports the development of self-powered devices for healthcare and security monitoring.
Novel Isoxazolylpyrimidine Derivatives: Design, Synthesis, Antifungal Activity and In‐Silico Studies.
Contributed computational studies to evaluate molecular interactions and biological activity of newly synthesized antifungal compounds. The findings identified promising candidates for further therapeutic development.
Unveiling the Role of Ionic States of Cesium halides for High-Performance Triboelectric Nanogenerators: Applications in UV-Sensitive Devices.
Investigated the electronic contribution insight into influence of effect of ionic halides contribution on charge generation and energy-harvesting performance in triboelectric nanogenerators.
Comprehensive Computational Study of a Novel Chromene-Trione Derivative Bioagent: Integrated Molecular Docking, Dynamics, Topology, and Quantum Chemical Analysis.
Contributed molecular simulation and computational analyses to evaluate the structural, energetic, and interaction properties of a novel bioactive compound with potential therapeutic applications.
Novel Chromone–Hydrazone Conjugates: Synthesis, In Silico evaluation and Cytotoxic Assessment against Hormone Dependent Breast Cancer cell lines.
Contributed computational evaluation of newly synthesized chromone–hydrazone derivatives and their interactions with biological targets, supporting their potential application as anticancer agents.
Investigation of Phe-tRNA interaction with EF-Tu in GDP/GTP nucleotide bound states: a molecular dynamics simulation study.
Studied the molecular interactions between Phe-tRNA and GDP-bound and GTP bound EF-Tu to understand the structural basis of translational processes and protein synthesis.
Molecular dynamics simulation studies and dynamic network analysis of Bacillus subtilis YsxC in GDP and GTP-Mg2+ bound states.
Investigated nucleotide-dependent structural dynamics and residue communication networks in YsxC, providing insights into its potential role during ribosome biogenesis.

Study biomolecular structure, dynamics, and function using molecular dynamics simulations and enhanced sampling techniques to elucidate how molecular motions regulate biological function, investigate the effects of mutations and different cellular conditions, and uncover molecular mechanisms associated with diseases.

Investigate the electronic structure, optical properties, and excited-state behavior of molecular systems using DFT and TD-DFT calculations.

Research Interests

Computational Biophysics Simulations

Density Functional Theory (DFT) and Time-Dependent DFT (TD-DFT)

Machine Learning Applications in Molecular simulations

NSTC International Internship Pilot Program (IIPP) Fellowship
Awarded by the National Science and Technology Council (NSTC), Taiwan, to conduct research at Taipei Medical University, Taiwan, under an international research internship program (September–November 2024).

DST–KSTePS Ph.D. Fellowship
Awarded by the Karnataka Science and Technology Promotion Society (KSTePS), Government of Karnataka.

Kavya K. M

Assistant Professor

Ph.D in Physics

School of Pure and Applied Sciences

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