Anugraha T K
|PhD Candidate
|Computational Biophysics & Enhanced Sampling Methods
Programming
Scientific Libraries
Simulation Tools
Specializations
Doctoral Researcher
University of California, Davis
Parallelizable GaMD
Achieved ~4× sampling speed-up and near-linear GPU scaling by integrating GaMD with Weighted Ensemble via Nvidia MPS, surpassing either method alone for free-energy convergence.
Performance comparison showing ~4× speedup achieved with MPS-enabled parallelization compared to standard implementation. Benchmarks performed on one NVIDIA A100 GPU (80 GB) with system size of 8,600 atoms in explicit water.
Predicting Hotspot Residues in Antigen–Antibody Complexes
Developed a computational pipeline for predicting antigen–antibody hotspot residues, ranking the top five residue pairs crucial to binding affinity, and expediting mutational studies for more efficient antibody engineering.
Comparative analysis of key residue pair interactions between Wuhan (yellow) and Omicron (green) variants, showing differential binding patterns that influence antibody recognition and effectiveness.
Machine Learning for Enhanced Sampling
Lead an ongoing ML-integrated MD project to enhance sampling efficiency and accuracy, with systematic comparisons aimed at establishing best practices for robust biomolecular simulations.
Alpha-1 Antitrypsin (AAT) Deficiency
Evaluated plant-derived recombinant AAT via umbrella sampling, showing therapeutic potential comparable to human AAT.
Ovarian Cancer Antibodies
Quantified FAS epitope occlusion via molecular dynamics, showing 80% occlusion when glycosylated vs. 40% when non-glycosylated, enabling selective antibody targeting of cancer cells (non-glycosylated FAS) while sparing healthy cells (glycosylated FAS).
Understanding why 2Rab binds to non-glycosylated FAS and not to glycosylated FAS
HIV-related GI Damage
Applied GaMD to reveal dual binding sites of 10-hydroxystearic acid on PPAR-α, demonstrating therapeutic potential in HIV-induced GI injury (Manuscript currently under second review at Nature).
Predicting Ligand Binding: Visualization of binding site interactions and residue dynamics
Key Features:
- First binding site (a): Shows interactions with residues Y314, L424, S480, and H440
- Second binding site (b): Demonstrates binding near residues D453, K266, and E251
- Time-resolved trajectories shown at 0 ns, 575 ns, and 1150 ns
- Binding paths highlighted in red and blue showing distinct interaction patterns
Dylan Kramer, Clarissa Rocha, Anugraha Thyagatur, Abhaya Dandekar, Roland Faller, Satya Dandekar. "Microbial Metabolite Restores Gut Barrier and Microbiome Diversity in Viral Infection." (Under second review at Nature).
Anugraha Thyagatur, Minami, S., Shah, P., McDonald, K. A., Nandi, S., & Faller, R. "Modeling the Influence of Glycosylation on the SARS-CoV-2 Spike Protein." Paper presented at the 2023 AIChE Annual Meeting, AIChE. (2023, November 7).
Anugraha Thyagatur, L.T. Mushongera. "Effect of Interface Orientation and Loading Direction on Cu-Nb Multilayered Nanocomposites." Journal of Materials Engineering and Performance, 32, 3371–3377 (2023).
Anugraha Thyagatur, L.T. Mushongera. "Effects of Interface Orientation on Deformation Mechanism in Cu-Nb Multilayered Nanocomposites." Journal of Molecular Modeling, 28, 166 (2022).
Anugraha Thyagatur, R. Gakhar, D. Chidambaram, P. Calderoni, M. Buric, L.T. Mushongera. "Thermodynamic Stability of Sapphire in Molten Chloride." Journal of the American Ceramic Society, (2022).
M. Jain, K. Yaddanapudi, Anugraha Thyagatur, K.J. Baldwin, M. Knezevic, N.A. Mara, I.J. Beyerlein. "High Strength and Stability of Bcc Nb/Mg Nanolaminates." Acta Materialia, (2023).
BioMADE Workshop 2024
Davis, CA, USA2024Presented: "Multiscale Modeling of SARS-CoV-2 Spike Protein Antigens: Exploring Conformational Dynamics to Inform Next-Gen Vaccine Designs."
2023 AIChE Annual Meeting
Orlando, FL, USANovember 2023Co-authored: "Modeling the Influence of Glycosylation on the SARS-CoV-2 Spike Protein."
TMS 2020 Annual Meeting
San Diego, CA, USA2020Presented: "Ductile vs. Brittle Behavior of Sapphire Using Nano-indentation and Micro-pillar Compression"
IMECE 2019
Salt Lake City, UT, USA2019Presented: "Structure and Properties of Pseudomorphically Transformed Bcc Mg in Mg-Nb Multilayer Nanocomposites"
Gordon Research Conference (GRC) Physical Metallurgy 2019
Hampshire, Boston, USA2019Poster: "Structure and Properties of bcc Mg Synthesized under extreme conditions"
NSF ACCESS
Awarded 40,000 GPU hours ($32,000 value) by NSF ACCESS for implementing and testing ParGaMD.
Center for Integrated Nanotechnology (CINT) User Proposal Grant
Awarded no-cost access at Los Alamos National Laboratory to investigate Mg/Nb interface-driven enhancements in Mg strength/ductility via in situ pillar compression in SEM.
Advanced Photon Source User Proposal Grant
Secured beamtime at Argonne National Laboratory to examine pressure–temperature effects on the compression behavior of Mg–Nb multilayer nanocomposites.
Summer Fellowship Programme
Awarded by the Indian Institute of Technology (IIT) Madras, 2017.
Branch Entry Scholarship
Awarded by the National Institute of Technology Karnataka, 2014.
Enhanced Sampling Methods
Developing and optimizing computational techniques to improve sampling efficiency in molecular dynamics simulations
Computational Biophysics
Applying computational methods to understand biological systems at the molecular level
Machine Learning in MD
Integrating machine learning techniques with molecular dynamics to enhance simulation accuracy and efficiency
Free Energy Calculations
Computing free energy landscapes to understand molecular interactions and binding processes