Curriculum vitae - Anupam Anand Ojha

Education

Doctor of Philosophy in Chemistry, University of California San Diego, CA, USA

September 2019 - June 2024

• CGPA 4.0/4.0
• Merck Research Awardee for Underrepresented Chemists of Color (2024)
• Merkin Graduate Fellow (2023)
• Teddy Traylor Awardee (2023)
• Distinguished Graduate Student Fellow (2022)
• Bonnie Reiss Carbon Neutrality Student Fellow (2021)
• Friends of the International Center Fellow (2021)

BS-MS, Indian Institute of Science Education and Research (IISER) Thiruvananthapuram, KL, India

August 2012 – June 2017

• CGPA 8.6/10.0
• Innovation in Science Pursuit for Inspired Research (INSPIRE) Fellow (2012 - 2017)
• Swiss Government Excellence Fellow (2017 - 2018)

Skills

• Programming: Python, MATLAB, R, MATHEMATICA, LATEX, AWK
• Software Proficiency: Amber, MOE, CHARMM, NAMD, ORCA, MOLPRO, VASP, Quantum ESPRESSO, Gaussian, RDKit, OpenEye, MOLDEN, COMSOL, VESTA, PyMOL, Chemcraft, Schrodinger, VCell, MCell, BrownDye, VMD, APBS, Avogadro, Gnuplot, RStudio, Jupyter, Spyder, Tableau, GitHub, cryoDRGN, RELION, cryoSPARC, OpenMM, AutoDock Vina, Q-Chem, rDock
• AI/ML Technologies: PyTorch, TensorFlow, Keras, scikit-learn

Industry Work Experience

Multiscale Modeling Scientist Intern, Genentech, Inc., San Francisco, CA, USA

June 2024 - September 2024

• Perform multi-scale molecular dynamics simulations for protein-protein and protein-ligand interactions, including large and conformational transitions.
• Build computational workflow to accelerate MD simulations using enhanced and adaptive sampling techniques.

Computer-Aided Drug Design Intern, Janssen Pharmaceutical Companies of Johnson and Johnson, La Jolla, CA, USA

June 2023 - August 2023

• Employed MSM, deep learning, and enhanced sampling methods to determine cellular permeability and rank ordering of protein degraders.
• Developed an end-to-end Python-based workflow for blind cellular permeability prediction of beyond rule-of-five protein degraders.

Research and Early Development Intern, Genentech, Inc., San Francisco, CA, USA

June 2022 - September 2022

• Performed enhanced MD simulations and MSM analysis on protein degraders to calculate transition rates between metastable states.
• Developed an end-to-end Python framework to generate customizable force field parameters for protein degraders.

Academic Research Experience

Merkin Graduate Fellow, Institute of Physics, University of Freiburg, Freiburg im Breisgau, Germany

April 2024 - June 2024

• Multiscale milestoning simulation approach with the dissipation-corrected targeted MD to estimate drug-target residence times for JAK-inhibitor complexes.

Visiting Researcher, Center for Computational Biology, Flatiron Institute, NY, USA

January 2024 - March 2024

• Leveraged cryo-EM image analysis and molecular simulations to investigate dynamic structural transformations in biological molecules.
• Developed integrative cryo-EM methodologies (ManifoldEM), incorporating deep learning and enhanced molecular simulations to formulate iterative dynamic workflows.

Graduate Research Assistant, Department of Chemistry and Biochemistry, UC San Diego, San Diego, CA, USA

November 2019 - June 2024

Published/submitted 11 research publications since 2020, with 7 first-author publications showcasing distinctive research understanding and scientific writing capabilities.

Method and Software Development Projects in Biophysics

• Developed the Markovian milestoning with Voronoi tessellations (MMVT) approach within the Simulation Enabled Estimation of Kinetic Rates (SEEKR) project, improving efficiency of computational predictions of drug-target (un)binding kinetics by 10-fold.
• Developed QMrebind, a method to quantum mechanically reparameterize force field parameters at the drug-target bound state to accurately predict drug-residence times with a multiscale milestoning approach.
• Developed GaMD-WE, a hybrid approach combining Gaussian-accelerated molecular dynamics (GaMD) and weighted ensemble (WE) simulations, enabling accurate and rapid sampling of thermodynamic and kinetic properties of biomolecular complexes by 2-fold.
• Developed DeepWEST, a hybrid method combining deep learning, Markov state models (MSM), and weighted ensemble (WE) simulations, improving the estimation of kinetic and thermodynamic properties of complex biomolecules.
• Employed chemoinformatics and machine learning to identify 8 physicochemical properties differentiating liver OATP- and kidney OAT-transported drugs, offering a molecular basis for informed drug selection.

Molecular Dynamics Simulation of Biomolecular Complexes

• Employed Markovian milestoning with Voronoi tessellations (MMVT) multiscale simulation approach to elucidate selectivity of JAK2 over JAK3 inhibitors and successful rank ordering of 8 JAK-inhibitors by their residence time.
• Employed a two-phase approach with long-scale Gaussian-accelerated molecular dynamics (GaMD) and weighted ensemble (WE) simulations to investigate the allosteric and dynamical effects of 5 disease-associated single-point LRRK2 mutations, providing insights for therapeutic interventions.
• Employed long-scale weighted ensemble (WE) simulations on SARS-CoV-2 spike protein to identify stabilizing mutations providing a more stable and immunogenic S2 construct.

Research Assistant, Centre for Nano and Material Science, Jain University, Bangalore, KA, India

September 2018 - July 2019

• Conducted ab-initio electronic structure calculations (DFT and HF) in ORCA software of a newly synthesized colorimetric chemosensor to determine selective recognition of copper against 10 other ions.

Research Assistant, Department of Chemistry, ETH Zürich, Zürich, Switzerland

August 2017 - August 2018

• Developed an end-to-end Python-based workflow to calculate concerted hydrogen transfer rates within water clusters of sizes 3-10 using ring-polymer instanton theory.

Master’s Research Project, Department of Chemistry, IISER Thiruvananthapuram, KL, India

August 2016 - April 2017

• Employed ab-initio electronic structure calculations in the Gaussian software to quantify binding free energies and rank order a series of 20 analytes interacting with metal-organic frameworks (MOFs) to describe selective sensing of amines.
• Employed ab-initio electronic structure calculations in the VASP software to calculate interaction energies of a series of glyphosates with Zr-based metal-organic frameworks.

Summer Research Intern, Center for Multidimensional Carbon Materials, Institute for Basic Science, Ulsan, South Korea

May 2016 - July 2016

• Performed ab-initio electronic structure calculations with hybrid functionals in Quantum ESPRESSO engine to calculate hydrogen diffusion rates in noble metal surfaces.
• Performed molecular dynamics and surface simulations to calculate the adsorption energies of alkanes onto noble metal surfaces.

Summer Research Intern, Department of Chemistry, IIT Kharagpur, WB, India

May 2015 - July 2015

• Conducted hybrid QM/MM enhanced molecular dynamics studies using NAMD simulation engine, elucidating substrate binding and mechanism of action of dapE-encoded N-succinyl-L, L- Diaminopimelic Acid Desuccinylase with 5 transition metal centers.

Summer Research Intern, Department of Chemistry, IACS, Kolkata, WB, India

May 2014 - July 2014

• Employed ab-initio electronic structure calculations (DFT and HF) in Gaussian to elucidate quantum tunneling phenomena and reactivity in a series of N-heterocyclic carbenes.

Summer Research Intern, Department of Chemistry, IACS, Kolkata, WB, India

May 2013 - July 2013

• Employed quantum mechanical calculations in the Gaussian software to quantify interactions of cyclooctatetraene and related molecules on different noble metal surfaces.

Fellowships and Awards

Merck Research Award for Underrepresented Chemists of Color (2024)

Award recognizing significant contributions of underrepresented chemists of color to chemical sciences and commitment to diversity in the field.

The Merck Research Award for Underrepresented Chemists of Color exemplifies Merck’s commitment to fostering diversity and inclusion in the scientific community. This prestigious award recognizes the outstanding contributions of young researchers to chemical sciences and provides opportunities for career development and networking within the scientific community. Award recipients gain access to mentorship from experienced professionals at Merck, who provide guidance, feedback, and valuable connections relevant to their research. Award recipients present their work at an award symposium, where they showcase their research to peers and mentors.

Merkin Graduate Fellowship, UC San Diego (2023)

$50,000 fellowship recognizing outstanding research excellence and financial support for conducting translational medicine research abroad and building international collaborations.

The Merkin Graduate Fellows Program offers a unique opportunity for UC San Diego graduate students to conduct innovative research abroad in areas related to human health and longevity. As a Merkin Graduate Fellow, students collaborate with researchers globally, aiming to drive bold advancements in medical research and clinical applications while shaping their personal and professional trajectory. This prestigious award includes a monthly stipend, funding for travel, and tuition coverage, enabling them to pursue transformative experiences in translational medicine.

Teddy Traylor Award, UC San Diego (2023)

$3,000 fellowship recognizing outstanding research excellence and financial support to attend scholarly conferences and meetings.

This merit-based award recognizes research excellence and was set up by Dr. Traylor’s colleagues and friends to honor his memory. The $3000 award assists bright, young investigators in pursuing their studies and traveling to scholarly meetings.

Distinguished Graduate Student Fellowship (2022)

$17,000 fellowship acknowledging exceptional research, providing comprehensive financial support for university fees, and a research travel grant.

The Department of Chemistry and Biochemistry at UC San Diego established the Distinguished Graduate Student Fellowship to recognize research excellence. This prestigious fellowship provides one-quarter of fellowship support (stipends and fees), as well as an additional $3,000 bonus for the Fellow to use towards research support.

Bonnie Reiss Carbon Neutrality Student Fellowship (2021)

$4,000 fellowship for contributing to the university goal of achieving zero net greenhouse gas emissions by 2025.

The UC President’s Bonnie Reiss Climate Action Fellowship Program empowers students to lead initiatives that advance the UC system’s climate action objectives. Open to both undergraduate and graduate students across all UC campuses, academic health centers, and affiliated institutions, this program fosters innovation and collaboration to address local climate challenges. Named in honor of the late Regent Bonnie Reiss, a fervent advocate for climate mitigation, the fellowship ensures that students’ efforts contribute to her enduring legacy of environmental stewardship.

Friends of the International Center Fellowship (2021)

$2,000 fellowship for outstanding graduate students pursuing international education, fostering friendship and cooperation within the global community.

Founded in 1961, the Friends of the International Center (Friends) Fellowship supports international education at UCSD in numerous ways, one of which is raising money for and awarding student scholarships. The fellowship awards a stipend of $2,000 to a selected number of outstanding graduate students.

Molecular Sciences Software Institute 2021-A “SEED” Software Fellowship (2021)

$42,057 fellowship to outstanding software scientists in biomolecular and macromolecular simulation, quantum chemistry, and materials science.

The Molecular Sciences Software Institute (MolSSI) fellowship is an esteemed six-month fellowship that recognizes exceptional graduate students dedicated to advancing software infrastructure in computational molecular sciences, including biomolecular and macromolecular simulation, quantum chemistry, and materials science. Fellows collaborate with MolSSI scientists to implement best practices in computational science, ensuring the robustness of their projects. They also receive specialized training in cutting-edge software design principles and tools, and participate in outreach and educational activities organized by MolSSI.

Swiss Government Excellence Scholarship (2017)

$26,317 fellowship from Govt. of Switzerland for outstanding researchers to conduct one-year research at ETH Zurich.

The Swiss Government Excellence Scholarships, awarded annually by the Swiss Confederation, facilitate international exchange and research collaboration between Switzerland and over 180 countries. These prestigious scholarships target young researchers and artists from abroad, offering opportunities for advanced studies and research in various fields including biomolecular and macromolecular simulation, quantum chemistry, and materials science. Administered by the Federal Commission for Scholarships for Foreign Students (FCS), the program provides specialized training, mentorship, and networking opportunities to recipients, ensuring the continued promotion of academic and scientific excellence.

Innovation in Science Pursuit for Inspired Research (INSPIRE) Fellowship (2012-2017)

$5,000 fellowship from Govt. of India for outstanding undergraduate students for five years.

The Innovation in Science Pursuit for Inspired Research (INSPIRE) fellowship, sponsored by the Department of Science and Technology (DST) India, is dedicated to nurturing outstanding young talents and strengthening India’s science and technology landscape. The INSPIRE fellowship offers students a unique opportunity to pursue their passion for basic and natural sciences. These scholarships target students at the undergraduate and postgraduate levels who aspire to build careers in research. Selected candidates for the fellowship receive substantial financial support, including a monthly stipend to cover living expenses and a summer research project grant, which provides an opportunity for hands-on research experience. The scholarship is tenable for a maximum of five years, covering undergraduate and graduate studies.

Positions of Responsibilities

Reviewer for the Journal of Biomolecular Structure and Dynamics

November 2022 - Present

UC San Diego Chemistry International Friendship Group (CIFG) representative

July 2023 - June 2024

Contributing to a community of international graduate students in fostering camaraderie and support.

UC San Diego Chemistry Graduate Student Council (CGSC) representative

July 2023 - June 2024

Advocating for graduate students through engagement in department meetings, seminar organization, and social events.

UC San Diego Chemistry Graduate Student Council (CGSC) representative

September 2019 - May 2020

Advocating for graduate students through engagement in department meetings, seminar organization, and social events.

UC San Diego EXperiential Projects for Accelerated Networking and Development (EXPAND) mentor

January 2023 - April 2023

Mentor for underrepresented undergraduate students to work closely towards a research project.

Graduate Student Representative at UC San Diego Senate for Academic Freedom

September 2021 - May 2022

Actively contributing to a committee tasked with examining and addressing factors impacting the academic freedom of university members.

Publications

Distinguishing Molecular Properties of OAT, OATP, and MRP Drug Substrates by Machine Learning

Anisha K. Nigam, Jeremiah D. Momper, Anupam Anand Ojha, and Sanjay K. Nigam. "Distinguishing Molecular Properties of OAT, OATP, and MRP Drug Substrates by Machine Learning." Pharmaceutics 16, no. 5 (2024): 592.

Simulation-Driven Design of Stabilized SARS-CoV-2 Spike S2 Immunogens

Xandra Nuqui, Lorenzo Casalino, Ling Zhou, Mohamed Shehata, Albert Wang, Alexandra L. Tse, Anupam Ojha, Fiona L. Kearns, Mia A. Rosenfeld, Emily Happy Miller, Cory M. Acreman, Surl-Hee Ahn, Kartik Chandran, Jason S. McLellan, Rommie E Amaro. "Simulation-Driven Design of Stabilized SARS-CoV-2 Spike S2 Immunogens." bioRxiv (2023): 2023-10.

An introductory tutorial to the SEEKR2 (Simulation enabled estimation of kinetic rates v. 2) multiscale milestoning software [Article v1. 0]

Anupam Anand Ojha, Lane William Votapka, Gary Alexander Huber, Shang Gao, and Rommie Elizabeth Amaro. "An introductory tutorial to the SEEKR2 (Simulation enabled estimation of kinetic rates v. 2) multiscale milestoning software [Article v1. 0]." Living Journal of Computational Molecular Science 5, no. 1 (2023): 2359-2359.

QMrebind: incorporating quantum mechanical force field reparameterization at the ligand binding site for improved drug-target kinetics through milestoning simulations

Anupam Anand Ojha, Lane William Votapka, and Rommie Elizabeth Amaro. "QMrebind: incorporating quantum mechanical force field reparameterization at the ligand binding site for improved drug-target kinetics through milestoning simulations." Chemical Science 14, no. 45 (2023): 13159-13175.

Selectivity and Ranking of Tight-Binding JAK-STAT Inhibitors Using Markovian Milestoning with Voronoi Tessellations

Anupam Anand Ojha, Ambuj Srivastava, Lane William Votapka, and Rommie E. Amaro. "Selectivity and ranking of tight-binding JAK-STAT inhibitors using Markovian milestoning with Voronoi tessellations." Journal of Chemical Information and Modeling 63, no. 8 (2023): 2469-2482.

DeepWEST: Deep Learning of Kinetic Models with the Weighted Ensemble Simulation Toolkit for Enhanced Sampling

Anupam Anand Ojha, Saumya Thakur, Surl-Hee Ahn, and Rommie E. Amaro. "DeepWEST: Deep learning of kinetic models with the Weighted Ensemble Simulation Toolkit for enhanced sampling." Journal of chemical theory and computation 19, no. 4 (2023): 1342-1359.

SEEKR2: Versatile Multiscale Milestoning Utilizing the OpenMM Molecular Dynamics Engine

Lane W. Votapka, Andrew M. Stokely, Anupam A. Ojha, and Rommie E. Amaro. "SEEKR2: Versatile multiscale milestoning utilizing the OpenMM molecular dynamics engine." Journal of chemical information and modeling 62, no. 13 (2022): 3253-3262.

Gaussian-accelerated molecular dynamics with the weighted ensemble method: A hybrid method improves thermodynamic and kinetic sampling

Surl-Hee Ahn, Anupam A. Ojha, Rommie E. Amaro, and J. Andrew McCammon. "Gaussian-accelerated molecular dynamics with the weighted ensemble method: A hybrid method improves thermodynamic and kinetic sampling." Journal of chemical theory and computation 17, no. 12 (2021): 7938-7951.

Molecular Properties of Drugs Handled by Kidney OATs and Liver OATPs Revealed by Chemoinformatics and Machine Learning: Implications for Kidney and Liver Disease

Anisha K. Nigam, Anupam A. Ojha, Julia G. Li, Da Shi, Vibha Bhatnagar, Kabir B. Nigam, Ruben Abagyan, and Sanjay K. Nigam. "Molecular properties of drugs handled by kidney OATs and liver OATPs revealed by chemoinformatics and machine learning: implications for kidney and liver disease." Pharmaceutics 13, no. 10 (2021): 1720.

Predicting Ligand Binding Kinetics Using a Markovian Milestoning with Voronoi Tessellations Multiscale Approach

Benjamin R. Jagger, Anupam A. Ojha, and Rommie E. Amaro. "Predicting ligand binding kinetics using a Markovian milestoning with Voronoi tessellations multiscale approach." Journal of Chemical Theory and Computation 16, no. 8 (2020): 5348-5357.

Paper based field deployable sensor for naked eye monitoring of copper (II) ions; elucidation of binding mechanism by DFT studies

Halali V. Vishaka, Manav Saxena, H. R. Chandan, Anupam Anand Ojha, and R. Geetha Balakrishna. "Paper based field deployable sensor for naked eye monitoring of copper (II) ions; elucidation of binding mechanism by DFT studies." Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 223 (2019): 117291.

Water-stable nanoscale zirconium-based metal-organic frameworks for the effective removal of glyphosate from aqueous media

Asha Pankajakshan, Mekhola Sinha, Anupam Anand Ojha, and Sukhendu Mandal. "Water-stable nanoscale zirconium-based metal–organic frameworks for the effective removal of glyphosate from aqueous media." ACS omega 3, no. 7 (2018): 7832-7839.

“Turn-on” fluorescence sensing and discriminative detection of aliphatic amines using a 5-fold-interpenetrated coordination polymer

Prabu Mani, Anupam Anand Ojha, Vennapusa Sivaranjana Reddy, and Sukhendu Mandal. "“Turn-on” fluorescence sensing and discriminative detection of aliphatic amines using a 5-fold-interpenetrated coordination polymer." Inorganic Chemistry 56, no. 12 (2017): 6772-6775.

Invited Talks

Advancements and challenges in multiscale milestoning methods for efficient and accurate prediction of biomolecular kinetics

March 18, 2024

Talk at American Chemical Society Spring 2024, New Orleans, Louisiana

Overcoming limitations in receptor-ligand (un)binding kinetic predictions: A QM-enhanced multiscale milestoning simulation framework integrating quantum mechanics, molecular dynamics, and Brownian dynamics

August 16, 2023

Talk at American Chemical Society Fall 2023, San Francisco, CA

Enhancing sampling efficiency in molecular dynamics simulations of complex biomolecules: Hybrid methods combining Gaussian-accelerated MD, weighted ensemble simulations, and deep learning of kinetic models

August 13, 2023

Talk at American Chemical Society Fall 2023, San Francisco, CA

Multiscale milestoning simulations with Voronoi tessellations approach to decipher selectivity and ranking among JAK-STAT pathway inhibitors with extended residence time

August 22, 2022

Talk at American Chemical Society Fall 2022, Chicago, IL

Deep learning of kinetic models with the Weighted Ensemble Simulation Toolkit for enhanced sampling

April 27, 2022

Talk at WESTPA Developer's Meeting, Department of Chemistry, University of Pittsburgh, Pittsburgh, PA

Gaussian-accelerated molecular dynamics with the weighted ensemble method: A hybrid method improves thermodynamic and kinetic sampling

December 08, 2021

Talk at WESTPA Developer's Meeting, Department of Chemistry, University of Pittsburgh, Pittsburgh, PA

Enhanced sampling approaches to gain insights into receptor-ligand binding and unbinding kinetics

November 10, 2021

Talk at Student Research Seminar, Department of Chemistry and Biochemistry, UC San Diego, San Diego, CA

Multiscale milestoning simulation approach for efficient protein-ligand binding and unbinding kinetics: Adding a quantum mechanical approach to reparameterize the bound state

August 25, 2021

Talk at American Chemical Society Fall 2021, Atlanta, GA

Teaching

Physical Biochemistry II: Quantum and Statistical Mechanics of Biomolecules (CHEM 126B)

Chemical Physics: Statistical Thermodynamics II (CHEM 132)

General Chemistry I (CHEM 6B)

Biophysical Thermodynamics (CHEM 126A)