From 3f51c70b91ea93b772bbfb39065071ce5fc1b786 Mon Sep 17 00:00:00 2001 From: A Anand Ojha Date: Tue, 14 May 2024 10:18:54 +0200 Subject: [PATCH] Update cv.md --- _pages/cv.md | 84 +++++++++++++++++++++++++++------------------------- 1 file changed, 44 insertions(+), 40 deletions(-) diff --git a/_pages/cv.md b/_pages/cv.md index 56fa0686f51db..9eabbaab861df 100644 --- a/_pages/cv.md +++ b/_pages/cv.md @@ -12,13 +12,14 @@ redirect_from: Curriculum vitae - Anupam Anand Ojha ====== -# Education +## Education +
-## Doctor of Philosophy in Chemistry +### Doctor of Philosophy in Chemistry **University of California, San Diego** *September 2019 - June 2024* -### Awards and Fellowships +#### Awards and Fellowships - **2024** Merck Research Award for Underrepresented Chemists of Color - **2023** Merkin Graduate Fellowship - **2023** Teddy Traylor Award @@ -26,57 +27,60 @@ Curriculum vitae - Anupam Anand Ojha - **2021** Bonnie Reiss Carbon Neutrality Student Fellowship - **2021** Friends of the International Center Fellowship -## BS-MS Dual Degree +### BS-MS Dual Degree **Indian Institute of Science Education and Research (IISER), Thiruvananthapuram** *August 2012 – June 2017* -### Fellowships +#### Fellowships - **2012-2017** Innovation in Science Pursuit for Inspired Research (INSPIRE) Fellowship - **2017** Swiss Government Excellence Scholarship -Skills -====== +## 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 +## Industry Work Experience +
-## 1. Multiscale Modeling Scientist Intern +### i. 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. -## 2. Computer-Aided Drug Design Intern +### ii. 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. -## 3. Research and Early Development Intern +### iii. 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 +## Academic Research Experience +
-## 1. Merkin Graduate Fellow +### i. 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. -## 2. Visiting Researcher +### ii. 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. -## 3. Graduate Research Assistant +### iii. 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. @@ -91,72 +95,71 @@ Skills - 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. -## 4. Research Assistant +### iv. 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. -## 5. Research Assistant +### v. 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. -## 6. Master’s Research Project +### vi. 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. -## 7. Summer Research Intern +### vii. 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. -## 8. Summer Research Intern +### viii. 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. -## 9. Summer Research Intern +### ix. 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. -## 10. Summer Research Intern +### x. 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 +
- -# Fellowships and Awards - -### 1. Merck Research Award for Underrepresented Chemists of Color (2024) +### i. Merck Research Award for Underrepresented Chemists of Color (2024) - This award recognizes significant contributions to chemical sciences and commitment to diversity in the field. -### 2. Merkin Graduate Fellowship, UC San Diego (2023) +### ii. 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. -### 3. Teddy Traylor Award, UC San Diego (2023) +### iii. Teddy Traylor Award, UC San Diego (2023) - $3,000 fellowship recognizing outstanding research excellence and financial support to attend scholarly conferences and meetings. -### 4. Distinguished Graduate Student Fellowship (2022) +### iv. Distinguished Graduate Student Fellowship (2022) - $17,000 fellowship acknowledging exceptional research, providing comprehensive financial support for university fees and a research travel grant. -### 5. Bonnie Reiss Carbon Neutrality Student Fellowship (2021) +### v. 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. -### 6. Friends of the International Center Fellowship (2021) +### vi. 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. -### 7. Molecular Sciences Software Institute 2021-A "SEED" Software Fellowship (2021) +### vii. 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. -### 8. Swiss Government Excellence Scholarship (2017) +### viii. Swiss Government Excellence Scholarship (2017) - $26,317 fellowship from Govt. of Switzerland for outstanding researchers to conduct one-year research at ETH Zurich. -### 9. Innovation in Science Pursuit for Inspired Research (INSPIRE) Fellowship (2012-2017) +### ix. 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. @@ -179,22 +182,23 @@ Teaching {% endfor %} # Positions of Responsibilities +
-### 1. November 2022 – Present: Reviewer for the Journal of Biomolecular Structure and Dynamics +### i. November 2022 – Present: Reviewer for the Journal of Biomolecular Structure and Dynamics Reviewer for the Journal of Biomolecular Structure and Dynamics. -### 2. July 2023 - June 2024: UC San Diego Chemistry International Friendship Group (CIFG) representative +### ii. July 2023 - June 2024: UC San Diego Chemistry International Friendship Group (CIFG) representative Contributing to a community of international graduate students in fostering camaraderie and support. -### 3. July 2023 - June 2024: UC San Diego Chemistry Graduate Student Council (CGSC) representative +### iii. July 2023 - June 2024: UC San Diego Chemistry Graduate Student Council (CGSC) representative Advocating for graduate students through engagement in department meetings, seminar organization, and social events. -### 4. September 2019 - May 2020: UC San Diego Chemistry Graduate Student Council (CGSC) representative +### iv. September 2019 - May 2020: UC San Diego Chemistry Graduate Student Council (CGSC) representative Advocating for graduate students through engagement in department meetings, seminar organization, and social events. -### 5. January 2023 - April 2023: UC San Diego EXperiential Projects for Accelerated Networking and Development (EXPAND) mentor +### v. January 2023 - April 2023: UC San Diego EXperiential Projects for Accelerated Networking and Development (EXPAND) mentor Mentor for underrepresented undergraduate students to work closely towards a research project. -### 6. September 2021 - May 2022: Graduate Student Representative at UC San Diego Senate for Academic Freedom +### vi. September 2021 - May 2022: Graduate Student Representative at UC San Diego Senate for Academic Freedom Actively contributing to a committee tasked with examining and addressing factors impacting the academic freedom of university members.