Update cv.md

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@@ -12,71 +12,75 @@ redirect_from:
 Curriculum vitae - Anupam Anand Ojha
 ======
 
-# Education
+## Education
+<hr style="height: 4px; border: none; background-color: black;">
 
-## 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
 - **2022** Distinguished Graduate Student Fellowship
 - **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
+<hr style="height: 4px; border: none; background-color: black;">
+
 * 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
+<hr style="height: 4px; border: none; background-color: black;">
 
-## 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
+<hr style="height: 4px; border: none; background-color: black;">
 
-## 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
+<hr style="height: 4px; border: none; background-color: black;">
 
-
-# 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 %}</ul>
 
 # Positions of Responsibilities
+<hr style="height: 4px; border: none; background-color: black;">
 
-### 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.