Updated

_config.yml

@@ -8,9 +8,9 @@
 
 # Basic Site Settings
 locale                   : "en-US"
-title                    : "Your Name / Site Title"
+title                    : "Anupam Anand Ojha"
 title_separator          : "-"
-name                     : &name "Your Name"
+name                     : &name "Anupam Anand Ojha"
 description              : &description "personal description"
 url                      : https://academicpages.github.io # the base hostname & protocol for your site e.g. "https://mmistakes.github.io"
 baseurl                  : "" # the subpath of your site, e.g. "/blog"
@@ -21,50 +21,50 @@ repository               : "academicpages/academicpages.github.io"
 #               Additional customization can be done by editing /_includes/author-profile.html
 author:
   # Biographic information
-  avatar           : "profile.png"
-  name             : "Your Sidebar Name"
+  avatar           : "aaojha.jpeg"
+  name             : "Anupam Anand Ojha"
   pronouns         : # example: "she/her"  
-  bio              : "Short biography for the left-hand sidebar"
-  location         : "Earth"
-  employer         : "Red Brick University"
+  bio              : "Computational Biophysicist | Structural Biologist"
+  location         : "San Diego, CA"
+  employer         : "UC San Diego"
   uri              : # URL
-  email            : "none@example.org" 
+  email            : "anandojha.002@gmail.com" 
 
   # Academic websites
   arxiv            : # URL - Update with the correct link to your profile
-  googlescholar    : "https://scholar.google.com/citations?user=PS_CX0AAAAAJ"
+  googlescholar    : "https://scholar.google.com/citations?user=BQ0WKs8AAAAJ&hl=en"
   impactstory      : # URL
-  orcid            : "http://orcid.org/yourorcidurl"
-  pubmed           : "https://www.ncbi.nlm.nih.gov/pubmed/?term=john+snow"
-  researchgate     : # URL
+  orcid            : "https://orcid.org/0000-0001-6588-3092"
+  pubmed           : # URL
+  researchgate     : "https://www.researchgate.net/profile/A-Anand-Ojha"
 
   # Repositories and software development
   bitbucket        : # Username - Update with your username on the site
   codepen          : # Username
   dribbble         : # Username
-  github           : "academicpages"
+  github           : "anandojha"
   kaggle           : # Username  
   stackoverflow    : # User number or user number and name (i.e., use "1" or "1/jeff-atwood")    
 
   # Social media
-  bluesky          : "bsky.app" # Replace this with you Bluesky username
-  facebook         : # Username
+  bluesky          : #
+  facebook         : "https://www.facebook.com/anandojha002/"
   flickr           : # Username
   foursquare       : # Username
   goodreads        : # Username
   google_plus      : # Username
   keybase          : # Username
-  instagram        : # Username
+  instagram        : "https://www.instagram.com/cross_meridian/"
   lastfm           : # Username
-  linkedin         : # Username
+  linkedin         : "https://www.linkedin.com/in/aaojha/"
   mastodon         : # URL
   medium           : # URL
   pinterest        : # Username
   soundcloud       : # Username
   steam            : # Username
   telegram         : # URL
   tumblr           : # Username
-  twitter          : # Username for X / Twitter
+  twitter          : "aaojha"
   vine             : # Username
   weibo            : # Username
   wikipedia        : # Username

_pages/cv.md

@@ -1,6 +1,6 @@
 ---
 layout: archive
-title: "CV"
+title: ""
 permalink: /cv/
 author_profile: true
 redirect_from:
@@ -9,37 +9,117 @@ redirect_from:
 
 {% include base_path %}
 
+Curriculum vitae - Anupam Anand Ojha
+======
+
 Education
 ======
-* Ph.D in Version Control Theory, GitHub University, 2018 (expected)
-* M.S. in Jekyll, GitHub University, 2014
-* B.S. in GitHub, GitHub University, 2012
+* Sept. 2019 - June 2024: Doctor of Philosophy in Chemistry, University of California San Diego
+  * Merck Research Award for Underrepresented Chemists of Color (2024)
+  * Merkin Graduate Fellowship (2023)
+  * Teddy Traylor Award (2023)
+  * Distinguished Graduate Student Fellowship (2022)
+  * Bonnie Reiss Carbon Neutrality Student Fellowship (2021)
+  * Friends of the International Center Fellowship (2021)
+
+* Aug. 2012 – June 2017: BS-MS, IISER Thiruvananthapuram
+  * Innovation in Science Pursuit for Inspired Research (INSPIRE) Fellowship (2012-2017)
+  * Swiss Government Excellence Scholarship (2017)
+
+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
 
-Work experience
+Industry Work Experience
 ======
-* Spring 2024: Academic Pages Collaborator
-  * Github University
-  * Duties includes: Updates and improvements to template
-  * Supervisor: The Users
+* June 2024 - September 2024: Multiscale Modeling Scientist Intern, Genentech, Inc., San Francisco, CA, USA
+  * Perform multi-scale molecular dynamics simulations for protein-protein and protein-ligand interactions, large and conformational transitions.
+  * Build computational workflow to accelerate MD simulations using enhanced and adaptive sampling techniques.
 
-* Fall 2015: Research Assistant
-  * Github University
-  * Duties included: Merging pull requests
-  * Supervisor: Professor Hub
+* June 2023 - August 2023: Computer-Aided Drug Design Intern, Janssen Pharmaceutical Companies of Johnson and Johnson, La Jolla, CA, USA
+    * 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.
+
+* June 2022 - September 2022: Research and Early Development Intern, Genentech, Inc., San Francisco, CA, USA
+    * 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 
+======
+* April 2024 - June 2024: Merkin Graduate Fellow, Institute of Physics, University of Freiburg, Freiburg im Breisgau, Germany
+  * Multiscale milestoning simulation approach with the dissipation-corrected targeted MD to estimate drug-target residence times for JAK-inhibitor complexes.
+
+* January 2024 - March 2024: Visiting Researcher, Center for Computational Biology, Flatiron Institute, NY, USA
+  * 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.
+
+* November 2019 - June 2024: Graduate Research Assistant, Department of Chemistry and Biochemistry, UC San Diego, San Diego, CA, USA
+  * 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.
 
-* Summer 2015: Research Assistant
-  * Github University
-  * Duties included: Tagging issues
-  * Supervisor: Professor Git
-
-Skills
+* September 2018 - July 2019: Research Assistant, Centre for Nano and Material Science, Jain University, Bangalore, KA, India
+  * 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.
+
+* August 2017 - August 2018: Research Assistant, Department of Chemistry, ETH Zürich, Zürich, Switzerland
+  * 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.
+
+* August 2016 - April 2017: Master’s Research Project, Department of Chemistry, IISER Thiruvananthapuram, KL, India
+  * 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.
+
+* May 2016 - July 2016: Summer Research Intern, Center for Multidimensional Carbon Materials, Institute for Basic Science, Ulsan, South Korea
+  * 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.
+
+* May 2015 - July 2015: Summer Research Intern, Department of Chemistry, IIT Kharagpur, WB, India
+  * 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.
+
+* May 2014 - July 2014: Summer Research Intern, Department of Chemistry, IACS, Kolkata, WB, India
+  * 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.
+
+* May 2013 - July 2013: Summer Research Intern, Department of Chemistry, IACS, Kolkata, WB, India
+  * Employed quantum mechanical calculations in the Gaussian software to quantify interactions of cyclooctatetraene and related molecules on different noble metal surfaces.
+
+Fellowships and Awards
 ======
-* Skill 1
-* Skill 2
-  * Sub-skill 2.1
-  * Sub-skill 2.2
-  * Sub-skill 2.3
-* Skill 3
+* Merck Research Award for Underrepresented Chemists of Color (2024): This award recognizes significant contributions to chemical 
+  sciences and commitment to diversity in the field.
+* 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.
+* Teddy Traylor Award, UC San Diego (2023): $3000 fellowship recognizing outstanding research excellence and financial support to 
+  attend scholarly conferences and meetings.
+* Distinguished Graduate Student Fellowship (2022): $17,000 fellowship acknowledging exceptional research, providing comprehensive 
+  financial support for university fees and a research travel grant.
+* 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.
+* 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.
+* 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.
+* Swiss Government Excellence Scholarship (2017): $26,317 fellowship from Govt. of Switzerland for outstanding researchers to conduct 
+  one-year research at ETH Zurich.
+* Innovation in Science Pursuit for Inspired Research (INSPIRE) Fellowship (2012-2017): $5000 fellowship from Govt. of India for 
+  outstanding undergraduate students for five years.
 
 Publications
 ======
@@ -59,6 +139,11 @@ Teaching
     {% include archive-single-cv.html %}
   {% endfor %}</ul>
 
-Service and leadership
+Positions of Responsibilities
 ======
-* Currently signed in to 43 different slack teams
+* November 2022 – Present: Reviewer for the Journal of Biomolecular Structure and Dynamics.
+* 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.
+* 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.
+* 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.
+* January 2023 - April 2023: UC San Diego EXperiential Projects for Accelerated Networking and Development (EXPAND) mentor for underrepresented undergraduate students to work closely towards a research project.
+* 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.

_portfolio/portfolio_1.md

@@ -0,0 +1,5 @@
+---
+title: "Anupam Anand Ojha and the Amaro Lab"
+excerpt: "<br/><img src='/images/p1.png'>"
+collection: portfolio
+---

_portfolio/portfolio_2.md

@@ -0,0 +1,5 @@
+---
+title: "Merck Research Award for Underrepresented Chemists of Color"
+excerpt: "<br/><img src='/images/p2.png'>"
+collection: portfolio
+---

_portfolio/portfolio_3.md

@@ -0,0 +1,5 @@
+---
+title: "Bouchet Graduate Honor Society: Honorable Mention"
+excerpt: "<br/><img src='/images/p3.png'>"
+collection: portfolio
+---

_portfolio/portfolio_4.md

@@ -0,0 +1,5 @@
+---
+title: "EXPAND Mentor and Carbon Neutrality Initiative Poster Winner"
+excerpt: "<br/><img src='/images/p4.png'>"
+collection: portfolio
+---

_portfolio/portfolio_5.md

@@ -0,0 +1,5 @@
+---
+title: "Molecular Sciences Software Institute Fellow"
+excerpt: "<br/><img src='/images/p5.png'>"
+collection: portfolio
+---

_portfolio/portfolio_6.md

@@ -0,0 +1,5 @@
+---
+title: "Teddy Traylor Awardee"
+excerpt: "<br/><img src='/images/p6.png'>"
+collection: portfolio
+---

_portfolio/portfolio_7.md

@@ -0,0 +1,5 @@
+---
+title: "Freinds of the International Center Fellow and Distinguished Graduate Fellow"
+excerpt: "<br/><img src='/images/p7.png'>"
+collection: portfolio
+---