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Summary

Post doctoral fellow skilled in molecular dynamics, modeling, methods development, and computer-aided drug design. Experienced in collaborative industry settings, with multiple internships in discovery chemistry and modeling teams.

Education

🎓 Doctor of Philosophy, Biophysics, University of Rochester , 2018 - 2024

🎓 Master of Science, Biophysics, University of Rochester, 2018 - 2021

🎓 Master of Science, Physics, NIT Calicut, 2016 - 2018

🎓 Bachelor of Science, Physics, St.Stephen's College, University of Delhi, 2013 - 2016

Research Experience

Post Doctoral Fellow

🏢 University of Maryland Baltimore, MacKerell Lab, Baltimore, MD

📆 July 2024 - Present

  • Developed ensemble learning and deep learning models to predict small molecule membrane permeability using physics-based SILCS continuum models with fragment-based 3D mapping of membranes of varying complexity. Feature engineered multiple novel molecular descriptors and assessed their effects on the explainability of models1

  • Lead optimization and High Throughput Virtual Screening of SCP2 inhibitors: Using Site Identification by Ligand Competitive Saturation (SILCS) platform, I led the fragment-based computational campaign to expand chemical modifications, corresponding SAR analysis on targets and off-targets with experimental collaboration2

  • In-silico designing of photoaffinity probes for target characterization and identification for the SCP2 campaign

  • Developing an in silico renal proximal tubule model for ADMET prediction with SILCS whole cell simulation

Graduate Research Student

🏢 University of Rochester Medical Center, Grossfield Lab Rochester, NY

📆 June 2019 - April 2024

  • Developed a computational method to estimate the free energy landscape of phase separation in the lipid bilayers from molecular dynamics (MD) simulations using enhanced sampling protocols3 🔸 Analyzed > 100 TB simulation data 🔸 Unsupervised Learning 🔸 Coarse Grained MD 🔸 Weighted Ensemble 🔸 GROMACS

  • Studied the MD finite-box size effects in constructing free energy landscapes of phase separating lipid bilayers4

  • Developed analysis schemes using statistical mechanics to track and visualize ultrafast dynamics of Rhodopsin upon light activation to interpret the XFEL experiments 🔸 Analyzed > 10000 short All-Atom simulations 🔸 NAMD 🔸 OpenMM 🔸 Cross-functional collaboration 🔸 Membrane-GPCR modeling 🔸 Python

Discovery Chemistry Co-op

🏢 Moderna, Computational Sciences Cambridge, MA - Part Time

📆 Jun 2023 - Oct 2023

  • Studied the role of ionizable lipids in lipid nanoparticles (LNPs) and their preferential interactions with RNA with NAMD3 All-Atom Molecular Dynamics simulations in AWS5 🔸 RNA-bilayer Modeling 🔸 Python suite for end-to-end large-scale data analysis

  • Generalized and automated in-house protocol for customized in-silico lipid bilayer model generation

Molecular Engineering and Modeling Co-op

🏢 Moderna, Computational Sciences Cambridge, MA - Full Time

📆 January 2022 - June 2022

  • Studied RNA - small molecule interaction via docking & Molecular Dynamics. Proposed and implemented a python analysis suite for initial validation of binding pocket interactions and ligand conformational dynamics

  • Benchmarked different alchemical and geometrical routes for RNA-small molecule binding free energy calculations. Implemented a test pipeline molecules that can be extended for an extensive ligand library screening

  • Studied RNA - lipid bilayer interactions with NAMD All-Atom Molecular Dynamics simulations

  • Proposed and initiated an internal pilot project that involved cross-functional teams 🔸 Schrödinger Glide, Maestero 🔸 BFEE2 🔸 AMBER Antechamber, GAFF2 🔸 Bitbucket 🔸 JupyterLab 🔸 AWS

Summer Research Fellow

🏢 JNCASR, Theoretical Sciences Unit Bangalore, India

📆 April 2018 - June 2018

  • Studied the sensitivity of population dynamics of bacteria towards the nutrient environment using modeling and numerical simulation. Modeled quorum sensing and chemotaxis behaviors and emulated racing conditions

Summer Research Fellow

🏢 JNCASR, Theoretical Sciences Unit Bangalore, India

📆 May 2017 - July 2017

  • Conducted metabolic network reconstructions and flux balance analyses on constrained-based in silico yeast models. Studied the effect of various metabolites on the yeast growth rates upon network perturbations

  • Integrated transcriptomic data into in silico models of Plasmodium falciparum to emulate multiple malaria variants in southeast Asia to understand the rise of drug resistance using cross-functional efforts

Other Relevant Experience

  • Software Contributions (2024 - Present) SILCS : Created protocols for handling complex user-input custom membranes for SILCS-Membrane tool that elimiated early runtime termination. Bug fixes, and beta-testing.

  • URBEST Trainee (2021 - 2024) University of Rochester initiative to Broaden Experiences in Scientific Training for early career scientists. Training on leadership and management skills for scientists via coursework, panel discussions, informational interviews, career stories, mentoring, and other personalized programs

  • UR2 Mentorship Program (2020 - 2022): A program run by graduate students to mentor and train first-generation undergraduates and those from less privileged backgrounds on tools and resources for a research career

  • Teaching Assistant, BPH509 - Molecular Biophysics (2020) Instructed students in theoretical, experimental, and computational methods to study macromolecules. Topics include statistical mechanics, optical melting experiments, dynamic programming algorithms, molecular dynamics, protein folding, and isothermal titration calorimetry

  • Open-source Contributions (2020 - 2023) LOOS : A lightweight object-oriented structure analysis library for MD simulations. WESTPA : The Weighted Ensemble Simulation Toolkit with Parallelization and Analysis. FLOPSS 2.0 : pipeline to compute Free energy Landscape Of Phase Separating Systems - to be released soon (Early version)

Relevant Publications

  1. Elizabeth S. Liedhegner, Caitlin Bauer, Nathalia Rocha Lainetti, Ashlin Poruthoor, Alexander MacKerell, Christopher Cunningham, Cecilia Hillard. Sterol Carrier Protein 2 (SCP-2), trafficker of endocannabinoids, interacts with the phytocannabinoids, cannabidiol (CBD) and cannabigerol (CBG). GRC Cannabinoid Function in the CNS, New Hampshire, August 2025 [Poster]

  2. Ashlin Poruhtoor, Alexander MacKerell Jr. Lessons learned from predicting drug permeability by bridging physics and machine learning using the SILCS methodology. ACS Fall Meeting 2025, Washington, D.C. [Poster]

  3. Ashlin Poruthoor, Akshara Sharma, Alan Grossfield. (2023). Understanding the Free Energy Landscape of Phase Separation in Lipid Bilayers using Molecular Dynamics. Biophysical Journal. 122. 10.1016/j.bpj.2023.09.012.

  4. Ashlin Poruthoor, Jack Stallone, Megan Miaro, Akshara Sharma, Alan Grossfield. (2024). System size effects on the free energy landscapes from molecular dynamics of phase-separating bilayers. J. Chem. Phys. 161, 145101

  5. Ashlin Poruthoor, Sepehr Dehghanighahnaviyeh, Semiha Bali, Mehtap Isik, Sreyoshi Sur. (2024). Interactions between ionizable amino lipids and a short RNA hairpin: Insights from molecular dynamics simulations for lipid nanoparticle optimization. Biophysical Journal. 123. 97a. 10.1016/j.bpj.2023.11.699. [Poster]