Rakesh Krishnan
Resume
Research Experience
University of Pennsylvania – Postdoctoral Fellow Aug 2023– Aug 2025
Supervisor: Prof. Cesar de la Fuente
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Studied antimicrobial resistance (AMR) and antimicrobial peptides (AMP) using various methods like simulations, bioinformatics, and data mining.
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Performed simulation on lipid bilayer and AMP system to study cell penetration viability and activity of AMPs against multiple bacterial strains.
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Performed enhanced sampling simulations of the lipid-peptide system to study the free energy of various lipid bilayers.
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Mined the intrinsically disordered proteome to find active AMPs in different bacterial strains.
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Worked on various collaborative projects on AMR, tumor immunity, and immunomodular activities.
IIT Bombay – Research Scholar, Associate and Postdoctoral Fellow Jan 2017–Jul 2023
Supervisor: Prof. Ranjith Padinhateeri
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Studied the role of non-specific interaction in the role of phase-separation of intrinsically disordered proteins.
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Simulated the phase-separation of protein and DNA-like polymer to understand the effect of phase-separation in the DNA-repair mechanism.
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Modeled and simulated the HP1 protein to understand the role of few interacting regions in heterochromatin formation.
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Collaborated with the experimental group to study the effect of protein interaction in the folding of IDP, alpha-synuclein.
Education
Ph.D., Computational Biophysics
Indian Institute of Technology Bombay, Mumbai, India
Jan 2017 – Apr 2023
Supervisor: Prof. Ranjith Padinhateeri
B.Tech., Bioinformatics
SASTRA University, Tanjore, India
Jul 2012 – May 2016
Teaching Assistant in Courses:
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Mathematical Biology
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Modeling Biological Systems and Processes
NPTEL Teaching Assistant:
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Introductory Mathematical Methods for Biologists (2020).
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Introductory Mathematical Methods for Biologists (2021)
Teaching Experience
Conferences/Poster/Talks
• Invited Talk at National Institute of Technology, AP, India, May 2026
• Invited Talk at CESGA, Spain (Virtual), Oct 2025
• Invited Talk at Biocogniz Academy, India (Virtual), Dec 2024
• Invited Talk at University of Pennsylvania, USA, Mar 2023
• IDPosters22 by IDP-Seminars, Nov 2022
• EMBO Workshop on Physics of cells: Physcell2022, Ein Gedi, Sep 2022
• International School on Biological Physics of Cells, Weizmann Institute of Science, Sep 2022
• 66th Annual Biophysical Society Annual Meeting, Mar 2022
• Multiscale simulation & math. modeling of complex biological systems, JNU India, Sep 2021
• CompFlu 2019, IISER Bhopal, Nov 2019
• Conference on Mathematical Biology, IMSC Chennai, Nov 2018
• National symposium on Frontiers in Modern Biology, IISER Kolkata, Jan 2018
Skills & Expertise
Programming languages: C, C++
Scripting languages: Python, shell script, tcl
Softwares simulations: LAMMPS, NAMD, GROMACS
Visualization Softwares: VMD, Pymol, Ovito
Operating Systems: Linux (Ubuntu), Windows, MacOS