Avijeet Kulshrestha

ANRF National Postdoctoral Fellow
National Centre for Biological Sciences
Tata Institute of Fundamental Research

I am a chemical engineer by training and received my Ph.D. from the Indian Institute of Science (IISc), Bangalore, where my doctoral research focused on biophysical modeling and simulation. During my Ph.D., I worked with Prof. K. G. Ayappa, Prof. Sudeep Punnathanam, and Prof. Rahul Roy, followed by postdoctoral research with Prof. Jeetain Mittal at Texas A&M University. In addition to my academic work, I have industry experience as a data analyst and data scientist at Accenture and Wells Fargo, respectively, which has shaped my interest in data-driven modeling.

Full CV can be found here

Research interest

Topics: Multiscale simulations of protein conformational changes associated with biomembranes and aggregation
Techniques: Molecular dynamics (MD) and Monte Carlo (MC) simulations, Coarse-grained and Structure-based modeling, Enhanced sampling methods, and Machine learning

Education

Ph.D. in Chemical Engineering (Jan 2018 - Oct 2023)

Indian Institute of Science Bangalore, CGPA: 8.0/10.0 (Advisors: K Ganapathy Ayappa and Sudeep N Punnathanam)

M.Tech. in Chemical Engineering (Jul 2015 - Jun 2017)

Indian Institute of Technology Roorkee, CGPA: 9.23/10.0 (Advisor: Sabina Khanam)

B.Tech. in Chemical Engineering (Jul 2011 - Jun 2015)

Dr. A.P.J. Abdul Kalam Technical University, Lucknow, CGPA: 7.87/10.0

Skills

Tools and Languages: Python, C, GitHub, LaTeX, Microsoft Office, Bash Scripting, Gromacs, Autodock, Plumed, GAMS
Quantitative Research: Statistics, Optimization, Molecular dynamics and Monte Carlo simulations, Kinetic modeling, Machine and Deep Learning
Languages: Hindi, English

Work experience

NPDF - Postdoctoral Fellow at NCBS, Bangalore, India (November 2025 --- Present)

Developing CG models to capture the viral fusion protein driven membrane fusion.

TIFR - Postdoctoral Fellow at NCBS, Bangalore, India (May 2025 --- October 2025)

I worked on capturing the large-scale conformational changes in the viral proteins using coarse-grained structure-based models.

Postdoctoral Researcher at Texas A&M University, USA (February 2024 --- April 2025)

Amyloid fibrils, which are associated with aging, are formed through various factors and contribute to the development of neurodegenerative diseases and cancer. My research focuses on investigating the fibrillation mechanism, the implications of conformational heterogeneity, capturing conformational changes, and understanding the thermodynamic and kinetic behavior using advanced sampling methods and specialized (non-transferable) structure-based models.

Program Associate at Wells Fargo, Bengaluru, India (Jul 2023 --- Dec 2023)

I was a part of the identity management and digital customer experience team. My primary role was to analyze the voice of customer surveys and identify the key drivers of login issues. I also worked on a behavioral biometric project that involved developing the ground truth model to assess the model's accuracy for keystroke and mouse movement data.

Business and Integration Architect Analyst at Accenture, Bengaluru, India (Jul 2017 --- Dec 2017)

During my brief tenure at Accenture, I received training in Tableau (a data visualization and business intelligence tool), machine learning, and automation.

Publications

A. Kulshrestha, S. N. Punnathanam, K. G. Ayappa, "Finite temperature string method with umbrella sampling using path collective variables: Application to secondary structure change in a protein” Soft Matter (2022), 18 (39), 7593-7603.
A. Kulshrestha, S. Maurya, T. Gupta, R. Roy, S. N. Punnathanam, K. G. Ayappa, "Conformational flexibility is a key determinant for the lytic activity of the pore-forming protein, Cytolysin A” J. Phys. Chem. B (2022), 127 (1), 69-84.
A. Kulshrestha, S. N. Punnathanam, K. G. Ayappa, "Cholesterol catalyzes unfolding in membrane inserted motifs of the pore forming protein cytolysin A” Biophysical Journal (2023), 122, 4068-4081.
A. Kulshrestha, Ph.D. Thesis, (2023) "Computational study of membrane driven secondary structural changes in proteins"
A. Kulshrestha, T. M. Phan, A. Rizuan, P. Mohanty, J. Mittal, "Multiscale Simulations Elucidate the Mechanism of Polyglutamine Aggregation and the Role of Flanking Domains in Fibril Polymorphism" J. Phys. Chem. B (2025), 129 (43), 11205-11219.
A. Kulshrestha, J. Mittal, "The shrinking nucleus: How polyglutamine length dictates nucleus size and stability" (under preparation)
A. Kulshrestha, A. Banerjee1, S. Lall, S. Gosavi, "Transmembrane domain acts as a kinetic regulator of SARS-CoV-2 spike conformational transition” (under preparation)
L. P. Jayanthi, A. Kulshrestha, S. Gosavi, "Kinetic accessibility influences the folding landscape of switchable proteins" (under preparation)
B. M. Nishant, A. Kulshrestha, S. N. Punnathanam, K. G. Ayappa, "Preferential binding of cardiolipin with N-terminus of CM15 influences the membrane insertion of the antimicrobial peptide" (under preparation)
A. Sannigrahi, D. Chakraborty, R. Moral, V. H. Rai, A. Kulshreshtha, M. V. Challil, K. G. Ayappa, S. Paul, R. Roy, "A lipid-based chaperone mechanism drives membrane pore formation by Cytolysin A" (under preparation)

Thesis projects

Ph.D. Thesis: Computational study of membrane driven secondary structural changes in proteins (Jan 2019 --- Oct 2023)

Biological processes involve protein conformational changes, some of which are mediated through cell membrane interactions, which are necessary to support essential life functions. There is an innate value in understanding the mechanism of these processes to develop therapeutic strategies in cases of malfunctioning or misfolding of proteins. Molecular dynamics (MD) simulation is an important tool that aids to probe the underlying mechanisms of a few microsecond-long processes; however, protein conformational changes occur at a much longer time scale. To overcome this limitation, I studied and developed a string method based approach to capture the transition state and the free energy associated with it. Subsequently, I applied the method to capture membrane driven conformational changes in a pore-forming toxin (PFT) and an antimicrobial peptide (AMP). In the PFT work, the study confirmed the experimental observation of cholesterol enhanced toxin activity by reporting a reduced free energy barrier with cholesterol. With the knowledge of the mechanism, I further studied the effect of point mutations on the PFT activity and showed that loss of flexibility correlates well with the loss of activity. In my AMP work, I studied the membrane insertion mechanism and the membrane components essential for the activity.

M.Tech. Thesis: Optimization of hydrogen distribution in refinery considering piping cost (Jul 2016 --- Jun 2017)

In my master's thesis, I worked on optimizing hydrogen distribution within a refinery using linear programming (LP) and nonlinear programming (NLP) constraint models. I used GAMS software to optimize (reduce) the overall cost and the external hydrogen demand.

Other projects

Physics-informed and data-driven identification of governing equations (Mar 2023 --- Jun 2023)

Often, it is difficult to identify if the ML based models have poor accuracy due to poor estimation of parameters or the model equations itself. Additionally, the developed models with good accuracy lack interpretation and generalization. It requires sparse techniques to find the parsimonious models; however, including the physical constraint helps in finding physically relevant models. I worked on developing an algorithm to identify the elementary reaction model equations with physical constraints from the given data.

Teaching and responsibilities

Teaching assistantship for chemical reaction engineering and molecular dynamics simulations subjects at IISc Bangalore
Organized a national level 5th biomembranes symposium held at IISc Bangalore 2022
Mass transfer laboratory teaching assistantship at IIT Roorkee

Internships and workshops

Martini3 online workshop (Sep 2021)
Rare Events summer school: Applications, Computation, and Theory at IISc (Jul 2019)
Free Energy Calculations workshop for Chemical and Biological Systems at IIT Kanpur (Mar 2018)
B.Tech. Industrial Internship at United Breweries Limited (Jun 2013 - Jul 2013)
Software development summer Training Program (BRiCS) at IIT Kanpur (Jun 2012 - Jul 2012)

Conference presentations

2026 NCBS Annual talk, Bangalore, India (January 2026)
2024 AIChE Annual Meeting, San Diego, USA (November 2022)
Physics of Life 2023 conference at Harrogate, UK (March 2023)
2022 AIChE Annual online Meeting (November 2022)
5th Biomembranes Symposium at IISc Bangalore (September 2022)
ACS online meeting 2022 (March 2022)
66th Biophysical Society online meeting 2022 (February 2022)
5th Prato online meeting (June 2021)
Statistical mechanics in chemistry and biology (SMCB) online meeting (January 2021)

Achievements and awards

Recipient of ANRF National Postdoctoral Fellowship (NPDF) (Nov 2025 - Oct 2027)
Recipient of K Ananth Swamy Memorial Research Award for the year of 2023 at IISc Bangalore (Sept 2023)
Recipient of MHRD fellowship during Ph.D. (Jan 2018 - Dec 2022)
Recipient of MHRD fellowship during M.Tech. (Jul 2015 - Jun 2017)
All India Rank-575 (96.38 percentile) in Graduate Aptitude Test in Engineering (GATE 2015) in Chemical Engineering (March 2015)

References

Dr. Shachi Gosavi, National Centre for Biological Sciences, Bangalore, India, Email: shachi@ncbs.res.in
Prof. Jeetain Mittal, Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas, Email: jeetain@tamu.edu
Prof. K Ganapathy Ayappa, Department of Chemical Engineering, Indian Institute of Science, Bangalore, Email: ayappa@iisc.ac.in, Contact: +91-80-2293 2769
Prof. Sudeep N Punnathanam, Department of Chemical Engineering, Indian Institute of Science, Bangalore, Email id: sudeep@iisc.ac.in, Contact: +91-80-2293 3109
Prof. Rahul Roy, Center for BioSystem Science and Engineering, Indian Institute of Science, Bangalore, Email id: rahulroy@iisc.ac.in, Contact: +91-80-2293 3109
Prof. Shabina Khanam, Department of Chemical Engineering, Indian Institute of Technology Roorkee, Email id: shabina.khanam@ch.iitr.ac.in, Contact: +91-1332-285157

Personal information

I was born and raised in Agra, Uttar Pradesh, India, and completed my B.Tech. at Dr. A. P. J. Abdul Kalam Technical University, Lucknow, and M.Tech. at IIT Roorkee, both in Chemical Engineering. Outside of research, I enjoy listening to classical music, practicing Hindustani classical vocals, and playing musical instruments. I also value staying active through exercise such as gym workouts, badminton, and swimming.

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