CV

• Topics: Multiscale simulations of protein conformational changes associated with biomembranes and misfolding

• Techniques: Molecular dynamics (MD) and Monte Carlo (MC) simulations, Coarse-grained and Structure-based modeling, Enhanced sampling methods, and Machine learning

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

• 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

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

• Working on capturing the large scale conformational changes in the viral proteins while accounting for the membrane fusion. 

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 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 major role was to rank the voice of customer surveys and identify the key drivers for login issues. I also worked on a behavioral biometric project that included the ground truth model development to assess the model for keystrokes and mouse moment data. 

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

• During my brief time at Accenture, I was trained in Tableau (a data visualization and business intelligence tool), machine learning, and automation.

1. 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. 

2. 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. 

3. 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.

4. 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)

5. A. Kulshrestha, Ph.D. Thesis, (2023) "Computational study of membrane driven secondary structural changes in proteins" 

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

Coarse-grained model to capture the conformational changes in proteins (Jul 2019 --- Dec 2019)

• MD simulations of a large system size often require coarse-graining to reduce the degrees of freedom and be able to simulate long time scale trajectories. Coarse graining of protein, however, is challenging as it destabilizes the protein and often requires an additional native bias to its structure. Elastic network based native biasing, as done in Martini 2.0 models, makes it challenging to study conformational changes. In my work, I utilized the double well potential idea of structure based models for biasing two metastable states of a protein that allows us to simulate the conformational change between two basins.

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 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 

• 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)

• 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)

• 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)

• 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. Sabina Khanam, Department of Chemical Engineering, Indian Institute of Technology Roorkee, Email id: sabina.khanam@ch.iitr.ac.in, Contact: +91-1332-285157