Principal Investigator

Srirupa Chakraborty

Assistant Professor

Department of Chemical Engineering

Department of Chemistry and Chemical Biology

Northeastern University

Srirupa Chakraborty is an Assistant Professor in the College of Engineering of Northeastern University, with a joint appointment in the College of Science. Her research interest is at the interface  of biophysics, computer science and chemical engineering. She focuses on solving critical biomedical questions through first-principles as well as data-driven approaches. Srirupa earned a B.S. in Physics from Presidency College, University of Calcutta (India), followed by an M.S. in Physics from the Indian Institute of Technology – Guwahati (India) and a Ph.D. in Biophysics from the State University of New York at Buffalo. Prior to joining Northeastern, she was a postdoctoral researcher at Los Alamos National Laboratory, NM. Her current CV can be found here

Doctoral Students

 Natesan Mani

Hello world, I am Natesan. I joined the SimBioSys lab in Spring 2022 and I’m in my second year of PhD. I did my Masters at the University of Houston where my research interest was in developing kinetic models to describe heterogenous catalytic reactions. My current interests lie in protein-protein docking and in modeling of the dynamics of biological macromolecules, including glycoproteins. Outside of the lab, I like exploring different cities and states in the US, hiking and cooking.

 Jason Kantorow

Hey! I’m Jason, a first year PhD student in the Chemical Engineering department at Northeastern. I officially joined the SimBioSys lab in January of 2023 where my interests land in the fields of biomolecular and pharmaceutical engineering; specifically, my project focuses on utilizing machine learning and high performance computational methods to predict glycoprotein interactions for use in drug delivery systems. I received my B.S. in Chemical Engineering from the University of Florida in May of 2022 where I previously worked on bioinformatic analysis of regenerative retinal neurons under the supervision of Dr. John Ash. When I’m not in the lab, my main hobbies include playing guitar and video games with my friends and I love a good nature walk or hike!

 Emma Stevens

Hi! I'm Emma, a first year PhD student in the Department of Chemistry and Chemical Biology here at Northeastern. I received my B.S. in Chemistry with a concentration in Biochemistry and a minor in Data Analytics from Emmanuel College in May of 2022. My undergraduate research, in the Dr. Allen Price Lab, focused on developing a machine learning model for particle recognition in single-molecule biophysical video data. I joined the SimBioSys lab in January of 2023 and am excited to apply my background in machine learning to the development of an explainable artificial intelligence model for predicting viral antibody-antigen binding interactions. This model will allow for the identification of specific residues that are important for binding and lend itself to novel protein engineering and vaccine design. Outside of research, I enjoy baking, taking walks around the city, and spending time with friends.

Masters Students

 Simran Pandey

Hi! I am Simran. I am a first year ChemE master’s student at Northeastern University. Having an interest in computational modeling led me to join the SimBioSys Lab in the spring of 2023. Currently, I am trying to develop atomistic and coarse-grained models of mucin and perform classical molecular dynamics simulations for studying interactions within the intestinal mucus barrier. In my spare time, I like to cook, sing, and practice yoga.

Simran is also a part of the Francesco Hung lab, co-advised by both the PIs.

Undergraduate Students

(Click on our names to know more about us)

Jiajia Fu

Greetings! I am Jiajia (Jia^2) Fu, a first year Bioengineering major at Northeastern University. My research focuses are molecular modeling and protein engineering for synthetic biology and environmental applications. I joined SymBioSys in Fall 2022 and am working on predicting lattice-model protein folding through quantum annealing computing. In my free time, I love nature photography, hiking and binging Star Trek. 

Nidhi Jadhav

Hi! I’m Nidhi, a first year studying Computer Science + Business Administration and minoring in Math! I’m incredibly passionate about utilizing exponential technologies to make an impact. At SimBioSys Lab, I’m working on an open-source pipeline to model viral glycan shield and their corresponding vulnerabilities, to make vaccine development more efficient.

Ishaan Subramanian

Hello! I’m Ishaan, currently a first year bioengineering student at Northeastern. I joined the lab in October 2022. My research focuses on developing new computational models to explain and predict antigen-antibody interactions. Right now, I am working on extracting specific amino acid interactions from protein structures we’ve collected. In my free time, I like to work out, play piano, and watch Formula 1 racing. 

Maxwell He

Hi! I’m Max, a third-year studying Computer Science and Biology at Northeastern. I am excited to apply machine learning and molecular dynamics (MD) simulation techniques to understand the complexities of antibody-antigen binding. I joined SimBioSys in the Spring of 2024 and am working on training viral docking models with decoy and unbound interaction states. Outside of the lab, I love playing music and taking photos.

Madison Weiss

Hi! My name is Maddie and I’m a second-year Computer Science and Biology major at Northeastern University. With a deep passion for computational biology, I’m thrilled to be joining the SimBioSys team this semester! I'm currently working on a project to enhance the efficiency of immunogen design: creating an open-source framework aimed at characterizing the glycan shield of viruses and identifying associated weaknesses.

Thomas Mourier

Hi! I’m Thomas, a first year undergraduate student at Northeastern pursuing a combined degree in Mechanical Engineering and Bioengineering. I joined the SimBioSys lab in October 2023 and I’m excited to learn more about machine learning and how it can help predict antibody-antigen binding interactions commonly found in viruses. When I’m not in the lab, I enjoy running long distances, Nordic skiing, and working on cars. Go Huskies!

Alexander Zambrowski

Hello! I’m Alex, a second year Chemical Engineering/Bioengineering student at Northeastern University, and I joined SimBioSys in Fall 2023. In the lab, my current research focus is on molecular dynamics modeling, and I’m working on modeling glycoproteins and other macromolecules. In my free time, I enjoy running, learning chess and puzzles, and, when it’s colder, skiing.

Aryan Jain

Hey! My name is Aryan, and I am currently a first-year student studying Data Science and Business Administration at Northeastern. I am excited to work on complex biological problems using a data-driven lens and apply machine learning programs to supplement them. I joined the SimBioSys lab in the fall of 2023 and am working on a program that creates probability matrices of viruses and the effectiveness of antibodies against them, focusing on making the program more accessible. In my free time, I love going out to explore the city, hanging out with friends, dancing, and doing community service.

Hayley Ha

Hi! My name is Hayley, and I am a second-year bioengineering student with a concentration in computational biology and minors in mathematics and data science. I am interested in learning more about computational modeling and data analysis in medical research. The current research I am working on at SimBioSys Lab is homology modeling for glycan shields. Some of my hobbies include reading, listening to music, golfing, and fencing.

Elliot Bangerter

Hi! I’m Elliot, a fourth-year Data Science and Biochemistry major at Northeastern. I joined the lab in January 2024 as part of my senior reserach course, and I will be working on machine learning models for scoring the cell penetrating ability of cell penetrating proteins containing glycans for various types of cells. Outside of the lab, I particularly enjoy running, soccer, and gaming.

High School Students

 Kenny Wong

Hello, I'm Kenny, currently a sophomore in high school. My overall research interest is in the interface of physics and biology. I am currently curating data for a machine learning project which predicts the properties of antibody-antigen interactions. Outside of school, hobbies include running on the cross country team, cooking, and watching T.V shows (especially South Park).  

Lab Alumni

 Raghavendran Suresh (MS, Chemical Engineering) : Currently PhD student at SUNY Buffalo

Sriram Velmurugan (MS, Biotechnology)

Ria Jansun (BS, Bioengineering and Biochemistry)

This could be you!

 Join the SimBioSys Lab!

Excited to look at the jigglings and wigglings of life through the virtual microscope? Curious about how structure defines function? Interested to be a part of interdisciplinary research, with biocomputing as your tool of choice? Come join us. Or stop by at the dungeons of Mugar to know more. 

The SymBioSys Lab supports and celebrates

Land Acknowledgement: We acknowledge the territory on which Northeastern University stands, which is the land of The Wampanoag and The Massachusett People. While visiting campus, please honor the continued efforts of the Native and Indigenous community leaders who work to preserve the history and culture of the tribes which make up Eastern Massachusetts and the surrounding region. Today, Boston is still home to many indigenous peoples, including the Mashpee Wampanoag and Wampanoag Tribe of Gay Head (Aquinnah), the Mi’kmaq and many more in our region.