People – Arup K. Chakraborty Group

ARUP K. CHAKRABORTY, PhD

John M. Deutch Institute Professor; Professor of Chemical Engineering, Physics & Chemistry, MIT

Core Faculty Member and former Founding Director, Institute for Medical Engineering and Science (IMES), MIT

Founding Steering Committee Member, Ragon Institute of MGH, MIT and Harvard

About

Arup K. Chakraborty is one of the 12 Institute Professors at MIT, the highest rank awarded to a MIT faculty member, and holds the John M. Deutch Institute Professorship. He is also a Professor of Chemical Engineering, Physics, and Chemistry at MIT. He served as the founding Director of MIT’s Institute for Medical Engineering and Science, and he is a founding member of the Ragon Institute of MIT, MGH, and Harvard. For over two decades now, Chakraborty’s work has largely focused on bringing together approaches from statistical physics, immunology, and virology. His interests span T cell signaling, development of the T cell repertoire, and a mechanistic understanding of virus evolution, antibody responses, and vaccine design. Since 2016, Chakraborty has also been interested in the role of phase separation in gene regulation. Chakraborty is one of only 26 individuals who are members of all three branches of the US National Academies – National Academy of Sciences, National Academy of Medicine, and National Academy of Engineering. He is also a Fellow of the American Academy of Arts & Sciences, and has received many other honors including the NIH Director’s Pioneer Award, the E. O. Lawrence Medal (DOE), a Guggenheim Fellowship, the Max Delbruck Prize in Biological Physics from the American Physical Society, the Colburn, Professional Progress, and Prausnitz Institute Lectureship from the AIChE, and three honorary doctorates. Chakraborty has received 7 awards for his classroom teaching and he is a co-author of the book “Viruses, Pandemics, & Immunity”. Chakraborty is a member of the Board of Governors of the Wellcome Trust, and serves as a consultant for biotechnology companies.

Meet the Team

Postdoctoral Associates

	Andriy Goychuk Postdoctoral Associate I am interested in the self-organized dynamics of living systems and their noisy response to external chemical and mechanical stimuli. To study these systems, I apply the methods and tools of theoretical biophysics, statistical mechanics, stochastic dynamics, and finite element simulations. Currently, I am working on the conformational dynamics of active polymers, and on the co-phase separation dynamics of proteins in the presence of energy-dissipating processes. Google Scholar \| LinkedIn \| GitHub \| ORCID
	Sam Melton Physics of Living Systems Fellow I am interested in information theory, evolvability, and learning. I did a PhD in Applied Mathematics at Harvard in Sharad Ramanathan's group working on inference and modeling gene regulatory networks in developmental biology. Now, I work on mathematical descriptions of T cell repertoires and their responses to pathogens.
	Saeed Mahdisoltani Postdoctoral Associate I am interested in studying adaptive immunity and affinity maturation within germinal centers. Using tools from nonequilibrium statistical physics, I currently work on modeling frameworks to optimize B cells’ response against highly mutable pathogens like HIV. Prior to MIT, I earned my DPhil in Theoretical Physics from the University of Oxford. Google Scholar \| LinkedIn
	Federica Ferretti Postdoctoral Associate I am a theoretical physicist interested in statistical modelling for biological systems. Prior to MIT, I earned my PhD from the University of Rome La Sapienza. My current work focuses on affinity maturation and optimization problems related to aspects of vaccinology. I develop and study mathematical models to better understand how the statistical features of the immune repertoire and of antigen-receptor affinity landscape can be manipulated to control the diversity and specificity of the antibody response. Google Scholar
	Yannick Omar (Fall 2023) Postdoctoral Associate I am currently working on gaining a deeper understanding of LAT condensates and their importance for T-cell activation. More broadly, my research interests include continuum mechanics, numerical methods for PDEs, and the physics of lipid membranes. Prior to joining MIT, I received my PhD in Chemical Engineering from UC Berkeley, where I worked on the electromechanics of lipid membranes. Google Scholar

Research Associates

	Leerang Yang Research Associate / PhD. Candidate I received BS in Chemical Engineering from Columbia University in 2016 and joined the Chakraborty Group in 2018. I am interested in understanding the complex dynamics of antibody response to viruses and vaccines through computational modeling. I apply this mechanistic understanding to help design more potent and variant-proof vaccination strategies. Google Scholar \| LinkedIn
	Pradeep Natarajan Research Associate / PhD. Candidate Before joining the Chakraborty Lab at MIT in 2018, I obtained a B.Tech./M.Tech. Dual Degree in Chemical Engineering at the Indian Institute of Technology Madras, India. Transcriptional proteins form phase-separated condensates at specific locations on the genome to regulate transcription, and RNA species can regulate these condensates. I use phase-field simulations and analytical theory to study how the interplay between multicomponent RNA-protein phase separation, genome organization, and irreversible reactions such as transcription lead to emergent transcriptional regulation. Insights from my research have broader implications in understanding how different cell types emerge during embryonic development and how cells turn cancerous. In addition to my research, I have also taken care of computing resources in the group and like learning about better software engineering practices, high-performance computing, and data science. Google Scholar \| LinkedIn \| Twitter
	Rose Yin Research Associate / PhD. Candidate I am a 4th year PhD student in Chemical Engineering, having gone straight from undergrad at Cornell University with a B.S. in Chemical Engineering. My main research focus is in understanding T cell immunology. My most recent project involved developing computational models to understand how collective T cell behavior can help explain why persistent infections lead to autoimmunity.
	Eric Wang Research Associate / PhD. Candidate I am a PhD student in the HST program, and I previously got my MPhil in chemistry from the University of Cambridge and my BS in bioengineering from the University of Maryland. My research focuses on using computational methods to design vaccines against mutable pathogens such as coronaviruses and HIV. Google Scholar
	Deepti Kannan Research Associate / PhD. Candidate I am a Physics PhD student interested in applying tools from statistical physics to study biophysical mechanisms underlying transcriptional control and the immune response. My latest project uses polymer simulations to investigate how active processes such as gene transcription can affect genome organization. Google Scholar
	Melbourne Tang Research Associate / MIT Undergraduate