(2au) Design and Control of Biological Assemblies By Leveraging Self-Organization

Summary: My research aims to model and engineer assemblies of biomolecules and cells, with a focus on self-organization by phase transitions, for applications to mechanism discovery, genetic/cellular therapeutics, bio-inspired material design, and synthetic biology.

Motivation: Assemblies are ubiquitous in life, from DNA molecules that make up our genome to cells that constitute our tissues. Self-organization by phase transitions has recently emerged as a key mechanism governing formation of biomolecular assemblies called condensates. Condensates are found in nearly all organisms and implicated in genome regulation, photosynthesis, development, and signaling, amongst other functions. Defects in phase behavior are increasingly found to be associated with a variety of developmental disorders and diseases. Despite their broad relevance to physiology and disease, there exists a big gap in our ability to understand, engineer, and control condensates.

Gap: A key bottleneck is the lack of physicochemical models to describe condensates. They are challenging to study since they (a) Form dynamic multiphase assemblies comprising hundreds of biomolecules with complex compositions and are subject to non-equilibrium regulation (b) Exhibit a wide gamut of physical and material states including examples of emulsions, micelles, gels, and active fluids in the crowded cellular/tissue environment and (c) Intrinsically span multiple scales with feedback mechanisms.

Proposal: I will establish a research program that develops quantitative multiscale frameworks, rooted in theory and computation, to model, design and engineer condensates. To accomplish this, I will embrace an interdisciplinary approach that integrates condensate biology, physics of soft matter, and my chemical engineering expertise in multiphase fluids, transport, and statistical thermodynamics. I will complement our work by building diverse collaborations, consistent with my past track-record.

Impact: Through improved understanding of condensates, we aim to contribute to (A) Rational discovery of genetic and cellular therapies for the expanding catalog of diseases linked to defects in biomolecular phase behavior, (B) Engineering of synthetic organelles to improve efficiency of biological pathways, and (C) Programmable design of biologically-derived and DNA materials for synthetic and clinical applications.

Research Interests:

My lab will model biomolecular assemblies by integrating (a) Theoretical approaches from statistical mechanics, multiphase fluids, and soft matter physics, (b) Simulations and machine-learning aided numerical methods, and (c) Statistical and data-driven models. Our initial research will be along 3 overlapping directions.

Focus 1: Our goal will be to describe how physical properties of condensates emerge from their many interacting constituents. Towards this, we will combine approaches from statistical thermodynamics, transport, and numerical simulation. Specific directions will focus on modeling/controlling dynamics of phase separation, inverse design of biomolecules for engineered condensates, and method development for probing multiphase and complex fluids.

Focus 2: Our goal will be to develop physical models of genome self-organization, a massive polymeric assembly in the crowded nucleus, in health and disease. Models will couple polymer simulations and non-equilibrium theories and be refined/tested with multiplexed genomics data-sets. Initial directions will be on modeling the role of RNA in gene regulation, deciphering interplay of nuclear condensates and genome function, and dissecting the mechanisms of long-range interactions in genome organization.

Focus 3: We will focus on leveraging principles of assembly (discerned in Foci 1-2) to tackle design of biological assemblies and circuits beyond condensates. We will leverage advances in machine-learning, coarse-grained simulations, and statistical mechanical approaches towards this. Our primary directions will be on engineering adaptable assemblies, modeling self-organization in tissues, and method development for inverse design of signaling circuits.

Research Experience:

NSF-Simons Postdoctoral Fellow (Harvard, 09/2020-Now): I am fortunate to lead an independent research program and co-mentor a small team at Harvard. Working closely with Prof. Michael P. Brenner, I am working to develop theories that predict emergent phase behavior in highly multicomponent liquids [1]. This work leverages surprising connections between multiphase thermodynamics and random-matrix theory. While nascent, by expanding to incorporate new theories and numerical methods, this model offers new routes to interrogate complex fluid assemblies (which my lab will explore in F1). Along with experimental collaborations, my second focus is on dissecting condensate assembly on flexible scaffolds like RNA and membranes (in prep). Through combining physical theories, in vitro experiments, and coarse-grained MD/MC simulations, we have begun to uncover the importance of RNA secondary structure and combinatorial interactions in driving composition of multicomponent assemblies. An exciting area for my lab will be expanding this nascent logic for biomolecular assemblies in genomic (F2) and synthetic (F3) contexts and discovering failure modes in disease.

PhD, ChemE (MIT, 2014-2020): I trained with Prof. Arup K. Chakraborty, where I established a new research program in the lab to investigate how phase separation regulates gene expression. To do this, I developed theoretical and computational frameworks based on coacervate chemistry, polymer physics, and statistical physics, in collaboration with experimental colleagues. By iterating model and experiment, we found: 1. Gene expression apparatus condenses to form droplets in living cells [5-6] 2. DNA and protein features facilitate dynamic and spatial control of condensate formation - providing a new model of enhancers - non-coding DNA elements that regulate genes - in health and pathology [3-4] and 3. A new mechanism of gene regulation that arises from coupling of non-equilibrium RNA-synthesis, hindered transport, and feedback on phase behavior [2]. Overall, I contributed to 8 articles, including 4 first/co-first author papers and a patent application with translational potential for drug discovery. Our work was listed as one of the top 10 scientific breakthroughs of 2018 by Science Magazine. This model of condensation has opened up several unknowns, particularly on the interplay between condensation and genome structure and role of active processes, both of which my lab will contribute to tackling (F2).

Teaching Interests

Philosophy: To me, teaching is an opportunity to empower and mold the next-generation of students - simultaneously a privilege and an important responsibility. As a teacher, I commit to use my position of power to foster diversity and inclusivity in the classroom and beyond.

Teaching interests: My training and love for chemical engineering equips me to teach a broad variety of classes. Of particular interest are courses that combine physical principles and computational approaches - such as transport, statistical thermodynamics, and fluids. I believe that cross-disciplinary training will be important for the modern chemical engineer - whose contributions span quantum and nano-material design, protein and tissue engineering and chemical plants and food processing. Based on my own interests, I aim to develop two courses: (A) Undergraduate focused course introducing the utility of chemical engineering concepts in life sciences and bioengineering and (2) Graduate-focused course that trains students in developing quantitative models to design and engineer cells.

Teaching experience: As a graduate student at MIT’s Chemical Engineering Dept, I served as a teaching assistant for undergraduate transport. I received the highest evaluations amongst teaching staff (6.7/7) and the Edward Merrill Outstanding Teaching Prize – a student-nominated award. I helped cofound the MIT Chemical Engineering Communication Lab – a team of students/postdocs led by professional science communicators. Working together, we developed workshops and open-access resources on topics including writing, presentation, and poster-design for the department (500+ students) and personally mentored over 20 undergraduates and graduates from diverse backgrounds. At MIT, I also earned a certificate from the Kaufman Teaching Center, where I enrolled in a class that emphasized holistic and inclusive course design and focused on principles of teaching pedagogy.

Selected Awards/fellowships

NSF-Simons Independent Fellowship, Harvard University 2020-2023
~$300k over 3 years

Edward W. Merill Outstanding Teaching Assistant Award, MIT (2018)
Student-nominated award for best TA in ChemE

Institute Silver Medal and Reliance Heat Transfer Prize, IIT-Madras (2013,2014)
University-wide recognition for academic/research excellence

Selected publications

1. K. Shrinivas^c, M. P. Brenner, Phase separation in fluids with many interacting components. PNAS. 118 (2021).

2. J. E. Henninger⁼, O. Oksuz⁼, K. Shrinivas⁼, I. Sagi, G. LeRoy, M. M. Zheng, J. O. Andrews, A. V. Zamudio, C. Lazaris, N. M. Hannett, T. I. Lee, P. A. Sharp, I. I. Cissé, A. K. Chakraborty^c, R. A. Young^c, RNA-Mediated Feedback Control of Transcriptional Condensates. Cell. 184, 207-225.e24 (2021).

3. K. Shrinivas⁼, B. R. Sabari⁼, E. L. Coffey, I. A. Klein, A. Boija, A. V. Zamudio, J. Schuijers, N. M. Hannett, P. A. Sharp^c, R. A. Young^c, A. K. Chakraborty^c, Enhancer features that drive formation of transcriptional condensates. Molecular Cell. 75, 549-561.e7 (2019).

4. A. Gao⁼, K. Shrinivas⁼, P. Lepeudry, H. I. Suzuki, P. A. Sharp^c, A. K. Chakraborty^c, Evolution of weak cooperative interactions for biological specificity. Proceedings of the National Academy of Sciences. 115, E11053–E11060 (2018).

5. B. R. Sabari⁼, A. Dall’Agnese⁼, A. Boija, I. A. Klein, E. L. Coffey, K. Shrinivas, B. J. Abraham, N. M. Hannett, A. V. Zamudio, J. C. Manteiga, C. H. Li, Y. E. Guo, D. S. Day, J. Schuijers, E. Vasile, S. Malik, D. Hnisz, T.I. Lee, I. I. Cisse, R. G. Roeder, P. A. Sharp, A. K. Chakraborty, R. A. Young^c, Coactivator condensation at super-enhancers links phase separation and gene control. Science. 361 (2018).

6. D. Hnisz⁼, K. Shrinivas⁼, R. A. Young^c, A. K. Chakraborty^c, P. A. Sharp^c, A Phase Separation Model for Transcriptional Control. Cell. 169, 13–23 (2017).

⁼co-first author, ^ccorresponding author, Google Scholar Profile