Random Walks Abhigyan Ray

In this episode, I converse with Dr. Christopher Rackauckas, the Research Affiliate and Co-PI of the Julia Lab at the Massachusetts Institute of Technology, Director of Modeling and Simulation at Julia Computing and Creator / Lead Developer of JuliaSim, Director of Scientific Research at Pumas-AI and Creator / Lead Developer of Pumas, and Lead Developer of the SciML Open Source Software Organization. As an undergraduate at Oberlin College, Chris was awarded the NSF S-STEM scholarship and the Margaret C. Etter Student Lecturer Award by the American Crystallographic Association, an award usually given for PhD dissertations, for his work on 3+1 dimensional incommensurate crystal structure. He completed his Masters and Ph.D. at the University of California, Irvine where his research doctoral focused on the methods for simulating stochastic biological models and detailing how the randomness inherent in biological organisms can be controlled using stochastic analysis and he was awarded the Mathematical and Computational Biology institutional fellowship, the National Science Foundation's Graduate Research Fellowship, the Ford Predoctoral Fellowship, the NIH T32 Predoctoral Training Grant, and the Data Science Initiative Summer Fellowship. 

Chris' research and software is focused on Scientific Machine Learning (SciML): the integration of domain models with artificial intelligence techniques like machine learning. By utilizing the structured scientific (differential equation) models together with the unstructured data-driven models of machine learning, our simulators can be accelerated, our science can better approximate the true systems, all while enjoying the robustness and explainability of mechanistic dynamical models. We indulge in a fantastic conversation on his wonderful Random Walks through science and life; brilliant research in building numerical methods and software for scientific machine learning, scientific machine learning as next-generation healthcare, and development of high performance solving of differential equations; straddling the industry-academia interface with great elan; mathematics as a progressive form of rock music; the revolutionary rise of computing in the last half a century; dealing with rejections and making progress when stuck; great mentors and prescient insights on mentorship; and many more things!!

In this episode, I converse with Prof. James Fraser at the University of California, San Francisco. James was an undergraduate at McGill University, where he worked in the lab of Dr. Francois Fagotto on Xenopus developmental biology. As a graduate student, with Tom Alber at UC Berkeley, James established room-temperature X-ray data collection techniques and electron density sampling strategies to define protein conformational ensembles essential for catalysis. Prior to starting an independent position at UCSF, he was a visiting EMBO Short Term Fellow in the lab of Dan Tawfik at the Weizmann Institute of Science in Israel and developed expertise in directed evolution and high-throughput assays of enzymatic or binding activity. In January 2011, James started his independent career as a QB3 at UCSF Fellow affiliated with the Department of Cellular and Molecular Pharmacology. In January 2013, he was appointed as an Assistant Professor in the Department of Bioengineering and Therapeutic Sciences and the California Institute for Quantitative Biosciences (QB3) with promotion to Associate Professor in 2016, and Full Professor in 2020. James is also a Faculty Scientist in the Molecular Biophysics and Integrated Bioimaging Division of Lawrence Berkeley National Lab. 

The long-term goals of James' research group is to understand how protein conformational ensembles are reshaped by perturbations, such as mutation and ligand binding, and to quantify how these perturbations impact protein function and organismal fitness. To accomplish these goals, they create new computational and biophysical approaches to study how proteins move between different conformational states. Additionally, the group uses two complementary approaches to study the relationship between protein conformational ensembles and function. To dissect consequences of mutations on organismal fitness, they use high-throughput systems biology and biophysical methods to analyze large sets of clinically or biophysically interesting mutations and to improve the ability to engineer new protein functions, they investigate changes to the conformational ensemble as new enzymatic and binding functions emerge from directed evolution studies. We indulge in a fascinating conversation on his enjoyable journey through science and life; foraying into academia from a family of non-academics; the thrill of methods development; the enormous influence of his brilliant mentors, friends, and collaborators; creating a more equitable, open, and just environment in science; and many more things!!

In this episode, I converse with Dr. Rocío Mercado, who's currently a postdoc in the Coley group at MIT. Previously, Rocío was a postdoc in the Molecular AI team at AstraZeneca, where she worked on the development of deep generative models for small molecule drug discovery. Before AstraZeneca, Rocío was a PhD student in Prof. Berend Smit’s molecular simulation group at UC Berkeley and EPFL and received her PhD in Chemistry from UC Berkeley in August 2018, and her BS in Chemistry from Caltech in June 2013.

Rocío's research expertise lies in data-driven molecular design, at the interface of computer science and chemistry and she's passionate about the development of computational tools which can be used to enhance the process of pharmaceutical drug discovery, such as deep molecular generative models and molecular optimization methods. We indulge in a riveting conversation on her phenomenal journey through science and life; thoroughly inspirational mentors; fascinating research; confronting the imposter syndrome; fostering a more equitable and just environment in science; and many more things!!

In this episode, I converse with Dr. Rubul Mout, a Research Fellow at Harvard Medical School and at the Stem Cell Program, Boston Children’s Hospital (BCH). Born, brought up, and educated in India, Dr. Mout moved to the United States to pursue his PhD from the University of Massachusetts, Amherst. Prior to joining Harvard/BCH, he was a Washington Research Foundation Innovation Fellow at the Institute for Protein Design, University of Washington. Dr. Mout is the inventor of numerous technologies in gene editing and protein design, and in the last decade he developed a technology for intracellular protein delivery and gene editing in mammalian cells, termed as the ‘E-tag’ method, which was in 2020, granted a patent by USPTO (the United States Patent and Trademark Office).

At Harvard/BCH, Dr. Mout works to engineer bone marrow stem cells (Hematopoietic stem cells, or HSCs) to cure genetic diseases of blood origin and uses various technologies, including techniques he invented in his prior research, to engineer these HSCs. In particular, he uses patient-derived induced pluripotent stem cells (iPSC) to differentiate them to HSC first, and then to produce and train T-cells that could potentially fight off many diseases. We indulge in a terrific conversation on his magnificent journey through science and life inspired by his innate curiosity; growing up in a poor peasant’s family in a far remote corner of Northeast India, near the Assam-Arunachal border; undertaking a majestic quest from Tinsukia to Mumbai to Amherst to Seattle to Boston; inspirational mentors like GK Johori, David Baker, Vincent Rotello, and George Daley; fantastic dedication to scientific outreach and activism; writing outstanding books including a popular bestseller that chronicled his splendid journey; and many more things!!  

In this episode, I converse with Crystal Lee, a PhD candidate at MIT and a Fellow at the Berkman Klein Center at Harvard University. Previously, Crystal was a visiting research scientist at the European Commission, and graduated with high honors from Stanford University. Crystal's research has been supported by the National Science Foundation, Social Science Research Council, and the MIT Programs for the Digital Humanities.

Crystal works broadly on topics related to the sociopolitical dimensions of computing, data visualization, and disability. She also conducts ethnographic and computational research on social media communities like COVID skeptics, Chinese cyber-nationalist fandoms, and data hoarders. We indulge in a fantastic conversation on her extraordinary research; the intricate relationship between politics and science; confronting the imposter syndrome; pioneering student activism and actively combating bias and discrimination in science through terrific endeavours to foster a more welcoming environment for underrepresented groups; science as a collaborative enterprise and disputing the notion of male white genius' revolutionising it; and many more things!!

In this episode, I converse with Dr. Teodoro Laino, a Distinguished Research Scientist and Manager at IBM Research. Teodoro received his degree in Theoretical Chemistry in 2001 at the University of Pisa and Scuola Normale Superiore di Pisa, and further completed his doctorate in 2006 in computational chemistry at the Scuola Normale Superiore di Pisa, Italy on "Multi-Grid QM/ MM Approaches in ab initio Molecular Dynamics", supervised by the legendary Prof. Michele Parrinello. From 2006 to 2008, he worked as a post-doctoral researcher in the research group of Prof. Jürg Hutter at the University of Zurich, where he developed algorithms for ab initio and classical molecular dynamics simulations. Since 2008, he has been working in the department of Cognitive Computing and Industry Solutions at the IBM Research - Zurich Laboratory.  

Teodoro's research focuses on complex material simulations for industrial-related problems (energy storage, life sciences and nano-electronics) and more recently, he has been interested in the application of machine learning/artificial intelligence technologies to chemistry and materials science problems with the purpose of developing customized solutions. We indulge in a very fascinating conversation on his terrific journey through science; fantastic mentors who inspired him; heading into theoretical chemistry at the cusp of revolution; confronting the ubiquitous imposter syndrome; the extraordinary impact of AI and ML in the natural sciences; the IBM RXN for chemistry platform; becoming an aviation pilot, and many more things!!