Random Walks

Abhigyan Ray

The process of science as a whole seems an interesting but daunting prospect. To explore the intricacies of science, join me for ~60 minutes each week as I indulge in a freewheeling conversation on science and myriad other things with an eclectic set of professors, graduate students, physician-scientists, journal editors, science communicators, ethicists, and anybody who does science! In our Random Walks, we delve deep into the numerous challenges doing science entails and how everyone charts a unique collaborative path through it. https://linktr.ee/randomwalks

Peregrination of a raconteur through maths, computing, and life with Chris Rackauckas (MIT)
24-12-2021
Peregrination of a raconteur through maths, computing, and life with Chris Rackauckas (MIT)
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!!
Developing methods to break new grounds in science and life with James Fraser (UCSF)
28-11-2021
Developing methods to break new grounds in science and life with James Fraser (UCSF)
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!!
Blazing an outstanding trail through science and life with Rubul Mout (Harvard)
01-11-2021
Blazing an outstanding trail through science and life with Rubul Mout (Harvard)
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!!
Automating and integrating synthesis and life with Teodoro Laino (IBM Research)
25-09-2021
Automating and integrating synthesis and life with Teodoro Laino (IBM Research)
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!!
Ruminations of a savant through science, art, and life with Siranush Babakhanova (Stanford)
29-08-2021
Ruminations of a savant through science, art, and life with Siranush Babakhanova (Stanford)
In this episode, I converse with Siranush Babakhanova, an artist, scientist, and engineer, creating physical and digital immersive paradigms that allow us to transcend the limitations of perception and comprehension. Siranush studied Physics and Computer Science at MIT; researched terraformation at NASA; and devised ways to read/non-invasively interact with microstructures in a brain at the Synthetic Neurobiology lab. In parallel, she also conglomerated the largest teams for fashion design and photography for MIT’s Infinite magazine and initiated award-winning (National Geographics, CAMIT) art-meets-science collaborations. Siranush is also an expert calligrapher, pianist, dancer, graphic designer, multimedia painter, and a polyglot versed in 7 languages. In the fall of 2020, Siranush joined the Stanford Biophysics PhD program as a Knight-Hennessy Scholar and National Science Foundation Graduate Research Fellow. Siranush is interested in innovative (cyber/bio) fashion design and implementation of novel materials and interfaces, creating new storytelling techniques (linguistic and semiotic) and mediums (oceanological), and making tools and experiences (choreographies, immersive environments) that help imagine the future of human experience. We indulge in a truly riveting conversation on her phenomenal journey through science and life; thoroughly inspirational mother; science as a gateway to the wider world in post-Soviet Armenia; winning a record six International Olympiad medals; eclectic research interests, right from working on exoatmosphere-wide simulations at NASA to designing tools for deep brain imaging and in situ proteomics; founding the Xapiens human augmentation initiative at MIT; heading to Stanford for grad school during pandemic times; chasing one's innate curiosity and thriving at the interface of interdisciplinarities'; and many more things!!
Breaking ceilings in life and science with Amy Zhang (UW Seattle)
25-08-2021
Breaking ceilings in life and science with Amy Zhang (UW Seattle)
In this episode, I converse with Prof. Amy X. Zhang, an assistant professor at the University of Washington's Allen School of Computer Science and Engineering. Previously, she was a Postdoc at Stanford University's Computer Science Department after completing her Ph.D. at MIT CSAIL in 2019, where she received the George Sprowls Best Ph.D. Thesis Award at MIT in computer science. During her Ph.D., she was an affiliate and 2018-19 Fellow at the Berkman Klein Center at Harvard University, a Google Ph.D. Fellow, and an NSF Graduate Research Fellow.Amy received an M.Phil. in Computer Science at the University of Cambridge on a Gates Fellowship and a B.S. in Computer Science at Rutgers University, where she was captain of the Division I Women's tennis team. Amy's research is in the field of human-computer interaction and social computing where she works on designing and building systems to improve discourse, collaboration, and understanding online, with applications to social media and online communities, news and civic engagement, education, and computer-supported cooperative work and collective action. Her work has received a best paper award at ACM CSCW, a best paper honorable mention award at ACM CHI, and has been profiled on BBC's Click television program, CBC radio, and featured in articles by ABC News, The Verge, New Scientist, and Poynter. She is a founding member of the Credibility Coalition, a group dedicated to research and standards for information credibility online. We indulge in a terrific conversation on her fantastic journey in science; fantastic mentors who inspired her; confronting the imposter syndrome; tennis; human-computer interaction; and many more things!!
Embarking on a serendipitous course of genome, science, and life with Vijay Ramani (UCSF)
15-08-2021
Embarking on a serendipitous course of genome, science, and life with Vijay Ramani (UCSF)
In this episode, I converse with Prof. Vijay Ramani, Principal Investigator and Sandler Fellow at the University of California, San Francisco. He finished his B.S.E. in Chemical Engineering at Princeton University, with minors in Quantitative & Computational Biology, and Engineering Biology and then spent a year as a Computational Biology intern at Sangamo BioSciences. Vijay went on to complete his PhD studies in Jay Shendure’s lab at the University of Washington, where he invented high-throughput molecular methods to study biological phenomena at scale. These methods included an assay for studying RNA structure, as well as single-cell genomic assays reliant on in situ DNA barcoding of intact cells and nuclei, to make genome-wide measurements in thousands of single-cells without ever resorting to single-cell isolation. Vijay's lab develops novel molecular technologies to understand the regulation of biology’s central dogma – the transfer of genetic information from DNA to RNA to protein. We indulge in a terrific conversation on his extremely fascinating journey through science and life; early familial influences to foray into science; partaking in OG genome editing before the CRISPR boom; fundamental research in industry; heading to UW for grad school and working with terrific mentors like Prof. Jay Shendure; starting as a PI straight out of grad school; prescient thoughts on structural changes required in academia; the far-reaching consequences of society's understanding of science; exciting future of biotech; and many more things!!
Seamlessly navigating intersectionalities in science and life with Yangyang Cheng (Yale)
11-08-2021
Seamlessly navigating intersectionalities in science and life with Yangyang Cheng (Yale)
In this episode, I converse with Yangyang Cheng, a Postdoctoral Fellow at Yale Law School's Paul Tsai China Center. Before joining Yale, she worked on the Large Hadron Collider (LHC) for over a decade and was a postdoctoral research associate at Cornell University and an LHC Physics Center Distinguished Researcher at Fermi National Accelerator Laboratory. Yangyang received her Ph.D. in physics from the University of Chicago in 2015, and her Bachelor’s in Science from the University of Science and Technology of China’s School for the Gifted Young. Yangyang is a regular columnist for SupChina and her writings have also appeared in The New York Times, The Guardian, Los Angeles Review of Books, VICE World News, Foreign Policy, MIT Technology Review, Bulletin of the Atomic Scientists, ChinaFile, and other publications.  Yangyang currently studies the ethics and governance of science in China and their global implications. We indulge in a splendid conversation on her extremely interesting and riveting journey through science and life; early fascinations about the fundamental questions of the universe and abstractions; pursuing Physics in a manner akin to a world-class athlete; her time on the ATLAS and CMS experiment at the Large Hadron Collider (LHC); exceptional mentors who inspired her; navigating rejections in life; diving into China studies straight from particle physics; future of fundamental curiosity-driven research; and many more things!!
Perambulations of a raconteuse through science and life with Meghana Ranganathan (MIT)
04-07-2021
Perambulations of a raconteuse through science and life with Meghana Ranganathan (MIT)
In this episode, I converse with Meghana Ranganathan, a fourth-year Ph.D student in Climate Science at the Department of Earth, Atmospheric, and Planetary Sciences at MIT. Meghana completed her undergraduate education at Swarthmore College and received a B.A. in mathematics, with a specialization in applied mathematics. Her past research has been on eclectic areas of interest, including focuses on El Nino-Southern Oscillation forecasting, statistical paleontology, and building queuing theory models for emergency rooms to identify bottlenecks in the intake process. Meghana is also passionate about diversity, equity, justice, and inclusion in STEM and has been actively involved in education and activism around issues of racism and colonialism in the geosciences.  Meghana's current research focuses on the dynamics and energetics of ice streams in West Antarctica, illuminating processes on the micro-scale and connecting micro-scale processes with macro-scale dynamics. We indulge in a fascinating conversation on her terrific journey in science; naturally discovering maths in college and flaws with mathematical pedagogy in schools; applying a mathematical lens to solving the pressing challenge of the day - climate change; grad school and confronting the ubiquitous imposter syndrome; the importance of lucid science communication; breathtaking research on glaciology; engaging communities on the ground; forays into writing and the storytelling aspect of science; and many more things!!
Unravelling the complex secrets in matter, science, and life with Sujit Datta (Princeton)
20-06-2021
Unravelling the complex secrets in matter, science, and life with Sujit Datta (Princeton)
In this episode, I converse with Prof. Sujit Datta, an Assistant Professor of Chemical and Biological Engineering at Princeton University. Sujit earned a BA in Mathematics and Physics, and an MS in Physics, in 2008 from the University of Pennsylvania. He earned his PhD in Physics in 2013 from Harvard, where he studied fluid dynamics and instabilities in porous media and colloidal microcapsules with David Weitz after which he finished a postdoc in Chemical Engineering at Caltech, where he studied the biophysics of the gut with Rustem Ismagilov. He joined the faculty at Princeton in 2017 and been the recipient of multiple awards like the NSF CAREER Award, AIChE 35 Under 35 Award, ACS Unilever Award, APS Andreas Acrivos Award in Fluid Dynamics. Sujit's lab studies soft and living materials in complex settings, motivated by challenges like water remediation, carbon sequestration, oil/gas recovery, and targeted drug delivery, and their work integrates microscopy, microfluidics, soft materials chemistry, and biophysical characterisation. We indulge in an ebullient conversation on his wonderful journey through science and life; from early fascinations with economics and philosophy to pivoting to maths and physics; fascination with science and the fundamental role of curiosity-driven basic science research in helping shape the world; his terrific set of mentors; kickboxing the stress out of his life; the importance of diversity and inclusion in all walks of life; and many more things!!
Pioneering a trailblazing pathway through the frontiers of science, medicine, and life with George Church (Harvard/MIT)
09-06-2021
Pioneering a trailblazing pathway through the frontiers of science, medicine, and life with George Church (Harvard/MIT)
In this episode, I converse with the legendary geneticist, an outstanding scientist, terrific engineer, inimitable mentor, and fantastic innovator Prof. George Church of Harvard and MIT. Church is a Professor of Genetics at Harvard Medical School and Professor of Health Sciences and Technology at Harvard University and the Massachusetts Institute of Technology (MIT). He has received multiple awards including the Bower Award and Prize for Achievement in Science from the Franklin Institute and election to the coveted National Academy of Sciences and Engineering for his pioneering contributions to science. He has co-authored over 600 publications, holds more than 150 patents, and published a book titled “Regenesis: How Synthetic Biology Will Reinvent Nature and Ourselves”, with more than 70 billion copies published. Church's lab researches at the frontiers of science and helped develop the methods for the first genome sequencing, and their subsequent work brought down the price of sequencing over 10-million-fold. His was one of the two groups that first got CRISPR-Cas9, subject of the latest Nobel Prize in Chemistry, to work for precise gene editing in human cells by a homologous recombination, and he has been behind countless other scientific innovations and disruptions, specifically in the world of precision genome sequencing. We indulge in an extremely riveting conversation on his absolutely stellar and thoroughly inspiring journey through science; early childhood inspirations and building his first computer in conjunction with an electrician family friend; foraying into biological sciences armed with strong physical and computational science skills right at the cusp of revolution; fascinating grad school experience, from flunking out of Duke to make giant strides at Harvard; inspirational mentors like Gail Martin, Wally Gilbert, and Sung-Hou Kim; disappointment with the Human Genome Project; breathtaking research that has hugely impacted the world; combating failures and rejections; the prospect of creating an actual living and breathing Jurassic Park; and many more things!!
Peregrinating a pioneering journey through science and life with Avanti Shrikumar (Stanford)
23-05-2021
Peregrinating a pioneering journey through science and life with Avanti Shrikumar (Stanford)
In this episode, I converse with Dr. Avanti Shrikumar, a Ram and Vijay Shriram Data Science Postdoctoral Fellow at Stanford Data Science, where she works with Prof. Karen Casciotti in the Department of Earth System Science at Stanford, Avanti completed her B.S. in Computer Science and Molecular Biology from MIT in 2013 and took a gap year to work on the healthcare team of Palantir Technologies before beginning her graduate studies in the Computer Science department at Stanford under the aegis of Prof. Anshul Kundaje. Avanti's current research focuses on developing and applying data science techniques to improve our understanding of oceanic nutrient cycling and during her PhD she helped develop machine learning methods, with a focus on deep learning, model interpretation, and applications to regulatory genomics. We indulge in a terrific conversation on her fantastic journey in science; early familial influences and childhood initiations into science; combating biases and dealing with the ubiquitous imposter syndrome; her brilliant research and the fantastic mentors who inspired her; the globally pressing challenge of climate change and the urgent need to combat it to prevent the doomsday scenario of spraying sulfur dioxide in the atmosphere; and many more things!! *Disclaimer: This episode was recorded early this year in the month of January but is being released now due to some extraneous reasons!