Ups and Downs
I am a mathematician by training, whose early work in topology, geometry and dynamics has found applications in high energy physics and theoretical biology. I have held the René Thom Chair in Mathematical Biology at the IHÉS since 2014, after having been
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I am a mathematician by training, whose early work in topology, geometry and dynamics has found applications in high energy physics and theoretical biology. I have held the René Thom Chair in Mathematical Biology at the IHÉS since 2014, after having been a frequent visiting professor there for decades. Since June, 2019, I have been studying viral glycoproteins, leading to the two papers Backbone free energy estimator applied to viral glycoproteins and Conserved high free energy sites in human coronavirus spike glycoprotein backbones, both in the Journal of Computational Biology. In the first, I propose a geometric method to predict promising targets for antiviral drugs or vaccines across all viruses, and the sequel applies these methods specifically to human coronaviruses, thus pushing forward the current efforts to fight SARS CoV-2, the virus causing COVID-19. These works are surveyed in a Scientific American article from May 19, 2020. The IHÉS asked me to recount how a pure mathematician has found his way to work on virology, and here is that story. My first paper on RNA was published in 1992, co-authored with my close friend and onetime colleague Mike Waterman, sometimes called the “father of computational biology.” We would celebrate (or bemoan) the beginning of each academic year at USC with a deep-sea fishing trip, for it is late summer when the yellowtail amberjack run in the warm waters off southern California. Waiting for something to bite, he mentioned his recent work, which I immediately recognized as a bastardized version of Poincaré duality. This led to our first paper on spaces of RNA secondary structures, which was well received but had no major impact until much later. But this set the ball in motion, and he invited me, over the next decades, to any seminar he thought might be accessible and of interest to me. Some years later, we ran a private meeting at USC on macromolecules funded by the bio-philanthropist Peter
R. C. Penner (*) Institut des Hautes Études Scientifiques, Le Bois-Marie, Bures-sur-Yvette, France e-mail: [email protected] © The Author(s), under exclusive license to Springer Nature Switzerland AG 2020 A. Wonders (ed.) Math in the Time of Corona, Mathematics Online First Collections, https://doi.org/10.1007/16618_2020_13
R. C. Penner
Preuss, and among the star-studded attendees was Alexeii Finkelstein, a leading world authority on protein, who plays crucial subsequent roles. We instantly became friends. His book entitled “Protein Physics: a course of lectures,” written with his teacher Oleg Ptitsyn, is a masterpiece, and I devoured it. Macromolecules—specifically, RNA and protein—were my gateway to biology, a separate and comprehensible piece of a dauntingly enormous puzzle. Macromolecules, after all, are essentially one-dimensional objects that interact along sites, just as are the strings of high-energy physics. And I immediately saw ways to extrapolate up 25 or so orders of magnitude, from the Planck scale to the Angstrom scale, the basic combinatorics of my earlier work in string theory.
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