Birthday Symposium for Bruce Donald
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Birthday Symposium for Bruce Donald Duke Gardens, Durham NC July 17, 2018 Morning Session to contribute to so many areas. Nevertheless, these areas are glad that he has done so. Introduction & Welcome Computational Structural Biology, Robotics and the Chittu Tripathy, Mark Hallen, Ryan Lilien. Algorithms In Between, What I’ve Learned from Bruce and How it Has Ramgopal Mettu, Associate Professor, Department of Changed My Science, Computer Science, Tulane University. Terrence Oas, Professor of Biochemistry, Duke univer- In this talk I’ll give a brief overview of my work in the sity. areas of algorithms, computational biology and most re- I will briefly summarize the impact of Bruce on both my cently, robotics. Algorithms for discrete (and continu- administrative as well as scientific life. I first encoun- ous) optimization are of course the common thread, but tered Bruce when I was leading the Bioinformatics and just as important is how a problem is chosen, modeled, Genomic Technology PhD Program. I will describe his and solved. While working with Bruce as a postdoc we willingness to help us apply for an NIH training grant. devised novel algorithms for NMR data interpretation I will also describe the impact that our interactions have that had both nice theoretical properties, and also worked had on my appreciation for continuous distributions and on actual experimental data. This experience provided a the role that they can play in interpretation of structural template for future work, and I’ll describe how my sub- NMR data. I will also mention the potential utility of sequent research has at least attempted to be both theo- this approach in the interpretation of structural data from retically interesting and practically relevant. other methods. Development of a Novel 3D-Topography Scanning From Robotics and Computational Geometry to and Analysis System for Firearm Forensics, Molecular Biology, Ryan Lilien, Founder, Cadre Forensics; Adjunct Profes- Jack Snoeyink, Professor of Computer Science, UNC sor of Computer Science, University of Toronto. Chapel Hill. I will describe my group’s work developing an accurate, Bruce Donald’s PhD thesis, “A Theory of Error Detection fast, and low-cost 3D imaging and analysis system for and Recovery: Robot Motion Planning with Uncertainty firearm forensics. Which is, of course, the next logi- in the Geometry of the Environment,” did not prefigure cal field to transition to after computational biology. As his excessive number of affiliations: “Professor of Com- portrayed in the movies, ammunition cycled through a puter Science at Duke University, Professor of Chem- firearm picks up small microscopic imperfections (i.e., istry, and Professor of Biochemistry in the Duke Univer- toolmarks) unique to that firearm. Microscopic exam- sity Medical Center. He is also Professor of Electrical ination of these marks allows firearm examiners to as- and Computer Engineering in the Duke Pratt School of sess the likelihood of common origin (e.g., the linking Engineering.” I’ll briefly explain why the foundational of a cartridge case found at a crime scene to a test fire work that Bruce did in computational geometry plays a from a suspect’s firearm). At Cadre, we are developing role in so many areas, but will leave it to him to explain a novel 3D scanning and analysis system for cartridge why he would want to make it official that he is supposed cases. Our system has been validated and is now in use 1 at the FBI’s primary firearm and toolmark laboratory in ology Facility; Director, NMRbox.org: National Center Quantico, VA. Experience supports the hypothesis that for Biomolecular NMR Data Processing and Analysis. 3D imaging methods such as ours has the potential to Bruce Donald made his mark in a number of areas be- greatly impact the criminal justice system. fore turning his attention to computational aspects of Cell-Shape Oscillations and Their Biological Rele- biomolecular NMR spectroscopy - but his influence is vance, most sorely needed in NMR as nowhere else. A curse of Glenn Edwards, Professor of Physics, Duke University. modern computational hardware is that it is possible to take dumb ideas and with enough brute force emit some- Bruce and I met while serving on Duke’s Academic Pro- thing...OK. However not everything that can be com- motions and Tenure Committee. I’ll start with a necessar- puted should. Bruce brings a sense and sensibility to ily cryptic comment about our shared experiences during computation in bioNMR that we as a field need to em- those three years. We also talked in brief about our re- ulate in order to truly succeed. Through an example search interests on those many walks to and from APT. (or two) I’ll show how bedrock principles embodied by Having Bruce’s attention during this Symposium, I’ll re- Bruce’s work could earn a new generation of assistant view some recent biophysics research on the mechanism professors tenure. for cell oscillations and cell ingression. This research uses mathematical and physical techniques that I did not The Ubiquitous Sparsity: From Modeling Protein learn as an undergraduate math major nor as a physics Structures Using Sparse NMR Data to Understand- graduate student. Consequently the target biological au- ing Customer Behavior, dience became rather narrow. In retrospect, this project is Chittu Tripathy, Staff Data Scientist, Walmart Labs. bit like a drum solo. My wife thinks drum solos are self My work in the D-Lab was mainly focused on using indulgent and detract from the musical experience. Gen- Sparse NMR data, specifically, the residual dipolar cou- erally I like drum solos, but are there drum solos in blue plings and residual chemical shift anisotropy data to de- grass? In any event, I anticipate Bruce really will un- termine the 3D protein structural folds at atomic resolu- derstand this mechanism, so this is an opportunity not to tion. After moving to an industry job, I only began to re- be missed. Now for the science: Cell-shape oscillations alize why modeling with sparse data is even more impor- have generated considerable interest.These oscillations tant. In past 5 years, I have worked on real-world prob- occur at low-Reynolds number and from this perspective lems involving millions of customers of two retail giants it was surprising that a band of oscillation frequencies of our time, Amazon and Walmart, primarily focusing on (5.7±0.9 mHz) has been resolved experimentally in am- modeling customer’s behavior and their interactions with nioserosa cells during Drosophila morphogenesis. This the products, ranging in domains such as last-mile logis- talk will review a molecular mechanism that: 1) identi- tics, personalization, customer-segmentation, targeting fies the key-attributes of a molecular contractile unit that with an aim to understand the ‘WHY’ behind a customer- leads to a unified mechanism for producing oscillations action. Sitting at the core of these problems, that are per- and the steady forces that promote ingression; 2) charac- ceived to derive inferences from the enormous amount of terizes a regulatory process that switches contractile units data, are a number of sparse-data problems. I will talk from oscillatory to steady-force production; and 3) incor- about some of the models I have worked on in the recent porates the role of actin cross-links in scaling piconewton past, and how my training in the D-lab naturally extends actomyosin forces to nanonewton intercellular forces. to this area. Afternoon Session 1 Protein Backbone and Protein Surface: New Solu- tions to Old Problems, NMR.Needs.Bruce (Pump up the Volume), Lincong Wang, College of Computer Science and Tech- Jeffrey Hoch, Joseph Meyerhoff Visiting Professor of nology, Jilin University, China. Chemical Physics, Weizmann Institute of Science; Pro- The first part of my talk focuses on a novel representation fessor of Molecular Biology and Biophysics, UConn of protein backbone as a polyline linking consecutive Health; Director, Gregory P. Mullen NMR Structural Bi- peptide plane centers. This representation is the basis of 2 a highly-accurate, distance-based algorithm for protein state designs with continuous flexibility, and designs with secondary structure element assignment that uses none extensive continuous backbone flexibility and advanced of backbone hydrogen bonds. Next I present the char- non-pairwise energy functions. acterization of protein-ligand interactions using solvent- A Computational Pipeline for Design of Novel RNA- excluded surface (SES) and a series of SES-defined phys- like Topologies, ical and geometrical properties. For example we have Swati Jain, Postdoctoral Associate, Department of proposed a new model for protein-protein interaction in- Chemistry, New York University. terfaces specified in terms of the large differences in SES-defined properties between completely-buried and Designing novel RNA topologies is important for thera- partially-buried surface atoms. peutic and industrial applications. I will describe a re- cent computational pipeline for design of novel RNA On the Topic of Velvet Paintings and Rotamer Hip- topologies we have developed based on our lab’s coarse- popotami (with Some Science), grained RNA-As-Graphs (RAG) framework, that rep- Jonathan Jou (JJ), Postdoctoral Research Associate at resents RNA secondary structures as tree graphs. We Duke. have previously enumerated possible graph topologies What follows will be 20ish minutes chronicling my time for graphs up to 13 vertices and identified RNA-like in the lab, highlighting personally memorable anecdotes, topologies among these. We developed a system- hopefully exciting science, and more than a few good lab atic design pipeline, using recently developed tools for memories. Topics include, but are not limited to: pro- graph-partitioning and fragment assembly (F-RAG). Fol- tein design, algorithms, lab photos, graduation gifts, the- lowing partitioning of the target graph, corresponding sis cover artwork, personal gaffes, and maybe even clip atomic fragments from our database of RNA substruc- from a music video, if I can get my hands on it.