Sean Seyler | People | Beckstein Lab

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Sean Seyler
Sep 24

Sean Seyler

Sean obtained his PhD in Physics in November 2017.

Sean is interested in the general statistical mechanical principles that underlie macromolecular transition events and, using a suite of computational approaches, seeks to identify their molecular-structural determinants—the atomistic mechanisms that characterize their behavior.

Proteins, such as membrane transporters or enzymes, are much like nanomachines that undergo structural changes—conformational transitions—between multiple states in order to perform chemical or mechanical work. These transitions are rare events that, due to the equilibrium sampling problem, are difficult to reproduce in equilibrium molecular dynamics (MD) simulation. The paradigm for studying these processes is the so-called structure-function connection; in principle, one should be able to infer a protein’s function given information about its structure (its “shape” and/or amino acid sequence). Sean is currently developing software tools and computational methods to generate and quantify conformational transition pathways and, ultimately, predict the kinetic transition rates.

Sean received his B.S. (2011) and M.Eng. (2012) in Engineering Physics from the School of Applied and Engineering Physics at Cornell University. He joined Beckstein Lab at Arizona State University in the Fall of 2012 to pursue his Ph.D. in physics. Sean is a 2016 Blue Waters Graduate Fellow and will focus on developing a hybrid continuum-atomistic numerical code for the simulation of biomacromolecules during the 2016-2017 academic year.

Outside the immediate scope of his research, Sean is interested in the statistical mechanics of non-equilibrium and nano-/meso-scale phenomena, such as fluctuating hydrodynamics and heterogeneous soft-matter systems. When not coding or performing simulations, he can be found mountain biking, cycling or hiking in the hills surrounding the Phoenix area, listening to new music, and playing tennis with the ASU Club Tennis team.

Publications

  1. N. Coudray, S. L. Seyler, R. Lasala, Z. Zhang, K. M. Clark, M. E. Dumont, A. Rohou, O. Beckstein and D. L. Stokes (2017). Structure of the SLC4 transporter Bor1p in an inward-facing conformation. Protein Science, 26: 130–145. doi: 10.1002/pro.3061
  2. R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein (2016). MDAnalysis: a Python package for the rapid analysis of molecular dynamics simulations. In S. Benthall and S. Rostrup, editors, Proceedings of the 15th Python in Science Conference, pages 102-109, Austin, TX. SciPy.
  3. S. L. Seyler, A. Kumar, M. F. Thorpe, O. Beckstein (2015). Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways. PLoS Computational Biology 11(10): e1004568. doi: 10.1371/journal.pcbi.1004568
  4. S. L. Seyler and O. Beckstein (2014). Sampling large conformational transitions: adenylate kinase as a testing ground. Molecular Simulation 40 (10-11), 855-877. doi: 10.1080/08927022.2014.919497
  5. S. L. Seyler (2015). Modeling dynamic ionization and radiation transport in a numerical magnetohydrodynamic code. M.Eng. Research Report, Cornell University, 2012. figshare. doi: 10.6084/m9.figshare.1619903

Presentations and posters

  1. 2017 Blue Waters Symposium, Sun River, OR, Talk: Developing a Hybrid Atomistic-Continuum Method for Simulating Large-scale Heterogeneous Biomolecular Systems, S. L. Seyler, C. E. Seyler and O. Beckstein, May 17, 2017.
  2. 2017 Blue Waters Symposium, Sun River, OR, Poster: Developing a Hybrid Atomistic-Continuum Method for Simulating Large-scale Heterogeneous Biomolecular Systems, S. L. Seyler, C. E. Seyler and O. Beckstein, May 16, 2017.
  3. 60th Annual Meeting of the Biophysical Society, Los Angeles, LA, Platform Presentation: Quantifying Macromolecular Transition Paths with Path Similarity Analysis, S. L. Seyler, A. Kumar, T. Colburn, M. F. Thorpe, and O. Beckstein, March 2, 2016.
  4. 2015 APS 4CS Meeting, Tempe, AZ, Contributed Talk: Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways, S. L. Seyler, A. Kumar, M. F. Thorpe, and O. Beckstein, October 17, 2015.
  5. BioPhest Meeting 2015, Arizona State University, Tempe, AZ, Talk: Path Similarity Analysis: a method
    for quantifying macromolecular transition paths,     S. L. Seyler, A. Kumar, M. F. Thorpe, and O. Beckstein, May 2, 2015.
  6. APS March Meeting 2015, San Antonio, TX, Poster: Quantifying macromolecular conformational transition pathways, S. L. Seyler, A. Kumar, M. F. Thorpe, and O. Beckstein, March 4, 2015.
  7. BioPhest Meeting 2014, University of Arizona, Tucson, AZ, Talk: Quantifying Conformational Transitions: An Application to Simulations of Apo Adenylate Kinase, S. L. Seyler, A. Kumar, M. F. Thorpe, and O. Beckstein, April 26, 2014.
  8. University of Pittsburgh, Department of Biological Sciences, Invited Seminar: Quantifying conformational transitions, S. L. Seyler, A. Kumar, M. F. Thorpe, and O. Beckstein, November 7, 2013.
  9. 2013 APS 4CS Meeting, Denver, CO, Contributed Talk: An approach to quantifying macromolecular transition pathways, S. L. Seyler, A. Kumar, M. F. Thorpe, and O. Beckstein, October 18, 2013.
  10. BioPhest Meeting 2013, Arizona State University, Tempe, AZ, Talk: Quantifying conformational transitions, S. L. Seyler and O. Beckstein, April 20, 2013.

Honors and Awards

  • CLAS Student Leader (2016) — Arizona State University, College of Liberal Arts and Sciences
  • Molecular Imaging Corporation Endowment (2016) — Arizona State University, Department of Physics
  • Blue Waters Graduate Fellow (2016-2017) — provides PhD students with a year of support, including a $38,000 stipend, up to $12,000 in tuition allowance, an allocation of up to 50,000 node-hours on the powerful Blue Waters petascale computing system, and funds for travel to a Blue Waters-sponsored symposium to present research progress and results.
  • Education Committee Travel Award (2016) — Biophysical Society — grant awarded to help defray travel expenses to the Biophysical Society 60th Annual Meeting.
  • 66th Lindau Nobel Laureate Meeting Young Researcher (2016)
  • Summer 2015 University Graduate Fellowship (summer 2015) — Arizona State University, Department of Physics — supports a PhD student to work on their research during the summer months and also provides additional flexibility to, for instance, attend conferences.
  • Shirley Chan Student Travel Award (Jan 2015) — American Physical Society, Division of Biological Physics
  • Wally Stoelzel Physics Fellowship (May 2014) — Arizona State University, Department of Physics — Stoelzel Physics Scholarships are awarded by Mr. Wally Stoelzel in honor of Professor Allen Wager, former chair of the Department of Physics, and Ms. Glenna Curtis, former department secretary.
  • David Delano Clark Award (May 2012) — Cornell University, Department of Applied and Engineering Physics — awarded annually to a student in Engineering Physics for best M.Eng. project.
  • Henri S. Sack Memorial Award (May 2012) — Cornell University, Department of Applied and Engineering Physics — awarded for top academic performance among Engineering Physics M.Eng. students.

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