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Giving Vitamins to the Most Basic Bacterium

POSTER

Abstract

This project revolves around the JCVI-syn3A and uses it as a platform to contribute to the understanding of the fundamental rules of life and how living things respond to changing environments and situations. The JCVI-syn3A is a minimal bacterial cell, i.e, it only contains genome essential for survival. The motivation behind the creation of the minimal cell is to create a simple cell that can be complexified to understand more complex cells and systems. This summer, we explored the JCVI-syn3A and used methods such as the Chemical Master Equation and Gillespie algorithm (a Monte Carlo Method for numerically generating trajectories of molecular populations) to simulate trajectories for processes such as the assembly of the ECF transporter. Due to the reduction in genome of the JCVI-syn3A, ECF transporters play an important part in the transportation of cofactors since the JCVI-syn3A cannot metabolize its cofactors and needs to transport cofactors from the external medium. Our aim was to simulate trajectories of the assembly of the ECF transporter under different conditions using Lattice Microbes (an implementation of the Gillespie algorithm using GPUs). From a biophysical standpoint, if we understand the assembly of such transporters, we can analyze the physical underpinnings of both their structure and the transportation they aide in. Future work may focus on determining the assembly models for all membrane protein complexes in the JCVI-syn3A and use these models for other complex cells.

Authors

  • Halona Dantes

    University of North Carolina at Chapel Hill

  • Kristin Rabosky

    Middle Tennessee State University, University of Alabama Tuscaloosa, Swarthmore College, CT Clinical Innovation Center, Department of Radiology, Mayo Clinic, Rochester, MN, Bard College, Wright State University, University of Michigan, University of Hawai'i-Manoa, Rice University, University of Alaska Fairbanks, University of Utah, South Dakota School of Mines and Technology, Furman University, University of Notre Dame, Theoretical Physics Division, Institute of High Energy Physics, the Chinese Academy of Sciences, Peng Huanwu Center for Fundamental Theory, University of Science and Technology China, University of Cambridge, University of Kansas, SLAC National Accelerator Laboratory, Planetary Science Institute, Iowa State University, College of Idaho, University of Washington, Bothell, Ottawa Hills High School, Case Western Reserve University, Yale University and Strasbourg Astronomical Observatory, Yale University, Korea Astronomy and Space Science Institute, NOIRLab, Purdue University, Korea Instotute for Advanced Study, Perimeter Institute, Rutgers University, University of Maryland, Juniata College, Columbia University, City University of New York / American Museum of Natural History, Columbia University / American Museum of Natural History, Morehead State University, Hofstra University, Occidental College, Georgia Institute of Technology, School of Physics and Astronomy, University of Minnesota, The Oskar Klein Centre, Department of Astronomy, University of Mississippi, Stanford/KIPAC/SLAC, University of Connecticut, Kansas State University, Vassar College, Penn State, Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Department of Physics, Worcester Polytechnic Institute, Clark University, University of Illinois at Urbana-Champaign, Rhodes College, Rensselaer Polytechnic Institute, Harvard University, Cornell University, Air Force Research Lab, Wright-Patterson AFB, Ohio 45433, Air Force Research Lab, Wright-Patterson AFB, Ohio 45433 & UES, Inc., 4401 Dayton-Xenia Rd, Dayton, OH 45432, Department of Physics, University of Dayton, Dayton Ohio & Air Force Research Lab, Wright-Patterson AFB, Ohio 45433, Los Alamos National Laboratory, Utah State University, Ramapo College of NJ, Brookhaven National Laboratory, Research Center of Topological Functional Materials and Henan Key Laboratory of Photovoltaic Materials, Henan Univers., Brookhaven National Laboratory, Montclair State University, Weber State University

  • Kristin Rabosky

    Middle Tennessee State University, University of Alabama Tuscaloosa, Swarthmore College, CT Clinical Innovation Center, Department of Radiology, Mayo Clinic, Rochester, MN, Bard College, Wright State University, University of Michigan, University of Hawai'i-Manoa, Rice University, University of Alaska Fairbanks, University of Utah, South Dakota School of Mines and Technology, Furman University, University of Notre Dame, Theoretical Physics Division, Institute of High Energy Physics, the Chinese Academy of Sciences, Peng Huanwu Center for Fundamental Theory, University of Science and Technology China, University of Cambridge, University of Kansas, SLAC National Accelerator Laboratory, Planetary Science Institute, Iowa State University, College of Idaho, University of Washington, Bothell, Ottawa Hills High School, Case Western Reserve University, Yale University and Strasbourg Astronomical Observatory, Yale University, Korea Astronomy and Space Science Institute, NOIRLab, Purdue University, Korea Instotute for Advanced Study, Perimeter Institute, Rutgers University, University of Maryland, Juniata College, Columbia University, City University of New York / American Museum of Natural History, Columbia University / American Museum of Natural History, Morehead State University, Hofstra University, Occidental College, Georgia Institute of Technology, School of Physics and Astronomy, University of Minnesota, The Oskar Klein Centre, Department of Astronomy, University of Mississippi, Stanford/KIPAC/SLAC, University of Connecticut, Kansas State University, Vassar College, Penn State, Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Department of Physics, Worcester Polytechnic Institute, Clark University, University of Illinois at Urbana-Champaign, Rhodes College, Rensselaer Polytechnic Institute, Harvard University, Cornell University, Air Force Research Lab, Wright-Patterson AFB, Ohio 45433, Air Force Research Lab, Wright-Patterson AFB, Ohio 45433 & UES, Inc., 4401 Dayton-Xenia Rd, Dayton, OH 45432, Department of Physics, University of Dayton, Dayton Ohio & Air Force Research Lab, Wright-Patterson AFB, Ohio 45433, Los Alamos National Laboratory, Utah State University, Ramapo College of NJ, Brookhaven National Laboratory, Research Center of Topological Functional Materials and Henan Key Laboratory of Photovoltaic Materials, Henan Univers., Brookhaven National Laboratory, Montclair State University, Weber State University