PHYSICAL & BIOLOGICAL CHEMISTRY
Ph.D., University of California, San Diego 2006
NIH Ruth Kirschstein Postdoctoral Fellow, University of Utah, 2006-2009
Research Assistant to Research Associate Professor, University of Chicago, 2010-2019
Phone: (801) 581-7485
Office: 4613 TBBC
Activities & Awards
- Telluride Summer Research Center Protons in Biology Conference Co-Chair, 2018-2020
- NIH Ruth Kirschtein Postdoctoral Fellow, 2006-2009
- ACS Phys. Chem. Postdoctoral Research Highlights, 2009
Biological systems wrap many layers of complexity and eons of evolution into finely tuned function, and arguably more complex, intermixed dysfunction. Our research aims to probe medically and environmentally relevant biological processes at the molecular level. Combining electronic structure data, ab initio and classical molecular dynamics simulation, enhanced free energy sampling methods, and kinetic models, we study processes across a range of time and length scales, ultimately revealing key mechanistic insight.
Our multiscale approach is used to characterize complex biophysical processes such as ATP hydrolysis in AAA ATPases, membrane permeation and lipid trafficking, protein targeting of lipid droplets, as well as a wide range of proton-coupled phenomena including charge transport in channels and transporters, redox-coupled proton pumping, and pH-dependent membrane interactions. Many of these projects involve chemical reactions in large biomolecular systems, for which we bridge the quantum and classical realms with QM/MM and reactive molecular dynamics simulations. Most projects are also complemented by close experimental collaborations.
- Aydin, R. Sun, J.M.J. Swanson, Mechanism of Mycolactone Toxin Membrane Permeation: Atomistic vs Coarse-Grained MARTINI Simulations, Biophys. J., 116 (12) (2019).
- B. Mayes, S. Lee, G.A. Voth, J.M.J. Swanson, Multiscale Kinetic Modeling Reveals an Ensemble of Cl-/H+ Exchange Pathways in ClC-ec1 Antiporter, J. Am. Chem. Soc., 140, 1793-1804 (2018).
- M.J. Swanson, Computational Means of Assessing Proton Pumping in Cytochrome c Oxidase (Complex IV), chapter in Mechanisms of Primary Energy Transduction in Biology, edited by Marten Wikström, Chemical Biology series from Royal Society of Chemistry, (2018).
- Liang, G.A. Voth, M Wikström, J.M.J. Swanson, Understanding the Essential Proton Pumping Kinetic Gates and Decoupling Mutations in Cytochrome c Oxidase, Proc. Natl. Acad. Sci. USA, 114, 5924-5929 (2017).
- Lee, R. Liang, G.A. Voth, J.M.J. Swanson, Computationally Efficient Multiscale Reactive Molecular Dynamics to Describe Amino Acid Deprotonation in Proteins, J. Chem. Theory Comput., 12 (2), 879-891 (2016).