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Jessica Swanson

Assistant Professor of ChemistrySwanson Photo

B.S. Biochemistry, University of California Davis

Ph.D. Physical/Theoretical Chemistry, University of California San Diego



Jessica Swanson's  Lab Page

Jessica Swanson's  Google Scholar Search

Biological Chemistry Program

Multiscale simulations of biomolecular systems, Membrane permeation, Lipid droplets, ATP hydrolysis, AAA+ ATPases, Charge transport, Channels and Antiporters


We study biological systems with computer simulations and a variety of multiscale computational methods. Although our interests are broad, we are currently focused characterizing biomolecular charge transport, membrane permeation, lipid droplets, pH-coupled processes, ATP hydrolysis and ATP-driven motion. In each of these projects we seek mechanistic insight by bridging time and length scales with electronic structure calculations, ab initio and classical molecular dynamics simulations, enhanced free energy sampling and kinetic modeling. We also work closely with experimental collaborators each step of the way, integrating experimental data, testing simulation results, predicting outcomes and ultimately synergistically characterizing each biomolecular process.



Selected Publications/References:

  1. Local Conformational Dynamics Regulating Transport Properties of a Cl-/H+ Antiporter, Z Wang, JMJ Swanson, GA Voth, J. Comput. Chem. 41 (6), 513-519 (2020).
  2. Dynamic Protonation Dramatically Affects the Membrane Permeability of Drug-Like Molecules, Z Yue, C Li, GA Voth, JMJ Swanson, Am. Chem. Soc.141 13421-13433 (2019).
  3. Mycolactone Toxin Membrane Permeation: Atomistic versus Coarse-Grained MARTINI Simulations, F Aydin, R Sun, JMJ Swanson, J., 117, 87-98 (2019).
  4. Proton Induced Conformational and Hydration Dynamics in the Influenza A M2 Channel, LC Watkins, R Liang, JMJ Swanson, WR DeGrado, GA Voth, Am. Chem. Soc.141 11667-11676 (2019).
  5. Multiscale Kinetic Modeling Reveals an Ensemble of Cl-/H+ Exchange Pathways in ClC-ec1 Antiporter, HB Mayes, S Lee, GA Voth, JMJ Swanson, Am. Chem. Soc., 140, 1793-1804 (2018).
  6. Modulating the Chemical Transport Properties of a Transmembrane Antiporter via Alternative Anion Flux, Z Wang, JMJ Swanson, GA Voth, Am. Chem. Soc.140, 16535-16543 (2018).
  7. Molecular Transport through Membranes: Accurate Permeability Coefficients from Multidimensional Potentials of Mean Force and Local Diffusion Constants, R Sun, Y Han, JMJ Swanson, JS Tan, JP Rose, GA Voth, Chem. Phys.149, 072310-1-11 (2018).
  8. Computational Means of Assessing Proton Pumping in Cytochrome c Oxidase (Complex IV)”,JMJ Swanson, chapter in Mechanisms of Primary Energy Transduction in Biology, edited by Marten Wikström, Chemical Biology series from Royal Society of Chemistry, (2018).
  9. Membrane Perturbing Properties of Toxin Mycolactone from Mycobacterium Ulcerans, C Lopez, C Unkefer, BI Swanson, JMJ Swanson, S Gnankaran, PLoS Comput. Biol., 14 (2), E1005972-1-22 (2018).
  10. Understanding the Essential Proton Pumping Kinetic Gates and Decoupling Mutations in Cytochrome c Oxidase, R Liang, GA Voth, M Wikström, JMJ Swanson, Natl. Acad. Sci. USA, 114, 5924-5929 (2017).
  11. Proton Movement and Coupling in the POT Family of Peptide Transporters, J Parker, C Li, A Brinth, Z Wang, L Vogeley, N Solcan, G Ledderboge-Vucnic, JMJ Swanson, M Caffrey, GA Voth, S Newstead, Natl. Acad. Sci. USA, 114 (50), 13182-13187 (2017).
  12. Acid Activation Mechanism of the Influenza A M2 Proton Channel, R Liang, JMJ Swanson, JJ Madsen, M Hong, WF DeGrado, GA Voth, Natl. Acad. Sci. USA, 113 (45), E6955–E6964 (2016).
  13. The Origin of Coupled Chloride and Proton Transport in a Cl/H+ Antiporter, S Lee, HB Mayes, JMJ Swanson, GA Voth, Am. Chem. Soc., 138, 14923−14930 (2016).
  14. Coupling Protein Dynamics with Proton Transport in Human Carbonic Anhydrase II, S Taraphder, CM Maupin, JMJ Swanson, GA Voth, Phys. Chem. B, 120, 8389−8404 (2016).
  15. Multiscale Simulations Reveal Key Features of the Proton Pumping Mechanism in Cytochrome c Oxidase, R Liang, JMJ Swanson, Y Peng, M Wikström, GA Voth, Natl. Acad. Sci. USA, 113 (27), 7420-7425 (2016).
  16. Multiscale Simulations Reveal Key Aspects of the Proton Transport Mechanism in the ClC-ec1 Antiporter, S Lee, JMJ Swanson, GA Voth, J., 110 (6), 1334-1345 (2016).
  17. Computationally Efficient Multiscale Reactive Molecular Dynamics to Describe Amino Acid Deprotonation in Proteins, S Lee, R Liang, GA Voth, JMJ Swanson, Chem. Theory Comput., 12 (2), 879-891 (2016).

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Last Updated: 10/1/20