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Jessica Swanson

Assistant Professor of Chemistry and Adjunct Assistant Professor of Biochemistry

Multiscale Simulations of Biomolecular Systems, Membrane Permeation, Lipid Droplets, ATP Hydrolysis, AAA+ ATPases, Charge Transport, Channels and Antiporters

Swanson Photo

 

Biological Chemistry Program

Education

B.S. Biochemistry, University of California Davis

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

Links

Lab Page

Google Scholar Search

j.swanson@utah.edu

 

Research

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.

 

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References (Selected Publications)

  1. Toward a Multipathway Perspective: pH-Dependent Kinetic Selection of Competing Pathways and the Role of the Internal Glutamate in Cl–/H+ Antiporters. Z Yue, A Bernardi, C Li, AV Mironenko, JMJ Swanson. The Journal of Physical Chemistry (2021)
  2. Improving the accuracy and convergence of drug permeation simulations via machine-learned collective variables. F Aydin, AEP Durumeric, GCA da Hora, JDM Nguyen, MI Oh, ...The Journal of Chemical Physics 155 (4), 045101 (2021)
  3. CycFlowDec: A Python module for decomposing flow networks using simple cycles. A Bernardi, JMJ Swanson. SoftwareX 14, 100676 (2021)
  4. Stressed lipid droplets: How neutral lipids relieve surface tension and membrane expansion drives protein association. S Kim, MI Oh, JMJ Swanson. The Journal of Physical Chemistry B (2021)
  5. The Surface and Hydration Properties of Lipid Droplets. S Kim, JMJ Swanson. Biophysical Journal 119 (10), 1958-1969 (2020)
  6. Determinants of endoplasmic reticulum-to-lipid droplet protein targeting. MJ Olarte, S Kim, ME Sharp, JMJ Swanson, RV Farese Jr, TC Walther. Developmental Cell 54 (4), 471-487. e7 (2020)
  7. Understanding and tracking the excess proton in Ab Initio simulations; Insights from IR spectra. C Li, JMJ Swanson. The Journal of Physical Chemistry B 124 (27), 5696-5708 (2020)
  8. Local conformational dynamics regulating transport properties of a Cl−/H+ antiporter. Z Wang, JMJ Swanson, GA Voth. Journal of computational chemistry 41 (6), 513-519 (2020)
  9. Understanding coupled ion exchange in ClC antiporters from the kinetic landscape of Cl-/H plus exchange. J Swanson. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 258 (2019)
  10. How proteins use hydration as a kinetic control knob in coupled ion exchange J Swanson ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 258 (2019)
  11. Integrating dynamic ionization into membrane permeation free energy landscapes and macroscopic permeability calculations. Z Yue, J Swanson. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 258 (2019)
  12. Dynamic protonation dramatically affects the membrane permeability of drug-like molecules. Z Yue, C Li, GA Voth, JMJ Swanson. Journal of the American Chemical Society 141 (34), 13421-13433 (2019)
  13. Mycolactone toxin membrane permeation: atomistic versus coarse-grained MARTINI simulations. F Aydin, R Sun, JMJ Swanson. Biophysical journal 117 (1), 87-98 (2019)
  14. Proton-induced conformational and hydration dynamics in the influenza A M2 channel. LC Watkins, R Liang, JMJ Swanson, WF DeGrado, GA Voth. Journal of the American Chemical Society 141 (29), 11667-11676 (2019)
  15. Modulating the Chemical Transport Properties of the CLC Antiporter via Alternative Anion Flux and Mutation. Z Wang, JMJ Swanson, GA Voth. Biophysical Journal 116 (3), 433a (2019)
  16. Modulating the chemical transport properties of a transmembrane antiporter via alternative anion flux. Z Wang, JMJ Swanson, GA Voth. Journal of the American Chemical Society 140 (48), 16535-16543 (2018)
  17. Automatic Construction of Collective Variables for Metadynamics Simulations of Drug Permeation through Lipid Membranes. F Aydin, JMJ Swanson, GA Voth. 2018 AIChE Annual Meeting (2018)
  18. 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. The Journal of chemical physics 149 (7), 072310 (2018)
  19. Multiscale Kinetic Modeling Reveals an Ensemble of Cl–/H+ Exchange Pathways in ClC-ec1 Antiporter. HB Mayes, S Lee, AD White, GA Voth, JMJ Swanson. Journal of the American Chemical Society 140 (5), 1793-1804     (2018)
  20. Membrane perturbing properties of toxin mycolactone from Mycobacterium ulcerans. CA López, CJ Unkefer, BI Swanson, JMJ Swanson, S Gnanakaran. PLoS computational biology 14 (2), e1005972 (2018)
  21. Multiscale Kinetic Modeling of a Cl−/H+ Antiporter: Integrating Simulation and Experiment to Characterize A Complex Ion Exchange Process. JM Swanson, HB Mayes, S Lee, GA Voth Biophysical Journal 114 (3), 7a (2018)
  22. Proton movement and coupling in the POT family of peptide transporters. JL Parker, C Li, A Brinth, Z Wang, L Vogeley, N Solcan, ...Proceedings of the National Academy of Sciences 114 (50), 13182-13187 (2017)
  23. Mechanisms of Primary Energy Transduction in Biology. C Moser, L Sazanov, V Zickermann, V Kaila, R Gennis, B Barquera, ... Royal Society of Chemistry (2017)
  24. Computational Means of Assessing Proton Pumping in Cytochrome c Oxidase (Complex IV). JMJ Swanson. Mechanisms of Primary Energy Transduction in Biology 5, 249 (2017)
  25. Understanding the essential proton-pumping kinetic gates and decoupling mutations in cytochrome c oxidase. R Liang, JMJ Swanson, M Wikström, GA Voth. Proceedings of the National Academy of Sciences 114 (23), 5924-5929 (2017)
  26. The Origin of Coupled Chloride and Proton Transport in a Cl-/H+ Antiporter. S Lee, HB Mayes, JMJ Swanson, GA Voth. Biophysical Journal 112 (3), 254a-255a (2017)
  27. The Origin of Coupled Chloride and Proton Transport in a Cl–/H+ Antiporter. S Lee, HB Mayes, JMJ Swanson, GA Voth. Journal of the American Chemical Society 138 (45), 14923-14930 (2016)
  28. Acid activation mechanism of the influenza A M2 proton channel. R Liang, JMJ Swanson, JJ Madsen, M Hong, WF DeGrado, GA Voth. Proceedings of the National Academy of Sciences 113 (45), E6955-E6964 (2016)
  29. Coupling protein dynamics with proton transport in human carbonic anhydrase II. S Taraphder, CM Maupin, JMJ Swanson, GA Voth. The Journal of Physical Chemistry B 120 (33), 8389-8404 (2016)
  30. Multiscale simulations reveal key features of the proton-pumping mechanism in cytochrome c oxidase. R Liang, JMJ Swanson, Y Peng, M Wikström, GA VothProceedings of the National Academy of Sciences 113 (27), 7420-7425 (2016)
  31. Multiscale simulations reveal key aspects of the proton transport mechanism in the ClC-ec1 antiporter. S Lee, JMJ Swanson, GA Voth. Biophysical journal 110 (6), 1334-1345 (2016)
  32. Computationally efficient multiscale reactive molecular dynamics to describe amino acid deprotonation in proteins. S Lee, R Liang, GA Voth, JMJ Swanson. Journal of chemical theory and computation 12 (2), 879-891 (2016)
  33. Hydrated excess protons can create their own water wires. Y Peng, JMJ Swanson, S Kang, R Zhou, GA Voth. The Journal of Physical Chemistry B 119 (29), 9212-9218 (2015)
  34. Multiscale Reactive Molecular Dynamics for Absolute pKa Predictions and Amino Acid Deprotonation. JG Nelson, Y Peng, DW Silverstein, JMJ Swanson. Journal of chemical theory and computation 10 (7), 2729-2737 (2014)
  35. Multiscale simulation reveals a multifaceted mechanism of proton permeation through the influenza A M2 proton channel. R Liang, H Li, JMJ Swanson, GA Voth. Proceedings of the National Academy of Sciences 111 (26), 9396-9401 (2014)
  36. Benchmark study of the SCC-DFTB approach for a biomolecular proton channel. R Liang, JMJ Swanson, GA Voth. Journal of chemical theory and computation 10 (1), 451-462 (2014)
  37. Using force-matching to reveal essential differences between density functionals in ab initio molecular dynamics simulations. S Izvekov, JMJ Swanson. The Journal of chemical physics 134 (19), 194109 (2011)
  38. Intricate Role of Water in Proton Transport through Cytochrome c Oxidase. HJ Lee, E Svahn, JMJ Swanson, H Lepp, GA Voth, P Brzezinski, ...Journal of the American Chemical Society 132 (45), 16225-16239 (2010)
  39. Role of charge transfer in the structure and dynamics of the hydrated proton. JMJ Swanson, J Simons, The Journal of Physical Chemistry B 113 (15), 5149-5161 (2009)
  40. Coarse-graining in interaction space: A systematic approach for replacing long-range electrostatics with short-range potentials. S Izvekov, JMJ Swanson, GA Voth. The Journal of Physical Chemistry B 112 (15), 4711-4724 (2008)
  41. Proton solvation and transport in aqueous and biomolecular systems: Insights from computer simulations. JMJ Swanson, CM Maupin, H Chen, MK Petersen, J Xu, Y Wu, GA Voth. The Journal of Physical Chemistry B 111 (17), 4300-4314 (2007)
  42. Optimizing the Poisson dielectric boundary with explicit solvent forces and energies: lessons learned with atom-centered dielectric functions. JMJ Swanson, JA Wagoner, NA Baker, JA McCammon. Journal of Chemical Theory and Computation 3 (1), 170-183 (2007)
  43. The entropic cost of proteinprotein association: a case study on acetylcholinestrase binding to fasciculin-2 (vol 89, L25, 2005). DDL Minh, JM Bui, C Chang, T Jain, JMJ Swanson, JA McCammon. BIOPHYSICAL JOURNAL 91 (2), 775-775 (2006)
  44. Coupling hydrophobicity, dispersion, and electrostatics in continuum solvent models. J Dzubiella, JMJ Swanson, JA McCammon. Physical review letters 96 (8), 087802 (2006)
  45. Coupling nonpolar and polar solvation free energies in implicit solvent models. J Dzubiella, JMJ Swanson, JA McCammon. The Journal of chemical physics 124 (8), 084905 (2006)
  46. The entropic cost of protein-protein association: a case study on acetylcholinesterase binding to fasciculin-2. DDL Minh, JM Bui, C Chang, T Jain, JMJ Swanson, JA McCammon. Biophysical journal 89 (4), L25-L27 (2005)
  47. Limitations of atom-centered dielectric functions in implicit solvent models. JMJ Swanson, J Mongan, JA McCammon. The Journal of Physical Chemistry B 109 (31), 14769-14772 (2005)
  48. Optimized radii for Poisson− Boltzmann calculations with the AMBER force field. JMJ Swanson, SA Adcock, JA McCammon. Journal of Chemical Theory and Computation 1 (3), 484-493 (2005)
  49. Revisiting free energy calculations: a theoretical connection to MM/PBSA and direct calculation of the association free energy. JMJ Swanson, RH Henchman, JA McCammon. Biophysical journal 86 (1), 67-74 (2004)
  50. Computer simulation of water in cytochrome c oxidase. X Zheng, DM Medvedev, J Swanson, AA Stuchebrukhov. Biochimica et Biophysica Acta (BBA)-Bioenergetics 1557, 99-107 (2003)
Last Updated: 9/23/21