J. Swanson

发表

Revisiting free energy calculations: a theoretical connection to MM/PBSA and direct calculation of the association free energy.

Richard H. Henchman, J. Mccammon, J. Swanson, 2004, Biophysical journal.

Understanding and Tracking the Excess Proton in Ab initio Simulations; Insights from IR Spectra.

J. Swanson, Chenghan Li, 2020, The journal of physical chemistry. B.

Determinants of Endoplasmic Reticulum-to-Lipid Droplet Protein Targeting.

J. Swanson, T. Walther, R. Farese, 2020, Developmental cell.

Optimized Radii for Poisson-Boltzmann Calculations with the AMBER Force Field.

J Andrew McCammon, Jessica M J Swanson, Stewart A. Adcock, 2005, Journal of chemical theory and computation.

Hydrated Excess Protons Can Create Their Own Water Wires

G. Voth, J. Swanson, R. Zhou, 2014, The journal of physical chemistry. B.

Multiscale simulation reveals a multifaceted mechanism of proton permeation through the influenza A M2 proton channel

Jessica M J Swanson, Gregory A Voth, Hui Li, 2014, Proceedings of the National Academy of Sciences.

Multiscale simulations reveal key features of the proton-pumping mechanism in cytochrome c oxidase

G. Voth, J. Swanson, M. Wikström, 2016, Proceedings of the National Academy of Sciences.

Computationally Efficient Multiscale Reactive Molecular Dynamics to Describe Amino Acid Deprotonation in Proteins

G. Voth, J. Swanson, Sangyun Lee, 2016, Journal of chemical theory and computation.

Creation and Characterization of Industrially Applicable de Novo Lager Yeast Hybrids with a Unique Genomic Architecture.

J. Swanson, T. Sierocinski, C. Brimacombe, 2020, Applied and environmental microbiology.

Mycolactone Toxin Membrane Permeation: Atomistic versus Coarse-Grained MARTINI Simulations.

J. Swanson, Fikret Aydin, Rui Sun, 2019, Biophysical journal.

Can Membrane Composition Traffic Toxins? Mycolactone and Preferential Membrane Interactions

J. Swanson, G. C. da Hora, John D M Nguyen, 2022, bioRxiv.

Mechanism of Mycolactone Toxin Membrane Permeation: Atomistic vs Coarse-Grained MARTINI Simulations

J. Swanson, Fikret Aydin, Rui Sun, 2018, bioRxiv.

Interaction of cytochrome c with cardiolipin: an infrared spectroscopic study.

J. Swanson, S. Choi, S. Choi, 1995, Biophysical chemistry.

Capturing the Liquid-Crystalline Phase Transformation: Implications for Protein Targeting to Sterol Ester-Rich Lipid Droplets

J. Swanson, R. Braun, 2022, bioRxiv.

The CYTOLD and ERTOLD pathways for lipid droplet-protein targeting.

Robert V Farese, J. Swanson, T. Walther, 2021, Trends in biochemical sciences.

Intricate role of water in proton transport through cytochrome c oxidase.

Gregory A. Voth, Jessica M. J. Swanson, Robert B. Gennis, 2010, Journal of the American Chemical Society.

Dynamic Protonation Dramatically Affects the Membrane Permeability of Drug-like Molecules.

Gregory A. Voth, Zhi Yue, Jessica M. J. Swanson, 2019, Journal of the American Chemical Society.

Proton solvation and transport in aqueous and biomolecular systems: insights from computer simulations.

Jessica M J Swanson, Gregory A Voth, C Mark Maupin, 2007, The journal of physical chemistry. B.

Highly conserved charge-pair networks in the mitochondrial carrier family.

J. Swanson, D. Nelson, C. Félix, 1998, Journal of molecular biology.

Industrially Applicable De Novo Lager Yeast Hybrids with a Unique Genomic Architecture: Creation and Characterization

J. Swanson, T. Sierocinski, C. Brimacombe, 2020, Applied and Environmental Microbiology.

Toward a Multipathway Perspective: pH-Dependent Kinetic Selection of Competing Pathways and the Role of the Internal Glutamate in Cl-/H+ Antiporters.

J. Swanson, Chenghan Li, A. V. Mironenko, 2021, The journal of physical chemistry. B.

Proton movement and coupling in the POT family of peptide transporters

G. Voth, J. Swanson, M. Caffrey, 2017, Proceedings of the National Academy of Sciences.

Acid activation mechanism of the influenza A M2 proton channel

G. Voth, W. DeGrado, J. Swanson, 2016, Proceedings of the National Academy of Sciences.

Understanding the essential proton-pumping kinetic gates and decoupling mutations in cytochrome c oxidase

G. Voth, J. Swanson, M. Wikström, 2017, Proceedings of the National Academy of Sciences.

Multiscale simulations reveal key features of the proton pumping mechanism in cytochrome c oxidase

G. Voth, J. Swanson, M. Wikström, 2016, bioRxiv.

Coupling Protein Dynamics with Proton Transport in Human Carbonic Anhydrase II

G. Voth, J. Swanson, C. M. Maupin, 2016, The journal of physical chemistry. B.

The entropic cost of protein-protein association: a case study on acetylcholinesterase binding to fasciculin-2.

David D L Minh, David D. L. Minh, J Andrew McCammon, 2005, Biophysical journal.

Computational Studies of Lipid Droplets

G. Voth, J. Swanson, Siyoung Kim, 2022, The journal of physical chemistry. B.

Coupling nonpolar and polar solvation free energies in implicit solvent models.

J A McCammon, J. Mccammon, J. Swanson, 2006, The Journal of chemical physics.

Coupling hydrophobicity, dispersion, and electrostatics in continuum solvent models.

J A McCammon, J. Mccammon, J. Swanson, 2005, Physical review letters.

Limitations of atom-centered dielectric functions in implicit solvent models.

J Andrew McCammon, Jessica M J Swanson, John Mongan, 2005, The journal of physical chemistry. B.

Role of charge transfer in the structure and dynamics of the hydrated proton.

Jessica M J Swanson, J. Simons, J. Swanson, 2009, The journal of physical chemistry. B.

The Surface and Hydration Properties of Lipid Droplets.

J. Swanson, Siyoung Kim, 2020, Biophysical journal.

Stressed Lipid Droplets: How Neutral Lipids Relieve Surface Tension and Membrane Expansion Drives Protein Association.

J. Swanson, Siyoung Kim, M. Oh, 2021, The journal of physical chemistry. B.

Tld1 is a novel regulator of triglyceride lipolysis that demarcates a lipid droplet subpopulation

J. Swanson, N. Speer, W. Henne, 2023, bioRxiv.

Coarse-graining in interaction space: a systematic approach for replacing long-range electrostatics with short-range potentials.

G. Voth, J. Swanson, S. Izvekov, 2008, The journal of physical chemistry. B.

Proton Induced Conformational and Hydration Dynamics in the Influenza A M2 Channel.

G. Voth, W. DeGrado, J. Swanson, 2019, Journal of the American Chemical Society.

Benchmark Study of the SCC-DFTB Approach for a Biomolecular Proton Channel.

G. Voth, J. Swanson, Ruibin Liang, 2014, Journal of chemical theory and computation.

Local conformational dynamics regulating transport properties of a Cl−/H+ antiporter

Zhi Wang, Jessica M J Swanson, Gregory A Voth, 2020, J. Comput. Chem..

Using force-matching to reveal essential differences between density functionals in ab initio molecular dynamics simulations.

J. Swanson, S. Izvekov, 2011, The Journal of chemical physics.

Membrane perturbing properties of toxin mycolactone from Mycobacterium ulcerans

Basil I. Swanson, S. Gnanakaran, Clifford J. Unkefer, 2018, PLoS Comput. Biol..

Computer simulation of water in cytochrome c oxidase.

J. Swanson, A. Stuchebrukhov, Xuehe Zheng, 2003, Biochimica et biophysica acta.

Optimizing the Poisson Dielectric Boundary with Explicit Solvent Forces and Energies: Lessons Learned with Atom-Centered Dielectric Functions.

Nathan A. Baker, Jessica M J Swanson, Nathan A Baker, 2007, Journal of chemical theory and computation.

Multiscale Reactive Molecular Dynamics for Absolute pKa Predictions and Amino Acid Deprotonation

J. Swanson, D. Silverstein, Yuxing Peng, 2014, Journal of chemical theory and computation.

Molecular transport through membranes: Accurate permeability coefficients from multidimensional potentials of mean force and local diffusion constants.

John P. Rose, Jeffrey S. Tan, G. Voth, 2018, The Journal of chemical physics.

CycFlowDec: A Python module for decomposing flow networks using simple cycles

Austen Bernardi, Jessica M.J. Swanson, J. Swanson, 2021, SoftwareX.

Multiscale Simulations Reveal Key Aspects of the Proton Transport Mechanism in the ClC-ec1 Antiporter.

Jessica M J Swanson, Gregory A Voth, G. Voth, 2016, Biophysical journal.

The Origin of Coupled Chloride and Proton Transport in a Cl–/H+ Antiporter

Gregory A. Voth, Heather B. Mayes, Jessica M. J. Swanson, 2016, bioRxiv.

Modulating the Chemical Transport Properties of a Transmembrane Antiporter via Alternative Anion Flux

G. Voth, J. Swanson, Zhi Wang, 2018, Journal of the American Chemical Society.

Mycolactone A vs. B: Multiscale Simulations Reveal the Roles of Localization and Association in Isomer-Specific Toxicity

J. Swanson, G. C. D. da Hora, John D. M. Nguyen, 2023, Toxins.

Improving the accuracy and convergence of drug permeation simulations via machine-learned collective variables.

Aleksander E. P. Durumeric, J. Swanson, Fikret Aydin, 2021, The Journal of chemical physics.

tICA-Metadynamics for Identifying Slow Dynamics in Membrane Permeation

J. Swanson, Myongin Oh, G. C. D. da Hora, 2023, bioRxiv.

Mycolactone A vs. B: Does localization or association explain isomer-specific toxicity?

J. Swanson, G. C. D. da Hora, John D. M. Nguyen, 2023, bioRxiv.

Intricate role of water in proton transport through cytochrome c oxidase.

G. Voth, R. Gennis, J. Swanson, 2010, Journal of the American Chemical Society.

Lasso Peptides: Exploring the Folding Landscape of Nature's Smallest Interlocked Motifs.

J. Swanson, A. G. Roberts, Myongin Oh, 2024, Journal of the American Chemical Society.

tICA-Metadynamics for Identifying Slow Dynamics in Membrane Permeation.

J. Swanson, Myongin Oh, Gabriel C. A. da Hora, 2023, Journal of Chemical Theory and Computation.

Dynamic Protonation Dramatically Affects the Membrane Permeability of Drug-like Molecules.

G. Voth, J. Swanson, Chenghan Li, 2019, Journal of the American Chemical Society.