PUBLICATIONS
- From Flux to Function: Extracting Mechanistic Insights from Ion Channels via IV and Iμ Analyses, H Weckel-
Dahman, R Carlsen, A Daum, JMJ Swanson, J. Phys. Chem. B (under review, 2025) - Mechanistic Insights into the Selective Targeting of MLX to Triacylglycerol-Rich Lipid Droplets, JR Braun,
JMJ Swanson, Biophys J (under review, 2025). bioRxiv: DOI: 10.1101/2024.07.15.603605 - Progress in Lipid Droplet Simulations: How Polarizability Shapes Triacylglycerol Behavior in Bulk and
Interfacial Environments, JR Braun, Jessica M. J. Swanson, J. Chem. Theory Comput. (2025) 21, 8235-8248. DOI: 10.1021/acs.jctc.5c00882 - Ion Channel Reaction Networks: Dielectric Screening and the Importance of Off-Pathway Flux, H Weckel-
Dahman, R Carlsen, A Daum, M He, TG Southam, JMJ Swanson, J. Chem. Theory Comput. Special Issue on
Markov State Modeling (2025) 21, 3700-3711. DOI: 10.1101/2025.03.06.637869 - In Silico Design of Foldable Lasso Peptides, JDM Nguyen, GCM da Hora, MC Mifflin, L Digal, AG Roberts,
JMJ Swanson, Biophys. J. (2025) 124, 1-16. DOI: 10.1016/j.bpj.2025.03.036 - Multiscale Responsive Kinetic Modeling: Quantifying Biomolecular Reaction Flux under Varying
Electrochemical Conditions, H Weckel-Dahman, R Carlsen, JMJ Swanson, J. Chem. Theory Comput. (2025)
21, 1, 374-389. PMC11312519. DOI: 10.1021/acs.jctc.4c00872 - News & Views: How nature ties peptide knots, AG Roberts, JMJ Swanson, Nature Chem Bio (2024) doi:
10.1038/s41589-024-01775-2 - Nernst Equilibrium, Rectification, and Saturation: Insights into Ion Channel Behavior, R Carlsen, H Weckel-
Dahman, JMJ Swanson Biophys. J. (2024) 123, 1-12. PMC11343188. DOI: 10.1101/2024.08.16.608320 - One Descriptor to Fold Them All: Harnessing Intuition and Machine Learning to Identify Transferable Lasso
Peptide Reaction Coordinates GCM da Hora, MI Oh, JDM Nguyen, JMJ Swanson, J. Phys. Chem.B (2024)
128(17): 4063-4075. *Cover Story. DOI: 10.1021/acs.jpcb.3c08492 - Lasso Peptides: Exploring the Folding Landscape of Nature’s Smallest Interlocked Motifs GCM da Hora, MI
Oh, MC Mifflin, L Digal, AG Roberts, JMJ Swanson, J. Am. Chem. Soc. (2024) 146 (7): 4444-4454. *Cover
Story. DOI: 10.1021/jacs.3c10126 - Tld1 is a novel regulator of triglyceride lipolysis that demarcates a lipid droplet subpopulation. Speer NO,
Braun JR, Reynolds EG, Swanson JMJ, Henne WM. J Cell Biol (2024) 223 (1): e202303026. PMC10028886. DOI: 10.1083/jcb.202303026 - tICA-Metadynamics for Identifying Slow Dynamics in Membrane Permeation, MI Oh, GCA da Hora, JMJ
Swanson, J. Chem. Theory Comput. (2023) 19 (23) 8886-8900. PMC11282584. DOI: 10.1021/acs.jctc.3c00526 - Mycolactone A vs. B: Multiscale Simulations Reveal the Roles of Localization and Association in Isomer-
Specific Toxicity, JDM Nguyen, GCA da Hora, JMJ Swanson, Toxins 15(8) 486-1-21 (2023). *Cover story. DOI: 10.3390/toxins15080486 - Can membrane composition traffic toxins? Mycolactone and preferential membrane interactions, GCM da
Hora, JDM Nguyen, JMJ Swanson, Biophys. J. 121 4260-4270 (2022). PMC9703097. DOI: 10.1016/j.bpj.2022.10.019 - Capturing the liquid-crystalline phase transformation: Implications for protein targeting to sterol ester-rich
lipid droplets, JR Braun, JMJ Swanson, Membranes 12 949 (2022). PMC9607156. DOI:10.3390/membranes12100949 - Computational Studies of Lipid Droplets, S. Kim, JMJ Swanson, GA Voth J Phys. Chem. B—Feature Article
126 2145-2154 (2022). PMC8957551. DOI: 10.1021/acs.jpcb.2c00292 - Multiscale Kinetic Analysis of Proteins, JMJ Swanson, Curr. Op. Struct. Biol. 72 169-175 (2021).
PMC9288830. DOI: 10.1016/j.sbi.2021.11.005 - The CYTOLD and ERTOLD pathways for lipid droplet–protein targeting, MJ Olarte, JMJ Swanson, TC
Walther, RV Farese, Trends Biochem. Sci. 47(1) 39-51 (2021). PMC8688270. DOI: 10.1016/j.tibs.2021.08.007 - Toward a Multi-pathway 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, J.
Phys. Chem. B 125, 7975-7984 (2021). PMC8409247. DOI: 10.1021/acs.jpcb.1c03304 - Improving the accuracy and convergence of drug permeation simulations via machine-learned collective
variables, F Aydin, AEP Durameric, GCA da Hora, JDM Nguyen, MI Oh, JMJ Swanson, J. Chem. Phys. 155,
045101-01-11 (2021). PMID34340389. DOI: 10.1063/5.0055489 - Stressed Lipid Droplets: How Neutral Lipids Relieve Surface Tension and Membrane Expansion Drives
Protein Association, S Kim, MI Oh, JMJ Swanson, J. Phys. Chem. B 125, 5572-5586 (2021). PMC8796793. DOI: 10.1021/acs.jpcb.1c01795 - CycFlowDec: A Python module for decomposing flow networks using simple cycles, A Bernardi, JMJ
Swanson, SoftwareX 14 (2021). PMC8545271. DOI: 10.1016/j.softx.2021.100676 - The Surface and Hydration Properties of Lipid Droplets, S Kim, JMJ Swanson, Biophys. J. 119, 1958-1969
(2020). PMC7732727. DOI: 10.1016/j.bpj.2020.10.001 - Determinants of Endoplasmic Reticulum-to-Lipid Droplet Protein Targeting, MJ Olarte, S Kim, ME Sharp,
JMJ Swanson, RV Farese, TC Walther, Dev. Cell 54, 471-487 (2020). PMC7696655. DOI: 10.1016/j.devcel.2020.07.001 - Understanding and Tracking the Excess Proton in Ab Initio Simulations; Insights from IR Spectra, C Li, GA
Voth, JMJ Swanson, J. Phys. Chem. B 124, 5696-5708 (2020). PMC7448536. DOI: 10.1021/acs.jpcb.0c03615
Full list of publications can be found here.