Publications

2026

  1. Lewis, A. L., Himberg, B., Torres-Sánchez, A., and Vanegas, J. M. Microscopic elasticity from MD. II. Liquid interfaces and lipid membranes. J. Chem. Phys. 164, 024111. (2026) [PDF]
  2. Lewis, A. L., Himberg, B., Torres-Sánchez, A., and Vanegas, J. M. Microscopic elasticity from MD. I. Bulk solid and fluid systems. J. Chem. Phys. 164, 024110. (2026) [PDF]
  3. Poudel, B., Whiting, J., Vanegas J. M., and Rempe, S. B. Thermal Degradation Energy Landscapes of Fluorofentanyls: Probing the Mechanisms and Energetics of Bond Breaking J. Phys. Chem. B 130, 3–10. (2026). [PDF]

2025

  1. Kwok, E., Khuu, P., Huang, E., Saadat, F., Urbaitel, E., Indrawan, J. S., Reardon, P. N., Vanegas, J. M., and Johnson, C. P. Disordered Ferlin C2A–C2B Linkers Bind Membranes and Encode Small Linear Motifs. J. Mol. Biol. 437, 169419. (2025) [PDF]
  2. Walker, D. R., Fujimura, G., Vanegas, J. M., and Barbar, E. J. Successful prediction of LC8 binding to intrinsically disordered proteins sheds light on AlphaFold’s black box. Front. Mol. Biosci. 12, 1531793. (2025) [PDF]
  3. Poudel, B., Whiting, J., Vanegas J. M., and Rempe, S. B. Thermal degradation energetics of fentanyl and its analogues: furanyl fentanyl and ortho -fluoro fentanyl. Phys. Chem. Chem. Phys. 27, 9631–9636. (2025). [PDF]

2024

  1. Poudel, B. and Vanegas, J. M. Structural Rearrangement of the AT1 Receptor Modulated by Membrane Thickness and Tension. J. Phys. Chem. B 128 (39) 9470-9481. (2024) [PDF]
  2. Prignano, L. A., Stevens, M. J., Vanegas, J. M., Rempe, S. B., and Dempski, R. E. Metadynamics Simulations Reveal Mechanisms of Na+ and Ca2+ Transport in Two Open States of the Channelrhodopsin Chimera. PLOS One 19 (9), e0309553. (2024) [PDF]
  3. Leverant, C. J., Richards, D., Spoerke, E. D., Alcala, R., Jiang, Y.-B., Percival, S. J., Vanegas, J. M., and Rempe, S. B. Nanoconfinement of Carbon Dioxide within Interfacial Aqueous/Ionic Liquid Systems. Langmuir 40 (20), 10615–10622. (2024) [PDF]
  4. Kim, S. W., Elsayed, M. M., Nichols, N. S., Lakoba, T., Vanegas, J. M., Wexler, C., Kotov, V. N., and Del Maestro, A. Atomically Thin Superfluid and Solid Phases for Atoms on Strained Graphene. Phys. Rev. B 109 (6), 064512. (2024) [PDF]

2023

  1. Poudel, B., Monteith, H. L., Sammon, J. P., Whiting, J. J., Moorman, M. W., Vanegas, J. M., and Rempe, S. B. Energetics of High Temperature Degradation of Fentanyl into Primary and Secondary Products. Phys. Chem. Chem. Phys. 25 (45), 30880–86. (2023) [PDF]
  2. Sharma, A., Leverant, C. J., Richards, D., Beamis, C. P., Spoerke, E. D., Percival, S. J., Rempe, S. L., and Vanegas, J. M. Transport and Energetics of Carbon Dioxide in Ionic Liquids at Aqueous Interfaces. J. Phys. Chem. B 127, 10573-10582. (2023) [PDF]
  3. Poudel, B., Rajeshwar T., R, and Vanegas, J. M. Membrane mediated mechanical stimuli produces distinct active-like states in the AT1 receptor. Nat. Commun. 14, 4690. (2023) [PDF]
  4. Sharma, A., Anishkin, A., Sukharev, S., and Vanegas, J. M. Tight hydrophobic core and flexible helices yield MscL with a high tension gating threshold and a membrane area mechanical strain buffer. Front. Chem. 11, 1159032. (2023) [PDF]
  5. Sharma, A., Chiang, R., Manginell, M., Nardi, I., Coker, E. N., Vanegas, J. M., Rempe, S. B., Bachand, G. D. Carbonic Anhydrase Robustness for Use in Nanoscale CO2 Capture Technologies. ACS Omega 8, 37830-37841. (2023) [PDF]
  6. Back, D., O'Donnell, T. J., Axt, K. K., Gurr, J. R., Vanegas, J. M., Williams, P. G., and Philmus, B. Identification, Heterologous Expression, and Characterization of the Tolypodiol Biosynthetic Gene Cluster Through an Integrated Approach. ACS Chem. Biol. 18, 1797–1807 (2023) [PDF]
  7. Kwok, E., Otto, S. C., Khuu, P., Carpenter, A. P., Codding, S. J., Reardon, P. N., Vanegas, J. M., Kumar, T. M., Kuykendall, C. J., Mehl, R. A., Baio, J., and Johnson, C. P. The Dysferlin C2A Domain Binds PI(4,5)P2 and Penetrates Membranes. J. Mol. Biol. 435, 168193 (2023) [PDF]
  8. Pirhadi, E., Vanegas, J. M., Farin, M., Schertzer, J. W., and Yong, X. Effect of Local Stress on Accurate Modeling of Bacterial Outer Membranes Using All-Atom Molecular Dynamics. J. Chem. Theory Comput. 19 (1), 363-372 (2023) [PDF]
  9. Elsayed, M. M., Kim, S. W. Vanegas, J. M., and Kotov, V. N. Polarization Charge around Impurities in Two-Dimensional Anisotropic Dirac Systems. Phys. Rev. B 108 (24), 245414 (2023) [PDF]

2022

  1. Vanegas, J. M., Peterson, D., Lakoba, T., and Kotov, V. N. Spinodal de-wetting of light liquids on graphene. J. Phys. Condens. Mat. 34, 175001 (2022) [PDF]
  2. Del Maestro, A. G., Wexler, C., Vanegas, J. M., Lakoba, T., and Kotov, V. N. A Perspective on Collective Properties of Atoms on 2D Materials. Adv. Electron. Mater., 8, 202100607 (2022) [PDF]

2021

  1. Yu, J., Lauricella, E., Elsayed, M., Shepherd Jr., K., Nichols, N. S., Lombardi, T., Kim, S.-W., Wexler, C., Vanegas, J. M., Lakoba, T., Kotov, V. N., and Del Maestro, A. G. Two-Dimensional Bose-Hubbard Model for Helium on Graphene. Phys. Rev. B 103, 235414 (2021) [PDF]
  2. **Rajeshwar T., R., Anishkin, A., Sukharev, S. and Vanegas, J.M. Mechanical Activation of MscL Revealed by a Locally Distributed Tension Molecular Dynamics Approach. Biophys. J. 19, 232-242 (2021) [PDF] **Highlighted under 'New and Notable' in the Biophys. J. January 2021 issue (see here).

2020

  1. Winkeljohn, C. M., Himberg, B., and Vanegas, J.M. Balance of Solvent and Chain Interactions Determines the Local Stress State of Simulated Membranes. J. Phys. Chem. B 124, 32, 6963–6971 (2020) [PDF]
  2. Lubkowski, J., Vanegas, J. M., Chan, W.-K., Lorenzi, P. L., Weinstein, J. N., Sukharev, S., Fushman, D., Rempe, S. B., Anishkin, A., and Wlodawer, A. The mechanism of catalysis by L-asparaginase. Biochemistry 59, 1927-1945 (2020) [PDF]

2019

  1. Chaudhari, M. I., Vanegas, J. M., Pratt, L. R., Muralidharan, A., and Rempe, S. B. Hydration Mimicry by Membrane Ion Channels Annu. Rev. Phys. Chem. 71, 1-25 (2020) [PDF]
  2. Torres-Sanchez, A., Vanegas, J. M., Purohit, P. K., Arroyo, M. Combined molecular/continuum modeling reveals the role of friction during fast unfolding of coiled-coil proteins Soft Matter 15, 4961-4975 (2019) [PDF]

2018

  1. Wen, P.-C., Vanegas, J. M., Rempe, S. B. and Tajkhorshid, E. Probing key elements of teixobactin–lipid II interactions in membranes Chem. Sci. 9, 6997-7008 (2018) [PDF]
  2. Fu, Y., Jiang, Y., Dunphy, D., Xiong, H., Coker, E., Chou, S., Zhang, H., Vanegas, J. M., Croissant, J., Cecchi, J., Rempe, S. B., and Brinker, C. J. Ultra-thin, enzymatic, nano-stabilized liquid membrane for CO2 separation. Nature Commun. 9, 990 (2018) [PDF]
  3. Vanegas, J. M., Heinrich, F., Rogers, D. M., Carson, B. D., La Bauve, S., Vernon, B. C., Akgun, B., Satija, S., Zheng, A., Kielian, M., Rempe, S. B., and Kent, M. S. Study of Dengue E insertion into lipid bilayers by neutron reflectivity and molecular dynamics simulations. Biochim. Biophys. Acta 1860, 1216 – 1230 (2018) [PDF]

2016

  1. Torres-Sanchez, A., Vanegas, J. M., and Arroyo, M. Geometric derivation of the microscopic stress: A covariant central force decomposition. J. Mech. Phys. Solids 93, 224 – 239 (2016) [PDF]

2015

  1. Torres-Sanchez, A., Vanegas, J. M., and Arroyo, M. Examining the mechanical equilibrium of microscopic stresses in molecular simulations. Phys. Rev. Lett. 114, 258102 (2015). [PDF]
  2. Anishkin, A., Vanegas, J. M., Rogers, D. M., Lorenzi, P. L., Chan, W. K., Purwaha, P., Weinstein, J. N., Sukharev, S., and Rempe, S. B. Catalytic role of the substrate defines specificity of therapeutic L-asparaginase. J. Mol. Biol. 427, (17), 2867–2885 (2015) [PDF]

2014

  1. Vanegas, J. M. and Arroyo, M. Force transduction and lipid binding in MscL: A continuum-molecular approach. PLoS ONE, 9 (12), e113947. (2014) [PDF]
  2. Vanegas, J. M., Torres-Sanchez, A., and Arroyo, M. Importance of force decomposition for local stress calculations in biomembrane molecular simulations. J. Chem. Theory Comput., 10, 691-702. (2014) [PDF]

2012

  1. Vanegas, J. M., Contreras, M. F., Faller, R., and Longo, M. L. Role of unsaturated lipid and ergosterol in ethanol tolerance of model yeast biomembranes. Biophys. J., 102, 507-516. (2012) [PDF]

2011

  1. Vanegas, J. M., Longo, M. L., and Faller, R. Crystalline, ordered and disordered lipid membranes: Convergence of stress profiles due to ergosterol. J. Am. Chem. Soc., 133, 3720-3723. (2011) [PDF]

2010

  1. Vanegas, J. M., Faller, R., and Longo, M. L. Influence of ethanol on lipid/sterol membranes: Phase diagram construction from AFM imaging. Langmuir, 26, 10415-10418. (2010) [PDF]

2009

  1. Goksu, I., Vanegas, J. M., Blanchette, C. D., Lin, W-C., and Longo, M. L. AFM for structure and dynamics of biomembranes. Biochim. Biophys. Acta, 1788, 254-266. (2009) [PDF]

Patents