Publications

(For a full list of Josh’s publications, including those prior to his time at MSU, go to Google Scholar, ORCID)

Highlights

  1. A Lipoxygenase 3 Mutation Reverses Growth Phenotypes in an Arabidopsis Plastid Lipase 3 Overexpression Line A Lipoxygenase 3 Mutation Reverses Growth Phenotypes in an Arabidopsis Plastid Lipase 3 Overexpression Line

    Mugume, Y., Cook, R., Hagerty, B., Liu, J., Alvord, Z. B., Danhof, L., Froehlich, J. E., Vermaas, J. V., & Benning, C. (2026). A Lipoxygenase 3 Mutation Reverses Growth Phenotypes in an Arabidopsis Plastid Lipase 3 Overexpression Line. PLOS One, 21(6), e0350738.

  2. Dynamics and Structural Responses to Cis–Trans Isomerization in Bacterial Lipid Bilayers Dynamics and Structural Responses to Cis–Trans Isomerization in Bacterial Lipid Bilayers

    Raza, S., Sievertsen, T. H., Jafari, M., & Vermaas, J. V. (2026). Dynamics and Structural Responses to Cis–Trans Isomerization in Bacterial Lipid Bilayers. ACS Omega, 11(1), 449–459.

  3. Evaluating the Transport Mechanism for Lignocellulosic Inhibitors in Zymomonas Mobilis Evaluating the Transport Mechanism for Lignocellulosic Inhibitors in <i>Zymomonas</i><i> Mobilis</i>

    Singh, N. K., & Vermaas, J. V. (2026). Evaluating the Transport Mechanism for Lignocellulosic Inhibitors in Zymomonas Mobilis. ACS Sustainable Chemistry & Engineering, 14(29), 13292–13302.

  4. Encapsulation in a Bacterial Microcompartment Shell Improves Thermal Stability of a Glycolytic Enzyme Encapsulation in a Bacterial Microcompartment Shell Improves Thermal Stability of a Glycolytic Enzyme

    Tefft, N. M., Yadav, N. S., Gruenberg Cross, M. C., Swiggett, C. D., Parent, K. N., Vermaas, J. V., & TerAvest, M. A. (2026). Encapsulation in a Bacterial Microcompartment Shell Improves Thermal Stability of a Glycolytic Enzyme. ACS Synth. Biol., 15(5), 1980–1992.

  5. Quantifying Chemically Modified Acetylation Induced Changes in the Plant Secondary Cell Wall Structure and Dynamics Quantifying Chemically Modified Acetylation Induced Changes in the Plant Secondary Cell Wall Structure and Dynamics

    Complementary work tracking ion diffusion within plant cell walls after acetylation.

    Barkarar, M., Sarkar, D., Hunt, C. G., & Vermaas, J. V. (2025). Quantifying Chemically Modified Acetylation Induced Changes in the Plant Secondary Cell Wall Structure and Dynamics. Biomacromolecules, 26(9), 5645–5656.

    This is a great example of undergraduate researchers doing cool work in the lab, as Murtaza has now moved on to bigger and better things!

  6. Identifying and Quantifying Membrane Interactions of the Protein Human Cis -prenyltransferase Identifying and Quantifying Membrane Interactions of the Protein Human <i>Cis</i> -prenyltransferase

    Boren, D. M., Kredi, S., Positselskaya, E., Giladi, M., Haitin, Y., & Vermaas, J. V. (2025). Identifying and Quantifying Membrane Interactions of the Protein Human Cis -prenyltransferase. Protein Science, 34(6), e70167.

  7. Molecular Modeling and Molecular Dynamics Simulation of a Packed and Intact Bacterial Microcompartment Molecular Modeling and Molecular Dynamics Simulation of a Packed and Intact Bacterial Microcompartment

    Wicked cool simulations of a whole 11M atom BMC system! We learned alot from this research that we think we can apply to further advance catalysis within BMCs.

    Raza, S., Yadav, N. S., Jussupow, A., Kerfeld, C. A., Feig, M., & Vermaas, J. V. (2025). Molecular Modeling and Molecular Dynamics Simulation of a Packed and Intact Bacterial Microcompartment. J. Phys. Chem. B, 129(50), 12811–12827.

    This particular research made the cover!

  8. Adaptative Survival of Aspergillus Fumigatus to Echinocandins Arises from Cell Wall Remodeling beyond β-1,3-Glucan Synthesis Inhibition Adaptative Survival of Aspergillus Fumigatus to Echinocandins Arises from Cell Wall Remodeling beyond β-1,3-Glucan Synthesis Inhibition

    Dickwella Widanage, M. C., Gautam, I., Sarkar, D., Mentink-Vigier, F., Vermaas, J. V., Ding, S.-Y., Lipton, A. S., Fontaine, T., Latgé, J.-P., Wang, P., & Wang, T. (2024). Adaptative Survival of Aspergillus Fumigatus to Echinocandins Arises from Cell Wall Remodeling beyond β-1,3-Glucan Synthesis Inhibition. Nat Commun, 15(1), 6382.

  9. PLAT Domain Protein 1 (PLAT1/PLAFP) Binds to the Arabidopsis Thaliana Plasma Membrane and Inserts a Lipid PLAT Domain Protein 1 (PLAT1/PLAFP) Binds to the Arabidopsis Thaliana Plasma Membrane and Inserts a Lipid

    Kulke, M., Kurtz, E., Boren, D. M., Olson, D. M., Koenig, A. M., Hoffmann-Benning, S., & Vermaas, J. V. (2024). PLAT Domain Protein 1 (PLAT1/PLAFP) Binds to the Arabidopsis Thaliana Plasma Membrane and Inserts a Lipid. Plant Science, 338, 111900.

  10. Electron Transfer in a Crystalline Cytochrome with Four Hemes Electron Transfer in a Crystalline Cytochrome with Four Hemes

    Parson, W. W., Huang, J., Kulke, M., Vermaas, J. V., & Kramer, D. M. (2024). Electron Transfer in a Crystalline Cytochrome with Four Hemes. The Journal of Chemical Physics, 160(6), 065101.

  11. Passive Permeability Controls Synthesis for the Allelochemical Sorgoleone in Sorghum Root Exudate Passive Permeability Controls Synthesis for the Allelochemical Sorgoleone in Sorghum Root Exudate

    Raza, S., Sievertsen, T. H., Okumoto, S., & Vermaas, J. V. (2024). Passive Permeability Controls Synthesis for the Allelochemical Sorgoleone in Sorghum Root Exudate. Phytochemistry, 217, 113891.

  12. Comparative Pore Structure and Dynamics for Bacterial Microcompartment Shell Protein Assemblies in Sheets or Shells Comparative Pore Structure and Dynamics for Bacterial Microcompartment Shell Protein Assemblies in Sheets or Shells

    Raza, S., Sarkar, D., Chan, L. J. G., Mae, J., Sutter, M., Petzold, C. J., Kerfeld, C. A., Ralston, C. Y., Gupta, S., & Vermaas, J. V. (2024). Comparative Pore Structure and Dynamics for Bacterial Microcompartment Shell Protein Assemblies in Sheets or Shells. ACS Omega, 9(33), 35503–35514.

  13. Atomic View of Photosynthetic Metabolite Permeability Pathways and Confinement in Cyanobacterial Carboxysomes Atomic View of Photosynthetic Metabolite Permeability Pathways and Confinement in Cyanobacterial Carboxysomes

    Through a combination of classical molecular dynamics simulations and atomic resolution Brownian dynamics, we determine the permeability for carboxysomes to photosynthetic metabolites and the rate of leakage from the carbon concentrating mechanism in cyanobacteria.

    Sarkar, D., Maffeo, C., Sutter, M., Aksimentiev, A., Kerfeld, C., & Vermaas, J. (2024). Atomic View of Photosynthetic Metabolite Permeability Pathways and Confinement in Cyanobacterial Carboxysomes. Proceedings of the National Academy of Sciences, 121(45), e2402277121.

    Kara did a fantastic news story on this work!

  14. Nanoscale Simulation of the Thylakoid Membrane Response to Extreme Temperatures Nanoscale Simulation of the Thylakoid Membrane Response to Extreme Temperatures

    Kulke, M., Weraduwage, S. M., Sharkey, T. D., & Vermaas, J. V. (2023). Nanoscale Simulation of the Thylakoid Membrane Response to Extreme Temperatures. Plant Cell & Environment, 46(8), 2273–2589.

  15. Long-Range Electron Transport Rates Depend on Wire Dimensions in Cytochrome Nanowires Long-Range Electron Transport Rates Depend on Wire Dimensions in Cytochrome Nanowires

    Kulke, M., Olson, D. M., Huang, J., Kramer, D. M., & Vermaas, J. V. (2023). Long-Range Electron Transport Rates Depend on Wire Dimensions in Cytochrome Nanowires. Small, 19(52), 2304013.

  16. Plant Terpenoid Permeability through Biological Membranes Explored via Molecular Simulations Plant Terpenoid Permeability through Biological Membranes Explored via Molecular Simulations

    Raza, S., Miller, M., Hamberger, B., & Vermaas, J. V. (2023). Plant Terpenoid Permeability through Biological Membranes Explored via Molecular Simulations. J. Phys. Chem. B, 127(5), 1144–1157.

  17. LongBondEliminator: A Molecular Simulation Tool to Remove Ring Penetrations in Biomolecular Simulation Systems LongBondEliminator: A Molecular Simulation Tool to Remove Ring Penetrations in Biomolecular Simulation Systems

    This is a cool tool to help relax away ring penetration artifacts that might arise when assembling a molecular simulation system.

    Sarkar, D., Kulke, M., & Vermaas, J. V. (2023). LongBondEliminator: A Molecular Simulation Tool to Remove Ring Penetrations in Biomolecular Simulation Systems. Biomolecules, 13(1), 107.

  18. Diffusion in Intact Secondary Cell Wall Models of Plants at Different Equilibrium Moisture Content Diffusion in Intact Secondary Cell Wall Models of Plants at Different Equilibrium Moisture Content

    In collaboration with a diverse research group from NREL and the Forest Products Lab, we measured diffusion for ions and cell wall components within models for secondary cell walls at different hydration levels. Unsurprisingly, more water to lubricate the cell wall raises diffusion. However, we predict a moisutre-induced glass transition at around 10-15% water content in secondary plant cell walls.

    Sarkar, D., Bu, L., Jakes, J. E., Zieba, J. K., Kaufman, I. D., Crowley, M. F., Ciesielski, P. N., & Vermaas, J. V. (2023). Diffusion in Intact Secondary Cell Wall Models of Plants at Different Equilibrium Moisture Content. The Cell Surface, 100105.

  19. Lignin Nanoparticle Morphology Depends on Polymer Properties and Solvent Composition: An Experimental and Computational Study Lignin Nanoparticle Morphology Depends on Polymer Properties and Solvent Composition: An Experimental and Computational Study

    Andeme Ela, R. C., Raza, S., Heiden, P. A., Vermaas, J. V., & Ong, R. G. (2022). Lignin Nanoparticle Morphology Depends on Polymer Properties and Solvent Composition: An Experimental and Computational Study. ACS Appl. Polym. Mater., 4(10), 6925–6935.

  20. Identification of a HTT-specific Binding Motif in DNAJB1 Essential for Suppression and Disaggregation of HTT Identification of a HTT-specific Binding Motif in DNAJB1 Essential for Suppression and Disaggregation of HTT

    Ayala Mariscal, S. M., Pigazzini, M. L., Richter, Y., Özel, M., Grothaus, I. L., Protze, J., Ziege, K., Kulke, M., ElBediwi, M., Vermaas, J. V., Colombi Ciacchi, L., Köppen, S., Liu, F., & Kirstein, J. (2022). Identification of a HTT-specific Binding Motif in DNAJB1 Essential for Suppression and Disaggregation of HTT. Nat Commun, 13(1), 4692.

  21. Reversible Unwrapping Algorithm for Constant-Pressure Molecular Dynamics Simulations Reversible Unwrapping Algorithm for Constant-Pressure Molecular Dynamics Simulations

    Kulke, M., & Vermaas, J. V. (2022). Reversible Unwrapping Algorithm for Constant-Pressure Molecular Dynamics Simulations. J. Chem. Theory Comput., 18(10), 6161–6171.

  22. ChAdOx1 Interacts with CAR and PF4 with Implications for Thrombosis with Thrombocytopenia Syndrome ChAdOx1 Interacts with CAR and PF4 with Implications for Thrombosis with Thrombocytopenia Syndrome

    Baker, A. T., Boyd, R. J., Sarkar, D., Teijeira-Crespo, A., Chan, C. K., Bates, E., Waraich, K., Vant, J., Wilson, E., Truong, C. D., Lipka-Lloyd, M., Fromme, P., Vermaas, J., Williams, D., Machiesky, L. A., Heurich, M., Nagalo, B. M., Coughlan, L., Umlauf, S., … Borad, M. J. (2021). ChAdOx1 Interacts with CAR and PF4 with Implications for Thrombosis with Thrombocytopenia Syndrome. Sci. Adv., 7(49), eabl8213.

 

Full List

  1. The Nanoscale Impact of Cyclopropane Fatty Acids and Hopanoids on Alcohol Tolerance in Clostridium Acetobutylicum and Zymomonas Mobilis
    Belagali, H., Singh, N. K., & Vermaas, J. V. (2026). The Nanoscale Impact of Cyclopropane Fatty Acids and Hopanoids on Alcohol Tolerance in Clostridium Acetobutylicum and Zymomonas Mobilis.

     

  2. Molecular DesignPrinciples for Photosystem I-BasedBiohybrid Solar Fuel Catalysts
    Emerson, M. D., Damaraju, S. N. S., Short, A. H., Alvord, Z. B., Palmer, Z. A., Mehra, H. S., Brininger, C. M., Vermaas, J. V., Utschig, L. M., & Gisriel, C. J. (2026). Molecular DesignPrinciples for Photosystem I-BasedBiohybrid Solar Fuel Catalysts. ACS Nano.

     

  3. Oxidative Stress-Responsive Cell Wall Remodeling Depends on Phosphate in Candida Albicans
    Jacob, A., Qi, W., Yarava, J. R., Barkarar, M., Withrow, A., Karai, A., Vermaas, J. V., Köhler, J. R., & Wang, T. (2026). Oxidative Stress-Responsive Cell Wall Remodeling Depends on Phosphate in Candida Albicans. Nat Commun.

     

  4. A Peripheral Carboxysome Component Regulates Cyanobacterial Glycogen Deposition
    MacCready, J. S., Boren, D. M., Santos-Merino, M., Sharpe, L. A., Lechno-Yossef, S., Vermaas, J. V., & Ducat, D. C. (2026). A Peripheral Carboxysome Component Regulates Cyanobacterial Glycogen Deposition. Proc. Natl. Acad. Sci., 123(34), e2607702123.

     

  5. A Lipoxygenase 3 Mutation Reverses Growth Phenotypes in an Arabidopsis Plastid Lipase 3 Overexpression Line
    Mugume, Y., Cook, R., Hagerty, B., Liu, J., Alvord, Z. B., Danhof, L., Froehlich, J. E., Vermaas, J. V., & Benning, C. (2026). A Lipoxygenase 3 Mutation Reverses Growth Phenotypes in an Arabidopsis Plastid Lipase 3 Overexpression Line. PLOS One, 21(6), e0350738.

     

  6. Dynamics and Structural Responses to Cis–Trans Isomerization in Bacterial Lipid Bilayers
    Raza, S., Sievertsen, T. H., Jafari, M., & Vermaas, J. V. (2026). Dynamics and Structural Responses to Cis–Trans Isomerization in Bacterial Lipid Bilayers. ACS Omega, 11(1), 449–459.

    This had a highlight by the unimitable Kara Headley!

     

  7. Screening for Residues in Atg11, a Central Organizer of Selective Autophagy in Yeast, Important for Binding with Atg9
    Sherpa, C. D., Woghiren, P., Leonello, E., Abdel-Khalek, M., Schuessler, B. J., Vermaas, J. V., & Backues, S. K. (2026). Screening for Residues in Atg11, a Central Organizer of Selective Autophagy in Yeast, Important for Binding with Atg9. MicroPublication Biology.

     

  8. A Conserved Sequence Insert of Fibrillins Is Involved in Plastoglobule Association and Lipid Binding
    Shivaiah, K.-K., Kithan-Lundquist, R., Kaneshiro, A. K., Boren, D. M., Susanto, F. A., Herrera-Tequia, A., Vermaas, J. V., & Lundquist, P. K. (2026). A Conserved Sequence Insert of Fibrillins Is Involved in Plastoglobule Association and Lipid Binding. Plant Cell Physiol., pcag047.

     

  9. Quantifying Membrane Structure and Dynamics during Bioproduct Production in Zymomonas Mobilis by Molecular Simulation
    Singh, N. K., & Vermaas, J. V. (2026). Quantifying Membrane Structure and Dynamics during Bioproduct Production in Zymomonas Mobilis by Molecular Simulation. J. Phys. Chem. B, 130(9), 2539–2553.

     

  10. Evaluating the Transport Mechanism for Lignocellulosic Inhibitors in Zymomonas Mobilis
    Singh, N. K., & Vermaas, J. V. (2026). Evaluating the Transport Mechanism for Lignocellulosic Inhibitors in Zymomonas Mobilis. ACS Sustainable Chemistry & Engineering, 14(29), 13292–13302.

     

  11. Encapsulation in a Bacterial Microcompartment Shell Improves Thermal Stability of a Glycolytic Enzyme
    Tefft, N. M., Yadav, N. S., Gruenberg Cross, M. C., Swiggett, C. D., Parent, K. N., Vermaas, J. V., & TerAvest, M. A. (2026). Encapsulation in a Bacterial Microcompartment Shell Improves Thermal Stability of a Glycolytic Enzyme. ACS Synth. Biol., 15(5), 1980–1992.

     

  12. Quantifying Selective Metabolite Transport for the Bacterial Microcompartment from Haliangium Ochraceum with Molecular Dynamics Simulations
    Yadav, N. S., Raza, S., Wang, Y., Landa, J. F., Hegg, E. L., Hausinger, R. P., & Vermaas, J. V. (2026). Quantifying Selective Metabolite Transport for the Bacterial Microcompartment from Haliangium Ochraceum with Molecular Dynamics Simulations. Nanoscale, 18, 6092–6104.

     

  13. Quantifying Chemically Modified Acetylation Induced Changes in the Plant Secondary Cell Wall Structure and Dynamics
    Barkarar, M., Sarkar, D., Hunt, C. G., & Vermaas, J. V. (2025). Quantifying Chemically Modified Acetylation Induced Changes in the Plant Secondary Cell Wall Structure and Dynamics. Biomacromolecules, 26(9), 5645–5656.

    This is a great example of undergraduate researchers doing cool work in the lab, as Murtaza has now moved on to bigger and better things!

     

  14. Identifying and Quantifying Membrane Interactions of the Protein Human Cis -prenyltransferase
    Boren, D. M., Kredi, S., Positselskaya, E., Giladi, M., Haitin, Y., & Vermaas, J. V. (2025). Identifying and Quantifying Membrane Interactions of the Protein Human Cis -prenyltransferase. Protein Science, 34(6), e70167.

    This is the paper that Duncan won the Tomashow Keegstra Award for!

     

  15. Anionic Lipids Regulate the Light-Harvesting Complex 1-Reaction Center Photocycle in Purple Bacteria
    Fiebig, O. C., Schmidt, G. P., Yadav, N. S., Wang, D., Nairat, M., Tang, H., Ji, Y., Prima, V., Sturgis, J. N., Vermaas, J. V., Harris, D., & Schlau-Cohen, G. S. (2025). Anionic Lipids Regulate the Light-Harvesting Complex 1-Reaction Center Photocycle in Purple Bacteria. J. Am. Chem. Soc., 147(40), 36706–36716.

     

  16. Synthesis, Function, and Genetic Variation of Sorgoleone, the Major Biological Nitrification Inhibitor in Sorghum
    Okumoto, S., Maharjan, B., Rajan, N., Xi, J., Baerson, S. R., Rooney, W. L., Thomson, M. J., Odeny, D. A., Yoshihashi, T., Vermaas, J. V., & Subbarao, G. V. (2025). Synthesis, Function, and Genetic Variation of Sorgoleone, the Major Biological Nitrification Inhibitor in Sorghum. Crop Science, 65(3), e70066.

     

  17. Molecular Modeling and Molecular Dynamics Simulation of a Packed and Intact Bacterial Microcompartment
    Raza, S., Yadav, N. S., Jussupow, A., Kerfeld, C. A., Feig, M., & Vermaas, J. V. (2025). Molecular Modeling and Molecular Dynamics Simulation of a Packed and Intact Bacterial Microcompartment. J. Phys. Chem. B, 129(50), 12811–12827.

    This particular research made the cover!

     

  18. IRE1 Regulates TOR Signaling via RIDD of RAPTOR1b to Coordinate Growth and Stress Adaptation
    Reagan, B. C., Kim, J. Y., Angelos, E., Vermaas, J. V., & Brandizzi, F. (2025). IRE1 Regulates TOR Signaling via RIDD of RAPTOR1b to Coordinate Growth and Stress Adaptation. Plant Biology.

     

  19. Increasing Thermostability of the Key Photorespiratory Enzyme Glycerate 3-kinase by Structure-based Recombination
    Roze, L. V., Antoniak, A., Sarkar, D., Liepman, A. H., Tejera-Nieves, M., Vermaas, J. V., & Walker, B. J. (2025). Increasing Thermostability of the Key Photorespiratory Enzyme Glycerate 3-kinase by Structure-based Recombination. Plant Biotechnology Journal, 23(2), 454–466.

     

  20. Jojoba LIPID DROPLET-ASSOCIATED PROTEIN 1 Facilitates the Efficient Packaging of Wax Esters into Lipid Droplets
    Whitehead, P., Raza, S., Miklaszewska, M., Hornung, E., Herrfurth, C., Nadella, R., Clews, A., Doner, N. M., Dyer, J. M., Mullen, R., Feussner, I., Vermaas, J. V., & Chapman, K. (2025). Jojoba LIPID DROPLET-ASSOCIATED PROTEIN 1 Facilitates the Efficient Packaging of Wax Esters into Lipid Droplets. The Plant Cell, 37(8), koaf115.

     

  21. Quantitative Measurement of Molecular Permeability to a Synthetic Bacterial Microcompartment Shell System
    Young, E. J., Kirst, H., Dwyer, M. E., Vermaas, J. V., & Kerfeld, C. A. (2025). Quantitative Measurement of Molecular Permeability to a Synthetic Bacterial Microcompartment Shell System. ACS Synth. Biol., 14(5), 1404–1413.

    This paper has a really cool cover associated with it!

     

  22. Structure Characterization of Bacterial Microcompartment Shells via X-ray Scattering and Coordinate Modeling: Evidence for Adventitious Capture of Cytoplasmic Proteins
    Zuo, X., Jussupow, A., Ponomarenko, N. S., Grant, T. D., Tefft, N. M., Yadav, N. S., Range, K. L., Ralston, C. Y., TerAvest, M. A., Sutter, M., Kerfeld, C. A., Vermaas, J. V., Feig, M., & Tiede, D. M. (2025). Structure Characterization of Bacterial Microcompartment Shells via X-ray Scattering and Coordinate Modeling: Evidence for Adventitious Capture of Cytoplasmic Proteins. ACS Appl. Bio Mater., 8(3), 2090–2103.

     

  23. Adaptative Survival of Aspergillus Fumigatus to Echinocandins Arises from Cell Wall Remodeling beyond β-1,3-Glucan Synthesis Inhibition
    Dickwella Widanage, M. C., Gautam, I., Sarkar, D., Mentink-Vigier, F., Vermaas, J. V., Ding, S.-Y., Lipton, A. S., Fontaine, T., Latgé, J.-P., Wang, P., & Wang, T. (2024). Adaptative Survival of Aspergillus Fumigatus to Echinocandins Arises from Cell Wall Remodeling beyond β-1,3-Glucan Synthesis Inhibition. Nat Commun, 15(1), 6382.

    This paper has a high-level overview written by the MSU communications team!

     

  24. PLAT Domain Protein 1 (PLAT1/PLAFP) Binds to the Arabidopsis Thaliana Plasma Membrane and Inserts a Lipid
    Kulke, M., Kurtz, E., Boren, D. M., Olson, D. M., Koenig, A. M., Hoffmann-Benning, S., & Vermaas, J. V. (2024). PLAT Domain Protein 1 (PLAT1/PLAFP) Binds to the Arabidopsis Thaliana Plasma Membrane and Inserts a Lipid. Plant Science, 338, 111900.

     

  25. Electron Transfer in a Crystalline Cytochrome with Four Hemes
    Parson, W. W., Huang, J., Kulke, M., Vermaas, J. V., & Kramer, D. M. (2024). Electron Transfer in a Crystalline Cytochrome with Four Hemes. The Journal of Chemical Physics, 160(6), 065101.

    This article was chosen for the journal cover, and the PRL has a great story about this research!

     

  26. Passive Permeability Controls Synthesis for the Allelochemical Sorgoleone in Sorghum Root Exudate
    Raza, S., Sievertsen, T. H., Okumoto, S., & Vermaas, J. V. (2024). Passive Permeability Controls Synthesis for the Allelochemical Sorgoleone in Sorghum Root Exudate. Phytochemistry, 217, 113891.

     

  27. Comparative Pore Structure and Dynamics for Bacterial Microcompartment Shell Protein Assemblies in Sheets or Shells
    Raza, S., Sarkar, D., Chan, L. J. G., Mae, J., Sutter, M., Petzold, C. J., Kerfeld, C. A., Ralston, C. Y., Gupta, S., & Vermaas, J. V. (2024). Comparative Pore Structure and Dynamics for Bacterial Microcompartment Shell Protein Assemblies in Sheets or Shells. ACS Omega, 9(33), 35503–35514.

    This paper was selected for a cover! We also have a news story to go along with the paper.

     

  28. Atomic View of Photosynthetic Metabolite Permeability Pathways and Confinement in Cyanobacterial Carboxysomes
    Sarkar, D., Maffeo, C., Sutter, M., Aksimentiev, A., Kerfeld, C., & Vermaas, J. (2024). Atomic View of Photosynthetic Metabolite Permeability Pathways and Confinement in Cyanobacterial Carboxysomes. Proceedings of the National Academy of Sciences, 121(45), e2402277121.

    Kara did a fantastic news story on this work!

     

  29. Atomistic Simulations of Polydisperse Lignin Melts Using Simple Polydisperse Residue Input Generator
    Sethuraman, V., Vermaas, J. V., Liang, L., Ragauskas, A. J., Smith, J. C., & Petridis, L. (2024). Atomistic Simulations of Polydisperse Lignin Melts Using Simple Polydisperse Residue Input Generator. Biomacromolecules, 25(2), 767–777.

     

  30. Electrochemical Cofactor Recycling of Bacterial Microcompartments
    Sutter, M., Utschig, L. M., Niklas, J., Paul, S., Kahan, D. N., Gupta, S., Poluektov, O. G., Ferlez, B. H., Tefft, N. M., TerAvest, M. A., Hickey, D. P., Vermaas, J. V., Ralston, C. Y., & Kerfeld, C. A. (2024). Electrochemical Cofactor Recycling of Bacterial Microcompartments. Proc. Natl. Acad. Sci. U.S.A., 121(49), e2414220121.

    There was a commentary that was published along with the paper.

     

  31. The Isoprene-responsive Phosphoproteome Provides New Insights into the Putative Signalling Pathways and Novel Roles of Isoprene
    Weraduwage, S. M., Whitten, D., Kulke, M., Sahu, A., Vermaas, J. V., & Sharkey, T. D. (2024). The Isoprene-responsive Phosphoproteome Provides New Insights into the Putative Signalling Pathways and Novel Roles of Isoprene. Plant Cell & Environment, 47(4), 1099–1117.

     

  32. Nanoscale Simulation of the Thylakoid Membrane Response to Extreme Temperatures
    Kulke, M., Weraduwage, S. M., Sharkey, T. D., & Vermaas, J. V. (2023). Nanoscale Simulation of the Thylakoid Membrane Response to Extreme Temperatures. Plant Cell & Environment, 46(8), 2273–2589.

    This work was featured as a PRL news article.

     

  33. Long-Range Electron Transport Rates Depend on Wire Dimensions in Cytochrome Nanowires
    Kulke, M., Olson, D. M., Huang, J., Kramer, D. M., & Vermaas, J. V. (2023). Long-Range Electron Transport Rates Depend on Wire Dimensions in Cytochrome Nanowires. Small, 19(52), 2304013.

    This research was picked up by MSU Today.

     

  34. Computing the Relative Affinity of Chlorophylls a and b to Light-Harvesting Complex II
    Ranepura, G. A., Mao, J., Vermaas, J. V., Wang, J., Gisriel, C. J., Wei, R. J., Ortiz-Soto, J., Uddin, M. R., Amin, M., Brudvig, G. W., & Gunner, M. R. (2023). Computing the Relative Affinity of Chlorophylls a and b to Light-Harvesting Complex II. J. Phys. Chem. B, 127(51), 10974–10986.

     

  35. Plant Terpenoid Permeability through Biological Membranes Explored via Molecular Simulations
    Raza, S., Miller, M., Hamberger, B., & Vermaas, J. V. (2023). Plant Terpenoid Permeability through Biological Membranes Explored via Molecular Simulations. J. Phys. Chem. B, 127(5), 1144–1157.

     

  36. SARS-CoV2 Billion-Compound Docking
    Rogers, D. M., Agarwal, R., Vermaas, J. V., Smith, M. D., Rajeshwar, R. T., Cooper, C., Sedova, A., Boehm, S., Baker, M., Glaser, J., & Smith, J. C. (2023). SARS-CoV2 Billion-Compound Docking. Sci Data, 10(1), 173.

     

  37. LongBondEliminator: A Molecular Simulation Tool to Remove Ring Penetrations in Biomolecular Simulation Systems
    Sarkar, D., Kulke, M., & Vermaas, J. V. (2023). LongBondEliminator: A Molecular Simulation Tool to Remove Ring Penetrations in Biomolecular Simulation Systems. Biomolecules, 13(1), 107.

     

  38. Atomistic Origins of Biomass Recalcitrance in Organosolv Pretreatment
    Sarkar, D., Santiago, I. J., & Vermaas, J. V. (2023). Atomistic Origins of Biomass Recalcitrance in Organosolv Pretreatment. Chemical Engineering Science, 118587.

     

  39. Diffusion in Intact Secondary Cell Wall Models of Plants at Different Equilibrium Moisture Content
    Sarkar, D., Bu, L., Jakes, J. E., Zieba, J. K., Kaufman, I. D., Crowley, M. F., Ciesielski, P. N., & Vermaas, J. V. (2023). Diffusion in Intact Secondary Cell Wall Models of Plants at Different Equilibrium Moisture Content. The Cell Surface, 100105.

     

  40. Adaptive Ensemble Refinement of Protein Structures in High Resolution Electron Microscopy Density Maps with Radical Augmented Molecular Dynamics Flexible Fitting
    Sarkar, D., Lee, H., Vant, J. W., Turilli, M., Vermaas, J. V., Jha, S., & Singharoy, A. (2023). Adaptive Ensemble Refinement of Protein Structures in High Resolution Electron Microscopy Density Maps with Radical Augmented Molecular Dynamics Flexible Fitting. J. Chem. Inf. Model., 63(18), 5834–5846.

     

  41. Characterization of Promoter Elements of Isoprene-responsive Genes and the Ability of Isoprene to Bind START Domain Transcription Factors
    Weraduwage, S. M., Sahu, A., Kulke, M., Vermaas, J. V., & Sharkey, T. D. (2023). Characterization of Promoter Elements of Isoprene-responsive Genes and the Ability of Isoprene to Bind START Domain Transcription Factors. Plant Direct, 7(2), e483.

     

  42. Lignin Nanoparticle Morphology Depends on Polymer Properties and Solvent Composition: An Experimental and Computational Study
    Andeme Ela, R. C., Raza, S., Heiden, P. A., Vermaas, J. V., & Ong, R. G. (2022). Lignin Nanoparticle Morphology Depends on Polymer Properties and Solvent Composition: An Experimental and Computational Study. ACS Appl. Polym. Mater., 4(10), 6925–6935.

     

  43. Identification of a HTT-specific Binding Motif in DNAJB1 Essential for Suppression and Disaggregation of HTT
    Ayala Mariscal, S. M., Pigazzini, M. L., Richter, Y., Özel, M., Grothaus, I. L., Protze, J., Ziege, K., Kulke, M., ElBediwi, M., Vermaas, J. V., Colombi Ciacchi, L., Köppen, S., Liu, F., & Kirstein, J. (2022). Identification of a HTT-specific Binding Motif in DNAJB1 Essential for Suppression and Disaggregation of HTT. Nat Commun, 13(1), 4692.

    Nature has a companion article that is less technical than a full-blown journal article.

     

  44. Reversible Unwrapping Algorithm for Constant-Pressure Molecular Dynamics Simulations
    Kulke, M., & Vermaas, J. V. (2022). Reversible Unwrapping Algorithm for Constant-Pressure Molecular Dynamics Simulations. J. Chem. Theory Comput., 18(10), 6161–6171.

     

  45. Lytic Polysaccharide Monooxygenase Increases Cellobiohydrolases Activity by Promoting Decrystallization of Cellulose Surface
    Uchiyama, T., Uchihashi, T., Ishida, T., Nakamura, A., Vermaas, J. V., Crowley, M. F., Samejima, M., Beckham, G. T., & Igarashi, K. (2022). Lytic Polysaccharide Monooxygenase Increases Cellobiohydrolases Activity by Promoting Decrystallization of Cellulose Surface. Sci. Adv., 8(51), eade5155.

     

  46. Exploring Cryo-Electron Microscopy with Molecular Dynamics
    Vant, J. W., Sarkar, D., Nguyen, J., Baker, A. T., Vermaas, J. V., & Singharoy, A. (2022). Exploring Cryo-Electron Microscopy with Molecular Dynamics. Biochemical Society Transactions, 50(1), 569–581.

     

  47. Assembly and Analysis of Cell-Scale Membrane Envelopes
    Vermaas, J. V., Mayne, C. G., Shinn, E., & Tajkhorshid, E. (2022). Assembly and Analysis of Cell-Scale Membrane Envelopes. J. Chem. Inf. Model., 62(3), 602–617.

     

  48. Molecular Simulation of Lignin-Related Aromatic Compound Permeation through Gram-Negative Bacterial Outer Membranes
    Vermaas, J. V., Crowley, M. F., & Beckham, G. T. (2022). Molecular Simulation of Lignin-Related Aromatic Compound Permeation through Gram-Negative Bacterial Outer Membranes. Journal of Biological Chemistry, 298(12), 102627.

     

  49. ChAdOx1 Interacts with CAR and PF4 with Implications for Thrombosis with Thrombocytopenia Syndrome
    Baker, A. T., Boyd, R. J., Sarkar, D., Teijeira-Crespo, A., Chan, C. K., Bates, E., Waraich, K., Vant, J., Wilson, E., Truong, C. D., Lipka-Lloyd, M., Fromme, P., Vermaas, J., Williams, D., Machiesky, L. A., Heurich, M., Nagalo, B. M., Coughlan, L., Umlauf, S., … Borad, M. J. (2021). ChAdOx1 Interacts with CAR and PF4 with Implications for Thrombosis with Thrombocytopenia Syndrome. Sci. Adv., 7(49), eabl8213.

    This work has been featured by the BBC, EurekaAlert, and MSU.

     

  50. High-Throughput Virtual Laboratory for Drug Discovery Using Massive Datasets
    Glaser, J., Vermaas, J. V., Rogers, D. M., Larkin, J., LeGrand, S., Boehm, S., Baker, M. B., Scheinberg, A., Tillack, A. F., Thavappiragasam, M., Sedova, A., & Hernandez, O. (2021). High-Throughput Virtual Laboratory for Drug Discovery Using Massive Datasets. The International Journal of High Performance Computing Applications, 35(5), 452–468.

     

  51. Inhibitor Binding Influences the Protonation States of Histidines in SARS-CoV-2 Main Protease
    Pavlova, A., Lynch, D. L., Daidone, I., Zanetti-Polzi, L., Smith, M. D., Chipot, C., Kneller, D. W., Kovalevsky, A., Coates, L., Golosov, A. A., Dickson, C. J., Velez-Vega, C., Duca, J. S., Vermaas, J. V., Pang, Y. T., Acharya, A., Parks, J. M., Smith, J. C., & Gumbart, J. C. (2021). Inhibitor Binding Influences the Protonation States of Histidines in SARS-CoV-2 Main Protease. Chemical Science, 12(4), 1513–1527.

     

  52. Supercomputing Pipelines Search for Therapeutics Against COVID-19
    Vermaas, J. V., Sedova, A., Baker, M., Boehm, S., Rogers, D., Larkin, J., Glaser, J., Smith, M., Hernandez, O., & Smith, J. (2021). Supercomputing Pipelines Search for Therapeutics Against COVID-19. Computing in Science & Engineering, 23(1), 7–16.

     

  53. Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to COVID-19
    Acharya, A., Agarwal, R., Baker, M. B., Baudry, J., Bhowmik, D., Boehm, S., Byler, K. G., Chen, S. Y., Coates, L., Cooper, C. J., Demerdash, O., Daidone, I., Eblen, J. D., Ellingson, S., Forli, S., Glaser, J., Gumbart, J. C., Gunnels, J., Hernandez, O., … Zanetti-Polzi, L. (2020). Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to COVID-19. J. Chem. Inf. Model., 60(12), 5832–5852.

     

  54. Advances in Multiscale Modeling of Lignocellulosic Biomass
    Ciesielski, P. N., Pecha, M. B., Lattanzi, A. M., Bharadwaj, V. S., Crowley, M. F., Bu, L., Vermaas, J. V., Steirer, K. X., & Crowley, M. F. (2020). Advances in Multiscale Modeling of Lignocellulosic Biomass. ACS Sustainable Chemistry & Engineering, 8(9), 3512–3531.

     

  55. GPU-Accelerated Drug Discovery with Docking on the Summit Supercomputer
    LeGrand, S., Scheinberg, A., Tillack, A. F., Thavappiragasam, M., Vermaas, J. V., Agarwal, R., Larkin, J., Poole, D., Santos-Martins, D., Solis-Vasquez, L., Koch, A., Forli, S., Hernandez, O., Smith, J. C., & Sedova, A. (2020). GPU-Accelerated Drug Discovery with Docking on the Summit Supercomputer. Proceedings of the 11th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics, 1–10.

     

  56. Mesoscale Reaction–Diffusion Phenomena Governing Lignin-First Biomass Fractionation
    Thornburg, N. E., Pecha, M. B., Brandner, D. G., Reed, M. L., Vermaas, J. V., Michener, W. E., Katahira, R., Vinzant, T. B., Foust, T. D., Donohoe, B. S., Román-Leshkov, Y., Ciesielski, P. N., & Beckham, G. T. (2020). Mesoscale Reaction–Diffusion Phenomena Governing Lignin-First Biomass Fractionation. ChemSusChem, 13(17), 4495–4509.

     

  57. Data-Guided Multi-Map Variables for Ensemble Refinement of Molecular Movies
    Vant, J. W., Sarkar, D., Streitwieser, E., Fiorin, G., Skeel, R., Vermaas, J. V., & Singharoy, A. (2020). Data-Guided Multi-Map Variables for Ensemble Refinement of Molecular Movies. The Journal of Chemical Physics, 153(21), 214102.

     

  58. Molecular Lignin Solubility and Structure in Organic Solvents
    Vermaas, J. V., Crowley, M. F., & Beckham, G. T. (2020). Molecular Lignin Solubility and Structure in Organic Solvents. ACS Sustainable Chemistry & Engineering, 8(48), 17839–17850.

     

  59. Lignin-KMC: A Toolkit for Simulating Lignin Biosynthesis
    Orella, M. J., Gani, T. Z. H., Vermaas, J. V., Stone, M. L., Anderson, E. M., Beckham, G. T., Brushett, F. R., & Román-Leshkov, Y. (2019). Lignin-KMC: A Toolkit for Simulating Lignin Biosynthesis. ACS Sustainable Chem. Eng., 7(22), 18313–18322.

     

  60. Systematic Parameterization of Lignin for the CHARMM Force Field
    Vermaas, J. V., Petridis, L., Ralph, J., Crowley, M. F., & Beckham, G. T. (2019). Systematic Parameterization of Lignin for the CHARMM Force Field. Green Chemistry, 21(1), 109–122.

     

  61. Automated Transformation of Lignin Topologies into Atomic Structures with LigninBuilder
    Vermaas, J. V., Dellon, L. D., Broadbelt, L. J., Beckham, G. T., & Crowley, M. F. (2019). Automated Transformation of Lignin Topologies into Atomic Structures with LigninBuilder. ACS Sustainable Chemistry and Engineering, 7(3), 3443–3453.

     

  62. Passive Membrane Transport of Lignin-Related Compounds
    Vermaas, J. V., Dixon, R. A., Chen, F., Mansfield, S. D., Boerjan, W., Ralph, J., Crowley, M. F., & Beckham, G. T. (2019). Passive Membrane Transport of Lignin-Related Compounds. Proceedings of the National Academy of Sciences of the United States of America, 116(46), 23117–23123.

     

  63. A Quantitative Molecular Atlas for Interactions Between Lignin and Cellulose
    Vermaas, J. V., Crowley, M. F., & Beckham, G. T. (2019). A Quantitative Molecular Atlas for Interactions Between Lignin and Cellulose. ACS Sustainable Chem. Eng., 7(24), 19570–19583.

     

  64. The Dissociation Mechanism of Processive Cellulases
    Vermaas, J. V., Kont, R., Beckham, G. T., Crowley, M. F., Gudmundsson, M., Sandgren, M., Ståhlberg, J., Väljamäe, P., & Knott, B. C. (2019). The Dissociation Mechanism of Processive Cellulases. Proceedings of the National Academy of Sciences of the United States of America, 116(46), 23061–23067.

     

  65. Characterizing Activity and Thermostability of GH5 Endoglucanase Chimeras from Mesophilic and Thermophilic Parents
    Zheng, F., Vermaas, J. V., Zheng, J., Wang, Y., Tu, T., Wang, X., Xie, X., Yao, B., Beckham, G. T., & Luo, H. (2019). Characterizing Activity and Thermostability of GH5 Endoglucanase Chimeras from Mesophilic and Thermophilic Parents. Applied and Environmental Microbiology, 85(5), e02079–18.

     

  66. Membrane Permeability of Terpenoids Explored with Molecular Simulation
    Vermaas, J. V., Bentley, G. J., Beckham, G. T., & Crowley, M. F. (2018). Membrane Permeability of Terpenoids Explored with Molecular Simulation. The Journal of Physical Chemistry B, 122(45), 10349–10361.

     

  67. Electrostatic Lock in the Transport Cycle of the Multidrug Resistance Transporter EmrE
    Vermaas, J. V., Rempe, S. B., & Tajkhorshid, E. (2018). Electrostatic Lock in the Transport Cycle of the Multidrug Resistance Transporter EmrE. Proceedings of the National Academy of Sciences of the United States of America, 115(32), E7502–E7511.

     

  68. Extension of the Highly Mobile Membrane Mimetic to Transmembrane Systems through Customized in Silico Solvents
    Vermaas, J. V., Pogorelov, T. V., & Tajkhorshid, E. (2017). Extension of the Highly Mobile Membrane Mimetic to Transmembrane Systems through Customized in Silico Solvents. The Journal of Physical Chemistry B, 121(15), 3764–3776.

     

  69. Membrane Permeability of Fatty Acyl Compounds Studied via Molecular Simulation
    Vermaas, J. V., Beckham, G. T., & Crowley, M. F. (2017). Membrane Permeability of Fatty Acyl Compounds Studied via Molecular Simulation. The Journal of Physical Chemistry B, 121(50), 11311–11324.

     

  70. Differential Membrane Binding Mechanics of Synaptotagmin Isoforms Observed in Atomic Detail
    Vermaas, J. V., & Tajkhorshid, E. (2017). Differential Membrane Binding Mechanics of Synaptotagmin Isoforms Observed in Atomic Detail. Biochemistry, 56(1), 281–293.

     

  71. Atomic-Level Description of Protein–Lipid Interactions Using an Accelerated Membrane Model
    Baylon, J. L., Vermaas, J. V., Muller, M. P., Arcario, M. J., Pogorelov, T. V., & Tajkhorshid, E. (2016). Atomic-Level Description of Protein–Lipid Interactions Using an Accelerated Membrane Model. Biochimica Et Biophysica Acta (BBA) - Biomembranes, 1858(7), 1573–1583.

     

  72. The Cellular Membrane as a Mediator for Small Molecule Interaction with Membrane Proteins
    Mayne, C. G., Arcario, M. J., Mahinthichaichan, P., Baylon, J. L., Vermaas, J. V., Navidpour, L., Wen, P.-C., Thangapandian, S., & Tajkhorshid, E. (2016). The Cellular Membrane as a Mediator for Small Molecule Interaction with Membrane Proteins. Biochimica Et Biophysica Acta (BBA) - Biomembranes, 1858(10), 2290–2304.

     

  73. Q-Band Electron-Nuclear Double Resonance Reveals Out-of-Plane Hydrogen Bonds Stabilize an Anionic Ubisemiquinone in Cytochrome Bo3 from Escherichia Coli
    Sun, C., Taguchi, A. T., Vermaas, J. V., Beal, N. J., O’Malley, P. J., Tajkhorshid, E., Gennis, R. B., & Dikanov, S. A. (2016). Q-Band Electron-Nuclear Double Resonance Reveals Out-of-Plane Hydrogen Bonds Stabilize an Anionic Ubisemiquinone in Cytochrome Bo3 from Escherichia Coli. Biochemistry, 55(40), 5714–5725.

     

  74. Chapter 7. Computational Characterization of Molecular Mechanisms of Membrane Transporter Function
    Trebesch, N., Vermaas, J. V., & Tajkhorshid, E. (2016). Chapter 7. Computational Characterization of Molecular Mechanisms of Membrane Transporter Function. In C. Domene (Ed.), Theoretical and Computational Chemistry Series (pp. 197–236). Royal Society of Chemistry.

     

  75. TopoGromacs: Automated Topology Conversion from CHARMM to GROMACS within VMD
    Vermaas, J. V., Hardy, D. J., Stone, J. E., Tajkhorshid, E., & Kohlmeyer, A. (2016). TopoGromacs: Automated Topology Conversion from CHARMM to GROMACS within VMD. Journal of Chemical Information and Modeling, 56(6), 1112–1116.

     

  76. Microscopic Characterization of Membrane Transporter Function by In Silico Modeling and Simulation
    Vermaas, J. V., Trebesch, N., Mayne, C. G., Thangapandian, S., Shekhar, M., Mahinthichaichan, P., Baylon, J. L., Jiang, T., Wang, Y., Muller, M. P., Shinn, E., Zhao, Z., Wen, P.-C., & Tajkhorshid, E. (2016). Microscopic Characterization of Membrane Transporter Function by In Silico Modeling and Simulation. In Methods in Enzymology (Vol. 578, pp. 373–428). Elsevier.

     

  77. CHARMM-GUI HMMM Builder for Membrane Simulations with the Highly Mobile Membrane-Mimetic Model
    Qi, Y., Cheng, X., Lee, J., Vermaas, J. V., Pogorelov, T. V., Tajkhorshid, E., Park, S., Klauda, J. B., & Im, W. (2015). CHARMM-GUI HMMM Builder for Membrane Simulations with the Highly Mobile Membrane-Mimetic Model. Biophysical Journal, 109(10), 2012–2022.

     

  78. Efficient Exploration of Membrane-Associated Phenomena at Atomic Resolution
    Vermaas, J. V., Baylon, J. L., Arcario, M. J., Muller, M. P., Wu, Z., Pogorelov, T. V., & Tajkhorshid, E. (2015). Efficient Exploration of Membrane-Associated Phenomena at Atomic Resolution. The Journal of Membrane Biology, 248(3), 563–582.

     

  79. Redox Potential Tuning through Differential Quinone Binding in the Photosynthetic Reaction Center of Rhodobacter Sphaeroides
    Vermaas, J. V., Taguchi, A. T., Dikanov, S. A., Wraight, C. A., & Tajkhorshid, E. (2015). Redox Potential Tuning through Differential Quinone Binding in the Photosynthetic Reaction Center of Rhodobacter Sphaeroides. Biochemistry, 54(12), 2104–2116.

     

  80. Effects of Lytic Polysaccharide Monooxygenase Oxidation on Cellulose Structure and Binding of Oxidized Cellulose Oligomers to Cellulases
    Vermaas, J. V., Crowley, M. F., Beckham, G. T., & Payne, C. M. (2015). Effects of Lytic Polysaccharide Monooxygenase Oxidation on Cellulose Structure and Binding of Oxidized Cellulose Oligomers to Cellulases. The Journal of Physical Chemistry B, 119(20), 6129–6143.

     

  81. Mechanism of Lignin Inhibition of Enzymatic Biomass Deconstruction
    Vermaas, J. V., Petridis, L., Qi, X., Schulz, R., Lindner, B., & Smith, J. C. (2015). Mechanism of Lignin Inhibition of Enzymatic Biomass Deconstruction. Biotechnol Biofuels, 8(1), 217.

     

  82. Partitioning of Amino Acids into a Model Membrane: Capturing the Interface
    Pogorelov, T. V., Vermaas, J. V., Arcario, M. J., & Tajkhorshid, E. (2014). Partitioning of Amino Acids into a Model Membrane: Capturing the Interface. The Journal of Physical Chemistry B, 118(6), 1481–1492.

     

  83. A Microscopic View of Phospholipid Insertion into Biological Membranes
    Vermaas, J. V., & Tajkhorshid, E. (2014). A Microscopic View of Phospholipid Insertion into Biological Membranes. J. Phys. Chem. B, 118(7), 1754–1764.

     

  84. Conformational Heterogeneity of α-Synuclein in Membrane.
    Vermaas, J. V., & Tajkhorshid, E. (2014). Conformational Heterogeneity of α-Synuclein in Membrane. Biochimica Et Biophysica Acta (BBA) - Biomembranes, 1838(12), 3107–3117.

     

  85. Beyond the Boltzmann Factor for Corrections to Scaling in Ferromagnetic Materials and Critical Fluids
    Chamberlin, R. V., Vermaas, J. V., & Wolf, G. H. (2009). Beyond the Boltzmann Factor for Corrections to Scaling in Ferromagnetic Materials and Critical Fluids. The European Physical Journal B, 71(1), 1–6.