Publications

• Nickels, J. D., Bonifer, K. S., Tindall, R. R., Yahya, A., Tan, L., Do, C., Davison, B. H., Elkins, J.G. “Improved chemical and isotopic labeling of biomembranes in Bacillus subtilis by leveraging CRISPRi inhibition of beta-ketoacyl-ACP synthase (fabF).” (2022) Front. Mol. Biosci. 9:1011981. doi: 10.3389/fmolb.2022.1011981
• Tan, L., Smith, M. D., Scott, H. L., Yahy, A., Elkins, J. G., Katsaras, J., O’Neill, H. M., Pingali, S. V., Smith, J. C., Davison, B. D., Nickels, J. D. “Modelling the partitioning of amphiphilic molecules and co-solvents in biomembranes.” (2022) J. Appl. Cryst. 55. doi.org/10.1107/S1600576722008998.
• Sawada, D., Nishiyama, Y., Shah, R., Forsyth, V. T., Mossou, E., O’Neill, H. M., Wada, M., Langan, P. “Untangling the threads of cellulose mercerization.” (2022) Nature Comm 13:6189. doi.org/10.1038/s41467-022-33812-w
• Meng, X., Wang, Y., Conte, A. G., Zhang, S., Ryu, J., Wie, J. J., Pu, Y., Davison, B. H., Yoo, H. G., Ragauskas, A. J. “Applications of biomass-derived solvents in biomass pretreatment – strategies, challenges, and prospects.” (2023) Bioresource Technol. 368: 128280, https://doi.org/10.1016/j.biortech.2022.128280.
• Li, R., Zheng, Y., Zhao, X., Yong, Q., Meng, X., Ragauskas, A. J., Huang, C. “Recent advances in biomass pretreatment using biphasic solvent system.” (2023) Green Chem 25: 2505-2523. DOI: 10.1039/d3gc00271c
• Tan, L., Scott, H. L., Smith, M. D., Pingali, S. V., O’Neill, H. M., Morrell-Falvey, J. L., Katsaras, J., Smith, J. C., Davison, B. H., Elkins, J. G., Nickels, J. D. “Amphiphilic Co-Solvents Modulate the Structure of Membrane Domains.” (2023) ACS Sust Chem Eng. 11: 1598-1609. doi.org/10.1021/acssuschemeng.2c06876
• Annamraju, A., Rajan, K., Zuo, X., Long, B. K., Pingali, S. V., Elder, T. J., Labbé, N. “Atomic Level Interactions and Suprastructural Configuration of Plant Cell Wall Polymers in Dialkylimidazolium Ionic Liquids.” (2023—in press) Biomacromol. DOI: 10.1021/acs.biomac.3c00047.
• Mohan, M., Smith, M. D., Demerdash, O. N., Simmons, B. A., Singh, S., Kidder, M. K., Smith, J. C. “Quantum Chemistry-Driven Machine Learning Approach for the Prediction of the Surface Tension and Speed of Sound in Ionic Liquids.” (2023) ACS Sust Chem Eng 11 (20): 7809-7821. DOI: 10.1021/acssuschemeng.3c00624
• Mohan, M., Smith, M. D., Demerdash, O., Kidder, M. K., Smith, J. C. “Predictive understanding of the surface tension and velocity of sound in ionic liquids using machine learning.” (2023) J. Chem. Phys. 158: 214502. doi.org/10.1063/5.0147052
• Mohan M, Demerdash O, Simmons BA, Smith JC, Kidder M, Singh S. “Accurate Prediction of Carbon Dioxide Capture by Deep Eutectic Solvents using Quantum Chemistry and a Neural Network.” (2023) Green Chemistry 25: 3475-3492. DOI: 10.1039/D2GC04425K.
• Song, Yan, Xianzhi Meng, Wei Jiang, Barbara R. Evans, Haoxi Ben, Yuanming Zhang, Yunqiao Pu et al. “Deuterium incorporation into cellulose: a mini-review of biological and chemical methods.” Cellulose (2022): 1-18.
• Liang, Luna, Yun-Yan Wang, Samarthya Bhagia, Vaidyanathan Sethuraman, Zhi Yang, Xianzhi Meng, Nathan Bryant et al. “Chemical and Morphological Structure of Transgenic Switchgrass Organosolv Lignin Extracted by Ethanol, Tetrahydrofuran, and γ-Valerolactone Pretreatments.” ACS Sustainable Chemistry & Engineering 10(28): 9041-9052 (2022).
• Yao, L.; Yang, H.; Meng X.; Ragauskas, A.J. (2022) “Toward a Fundamental Understanding of the Role of Lignin in the Biorefinery Process.” Frontiers in Energy Res 9:895.
• Huang, C., Jiang, X., Shen, X., Hu, J., Tang, W., Wu, X., Ragauskas, A., Jameel, H., Meng, X., Yong, Q. “Lignin-Enzyme Interaction: A Roadblock for Efficient Enzymatic Hydrolysis of Lignocellulosics. ” (2022) Renewable and Sustainable Energy Reviews 154:111822.
• Yang, Z., Foston, M.B., O’Neill, H., Urban, V.S., Ragauskas, A., Evans, B.R, Davison, B.H., and Pingali, S. V. “Structural Reorganization of Non-Cellulosic Polymers Observed in situ during Dilute Acid Pretreatment by Small Angle Neutron Scattering.” ACS Sust Chem Eng (2021).
• Tan, L., Elkins, J.G., Davison, B.H., Kelley, E.G., and Nickels, J. “Implementation of a Self- Consistent Slab Model of Bilayer Structure in the SasView Suite.” (2021). J Appl Cryst 54:364–370.
• Smith, M.D., and Smith, J. C. “Effects of Sodium and Calcium Chloride Ionic Stresses on Model Yeast Membranes Revealed by Molecular Dynamics Simulation.” (2021) Chem Physics Lipids 233:104980.
• Chen, P., Li, Y., Nishiyama, Y., Pingali, S. V., O’Neill, H. M., Zhang, Q., Berglund, L. A. “Small Angle Neutron Scattering Shows Nanoscale PMMA Distribution in Transparent Wood ” (2021)Nano Lett (21) 7:2883–2890.
• Zhu, Y., Rodriguez, N. P., Kojima, Y., Yoshida, M., Zhang, J., Jellison, J., Pingali, S. V., O’Neill, H., and Goodell, B. “Nanostructural Analysis of Enzymatic and Non-Enzymatic Brown-Rot Fungal Deconstruction of the Lignocellulose Cell Wall.” (2020) Front Microbiol 11:1389.
• Vural, , Smith, J. C., and Petridis, L. “Polymer Principles Behind Solubilizing Lignin with Organic Cosolvents for Bioenergy.” (2020) Green Chem 22:4331–4340.
• Meng, , Bhagia, S., Wang, Y., Zhou, Y., Pu, Y., Dunlap, J. R., Shuai, L., Ragauskas, A. J., Yoo, C.“Effects of the Advanced Organosolv Pretreatment Strategies on Structural Properties of Woody Biomass.” (2020)Industrial Crops and Products 146, 112144.
• Smith, M. D., Pingali, S. V., Elkins, J. G., Bolmatov, D., Standaert, R. F., Nickels, J. D., Urban, V. S., Katsaras, J., Davison, B., Smith, J. C., and Petridis, L. “Solvent-Induced Membrane Stress in Biofuel Production: Molecular Insights from Small-Angle Scattering and All-Atom Molecular Dynamics Simulations.” (2020) Green Chem22:8278–8288. Journal back cover.
• Pingali, S. V., Smith, M. D., Liu, S. H., Rawal, T. B., Pu, Y., Shah, R., Evans, B. R., Urban, V. S., Davison, H., Cai, C. M., Ragauskas, A. J., O’Neill, H. M., Smith, J. C., and Petridis, L.“Deconstruction of Biomass Enabled by Local Demixing of Cosolvents at Cellulose and Lignin Surfaces.” (2020)PNAS 117:16776–16781.
• Agarwal, , Smith, M. D., and Smith, J. C. “Capturing Deuteration Effects in a Molecular Mechanics Force Field: Deuterated THF and the THF–Water Miscibility Gap.” (2020) J Chem Theory Comput. 16:2529–2540.
• Nickels, J. D., Poudel, S., Chatterjee, S., Farmer, A., Cordner, D., Campagna, S. R., Giannone, R. J., Hettich, R. J., Myles, D. A. A., Standaert, R. F., Katsaras, J., Elkins, J. G., and Davison. B. H. “Impact of Fatty Acid Labeling of Bacillus subtilis Membranes on the Cellular Lipidome and Proteome.” (2020) Frontiers Microbiol:Systems Microbiol 11:914.
• Agarwal, R., Shrestha, U. R., Chu, X.-Q., Petridis, L., and Smith, J. C. “Mesophilic Pyrophosphatase Function at High Temperature: A Molecular Dynamics Simulation Study.” (2020) Biophys J 119:142–150.
• Vural, D., “Dynamics of Lignin: Molecular Dynamics and Neutron Scattering” In Understanding Lignocellulose: Synergistic Computational and Analytic Methods, ACS Symposium Series 1338, Ed. MicholasDean Smith, Chapter 4, 49–67, ACS Publications, Washington D.C. (2019).
• Patri, A., Mostofian, B., Pu, Y., Ciaffone, N., Soliman, M., Tetard, L., Smith, M. D., Cheng, X., Kumar, ,Ragauskas, A. J., Wyman, C. E., Smith, J. C., Petridis, L., Cai, C. M. “A Multifunctional Cosolvent Pair Reveals Molecular Principles of Biomass Deconstruction.” (2019) J. Am. Chem. Soc.141 (32), 12545–12557.
• Ding, J., Yoo, C. G., Pu, Y., Meng, X., Bhagia, S., Yu, C., Ragauskas, A. J. “Cellulolytic Enzyme- Aided Hemicellulose Extraction and Its Characteristics from Switchgrass.” (2019) Green Chemistry 21:3902–3910.
• Vermaas, J. V., Petridis, L., Ralph, J., Crowley, M. F. and Beckham, G. T. “Systematic parameterization of lignin for the CHARMM force field.” (2019) Green Chemistry 21:109–122.
• Kothari, N., Bhagia, S., Zaher, M., Pu, Y., Mittal, A., Yoo, C. G., Himmel, M. E., Ragauskas, A. J., Kumar, R., Wyman, C. E. “Cellulose Hydrolysis by Clostridium Thermocellum is Agnostic to Substrate Structural Properties in Contrast to Fungal Cellulases” (2019) Green Chemistry 21(10):2810–2822.
• Paeslack, Smith, J. C., Heyden, M., Schaefer, L. V. “Hydration-Mediated Stiffening of Collective Membrane Dynamics by Cholesterol.” (2019) Physical Chemistry Chemical Physics 21(20):10370–10376.
• Evans, B. R., Foston, M., O’Neill, H. M., Reeves, D., Rempe, C., McGrath, K., Ragauskas, A. J., and Davison, B. H. “Production of Deuterated Biomass by Cultivation of Lemna minor (duckweed) in D₂O.” (2019) Planta 249:1465–1475.
• Shah, R., Huan, S., Pingali, S. V., Sawada, D., Kim, S., Evans, B. R., Davison, B. H., O’Neill, H.“Hemicellulose-Cellulose Composites Reveal Differences in Cellulose Organization After Dilute Acid” (2019) Biomacromolecules 20(2):893–903.
• Petridis, L., Smith, J. C. “Molecular-level Driving Forces in Lignocellulosic Biomass Deconstruction for Bioenergy.“(2018) Nature Reviews Chemistry 2:382–389.
• Satlewal A., Agrawal R., Bhagia S., Sangoro J., and Ragauskas A.J., “Natural Deep Eutectic Solvents for Lignocellulosic Biomass Pretreatment: Recent Developments, Challenges and Novel Opportunities.” (2018) Biotechnol. Adv. 36(8):2032–2050.
• Bhagia, S., Meng, X., Evans, B.R., JR Dunlap, J.R., Bali, G., Chen, J., Reeves, K.S., Ho, HCH., Davison, B.H., Ragauskas, A.J. ‘Ultrastructure and Enzymatic Hydrolysis of Deuterated Switchgrass.” (2018) Rep. 8:13226
• Vural, D., Smith, J.C., L Petridis, L. “Dynamics of the Lignin Glass Transition.” (2018) Phys. Chem. Chem. Phys. 20:20504-20512.
• Vural, D., Smith J.C., Glyde, H. “Determination of Dynamical Heterogeneity from Dynamic Neutron Scattering of Proteins.” (2018) J. 114:2397-2407.
• Smith, M.D., Cai, C., Cheng, X., Petridis, L., Smith, J.C. “Phase-dependent solvation of xylan in tetrahydrofuran-water enables synergistic processing of lignocellulosic biomass.” (2018) Green Chem. 20:1602-1620.
• Smith, J.C., Tan, P., Petridis, L., Hong, L. “Dynamic Neutron Scattering by Biological Systems.” (2018) Rev. Biophysics 47:335-354.
• Vural, D., Gainaru, C., O’Neill, H., Pu, Y., Smith, MD., Pingali, S.V.,  Mamontov, E., Davison, B.H., Sokolov, A.P., Ragauskas, A.J., Smith, J.C., Petridis, L. “Impact of hydration and temperature history on the structure and dynamics of lignin.” (2018) Green Chem. 20:1602-1611.
• Sawada, D., Kalluri, U., O’Neill, H., Urban, V., Langan, P., Davison, B.H, Pingali, SV. “Tension wood structure and morphology conducive for better enzymatic digestion.” (2018) Biofuels 11:44.
• Kumar, R., Bhagia, S., Smith, M.D., Petridis, L., Ong, R., Cai, C.M., Mittal, A., Himmel, M.E., Balan, V., Dale, B.D., Ragauskas, A.J., Smith, J.C., Wyman, C.E. “Cellulose-Hemicellulose Interactions at Elevated Temperatures Increase Cellulose Recalcitrance to Biological Conversion.” (2018) Green Chem. 20:921-934.
• Moyer, P., Smith M.D., Abdoulmoumine, M., Chmely, S.C., Smith, J.C., Petridis, L., Labbé, N. “Relationship between lignocellulosic biomass solubilization and physicochemical properties of ionic liquids composed of 3-methylimidazolium cations and carboxylate anions.” (2018) Chem. Chem. Phys. 20:2508-2516.
• Meng, X., Pu, Y., Sannigrahi, P., Li, M., Cao, S., Ragauskas, A.J. “The nature of hololignin.” (2018) ACS Sust. Chem. Eng. 6(1):957-964.
• Smith, M.D., Cheng, X., Petridis, L., Mostofian, B., Smith, J.C. “Organosolv-Water Cosolvent Phase Separation on Cellulose and its Influence on the Physical Deconstruction of Cellulose: A Molecular Dynamics Analysis.” (2017) Rep. 7 (1):14494.
• Evans, B.R., Bali, G., Ragauskas, A.J., Shah, R., O’Neill, H., Howard, C.,  Lavenhouse, F., Ramirez, D., Weston, K., Ramey, K., Cangemi, V., Kinney, B., Partee, C., Ware, T., Davison, B.H. “Alleopathic effects of exogenous phenylalanine: A comparison of four monocot species.” (2017) Planta 246 (4):673 – 685.
• Meng, X., Evans, B.R., Yoo, C.G., Pu, Y., Davison, B.H., Ragauskas, A.J. “Effect of in Vivo Deuteration on Structure of Switchgrass Lignin.” (2017) ACS Sust. Chem. Eng. 5(9):8004 – 8010.
• O’Neill, H., Pingali, S.V., Petridis, L., He, J., Evans, B.R., Mamontov, E., Hong, L., Urban, V., Langan, P., Smith, J.C., Davison, B.H. “Dynamics of water bound to crystalline cellulose.” (2017) Rep. 7:11840.
• Goodell, B., Zhu. Y., Kim, S., Kafle, K., Eastwood, D., Daniel, G., Jellison, J., Yoshida, M., Groom, L., Pingali, S.V., O’Neill, H. “Modification of the nanostructure of lignocellulose cell walls via a non-enzymatic lignocellulose deconstruction system in brown-rot wood decay fungi.” (2017) Biofuels 10:179.
• Pingali, S.V., Urban, V.S., Heller, W.T., McGaughey, J., O’Neill, H., Foston, M.B., Li, H., Wyman, C.E., Myles, D.A., Langan, P., Ragauskas, A.J., Davison, B.H., Evans, B.R. “Understanding Multiscale Structural Changes During Dilute Acid Pretreatment of Switchgrass and Poplar.” (2017) ACS Sust. Chem. Eng 5(1):426 -435.