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Mark Maupin
Data Scientist

Mark Maupin is the Systems Modeling Team Lead in the Computing, Analytics, and Modeling Group within the Integrated Discovery Sciences Directorate at Pacific Northwest National Laboratory (PNNL). He joined PNNL in 2023 as a data scientist in the National Security Directorate's Chemical and Biological Signatures Group and transitioned to his current leadership role in 2026. His expertise spans multiscale modeling, machine learning, computational toxicology, and protein complex prediction.

In 2026, Mark also became a Campaign Lead for EMSL's Community Science Campaigns, where he is advancing efforts to make molecular modeling more accessible through streamlined, user-focused workflows. His work aims to bring truly multiscale simulation tools into practice, connecting modeling approaches across scales to accelerate scientific discovery.

Before joining PNNL, Mark spent six years as a senior scientist in Corporate Functions R&D at Procter & Gamble. There, he developed pharmacokinetic/pharmacodynamic (PK/PD) models to predict microbial efficacy and integrated multiscale modeling with machine learning to understand and forecast microbial and viral behavior.

Grounded in physical chemistry, Mark earned his PhD from the University of Utah and conducted postdoctoral research on interfacial phenomena using ab initio molecular dynamics. From 2010 to 2017, he led an independently-funded research group at Colorado School of Mines, investigating ligand-gated ion channels, proton-conducting membranes, ionic liquids, and cellulase enzymes. Across industry, academia, and national laboratory research, he has brought together computational methods and interdisciplinary expertise to tackle complex scientific challenges.

Research Interests

  • Multiscale modeling
  • Method development
  • Computational toxicology
  • Artificial intelligence
  • Machine learning 

Education

  • PhD in Chemistry, University of Utah, 2008
  • MS in Chemistry, Boise State University, 2002
  • BS in Chemistry, Boise State University, 2000

Awards and Recognition

  • P&G CEO Award, 2022
  • Henry Eyring Research Fellow, 2002

Affiliations and Professional Service

  • American Chemical Society
  • AAAS-Pacific Division Chair of Computer and Information Sciences Section, 2012–2015

Publications

2026

  • I. Ahmed, S. J. Fox, C. M. Maupin, O. Todini, D. Amirkulova, "Molecular Modelling of Surfactant Interactions on Phospholipid Bilayers Mimicking Corneal Epithelium", Journal of Chemical Theory and Computation, 2026, 22, 7966-7980, DOI.10.1021/acs.jctc.6c00863
     
  • S. Masirevic, J. K. Marzinek, M. L. Y. Kong, G. Lin, H. Chen, J. Liu, C. Chua, C. M. Maupin, C. S. Verma, S. J. Fox, P. J. Bond, "A Multiscale Framework for Uncovering Surfactant-Mediated Viral Capsid Disruption", Cell Reports Physical Science, 2026, 7, 103324, DOI.10.1016/j.xcrp.2026.103324
     
  • G. Panapitiya, P. Gao, C. M. Maupin, E. G. Saldanha, "FragNet: A Graph Neural Network for Molecular Property Prediction with Four Levels of Interpretability", J. Am. Chem. Soc., 2026, 148, 9930-9950, DOI.10.1021/jacs.5c22620

2025

  • Masirevic, S., J. K., Marzinek, J. Liu, C. M. Maupin, S. J. Fox, C. S. Verma, P. J. Bond. 2025. “Unravelling the dynamics of the maturation protein in MS2 bacteriophage via molecular simulations.” Scientific Reports 15: 35133. DOI:10.1038/s41598-025-19036-0
     
  • Cesaro, A., F. Wan, H. Shi, K. Wang, C. M. Maupin, M. L. Barker, J. Liu, S. J. Fox, J. Yeo, and Cesar de la Fuente-Nunez. 2025. “Antiviral discovery using sparse datasets by integrating experiments, molecular simulations, and machine learning.” Cell Reports Physical Science 6: 102554. DOI:10.1016/j.xcrp.2025.102554

2024

  • Bennett, W. F. D., A. Bernardi, T. N. Ozturk, H. I. Ingolfsson, S. J. Fox, D. Sun, and C. M. Maupin. 2024. “ezAlign: A Tool for Converting Coarse-Grained Molecular Dynamics Structures to Atomistic Resolution for Multiscale Modeling.” Molecules 29 (15): 3557. DOI: 10.3390/molecules29153557

2022

  • Bennett, W. F. D., S. J. Fox, D. Sun, and C. M. Maupin. 2022. “Bacterial Membranes Are More Perturbed by the Asymmetric Versus Symmetric Loading of Amphiphilic Molecules.” Membranes 12: 350. DOI: 10.3390/membranes12040350

2020

  • Kusoglu, A., K. Vezzu, G. A. Hegde, G. Nawn, A. R. Motz, H. N. Sarode, G. M. Haugen, Y. Yang, S. Seifert, M. A. Yandrasits, S. Hamrock, C. M. Maupin, A. Z. Weber, V. Di Noto, and A. M. Herring. 2020. “Transport and Morphology of a Proton Exchange Membrane Based on a Doubly Functionalized Perfluorosulfonic Imide Side Chain Perfluorinated Polymer.” Chem. Mater. 32: 38–59. DOI:10.1021/acs.chemmater.8b05012

2019

  • Divekar, A. G., M. -C. Kuo, A. M. Park, A. R. Motz, Z. S. Page-Belknap, Z. Owczarczyk, H. Long, S. Seifert, C. M. Maupin, M. A. Yandrasits, Y. Yang, B. S. Pivovar, and A. M. Herring. 2019. “The impact of alkyl tri-methyl ammonium side chains on perfluorinated ionic membranes for electrochemical applications.” J. Polym. Sci., Part B: Polym. Phys. 57: 700–712. DOI: 10.1002/polyb.24825 

2018

  • Ta, A. T., G. A. Hegde, B. D. Etz, A. G. Baldwin, Y. Yang, J. C. Shafer, M. P. Jensen, C. M. Maupin, and S. Vyas. 2018. “Solvation Dynamics of HEHEHP Ligand at the Liquid-Liquid Interface.” J. Phys. Chem. B. 122 (22): 5,999–6,006. DOI: 10.1021/acs.jpcb.8b0316

2017

  • Motz, A. R., A. M. Herring, S. Vyas, and C. M. Maupin. 2017. “Quantum Mechanical Study of the Reaction Mechanism for 2π-2π Cycloaddition of Fluorinated Methylene Groups.” J. Org. Chem. 82: 6,578–6,585. DOI: 10.1021/acs.joc.7b00597
     
  • Saqib, N., C. J. Silva, C. Mark Maupin, and J. M. Porter. 2017. “A Novel Optical Diagnostic for In Situ Measurements of Lithium Polysulfides in Battery Electrolytes.” Appl. Spectrosc. 71: 1,593–1,599. DOI: 10.1177/0003702816684638
     
  • Schutt, T. C., G. A. Hegde, V. S. Bharadwaj, A. J. Johns, and C. M. Maupin. 2017. “Impact of Water-Dilution on the Biomass Solvation Properties of the Ionic Liquid 1-Methyltriethoxy-3-Ethylimidazolium Acetate.” J. Phys. Chem. B. 121: 843–853. DOI: 10.1021/acs.jpcb.6b09101

2016

  • Warrier, P., M. N. Khan, V. Srivastava, C. M. Maupin, and C. A. Koh. 2016. “Overview: Nucleation of Clathrate Hydrates.” J. Chem. Phys. 145: 211705. DOI: 10.1063/1.4968590
     
  • Schutt, T. C., V. S. Bharadwaj, G. A. Hegde, A. J. Johns, and C. M. Maupin. 2016. “In Silico Insights into the Solvation Characteristics of the Ionic Liquid 1-Methyltriethoxy-3-Ethylimidazolium Acetate for Cellulosic Biomass.” Phys. Chem. Chem. Phys. 18: 23,715–23,726. DOI: 10.1039/c6cp03235d
     
  • Taraphder, S., C. M. Maupin, J. M. J. Swanson, and G. A. Voth. 2016. “Coupling Protein Dynamics with Proton Transport in Human Carbonic Anhydrase II.” J. Phys. Chem. B. 120: 8,389–8,404. DOI: 10.1021/acs.jpcb.6b02166
     
  • Hegde, G. A., V. S. Bharadwaj, C. L. Kinsinger, T. C. Schutt, N. R. Pissierra, and C. M. Maupin. 2016. “Impact of Water Dilution and Cation Tail Length on Ionic Liquid Characteristics: Interplay between Polar and Non-Polar Interactions.” J. Chem. Phys. 145: 064504. DOI: 10.1063/1.4960511
     
  • Liu, Y., B. Zhang, C. L. Kinsinger, Y. Yang, S. Seifert, Y. Yan, C. M. Maupin, M. Liberatore, and A. M. Herring. 2016. “Anion Exchange Membranes Composed of a Poly(2,6-Dimethyl-1,4-Phenylene Oxide) Random Copolymer Functionalized with a Bulky Phosphonium Cation.” J. Membr. Sci. 506: 50–59. DOI: 10.1016/j.memsci.2016.01.042
     
  • * Slingsby, J. G., N. A. Rorrer, L. Krishna, E. S. Toberer, C. A. Koh, and C. M. Maupin.,2016. “Dynamic Free Energy Surfaces for Sodium Diffusion in Type II Silicon Clathrates.” Phys. Chem. Chem. Phys. 18: 5,121–5,128. DOI: 10.1039/C5CP06066D 

2015

  • Kinsinger, C. L., Y. Liu, Y. Yang, S. Seifert, D. M. Knauss, A. M. Herring, and C. M. Maupin. 2015. “Random and Block Sulfonated Polyaramides as Advanced Proton Exchange Membranes.” J. Phys. Chem. C. 119: 24,724–24,732. DOI: 10.1021/acs.jpcc.5b06857
     
  • * Bharadwaj, V. S.. N. M. Eagan, N. M. Wang, M. W. Liberatore, and C. M. Maupin. 2015. “Molecular Simulations of Fatty-Acid Methyl Esters and Representative Biodiesel Mixtures.” Chem. Phys. Chem.16: 2,810–2,817. DOI: 10.1002/cphc.201500453
     
  • Schutt, T. C., V. S. Bharadwaj, D. M. Granum, and C. M. Maupin. 2015. “The Impact of Active Site Protonation on Substrate Ring Conformation in Melanocarpus albomyces cellobiohydrolase Cel7B.” Phys. Chem. Chem. Phys. 17: 16,947–16,958. DOI: 10.1039/C5CP01801C
     
  • Bharadwaj, V. S., T. C. Schutt, T. C. Ashurst, and C. M. Maupin. 2015. “Elucidating the Conformational Energetics of Glucose and Cellobiose in Ionic Liquids.” Phys. Chem. Chem. Phys. 17: 10,668–10,678. DOI: 10.1039/C5CP00118H
     
  • * Bharadwaj, V. S., S. Vyas, S. M. Villano, C. M. Maupin, and A. M. Dean. 2015. “Unravelling the Impact of Hydrocarbon Structure on the Fumarate Addition Mechanism – a gas‐phase ab initio study.” Phys. Chem. Chem. Phys. 17: 4,054–4066. DOI: 10.1039/C4CP04317K 
     
  • Slingsby, J. G., S. Vyas, and C. M. Maupin. 2015. “A Charge-Modified General Amber Force Field for Phospholipids: Improved Structural Properties in the Tensionless Ensemble.” Mol. Simulat. 41: 1,449–1,458. DOI:10.1080/08927022.2014.985675

2014

  • Sambasivarao, S. V., Y. Liu, J. L. Horan, S. Seifert, A. M. Herring, and C. M. Maupin. 2014. “Enhancing Proton Transport and Membrane Lifetimes in Perfluorosulfonic Acid Proton Exchange Membranes: A Combined Computational and Experimental Evaluation of the Structure and Morphology Changes Due to H3PW12O40 Doping.” J. Phys. Chem. C. 118: 20,193–20,202. DOI:10.1021/jp5059325
     
  • Vyas, S., C. Dreyer, J. Slingsby, D. Bicknase, J. M. Porter, and C. M. Maupin. 2014. “Electronic Structure and Spectroscopic Analysis of 1-Ethyl-3-methylimidazolium Bis(trifluoromethylsulfonyl)imide Ion Pair. J. Phys. Chem. A. 118: 6,873–6,882. DOI:10.1021/jp5035689
     
  • * Granum, D. M., T. C. Schutt, and C. M. Maupin. 2014. “Computational Evaluation of the Dynamic Fluctuations of Peripheral Loops Enclosing the Catalytic Tunnel of a Family 7 Cellobiohydrolase.” J. Phys. Chem. B. 118: 5,340–5,349. DOI: 10.1021/jp5011555
     
  • Aggarwal, M., B. Kondeti, C. Tu, C. M. Maupin, D. N. Silverman, and R. McKenna. 2014. “Structural insight into activity enhancement and inhibition of H64A carbonic anhydrase II by imidazoles.” IUCrJ 1: 129–135. DOI: 10.1107/S2052252514004096
     
  • Porter, J. M., C. B. Dreyer, D. Bicknase, S. Vyas, C. M. Maupin, J. Poshusta, and J. Martin. 2014. “Optical Measurements of Impurities in Room-Temperature Ionic Liquids.” J. Quant. Spectrosc. Radiat. Transfer. 113: 300–310. DOI: 10.1016/j.jqsrt.2013.08.015
     
  • * Sambasivarao, S. V., J. Roberts, V. S. Bharadwaj, J. G. Slingsby, C. Rohleder, C. Mallory, J. R. Groome, O. M. McDougal, and C. M. Maupin. 2014. “Acetylcholine Promotes Binding of a-Conotoxin MII for a3b2 Nicotinic Acetylcholine Receptors.” ChemBioChem. DOI: 10.1002/cbic.201300577 
     
  • Granum, D. M., S. Vyas, S. V. Sambasivarao, and C. M. Maupin. 2014. “Computational Evaluation of Charge Coupling and Hydrogen Bonding in the Active Site of a Family 7 Cellobiohydrolase.” J. Phys. Chem. B. DOI: 10.1021/jp408536s
     
  • Liu, Y., S. V. Sambasivarao, J. L. Horan, Y. Yang, C. M. Maupin, and A. M. Herring. 2014. “A Combined Theoretical and Experimental Investigation of the Transport Properties of Water in a Perfluorosulfonic Acid Proton Exchange Membrane Doped with Heteropoly Acids, H3PW12O40 or H4SiW12O40.” J. Phys. Chem. C. 118 (2): 854–863. DOI: 10.1021/jp4099232
     
  • Sambasivarao, S. V., D. M. Granum, H. Wang, and C. M. Maupin. 2014. “Identifying the Enzymatic Mode of Action for Cellulase Enzymes by Means of Docking Calculations and a Machine Learning Algorithm.” AIMS Molecular Science. DOI: 10.3934/molsci.2014.1.59 
     
  • McDougal, O. M., N. Cornia, S. V. Sambasivarao, A. Remm, C. Mallory, J. T. Oxford, C. M. Maupin, and T. Andersen. 2014. “Homology Modeling and Molecular Docking for the Science Curriculum.” Biochem. Mol. Biol. Edu. 42: 179–182. DOI:10.1002/bmb.20767

2013

  • McDougal, O. M. D. M. Granum, M. Swartz, C. Rohleder, and C. M. Maupin. 2013. “pKa Determination of Histidine Residues in α-Conotoxin MII Peptides by 1H NMR and Constant pH Molecular Dynamics Simulation.” J. Phys. Chem. B. 117: 2,653–2,661. DOI: 10.1021/jp3117227
     
  • Choi, T. H., R. Liang, C. M. Maupin, and G. A. Voth. 2013. “Application of the SCC-DFTB Method to Hydroxide Water Clusters and Aqueous Hydroxide Solutions.” J. Phys. Chem. B. 117: 5,165–5,179. DOI: 10.1021/jp400953a
     
  • Bharadwaj, V. S., A. M. Dean, and C. M. Maupin. 2013. “Insights into the Glycyl Radical Enzyme Active Site of Benzylsuccinate Synthase: A Computational Study.” J. Am. Chem. Soc. 135: 12,279–12,288. DOI: 10.1021/ja404842r

2012

  • Dorgan, J. R., N. A. Rorrer, C. M. Maupin. 2012. “Parameter Free Prediction of Rheological Properties of Homopolymer Melts by Dynamical Monte Carlo Simulation.” Macromolecules 45: 8,833–8,840. DOI: 10.1021/ma301307d

2011

  • Maupin, C. M., N. Castillo, S. Taraphder, C. Tu, R. McKenna, D. N. Silverman, and G. A. Voth. 2011. “Chemical Rescue of Enzymes: Proton Transfer in Mutants of Human Carbonic Anhydrase II.” J. Am. Chem. Soc. 133: 6,223–6,234. DOI: 10.1021/ja1097594

2010

  • Knight, C., C. M. Maupin, and G. A. Voth. 2010. “Defining Condensed Phase Reactive Force Fields from ab initio Molecular Dynamics Simulations: The Case of the Hydrated Excess Proton.” J. Chem. Theory Comput. 6: 3,223–3,232. DOI: 10.1021/ct1004438
     
  • Maupin, C. M., B. Aradi, and G. A. Voth. 2010. “The Self-Consistent Charge Density Functional Tight Binding Method Applied to Liquid Water and the Hydrated Excess Proton: Benchmark Simulations.” J. Phys. Chem. A. 114: 6,922–6,931. DOI: 10.1021/jp1010555
     
  • Maupin, C. M., and G. A. Voth. 2010. “Proton Transport in Carbonic Anhydrase: Insights from Molecular Simulation.” Biochimica et Biophysica Acta (BBA) – Proteins & Proteomics 1804: 332–342. DOI: 10.1016/j.bbapap.2009.09.006

2009

  • Maupin, C. M., J. Zheng, C. Tu, R. McKenna, D. N. Silverman, and G. A. Voth. 2009. “Effect of Active-site Mutations at Asn67 on the Proton Transfer Mechanism of Human Carbonic Anhydrase II.” Biochemistry 48: 7,996–8,005. DOI: 10.1021/bi901037u 
     
  • Maupin, C. M., R. McKenna, D. N. Silverman, and G. A. Voth. 2009. “Elucidation of the Proton Transport Mechanism in Human Carbonic Anhydrase II.” J. Am. Chem. Soc. 131: 7,598–7,608. DOI: 10.1021/ja8091938 

2008

  • Maupin, C. M., M. G. Saunders, I. F. Thorpe, R. McKenna, D. N. Silverman, and G. A. Voth. 2008. “Origins of Enhanced Proton Transfer in the Y7F Mutant of Human Carbonic Anhydrase II.” J. Am. Chem. Soc. 130: 11,399–11,408. DOI: 10.1021/ja802264j 

2007

  • Swanson, J. M. J., C. M. Maupin, H. Chen, M. K. Petersen, J. Xu, Y. Wu, and G. A. Voth. 2007. “Proton Solvation and Transport in Aqueous and Biomolecular Systems: Insights from Computer Simulations.” J. Phys. Chem. B. 111: 4,300–4,314. DOI: 10.1021/jp070104x
     
  • Maupin, C. M., and G. A. Voth. 2007. “Preferred Orientation of His-64 in Human Carbonic Anhydrase II.” Biochemistry 46: 2,938–2,947. DOI: 10.1021/bi062170f 
     
  • Fisher, Z. S., C. M. Maupin, L. Govindasamy, M. Budayova-Spano, C. Tu, M. Agbandje-McKenna, D. N. Silverman, G. A. Voth, and R. McKenna. 2007. “Atomic Crystal and Molecular Dynamics Simulation Structures of Human Carbonic Anhydrase II: Insights into the Proton Transfer Mechanism.” Biochemistry 46: 2,930–2,937. DOI: 10.1021/bi062066y

2006

  • Maupin, C. M., K. F. Wong, A. V. Soudackov, S. Kim, and G. A. Voth. 2006. “A Multistate Empirical Valence Bond Description of Protonatable Amino Acids.” J. Phys. Chem. A. 110: 631–639. DOI: 10.1021/jp053596r