Laboratory Fellow
National Security
Laboratory Fellow
National Security


Nathan Baker, Ph.D., is a Laboratory Fellow in the Computing & Analytics Division at Pacific Northwest National Laboratory (PNNL). He is also a University of Washington (UW) / PNNL Distinguished Faculty Fellow with the Department of Applied Mathematics at UW. Dr. Baker was previously a Visiting Faculty member in the Brown University Division of Applied Mathematics, and an Associate Professor of Biochemistry & Molecular Biophysics at Washington University in St. Louis.

Dr. Baker’s current research focuses on national security subjects as well as basic research on developing new algorithms and mathematical methods in biophysics, quantum information sciences, and data science. His research projects have included computational methods for modeling solvation in biomolecular systems, mathematical methods for mesoscale materials modeling, and development of methods for signature discovery. His research has included funded from the National Institutes of Health, U.S. Department of Energy, and National Science Foundation.

Dr. Baker has served as co-principal investigator and project manager for the DOE Advanced Scientific Computing Research CM4: Collaboratory on Mathematics for Mesoscopic Modeling of Materials and as lead for the Signature Discovery Initiative at PNNL. From 2016 to 2019, he served as the Director for the Advanced Computing, Mathematics, and Data Division at PNNL—a division of 100+ researchers in applied mathematics, data science, and high-performance computing. Dr. Baker also managed the Applied Statistics and Computational Modeling Group at PNNL from 2013 to 2015, which comprised approximately 50 staff with expertise in statistics, mathematics, and operations research.

Dr. Baker has served on review panels for various agencies, including as a member of the NIH Macromolecular Structure and Function D study section. He is current an editorial board member for Communications of the Association for Computing Machinery and serves on the editorial board for NPG Scientific Data. Dr. Baker previously served as associate editor and editorial board member for Biophysical Journal, editor-in-chief for Computational Science and Discovery, and section editor for Annual Reports in Computational Chemistry. He has authored more than 100 peer-reviewed publications.

Dr. Baker is a Fellow of the American Association for the Advancement of Science and a member of the Washington State Academy of Sciences. He has been awarded the Hewlett-Packard Junior Faculty Excellence Award by the American Chemical Society, the National Cancer Institute caBIG Connecting Collaborators Award, and an Alfred P. Sloan Research Fellowship. He earned his doctorate in physical chemistry from the University of California, San Diego.

Research Interest

  • Applied mathematics
  • Computational biophysics
  • Computational chemistry
  • Quantum information sciences


  • Ph.D., Physical Chemistry, University of California, San Diego
  • B.S., Chemistry, University of Iowa

Affiliations and Professional Service

  • American Chemical Society
  • Association for Computing Machinery
  • Biophysical Society
  • Institute of Electrical and Electronics Engineers
  • Society for Industrial and Applied Mathematics
  • Washington State Academy of Sciences

Awards and Recognitions

  • Fellow, American Association for the Advancement of Science
  • Hewlett-Packard Junior Faculty Excellence Award (American Chemical Society)
  • National Cancer Institute caBIG Connecting Collaborators Award
  • Alfred P. Sloan Research Fellowship
  • Howard Hughes Medical Institute Graduate Fellowship
  • Barry Goldwater Undergraduate Fellowship



  • Bauman N.P., H. Liu, E.J. Bylaska, S. Krishnamoorthy, G. Low, C.E. Granade, and N.O. Wiebe, et al. 2021. "Toward quantum computing for high-energy excited states in molecular systems: quantum phase estimations of core-level states." Journal of Chemical Theory and Computation 17, no. 1:201-210. PNNL-SA-154437. doi:10.1021/acs.jctc.0c00909


  • Grogan F.C., H. Lei, X. Li, and N.A. Baker. 2020. "Data-driven molecular modeling with the generalized Langevin equation." Journal of Computational Physics 418. PNNL-SA-149702. doi:10.1016/
  • Laureanti J.A., J.M. Brandi-Lozano, E.C. Offor, D.W. Engel, R.J. Rallo Moya, B. Ginovska, and X. Martinez, et al. 2020. "Visualizing biomolecular electrostatics in virtual reality with UnityMol-APBS." Protein Science 29, no. 1:237-246. PNNL-SA-146891. doi:10.1002/pro.3773
  • Visweswara Sathanur A., and N.A. Baker. 2020. "A Clustering-based biased Monte Carlo Approach to Protein Titration Curve Prediction." In IEEE International Conference on Machine Learning and Applications (ICMLA 2020), December 14-17, 2020, Miami, FL, 179-184. Piscataway, New Jersey:IEEE. PNNL-SA-154142.  doi:10.1109/ICMLA51294.2020.00037


  • Lei H., J. Li, P. Gao, P. Stinis, and N.A. Baker. 2019. "A data-driven framework for sparsity-enhanced surrogates with arbitrary mutually dependent randomness." Computer Methods in Applied Mechanics and Engineering 350. PNNL-SA-134010. doi:10.1016/j.cma.2019.03.014


  • Goh G.B., C.M. Siegel, A. Vishnu, N.O. Hodas, and N.A. Baker. 2018. "How Much Chemistry Does a Deep Neural Network Need to Know to Make Accurate Predictions?" In IEEE Winter Conference on Applications of Computer Vision (WACV 2018), March 12-15, 2018, Lake Tahoe, NV, 1340-1349. Piscataway, New Jersey: IEEE. PNNL-SA-127201.  doi:10.1109/WACV.2018.00151
  • Jurrus E.R., D.W. Engel, K.T. Star, K.E. Monson, J.M. Brandi-Lozano, L. Felberg, and D.H. Brookes, et al. 2018. "Improvements to the APBS biomolecular solvation software suite." Protein Science 27, no. 1:112-128. PNNL-SA-127254. doi:10.1002/pro.3280
  • Yang X., H. Lei, P. Gao, D.G. Thomas, D.L. Mobley, and N.A. Baker. 2018. "Atomic radius and charge parameter uncertainty in biomolecular solvation energy calculations." Journal of Chemical Theory and Computation 14, no. 2:759-767. PNNL-SA-126404. doi:10.1021/acs.jctc.7b00905


  • Felberg L.E., D.H. Brookes, E. Yap, E.R. Jurrus, N.A. Baker, and T. Head-Gordon. 2017. "PB-AM: An Open-Source, Fully Analytical Linear Poisson-Boltzmann Solver." Journal of Computational Chemistry 38, no. 15:1275-1282. PNNL-SA-120107. doi:10.1002/jcc.24528
  • Katz A.M., I.S. Tolokh, S. Pabit, N.A. Baker, A. Onufriev, and L. Pollack. 2017. "Spermine condenses DNA, but not RNA duplexes." Biophysical Journal 112, no. 1:22-30. PNNL-SA-122618. doi:10.1016/j.bpj.2016.11.018


  • Gunner M.R., and N.A. Baker. 2016. "Continuum Electrostatics Approaches to Calculating pKas and Ems in Proteins." In Methods in Enzymology: Computational Approaches for Studying Enzyme Mechanism Part B, edited by GA Voth. 1-20. Cambridge, Massachusetts:Elsevier. PNNL-SA-116401. doi:10.1016/bs.mie.2016.05.052
  • Jurrus E.R., N.O. Hodas, N.A. Baker, T.P. Marrinan, and M.D. Hoover. 2016. "Adaptive Visual Sort and Summary of Micrographic Images of Nanoparticles for Forensic Analysis." In 2016 IEEE International Symposium on Technologies for Homeland Security, May 10-11, 2016, Waltham, MA. Piscataway, New Jersey:IEEE. PNNL-SA-114724.doi:10.1109/THS.2016.7568959
  • Lei H., N.A. Baker, and X. Li. 2016. "Data-driven Parameterization of the Generalized Langevin Equation." Proceedings of the National Academy of Sciences of the United States of America 113, no. 50:14183-14188. PNNL-SA-118385. doi:10.1073/pnas.1609587113
  • Lei H., N.A. Baker, L. Wu, G.K. Schenter, C.J. Mundy, and A.M. Tartakovsky. 2016. "Smoothed Dissipative Particle Dynamics model for mesoscopic multiphase flows in the presence of thermal fluctuations." Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics 94, no. 2:023304. PNNL-SA-114207. doi:10.1103/PhysRevE.94.023304
  • Pabit S., A.M. Katz, I.S. Tolokh, A. Drozdetski, N.A. Baker, A. Onufriev, and L. Pollack. 2016. "Understanding Nucleic Acid Structural Changes by Comparing Wide-Angle X-ray Scattering (WAXS) Experiments to Molecular Dynamics Simulations." Journal of Chemical Physics 144, no. 20:Article No. 205102. PNNL-SA-115068. doi:10.1063/1.4950814
  • Purvine E., K.E. Monson, E.R. Jurrus, K.T. Star, and N.A. Baker. 2016. "Energy Minimization of Discrete Protein Titration State Models Using Graph Theory." Journal of Physical Chemistry B 120, no. 33:8354-8360. PNNL-SA-111332. doi:10.1021/acs.jpcb.6b02059
  • Sushko M.L., D.G. Thomas, S. Pabit, L. Pollack, A. Onufriev, and N.A. Baker. 2016. "The role of correlation and solvation in ion interactions with B-DNA." Biophysical Journal 110, no. 2:315-326. PNNL-SA-110226. doi:10.1016/j.bpj.2015.12.011
  • Tolokh I.S., A. Drozdetski, L. Pollack, N.A. Baker, and A. Onufriev. 2016. "Multi-shell model of ion-induced nucleic acid condensation." Journal of Chemical Physics 144, no. 15:Article No. 155101. PNNL-SA-114165. doi:10.1063/1.4945382
  • Wei G., and N.A. Baker. 2016. "Differential geometry-based solvation and electrolyte transport models for biomolecular modeling: a review." In Many-Body Effects and Electrostatics in Biomolecules, edited by Q Cui, M Meuwly and P Ren. 417-461. Singapore:Pan Stanford Publishing. PNNL-SA-106886. doi:10.1201/b21343-15
  • Yang X., H. Lei, N.A. Baker, and G. Lin. 2016. "Enhancing Sparsity of Hermite Polynomial Expansions by Iterative Rotations." Journal of Computational Physics 307. PNNL-SA-110981. doi:10.1016/


  • Harper B., D.G. Thomas, S. Chikkagoudar, N.A. Baker, K. Tang, A. Heredia-Langner, and R.D. Lins, et al. 2015. "Comparative hazard analysis and toxicological modeling of diverse nanomaterials using the embryonic zebrafish (EZ) metric of toxicity." Journal of Nanoparticle Research 17, no. 6:Article No. 250. PNNL-SA-101181. doi:10.1007/s11051-015-3051-0
  • Lei H., X. Yang, B. Zheng, and N.A. Baker. 2015. "Constructing Surrogate Models of Complex Systems with Enhanced Sparsity: Quantifying the influence of conformational uncertainty in biomolecular solvation." Multiscale Modeling & Simulation 13, no. 4:1327-1353. PNNL-SA-104506. doi:10.1137/140981587
  • Pan W., M.D. Daily, and N.A. Baker. 2015. "Numerical calculation of protein-ligand binding rates through solution of the Smoluchowski equation using smooth particle hydrodynamics." BMC Biophysics 8. PNNL-SA-107569. doi:10.1186/s13628-015-0021-y


  • Bielska A., B.N. Olsen, S.E. Gale, L. Mydock-McGrane, K. Krishnan, N.A. Baker, and P.H. Schlesinger, et al. 2014. "Side-Chain Oxysterols Modulate Cholesterol Accessibility through Membrane Remodeling." Biochemistry 53, no. 18:3042-3051. PNWD-SA-10254. doi:10.1021/bi5000096
  • Daily M.D., B.N. Olsen, P.H. Schlesinger, D.S. Ory, and N.A. Baker. 2014. "Improved Coarse-Grained Modeling of Cholesterol-Containing Lipid Bilayers." Journal of Chemical Theory and Computation 10, no. 5:2137-2150. PNWD-SA-10252. doi:10.1021/ct401028g
  • Gosink L.J., E.A. Hogan, T.C. Pulsipher, and N.A. Baker. 2014. "Bayesian model aggregation for ensemble-based estimates of protein pKa values." Proteins. Structure, Function, and Bioinformatics 82, no. 3:354-363. PNNL-SA-95333. doi:10.1002/prot.24390
  • Pham C., D.G. Thomas, J. Beiser, L. Mitchell, J. Huang, A. Senpan, and G. Hu, et al. 2014. "Application of a hemolysis assay for analysis of complement activation by perfluorocarbon nanoparticles." Nanomedicine: Nanotechnology, Biology and Medicine 10, no. 3:651-660. PNWD-SA-10120. doi:10.1016/j.nano.2013.10.012
  • Thomas D.G., S. Chikkagoudar, A. Heredia-Langner, M.F. Tardiff, Z. Xu, D. Hourcade, and C. Pham, et al. 2014. "Physicochemical signatures of nanoparticle-dependent complement activation." Computational Science and Discovery 7, no. 1:Article No. 015003. PNNL-SA-99801. doi:10.1088/1749-4699/7/1/015003
  • Tolokh I.S., S. Pabit, A.M. Katz, Y. Chen, A. Drozdetski, N.A. Baker, and L. Pollack, et al. 2014. "Why double-stranded RNA resists condensation." Nucleic Acids Research 42, no. 16:10823-10831. PNNL-SA-102401. doi:10.1093/nar/gku756


  • Baker N.A., J. Klemm, S. Harper, S. Gaheen, M. Heiskanen, P. Rocca-Serra, and S.A. Sansone. 2013. "Standardizng Data." Nature Nanotechnology 8, no. 2:73-74. PNNL-SA-92648. doi:10.1038/nnano.2013.12
  • Baker N.A., J.L. Barr, G.T. Bonheyo, C.A. Joslyn, K. Krishnaswami, M. Oxley, and R.W. Quadrel, et al. 2013. "Research towards a systematic signature discovery process." In IEEE International Conference on Intelligence and Security Informatics (ISI 2013), June 4-7, 2013, Seattle, Washington, edited by K Glass, et al, 301-308. Piscataway, New Jersey:IEEE. PNNL-SA-94543. doi:10.1109/ISI.2013.6578848
  • Chakraborty S., B.J. Rao, N.A. Baker, and B. Asgeirsson. 2013. "Structural phylogeny by profile extraction and multiple superimposition using electrostatic congruence as a discriminator." Intrinsically Disordered Proteins 1. PNNL-SA-96283. doi:10.4161/idp.25463
  • Daily M.D., J. Chun, A. Heredia-Langner, G. Wei, and N.A. Baker. 2013. "Origin of parameter degeneracy and molecular shape relationships in geometric-flow calculations of solvation free energies." Journal of Chemical Physics 139, no. 20:Article No. 204108. PNWD-SA-10185. doi:10.1063/1.4832900
  • Harper S., J.E. Hutchison, N.A. Baker, M. Ostraat, S. Tinkle, J.A. Steevens, and M.D. Hoover, et al. 2013. "Nanoinformatics workshop report: Current resources, community needs, and the proposal of a collaborative framework for data sharing and information integration." Computational Science and Discovery 6, no. 1:Article No. 014008. PNWD-SA-10154. doi:10.1088/1749-4699/6/1/014008
  • Olsen B.N., A. Bielska, T. Lee, M.D. Daily, D.F. Covey, P.H. Schlesinger, and N.A. Baker, et al. 2013. "The Structural Basis of Cholesterol Activity in Membranes." Biophysical Journal 105, no. 8:1838-1847. PNNL-SA-91384. doi:10.1016/j.bpj.2013.08.042
  • Thomas D.G., J. Chun, Z. Chen, G. Wei, and N.A. Baker. 2013. "Parameterization of a Geometric Flow Implicit Solvation Model." Journal of Computational Chemistry 34, no. 8:687-695. PNWD-SA-9830. doi:10.1002/jcc.23181
  • Thomas D.G., S. Gaheen, S. Harper, M. Fritts, F. Klaessig, E. Hahn-Dantona, and D. Paik, et al. 2013. "ISA-TAB-Nano: A Specification for Sharing Nanomaterial Research Data in Spreadsheet-based Format." BMC Bioinformatics 13. PNWD-SA-9668. doi:10.1186/1472-6750-13-2


  • Chen Z., S. Zhao, J. Chun, D.G. Thomas, N.A. Baker, P.W. Bates, and G. Wei. 2012. "Variational approach for nonpolar solvation analysis." Journal of Chemical Physics 137, no. 8:Article No. 084101. PNWD-SA-9814. doi:10.1063/1.4745084
  • Jacob F., J. Gray, A.S. Wynne, Y. Liu, and N.A. Baker. 2012. "Domain-Specific Languages for Composing Signature Discovery Workflows." In DSM '12: Proceedings of the 2012 Workshop on Domain-Specific Modeling, October 22, 2012, Tucson, Arizona, 61-64. New York, New York:The ACM. PNNL-SA-90243. doi:10.1145/2420918.2420934
  • Konecny R., N.A. Baker, and J.A. McCammon. 2012. "iAPBS: a programming interface to Adaptive Poisson-Boltzmann Solver." Computational Science and Discovery 5. PNNL-SA-88092. doi:10.1088/1749-4699/5/1/015005
  • Lee S., P.H. Schlesinger, S.A. Wickline, G.M. Lanza, and N.A. Baker. 2012. "Simulation of fusion-mediated nanoemulsion interactions with model lipid bilayers." Soft Matter 8, no. 26:7024-7035. PNWD-SA-9677. doi:10.1021/jp103228c
  • Maojo V., M. Fritts, F. Martin-Sanchez, D. De la Iglesia, R. Cachau, M. Garcia-Remesal, and J. Crespo, et al. 2012. "Nanoinformatics: Developing New Computing Applications for Nanomedicine." Computing 94, no. 6:521-539. PNWD-SA-9371. doi:10.1007/s00607-012-0191-2
  • Maojo V., M. Fritts, F. Martin-Sanchez, D. De la Iglesia, R. Cachau, M. Garcia-Remesal, and J. Crespo, et al. 2012. "Nanoinformatics: developing new computing applications for nanomedicine." Computing 94, no. 6:521-539. PNWD-SA-9822. doi:10.1007/s00607-012-0191-2
  • Olsen B.N., P.H. Schlesinger, D.S. Ory, and N.A. Baker. 2012. "Side-chain oxysterols: From cells to membranes to molecules." Biochimica et Biophysica Acta--Biomembranes 1818, no. 2:330-336. PNWD-SA-9421. doi:10.1016/j.bbamem.2011.06.014
  • Ren P., J. Chun, D.G. Thomas, M. Schnieders, M. Marucho, J. Zhang, and N.A. Baker. 2012. "Biomolecular electrostatics and solvation: a computational perspective." Quarterly Reviews of Biophysics 45, no. 4:427-491. PNNL-SA-84152. doi:10.1017/S003358351200011X
  • Thomas D.G., S. Chikkagoudar, A.R. Chappell, and N.A. Baker. 2012. "Annotating the structure and components of a nanoparticle formulation using computable string expressions." In IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW 2012): October 4-7, 2012, Philadelphia, PA, 889-894. Piscataway, New Jersey:IEEE. PNWD-SA-9974. doi:10.1109/BIBMW.2012.6470259


  • Alexov E., E.L. Mehler, N.A. Baker, A. Baptista, Y. Huang, F. Milletti, and J.E. Nielsen, et al. 2011. "Progress in the prediction of pKa values in proteins." Proteins. Structure, Function, and Bioinformatics 79, no. 12:3260-3275. PNNL-SA-82965. doi:10.1002/prot.23189
  • Carstensen T., D. Farrell, Y. Huang, N.A. Baker, and J.E. Nielsen. 2011. "On the development of protein pKa calculation algorithms." Proteins. Structure, Function, and Bioinformatics 79, no. 12:3287-3298. PNNL-SA-77764. doi:10.1002/prot.23091
  • Chen Z., N.A. Baker, and G. Wei. 2011. "Differential geometry based solvation model II: Lagrangian formulation." Journal of Mathematical Biology 63, no. 6:1139-1200. PNWD-SA-9235. doi:10.1007/s00285-011-0402-z
  • Hossain K., C. Bailey-Kellogg, A.M. Friedman, M.J. Bradley, N.A. Baker, and N. Ramakrishnan. 2011. "Using Physicochemical Properties of Amino Acids to induce Graphical Models of Residue Couplings." In Proceedings of the 10th International Workshop on Data Mining in Bioinformatics (BioKDD 2011), August 21 - 24, 2011, San Diego, California, Article No. 3. New York, New York:ACM. PNWD-SA-9474. doi:10.1145/2003351.2003354
  • Lee S., P.H. Schlesinger, S.A. Wickline, G.M. Lanza, and N.A. Baker. 2011. "Interaction of Melittin Peptides with Perfluorocarbon Nanoemulsion Particles." The Journal of Physical Chemistry Letters 115, no. 51:15271-15279. PNWD-SA-9463. doi:10.1021/jp209543c
  • Olsen B.N., P.H. Schlesinger, D.S. Ory, and N.A. Baker. 2011. "25-Hydroxycholesterol Increases the Availability of Cholesterol in Phospholipid Membranes." Biophysical Journal 100, no. 4:948-956. PNNL-SA-73859. doi:10.1016/j.bpj.2010.12.3728
  • Thomas D.G., F. Klaessig, S. Harper, M. Fritts, M.D. Hoover, S. Gaheen, and T. Stokes, et al. 2011. "Informatics and Standards for Nanomedicine Technology." Wiley Interdisciplinary Reviews. Nanomedicine and Nanobiotechnology 3, no. 5:511-532. PNWD-SA-9296. doi:10.1002/wnan.152
  • Unni S., Y. Huang, R.M. Hanson, M. Tobias, S. Krishnan, W. Li, and J.E. Nielsen, et al. 2011. "Web servers and services for electrostatics calculations with APBS and PDB2PQR." Journal of Computational Chemistry 32, no. 7:1488-1491. PNNL-SA-74115. doi:10.1002/jcc.21720


  • Callenberg K.M., O.P. Choudhary, G.L. de Forest, D.W. Gohara, N.A. Baker, and M. Grabe. 2010. "APBSmem: A graphical interface for electrostatic calculations at the membrane." PLoS One 5, no. 9:Article No. e12722. PNWD-SA-9058. doi:10.1371/journal.pone.0012722
  • Chen Z., N.A. Baker, and G. Wei. 2010. "Differential geometry based solvation model I: Eulerian formulation." Journal of Computational Physics 229, no. 22:8231-8258. PNWD-SA-9173. doi:10.1016/