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Nathan

Nathan Baker

Physical & Computational Sciences
Division Director
Pacific Northwest National Laboratory
PO Box 999
MSIN: K7-90
Richland, WA 99352

Biography

Nathan Baker, Ph.D. is the Director of the Advanced Computing, Mathematics, and Data Division at Pacific Northwest National Laboratory (PNNL) and a Visiting Faculty member at Brown University.

His research interests include the development of new algorithms and mathematical methods in biophysics, nanotechnology, and informatics. Current research projects include new computational methods for modeling solvation in biomolecular systems (http://www.poissonboltzmann.org/), mathematical methods for mesoscale materials modeling (http://www.pnnl.gov/computing/cm4/), and development of new methods for signature discovery (http://signatures.pnnl.gov). His research is primarily funded by the National Institutes of Health and the Department of Energy.

Dr. Baker serves as co-PI and project manager for the DOE ASCR Collaboratory on Mathematics for Mesoscopic Modeling of Materials (CM4) and served as Lead for the Signature Discovery Initiative at PNNL. He 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 numerous review panels for agencies including NIH, NSF, DOE, and DTRA and is currently a member of the NIH Macromolecular Structure and Function D study section. He is currently an Associate Editor for Biophysical Journal, serves on the editorial board for NPG Scientific Data, and has previously served as Editor-in-Chief for the Computational Science and Discovery journal and Section Editor for Annual Reports in Computational Chemistry. Dr. Baker is the author of over 80 peer-reviewed publications. He is a Fellow of the American Association for the Advancement of Science, 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.

Research Interests

  • Applied mathematics
  • Signature discovery
  • Solvation
  • Computational biophysics
  • Nanoinformatics

Education and Credentials

  • PhD, Physical Chemistry, University of California San Diego
  • BS, Chemistry, University of Iowa

Affiliations and Professional Service

  • American Chemical Society
  • Association for Computing Machinery
  • Biophysical Society
  • IEEE
  • Society for Industrial and Applied Mathematics

Awards and Recognitions

  • Fellow of the 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
  • HHMI Graduate Fellowship
  • Barry Goldwater Undergraduate Fellowship

PNNL Publications

2017

  • Felberg LE, DH Brookes, EH Yap, ER Jurrus, NA Baker, and T Head-Gordon. 2017. "PB-AM: An Open-Source, Fully Analytical Linear Poisson-Boltzmann Solver." Journal of Computational Chemistry 38(15):1275-1282.  doi:10.1002/jcc.24528
  • Katz AM, IS Tolokh, S Pabit, NA Baker, A Onufriev, and L Pollack. 2017. "Spermine condenses DNA, but not RNA duplexes." Biophysical Journal 112(1):22-30.  doi:10.1016/j.bpj.2016.11.018

2016

  • Lei H, NA 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(50):14183-14188.  doi:10.1073/pnas.1609587113
  • Lei H, NA Baker, L Wu, GK Schenter, CJ Mundy, and AM 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(2):023304.  doi:10.1103/PhysRevE.94.023304
  • Gunner MR, and NA Baker. 2016. "Continuum Electrostatics Approaches to Calculating pKas and Ems in Proteins." Chapter 1 in Methods in Enzymology: Computational Approaches for Studying Enzyme Mechanism Part B, vol. 578, ed. GA Voth, pp. 1-20.  Elsevier, CAMBRIDGE, MA.  doi:10.1016/bs.mie.2016.05.052
  • Jurrus ER, NO Hodas, NA Baker, TP Marrinan, and MD 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.  IEEE, PISCATAWAY, NJ.  doi:10.1109/THS.2016.7568959
  • Pabit S, AM Katz, IS Tolokh, A Drozdetski, NA 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(20):Article No. 205102.  doi:10.1063/1.4950814
  • Purvine EAH, KE Monson, ER Jurrus, KT Star, and NA Baker. 2016. "Energy Minimization of Discrete Protein Titration State Models Using Graph Theory." Journal of Physical Chemistry B 120(33):8354-8360.  doi:10.1021/acs.jpcb.6b02059
  • Sushko ML, DG Thomas, S Pabit, L Pollack, A Onufriev, and NA Baker. 2016. "The role of correlation and solvation in ion interactions with B-DNA." Biophysical Journal 110(2):315-326.  doi:10.1016/j.bpj.2015.12.011
  • Tolokh IS, A Drozdetski, L Pollack, NA Baker, and A Onufriev. 2016. "Multi-shell model of ion-induced nucleic acid condensation." Journal of Chemical Physics 144(15):Article No. 155101.  doi:10.1063/1.4945382
  • Wei G, and NA Baker. 2016. "Differential geometry-based solvation and electrolyte transport models for biomolecular modeling: a review." Chapter 12 in Many-Body Effects and Electrostatics in Biomolecules, ed. Q Cui, M Meuwly and P Ren, pp. 417-461.  Pan Stanford Publishing, Singapore.  doi:10.1201/b21343-15
  • Yang X, H Lei, NA Baker, and G Lin. 2016. "Enhancing Sparsity of Hermite Polynomial Expansions by Iterative Rotations." Journal of Computational Physics 307:94-109.  doi:10.1016/j.jcp.2015.11.038

2015

  • Lei H, X Yang, B Zheng, and NA Baker. 2015. "Constructing Surrogate Models of Complex Systems with Enhanced Sparsity: Quantifying the influence of conformational uncertainty in biomolecular solvation." Multiscale Modeling & Simulation 13(4):1327-1353.  doi:10.1137/140981587
  • Lei H, X Yang, B Zheng, G Lin, and NA Baker. 2015. "Constructing Surrogate Models of Complex Systems with Enhanced Sparsity: Quantifying the Influence of Conformational Uncertainty in Biomolecular Solvation." Multiscale Modeling & Simulation 13(4):1327-1353.  doi:10.1137/140981587
  • Harper B, DG Thomas, S Chikkagoudar, NA Baker, K Tang, A Heredia-Langner, RD Lins, and S Harper. 2015. "Comparative hazard analysis and toxicological modeling of diverse nanomaterials using the embryonic zebrafish (EZ) metric of toxicity." Journal of Nanoparticle Research 17(6):Article No. 250.  doi:10.1007/s11051-015-3051-0
  • Pan W, MD Daily, and NA Baker. 2015. "Numerical calculation of protein-ligand binding rates through solution of the Smoluchowski equation using smooth particle hydrodynamics." BMC Biophysics 8:Article No. 7.  doi:10.1186/s13628-015-0021-y

2014

  • Gosink LJ, EA Hogan, TC Pulsipher, and NA Baker. 2014. "Bayesian model aggregation for ensemble-based estimates of protein pKa values." Proteins. Structure, Function, and Bioinformatics 82(3):354-363.  doi:10.1002/prot.24390
  • Bielska A, BN Olsen, SE Gale, L Mydock-McGrane, K Krishnan, NA Baker, PH Schlesinger, DF Covey, and DS Ory. 2014. "Side-Chain Oxysterols Modulate Cholesterol Accessibility through Membrane Remodeling." Biochemistry 53(18):3042-3051.  doi:10.1021/bi5000096
  • Daily MD, BN Olsen, PH Schlesinger, DS Ory, and NA Baker. 2014. "Improved Coarse-Grained Modeling of Cholesterol-Containing Lipid Bilayers." Journal of Chemical Theory and Computation 10(5):2137-2150.  doi:10.1021/ct401028g
  • Daily MD, BN Olsen, PH Schlesinger, DS Ory, and NA Baker. 2014. "Improved Coarse-Grained Modeling of Cholesterol-Containing Lipid Bilayers." Journal of Chemical Theory and Computation 10(5):2137-2150.  doi:10.1021/ct401028g
  • Pham C, DG Thomas, J Beiser, L Mitchell, J Huang, A Senpan, G Hu, M Gordon, NA Baker, D Pan, GM Lanza, and D Hourcade. 2014. "Application of a hemolysis assay for analysis of complement activation by perfluorocarbon nanoparticles." Nanomedicine: Nanotechnology, Biology and Medicine 10(3):651-660.  doi:10.1016/j.nano.2013.10.012
  • Thomas DG, S Chikkagoudar, A Heredia-Langner, MF Tardiff, Z Xu, D Hourcade, C Pham, GM Lanza, KQ Weinberger, and NA Baker. 2014. "Physicochemical signatures of nanoparticle-dependent complement activation." Computational Science and Discovery 7(1):Article No. 015003.  doi:10.1088/1749-4699/7/1/015003
  • Tolokh IS, S Pabit, AM Katz, Y Chen, A Drozdetski, NA Baker, L Pollack, and A Onufriev. 2014. "Why double-stranded RNA resists condensation." Nucleic Acids Research 42(16):10823-10831.  doi:10.1093/nar/gku756

2013

  • Baker NA, J Klemm, S Harper, S Gaheen, M Heiskanen, P Rocca-Serra, and SA Sansone. 2013. "Standardizng Data." Nature Nanotechnology 8(2):73-74.  doi:10.1038/nnano.2013.12
  • Baker NA, JL Barr, GT Bonheyo, CA Joslyn, K Krishnaswami, M Oxley, RW Quadrel, LH Sego, MF Tardiff, and AS Wynne. 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, ed. K Glass, et al, pp. 301-308.  IEEE, Piscataway, NJ.  doi:10.1109/ISI.2013.6578848
  • Chakraborty S, BJ Rao, NA Baker, and B Asgeirsson. 2013. "Structural phylogeny by profile extraction and multiple superimposition using electrostatic congruence as a discriminator." Intrinsically Disordered Proteins 1:69-81.  doi:10.4161/idp.25463
  • Daily MD, J Chun, A Heredia-Langner, G Wei, and NA Baker. 2013. "Origin of parameter degeneracy and molecular shape relationships in geometric-flow calculations of solvation free energies." Journal of Chemical Physics 139(20):Article No. 204108.  doi:10.1063/1.4832900
  • Harper S, JE Hutchison, NA Baker, M Ostraat, S Tinkle, JA Steevens, MD Hoover, J Adamick, K Rajan, S Gaheen, Y Cohen, A Nel, R Cachau, and M Tuominen. 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(1):Article No. 014008.  doi:10.1088/1749-4699/6/1/014008
  • Harper S, JE Hutchison, NA Baker, M Ostraat, S Tinkle, JA Steevens, MD Hoover, J Adamick, K Rajan, S Gaheen, Y Cohen, A Nel, R Cachau, and M Tuominen. 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(1):Article No. 014008.  doi:10.1088/1749-4699/6/1/014008
  • Olsen BN, A Bielska, T Lee, MD Daily, DF Covey, PH Schlesinger, NA Baker, and DS Ory. 2013. "The Structural Basis of Cholesterol Activity in Membranes." Biophysical Journal 105(8):1838-1847.  doi:10.1016/j.bpj.2013.08.042
  • Thomas DG, J Chun, Z Chen, G Wei, and NA Baker. 2013. "Parameterization of a Geometric Flow Implicit Solvation Model." Journal of Computational Chemistry 34(8):687-695.  doi:10.1002/jcc.23181
  • Thomas DG, S Gaheen, S Harper, M Fritts, F Klaessig, E Hahn-Dantona, D Paik, S Pan, G Stafford, E Freund, J Klemm, and NA Baker. 2013. "ISA-TAB-Nano: A Specification for Sharing Nanomaterial Research Data in Spreadsheet-based Format." BMC Bioinformatics 13:Article No. 2.  doi:10.1186/1472-6750-13-2

2012

  • Jacob F, J Gray, AS Wynne, YJ Liu, and NA 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, pp. 61-64.  The ACM, New York, NY.  doi:10.1145/2420918.2420934
  • Chen Z, S Zhao, J Chun, DG Thomas, NA Baker, PW Bates, and G Wei. 2012. "Variational approach for nonpolar solvation analysis." Journal of Chemical Physics 137(8):Article No. 084101.  doi:10.1063/1.4745084
  • Konecny R, NA Baker, and JA McCammon. 2012. "iAPBS: a programming interface to Adaptive Poisson-Boltzmann Solver." Computational Science and Discovery 5:Article No. 015005.  doi:10.1088/1749-4699/5/1/015005
  • Lee SJ, PH Schlesinger, SA Wickline, GM Lanza, and NA Baker. 2012. "Simulation of fusion-mediated nanoemulsion interactions with model lipid bilayers." Soft Matter 8(26):7024-7035.  doi:10.1021/jp103228c
  • Maojo V, M Fritts, F Martin-Sanchez, D De la Iglesia, R Cachau, M Garcia-Remesal, J Crespo, JA Mitchell, A Anguita, NA Baker, JM Barreiro, S Benitez, G de la Calle, JC Facelli, P Ghazal, A Geissbuhler, D Gonzalez-Nilo, N Graf, P Grangeat, I Hermosilla, R Hussein, J Kern, S Koch, Y Legre, V Lopez-Alonso, G Lopez-Campos, L Milanesi, V Moustakis, C Munteanu, P Otero, A Pazos, D Perez-Rey, G Potamius, F Sanz, and C Kulikowski. 2012. "Nanoinformatics: Developing New Computing Applications for Nanomedicine." Computing 94(6):521-539.  doi:10.1007/s00607-012-0191-2
  • Maojo V, M Fritts, F Martin-Sanchez, D De la Iglesia, R Cachau, M Garcia-Remesal, J Crespo, JA Mitchell, A Anguita, NA Baker, JM Barreiro, S Benitez, G de la Calle, JC Facelli, P Ghazal, A Geissbuhler, F Gonzalez-Nilo, N Graf, P Grangeat, I Hermosilla, R Hussein, J Kern, S Koch, Y Legre, V Lopez-Alonso, G Lopez-Campos, L Milanesi, V Moustakis, C Munteanu, P Otero, A Pazos, D Perez-Rey, G Potamius, F Sanz, and C Kulikowski. 2012. "Nanoinformatics: developing new computing applications for nanomedicine." Computing 94(6):521-539.  doi:10.1007/s00607-012-0191-2
  • Olsen BN, PH Schlesinger, DS Ory, and NA Baker. 2012. "Side-chain oxysterols: From cells to membranes to molecules." Biochimica et Biophysica Acta--Biomembranes 1818(2):330-336.  doi:10.1016/j.bbamem.2011.06.014
  • Ren P, J Chun, DG Thomas, M Schnieders, M Marucho, J Zhang, and NA Baker. 2012. "Biomolecular electrostatics and solvation: a computational perspective." Quarterly Reviews of Biophysics 45(4):427-491.  doi:10.1017/S003358351200011X
  • Thomas DG, S Chikkagoudar, AR Chappell, and NA 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, pp. 889-894.  IEEE, Piscataway, NJ.  doi:10.1109/BIBMW.2012.6470259

2011

  • Alexov E, EL Mehler, NA Baker, A Baptista, Y Huang, F Milletti, JE Nielsen, D Farrell, T Carstensen, MH Olsson, JK Shen, J Warwicker, S Williams, and JM Word. 2011. "Progress in the prediction of pKa values in proteins." Proteins. Structure, Function, and Bioinformatics 79(12):3260-3275.  doi:10.1002/prot.23189
  • Carstensen T, D Farrell, Y Huang, NA Baker, and JE Nielsen. 2011. "On the development of protein pKa calculation algorithms." Proteins. Structure, Function, and Bioinformatics 79(12):3287-3298.  doi:10.1002/prot.23091
  • Chen Z, NA Baker, and G Wei. 2011. "Differential geometry based solvation model II: Lagrangian formulation." Journal of Mathematical Biology 63(6):1139-1200.  doi:10.1007/s00285-011-0402-z
  • Hossain KSMT, C Bailey-Kellogg, AM Friedman, MJ Bradley, NA 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, p. Article No. 3.  ACM , New York, NY.  doi:10.1145/2003351.2003354
  • Lee SJ, PH Schlesinger, SA Wickline, GM Lanza, and NA Baker. 2011. "Interaction of Melittin Peptides with Perfluorocarbon Nanoemulsion Particles." The Journal of Physical Chemistry Letters 115(51):15271-15279.  doi:10.1021/jp209543c
  • Olsen BN, PH Schlesinger, DS Ory, and NA Baker. 2011. "25-Hydroxycholesterol Increases the Availability of Cholesterol in Phospholipid Membranes." Biophysical Journal 100(4):948-956.  doi:10.1016/j.bpj.2010.12.3728
  • Thomas DG, F Klaessig, S Harper, M Fritts, MD Hoover, S Gaheen, T Stokes, R Reznik-Zellen, E Freund, J Klemm, D Paik, and NA Baker. 2011. "Informatics and Standards for Nanomedicine Technology." Wiley Interdisciplinary Reviews. Nanomedicine and Nanobiotechnology 3(5):511-532.  doi:10.1002/wnan.152
  • Unni S, Y Huang, RM Hanson, M Tobias, S Krishnan, W Li, JE Nielsen, and NA Baker. 2011. "Web servers and services for electrostatics calculations with APBS and PDB2PQR." Journal of Computational Chemistry 32(7):1488-1491.  doi:10.1002/jcc.21720

2010

  • Callenberg KM, OP Choudhary, GL de Forest, DW Gohara, NA Baker, and M Grabe. 2010. "APBSmem: A graphical interface for electrostatic calculations at the membrane." PLoS One 5(9):Article No. e12722.  doi:10.1371/journal.pone.0012722
  • Chen Z, NA Baker, and G Wei. 2010. "Differential geometry based solvation model I: Eulerian formulation." Journal of Computational Physics 229(22):8231-8258.  doi:10.1016/j.jcp.2010.06.036

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