Curriculum Vitae (17-Jul-2008)

Personal information

• Name: Nathan Andrew Baker
• Address: Department of Biochemistry and Molecular Biophysics
  • Center for Computational Biology
  • 700 S. Euclid Ave.
  • Room 113, Campus Box 8036
  • St. Louis, MO 63110 USA
  • Phone: (314) 362-2040, Fax: (314) 362-0234
  • E-mail: baker@ccb.wustl.edu, Web: http://cholla.wustl.edu/

Education

• B.S. in Chemistry: University of Iowa (May-1997)
  • GPA: 4.0, honors, highest distinction
  • Advisor: Daniel Quinn, Department of Chemistry
• Ph.D. in Physical chemistry: University of California at San Diego (Apr-2001)
  • GPA: 4.0
  • Advisor: J. Andrew McCammon, Department of Chemistry and Biochemistry
  • Advisor: Michael Holst, Department of Mathematics
• Postdoctoral research in Computational Biology: University of California at San Diego (Jun-2002)
  • Advisor: J. Andrew McCammon, Department of Chemistry and Biochemistry
  • Advisor: Michael Holst, Department of Mathematics

Professional experience

• Research assistant (Jan-1994 to Aug-1997)
  • D.M. Quinn research group, University of Iowa
• Teaching assistant (Sep-1996 to May-1997)
  • Department of Chemistry, University of Iowa
• Graduate research fellow (Sep-1997 to Apr-2001)
  • J.A. McCammon research group, University of California at San Diego
• Teaching assistant (Jan-1998 to Mar-1999)
  • Department of Chemistry and Biochemistry, University of California at San Diego
• Graduate research fellow (Jan-1999 to Apr-2001)
  • M.J. Holst research group, University of California at San Diego
• Postdoctoral researcher (Apr-2001 to Jun-2002)
  • J.A. McCammon research group, University of California at San Diego
• Assistant professor (Jul-2002 to Dec-2006)
  • Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis
• Consultant (Oct-2004 to Nov-2004)
  • Gelsus, Inc.
• Associate professor (Dec-2006 to present)
  • Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis

Selected honors

• Undergraduate fellowship (1995 to 1997)
  • Barry M. Goldwater fund
• Predoctoral fellowship (1997 to 2001)
  • Howard Hughes Medical Institute
• Collegiate scholar (May-1997)
  • University of Iowa
• Predoctoral fellowship (1999 to 2001)
  • Burroughs-Wellcome La Jolla Interfaces in Science
• Kamen award for outstanding Ph.D. thesis in the biological sciences (2001)
  • University of California at San Diego
• Research fellow (2004 to 2006)
  • Alfred P. Sloan Foundation
• Hewlett-Packard Junior Faculty Excellence Award (2007)
  • American Chemical Society

Professional organizations

• American Chemical Society (1994 to present)
• American Physical Society (1999 to present)
• Society for Industrial and Applied Mathematics (2000 to present)
• Biophysical Society (2001 to present)
• International Society for Computational Biology (2007 to present)

Educational contributions

Postdoctoral researchers

• Seongeun Yang (Sep-2002 to Feb-2003) Washington University in St. Louis, Postdoctoral researcher.
• Yuhua Song (Dec-2002 to Aug-2006) Washington University in St. Louis, Postdoctoral researcher. Currently faculty member at Univ. of Alabama.
• Feng Dong (Aug-2005 to Aug-2007) Washington University in St. Louis, Postdoctoral researcher. Currently senior research biochemist at Merck.

Graduate students

• Michael Bradley (Jan-2003 to present) Washington University in St. Louis, Molecular biophysics. Joint with Peter Chivers group.
• Rachel Rice (Dec-2003 to present) Washington University in St. Louis, Molecular biophysics.
• Sun Joo Lee (Jun-2005 to present) Washington University in St. Louis, Molecular biophysics.
• Brett Olsen (Jan-2006 to present) Washington University in St. Louis, Cell biology.

Other students and researchers

• Todd Dolinsky (Oct-2002 to Aug-2006) Washington University in St. Louis, Programmer. Currently software engineer at Opsware, Inc..
• Jason Wagoner (Dec-2002 to Jul-2006) Washington University in St. Louis, Undergraduate research assistant. Currently graduate student at Stanford.
• Prachi Mayenkar (Jun-2004 to Aug-2004) Parkway North High School, STARS program researcher. Recipient of "Excellence in Research" award for summer research in our group.
• Eric Mintun (Jun-2005 to Aug-2005) Thomas Jefferson High School, Summer high school student researcher.
• Jeff Poskin (Jun-2005 to Aug-2005) Washington University, Biomedical Summer Scholars Program pre-freshman researcher.
• Peter Jones (Jan-2006 to present) Washington University in St. Louis, Programmer.
• David Gohara (May-2006 to present) Washington University in St. Louis, Programmer. Joint with Jay Ponder group.
• Tom Richner (Jan-2007 to May-2008) Washington University in St. Louis, Undergraduate research assistant.
• Samir Unni (Jun-2007 to present) Parkway West High School, Washington University in St. Louis, STARS program researcher and undergraduate researcher.
• Yong Huang (Sep-2007 to present) Washington University in St. Louis, Programmer.
• Stephen Gradwohl (Sep-2007 to present) Washington University in St. Louis, Undergraduate research assistant.
• Michal Lijowski (Jan-2008 to present) Washington University in St. Louis, Data Analyst.
• Sechin Jain (Apr-2008 to present) Washington University in St. Louis, Undergraduate research assistant.

Member of thesis committees for 24 other students.

Teaching

• Computational Biophysics and Systems Biology, Notre Dame CSE 40531/60531, J. Izaguirre
  • (Spring-2006)
• Ethics and Research Science, Bio 5011, N. Baker and P. Schlesinger
  • (Spring-2007)
• Introduction to Biomedical Engineering, BME 140, F. Yin
  • (Fall-2003, Fall-2004, Fall-2005, Fall-2006, Fall-2007)
• Introduction to Biomolecular Statistical Thermodynamics, BME 531, R. Pappu
  • (Spring-2005)
• Macromolecular Interactions, Bio 5312, T. Lohman
  • (Spring-2003, Spring-2004, Spring-2005, Spring-2006, Spring-2007, Spring-2008)
• Mathematical Methods for Biophysics and Biochemistry, Summer discussion group, N. Baker
  • (Summer-2004)
• Mathematical Methods for Biophysics and Biochemistry, Bio 5329, N. Baker
  • (Fall-2004, Fall-2005, Fall-2006, Fall-2007)
• Modeling Biomolecular Systems, BME 5290N, D. Sept
  • (Fall-2004)
• Modeling Biomolecular Systems I, Bio 5476, J. Ponder
  • (Spring-2004, Spring-2005, Spring-2006)
• Modeling Biomolecular Systems II, BME 540, D. Sept
  • (Fall-2004, Fall-2005)
• Molecular Electrostatics and Diffusion, National Biomedical Computation Resource Summer Institute, N. Baker and Y. Cheng
  • (Summer-2006, Summer-2007)
• Protein Structure and Function, Bio 5325, J. Ponder
  • (Fall-2002, Fall-2003, Fall-2005, Fall-2006, Fall-2007)
• Special Topics in Computational Biology, Bio 5497, G. Stormo
  • (Fall-2004, Fall-2005, Fall-2006)

Professional contributions

Administrative responsibilities

• Computer center development (1999 to 2001)
  • Keck II San Diego Supercomputer Center Satellite, University of California at San Diego
• Teaching lab development (2002)
  • Center for Computational Biology, Washington University in St. Louis
• Seminar co-organizer (2003 to 2008)
  • Center for Computational Biology, Washington University in St. Louis
• Director (Sep-2005 to Aug-2010)
  • Siteman Cancer Center for Nanotechnology Excellence Biocomputing Core, Washington University in St. Louis
• Co-organizer (May-2006)
  • ICAM/CCB Multiscale Interactions and Dynamics in Biological Systems Workshop, Institute for Complex Adaptive Matter
• Organizer and chair (Mar-2007)
  • Early Careers Panel Discussion: Negotiating the Transition to Non-Traditional Careers, Biophysical Society
• Director (Jul-2007 to present)
  • Molecular Biophysics graduate program, Washington University in St. Louis
• Co-organizer (Jun-2008)
  • Bridging Research and Teaching Workshop: Innovation at the Crossroads of Chemistry, Physics, and Biology, Washington University in St. Louis

Community service

• Mentor (2004 to 2007)
  • Students and Teachers as Researchers (STARs) program
• Mentor (2005)
  • Biomedical Summer Scholars Program
• Webmaster (2005 to present)
  • Ethical Society Nursery School
• Mentor (2006 to present)
  • St. Louis Junior Academy of Science
• Member (2006 to present)
  • Technology Committee, Our Lady of Lourdes School

University committees

• Faculty computational search committee (2002 to 2003)
  • Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis
• Oversight committee (2004)
  • Center for Scientific Parallel Computing, Washington University in St. Louis
• Admissions committee (2004 to 2007)
  • Division of Biology and Biomedical Sciences Graduate Program, Washington University in St. Louis
• Steering committee (2004 to present)
  • Molecular Biophysics Graduate Program, Washington University in St. Louis
• Faculty search committee (2006 to 2007)
  • Department of Mechanical and Aerospace Engineering, Washington University in St. Louis
• Faculty computational search committee (2006 to 2007)
  • Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis
• Liaison Committee on Medical Education Library and IT Committee (2006)
  • School of Medicine, Washington University in St. Louis
• Education Planning Committee, DBBS Workgroup (2007)
  • Division of Biology and Biomedical Sciences Graduate Program, Washington University in St. Louis
• Program and student affairs committee (2007 to present)
  • Division of Biology and Biomedical Sciences Graduate Program, Washington University in St. Louis
• Faculty single molecule search committee (2007 to present)
  • Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis
• Chair, Scientific Collaboration Panel Discussion (Mar-2008)
  • Annual Conference on Effective Research Management, Washington University in St. Louis

National committees

• Member (2004 to 2007)
  • Early Careers Committee, Biophysical Society
• Member (2005 to present)
  • Program Committee, Biophysical Society
• Ad hoc member (Jul-2005)
  • Special study section (RFA-CA-05-026), National Cancer Institute
• Member (2006 to present)
  • Nanotechnology Alliance Informatics Working Group, National Cancer Institute, National Institutes of Health
• Ad hoc member (Mar-2006)
  • MABS study section, National Institutes of Health
• Ad hoc member (Jun-2006 to Nov-2006)
  • ZRG1 F14A study section, National Institutes of Health
• Member (2007 to 2010)
  • Committee for Professional Opportunities for Women, Biophysical Society
• Organizer and chair (Mar-2007)
  • Early Careers Panel Discussion: Negotiating the Transition to Non-Traditional Careers, Biophysical Society
• Ad hoc member (Jun-2007)
  • MSFD study section, National Institutes of Health
• Ad hoc member (Oct-2007)
  • ZRG1 BSTQ study section, National Institutes of Health
• Panelist (Feb-2008)
  • CPOW "Transition from Postdoc to Faculty Lunch", Biophysical Society
• Member (Apr-2008 to present)
  • caBIG Nanotechnology Informatics Working Group, National Cancer Institute, National Institutes of Health
• Member (Jul-2008 to Jun-2011)
  • Editorial Board, Biophysical Society

Editorial positions

• Contributor (2008 to present)
  • Topic page, Scirus.com
• Member (2008 to present)
  • Faculty of 1000 Biology
• Section Editor (2008 to present)
  • Annual Reports in Computational Chemistry, American Chemical Society
• Editorial Board Member (Jul-2008 to Jun-2011)
  • Biophysical Society

Manuscript reviews

• Acta Crystallographica, Annals of Biomedical Engineering, Biochemistry, Bioinformatics, Bioorganic and Medicinal Chemistry Letters, Biophysical Chemistry, Biophysical Journal, Biopolymers, Journal of Chemical Physics, Journal of Chemical Theory and Computation, Journal of Computational Chemistry, Journal of Computational Physics, Journal of Computer-Aided Molecular Design, Journal of General Physiology, Journal of Molecular Biology, Journal of Molecular Graphics and Modeling, Journal of Neurophysiology, Journal of Physical Chemistry, Journal of Physical Chemistry B, Journal of Physics: Condensed Matter, Journal of Theoretical Biology, Journal of the American Chemical Society, Nature Nanotechnology, Nucleic Acids Research, Physical Biology, Physical Chemistry Chemical Physics, Proceedings of the National Academy of Sciences, Protein Engineering, Protein Science, Proteins, Structure

Grant reviews

• American Chemical Society Petroleum Research Fund, National Institutes of Health, National Science Foundation, United States Civilian Research and Development Foundation, United States-Israel Binational Science Foundation

Research contributions

Current research

Our research uses the methods of theoretical and computational science to study the physical phenomena underlying the behavior of biological systems. Such studies offer insight into the basic mechanisms of biomolecular dynamics and function and provide a foundation for new tools and algorithms to complement experimental research.

Understanding biomolecular solvation. The properties of biomolecules are strongly affected by their surrounding aqueous and ionic environment. Our research in solvation focuses on the development and application of accurate continuum solvent models for biomolecules. First, we continue to develop the APBS and PDB2PQR software packages which implement Poisson-Boltzmann electrostatics and various nonpolar models of continuum solvation. Second, we are working on improved continuum models for both polar and nonpolar solvation. Finally, we are developing multiscale treatments of solvation with particular emphasis on the influence of ionic species on nucleic acid structure and dynamics.

Allostery and energy flow in biomolecules. Proteins communicate information (e.g., ligand binding, etc.) over large distances through mechanisms that are often poorly understood. We are employing biophysical simulation techniques to study the molecular foundations of allosteric communication in protein systems. Initial work is focused on the NikR protein, a regulatory protein found in several bacteria species, and thrombin, an essential component in the blood clotting cascade.

Small molecule effects on biomembrane electrostatics and mechanics. We are interested in the ability of small molecules to perturb the electrical and mechanical properties of biological membranes. The mechanism of this perturbation is not well understood but has a significant impact on biomembrane functions, including membrane channel function and cellular electrophysiology. Initial studies on salicylate, a metabolite of aspirin, have revealed an interesting mechanism for its effects on membrane electrostatics and mechanics. We are now broadening these studies to examine other amphiphilic molecules known to affect membrane capacitance, bending modulus, and electrostatic potential.

Nanotechnology-based cancer therapeutics. We are part of the Siteman Cancer Center for Nanotechnology Excellence effort to develop nanoparticle-based technology for the delivery of therapeutic and diagnostic chemicals in a selective and efficient manner. One aspect of our research in this area is the development of databases, vocabularies, and ontologies to describe the physical and functional properties for a variety of nanoparticle platforms. A second area of research is the development of multiscale simulations for understanding the mechanism of nanoemulsion function and interaction with lipid membranes.

Research grants

• Howard Hughes Medical Institute (Aug-1997 to Jul-2001).
  • N. Baker, PI. Predoctoral fellowship
• National Partnership for Advanced Computational Infrastructure (Oct-2002 to Oct-2003).
  • Role: Investigator. A. Olson, PI. Large-scale Analysis of Macromolecular Assemblies in a Distributed Terascale Environment
• National Institutes of Health (NIGMS) (Dec-2003 to Dec-2008).
  • N. Baker, PI. APBS: Nanoscale biomolecular electrostatics software (R01 GM069702)
• Alfred P. Sloan Foundation (2004 to 2006).
  • N. Baker, PI. Research fellowship
• National Institutes of Health (NCRR) (May-2004 to May-2009).
  • Role: Investigator. P. Arzberger, PI. The National Biomedical Computation Resource (P41 RR08605)
• National Academies Keck Futures Initiative (May-2005 to Jun-2007).
  • N. Baker, PI. Molecular Engineering of Thrombin-Based Nanocatalysts
• Partnership for Advanced Computational Infrastructure (Aug-2005 to Aug-2006).
  • Role: Investigator. N. Baker, PI. Molecular simulation of amphiphile effects on biological membrane electrostatics and mechanics
• National Institutes of Health (NCI) (Sep-2005 to Aug-2010).
  • Role: Investigator and Core Director. S. Wickline, PI. The Siteman Center of Cancer Nanotechnology Excellence (U54 CA119342)
• National Science Foundation (MCB) (Feb-2006 to Feb-2009).
  • Role: Investigator. P. Chivers, PI. Allosteric Regulation of the Nickel-dependent NikR Repressor (MCB-0520877)
• TeraGrid (Jul-2006 to Jul-2007).
  • N. Baker, PI. Small molecule perturbation of biological membranes: electrostatics, mechanics, and dynamics (MCB060053)
• Children's Discovery Institute (Feb-2007 to Jan-2009).
  • Role: Investigator. A. Doctor, PI. Loss of Vascular Control in Pediatric Lung Injury: Disruption of NO Biotransport by Oxidative Stress
• National Institutes of Health (NCI) (Oct-2007 to Sep-2008).
  • N. Baker, PI. caNanoLab Data Submission Support (SAIC sub-contract)
• TeraGrid (Apr-2008 to Mar-2009).
  • N. Baker, PI. Molecular simulations of small molecule-bilayer interactions and biomolecular allostery (TG-MCA08X003)
• Defense Threat Reduction Agency (May-2008 to Apr-2010).
  • Role: Investigator. T. Rosenberry, PI. New Inhibitors of Acetylcholinesterase that Block Inactivation by Organophosphates (HDTRA1-08-C-0015)
• National Institutes of Health (NCI) (Jun-2008 to Feb-2009).
  • N. Baker, PI. caBIG Nanotechnology Informatics Working Group Subject Matter expert (caBIG sub-contract)

Research articles

1. Feaster SR, Lee K, Baker N, Hui DY, Quinn DM. Molecular recognition by cholesterol esterase of active site ligands: structure-reactivity effects for inhibition by aryl carbamates and subsequent carbamylenzyme turnover. Biochemistry, 35, 16723-16734, 1996. (http://dx.doi.org/10.1021/bi961677v)
2. Baker NA, McCammon JA. Non-Boltzmann rate distributions in stochastically gated reactions. J Phys Chem B, 103, 615-617, 1999. (http://dx.doi.org/10.1021/jp984151o)
3. Baker NA, Helms V, McCammon JA. Dynamical properties of fasciculin-2. Proteins, 36, 447-453, 1999. (http://tinyurl.com/3vtyh)
4. Baker NA, Hunenberger PH, McCammon JA. Polarization around an ion in a dielectric continuum with truncated electrostatic interactions. J Chem Phys, 110, 10679-10692, 1999. (http://dx.doi.org/10.1063/1.479013)
5. Malany S, Baker N, Verweyst M, Medhekar R, Quinn DM, Velan B, Kronman C, Shafferman A. Theoretical and experimental investigations of electrostatic effects on acetylcholinesterase catalysis and inhibition. Chem-Biol Interact, 120, 99-110, 1999. (http://dx.doi.org/10.1016/S0009-2797(99)00018-6)
6. Baker N, Holst M, Wang F. Adaptive multilevel finite element solution of the Poisson-Boltzmann equation II: refinement schemes based on solvent accessible surfaces. J Comput Chem, 21, 1343-1352, 2000. (http://tinyurl.com/3n92c)
7. Holst M, Baker N, Wang F. Adaptive multilevel finite element solution of the Poisson-Boltzmann equation I: algorithms and examples . J Comput Chem, 21, 1319-1342, 2000. (http://tinyurl.com/3uzq4)
8. Quinn DM, Feaster SR, Nair HK, Baker NA, Radic D, Taylor P. Delineation and decomposition of energies involved in quaternary ammonium binding in the active site of acetylcholinesterase. J Am Chem Soc, 122, 2975-2980, 2000. (http://dx.doi.org/10.1021/ja9933588)
9. Baker NA, Sept D, Holst MJ, McCammon JA. The adaptive multilevel finite element solution of the Poisson-Boltzmann equation on massively parallel computers . IBM J Res Devel, 45, 427-438, 2001. (http://dx.doi.org/10.1147/rd.453.0427)
10. Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci USA, 98, 10037-10041, 2001. (http://dx.doi.org/10.1073/pnas.181342398)
11. Lin JH, Baker NA, McCammon JA. Bridging implicit and explicit solvent approaches for membrane electrostatics. Biophys J, 83, 1374-1379, 2002. (http://www.biophysj.org/cgi/content/abstract/83/3/1374)
12. Ma C, Baker NA, Joseph S, McCammon JA. Binding of aminoglycoside antibiotics to the small ribosomal subunit: a continuum electrostatics investigation. J Am Chem Soc, 124, 1438-1442, 2002. (http://tinyurl.com/48l3bp)
13. Sept D, Baker NA, McCammon JA. The physical basis of microtubule stability. Protein Sci, 12, 2257-2261, 2003. (http://www.proteinscience.org/cgi/content/abstract/12/10/2257)
14. Tai K, Bond SD, MacMillan HR, Baker NA, Holst MJ, McCammon JA. Finite element simulations of acetylcholine diffusion in neuromuscular junctions. Biophys J, 84, 2234-2241, 2003. (http://www.biophysj.org/cgi/content/abstract/84/4/2234)
15. Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA. PDB2PQR: an automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res, 32, W665-W667, 2004. (http://tinyurl.com/4kcyc)
16. Dolinsky TJ, Karplus K, Burgers PMJ, Baker NA. SPrCY: comparison of structural predictions in the S. cerevisiae genome. Bioinformatics, 20, 2312-2314, 2004. (http://dx.doi.org/10.1093/bioinformatics/bth223)
17. Song Y, Zhang Y, Shen T, Bajaj CL, McCammon JA, Baker NA. Finite element solution of the steady-state Smoluchowksi equation for rate constant calculations. Biophys J, 86, 2017-2029, 2004. (http://www.biophysj.org/cgi/content/abstract/86/4/2017)
18. Song Y, Zhang Y, Bajaj C, Baker NA. Continuum diffusion reaction rate calculations of wild type and mutant mouse acetylcholinesterase: adaptive finite element analysis. Biophys J, 87, 1558-1566, 2004. (http://www.biophysj.org/cgi/content/abstract/87/3/1558)
19. Vitalis A, Baker NA, McCammon JA. ISIM: a program for grand canonical Monte Carlo simulations of the ionic environment of biomolecules . Mol Sim, 30, 45-61, 2004. (http://tinyurl.com/5986l)
20. Wagoner J, Baker NA. Solvation forces on biomolecular structures: a comparison of explicit solvent and Poisson-Boltzmann models. J Comput Chem, 25, 1623-1629, 2004. (http://dx.doi.org/10.1002/jcc.20089)
21. Zhang D, Konecny R, Baker NA, McCammon JA. Electrostatic interaction between RNA and protein capsid in CCMV simulated by a coarse-grain RNA model and a Monte Carlo approach. Biopolymers, 75, 325-337, 2004. (http://dx.doi.org/10.1002/bip.20120)
22. Showalter SA, Baker NA, Tang C, Hall KB. Iron responsive element RNA flexibility described by NMR and isotropic reorientational eigenmode dynamics. J Biomol NMR, 32, 179-193, 2005. (http://dx.doi.org/10.1007/s10858-005-7948-2)
23. Song Y, Guallar V, Baker NA. Molecular dynamics simulations of salicylate effects on the micro- and mesoscopic properties of a dipalmitoylphosphatidylcholine bilayer. Biochemistry, 44, 13425-13438, 2005. (http://dx.doi.org/10.1021/bi0506829)
24. Zhang D, Suen J, Zhang Y, Song Y, Radic Z, Taylor P, Holst MJ, Bajaj C, Baker NA, McCammon JA. Tetrameric mouse acetylcholinesterase: continuum diffusion rate calculations by solving the steady-state Smoluchowski equation using finite element methods. Biophys J, 88, 1659-1666, 2005. (http://dx.doi.org/10.1529/biophysj.104.053850)
25. Konecny R, Trylska J, Tama F, Zhang D, Baker NA, Brooks CL III, McCammon JA. Electrostatic properties of cowpea chlorotic mottle virus and cucumber mosaic virus capsids. Biopolymers, 82, 106-120, 2006. (http://dx.doi.org/10.1002/bip.20409)
26. Wagoner JA, Baker NA. Assessing implicit models for nonpolar mean solvation forces: the importance of dispersion and volume terms. Proc Natl Acad Sci USA, 103, 8331-8336, 2006. (http://dx.doi.org/10.1073/pnas.0600118103)
27. Wong CJ, Rice RL, Baker NA, Ju T, Lohman TM. Probing 3'-ssDNA loop formation in E. coli RecBCD/RecBC-DNA complexes using non-natural DNA: a model for "Chi" recognition complexes. J Mol Biol, 362, 26-43, 2006. (http://dx.doi.org/10.1016/j.jmb.2006.07.016)
28. Zhang X, Bajaj CL, Kwon B, Dolinsky TJ, Nielsen JE, Baker NA. Application of new multi-resolution methods for the comparison of biomolecular electrostatic properties in the absence of global structural similarity. Multiscale Model Sim, 5, 1196-1213, 2006. (http://dx.doi.org/10.1137/050647670)
29. Cerutti DS, Baker NA, McCammon JA. Solvent Reaction Field Potential inside an Uncharged Globular Protein: A Bridge between Implicit and Explicit Solvent Models?. J Chem Phys, 127, 155101, 2007. (http://dx.doi.org/10.1063/1.2771171)
30. Cheng Y, Suen JK, Zhang D, Bond SD, Zhang Y, Song Y, Baker NA, Bajaj CL, Holst MJ, McCammon JA. Finite element analysis of the time-dependent Smoluchowski equation for acetylcholinesterase reaction rate calculations. Biophys J, 92, 3397-406, 2007. (http://dx.doi.org/10.1529/biophysj.106.102533)
31. Dolinsky TJ, Czodrowski P, Li H, Nielsen JE, Jensen JH, Klebe G, Baker NA. PDB2PQR: Expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res, 35, W522-5, 2007. (http://dx.doi.org/10.1093/nar/gkm276)
32. Schnieders MJ, Baker NA, Ren P, Ponder JW. Polarizable Atomic Multipole Solutes in a Poisson-Boltzmann Continuum. J Chem Phys, 126, 124114, 2007. (http://dx.doi.org/10.1063/1.2714528)
33. Swanson JMJ, Wagoner JA, Baker NA, McCammon JA. Optimizing the Poisson dielectric boundary with explicit solvent forces and energies: lessons learned with atom-centered dielectric functions. J Chem Theory Comput, 3, 170-183, 2007. (http://dx.doi.org/10.1021/ct600216k)
34. Bradley MJ, Chivers PT, Baker NA. Molecular dynamics simulation of the Escherichia coli NikR protein: Equilibrium conformational fluctuations reveal inter-domain allosteric communication pathways. Journal of Molecular Biology, 378, 1155-1173, 2008. (http://dx.doi.org/10.1016/j.jmb.2008.03.010)
35. Lee S-J, Song Y, Baker NA. Molecular dynamics simulations of asymmetric NaCl and KCl solutions separated by phosphatidylcholine bilayers: potential drops and structural changes induced by strong Na+-lipid interactions and finite size effects. Biophysical Journal, 94, 3565-76, 2008. (http://dx.doi.org/10.1529/biophysj.107.116335)
36. Dong F, Wagoner JA, Baker NA. Assessing the performance of implicit solvation models at a nucleic acid surface. Phys Chem Chem Phys, in press. (http://dx.doi.org/10.1039/b807384h)

Review articles

1. Baker NA. Poisson-Boltzmann methods for biomolecular electrostatics. Methods in Enzymology, 383, 94-118, 2004. (http://dx.doi.org/10.1016/S0076-6879(04)83005-2)
2. Baker NA. Improving implicit solvent simulations: a Poisson-centric view. Curr Opin Struct Biol, 15, 137-143, 2005. (http://dx.doi.org/10.1016/j.sbi.2005.02.001)
3. Dong F, Olsen B, Baker NA. Computational Methods for Biomolecular Electrostatics. Methods in Cell Biology: Biophysical Tools for Biologists, 84, 843-870, 2008. (http://dx.doi.org/10.1016/S0091-679X(07)84026-X)

Book sections

1. Medhekar R, Baker N, Kearney W, Sando K, Quinn DM. Low-barrier hydrogen bond in the catalytic triad of serine esterases. In: Doctor BP, Quinn DM, Rotundo R, Taylor P, Eds. Structure and function of cholinesterases and related proteins. Plenum Press: New York (1998) .
2. Quinn DM, Medhekar R, Baker N. Ester hydrolysis. In: Poulter CD, Eds. Comprehensive natural products chemistry: enzymes, enzyme mechanisms, proteins, and aspects of NO chemistry . Elsevier Science: Oxford (1999) .
3. Baker N, Tai K, Henchman R, Sept D, Elcock A, Holst M, McCammon JA. Mathematics and molecular neurobiology. In: Gan HH, Schlick T, Eds. Computational Methods for Macromolecules: Challenges and Applications. Springer-Verlag: New York (2002) .
4. Baker NA, McCammon JA. Electrostatic interactions. In: Weissig H, Bourne PE, Eds. Structural Bioinformatics. John Wiley and Sons: New York (2003) .
5. Baker NA. Biomolecular applications of Poisson-Boltzmann methods . In: Lipkowitz KB, Larter R, Cundari TR, Eds. Reviews in Computational Chemistry. John Wiley and Sons: Hoboken, NJ (2005) .
6. Baker NA, Bashford D, Case DA. Implicit solvent electrostatics in biomolecular simulation. In: Leimkuhler B, Chipot C, Elber R, Laaksonen A, Mark A, Schlick T, Schutte C, Skeel R, Eds. New Algorithms for Macromolecular Simulation. Springer-Verlag: Berlin (2006) .

Selected invited presentations (last 2 years; of 54 total)

1. Baker NA. Biocomplexity Institute Seminar, University of Indiana. Jan-2006, Talk.
2. Baker NA. Theoretical and Computational Biophysics Seminar, University of Illinois Urbana-Champaign. Jan-2006, Talk.
3. Baker NA. Bioinformatics Institute, Agency for Science, Technology, and Research (A*STAR Biopolis), Singapore. Apr-2006, Visiting scientist lecture series.
4. Baker NA. Computer Science and Engineering Seminar Series, University of Notre Dame. Apr-2006, Talk.
5. Baker NA. National Biomedical Computation Resource Summer Institute. Aug-2006, Workshop.
6. Wagoner JA, Dong F, Baker NA*. Gibbs Conference on Biothermodynamics. Oct-2006, Talk.
7. Baker NA. Future of Biomolecular Simulations: From Ab Initio to Nano-molecular Machines, National Center for Computational Sciences, Oak Ridge National Lab. Dec-2006, Talk.
8. Olsen B, Song Y, Lee SJ, Tieleman DP, Baker NA*. American Chemical Society National Meeting. Mar-2007, Talk.
9. Dong F, Wagoner JA, Baker NA*. American Chemical Society National Meeting. Mar-2007, Talk.
10. Thomas D, Jones P, Pappu R, Sept D, Baker N*. Trans-NIH Nano Task Force Meeting. May-2007, Talk.
11. Baker NA. Biophysical Evenings, Washington University in St. Louis. May-2007, Talk.
12. Baker NA. Seminar, Integrated DNA Technologies. Jul-2007, Talk.
13. Baker NA. National Biomedical Computation Resource Summer Institute Mini-Symposium. Jul-2007, Talk.
14. Baker NA. Mathematics of DNA Structure, Function, and Interactions, Institute for Mathematics and its Applications. Sep-2007, Talk.
15. Baker NA* et al. National Cancer Institute Nanotechnology Alliance Meeting. Oct-2007, Talk.
16. Baker NA. Seminar, University of Kansas. Nov-2007, Talk.
17. Baker NA. Quantitative Biology and Modeling/Dept. of Mathematics Seminar, Michigan State University. Dec-2007, Talk.
18. Baker NA. Protein Folding Workshop, Institute for Mathematics and its Applications. Jan-2008, Talk.
19. Baker NA. Mechanical Engineering Seminar, Washington University. Feb-2008, Talk.
20. Baker NA. Seminar, Conway Institute, University College Dublin. Mar-2008, Talk.
21. Wagoner J, Dong F, Cerutti D, McCammon JA, Baker N*. American Chemical Society National Meeting. Apr-2008, Talk.
22. Bradley M, Rice R, Chivers P, Di Cera E, Baker N*. American Chemical Society National Meeting. Apr-2008, Talk.
23. Wagoner J, Dong F, Baker NA*. Biopolymers Gordon Research Conference. Jun-2008, Talk.
24. Thomas DG, Jones PL, Pappu RV, Baker NA*. caBIG Annual Meeting. Jun-2008, Talk.
25. Wagoner J, Dong F, Baker NA*. Protein Electrostatics Workshop, Telluride Science Research Center. Jul-2008, Talk.
26. Baker NA. Seminar, Department of Biological Science, Florida State University. Jul-2008, Talk.

Selected contributed presentations (last 2 years; of 35 total)

1. Wagoner JA*, Baker NA. Biophysical Society Meeting. Feb-2006, Poster.
2. Song Y*, Baker NA. Biophysical Society Meeting. Feb-2006, Poster.
3. Bradley M*, Chivers P, Baker N. Gibbs Conference on Biothermodynamics. Oct-2006, Poster.
4. Dong F*, Wagoner J, Baker NA. Gibbs Conference on Biothermodynamics. Oct-2006, Poster.
5. Olsen B*, Lee SJ*, Song Y, Baker NA. Gibbs Conference on Biothermodynamics. Oct-2006, Poster.
6. Thomas D, Sim H, Jones P, Pappu R, Sept D, Baker N*. Nanotechnology and the Life Sciences Symposium. Mar-2007, Talk and poster.
7. Lee SJ, Song Y, Baker NA*. Biophysical Society Meeting. Mar-2007, Poster.
8. Rice RL*, Baker NA. Biophysical Society Meeting. Mar-2007, Poster.
9. Thomas D, Sim H, Jones P, Sept D, Pappu R, Baker NA*. National Cancer Institute Nanotechnology Alliance Meeting. Oct-2007, Talk.
10. Li P-C*, Bradley MJ, Baker NA, Sept D. Gibbs Conference on Biothermodynamics. Oct-2007, Poster.
11. Bradley M*, Chivers P, Baker N. Gibbs Conference on Biothermodynamics. Oct-2007, Poster.
12. Olsen B*, Song Y, Tieleman DP, Baker N. Gibbs Conference on Biothermodynamics. Oct-2007, Poster.
13. Hahn-Dantona EA*, Fritts MJ, Patri AK, Baker NA, Thomas DG, Hartel FW. Nanobiology Think Tank Meeting. May-2008, Poster.
14. Paik D* et al. caBIG Annual Meeting. Jun-2008, Poster.
15. Paik D* et al. Radiological Society of North America 94th Scientific Sessions. Nov-2008, Poster.