Paul S. Nerenberg Division of Geological and Planetary Sciences California Institute of Technology 1200 E California Blvd, MC 150-­‐21, Pasadena, CA 91125 office: 626.395.6367 / cell: 617.529.3930 e-­‐mail: psn@caltech.edu http://www.gps.caltech.edu/~psn Education Ph.D. in Physics, Massachusetts Institute of Technology (MIT), February 2010. Thesis title: “The Mechanism of Collagenolysis: A Substrate-­‐centric View”, advisor: Prof. Collin Stultz. B.S. in Physics with University and Department honors, Johns Hopkins University (JHU), May 2004. Academic Positions Research Assistant Professor of Planetary Science, Division of Geological and Planetary Sciences, California Institute of Technology, 07/2014 – present. Visiting Assistant Professor of Physics, W.M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, 08/2011 – 06/2014. Research Experience Postdoctoral scholar with Prof. Teresa Head-­‐Gordon, California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, 03/2010 – 07/2011. Graduate research assistant with Prof. Collin Stultz, Dept. of Electrical Engineering and Computer Science and Harvard-­‐MIT Division of Health Sciences and Technology, MIT, 09/2006 – 01/2010. Graduate research assistant, Plasma Science and Fusion Center, MIT, 09/2004 – 05/2006. REU student with Prof. Jim Houck, Dept. of Astronomy, Cornell University, 06/2003 – 08/2003. Undergraduate research assistant with Prof. Cila Herman (STILLMix Project), Dept. of Mechanical Engineering, JHU, 09/2002 – 06/2003. Teaching Experience As visiting assistant professor at Claremont McKenna, Pitzer, and Scripps Colleges: •
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Spring 2014: Physics 34 – Principles of Physics, one integrated lecture-­‐lab section. Physics 31 – General Physics, one lab section. Fall 2013: Physics 30 – General Physics, two lecture sections and one lab section. Chemistry 29 – Accelerated General Chemistry, one lecture section and one lab section (co-­‐taught with Prof. Robert Kojima). Spring 2013: Physics 31 – General Physics, one lecture section and one lab section. Physics 178 – Biophysics, one lecture section. Fall 2012: Physics 30 – General Physics, one lecture section and one lab section. Physics 114 – Quantum Mechanics, one lecture section. Spring 2012: Physics 31 – General Physics, one lecture section and two lab sections. Fall 2011: Physics 30 – General Physics, one lecture section and three lab sections. As guest lecturer at UC Berkeley (Fall 2010): BE 143/243 – Computational Methods in Biology with Prof. Teresa Head-­‐Gordon. Teaching Experience (cont.) As graduate teaching assistant at MIT: •
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Fall 2008: 6.502 – Introduction to Molecular Simulations with Prof. Collin Stultz. Spring 2008: 8.02 – Physics II with Prof. Eric Hudson (now at Penn State). Fall 2007: 8.01 – Physics I with Dr. Peter Dourmashkin. Spring 2007: 8.02 – Physics II with Prof. Robert Simcoe. Fall 2006: 8.01 – Physics I with Prof. Alan Guth. Fall 2006 – Spring 2008: Media Lab Freshman-­‐Year Program with Dr. Michael Bove. Publications %
Undergraduate student author. * Both authors contributed equally to this work. 1. Nerenberg PS, Kretchmer JS, Karelina M, and Miller TF. The Solvation and Aggregation of Atmospheric Molecules in the Lakes of Titan. In preparation, 2014. 2. Yedvabny E, Nerenberg PS, So C%, and Head-­‐Gordon T. The Disordered Structural Ensembles of Vasopressin and Oxytocin and Their Mutants. Journal of Physical Chemistry B 2014; under review. 3. Chapman DE%*, Steck JK%*, and Nerenberg PS. Optimizing Protein-­‐Protein van der Waals Interactions for the AMBER ff9x/ff12 Force Field. Journal of Chemical Theory and Computation 2014; 10:273-­‐281. 4. Liguori N, Nerenberg PS, and Head-­‐Gordon T. Embedding Aβ42 in Heterogenous Membranes Depends on Cholesterol Asymmetries. Biophysical Journal 2013; 105:899-­‐910. 5. Nerenberg PS, Jo B%, So C%, Tripathy A%, and Head-­‐Gordon T. Optimizing Solute–Water van der Waals Interactions To Reproduce Solvation Free Energies. Journal of Physical Chemistry B 2012; 116:4524-­‐4534. 6. Ball KA, Phillips AH, Nerenberg PS, Fawzi NL, Wemmer DE, and Head-­‐Gordon T. Homogenous and Heterogeneous Tertiary Structure Ensembles of Amyloid-­‐β Peptides. Biochemistry 2011; 50:7612-­‐7628. 7. Nerenberg PS and Head-­‐Gordon T. Optimizing Protein-­‐Solvent Force Fields to Reproduce Intrinsic Conformational Preferences of Model Peptides. Journal of Chemical Theory and Computation 2011; 7:1220-­‐1230. 8. Chen MM, Bartlett AI, Nerenberg PS, Friel CT, Hackenberger CPR, Stultz CM, Radford SE, and Imperiali B. The effects of N-­‐linked glycosylation on protein folding kinetics and thermodynamics: a combined experimental and computational analysis. Proceedings of the National Academy of Sciences 2010; 107:22528-­‐22533. 9. Salsas-­‐Escat R*, Nerenberg PS*, and Stultz CM. Cleavage site specificity and conformational selection in type I collagen degradation. Biochemistry 2010; 49:4147-­‐4158. 10. Gurry T, Nerenberg PS, and Stultz CM. The contribution of interchain salt bridges to triple-­‐helical stability in collagen. Biophysical Journal 2010; 98:2634-­‐2643. 11. Phillips CM, Nerenberg PS, Drennan CL, and Stultz CM. The Physical Basis of Metal Binding Specificity in E. coli NikR. Journal of the American Chemical Society 2009; 131:10220-­‐10228. 12. Nerenberg PS and Stultz CM. Differential Unfolding of α1 and α2 Chains in Type I Collagen and Collagenolysis. Journal of Molecular Biology 2008; 382:246-­‐256. 13. Nerenberg PS, Salsas-­‐Escat R, Stultz CM. Do collagenases unwind triple-­‐helical collagen prior to peptide bond hydrolysis? Reinterpreting experimental observations with mathematical models. Proteins 2008; 70:1154-­‐1161. 14. Nerenberg PS, Salsas-­‐Escat R, Stultz CM. Collagen – A Necessary Accomplice in the Metastatic Process. Cancer Genomics and Proteomics 2007; 4:319-­‐328. Funding SI2-­‐CHE: Development and Deployment of Chemical Software for Advanced Potential Energy Surfaces. (PI, NSF award #1265660/1453123, $57k, 05/2013 – 04/2016.) A joint US/UK effort of 12 PIs funded by the NSF and EPSRC to develop software infrastructure and computationally inexpensive polarizable force fields for MD simulations. Activities include force field development, grand challenge modeling, and leading an annual training workshop in biomolecular simulations for undergraduate students. Computing Time Allocations Next-­‐Generation Fixed-­‐Charge Force Fields. (PI, DOE NERSC m1912, 500k MPP hours in 2014.) Allocation to develop new fixed-­‐charge force fields for simulating molecular systems relevant to both biology and planetary science. BI/BII Stabilization in Methylated DNA. (PI, DOE NERSC m1898, 500k MPP hours in 2014.) Allocation to investigate the impact of cytosine methylation on B-­‐DNA structure and thermodynamics. Previous allocations: NSF XSEDE TG-­‐MCB130157 (PI, 2013-­‐2014); DOE NERSC m1566 (PI, 2012-­‐2014); DOE NERSC m1174 (co-­‐PI, 2011-­‐2013). Mentoring Experience #
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Keck Science undergraduates (2012-­‐14): Dail Chapman# (Scripps), Roxanne Fries# (CMC), Kiley Lawrence# (Scripps), Crystal Lim (CMC), Georgia Macy# (Scripps), Jonathan Steck# (CMC), Patrick Shultz (CMC), David Wych (CMC) UC Berkeley undergraduates (2010-­‐11): Brian Jo, Clare So, Ajay Tripathy Visiting students at UC Berkeley (2010-­‐11): Nicoletta Liguori (Roma Tre University MS), Lin Mao (Zhejiang Univ. undergrad.) MIT undergraduates (2008-­‐09): Anjali Muralidhar, Steven Pennybaker, William Wyatt Visiting students at MIT (2008-­‐09): Gadini Delisca (Howard Univ. undergrad.), Thomas Gurry (Cambridge Univ. MPhil) Academic and University Service •
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Reviewer for Journal of Chemical Theory and Computation and PLoS ONE. Organizer, Claremont Colleges’ Software Carpentry programming bootcamp, 2014. Judge, California State University Student Research Competition, 2013. Chair, Gordon-­‐Kenan Research Seminar on Collagen, 2011. Co-­‐Editor, PER (Physics Education Research) Jobs website, 2008-­‐2012. Graduate Representative, Dean of Student Life Selection Committee, MIT, 2007-­‐08. Graduate Representative, DAPER Athletics Board, MIT, 2005-­‐07. Awards and Honors •
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Buechner Teaching Prize, Department of Physics, MIT, 2008. Graduate Student Life Grant, MIT, 2006 and 2007. Donald E. Kerr Memorial Medal, Department of Physics and Astronomy, JHU, 2004. Phi Beta Kappa Society, 2004. Sigma Pi Sigma Society, 2003. Provost’s Undergraduate Research Award, JHU, 2003. Posters, Presentations, and Colloquia Colloquium Dept. of Physics, CSU San Marcos; Feb. 24, 2014. Colloquium Dept. of Physics and Astronomy, CSU Sacramento; Feb. 18, 2014. Poster 58th Annual Meeting of The Biophysical Society (San Francisco, CA); Feb. 15-­‐19, 2014. Colloquium Dept. of Physics, University of San Diego; Feb. 4, 2014. Colloquium Depts. of Biology and Physics, University of Puget Sound; Dec. 5, 2013. Colloquium Summer Research Seminar, Cal Poly Pomona; July 10, 2013. Poster Gordon Research Conference: Biomolecular NMR (Mount Snow, VT); June 2-­‐7, 2013. Colloquium Dept. of Physics and Astronomy, CSU Los Angeles; April 11, 2013. Colloquium W.M. Keck Science Dept., CMC, Pitzer, and Scripps Colleges; Feb. 9, 2012. Poster 55th Annual Meeting of The Biophysical Society (Baltimore, MD); Mar. 5-­‐9, 2011. Colloquium Dept. of Physics, Harvey Mudd College; Nov. 30, 2010. Colloquium Dept. of Physics, Lafayette College; Dec. 10, 2009. Poster 23rd Symposium of The Protein Society (Boston, MA); July 25-­‐29, 2009. Presentation Gordon Research Conference: Collagen (New London, NH); July 19-­‐24, 2009. Poster Gordon Research Conference: Collagen (New London, NH); July 19-­‐24, 2009. Poster 53rd Annual Meeting of The Biophysical Society (Boston, MA); Feb. 28 -­‐Mar. 4, 2009. Poster 22nd Symposium of The Protein Society (San Diego, CA); July 19-­‐23, 2008.