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Peter L. Freddolino, Ph.D Peter L. Freddolino, Ph.D. Postdoctoral Research Scientist Department of Systems Biology, Columbia University Contact 406 Russ Berrie Pavilion Voice: +1 (609) 439-1811 Information Columbia University Fax: +1 (212) 851-5149 1150 St. Nicholas Avenue Email: [email protected] New York, NY 10032 Website: http://tavazoielab.c2b2.columbia.edu/petefred Education University of Illinois at Urbana-Champaign, Urbana, Illinois, 2004-2009 Ph.D., Biophysics and Computational Biology GPA: 4.0 Advisor: Klaus Schulten Thesis title: \Application of all-atom and coarse-grained molecular dynamics to long timescale structural transitions of proteins" Completed additional option in Computational Science and Engineering (see http://cse.illinois.edu/programs) California Institute of Technology, Pasadena, California, 2000-2004 B.S. with Honors, Biology GPA: 4.0 Research Postdoctoral Research Scientist with Dr. Saeed Tavazoie, Columbia University Experience (2011-present) and Princeton University (2009-2011) • Development of methods for genome-scale profiling of DNA binding protein locations under physiological conditions • Identification of mechanisms for rapid microbial adaptation to stressful conditions • Investigation of the fitness landscape effects of perturbation of Rho-dependent termi- nation in E. coli • Identification of anticipatory behavior evolutionarily hard-wired into bacterial genetic regulatory networks Graduate Research Fellow with Dr. Klaus Schulten, University of Illinois at Urbana-Champaign, 2004-2009 • Molecular dynamics and QM/MM investigation of light-induced receptor activation in LOV domains • Investigation of satellite tobacco mosaic virus assembly and disassembly through molec- ular dynamics simulations and single molecule fluorescence microscopy (with Prof. T. Ha, University of Illinois) • Development of coarse-grained models for large polymeric biological assemblies • Modeling of switching in the bacterial flagellum using multiscale simulations and com- bined crystallographic and cryo-EM data • Coarse-grained simulation of high density lipoprotein particle assembly mechanisms • Molecular dynamics analysis of ligand binding and ligand-induced structural changes in the NR3A NMDA receptor Freddolino { Curriculum vitae { Page 1 of 8 • Investigation of the protein folding processes for the villin headpiece and WW domain using molecular dynamics simulations Undergraduate Research Assistant with Dr. William A. Goddard III, California Institute of Technology, 2001-2004 • Development of methods for structure prediction of GPCRs • Structural prediction and virtual ligand screening for the β adrenergic receptor family Honors and NIH Pathway to Independence Award (K99, 2013{2015; pending R00, 2015{2018, with Awards option for earlier conversion to R00) Beckman Fellowship, University of Illinois at Urbana-Champaign, 2008-2009 National Science Foundation Graduate Research Fellowship, 2004-2009 Distinguished Fellowship, University of Illinois at Urbana-Champaign, 2004-2007 Sigma Xi Award for Undergraduate Research, California Institute of Technology, 2004 (awarded to one graduating senior each year) President's Scholarship, California Institute of Technology, 2000-2004 Journal H-index: 21 (ISI Web of Science), 22 (Google Scholar) Articles See my Google Scholar page for full text links and citation information 33. P. Freddolino, H. Goodarzi, and S. Tavazoie. Revealing the genetic basis of natural bacterial phenotypic divergence. J. Bacteriol., in press, 2013. 32. A. Hottes, P. Freddolino, A. Khare, Z. Donnell, J. Liu, and S. Tavazoie. Bacterial Adaptation Through Loss of Function. PLoS Genetics, 9(7): e1003617, 2013. 31. P. Freddolino, K. Gardner, and K. Schulten. Signaling mechanisms of LOV do- mains: New insights from molecular dynamics studies. Photochem. Photobiol. Sci., 12:1158{1170, 2013. 30. P. Freddolino and S. Tavazoie. The Dawn of Virtual Cell Biology. Cell 150:248{250, 2012. 29. P. Freddolino and S. Tavazoie. Beyond Homeostasis: A Predictive-Dynamic Frame- work for Understanding Cellular Behavior. Ann. Rev. Cell. Dev. Biol., 28:363-384, 2012. 28. P. Freddolino, H. Goodarzi, and S. Tavazoie. Fitness Landscape Transformation through a Single Amino Acid Change in the Rho Terminator. PLoS Genetics 8(5):e1002744, 2012. 27. Y. Liu, J. Str¨umpfer, P. Freddolino, M. Gruebele, and K. Schulten. Structural Char- acterization of λ-Repressor Folding from All-Atom Molecular Dynamics Simulations. J. Phys. Chem. Lett. 3:1117{1123, 2012. 26. P. Freddolino, S. Amini, and S. Tavazoie. Newly Identified Genetic Variations in Common Escherichia coli MG1655 Stock Cultures. J. Bacteriol., 194:303{306, 2012. 25. E. Schreiner, L. Trabuco, P. Freddolino, and K. Schulten. Stereochemical errors and Freddolino { Curriculum vitae { Page 2 of 8 their implications for molecular dynamics simulations. BMC Bioinformatics, 12:190, 2011. 24. S.-H. Song, P. Freddolino, A. Nash, E. Carroll, K. Schulten, K. Gardner, and D. Larsen. Modulating LOV Domain Photodynamics with a Residue Alteration out- side the Chromophore Binding Site. Biochemistry, 50:2411{2423, 2011. 23. P. Freddolino, C. Harrison, Y. Liu, and K. Schulten. Challenges in protein folding simulations: Force field, timescale, sampling, and analysis. Nature Physics, 6:751{758, 2010. 22. D. Cerutti, P. Freddolino, R. Duke, and D. Case. Simulations of a Protein Crystal with a High Resolution X-ray Structure: Evaluation of Force Fields and Water Models J. Phys. Chem. B, 114:12811{12824, 2010. 21. A. Rajan, P. Freddolino and K. Schulten. Going beyond clustering in MD trajectory analysis: an application to villin headpiece folding. PLoS One, 5:e9890, 2010. 20. P. Freddolino and K. Schulten. Common structural transitions in explicit-solvent simulations of villin headpiece folding. Biophysical Journal, 97:2338-2347, 2009. 19. P. Freddolino, S. Park, B. Roux, and K. Schulten. Force field bias in protein folding simulations. Biophysical Journal, 96:3772{378, 2009. 18. D. S. Cerutti, R. Duke, P. Freddolino, H. Fan, and T. Lybrand. A Vulnerability in Popular Molecular Dynamics Packages Concerning Langevin and Andersen Dynamics. J. Chem. Theor. Comput., 4:1669-1680, 2008. 17. Y. Yao, C. B. Harrison, P. Freddolino, K. Schulten, and M. L. Mayer. Molecular mechanisms of ligand recognition by NR3 subtype glutamate receptors. EMBO Jour- nal, 27:2158-2170, 2008. 16. P. Freddolino, F. Liu, M. Gruebele, and K. Schulten. Ten-microsecond MD simula- tion of a fast-folding WW domain. Biophysical Journal, 94:L75-L77, 2008. 15. J. Stone, J. Phillips, P. Freddolino, D. Hardy, L. Trabuco, and K. Schulten. Accel- erating molecular modeling applications with graphics processors. J. Comp. Chem., 28:2618-2640, 2007. 14. A. Shih, P. Freddolino, S. Sligar, and K. Schulten. Disassembly of nanodiscs with cholate. Nano Letters, 7:1692-1696, 2007. 13. A. Shih, A. Arkhipov, P. Freddolino, S. Sligar, and K. Schulten. Assembly of lipids and proteins into lipoprotein particles. J. Phys. Chem. B, 111:11095-11104, 2007. 12. A. Shih, P. Freddolino, A. Arkhipov, and K. Schulten. Assembly of lipoprotein particles revealed by coarse-grained molecular dynamics simulations. J. Struct. Biol., 157:579-592, 2007. 11. A. Arkhipov, P. Freddolino, and K. Schulten. Stability and dynamics of virus cap- sids described by coarse-grained modeling. Structure, 14:1767-1777, 2006. 10. P. Freddolino, M. Dittrich, and K. Schulten. Dynamic switching mechanisms in LOV1 and LOV2 domains of plant phototropins. Biophysical Journal, 91:3630-3639, 2006. 9. P. Spijker, N. Vaidehi, P. Freddolino, P. Hilbers, and W. Goddard III. Dynamic behavior of fully solvated beta2-adrenergic receptor, embedded in the membrane with bound agonist or antagonist. PNAS 103:4882-4887, 2006. Freddolino { Curriculum vitae { Page 3 of 8 8. A. Arkhipov, P. Freddolino, K. Imada, K. Namba, and K. Schulten. Coarse-grained molecular dynamics simulations of a rotating bacterial flagellum. Biophysical Journal, 91:4589-4597, 2006. 7. P. Freddolino, A. Arkhipov, S. Larson, A. McPherson, and K. Schulten. Molecu- lar dynamics simulations of the complete satellite tobacco mosaic virus. Structure, 14:437-449, 2006. 6. D. Lu, A. Aksimentiev, A. Shih, E. Cruz-Chu, P. Freddolino, A. Arkhipov, and K. Schulten. The role of molecular modeling in bionanotechnology. Physical Biology, 3:S40-S53, 2006. 5. A. Shih, A. Arkhipov, P. Freddolino, and K. Schulten. Coarse grained protein-lipid model with application to lipoprotein particles. J. Phys. Chem. B, 110:3674-3684, 2006. 4. M. Dittrich, P. Freddolino, and K. Schulten. When light falls in LOV: A quantum mechanical/molecular mechanical study of photoexcitation in Phot-LOV1 of Chlamy- domonas reinhardtii. J. Phys. Chem. B, 109:13006-13013, 2005. 3. P. Freddolino, M. Kalani, N. Vaidehi, W. Floriano, S. Hall, R. Trabanino, V. Kam, and W. Goddard III. Predicted 3D structure for the human β2 adrenergic receptor and its binding site for agonists and antagonists. PNAS 101:2736-2741, 2004. 2. M. Kalani, N. Vaidehi, S. Hall, R. Trabanino, P. Freddolino, M. Kalani, W. Flo- riano, V. Kam, and W. Goddard III. The predicted 3D structure of the human D2 dopamine receptor and the binding site and binding affinities for agonists and antag- onists. PNAS 101:3815-2820, 2004. 1. N. Vaidehi, W. Floriano, R. Trabanino, S. Hall, P. Freddolino, E. Choi, G. Za- manakos, and W. Goddard III. Prediction of structure and function of G protein- coupled receptors. PNAS 99:12622-12627, 2002. Book Chapters 2. A. Shih, P. Freddolino, A. Arkhipov, S. Sligar, and K. Schulten. Molecular model- ing of the structural
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