This page is no longer current. I am now a member of the Tavazoie lab at Columbia University as a postdoctoral research associate. My current research page and contact information can be found here.


Education:

*Ph.D. in Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, 2009
* B.S. with Honors in Biology, California Institute of Technology, 2004

Research Interests:



Publications:

  1. Publications Database Common structural transitions in explicit-solvent simulations of villin headpiece folding. Peter L. Freddolino and Klaus Schulten. Biophysical Journal, 97:2338-2347, 2009.
  2. Publications Database Force field bias in protein folding simulations. Peter L. Freddolino, Sanghyun Park, Benoit Roux, and Klaus Schulten. Biophysical Journal, 96:3772-3780, 2009.
  3. A Vulnerability in Popular Molecular Dynamics Packages Concerning Langevin and Andersen Dynamics. David S. Cerutti, Robert Duke, Peter L. Freddolino, Hao Fan, and Terry P. Lybrand. J. Chem. Theor. Compu. 4:1669-1680, 2008.

  4. Publications Database Molecular mechanisms of ligand recognition by NR3 subtype glutamate receptors. Yongneng Yao, Christopher B. Harrison, Peter L. Freddolino, Klaus Schulten, and Mark L. Mayer. EMBO Journal, 27:2158-2170, 2008.
  5. Publications Database Ten-microsecond molecular dynamics simulation of a fast-folding WW domain. Peter L. Freddolino, Feng Liu, Martin Gruebele, and Klaus Schulten. Biophysical Journal, 94:L75-L77, 2008.
  6. Publications Database Molecular modeling of the structural properties and formation of high-density lipoprotein particles. Amy Y. Shih, Peter L. Freddolino, Anton Arkhipov, Stephen G. Sligar, and Klaus Schulten. In Scott Feller, editor, Current Topics in Membranes: Computational Modeling of Membrane Bilayers, chapter 11, pp. 313-342. Elsevier, 2008.
  7. Publications Database Application of residue-based and shape-based coarse graining to biomolecular simulations. Peter L. Freddolino, Anton Arkhipov, Amy Y. Shih, Ying Yin, Zhongzhou Chen, and Klaus Schulten. In Gregory A. Voth, editor, Coarse-Graining of Condensed Phase and Biomolecular Systems, chapter 20, pp. 299-315. Chapman and Hall/CRC Press, Taylor and Francis Group, 2008.
  8. Publications Database Accelerating molecular modeling applications with graphics processors. John E. Stone, James C. Phillips, Peter L. Freddolino, David J. Hardy, Leonardo G. Trabuco, and Klaus Schulten. Journal of Computational Chemistry, 28:2618-2640, 2007.
  9. Publications Database Disassembly of nanodiscs with cholate. Amy Y. Shih, Peter L. Freddolino, Stephen G. Sligar, and Klaus Schulten. Nano Letters, 7:1692-1696, 2007.
  10. Publications Database Assembly of lipids and proteins into lipoprotein particles. Amy Y. Shih, Anton Arkhipov, Peter L. Freddolino, Stephen G. Sligar, and Klaus Schulten. Journal of Physical Chemistry B, 111:11095-11104, 2007.
  11. Publications Database Assembly of lipoprotein particles revealed by coarse-grained molecular dynamics simulations. Amy Y. Shih, Peter L. Freddolino, Anton Arkhipov, and Klaus Schulten. Journal of Structural Biology, 157:579-592, 2007.
  12. Publications Database Coarse-grained molecular dynamics simulations of a rotating bacterial flagellum. Anton Arkhipov, Peter L. Freddolino, Katsumi Imada, Keiichi Namba, and Klaus Schulten. Biophysical Journal, 91:4589-4597, 2006.
  13. Publications Database Stability and dynamics of virus capsids described by coarse-grained modeling. Anton Arkhipov, Peter L. Freddolino, and Klaus Schulten. Structure, 14:1767-1777, 2006.
  14. Publications Database Dynamic switching mechanisms in LOV1 and LOV2 domains of plant phototropins. Peter L. Freddolino, Markus Dittrich, and Klaus Schulten. Biophysical Journal, 91:3630-3639, 2006.
  15. Publications Database The role of molecular modeling in bionanotechnology. Deyu Lu, Aleksei Aksimentiev, Amy Y. Shih, Eduardo Cruz-Chu, Peter L. Freddolino, Anton Arkhipov, and Klaus Schulten. Physical Biology, 3:S40-S53, 2006.
  16. Publications Database Molecular dynamics simulations of the complete satellite tobacco mosaic virus. Peter L. Freddolino, Anton S. Arkhipov, Steven B. Larson, Alexander McPherson, and Klaus Schulten. Structure, 14:437-449, 2006.
  17. Publications Database Coarse grained protein-lipid model with application to lipoprotein particles. Amy Y. Shih, Anton Arkhipov, Peter L. Freddolino, and Klaus Schulten. Journal of Physical Chemistry B, 110:3674-3684, 2006.
  18. Publications Database When light falls in LOV: A quantum mechanical/molecular mechanical study of photoexcitation in Phot-LOV1 of Chlamydomonas reinhardtii. Markus Dittrich, Peter L. Freddolino, and Klaus Schulten. Journal of Physical Chemistry B, 109:13006-13013, 2005.

  19. Non-TCBG publications:
  20. Dynamic behavior of fully solvated beta2-adrenergic receptor, embedded in the membrane with bound agonist or antagonist Peter Spijker, Nagarajan Vaidehi, Peter L. Freddolino, Peter A. J. Hilbers, and William A. Goddard, III. PNAS 103:4882-4887, 2006.

  21. The predicted 3D structure of the human D2 dopamine receptor and the binding site and binding affinities for agonists and antagonists. M. Yashar S. Kalani, Nagarajan Vaidehi, Spencer E. Hall, Rene J. Trabanino, Peter L. Freddolino, Maziyar A. Kalani, Wely B. Floriano, Victor Wai Tak Kam and William A. Goddard, III. PNAS 101:3815-2820, 2004.

  22. Predicted 3D structure for the human B2 adrenergic receptor and its binding site for agonists and antagonists.Peter L. Freddolino, M. Yashar S. Kalani, Nagarajan Vaidehi, Wely B. Floriano, Spencer E. Hall, Rene J. Trabanino, Victor Wai Tak Kam and William A. Goddard, III. PNAS 101:2736-2741, 2004.

  23. Prediction of structure and function of G protein-coupled receptors. Nagarajan Vaidehi, Wely B. Floriano, Rene Trabanino, Spencer E. Hall, Peter Freddolino, Eun Jung Choi, Georgios Zamanakos, and William A. Goddard III. PNAS 99:12622-12627, 2002.


Presentations:

Posters

Talks

  • Coarse-grained Molecular Dynamics: Approaches, potential, and limitations. Seminar, T. Martinez Laboratory, August 12th, 2007.
  • All-atom Molecular Dynamics Study of a Complete Virus. Theoretical and Computational Biophysics Group Seminar, Beckman Institute, UIUC, April 10th, 2006.
  • Structure and Function Predictions for Beta Adrenergic Receptors, MSC 2004

Software:

VMD Plugins


Awards

  • Beckman Institute Graduate Fellowship (2008-2009)
  • NSF Graduate Research Fellowship (2004-2008)
  • UIUC Alumni Distinguished Fellowship (2004-2007)
  • Poster Prize, 2004 UIUC Molecular Biophysics Symposium
  • Sigma Xi Award for Undergraduate Research (2004)
  • Caltech President's Scholarship (2000-2004)