• Home

• Overview

• Highlights

• Bringing Physics To Life

• Bringing Computing To Life

• Picture and Movie Galleries

• TCB Group Members

• Publications

• Research

• Software

• Outreach

Peter Freddolino

I am now a member of the Tavazoie lab at Columbia as a postdoctoral associate. This page is thus no longer current; it will redirect to my new homepage once one has been completed.

Up to date contact information for me can be found in the Columbia university directory.

---

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:

• Molecular dynamics and QM/MM studies of photoreceptor activation in the LOV domain
• Development of Coarse Grain MD methodology for study of very large systems and very long time scales
• Large scale molecular dynamics studies on Satellite Tobacco Mosaic Virus
• Coarse grain simulations of Nanodiscs and High Density Lipoprotein (HDL)
• Development of tools to simplify the setup and analysis of molecular dynamics simulations, in the form of VMD plugins (see Software, below).
• Molecular dynamics simulations of protein folding

---

Publications:

1. Common structural transitions in explicit-solvent simulations of villin headpiece folding. Peter L. Freddolino and Klaus Schulten. Biophysical Journal, 97:2338-2347, 2009.

2. 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. 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. 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. 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. 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. 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. Disassembly of nanodiscs with cholate. Amy Y. Shih, Peter L. Freddolino, Stephen G. Sligar, and Klaus Schulten. Nano Letters, 7:1692-1696, 2007.

10. 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. 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. 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. 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. 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. 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. 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. 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. 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.


Non-TCBG publications:


19. 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.

20. 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.

21. 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.

22. 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

• Microsecond explicit solvent molecular dynamics simulations of protein folding. 2009 Biophysical Society Annual Meeting, Boston, MA.
• Agonist binding and allostery in the NR3A subunit of NMDA receptors, 2008 Gordon Research Conference on Biomolecular Interactions and Methods, Ventura, CA.
• Coarse-grained molecular dynamics simulations of rotation-induced structural transitions in the bacterial flagellum. 2007 Biophysical Society Annual Meeting 2007, Baltimore, MD.
• Molecular Dynamics Simulations of the Complete Satellite Tobacco Mosaic Virus, 2006 Biophysical Society Annual Meeting, Salt Lake City, UT.
• Structurally Derived Amino Acid Substitution Matrices, 2004 UIUC Molecular Biophysics Research Symposium

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:

• Ionize

VMD Plugins

• NAMDEnergy
• AutoPSF
• Molefacture
• Molfile plugins (BGF, MOL2, XBGF)

---

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)

Beckman Institute for Advanced Science and Technology // National Institutes of Health // National Science Foundation // Physics, Computer Science, and Biophysics at UIUC
Contact Us // Material on this page is copyrighted; contact Webmaster for more information. // Document last modified on 10 Sep 2011 // 13921 accesses since 20 Mar 2006 .