CURRICULUM VITAE

Margaret Shun Cheung

617 Science & Research I Email: mscheung@uh.edu

Department of Physics Phone: (713) 743-8358

University of Houston Fax: (713) 743-3589

Houston, TX, 77204 http://www.phys.uh.edu/~mscheung/

EDUCATION

National Taiwan University, B.Sci. Chemistry, 1994

University of California at San Diego, Ph.D., Physics, 2003

CURRENT RESEARCH POSITION

Assistant Professor, September 2006-present

Department of Physics, University of Houston

PAST RESEARCH POSITION

Alfred P. Sloan Postdoctoral Fellow, 2003-2006

Effects of crowding and confinement on protein-protein interaction

Institute for Physical Science and Technology

University of Maryland

Advisor: Prof. Devarajan Thirumalai

Graduate Researcher, 1997-2003

Energy landscape aspect of protein folding dynamics relevant to molecular functions
Department of Physics and the Center for Theoretical Biological Physics

University of California at San Diego

Advisor: Prof. Jose¡¦ N. Onuchic

AWARDS AND HONORS

• Book Coupon Award, 1990-1991
• President of the Chemistry Undergraduate Student Association, 1992
• Alfred P. Sloan Foundation Postdoctoral Fellowship in Computational Biology and Bioinformatics, 2003-2005
• University of Houston New Faculty Award, 2006

TEACHING

• University of Maryland High-Performance Computing for Biology, (CHPH) 718G, Winter 2006
• University of Houston Biological Physics (PHYS) 7397, Spring 2007
• University of Houston Statistical Physics (PHYS) 6327, Spring 2008
• University of Houston Introductory General Physics (PHYS)1301, Fall 2008
• University of Houston Statistical Physics (PHYS) 6327, Spring 2009

MENTORED STUDENTS

Shaoqing Zhang (graduate student, UH Physics, 2006-2007)

Buddhi Tilakaratne (graduate student, UH Physics, 2007-2008)

Antonios Samiotakis (Ph.D. student, UH Physics, 2007-present)

Qian Wang (Ph.D. student, UH Physics, 2008-present)

Jack Liang (Ph.D. student, UH Physics, 2009-present)

Soniya Yambem (graduate student, UH Physics, Summer 2008)

Marc Gonzalez (undergrad, UH Physics, Summer 2007)

Byron Hoffman (undergrad, UH Physics, Summer 2008)

Nathaniel Morgan (undergrad, UH Physics, Fall 2008-Spring 2009)

Megan Scoppa (undergrad, UH Biochemistry, Spring 2009-present)

Syed Razavi (undergrad, UH Chemical and Biomolecular Engineering, Summer 2009-current)

Rizwan Tai (undergrad, UH Political Sci. Summer 2009)

Faheem Shahid (undergrad, UH Mechanical Engineering, Summer 2009)

Tyler Quarton (undergrad, UH Biochemistry, Fall 2009-current)

Brian Bush (undergrad, UH Physics, Fall 2009-current)

POSTDOCS

Dirar Homouz (Postdoc, June 2007-May 2009)

GRANTS

University of Houston, ACS Petroleum New Faculty Grant, TcSUH seed grant, UH Grants to Enhance and Advance Research (GEAR), FDIP, Grant-in-aid from the Wright-Patterson Air Force Base, TeraGrid computing resources, and the National Science Foundation (MCB0919974, 2009-2013)

Journal Publications before 2006:

1. M. S. Cheung, I. Daizadeh, A. A. Stuchebrukhov, P. F. Heelis ¡§Pathways of Electron Transfer in E. coli DNA Photolyase¡¨, Biophys. J., 76, 1241-1249 (1999)

The prediction was later experimentally verified (Aubert et al, Nature, 405, 586-590, 2000).

2. M. S. Cheung, A. E. García, J. N. Onuchic ¡§Protein folding mediated by solvation: water expelling and formation of the hydrophobic core occurs after the structure collapse¡¨ Proc. Natl. Acad. Sci. U. S. A., 99, 685-690 (2002).

¡P This paper has 152 citations since being published.

3. C. Guo, M. S. Cheung, H. Levine, D. A. Kessler ¡§Mechanisms underlying sequence-independent beta-sheet formation¡¨ J. Chem. Phys. 116, 4353-4365 (2002).

4. M. S. Cheung, J. M. Finke, B. Callahan, J. N. Onuchic ¡§Exploring the interplay of topology and secondary structural formation in the protein folding problem¡¨ J. Phys. Chem., B, 107, 11193-11200 (2003).

5. M. S. Cheung, L. L. Chavez, J. N. Onuchic ¡§The Energy Landscape for Protein Folding and Possible Connections to Function¡¨ Polymer, 45, 547-555 (2004).

6. A. Fernandez-Escamilla, M. S. Cheung, M. C. Vega, M. Wilmanns, J. N. Onuchic, L. Serrano ¡§Solvation in protein folding analysis, combination of theoretical and experimental approaches¡¨ Proc. Natl. Acad. Sci. U. S. A., 101, 2834-2839 (2004).

7. J. M. Finke, M. S. Cheung, J. N. Onuchic. ¡§A structural model of polyglutamine determined from a host-guest method combining experiments and landscape theory¡¨ Biophys. J. 87, 1900-1918 (2004).

8. S. Yang, S. S. Cho, Y. Levy, M. S. Cheung, H. Levine, P. G. Wolynes, J. N. Onuchic. ¡§Domain swapping is a consequence of minimal frustration¡¨. Proc. Natl. Acad. Sci. U. S. A., 101, 13786-13791 (2004).

9. M. S. Cheung, D. Klimov, D. Thirumalai. ¡§Molecular crowding enhances native state stability and refolding rates¡¨. Proc. Natl. Acad. Sci. U. S. A., 102, 4753-4758 (2005).

¡P This paper was highlighted by Journal of Cell Biology in the April 11^th, 2005 issue.

10. J. Chahine, M. S. Cheung. ¡§Computational studies of the reversible domain swapping of p13suc1¡¨, Biophys. J. 89, 1-9 (2005).

11. M. S. Cheung, D. Thirumalai. ¡§Nanopore-protein interactions dramatically alter stability and yield of the native state in restricted spaces¡¨, J. Mol. Biol. 357, 632-643 (2006).

Journal publications after 2006:

12. M. E. Sardiu, M. S. Cheung, Y.-K. Yu. ¡§Cysteine-Cysteine contact preference leads to target-focusing in protein folding¡¨, Biophys.. J. 93 1-14 (2007).

13. M. S. Cheung, D. Thirumalai, ¡§Crowding and confinement effects on structures of the transition state ensemble in proteins¡¨, J. Phys. Chem. B.111 8250-8257 (2007)..

14. S.-Q.Zhang, M. S. Cheung, ¡§Manipulating Biopolymer Dynamics by Anisotropic Nanoconfinement¡¨, Nano Letters, 7, 3438-3442 (2007).

¡P This paper is in Research Highlights, Nature Nanotechnology web Oct 26^th 2007 release.

15. L. Stagg, S.-Q.Zhang, M. S. Cheung, P. Wittung-Stafshede, ¡§Molecular crowding enhances native structure and stability of £\/£] protein flavodoxin¡¨, Proc. Natl. Acad. Sci. U. S. A., 104, 18976-18981 (2007).

16. D. Homouz, M. Perham, A. Samiotakis, M. S. Cheung, P. Wittung-Stafshede. ¡§Crowded, cell-like environment induces shape changes in aspherical protein¡¨, Proc. Natl. Acad. Sci. U. S. A.,105, 11754-11759 (2008).

¡P It was featured in Chemical & Engineering News, Aug 18^th 08, issue

¡P It was featured in Research Highlights in Nature (vol 454, p21, 2008).

¡P It was featured in Research Highlights of 2008 in Nature.

17. N. Kanna, J. Subhlok, E. Gabriel, M. S. Cheung, D. Anderson, ¡§Redundancy tolerant communication on volatile nodes¡¨, technical reports,UH-CS-08-17 (2008).

18. D. Homouz, L. Stagg, P. Wittung-Stafshede, M. S. Cheung, ¡§Macromolecular crowding modulates folding mechanism of £\/£] protein apoflavodoxin¡¨, Biophys. J., 96, 671-680 (2009).

19. A. Samiotakis, P. Wittung-Stafshede, M. S. Cheung, ¡§Folding, stability and shape of proteins in crowded environments: Experimental and computational approaches¡¨, Int. J. Mol. Sci. 10, 572-588 (2009).

20. A. Kudlay, M. S. Cheung, D. Thirumalai, ¡§Crowding effects on the structural transitions in a flexible helical homopolymer¡¨, Phys. Rev. Letts. 102, 118101 (2009).

21. D. Homouz, H. Sanabria, M. N. Waxham, M. S. Cheung, ¡§Modulation of calmodulin plasticity by the effect of macromolecular crowding¡¨, J. Mol. Biol. 391, 933-943 (2009).

22. D. Homouz, B. Hoffman, M. S. Cheung, ¡§Hydrophobic interactions of hexane in nanosized water droplets¡¨, J. Phys. Chem. B, 113, 12337-12342 (2009).

¡P Byron Hoffman was an undergraduate from the Department of Physics, UH.

23. L. Stagg, A. Samiotakis, M. S. Cheung, P. Wittung-Stafshede, ¡§Residue specific analysis of frustration in folding landscape of repeat beta/alpha protein apoflavodoxin¡¨, submitted (2009).

24. Q. Wang, G. Hong, G. R. Johnson, R. Pachter, M. S. Cheung, ¡§ Molecular mechanisms of peptide translocation across micelles: A case study of cell-penetrating peptide and antimicrobial peptide", submitted (2009)

Membership in Professional Societies:

American Physical Society, Physics Teacher Education Coalition, American Chemical Society, Protein Society and Biophysical Society.

Departmental Services:

Website committee (Fall 2006-), graduate studies committee (Spring 2007-), high-school outreach programs (Spring 2008-), and faculty search committee (Fall 2008, Spring 2009).

Other Activities:

• Reviewer for Biophysical Journal, Proteins: Structure, Function, and Bioinformatics, Protein Science, Proceedings of the National Academy of Sciences, Physical Biology, Journal of Physical Chemistry B, International Journal of Molecular Sciences, Physical Review E, Biochemistry and Cell Biology, PLoS Computational Biology, and Nano Letters.

• Proposal reviewer for the Division of Materials Research from the National Science Foundation, the Department of Energy, and the Petroleum Research Foundation.

Invited talks and Seminar:

¡P ¡§Pathways of electron transfer in E. coli DNA Photolyase¡¨, invited talk. Lawrence Berkeley National Lab, Berkeley, CA, Spring 1997.

¡P ¡§Studying protein dynamics using minimalist model with desolvation effect¡¨, invited talk. The 221^st National Meeting for the American Chemical Society, San Diego, CA, April 2001.

¡P ¡§Protein folding with desolvation effect¡¨, Biocomplexity seminar. Physics Department, University of California, San Diego, CA, May 2001.

¡P ¡§Solvation in protein folding analysis, combination of theoretical and experimental approaches¡¨, CSCAMM (Center for scientific computational and mathematical modeling) seminar. University of Maryland, College Park, MD, October 2003.

¡P ¡§Exploring the protein folding funnel landscape: theory meets experiments¡¨, invited talk, ISCANA (International Symposium on Clusters and Nano Assemblies: Physical and Biological Systems), Virginia Commonwealth University, Richmond, VA, November 2003.

¡P ¡§Solvation in protein folding analysis, combination of theoretical and experimental approaches¡¨, invited talk. The 48^th annual meeting for the Biophysical Society, Baltimore, MD, February 2004.

¡P ¡§Life in a crowd: macromolecular crowding and confinement effects on protein interactions in living systems¡¨, invited talk, Department of Physics, University of Houston, TX, November 2005.

¡P ¡§Life in a crowd: macromolecular crowding and confinement effects on protein interactions in living systems¡¨, Biophysics seminar, Institute for Physical Science and Technology, University of Maryland, College Park, MD, November 2005.

¡P ¡§Life in a crowd: macromolecular crowding and confinement effects on protein interactions in living systems¡¨, invited talk, Department of Chemistry, University of Pittsburgh, PA, December 2005.

¡P ¡§Life in a crowd: macromolecular crowding and confinement effects on protein interactions in living systems¡¨, invited talk, Department of Chemistry, University of Utah, UT, December 2005.

¡P ¡§Life in a crowd: macromolecular crowding and confinement effects on protein interactions in living systems¡¨, invited talk, Department of Chemistry, University of Cincinnati, OH, December 2005.

¡P ¡§Life in a crowd: macromolecular crowding and confinement effects on protein interactions in living systems¡¨, invited talk, Department of Physics, University of Michigan, MI, January 2006.

¡P ¡§Life in a crowd: macromolecular crowding and confinement effects on protein interactions in living systems¡¨, invited talk, Dana-Farber Cancer Institute and Department of Biostatistics, Harvard University School of Public Health, MA, January 2006.

¡P ¡§Life in a crowd: macromolecular crowding and confinement effects on protein interactions in living systems¡¨, invited talk, Department of Physics and Astronomy, Iowa State University, IA, January 2006.

¡P ¡§Life in a crowd: macromolecular crowding and confinement effects on protein interactions in living systems¡¨, invited talk, Center for Bioinformatics, Department of Molecular Biosciences, and Department of Chemistry, University of Kansas, KS, February 2006.

¡P ¡§Life in a crowd: macromolecular crowding and confinement effects on protein interactions in living systems¡¨, invited talk, Department of Chemistry and Department of Computer Science, University of California at Irvine, CA, February 2006.

¡P ¡§Life in a crowd: macromolecular crowding and confinement effects on protein interactions in living systems¡¨, invited talk, Department of Bioengineering,

Rice University, TX, February 2006.

¡P ¡§Life in a crowd: macromolecular crowding and confinement effects on protein interactions in living systems¡¨, invited talk, Department of Physics, University of California at Berkeley, CA, February 2006.

¡P ¡§Life in a crowd: macromolecular crowding and confinement effects on protein interactions in living systems¡¨, invited talk, Department of Physics, Virginia Tech, VA, February 2006.

¡P ¡§Life in a crowd: macromolecular crowding and confinement effects on protein interactions in living systems¡¨, invited talk, Department of Physics, Massachusetts Institute of Technology, MA, February 2006.

¡P ¡§Life in a crowd: macromolecular crowding and confinement effects on protein interactions in living systems¡¨, invited talk, Department of Physics, George Washington University, Washington DC, November 2006.

¡P ¡§Life in a crowd: macromolecular crowding and confinement effects on protein interactions in living systems¡¨, invited talk, American Physical Society March Meeting, Denver, CO, March 2007.

¡P ¡§Life in a crowd: macromolecular crowding and confinement effects on protein interactions in living systems¡¨, invited talk, The 51^st annual meeting for the Biophysical Society, Baltimore, MD, March 2007.

¡P ¡§Life in a crowd: macromolecular crowding and confinement effects on protein interactions in living systems¡¨, invited talk, Keck Seminar, Rice University, Houston, TX, March 2007.

¡P ¡§Manipulating Biopolymer Dynamics by Anistropic Nanoconfinement¡¨, invited speaker in Nano Summit 2007: Rising Stars of Texas, Texas A&M, College Station, TX, August 2007.

¡P ¡§Manipulating biopolymer dynamics by anisotropic nanoconfinement¡¨, invited talk, Department of Physics and Engineering, Monterrey Tech, Mexico, October, 2007.

¡P ¡§Life in a crowd: macromolecular crowding and confinement effects on protein interactions in living systems¡¨, invited talk, Mechanical Engineering, University of Houston, Houston, TX, November, 2007.

¡P ¡§Simulating protein folding dynamics in crowded and porous media¡¨, invited speaker, Gordon Research Conference on Protein Folding Dynamics, Ventura, CA, January, 2008.

¡P ¡§Simulating protein folding dynamics in crowded and porous media¡¨, colloquium talk, Physics and Physical Sciences, University of Houston at Clear Lake, Houston, TX, January 2008.

¡P ¡§Simulating protein folding dynamics in crowded and porous media¡¨, colloquium talk, Department of Physics, University of Houston, Houston, TX, February 2008.

¡P ¡§Simulating protein folding dynamics in crowded and porous media¡¨, invited speaker, 16th Texan Folders Meeting, Navasota, TX, March 2008.

¡P ¡§Mesoscopic modeling of biomolecules¡¨, TcSUH bi-weekly seminars, University of Houston, Houston, TX, June 2008.

¡P ¡§Protein dynamics and conformational changes in crowded, cell-like environment¡¨, Colloquium, Department of Chemistry, University of California, Davis, CA, October 2008.

¡P ¡§Protein dynamics and conformational changes in crowded, cell-like environment¡¨, Biophysics seminar, Department of Physics, Rice University, Houston, TX, October 2008.

¡P ¡§HPC for soft and living matter¡¨, Supercomputing 08, Austin, TX, November 2008.

¡P ¡§Protein dynamics and conformational changes in crowded, cell-like environment¡¨, Informal seminar, Center for Extracellular Matrix Biology, Institute of Biosciences and Technology, Houston, TX, January 2009.

¡P ¡§Protein dynamics and conformational changes in crowded, cell-like environment¡¨, Colloquium, Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, March 2009.

¡P ¡§How soft matter becomes living matter? What matters lies in a crowd¡¨ Tutorial Session in Opportunities in Biological Physics, APS March Meeting, Pittsburgh, PA, March 2009.

¡P ¡§Crowded, cell-like environment induces shape changes in aspherical protein¡¨, Invited speaker, Focus Session, APS March Meeting, Pittsburgh, PA, March 2009.

¡P ¡§Life in a Crowd¡¨, Colloquium, Department of Physics, Texas Southern University, Houston, TX, April 2009.

¡P ¡§Modulation of Calmodulin Plasticity by the Effect of Macromolecular Crowding¡¨, TcSUH bi-weekly seminars, University of Houston, Houston, TX, May 2009.

¡P ¡§Crowded, cell-like environment induces shape changes in aspherical protein¡¨, Colloquium, Department of Biology and Biochemistry, University of Houston, Houston, TX, October 2009.