Publication list 1. Chu, J.-W., Izvekov, S., Noid, W.G., Ayton, G.S., and Voth, G.A., The multiscale coarse-grain approach based on the force matching method: Theoretical derivation, numerical implementation, and examples of application. In Preparation, 2007. 2. Chu, J.-W., Izvekov, S., and Voth, G.A., The multiscale challenge for biomolecular systems: Coarse-grained modeling Mol. Simulat., 2006. 32(3-4): p. 211-218. 3. Chu, J.-W., Ayton, G.S., and Voth, G.A., Emerging methods for multiscale simulation of biomolecular systems. Mol. Phys. , 2006. In Press. 4. Noid, W.G., Chu, J.-W., Ayton, G.S., and Voth, G.A., Multiscale coarse-graining and structural correlations: Connections to liquid state theory. J. Phys. Chem. B, in press, 2007. 5. Mirijanian, D.T., Chu, J.-W., Ayton, G.S., and Voth, G.A., Atomistic and coarse-grained analysis of double spectrin repeat units: The molecular origins of flexibility J. Mol. Biol., 2007. 365(2): p. 12. 6. Chu, J.-W. and Voth, G.A., Coarse-grained modeling of the actin filament derived from atomistic-scale simulations. Biophys. J., 2006. 90(2): p. 1572-1582. 7. Chu, J.-W. and Voth, G.A., Allostery of actin filaments: Molecular dynamics simulations and coarse-grained analysis. Proc. Natl. Acad. Sci. U. S. A., 2005. 102(37): p. 13111-13116. 8. Yin, J., Chu, J.-W., Ricci, M.S., Brems, D.N., Wang, D.I.C., and Trout, B.L., Effects of excipients on hydrogen peroxide induced oxidation of methionine residues in granulocyte colony-stimulating factor. Pharm. Res., 2005. 22: p. 141-147. 9. Yin, J., Chu, J.-W., Ricci, M.S., Brems, D.N., Wang, D.I.C., and Trout, B.L., Effects of antioxidants on the non-site-specific oxidation of methionine residues in granulocyte colony-stimulating factor (g-csf) and human parathyroid hormone (hpth) fragment 13-34. Pharm. Res., 2004. 21(2377-2383). 10. Chu, J.-W., Yin, J., Wang, D.I.C., and Trout, B.L., A atructural and mechanistic study of the oxidation of methionine residues in hpth(1-34) via experiments and simulations. Biochemistry, 2004. 43(44): p. 14139-14148. 11. Chu, J.-W., Yin, J., Wang, D.I.C., and Trout, B.L., Molecular dynamics simulations and oxidation rates of methionine residues of granulocyte colony-stimulating factor at different ph values. Biochemistry, 2004. 43(4): p. 1019-1029. 12. Chu, J.-W., Yin, J., Brooks, B.R., Wang, D.I.C., Ricci, M.S., Brems, D.N., and Trout, B.L., A comprehensive picture of non-site specific oxidation of methionine residues by peroxides in protein pharmaceuticals. J. Pharm. Sci., 2004. 93(12): p. 3096-3102. 13. Chu, J.-W. and Trout, B.L., On the mechanisms of oxidation of organic sulfides by h2o2 in aqueous solutions. J. Am. Chem. Soc., 2004. 126(3): p. 900-908. 14. Chu, J.-W., Brooks, B.R., and Trout, B.L., Oxidation of methionine residues in aqueous solutions: Free methionine and methionine in granulocyte colony-stimulating factor. J. Am. Chem. Soc., 2004. 126(50): p. 16601-16607. 15. Chu, J.-W., Trout, B.L., and Brooks, B.R., A super-linear minimization scheme for the nudged elastic band method. J. Chem. Phys., 2003. 119(24): p. 12708-12717. 16. Chu, J.-W., Lin, W.-H., Lee, E., and Hsu, J.-P., Electrophoresis of a sphere in a spherical cavity at arbitrary electrical potentials. Langmuir, 2001. 17(20): p. 6289-6297. 17. Lee, E., Chu, J.-W., and Hsu, J.-P., Electrophoretic mobility of a concentrated suspension of spherical particles. J. Colloid Interface Sci., 1999. 209(1): p. 240-246. 18. Lee, E., Chu, J.-W., and Hsu, J.-P., Sedimentation potential of a concentrated spherical colloidal suspension. J. Chem. Phys., 1999. 110(23): p. 11643-11651. 19. Lee, E., Chu, J.-W., and Hsu, J.-P., Electrophoretic mobility of a sphere in a spherical cavity. J. Colloid Interface Sci., 1998. 205(1): p. 65-76. 20. Lee, E., Chu, J.-W., and Hsu, J.-P., Electrophoretic mobility of a spherical particle in a spherical cavity. J. Colloid Interface Sci., 1997. 196(2): p. 316-320. INVITED TALKS 1. C4 workshop 2006, ETH Zürich, Switzerland, January 4, 2007 2. Computational Biology Symposium, Rice University, Houston, TX, December 10, 2006 3. The Ohio State University, Department of Chemical Engineering, Columbus, OH, January 19, 2006 4. The Pennsylvania State University, Department of Chemical Engineering, University Park, PA, January 26, 2006 5. Georgia Institute of Technology, Department of Chemical and Biomolecular Engineering, Atlanta, GA, February 1, 2006 6. University of Pennsylvania, Department of Chemical and Biomolecular Engineering, Philadelphia, PA, February, 8, 2006 7. University of Illinois at Urbana Champaign, Department of Chemical and Biomolecular Engineering, Philadelphia, PA, February, 14, 2006 8. University of Massachusetts-Amherst, Department of Chemical Engineering, Amherst, MA, February, 21, 2006 9. University of Florida, Department of Chemical Engineering, Gainesville, FL, February, 22, 2006 10. Stanford University, Department of Chemical Engineering, Stanford, CA, March, 7, 2006 11. University of Houston, Department of Chemical Engineering, Houston, TX, March, 9, 2006 12. University of California, Irvine, Department of Chemical and Material Science, Irvine, CA, March, 16, 2006 13. University of California, Berkeley, Department of Chemical Engineering, Philadelphia, CA, March, 23, 2006 14. Stanford University, Department of Bioengineering, Stanford, CA, April, 17, 2006 PRESENTATIONS 1. Chu J-W and Voth CA: “Exploring the Allostery of Actin Filaments via Molecular Dynamics Simulations and Coarse-Grained Analysis” American Institute of Chemical Engineers 2005 annual meeting, Cincinetti, OH, USA 2. Chu J-W and Voth CA: “Coarse-Graining the Actin Filament from Atomistic Simulations” American Institute of Chemical Engineers 2005 annual meeting, Cincinetti, OH, USA 3. Chu J-W, Yin J, Wang DIC, and Trout BL: “On the Oxidation of Methionine Residues during the Storage of Protein Pharmaceuticals in an Aqueous Solution”, American Chemical Society, the 227th Annual Meeting, 2004, Anaheim, USA. 4. Chu J-W, Brooks BR, and Trout BL: “Combined OM/MM Studies and Free Energy Simulations on the Oxidation of Methionine Residues in Granulocyte Colony Stimulating Factor”, American Chemical Society, the 227th Annual Meeting, 2004, Anaheim, USA. 5. Chu J-W, Brooks BR, and Trout BL: “Computer Simulations of Transition Processes in Complex Systems”, American Institute of Chemical Engineers 2003 annual meeting, San Francisco, USA. 6. Chu J-W, Brooks BR, and Trout BL: “A Super-Linear Minimization Scheme for the Nudged Elastic Band Method”, the Emerging technology in Computational Chemistry Symposium, American Chemical Society, the 226th Annual Meeting, 2003, New York, NY, USA. 7. Chu J-W, Wang DIC, and Trout BL: “Theoretical Studies on the Oxidation Instability of Therapeutic Proteins”, 2003 Colorado Protein Stability Conference, July 2003, Breckenridge, CO, USA. 8. Chu J-W and Trout BL: “The Mechanisms and Kinetics of Oxygen Binding to Methionine Groups in Proteins via ab initio Calculations” American Chemical Society, the 223rd Annual Meeting, April 2002, Orlando, FL, USA.