PUBLICATIONS

49. Shang, B.Z., Chang, R., and Chu, J.-W., Systems-level modeling with molecular resolution elucidates the rate-limiting mechanisms of cellulose decomposition by cellobiohydrolases. J. Biol. Chem. (2013), DOI: 10.1074/jbc.M113.497412.
48. Haas, R.K., Yang, H., and Chu, J.-W., Expectation-Maximization of the Potential of Mean Force and Diffusion Coefficient in Langevin Dynamics from Single-Molecule FRET Data Photon by Photon. J. Phys. Chem. B (2013) DOI: 10.1021/jp405983d.
47. Haas, R.K., Yang, H., and Chu, J.-W., Fisher Information Metric for the Langevin Equation and Least Informative Models of Continuous Stochastic Dynamics. J. Chem. Phys. (2013), 139, 121931.
46. Lin, Y., Beckham, G.T., Himmel, M.E., F., C.M.L., and Chu, J.-W., Endoglucanase Peripheral Loops Facilitate Complexation of Glucan Chains on Cellulose via Adaptive Coupling to the Emergent Substrate Structures. J. Phys. Chem. B (2013), 117, 10750–10758.
45. Voulgarakis, N.K., Shang, B.Z., and Chu, J.-W., Linking hydrophobicity and hydrodynamics by the hybrid fluctuating hydrodynamics and molecular dynamics methodologies. Phys. Rev. E (2013) 88, 023305.
44. Chung, T. Y.; Ning, N.; Chu, J.-W.; Graves, D. B.; Bartis, E.; Seog, J.; Oehrlein, G. S., Plasma Deactivation of Endotoxic Biomolecules: Vacuum Ultraviolet Photon and Radical Beam Effects on Lipid A. Plasma Process. Polym. (2013), 10, 167-180.
43. Gross, A. S.; Bell, A. T.; Chu, J.-W., Preferential Interactions between Lithium Chloride and Glucan Chains in N,N-Dimethylacetamide Drive Cellulose Dissolution. J. Phys. Chem. B (2013), 177, 3280-3286.

42. Shang, B. Z.; Voulgarakis, N. K.; Chu, J.-W., Fluctuating Hydrodynamics for Multiscale Simulation: Energy and Heat Transfer.J. Chem. Phys. (2012), 137, 044117.
41. Chang, R.; Gross, S. A.; Chu, J.-W., Degree of Polymerization of Glucan Chains Shapes the Melting and Structure Fluctuations of a Cellulose Microfibril. J. Phem. Chem. B (2012), 116, 8074-8083.
40. Gross, S. A.; Bell, A. T.; Chu, J.-W., Entropy of Cellulose Dissolution in Water and in the Ionic Liquid 1-Butyl-3-Methylimidazolim Chloride. Phys. Chem. Chem. Phys. (2012), 14, 8425-8430.
39. Hanson, J. A.; Brokaw, J. B.; Hayden, C. C.; Chu, J.-W.; Yang, H., Structural distributions from single-molecule measurements as a tool for molecular mechanics. Chem. Phys. (2012), 396, 61–71.

38. Lin, Y.; Silvestre-Ryan, J.; Himmel, M. E.; Crowley, M. F.; Beckham, G. T.; Chu, J.-W., Protein Allostery at the Solid-Liquid Interface: Endoglucanase Attachment to Cellulose Affects Glucan Clenching in the Binding Cleft. J. Am. Chem. Soc. (2011), 133, 16617-16624.
37. Cho, H. M.; Gross, A. S.; Chu, J.-W., Dissecting Force Interactions in Cellulose Deconstruction Reveals the Required Solvent Versatility for Overcoming Biomass Recalcitrance. J. Am. Chem. Soc. (2011), 133, 14033-14041.
36. Gross, S. A.; Bell, A. T.; Chu, J.-W., The Thermodynamics of Cellulose Solvation in Water and the Ionic Liquid 1-Butyl-3-Methylimidazolim Chloride. J. Phys. Chem. B (2011), 155, 13433-13440.
35. Shang, B. Z.; Voulgarakis, N. K.; Chu, J.-W., Fluctuating Hydrodynamics for Multiscale Simulation of Inhomogeneous Fluids – Mapping All­Atom Molecular Dynamics to Capillary Waves. J. Chem. Phys. (2011), 135, 044111.
34. Silvestre-Ryan, J.; Lin, Y.; Chu, J.-W., “Fluctuograms” Reveal the Intermittent Intra-Protein Communication in Subtilisin Carlsberg and Correlate Mechanical Coupling with Co-Evolution. Plos Comput. Biol. (2011), 7, e1002023.

33. Gross, A. S.; Chu, J.-W., On the Molecular Origins of Biomass Recalcitrance: The Interaction Network and Solvation Structures of Cellulose Microfibrils. J. Phys. Chem. B (2010), 114, 13333-13341.
32. Brokaw, J. B.; Chu, J.-W., On the Roles of Substrate Binding and Hinge Unfolding in Conformational Changes of Adenylate Kinase. Biophys. J. (2010), 99, 3420-3429.
31. Voulgarakis, N. K.; Satish, S.; Chu, J.-W., Modelling the viscoelasticity and thermal fluctuations of fluids at the nanoscale. Mol. Simulat. (2010), 36, 552-559.

30. Voulgarakis, N. K.; Chu, J.-W., Modeling the Nanoscale Viscoelasticity of Fluids by Bridging non-Markovian Fluctuating Hydrodynamics and Molecular Dynamics Simulations. J. Chem. Phys. (2009), 131, 234115.
29. Voulgarakis, N. K.; Chu, J.-W., Bridging Fluctuating Hydrodynamics and Molecular Dynamics Simulations of Fluids. J. Chem. Phys. (2009), 130, 134111.
28. Cho, H. M.; Chu, J.-W., Inversion of Radial Distribution Functions to Pair Forces by Solving the Yvon-Born-Green Equation Iteratively. J. Chem. Phys. (2009), 131, 134107.
27. Haas, R. K.; Chu, J.-W., Decomposition of energy and free energy changes by following the flow of work along reaction path.J. Chem. Phys. (2009), 131, 144105.
26. Brokaw, J. B.; Haas, K. R.; Chu, J.-W., Reaction Path Optimization with Holonomic Constraints and Kinetic-Energy Potentials.J. Chem. Theory Comput. (2009), 5, 2050–2061.
25.  Cho, H. and Chu, J.-W. On the development of state-specific coarse-grained potentials of water, in Modeling solvent environments: Applications to simulations of biomolecules, M. Feig, Editor. 2009, WILEY-VCH Verlag GmbH & Co: Weinheim, Germany.

24. Noid, W. G.; Liu, P.; Wang, Y.; Chu, J.-W.; Ayton, G. S.; Izvekov, S.; Andersen, H. C.; Voth, G. A., The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models. J. Chem. Phys. (2008), 128, 244115.
23. Noid, W. G.; Chu, J.-W.; Ayton, G. S.; Krishna, V.; Izvekov, S.; Voth, G. A.; Das, A.; Andersen, H. C., The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models. J. Chem. Phys. (2008), 128, 244114.
22. Gebremichael, Y.; Chu, J.-W.; Voth, G. A., Intrinsic bending and structural rearrangement of tubulin dimer: Molecular dynamics simulations and coarse-grained analysis. Biophys. J. (2008), 95, 2487-2499.

21. Hanson, J. A.; Duclerstacit, K.; Watkins, L. P.; Bhattacharyya, S.; Brokaw, J.; Chu, J.-W.; Yang, H., Illuminating the mechanistic roles of enzyme conformational dynamics. Proc. Natl. Acad. Sci. USA (2007), 104, 18055-18060.
20. Noid, W. G.; Chu, J.-W.; Ayton, G. S.; Voth, G. A., Multiscale coarse-graining and structural correlations: Connections to liquid-state theory. In J. Phys. Chem. B, 2007; Vol. 111, pp 4116-4127.
19. Mirijanian, D. T.; Chu, J.-W.; Ayton, G. S.; Voth, G. A., Atomistic and coarse-grained analysis of double spectrin repeat units: The molecular origins of flexibility. J. Mol. Biol. (2007), 365, 523-534.
18. Chu, J.-W.; Voth, G. A., Coarse-grained free energy functions for studying protein conformational changes: A double-well network model. Biophys. J. (2007), 93, 3860-3871.
17. Chu, J.-W.; Ayton, G. S.; Izvekov, S.; Voth, G. A., Emerging methods for multiscale simulation of biomolecular systems. Mol. Phys. (2007), 105, 167-175.

16. Chu, J.-W.; Voth, G. A., Coarse-grained modeling of the actin filament derived from atomistic-scale simulations. Biophys. J.(2006), 90, 1572-1582.
15. Chu, J.; Izveko, S.; Voth, G., The multiscale challenge for biomolecular systems: coarse-grained modeling. Mol. Simulat.(2006), 32, 211-218.

14. Chu, J.-W.; Voth, G. A., Allostery of actin filaments: Molecular dynamics simulations and coarse-grained analysis. Proc. Natl. Acad. Sci. USA. (2005), 102, 13111-13116.
13. Yin, J.; Chu, J.-W.; Ricci, M.; Brems, D.; Wang, D.; Trout, B., Effects of excipients on the hydrogen peroxide-induced oxidation of methionine residues in granulocyte colony-stimulating factor. Pharm. Res. (2005), 22, 141-147.

12. Yin, J.; Chu, J.-W.; Ricci, M.; Brems, D.; Wang, D.; Trout, B., Effects of antioxidants on the hydrogen peroxide-mediated oxidation of methionine residues in granulocyte colony-stimulating factor and human parathyroid hormone fragment 13-34. Pharm. Res. (2004), 21, 2377-2383.
11. Chu, J.-W.; Yin, J.; Wang, D. I. C.; Trout, B. L., A structural and mechanistic study of the oxidation of methionine residues in hPTH(1-34) via experiments and simulations. Biochemistry-US (2004), 43, 14139-14148.
10. Chu, J.-W.; Yin, J.; Wang, D. I. C.; Trout, B. L., Molecular dynamics simulations and oxidation rates of methionine residues of granulocyte colony-stimulating factor at different pH values. Biochemistry-US (2004), 43, 1019-1029.
9.   Chu, J.-W.; Yin, J.; Brooks, B. R.; Wang, D. I. C.; Ricci, M. S.; Brems, D. N.; Trout, B. L., A comprehensive picture of non-site specific oxidation of methionine residues by peroxides in protein pharmaceuticals. J. Pharm. Sci.-US. (2004), 93, 3096-3102.
8.   Chu, J.-W.; Trout, B. L., On the mechanisms of oxidation of organic sulfides by hydrogen peroxide in aqueous solutions. J. Am. Chem. Soc. (2004), 126, 900-908.
7.   Chu, J.-W.; Brooks, B. R.; 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, 16601-16607.

6.   Chu, J.-W.; Trout, B.; Brooks, B., A super-linear minimization scheme for the nudged elastic band method. J. Chem. Phys.(2003), 119, 12708-12717.
5.   Chu, J.-W.; Lin, W. H.; Lee, E.; Hsu, J. P., Electrophoresis of a sphere in a spherical cavity at arbitrary electrical potentials.Langmuir (2001), 17, 6289-6297.
4.   Lee, E.; Chu, J.-W.; Hsu, J. P., Electrophoretic mobility of a concentrated suspension of spherical particles. J. Colloid Interface Sci. (1999), 209, 240-246.
3.   Lee, E.; Chu, J.-W.; Hsu, J., Sedimentation potential of a concentrated spherical colloidal suspension. J. Chem. Phys. (1999),110, 11643-11651.
2.   Lee, E.; Chu, J.-W.; Hsu, J. P., Electrophoretic mobility of a sphere in a spherical cavity. J. Colloid Interf. Sci. (1998), 205, 65-76.
1.   Lee, E.; Chu, J.-W.; Hsu, J., Electrophoretic mobility of a spherical particle in a spherical cavity. J. Colloid Interf. Sci. (1997),196, 316-320.