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    22837 Publications
    3073 Total Profiles
    23 Edited Profiles

    Chu, Jhih-Wei

    TitleBiological Faculty Engineer
    SchoolLawrence Berkeley National Lab
    DepartmentPhysical Biosciences
    Address1 Cyclotron Road
    Berkeley CA 94720
    Phone510/642-4398

       Bibliographic 
       Publications
      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can sign in to make corrections and additions, or contact us for help.
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      1. Chung PW, Charmot A, Click T, Lin Y, Bae Y, Chu JW, Katz A. Importance of Internal Porosity for Glucan Adsorption in Mesoporous Carbon Materials. Langmuir. 2015 Jul 7; 31(26):7288-95.
        View in: PubMed
      2. Persson RA, Voulgarakis NK, Chu JW. Dynamic mesoscale model of dipolar fluids via fluctuating hydrodynamics. J Chem Phys. 2014 Nov 7; 141(17):174105.
        View in: PubMed
      3. Haas KR, Yang H, Chu JW. Analysis of trajectory entropy for continuous stochastic processes at equilibrium. J Phys Chem B. 2014 Jul 17; 118(28):8099-107.
        View in: PubMed
      4. Haas KR, Yang H, Chu JW. Trajectory Entropy of Continuous Stochastic Processes at Equilibrium. J Phys Chem Lett. 2014 Mar 20; 5(6):999-1003.
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      5. Tan YW, Hanson JA, Chu JW, Yang H. Confocal single-molecule FRET for protein conformational dynamics. Methods Mol Biol. 2014; 1084:51-62.
        View in: PubMed
      6. Haas KR, Yang H, Chu JW. Fisher information metric for the Langevin equation and least informative models of continuous stochastic dynamics. J Chem Phys. 2013 Sep 28; 139(12):121931.
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      7. Haas KR, Yang H, Chu JW. 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 Dec 12; 117(49):15591-605.
        View in: PubMed
      8. Lin Y, Beckham GT, Himmel ME, Crowley MF, Chu JW. Endoglucanase Peripheral Loops Facilitate Complexation of Glucan Chains on Cellulose via Adaptive Coupling to the Emergent Substrate Structures. J Phys Chem B. 2013 Sep 19; 117(37):10750-8.
        View in: PubMed
      9. Voulgarakis NK, Shang BZ, Chu JW. Linking hydrophobicity and hydrodynamics by the hybrid fluctuating hydrodynamics and molecular dynamics methodologies. Phys Rev E Stat Nonlin Soft Matter Phys. 2013 Aug; 88(2):023305.
        View in: PubMed
      10. Shang BZ, Chang R, Chu JW. Systems-level modeling with molecular resolution elucidates the rate-limiting mechanisms of cellulose decomposition by cellobiohydrolases. J Biol Chem. 2013 Oct 4; 288(40):29081-9.
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      11. Gross AS, Bell AT, Chu JW. Preferential interactions between lithium chloride and glucan chains in N,N-dimethylacetamide drive cellulose dissolution. J Phys Chem B. 2013 Mar 28; 117(12):3280-6.
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      12. Shang BZ, Voulgarakis NK, Chu JW. Fluctuating hydrodynamics for multiscale modeling and simulation: energy and heat transfer in molecular fluids. J Chem Phys. 2012 Jul 28; 137(4):044117.
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      13. Chang R, Gross AS, Chu JW. Degree of polymerization of glucan chains shapes the structure fluctuations and melting thermodynamics of a cellulose microfibril. J Phys Chem B. 2012 Jul 19; 116(28):8074-83.
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      14. Gross AS, Bell AT, Chu JW. Entropy of cellulose dissolution in water and in the ionic liquid 1-butyl-3-methylimidazolim chloride. Phys Chem Chem Phys. 2012 Jun 21; 14(23):8425-30.
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      15. Gross AS, Bell AT, Chu JW. Thermodynamics of cellulose solvation in water and the ionic liquid 1-butyl-3-methylimidazolim chloride. J Phys Chem B. 2011 Nov 24; 115(46):13433-40.
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      16. Lin Y, Silvestre-Ryan J, Himmel ME, Crowley MF, Beckham GT, Chu JW. Protein allostery at the solid-liquid interface: endoglucanase attachment to cellulose affects glucan clenching in the binding cleft. J Am Chem Soc. 2011 Oct 19; 133(41):16617-24.
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      17. Cho HM, Gross AS, Chu JW. Dissecting force interactions in cellulose deconstruction reveals the required solvent versatility for overcoming biomass recalcitrance. J Am Chem Soc. 2011 Sep 7; 133(35):14033-41.
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      18. Shang BZ, Voulgarakis NK, Chu JW. Fluctuating hydrodynamics for multiscale simulation of inhomogeneous fluids: mapping all-atom molecular dynamics to capillary waves. J Chem Phys. 2011 Jul 28; 135(4):044111.
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      19. Silvestre-Ryan J, Lin Y, Chu JW. "Fluctuograms" reveal the intermittent intra-protein communication in subtilisin Carlsberg and correlate mechanical coupling with co-evolution. PLoS Comput Biol. 2011 Mar; 7(3):e1002023.
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      20. Brokaw JB, Chu JW. On the roles of substrate binding and hinge unfolding in conformational changes of adenylate kinase. Biophys J. 2010 Nov 17; 99(10):3420-9.
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      21. Gross AS, Chu JW. On the molecular origins of biomass recalcitrance: the interaction network and solvation structures of cellulose microfibrils. J Phys Chem B. 2010 Oct 28; 114(42):13333-41.
        View in: PubMed
      22. Voulgarakis NK, Satish S, Chu JW. Modeling the nanoscale viscoelasticity of fluids by bridging non-Markovian fluctuating hydrodynamics and molecular dynamics simulations. J Chem Phys. 2009 Dec 21; 131(23):234115.
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      23. Haas K, Chu JW. Decomposition of energy and free energy changes by following the flow of work along reaction path. J Chem Phys. 2009 Oct 14; 131(14):144105.
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      24. Cho HM, Chu JW. Inversion of radial distribution functions to pair forces by solving the Yvon-Born-Green equation iteratively. J Chem Phys. 2009 Oct 7; 131(13):134107.
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      25. Brokaw JB, Haas KR, Chu JW. Reaction Path Optimization with Holonomic Constraints and Kinetic Energy Potentials. J Chem Theory Comput. 2009 Aug 11; 5(8):2050-61.
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      26. Voulgarakis NK, Chu JW. Bridging fluctuating hydrodynamics and molecular dynamics simulations of fluids. J Chem Phys. 2009 Apr 7; 130(13):134111.
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      27. Noid WG, Chu JW, Ayton GS, Krishna V, Izvekov S, Voth GA, Das A, Andersen HC. The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models. J Chem Phys. 2008 Jun 28; 128(24):244114.
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      28. Noid WG, Liu P, Wang Y, Chu JW, Ayton GS, Izvekov S, Andersen HC, Voth GA. The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models. J Chem Phys. 2008 Jun 28; 128(24):244115.
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      29. Gebremichael Y, Chu JW, Voth GA. Intrinsic bending and structural rearrangement of tubulin dimer: molecular dynamics simulations and coarse-grained analysis. Biophys J. 2008 Sep; 95(5):2487-99.
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      30. Hanson JA, Duderstadt K, Watkins LP, Bhattacharyya S, Brokaw J, Chu JW, Yang H. Illuminating the mechanistic roles of enzyme conformational dynamics. Proc Natl Acad Sci U S A. 2007 Nov 13; 104(46):18055-60.
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      31. Chu JW, Voth GA. Coarse-grained free energy functions for studying protein conformational changes: a double-well network model. Biophys J. 2007 Dec 1; 93(11):3860-71.
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      32. Noid WG, Chu JW, Ayton GS, Voth GA. Multiscale coarse-graining and structural correlations: connections to liquid-state theory. J Phys Chem B. 2007 Apr 26; 111(16):4116-27.
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      33. Mirijanian DT, Chu JW, Ayton GS, Voth GA. Atomistic and coarse-grained analysis of double spectrin repeat units: the molecular origins of flexibility. J Mol Biol. 2007 Jan 12; 365(2):523-34.
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      34. Chu JW, Voth GA. Coarse-grained modeling of the actin filament derived from atomistic-scale simulations. Biophys J. 2006 Mar 1; 90(5):1572-82.
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      35. Chu JW, Voth GA. Allostery of actin filaments: molecular dynamics simulations and coarse-grained analysis. Proc Natl Acad Sci U S A. 2005 Sep 13; 102(37):13111-6.
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      36. Yin J, Chu JW, Ricci MS, Brems DN, Wang DI, Trout BL. Effects of excipients on the hydrogen peroxide-induced oxidation of methionine residues in granulocyte colony-stimulating factor. Pharm Res. 2005 Jan; 22(1):141-7.
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      37. Chu JW, Brooks BR, Trout BL. Oxidation of methionine residues in aqueous solutions: free methionine and methionine in granulocyte colony-stimulating factor. J Am Chem Soc. 2004 Dec 22; 126(50):16601-7.
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      38. Yin J, Chu JW, Ricci MS, Brems DN, Wang DI, Trout BL. 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 Dec; 21(12):2377-83.
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      39. Chu JW, Yin J, Brooks BR, Wang DI, Ricci MS, Brems DN, Trout BL. A comprehensive picture of non-site specific oxidation of methionine residues by peroxides in protein pharmaceuticals. J Pharm Sci. 2004 Dec; 93(12):3096-102.
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      40. Chu JW, Yin J, Wang DI, Trout BL. A structural and mechanistic study of the oxidation of methionine residues in hPTH(1-34) via experiments and simulations. Biochemistry. 2004 Nov 9; 43(44):14139-48.
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      41. Chu JW, Yin J, Wang DI, Trout BL. Molecular dynamics simulations and oxidation rates of methionine residues of granulocyte colony-stimulating factor at different pH values. Biochemistry. 2004 Feb 3; 43(4):1019-29.
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      42. Chu JW, Trout BL. On the mechanisms of oxidation of organic sulfides by H2O2 in aqueous solutions. J Am Chem Soc. 2004 Jan 28; 126(3):900-8.
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