Hue Sun CHAN - Scientific Publications

    Refereed journal articles, reviews, and book chapters (1986 to present)
    Invited talks, seminars and abstracts are listed separately (Please click here for Presentations)
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    A partial list of the following publications is available at PubMed.
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    1. Z. Shen, B. Jia, Y. Xu, J. Wessén, T. Pal, H.S. Chan, S. Du and M. Zhang (2023) Biological condensates form percolated networks with molecular motion properties distinctly different from dilute solutions. eLife, in press (accepted for publication) [Accepted manuscript: elifesciences.org/articles/81907] [Preprint version: bioRχiv:2022.07.20.500769].

    1. J. Wessén, S. Das, T. Pal and H.S. Chan (2022) Analytical Formulation and Field-Theoretic Simulation of Sequence-Specific Phase Separation of Proteinlike Heteropolymers with Short- and Long-Spatial-Range Interactions. Journal of Physical Chemistry B 126, 9222-9245 [doi:10.1021/acs.jpcb.2c06181] [Preprint version: q-bioBM-arXiv:2209.04016].

    1. J. Wessén, T. Pal and H.S. Chan (2022) Field Theory Description of Ion Association in Phase Separation of Polyampholytes. Journal of Chemical Physics 156, 194903 [doi:10.1063/5.0088326] [pdf file] [Preprint version: cond-mat.soft-arXiv:2201.11834].

    1. H. Cinar, R. Oliva, H. Wu, M. Zhang, H.S. Chan and R. Winter (2022) Effects of Cosolvents and Crowding Agents on the Stability and Phase Transition Kinetics of the SynGAP/PSD-95 Condensate Model of Postsynaptic Densities. Journal of Physical Chemistry B 126, 1734-1741 [doi:10.1021/acs.jpcb.2c00794].

    1. Y.-H. Lin, J. Wessén, T. Pal, S. Das and H.S. Chan (2022) Numerical Techniques for Applications of Analytical Theories to Sequence-Dependent Phase Separations of Intrinsically Disordered Proteins. In: Phase-Separated Biomolecular Condensates, Methods and Protocols; edited by H.-X. Zhou, J.-H. Spille and P.R. Banerjee, Methods in Molecular Biology (Springer-Nature), Volume 2563, Chapter 3, pp.51-94 [doi:10.1007/978-1-0716-2663-4_3] [Preprint version: q-bioBM-arXiv:2201.01920].

    1. Y.-H. Lin, H. Wu, B. Jia, M. Zhang and H.S. Chan (2022) Assembly of Model Postsynaptic Densities Involves Interactions Auxiliary to Stoichiometric Binding. Biophysical Journal 121, 157-171 [doi:10.1016/j.bpj.2021.10.008] [Preprint version: q-bio.BM-arXiv:2110.02937].

    1. J. Song, J. Li and H.S. Chan (2021) Small-Angle X-Ray Scattering Signatures of Conformational Heterogeneity and Homogeneity of Disordered Protein Ensembles. Journal of Physical Chemistry B 125, 6451-6478 [doi:10.1021/acs.jpcb.1c02435] [Preprint version: q-bio.BM-arXiv:2105.13427].

    1. J. Wessén, T. Pal, S. Das, Y.-H. Lin and H.S. Chan (2021) A Simple Explicit-Solvent Model of Polyampholyte Phase Behaviors and its Ramifications for Dielectric Effects in Biomolecular Condensates. Journal of Physical Chemistry B 125, 4337-4358 [doi:10.1021/acs.jpcb.1c00954] (cover image). [Preprint version: q-bio.BM-arXiv:2102.03687].

    1. T. Pal, J. Wessén, S. Das and H.S. Chan (2021) Subcompartmentalization of Polyampholyte Species in Organelle-Like Condensates is Promoted by Charge-Pattern Mismatch and Strong Excluded-Volume Interaction. Physical Review E 103, 042406 [doi:10.1103/PhysRevE.103.042406] [Preprint version: q-bio.BM-arXiv:2006.12776] [Download combined pdf file for Main Text & Supplemental Material].

    1. S. Das, Y.-H. Lin, R.M. Vernon, J.D. Forman-Kay and H.S. Chan (2020) Comparative Roles of Charge, π, and Hydrophobic Interactions in Sequence-Dependent Phase Separation of Intrinsically Disordered Proteins. Proceedings of the National Academy of Sciences, USA 117, 28795-28805 [doi:10.1073/pnas.2008122117] [Preprint version: q-bio.BM-arXiv:2005.06712].

    1. H. Cinar, R. Oliva, Y.-H. Lin, X. Chen, M. Zhang, H.S. Chan and R. Winter (2020). Pressure Sensitivity of SynGAP/PSD-95 Condensates as a Model for Postsynaptic Densities and its Biophysical and Neurological Ramifications. Chemistry, A European Journal (Chem. Eur. J.) 26, 11024-11031 [doi:10.1002/chem.201905269] (pdf with cover image).

    1. A.N. Amin, Y.-H. Lin, S. Das and H.S. Chan (2020). Analytical Theory for Sequence-Specific Binary Fuzzy Complexes of Charged Intrinsically Disordered Proteins. Journal of Physical Chemistry B 124, 6709-6720. [doi:10.1021/acs.jpcb.0c04575] (cover image). [Preprint version: q-bio-arXiv:1910.11194].

    1. Y.-H. Lin, J.P. Brady, H.S. Chan and K. Ghosh (2020). A Unified Analytical Theory of Heteropolymers for Sequence-Specific Phase Behaviors of Polyelectrolytes and Polyampholytes. Journal of Chemical Physics 152, 045102. [doi:10.1063/1.5139661] [Preprint version: q-bio-arXiv:1908.09726].

    1. H. Cinar, Z. Fetahaj, S. Cinar, R.M. Vernon, H.S. Chan and R. Winter (2019). Temperature, Hydrostatic Pressure, and Osmolyte Effects on Liquid-Liquid Phase Separation in Protein Condensates: Physical Chemistry and Biological Implications. Chemistry, A European Journal (Chem. Eur. J.) 25, 13049-13069 [doi:10.1002/chem.201902210].

    1. S. Cinar, H. Cinar, H.S. Chan and R. Winter (2019). Pressure-Sensitive and Osmolyte-Modulated Liquid-Liquid Phase Separation of Eye-Lens γ-Crystallins. Journal of the American Chemical Society 141, 7347-7354 [doi:10.1021/jacs.8b13636].

    1. S. Das, A.N. Amin, Y.-H. Lin and H.S. Chan (2018). Coarse-Grained Residue-Based Models of Disordered Protein Condensates: Utility and Limitations of Simple Charge Pattern Parameters. Physical Chemistry Chemical Physics 20, 28558-28574 doi:10.1039/C8CP05095C; [arXiv versions: q-bio-arXiv:1808.10023].

    1. H. Cinar, S. Cinar, H.S. Chan and R. Winter (2018). Pressure-Induced Dissolution and Reentrant Formation of Condensed, Liquid-Liquid Phase-Separated Elastomeric α-Elastin. Chemistry, A European Journal (Chem. Eur. J.) 24, 8286-8291; doi:10.1002/chem.201801643 (cover image).

    1. Y.-H. Lin, J.D. Forman-Kay and H.S. Chan (2018). Theories for Sequence-Dependent Phase Behaviors of Biomolecular Condensates. Biochemistry 57, 2499-2508; doi:10.1021/acs.biochem.8b00058.

    1. S. Das, A. Eisen, Y.-H. Lin and H.S. Chan (2018). A Lattice Model of Charge-Pattern-Dependent Polyampholyte Phase Separation. Journal of Physical Chemistry B 122, 5418-5431; doi:10.1021/acs.jpcb.7b11723. Correction for a typographical error: 122, 8111 (2018); doi:10.1021/acs.jpcb.8b07367.

    1. L. Huynh, C. Neale, R. Pomès and H.S. Chan (2017). Molecular Recognition and Packing Frustration in a Helical Protein. PLoS (Public Library of Science) Computational Biology 13(12):e1005909 [Download combined pdf file for article, supporting text, and supporting figures] [Journal webpage for the html version of the article].

    1. Y.-H. Lin, J.P. Brady, J.D. Forman-Kay and H.S. Chan (2017). Charge Pattern Matching as a "Fuzzy" Mode of Molecular Recognition for the Functional Phase Separations of Intrinsically Disordered Proteins. New Journal of Physics 19, 115003 [Download pdf file]. (This paper is an article in the journal's Focus on Phase Transitions in Cells: From Metastable Droplets to Cytoplasmic Assemblies Special Issue). [record of arXiv preprints: q-bio-arXiv:1707.08990].

    1. J. Song, G.-N. Gomes, T. Shi, C.C. Gradinaru and H.S. Chan (2017). Conformational Heterogeneity and FRET Data Interpretation for Dimensions of Unfolded Proteins. Biophysical Journal 113, 1012-1024 [Download combined pdf file for Main Text & Supplemental Information].

    1. J.P. Brady, P.J. Farber, A. Sekhar, Y.-H. Lin, R. Huang, A. Bah, T.J. Nott, H.S. Chan, A.J. Baldwin, J.D. Forman-Kay and L.E. Kay (2017). Structural and Hydrodynamic Properties of An Intrinsically Disordered Region of A Germ-Cell Specific Protein on Phase Separation. Proceedings of the National Academy of Sciences, USA 114, E8194-E8203 [Download combined pdf file for Main Text & Supporting Information].

    1. J. Hu, T. Chen, M. Wang, H.S. Chan and Z. Zhang (2017). A Critical Comparison of Coarse-Grained Structure-Based Approaches and Atomic Models of Protein Folding. Physical Chemistry Chemical Physics 19, 13629-13639 [pdf file]. Correction for typographical errors: 19, 18102 (2017) [pdf for Correction].

    1. Y.-H. Lin and H.S. Chan (2017). Phase Separation and Single-Chain Compactness of Charged Disordered Proteins are Strongly Correlated. Biophysical Journal (Biophysical Letter) 112, 2043-2046 [pdf file].

    1. V. Csizmok, S. Orlicky, J. Cheng, J. Song, A. Bah, N. Delgoshaie, H. Lin, T. Mittag, F. Sicheri, H.S. Chan, M. Tyers and J.D. Forman-Kay (2017). An Allosteric Conduit Facilitates Dynamic Multisite Substrate Recognition by the SCFCdc4 Ubiquitin Ligase. Nature Communications 8, 13943; doi: 10.1038/ncomms13943 [Download combined pdf file for Main Text and Supplementary Information], [Journal webpage for the html version of the article].

    1. Y.-H. Lin, J. Song, J.D. Forman-Kay and H.S. Chan (2017). Random-Phase-Approximation Theory for Sequence-Dependent, Biologically Functional Liquid-Liquid Phase Separation of Intrinsically Disordered Proteins. Journal of Molecular Liquids 228, 176-193 [published online September 26, 2016: doi:10.1016/j.molliq.2016.09.090] [Download pdf file]; Corrigendum for typographical errors: 273, 676 (2019) [pdf file for Corrigendum].

    1. H. Krobath, T. Chen and H.S. Chan (2016). Volumetric Physics of Polypeptide Coil-Helix Transitions. Biochemistry 55, 6269-6281 (doi:10.1021/acs.biochem.6b00802) [Download combined pdf file for Main Text & Supporting Information].

    1. Y.-H. Lin, J.D. Forman-Kay and H.S. Chan (2016). Sequence-Specific Polyampholyte Phase Separation in Membraneless Organelles. Physical Review Letters 117, Art. No. 178101. [Download pdf file].

    1. H.S. Chan and Z. Liu (2016). Thermodynamics and Kinetics of TopoII Action: A Consensus on T-Segment Curvature Selection? Comment on "Disentangling DNA Molecules" by Alexander Vologodskii. Physics of Life Reviews 18, 135-138. [Download pdf file].

    1. T. Sikosek, H. Krobath and H.S. Chan (2016). Theoretical Insights into the Biophysics of Protein Bi-Stability and Evolutionary Switches. PLoS (Public Library of Science) Computational Biology 12(6):e1004960. [Download pdf file for article] [Download combined pdf file for article, supporting text, and supporting figures] [Journal webpage for the html version of the article] [PLoS Comput Biol homepage image on June 2, 2016].

    1. A. Mazouchi, Z. Zhang, A. Bahram, G.-N. Gomes, H. Lin, J. Song, H.S. Chan, J.D. Forman-Kay and C.C. Gradinaru (2016). Conformations of a Metastable SH3 Domain Characterized by smFRET and an Excluded-Volume Polymer Model. Biophysical Journal 110, 1510-1522 [Download combined pdf file for Main Text & Supplemental Information].

    1. J. Song, G.-N. Gomes, C.C. Gradinaru and H.S. Chan (2015). An Adequate Account of Excluded Volume is Necessary to Infer Compactness and Asphericity of Disordered Proteins by Förster Resonance Energy Transfer. Journal of Physical Chemistry B 119, 15191-15202 (doi:10.1021/acs.jpcb.5b09133) [Download combined pdf file for Main Text & Supporting Information].

    1. T. Chen and H.S. Chan (2015). Native Contact Density and Nonnative Hydrophobic Effects in the Folding of Bacterial Immunity Proteins. PLoS (Public Library of Science) Computational Biology 11(5): e1004260. [Download pdf file for article and high-resolution main-text and supporting figures] [Journal webpage for the html version of the article].

    1. Z. Liu and H.S. Chan (2015). Consistent Rationalization of Type-2 Topoisomerases' Unknotting, Decatenating, Supercoil-Relaxing Actions and Their Scaling Relation. Journal of Physics: Condensed Matter 27, 354103. [pdf]; Erratum for minor typographical errors: 27, 459601 (2015) [pdf for Erratum]. [Download single pdf file for Article and Erratum].

    1. T. Chen, J. Song and H.S. Chan (2015). Theoretical Perspectives on Nonnative Interactions and Intrinsic Disorder in Protein Folding and Binding. Current Opinion in Structural Biology 30, 32-42. [Download pdf file].

    1. T. Sikosek and H.S. Chan (2014). Biophysics of Protein Evolution and Evolutionary Protein Biophysics. Journal of the Royal Society Interface 11, 20140419. [Download pdf file]; [Journal webpage (free access)]; Correction for minor typographical errors: 12, 20150915 (2015) [pdf for Correction]. [Download single pdf file for Article and Correction].

    1. C.L. Dias and H.S. Chan (2014). Pressure-Dependent Properties of Elementary Hydrophobic Interactions: Ramifications for Activation Properties of Protein Folding. Journal of Physical Chemistry B 118, 7488-7509. [Download pdf file]; [Journal webpage].

    1. T. Chen and H.S. Chan (2014). Effects of Desolvation Barriers and Sidechains on Local-Nonlocal Coupling and Chevron Behaviors in Coarse-Grained Models of Protein Folding. Physical Chemistry Chemical Physics 16, 6460-6479. [Download pdf file].

    1. H. Kaya, Z. Uzunoğlu and H.S. Chan (2013). Spatial Ranges of Driving Forces are a Key Determinant of Protein Folding Cooperativity and Rate Diversity. Physical Review E 88, 044701. [Download pdf file].

    1. J. Song, S.C. Ng, P. Tompa, K.A.W. Lee and H.S. Chan (2013). Polycation-π Interactions are a Driving Force for Molecular Recognition by an Intrinsically Disordered Oncoprotein Family. PLoS (Public Library of Science) Computational Biology 9(9): e1003239. [Download combined pdf file for Main Text & Supporting Information] [Journal website with links to pdf for the article and Supporting Information].

    1. Z. Zhang and H.S. Chan (2012). Transition Paths, Diffusive Processes, and Preequilibria of Protein Folding. Proceedings of the National Academy of Sciences, USA 109, 20919-20924. [Download combined pdf file for Main Text & Supporting Information].

    1. T. Sikosek, E. Bornberg-Bauer and H.S. Chan (2012). Evolutionary Dynamics on Protein Bi-Stability Landscapes can Potentially Resolve Adaptive Conflicts. PLoS (Public Library of Science) Computational Biology 8(9): e1002659. [Download pdf file] [Journal website with links to Supporting Information].

    1. A.A. Beharry, T. Chen, M.S. Al-Abdul-Wahid, S. Samanta, K. Davidov, O. Sadovski, A. Ali, S.B. Chen, R.S. Prosser, H.S. Chan and G.A. Woolley (2012). Quantitative Analysis of the Effects of Photoswitchable Distance Constraints on the Structure of a Globular Protein. Biochemistry 51, 6421-6431. [Download pdf file] [Supporting Information].

    1. T. Sikosek, H.S. Chan and E. Bornberg-Bauer (2012). Escape from Adaptive Conflict Follows from Weak Functional Trade-Offs and Mutational Robustness. Proceedings of the National Academy of Sciences, USA 109, 14888-14893. [Download pdf file] [Download Supporting Information (text, figures, tables)] [PNAS website for complete Supporting Information (text, figures, tables and movies)].

    1. A. Zarrine-Afsar, Z. Zhang, K.L. Schweiker, G.I. Makhatadze, A.R. Davidson and H.S. Chan (2012). Kinetic Consequences of Native State Optimization of Surface-Exposed Electrostatic Interactions in the Fyn SH3 Domain. Proteins: Structure, Function, and Bioinformatics 80, 858-870. [Download pdf file].

    1. C.L. Dias, M. Karttunen and H.S. Chan (2011). Hydrophobic Interactions in the Formation of Secondary Structures in Small Peptides. Physical Review E 84, 041931. [Download pdf file].

    1. H.S. Chan, Z. Zhang, S. Wallin and Z. Liu (2011). Cooperativity, Local-Nonlocal Coupling, and Nonnative Interactions: Principles of Protein Folding from Coarse-Grained Models. Annual Review of Physical Chemistry 62, 301-326. [Download article from journal website].

    1. H.S. Chan (2011). Short-Range Contact Preferences and Long-Range Indifference: Is Protein Folding Stoichiometry Driven? Journal of Biomolecular Structure & Dynamics 28, 603-605. [Download pdf file].

    1. Z. Liu, L. Zechiedrich and H.S. Chan (2010). Action at Hooked or Twisted-Hooked DNA Juxtapositions Rationalizes Unlinking Preference of Type-2 Topoisomerases. Journal of Molecular Biology 400, 963-982. [Download pdf file] [Supplementary Data].

    1. M.S. Kimber, A.Y.H. Yu, M. Borg, E. Leung, H.S. Chan and W.A. Houry (2010). Structural and Theoretical Studies Indicate that the Cylindrical Protease ClpP Samples Extended and Compact Conformations. Structure 18, 798-808. [Download pdf file] [Supplementary Information] [Link to journal website for supplementary movies].

    1. H.S. Chan and G.L. Lukacs (2010). Introduction to the Special Issue on the 52nd Annual Meeting of the Canadian Society of Biochemistry, Molecular & Cellular Biology (CSBMCB). Biochemistry and Cell Biology 88, No. 2, pp.v-viii. [pdf file.]

    1. T. Chen, D. Vernazobres, T. Yomo, E. Bornberg-Bauer and H.S. Chan (2010). Evolvability and Single-Genotype Fluctuation in Phenotypic Properties: A Simple Heteropolymer Model. Biophysical Journal 98, 2487-2496. [Download pdf file] [Supporting Material].

    1. Z. Liu, L. Zechiedrich and H.S. Chan (2010). Local Site Preference Rationalizes Disentangling by DNA Topoisomerases. Physical Review E 81, 031902. [Download pdf file.]

    1. Z. Zhang and H.S. Chan (2010). Competition Between Native Topology and Nonnative Interactions in Simple and Complex Folding Kinetics of Natural and Designed Proteins. Proceedings of the National Academy of Sciences, USA 107, 2920-2925. [Download pdf file] [Supporting Information].

    1. A. Ferguson, Z. Liu and H.S. Chan (2009). Desolvation Barrier Effects are a Likely Contributor to the Remarkable Diversity in the Folding Rates of Small Proteins. Journal of Molecular Biology 389, 619-636 [Download pdf file]; Addendum: 392, 242 (2009) [pdf file for Addendum]; Corrigendum: 401, 153 (2010) [pdf file for Corrigendum].

    1. A. Badasyan, Z. Liu and H.S. Chan (2009). Interplaying Roles of Native Topology and Chain Length in Marginally Cooperative and Noncooperative Folding of Small Protein Fragments. International Journal of Quantum Chemistry 109, 3482-3499. [Download pdf file.]

    1. H.S. Chan and Z. Zhang (2009). Liaison Amid Disorder: Non-native Interactions May Underpin Long-Range Coupling in Proteins. Journal of Biology (BioMed Central) 8:27. [Download pdf file.]

    1. Z. Liu, R.W. Deibler, H.S. Chan and L. Zechiedrich (2009). The Why and How of DNA Unlinking. Nucleic Acids Research 37, 661-671. [Download pdf file]; (cover image).

    1. Z. Zhang and H.S. Chan (2009). Native Topology of the Designed Protein Top7 is not Conducive to Cooperative Folding. Biophysical Journal 96, L25-L27. [Download pdf file.]

    1. A. Badasyan, Z. Liu and H.S. Chan (2008). Probing Possible Downhill Folding: Native Contact Topology Likely Places a Significant Constraint on the Folding Cooperativity of Proteins with ~ 40 Residues. Journal of Molecular Biology 384, 512-530. [Download pdf file.]

    1. A. Zarrine-Afsar, S. Wallin, A.M. Neculai, P. Neudecker, P.L. Howell, A.R. Davidson and H.S. Chan (2008). Theoretical and Experimental Demonstration of the Importance of Specific Nonnative Interactions in Protein Folding. Proceedings of the National Academy of Sciences, USA 105, 9999-10004. [Download pdf file] [Supporting Information].

    1. Z. Liu and H.S. Chan (2008). Efficient Chain Moves for Monte Carlo Simulations of a Wormlike DNA Model: Excluded Volume, Supercoils, Site Juxtapositions, Knots and Comparisons with Random-Flight and Lattice Models. Journal of Chemical Physics 128, 145104 [Download pdf file]; Erratum: 131, 049902 (2009) [pdf file for Erratum].

    1. M. Borg, T. Mittag, T. Pawson, M. Tyers, J.D. Forman-Kay and H.S. Chan (2007). Polyelectrostatic Interactions of Disordered Ligands Suggest a Physical Basis for Ultrasensitivity. Proceedings of the National Academy of Sciences, USA 104, 9650-9655. [Download pdf file.] [Download pdf file for Supporting Information - Appendix.]

    1. R. Wroe, H.S. Chan and E. Bornberg-Bauer (2007). A Structural Model of Latent Evolutionary Potentials Underlying Neutral Networks in Proteins. HFSP Journal (published by the Human Frontier Science Program) 1, 79-87. [Download pdf file]; (cover image).

    1. J. L. MacCallum, M. Sabaye Moghaddam, H.S. Chan and D.P. Tieleman (2007). Hydrophobic Association of α-Helices, Steric Dewetting and Enthalpic Barriers to Protein Folding. Proceedings of the National Academy of Sciences, USA 104, 6206-6210. [Download pdf file.] (Research reported in this publication has benefited from the CISS-3 Canada-wide distributive computing project.) Correction: 105, 19561 (2008) [top of right column of pdf].

    1. M. Sabaye Moghaddam and H.S. Chan (2007). Pressure and Temperature Dependence of Hydrophobic Hydration: Volumetric, Compressibility, and Thermodynamic Signatures. Journal of Chemical Physics 126, 114507. [pdf file.]

    1. M. Sabaye Moghaddam and H.S. Chan (2006). Selective Adsorption of Block Copolymers on Patterned Surfaces. Journal of Chemical Physics 125, 164909. [pdf file.]

    1. M. Knott and H.S. Chan (2006). Criteria for Downhill Protein Folding: Calorimetry, Chevron Plot, Kinetic Relaxation, and Single-Molecule Radius of Gyration in Chain Models with Subdued Degrees of Cooperativity. Proteins: Structure, Function, and Bioinformatics 65, 373-391. [Download pdf file.]

    1. Z. Liu, J.K. Mann, E.L. Zechiedrich and H.S. Chan (2006). Topological Information Embodied in Local Juxtaposition Geometry Provides a Statistical Mechanical Basis for Unknotting by Type-2 DNA Topoisomerases. Journal of Molecular Biology 361, 268-285. [Download pdf file]; (cover image).

    1. Z. Liu, E.L. Zechiedrich and H.S. Chan (2006). Inferring Global Topology from Local Juxtaposition Geometry: Interlinking Polymer Rings and Ramifications for Topoisomerase Action. Biophysical Journal 90, 2344-2355. [Download pdf file.]

    1. S. Wallin and H.S. Chan (2006). Conformational Entropic Barriers in Topology-Dependent Protein Folding: Perspectives from a Simple Native-Centric Polymer Model. Journal of Physics: Condensed Matter 18, S307-S328. [Download pdf file.] (Link to journal website) [Special Issue Table of Contents] Corrigendum: 21, 329801 (2009) [pdf file for Corrigendum].

    1. S. Shimizu, M. Sabaye Moghaddam and H.S. Chan (2005). Comment on "Molecular Origin of Anticooperativity in Hydrophobic Association." Journal of Physical Chemistry B 109, 21220-21221. [Download pdf file.]

    1. Z. Liu and H.S. Chan (2005). Solvation and Desolvation Effects in Protein Folding: Native Flexibility, Kinetic Cooperativity, and Enthalpic Barriers under Isostability Conditions. Physical Biology 2, S75-S85. [Download pdf file.] (Link to journal website) [Special Issue Table of Contents]

    1. Z. Liu and H.S. Chan (2005). Desolvation is a Likely Origin of Robust Enthalpic Barriers to Protein Folding. Journal of Molecular Biology 349, 872-889. [Download pdf file.]

    1. S. Wallin and H.S. Chan (2005). A Critical Assessment of the Topomer Search Model of Protein Folding Using a Continuum Explicit-Chain Model with Extensive Conformational Sampling. Protein Science 14, 1643-1660. [Download pdf file.]

    1. H. Kaya, Z. Liu and H.S. Chan (2005). Chevron Behavior and Isostable Enthalpic Barriers in Protein Folding: Successes and Limitations of Simple Go-like Modeling. Biophysical Journal 89, 520-535. [Download pdf file.]

    1. H.S. Chan (2005). Simplified Models of Protein Folding. In: Handbook of Materials Modeling, edited by S. Yip (Springer, The Netherlands), Chapter 5.16, pp.1823-1836.

    1. R. Wroe, E. Bornberg-Bauer and H.S. Chan (2005). Comparing Folding Codes in Simple Heteropolymer Models of Protein Evolutionary Landscape: Robustness of the Superfunnel Paradigm. Biophysical Journal 88, 118-131. [Download pdf file.]

    1. M. Sabaye Moghaddam, S. Shimizu and H.S. Chan (2005). Temperature Dependence of Three-Body Hydrophobic Interactions: Potential of Mean Force, Enthalpy, Entropy, Heat Capacity, and Nonadditivity. Journal of the American Chemical Society 127, 303-316 [Download pdf file]; Correction: 127, 2363 (2005) [pdf file for Correction].

    1. H. Kaya and H.S. Chan (2005). Explicit-Chain Model of Native-State Hydrogen Exchange: Implications for Event Ordering and Cooperativity in Protein Folding. Proteins: Structure, Function, and Bioinformatics 58, 31-44. [Download pdf file.]

    1. J.E. Ollerenshaw, H. Kaya, H.S. Chan and L.E. Kay (2004). Sparsely Populated Folding Intermediates of the Fyn SH3 Domain: Matching Native-Centric Essential Dynamics and Experiment. Proceedings of the National Academy of Sciences, USA 101, 14748-14753. [Download pdf file.]

    1. M. Knott and H.S. Chan (2004). Exploring the Effects of Hydrogen Bonding and Hydrophobic Interactions on the Foldability and Cooperativity of Helical Proteins Using a Simplifed Atomic Model. Chemical Physics 307, 187-199. [Download pdf file.]

    1. H.S. Chan (2004). Physics of Protein Folding. Physics in Canada Vol. 60, No. 2 (March/April issue), 195-201. [Download pdf file.]

    1. H.S. Chan, S. Shimizu and H. Kaya (2004). Cooperativity Principles in Protein Folding. Methods in Enzymology 380, 350-379. [Download pdf file.]

    1. M. Knott, H. Kaya and H.S. Chan (2004). Energetics of Protein Thermodynamic Cooperativity: Contributions of Local and Nonlocal Interactions. Polymer 45, 623-632. [Download pdf file.]

    1. H.S. Chan (2003). Review of Protein Physics: A Course of Lectures by A. V. Finkelstein & O. B. Ptitsyn [354 p., Academic Press, London and San Diego (California), 2002]. The Quarterly Review of Biology Vol. 78, No. 4, 472-473 (December issue; The University of Chicago Press). [Download pdf file.]

    1. H. Kaya and H.S. Chan (2003). Contact Order Dependent Protein Folding Rates: Kinetic Consequences of a Cooperative Interplay Between Favorable Nonlocal Interactions and Local Conformational Preferences. Proteins: Structure, Function, and Genetics 52, 524-533. [Download pdf file.] [Download separate pdf copy of the cover image and legend (not included in the preceding pdf file for this article).]

    1. H. Kaya and H.S. Chan (2003). Simple Two-State Protein Folding Kinetics Requires Near-Levinthal Thermodynamic Cooperativity. Proteins: Structure, Function, and Genetics 52, 510-523. [Download pdf file.]

    1. H. Kaya and H.S. Chan (2003). Origins of Chevron Rollovers in Non-Two-State Protein Folding Kinetics. Physical Review Letters 90, Art. No. 258104. [Download GZipped PS (postscript) file.]

    1. H. Kaya and H.S. Chan (2003). Solvation Effects and Driving Forces for Protein Thermodynamic and Kinetic Cooperativity: How Adequate is Native-Centric Topological Modeling? Journal of Molecular Biology 326, 911-931. [Download pdf file.] Corrigendum: 337, 1069-1070 (2004) [pdf file for Corrigendum].

    1. H.S. Chan and E. Bornberg-Bauer (2002). Perspectives on Protein Evolution from Simple Exact Models. Applied Bioinformatics 1, 121-144. [Download pdf file.]

    1. S. Shimizu and H.S. Chan (2002). Origins of Protein Denatured State Compactness and Hydrophobic Clustering in Aqueous Urea: Inferences from Nonpolar Potentials of Mean Force. Proteins: Structure, Function, and Genetics 49, 560-566. [Download pdf file.]

    1. S. Shimizu and H.S. Chan (2002). Anti-Cooperativity and Cooperativity in Hydrophobic Interactions: Three-Body Free Energy Landscapes and Comparison with Implicit-Solvent Potential Functions for Proteins. Proteins: Structure, Function, and Genetics 48, 15-30. [Download postscript file.] [pdf file with color figure.] Erratum: 49, 294 (2002) [pdf file for Erratum].

    1. S. Shimizu and H.S. Chan (2002). Reply to ``Comment on `Anti-Cooperativity in Hydrophobic Interactions: A Simulation Study of Spatial Dependence of Three-Body Effects and Beyond' '' [J. Chem. Phys. 116, 2665 (2002)]. Journal of Chemical Physics 116, 2668-2669. [Download postscript file.]

    1. Y. Cui, W.H. Wong, E. Bornberg-Bauer and H.S. Chan (2002). Recombinatoric Exploration of Novel Folded Structures: A Heteropolymer-Based Model of Protein Evolutionary Landscapes. Proceedings of the National Academy of Sciences, USA 99, 809-814. [Download postscript file]; [PNAS webpage with link to Supporting Figure 7].

    1. H. Kaya and H.S. Chan (2002). Towards a Consistent Modeling of Protein Thermodynamic and Kinetic Cooperativity: How Applicable is the Transition State Picture to Folding and Unfolding? Journal of Molecular Biology 315, 899-909. [Download postscript file. Note that in Figure 2 of this postscript version, the shading is much fainter than that in the printed journal article. For better quality, click here to download postscript file for Figure 2.]

    1. H.S. Chan, H. Kaya and S. Shimizu (2002). Computational Methods for Protein Folding: Scaling a Hierarchy of Complexities. In: Current Topics in Computational Molecular Biology, edited by T. Jiang, Y. Xu & M.Q. Zhang (The MIT Press, Cambridge, Massachusetts, U.S.A.), Chapter 16, pp.403-447.

    1. S. Shimizu and H.S. Chan (2001). Statistical Mechanics of Solvophobic Aggregation: Additive and Cooperative Effects. Journal of Chemical Physics 115, 3424-3431. [Download postscript file.]

    1. S. Shimizu and H.S. Chan (2001). Anti-Cooperativity in Hydrophobic Interactions: A Simulation Study of Spatial Dependence of Three-Body Effects and Beyond. Journal of Chemical Physics 115, 1414-1421. [Download postscript file.]

    1. P.M. Harrison, H.S. Chan, S.B. Prusiner and F.E. Cohen (2001). Conformational Propagation with Prion-like Characteristics in a Simple Model of Protein Folding. Protein Science 10, 819-835. [Download postscript file.]

    1. S. Shimizu and H.S. Chan (2001). Configuration-Dependent Heat Capacity of Pairwise Hydrophobic Interactions. Journal of the American Chemical Society 123, 2083-2084. [Download postscript file.]

    1. H.S. Chan (2001). Amino Acid Side-chain Hydrophobicity. In: Encyclopedia of Life Sciences (Nature Publishing Group, London, U.K.; www.els.net). [postscript file.]

    1. H. Kaya and H.S. Chan (2000). Energetic Components of Cooperative Protein Folding. Physical Review Letters 85, 4823-4826. [Download postscript file.]

    1. S. Shimizu and H.S. Chan (2000). Temperature Dependence of Hydrophobic Interactions: A Mean Force Perspective, Effects of Water Density, and Non-Additivity of Thermodynamic Signatures. Journal of Chemical Physics 113, 4683-4700. [Download postscript file.] Erratum: 116, 8636 (2002) [postscript file for Erratum].

    1. H. Kaya and H.S. Chan (2000). Polymer Principles of Protein Calorimetric Two-State Cooperativity. Proteins: Structure, Function, and Genetics 40, 637-661. [Download postscript file.] Erratum: 43, 523 (2001) [postscript file for Erratum].

    1. H.S. Chan (2000). Modeling Protein Density of States: Additive Hydrophobic Effects are Insufficient for Calorimetric Two-State Cooperativity. Proteins: Structure, Function, and Genetics 40, 543-571. [Download postscript file.]

    1. R. Brem, H.S. Chan and K.A. Dill (2000). Extracting Microscopic Energies from Oil-Phase Solvation Experiments. Journal of Physical Chemistry B 104, 7471-7482. [Download postscript file.]

    1. H.S. Chan (1999). Folding Alphabets. Nature Structural Biology 6, 994-996. [Download pdf file.]

    1. E. Bornberg-Bauer and H.S. Chan (1999). Modeling Evolutionary Landscapes: Mutational Stability, Topology and Superfunnels in Sequence Space. Proceedings of the National Academy of Sciences, USA 96, 10689-10694. [Download postscript file.]

    1. P.M. Harrison, H.S. Chan, S.B. Prusiner and F.E. Cohen (1999). Thermodynamics of Model Prions and its Implications for the Problem of Prion Protein Folding. Journal of Molecular Biology 286, 593-606. [Download pdf file.]

    1. H.S. Chan (1999). Review of The Art of Molecular Dynamics Simulation by D. C. Rapaport (400 p., Cambridge University Press, U.K., 1997). The Quarterly Review of Biology Vol. 74, No. 1, 65 (March issue; The University of Chicago Press). [Download pdf file.]

    1. H.S. Chan (1998). Modelling Protein Folding by Monte Carlo Dynamics: Chevron Plots, Chevron Rollover, and Non-Arrhenius Kinetics. In: Monte Carlo Approach to Biopolymers and Protein Folding, edited by P. Grassberger, G.T. Barkema & W. Nadler. (World Scientific, Singapore) pp.29-44.

    1. D.R. DeVido, J.G. Dorsey, H.S. Chan and K.A. Dill (1998). Oil/Water Partitioning has a Different Thermodynamic Signature When the Oil Solvent Chains are Aligned than when they are Amorphous. Journal of Physical Chemistry B 102, 7272-7279. [Download postscript file.]

    1. H.S. Chan (1998). Protein Folding: Matching Speed and Locality. Nature 392, 761-763. [Download pdf file.]

    1. H.S. Chan and K.A. Dill (1998). Protein Folding in the Landscape Perspective: Chevron Plots and Non-Arrhenius Kinetics. Proteins: Structure, Function, and Genetics 30, 2-33. [Download postscript file.]

    1. H.S. Chan and K.A. Dill (1997). Solvation: How to Obtain Microscopic Energies from Partitioning and Solvation Experiments. Annual Review of Biophysics & Biomolecular Structure 26, 425-459. [Download pdf file.]

    1. K.A. Dill and H.S. Chan (1997). From Levinthal to Pathways to Funnels. Nature Structural Biology 4, 10-19. [pdf file (5.3 MB).]

    1. H.S. Chan and K.A. Dill (1996). A Simple Model of Chaperonin-Mediated Protein Folding. Proteins: Structure, Function, and Genetics 24, 345-351. [Download pdf file.]

    1. H.S. Chan and K.A. Dill (1996). Comparing Folding Codes for Proteins and Polymers. Proteins: Structure, Function, and Genetics 24, 335-344. [Download pdf file.]

    1. K.A. Dill, H.S. Chan and K. Yue (1995). The Protein Folding Problem: Searching Conformations of Compact Chain Molecules. Macromolecular Symposia 98, 615-617.

    1. A.E. Krukowski, H.S. Chan and K.A. Dill (1995). An Exact Lattice Model of Complex Solutions: Chemical Potentials Depend on Solute and Solvent Shape. Journal of Chemical Physics 103, 10675-10688. [Download postscript file.]

    1. S. Sun, R. Brem, H.S. Chan and K.A. Dill (1995). Designing Amino Acid Sequences to Fold with Good Hydrophobic Cores. Protein Engineering 8, 1205-1213. [pdf file.]

    1. H.S. Chan (1995). Kinetics of Protein Folding. Nature 373, 664-665. [Download pdf file.]

    1. H.S. Chan, S. Bromberg and K.A. Dill (1995). Models of Cooperativity in Protein Folding. Philosophical Transactions of the Royal Society of London, Series B 348, 61-70. [Download pdf file.]

    1. K.A. Dill, S. Bromberg, K. Yue, K.M. Fiebig, D.P. Yee, P.D. Thomas and H.S. Chan (1995). Principles of Protein Folding --- A Perspective from Simple Exact Models. Protein Science 4, 561-602. [Download pdf file (16 MB).]

    1. K. Yue, K.M. Fiebig, P.D. Thomas, H.S. Chan, E.I. Shakhnovich and K.A. Dill (1995). A Test of Lattice Protein Folding Algorithms. Proceedings of the National Academy of Sciences, USA 92, 325-329. [Download pdf file.]

    1. D.P. Yee, H.S. Chan, T.F. Havel and K.A. Dill (1994). Does Compactness Induce Secondary Structure in Proteins? A Study of Poly-Alanine Chains Computed by Distance Geometry. Journal of Molecular Biology 241, 557-573. [Download pdf file.]

    1. H.S. Chan and K.A. Dill (1994). Solvation: Effects of Molecular Size and Shape. Journal of Chemical Physics 101, 7007-7026. [Download postscript file.]

    1. H.S. Chan and K.A. Dill (1994). Transition States and Folding Dynamics of Proteins and Heteropolymers. Journal of Chemical Physics 100, 9238-9257. [Download postscript file.]

    1. H.S. Chan and K.A. Dill (1993). Energy Landscapes and the Collapse Dynamics of Homopolymers. Journal of Chemical Physics 99, 2116-2127. [Download postscript file.]

    1. D. Baker, H.S. Chan and K.A. Dill (1993). Coordinate-Space Formulation of Polymer Lattice Cluster Theory. Journal of Chemical Physics 98, 9951-9962. [Download postscript file.]

    1. H.S. Chan and K.A. Dill (1993). The Protein Folding Problem. Physics Today Vol. 46, No. 2, 24-32 (February issue). [pdf file (4.9 MB).] [See also Vol. 47, No. 2, 124-125 (February 1994).] Reprinted in Japanese in Parity, the Japanese Physical Science Magazine, 8(12), 24-35 (December 1993).

    1. K.A. Dill, K.M. Fiebig and H.S. Chan (1993). Cooperativity in Protein Folding Kinetics. Proceedings of the National Academy of Sciences, USA 90, 1942-1946. [Download pdf file.]

    1. H.S. Chan, K.A. Dill and D. Shortle (1992). Statistical Mechanics and Protein Folding. In: Princeton Lectures on Biophysics, edited by W. Bialek (World Scientific, Singapore) pp.69-173.

    1. D. Shortle, H.S. Chan and K.A. Dill (1992). Modeling the Effects of Mutations on the Denatured States of Proteins. Protein Science 1, 201-215. [pdf file.]

    1. R. Miller, C.A. Danko, M.J. Fasolka, A.C. Balazs, H.S. Chan and K.A. Dill (1992). Folding Kinetics of Proteins and Copolymers. Journal of Chemical Physics 96, 768-780. [Download pdf file.]

    1. H.S. Chan and K.A. Dill (1991). Polymer Principles in Protein Structure and Stability. Annual Review of Biophysics and Biophysical Chemistry 20, 447-490. [Download pdf file.]

    1. H.S. Chan and K.A. Dill (1991). Sequence Space Soup of Proteins and Copolymers. Journal of Chemical Physics 95, 3775-3787. [Download pdf file.]

    1. H.S. Chan, M.R. Wattenbarger, D.F. Evans, V.A. Bloomfield and K.A. Dill (1991). Enhanced Structure in Polymers at Interfaces. Journal of Chemical Physics 94, 8542-8557 [Download pdf file]; Erratum: 96, 3361 (1992) [pdf file for Erratum].

    1. M.R. Wattenbarger, H.S. Chan, D.F. Evans, V.A. Bloomfield and K.A. Dill (1990). Surface-Induced Enhancement of Internal Structure in Polymers and Proteins. Journal of Chemical Physics 93, 8343-8351. [Download pdf file.]

    1. H.S. Chan and K.A. Dill (1990). Origins of Structure in Globular Proteins. Proceedings of the National Academy of Sciences USA 87, 6388-6392. [Download pdf file.]

    1. H.S. Chan and K.A. Dill (1990). The Effects of Internal Constraints on the Configurations of Chain Molecules. Journal of Chemical Physics 92, 3118-3135 [Download pdf file]; Erratum: 107, 10353 (1997) [pdf file for Erratum].

    1. H.S. Chan and K.A. Dill (1989). Compact Polymers. Macromolecules 22, 4559-4573 [Download pdf file]; Reprinted in: Conformations and Forces in Protein Folding, edited by B.T. Nall and K.A. Dill (American Association for the Advancement of Science, Washington, D.C., 1991, pp.43-66).

    1. H.S. Chan and K.A. Dill (1989). Intra-Chain Loops in Polymers: Effects of Excluded Volume. Journal of Chemical Physics 90, 492-509 [Download pdf file]; Errata: 96, 3361 (1992) [pdf file for Erratum]; 107, 10353 (1997) [pdf file for Erratum].

    1. H.S. Chan and M.B. Halpern (1987). Continuum-Regularized Quantum Gravity. Zeitschrift Für Physik C36, 669-693. [Download pdf file.]

    1. H.S. Chan (1987). Continuum Regularization of Gauge Theory with Fermions (Ph.D. Thesis). [Lawrence Berkeley Laboratory Report No. 23418, April 1987 UMI order number: 8726161; pdf file (from the SPIRES-HEP database).]

    1. Z. Bern, H.S. Chan and M.B. Halpern (1987). Non-Grassmann Formulation of Regularized Gauge Theory with Fermions. Zeitschrift Für Physik C34, 267-276. [Download pdf file.]

    1. Z. Bern, H.S. Chan and M.B. Halpern (1986). Continuum Regularization of Gauge Theory with Fermions. Zeitschrift Für Physik C33, 77-88. [Download pdf file.]

    1. H.S. Chan (1986). Diagrammatic Expansions for the Yang-Mills Ground State. Nuclear Physics B278, 721-737 [Download pdf file]; Erratum: B287, 852 (1987) [pdf file for Erratum].

    1. H.S. Chan (1986). Temporal-Gauge Finite-Time Feynman Rules and Gauss's Law. Physical Review D34, 2433-2439. [Download pdf file.]

    1. H.S. Chan and M.B. Halpern (1986). New Ghost-Free Infrared-Soft Gauges. Physical Review D33, 540-547. [Download pdf file.]

    1. Z. Bern and H.S. Chan (1986). Perturbative Analysis of QCD4 Maps. Nuclear Physics B266, 509-535. [Download pdf file.]




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