Publications

1. J. E. Gonzales II, W. Hwang, and B. R. Brooks, "A Parallel CUDA Implementation of the Gauss-Legendre-Spherical-t Method for Electrostatic Interactions," J Chem Phys. 162 222501 (2025).  link
2. W. Hwang, J. E. Gonzales II, and B. R. Brooks, "Gauss-Legendre-Spherical-t (GLST) Cubature-Based Factorization of Long-Range Electrostatics in Simulations," J Chem Phys. 162 224102 (2025).  link
3. J. E. Gonzales, I. Kim, A. Bastiray, W. Hwang, and J.-H. Cho, "Evolutionary rewiring of the dynamic network underpinning allosteric epistasis in NS1 of influenza A virus," Proc. Natl. Acad. Sci. USA 122 e2410813122 (2025).  Access
4. R. J. Mallis, K. Brazin, J. S. Duke-Cohan, A. Akitsu, H. M. Stephens, A. C. Chang-Gonzalez, D. J. Masi, E. H. Kirkpatrick, E. L. Holliday, Y. Feng, K. J. Zienkiewicz, J. J. Lee, V. Cinella, K. I. Uberoy, K. Tan, G. Wagner, H. Arthanari, W. Hwang, M. J. Lang, and E. L. Reinherz, "Biophysical and Structural Features of αβ T-Cell Receptor Mechanosensing: A Paradigmatic Shift in Understanding T-Cell Activation," Immunol. Rev. 329 e13432 (2025).  Access
5. W. Hwang, S. L. Austin, A. Blondel, E. D. Boittier, S. Boresch, M. Buck, J. Buckner, A. Caflisch, H.-T. Chang, X. Cheng, Y. K. Choi, J,-W. Chu, M. Crowley, Q. Cui, A. Damjanovic, Y. Deng, M. Devereux, X. Ding, M. Feig, J. Gao, D. R. Glowacki, J. E. Gonzales II, M. B, Hamaneh, E. D. Harder, R. L. Hayes, J. Huang, Y. Huang, P. S. Hudson, W. Im, S. M. Islam, W. Jiang, M. R. Jones, S. K&amul;ser, F. L. Kearns, N. R. Kern, J. B. Klauda, T. Lazaridis, J. Lee, J. A. Lemkul, X. Liu, Y. Luo, A. D. MacKerell, Jr., D. T. Major, M. Meuwly, K. Nam, L. Nilsson, V. Ovchinnikov, E. Paci, S. Park, R. W. Pastor, A. R. Pittman, C. B. Post, S. Prasad, J. Pu, Y. Qi, T. Rathinavelan, D. R. Roe, B. Roux, C. N. Rowley, J. Shen, A. C. Simmonett, A. J. Sodt, K. T&omul;pfer, M. Upadhyay, A. van der Vaart, L. I. Vazquez-Salazar, R. M. Venable, L. C. Warrensford, H. L. Woodcock, Y. Wu, C. L. Brooks III, B. R. Brooks, M. Karplus, "CHARMM at 45: Enhancements in accessibility, functionality, and speed" J. Phys. Chem. B 128 (2024).  Access
6. A. Akitsu, E. Kobayashi, Y. Feng, H. M. Stephens, K. N. Brazin, D. J. Masi, E. H. Kirpatrick, R. J. Mallis, J. S. Duke-Cohan, M. A. Booker, V. Cinella, W. W. Feng, E. L. Holliday, J. J. Lee, K. J. Zienkiewicz, M. Y. Tolstorukov, W. Hwang, M. J. Lang, and E. L. Reinherz, "Parsing digital or analogue TCR performance through piconewton forces,'' Sci. Adv. 10 eado4313 (2024).  Access
7. A. C. Chang-Gonzalez, A. Akitsu, R. J. Mallis, M. J. Lang, E. L. Reinherz, and W. Hwang, "Load-based divergence in the dynamic allostery of two TCRs recognizing the same pMHC,''
   eLife 13 RP104280 (2024).  Access
8. A. C. Chang-Gonzalez, R. J. Mallis, M. J. Lang, E. L. Reinherz, and W. Hwang, "Asymmetric framework motion of TCRαβ controls load-dependent peptide discrimination,''
   eLife 13 e91881 (2024).  Access
9. K. Tan, J. Chen, Y. Kak, Y. Wang, L. Donius, R. A. Khan, X. Li, H. Richter, M. S. Seaman, T. Walz, W. Hwang, E. L. Reinherz, and M. Kim, "Inadequate structural constraint on Fab approach rather than paratope elicitation limits HIV-1 MPER vaccine utility,''
   Nat. Comm. 14 7218 (2023).  Access
10. E. L. Reinherz, W. Hwang, and M. J. Lang, "Harnessing αβ T cell receptor mechanobiology to achieve the promise of immuno­oncology"
    Proc. Natl. Acad. Sci. USA 120 e2215694120 (2023).   Access
11. J. Shi, J.-H. Cho, and W. Hwang, "Heterogeneous and allosteric role of surface hydration for protein-ligand binding"
    J. Chem. Theory Comput. 19 1875-1887 (2023).   Access   Journal Cover
12. J. S. Duke-Cohan, A. Akitsu, R. J. Mallis, C. M. Messier, P. H. Lizotte, J. C. Aster, W. Hwang, M. J. Lang, and E. L. Reinherz, "Pre-T cell receptor Self-MHC Sampling Restricts Thymocyte Dedifferentiation,"
    Nature 613 565-574 (2023).   Link   PDF   Nature News and Views
13. A. C. Chang-Gonzalez, H. C. Gibbs, A. C. Lekven, A. T. Yeh, and W. Hwang, "Building 3-Dimensional Model of Early-Stage Zebrafish Embryo Brain,"
    Biophys. Rep. 1 e100003 (2021).   Access   Journal Cover
14. R. J. Mallis, J. S. Duke-Cohan, D. K. Das, A. Akitsu, A. M. Luoma, D. Banik, H. M. Stephens, P. W. Tetteh, C. D. Castro, S. Krahnke, R. E. Hussey, B. Lawney, K. N. Brazin, P. A. Reche, W. Hwang, E. J. Adams, M. J. Lang, and E. L. Reinherz, "Molecular design of the γδT cell receptor ectodomain encodes biologically fit ligand recognition in the absence of mechanosensing,"
    Proc. Natl. Acad. Sci. USA 118 e2023050118 (2021).   Access
15. M. A. Herman, B. R. Aiello, J. D. DeLong, H. Garcia-Ruiz A. L. González, W. Hwang, C. McBeth, E. A. Stojkovíc, M. A. Trakselis and N. Yakoby, "A unifying framework for understanding biological structures and functions across levels of biological organization,"
    J. Integ. Comparat. Biol. 61 2038-2047 (2021).   Link   PDF
16. X. Li, R. Mizsei, K. Tan, R. J. Mallis, J. S. Duke-Cohan, A. Akitsu, P. W. Tetteh, A. Dubey, W. Hwang, G. Wagner, M. J. Lang, H. Arthanari, J.-H. Wang, and E. L. Reinherz, "Pre-T cell receptors topologically sample self-ligands during the β-selection phase of thymocyte development"
    Science 371 181-185 (2021).   Link   PDF
17. W. Hwang, R. J. Mallis, M. J. Lang, and E. L. Reinherz, "The αβTCR mechanosensor exploits dynamic ectodomain allostery to optimize its ligand recognition site"
    Proc. Natl. Acad. Sci. USA 117 21336-21345 (2020).   Link   PDF
18. J. Shi, Q. Shen, J.-H. Cho, and W. Hwang, "Entropy Hotspots for the Binding of Intrinsically Disordered Ligands to a Receptor Domain"
    Biophys. J. 118 2502-2512 (2020).   Access
19. J.-H. Cho, B. Zhao, J. Shi, N. Savage, Q. Shen, J. Byrnes, L. Yang, W. Hwang, and P. Li, "Molecular recognition of a host protein by NS1 of pandemic and seasonal influenza A viruses"
    Proc. Natl. Acad. Sci. USA 117 6550-6558 (2020).   Link   PDF
20. W. Hwang and M. Karplus, "Structural Basis for Power Stroke vs. Brownian Ratchet Mechanisms of Motor Proteins"
    Proc. Natl. Acad. Sci. USA 116 19777-19785 (2019).   Link   PDF
21. R. J. Mallis, K. N. Brazin, J. S. Duke-Cohan, W. Hwang, J. Wang, G. Wagner, H. Arthanari, M. J. Lang, and E. L. Reinherz, "NMR: An Essential Structural Tool for Integrative Studies of T Cell Development, pMHC Ligand Recognition and TCR Mechanobiology"
    J. Biomolec. NMR 73 319-332 (2019).   Link   PDF
22. E. Eryilmaz, W. Teizer, and W. Hwang, "Macromolecular and nanoscale investigation of intermolecular interactions driving the self-assembly of collagen," Biomed. Phys. Eng. Express 5 045005 (2019).   Link   PDF
23. B. Kang, S. Jo, J. Baek, F. Nakamura, W. Hwang, and H. Lee, "Role of Mechanical Flow for Actin Network Organization"
    Acta Biomater. 90 217--224 (2019).   Link   PDF
24. X. Teng and W. Hwang, "Effect of methylation on local mechanics and hydration structure of DNA"
    Biophys. J. 114 1791-1803 (2018).   Link   PDF   Journal Cover
25. Q. Shen, J. Shi, D. Zeng, B. Zhao, P. Li, W. Hwang and J-H Cho, "Molecular mechanisms of tight binding through fuzzy interactions"
    Biophys. J. 114 1313-1320 (2018).   Link   PDF
26. W. Hwang, M. J. Lang, and M. Karplus, "Kinesin motility is driven by subdomain dynamics"
    eLife 6 e28948 (2017).   Access
27. D. N. Reinemann, E. G. Sturgill, D. K. Das, M. S. Degen, Z. Vörös, W. Hwang, R. Ohi, and M. J. Lang, "Collective Force Regulation in Anti-Parallel Microtubule Gliding by Dimeric Kif15 Kinesin Motors"
    Curr. Biol. 27 2810--2820 (2017).   Link   PDF
28. H. C. Gibbs, A. C. Chang-Gonzalez, W. Hwang, A. T. Yeh, and A. C. Lekven, "Midbrain-hindbrain boundary morphogenesis: At the intersection of Wnt and Fgf signaling"
    Front. Neuroanat. 11 64 (2017).   Access
29. E. Eryilmaz, W. Teizer, and W. Hwang, "In vitro analysis of the co-assembly of type-I and type-III collagen"
    Cell. Molec. Bioeng. 10 41-53 (2017).   Link   PDF   Journal Cover
30. X. Teng and W. Hwang, "Elastic energy partitioning in DNA deformation and binding to proteins"
    ACS Nano 10 170-180 (2016).   Link   PDF
31. K. Kim, A. Sikora, H. Nakazawa, M. Umetsu, W. Hwang, and W. Teizer, "Isomorphic coalescence of aster cores formed in vitro from microtubules and kinesin motors"
    Phys. Biol. 13 056002 (2016).   Link   PDF
32. A. Sikora, F. F. Canova, K. Kim, H. Nakazawa, M. Umetsu, I.\ Kumagai, T. Adschiri, W. Hwang, and W. Teizer, "Behavior of Kinesin Driven Quantum Dots Trapped in a Microtubule Loop"
    ACS Nano 9 11003-11013 (2015).   Link   PDF
33. K. N. Brazin, R. J. Mallis, D. K. Das, Y. Feng, W. Hwang, J.-H. Wang, G. Wagner, M. J. Lang and E. L. Reinherz, "Structural features of the αβTCR mechanotransduction apparatus that promote pMHC discrimination"
    Front. Immunol. 6 441 (2015).   Access
34. K. Kim, A. Sikora, K. S. Nakayama, M. Umetsu, W. Hwang and W. Teizer, "Electric field-induced reversible trapping of microtubules along metallic glass microwire electrodes"
    J. Appl. Phys. 117 144701 (2015).   Link   PDF
35. W. Hwang and E. Eryilmaz, "Kinetic signature of fractal-like filament networks formed by orientational linear epitaxy"
    Phys. Rev. Lett. 113 025502 (2014).   Link   PDF   Journal Cover
36. X. Teng and W. Hwang, "Chain Registry and Load-Dependent Conformational Dynamics of Collagen"
    Biomacromolec. 15 3019-3029 (2014).   Link   PDF
37. E. G. Sturgill, D. K. Das, Y. Takizawa, Y. Shin, S. Collier, M. D. Ohi, W. Hwang, M. J. Lang and R. Ohi, "Kinesin-12 Kif15 targets kinetochore-fibers via an intrinsic two-step mechanism"
    Curr. Biol. 24 2307-2313 (2014).   Access
38. A. Sikora, J. Ramón-Azcón, K. Kim, K. Reaves, H. Nakazawa, M. Umetsu, I. Kumagai, T. Adschiri, H. Shiku, T. Matsue, W. Hwang and W. Teizer, "Molecular motor-powered shuttles along multi-walled carbon nanotube tracks"
    Nano Lett. 14 876-881 (2014).   Link   PDF
39. K. Kim, A. Sikora, K. S. Nakayama, H. Nakazawa, M. Umetsu, W. Hwang, and W. Teizer, "Functional localization of kinesin/microtubule-based motility system along 2 metallic glass microwires"
    Appl. Phys. Lett. 105 143701 (2014).   Link   PDF
40. K. Kim, A. Liao, A. Sikora, D. Oliveira, H. Nakazawa, M. Umetsu, I. Kumagai, T. Adschiri, W. Hwang, and W. Teizer, "Microtubule shuttles on kinesin-coated glass micro-wire tracks"
    Biomed. Microdev. 16 501-508 (2014).   Link   PDF
41. N. Varongchayakul, S. Johnson, T. Quabili, J. Cappello, H. Ghandehari, S. Solares, W. Hwang, and J. Seog, "Direct observation of amyloid nucleation under nanomechanical stretching"
    ACS Nano 7 7734-7743 (2013).   Link   PDF
42. W. R. Hesse, M. Steiner, M. L. Wohlever, R. D. Kamm, W. Hwang, and M. J. Lang, "Modular Aspects of Kinesin Force Generation Machinery"
    Biophys. J. 104 1969-1978 (2013).   Link   PDF
43. W. Hwang and M. J. Lang, "Nucleotide-Dependent Control of Internal Strains in Ring-Shaped AAA+ Motors"
    Cell. Molec. Bioeng. 6 65-73 (2013).   Link   PDF
44. A. Sikora, D. Oliveira, K. Kim, A. L. Liao, M. Umetsu, I. Kumagai, T. Adschiri, W. Hwang and W. Teizer, "Quantum Dot Motion on Microtubules"
    Chem. Lett. 41 1215-1217 (2012).   Link   PDF
45. K. M. Ravikumar and W. Hwang, "Role of Hydration Force in the Self-Assembly of Collagens and Amyloid Steric Zipper Filaments"
    J. Am. Chem. Soc. 133 11766-11773 (2011)   Link   PDF
46. S. K. Lakkaraju and W. Hwang, "Hysteresis-based mechanism for the directed motility of the Ncd motor"
    Biophys. J. 101 1105-1113 (2011).   Access
47. W. Leow and W. Hwang, "Epitaxially Guided Assembly of Collagen Layers on Mica Surfaces"
    Langmuir 27 10907-10913 (2011).   Link   PDF
48. T. Kim, W. Hwang, and R. D. Kamm, "Dynamic Role of Cross-linking Proteins in Actin Rheology"
    Biophys. J. 101 1597-1603 (2011).   Access
49. J. M. Hirshburg, K. M. Ravikumar, W. Hwang and A. T. Yeh, "Molecular basis for optical clearing of collagenous tissues"
    J. Biomed. Optics 15, 055002 (2010).   Access
50. G. Bao, R. D. Kamm, W. Thomas, W. Hwang, D. A. Fletcher, A. Grodzinsky, C. Zhu, and M, R. K. Mofrad, "Molecular Biomechanics: The Molecular Basis of How Forces Regulate Cellular Function"
    Cell. Molec. Bioeng. 3 91-105 (2010).   Link   PDF
51. M. J. Lang and W. Hwang, "Motor Proteins: Kinesin Drives with an Underhead Cam"
    Curr. Biol. 20 R408-R410 (2010).   Access
52. S. K. Lakkaraju and W. Hwang, "Critical buckling length versus persistence length: What governs biofilament conformation?"
    Phys. Rev. Lett. 102 118102 (2009).   Link   PDF
53. J. Park, B. Kahng, and W. Hwang, "Thermodynamic selection of steric zipper patterns in the amyloid cross-β spine"
    PLoS Comp. Biol. 5 e1000492 (2009).   Access
54. J. A. Noel, W. Teizer, and W. Hwang, "Surface manipulation of microtubules using self-assembled monolayers and electrophoresis"
    ACS Nano 3 1938-1946 (2009).   Link   PDF
55. J. A. Noel, W. Teizer, and W. Hwang, "Antifouling self-assembled monolayers on microelectrodes for patterning biomolecules"
    J. Visualized Exp. 30 doi:10.3791/1390 (2009).   Access
56. T. Kim, W. Hwang, H. Lee, and R. D. Kamm, "Computational analysis of viscoelastic properties of crosslinked actin networks"
    PLoS Comp. Biol. 5 e1000439 (2009).   Access
57. W. Hwang and M. J. Lang, "Mechanical design of translocating motor proteins"
    Cell Biochem. Biophys. 54 11-22 (2009)   Link   PDF
58. M.-E. Aubin-Tam, W. Hwang, and K. Hamad-Schifferli, "Site-directed nanoparticle labeling of cytochrome c"
    Proc. Natl. Acad. Sci. USA 106 4095-4100 (2009).   Access
59. S. K. Lakkaraju and W. Hwang, "Modulation of elasticity in functionally distinct domains of the tropomyosin coiled-coil"
    Cell. Molec. Bioeng. 2 57-65 (2009).   Link   PDF
60. T. Kim, W. Hwang, and R. D. Kamm, "Computational analysis of a cross-linked actin-like network"
    Exp. Mech. 49 91-104 (2009).   Link   PDF
61. F. Taraballi, M. Campione, A. Sassella, A. L. Vescovi, A. Paleari, W. Hwang, and F. Gelain, "Effect of functionalization on the self-assembling propensity of β-sheet forming peptides"
    Soft Matter 5 660-668 (2009).   Link   PDF
62. A. S. Khalil, D. C. Appleyard, A. K. Labno, A. Georges, M. Karplus, A. M. Belcher, W. Hwang, and M. J. Lang, "Kinesin's cover-neck bundle folds forward to generate force"
    Proc. Natl. Acad. Sci. USA 105 19247-19252 (2008).   Access
63. K. M. Ravikumar and W. Hwang, "Region-specific role of water in collagen unwinding and assembly"
    Proteins: Struct. Func. Bioinf. 72 1320-1332 (2008).   Link   PDF
64. W. Hwang, M. J. Lang, and M. Karplus, "Force generation in kinesin hinges on cover-neck bundle formation"
    Structure 16 62-71 (2008).   Access   Journal Cover
65. W. Hwang, "Calculation of conformation-dependent biomolecular forces"
    J. Chem. Phys. 127 175104 (2007).   Link   PDF
66. K. M. Ravikumar, J. D. Humphrey, and W. Hwang, "Spontaneous unwinding of a labile domain in a collagen triple helix"
    J. Mech. Mater. Struct. 2 999-1010 (2007).   Access
67. J. Park, B. Kahng, R. D. Kamm, and W. Hwang, "Atomistic simulation approach to a continuum description of self-assembled β-sheet filaments"
    Biophys. J. 90 2510-2524 (2006).   Access
68. A. Lomander, W. Hwang, and S. Zhang, "Hierarchical self-assembly of a coiled-coil peptide into fractal structure"
    Nano. Lett. 5 1255-1260 (2005).   Link   PDF
69. W. Hwang, S. Zhang, R. D. Kamm, and M. Karplus, "Kinetic control of dimer structure formation in amyloid fibrillogenesis"
    Proc. Natl. Acad. Sci. USA 101 12916-12921 (2004).   Access
70. J. R. Lu, S. Perumal, I. Hopkinson, J. R. P. Webster, J. Penfold, W. Hwang, and S. Zhang, "Interfacial nano-structuring of designed peptides regulated by solution pH"
    J. Am. Chem. Soc. 126 8940-8947 (2004).   Link   PDF
71. W. Hwang, D. M. Marini, R. D. Kamm, and S. Zhang, "Supramolecular Structure of Helical Ribbons Self-Assembled from a β-Sheet Peptide"
    J. Chem. Phys. 118 389-397 (2003).   Link   PDF
72. S. Zhang, D. M. Marini, W. Hwang, and S. Santoso, "Design of Nano Biological Materials through Self-Assembly of Peptides and Proteins"
    Curr. Opin. Chem. Biol. 6 865-871 (2002).   Link   PDF
73. S. Santoso, W. Hwang, W. Hartman, and S. Zhang, "Self-assembly of Surfactant-like Peptides with Variable Glycine Tails to Form Nanotubes and Nanovesicles"
    Nano Lett. 2, 687-691 (2002).   Link   PDF
74. D. M. Marini, W. Hwang, S. Zhang, D. A. Lauffenburger, and R. D. Kamm, "Left-Handed Helical Ribbon Intermediates in the Self-Assembly of a β-Sheet Peptide"
    Nano Lett. 2, 295-299 (2002).   Link   PDF
75. W. Hwang, P. Krapivsky, and S. Redner "Fitness versus Longevity in Age-Structured Population Dynamics"
    J. Math. Biol. 44, 375-393 (2002).   Link   PDF
76. W. Hwang and S. Redner, "Dissolution in a Field"
    Phys. Rev. E 64, 041606 (2001).   Link   PDF
77. W. Hwang and S. Redner, "Infiltration Through Porous Media"
    Phys. Rev. E 63, 021508 (2001).   Link   PDF
78. W. Hwang, P. Krapivsky and S. Redner, "Does Good Mutation Help You Live Longer?"
    Phys. Rev. Lett. 83, 1251-1254 (1999).   Link   PDF
79. S. Kwon, W. Hwang, and H. Park "Dynamic Behavior of Driven Interfaces in Models with Two Absorbing States"
    Phys. Rev. E 59, 4949-4952 (1999).   Link   PDF
80. W. Hwang and H. Park "Interacting Monomer-Dimer Model with Infinitely Many Absorbing States"
    Phys. Rev. E 59, 4683-4686 (1999).   Link   PDF
81. W. Hwang, S. Kwon, H. Park, and H. Park "Critical Phenomena of Nonequilibrium Dynamical Systems with Two Absorbing States"
    Phys. Rev. E 57, 6438-6450 (1998).   Link   PDF