Publications

97. J. C. Chang, Y. Liu, and Tom Chou, High-resolution reconstruction of cellular traction-force distributions: the role of physical constraints and compressed optimization, In Press: Biophysical Journal, (2017). (pdf)

96. Yao-Li Chuang, Tom Chou, and M. R. D'Orsogna, Age-structured social interactions enhance radicalization and extremism, Submitted To: Journal of Mathematical Sociology, (2017). (pdf)

95. J. De Anda, E. Y. Lee, C. K. Lee, R. Bennett, X. Ji, Mark C. Harrison, S. Soltani, M. C. Harrison, A. E. Baker, Y. Luo, Tom Chou, G. A. O'Toole, A. M. Armani, R. Golestanian, and G. C. L. Wong, High-speed 4D computational microscopy of flagellum-driven surface motility in Pseudomonas aeruginosa, ACS Nano, 11, 9340--9351, (2017). (pdf)

94. Lae Un Kim, Maria D'Orsogna, and Tom Chou, Perturbing the hypothalamic-pituitary-adrenal stress response system: mathematical modeling to improve diagnosis of post-traumatic and related stress disorders, In Press: Computational Psychiatry, (2017). (pdf)

93. Song Xu, S. Kim, I. S. Y. Chen, and Tom Chou, Mapping clone extinction and resurrection to intermittent hematopoietic stem cell differentiation: Analysis of a decade-long clone tracking study in rhesus macaque, Under revision: PLoS Computational Biology, (2017). (pdf)

92. Sam C. P. Norris, Tom Chou, and Andrea M. Kasko, Diffusion of photoabsorbing degradation byproducts in photodegradable polymer networks, Macromolecular Theory and Simulation, 26, 1700007, (2017). (pdf)

91. G. Suryawanshi, Song Xu, Yiming Xie, Tom Chou, Namshin Kim, Irvin S.Y. Chen, and Sanggu Kim, Bidirectional Retroviral Integration Site PCR Methodology and Quantitative Data Analysis Workflow, Journal of Visualized Experiments, 124, e55812, (2017). (pdf)

90. Yao-Li Chuang, M. R. D'Orsogna, and Tom Chou, A bistable belief model for radicalization and conflict, Quarterly of Applied Mathematics, LXXV, 19-37 (2016). (pdf)

89. Bhaven Mistry, M. D'Orsogna, N. Webb, B. Lee, and Tom Chou, Quantifying sensitivity of HIV-1 viral entry to receptor and coreceptor expression through kinetic models, Journal of Physical Chemistry B, 120, 6189-6199 (2016). (pdf)

88. Tom Chou and C. D. Greenman, A hierarchical kinetic theory of birth, death, and fission in age-structured interacting populations, Journal of Statistical Physics, 164, 49-76, (2016). (pdf)

87. Lae-Un Kim, Maria R. D'Orsogna, and Tom Chou, Neuroendocrine dynamics in stress disorder: models of timing, onset, and treatment, BMC Biology Direct, 11, 13 (2016). (pdf)

86. Yao-li Chuang, Maria R. D'Orsogna, and Tom Chou, Swarming in viscous fluids: three-dimensional patterns in swimmer- and force-induced flows, Physical Review E, 93, 043112, (2016). (pdf)

85. Chris D. Greenman and Tom Chou, A kinetic theory of age-structured stochastic birth-death processes, Physical Review E, 93, 012112, (2016). (pdf)

84. Joshua C. Chang, Pak-Wing Fok, and Tom Chou, Bayesian Uncertainty Quantification for Bond Energies and Mobilities Using Path Integral Analysis, Biophysical Journal, 109, 966-974 (2015). (pdf)

83. S. Goyal, S. Kim, I. Chen, and Tom Chou, Mechanisms of blood homeostasis: lineage tracking and a neutral model of cell populations in rhesus macaque, BMC Biology, 13, 85, (2015). (pdf)

82. Tom Chou and Yu Wang, First passage times in differentiation and evolution in the presence of bottlenecks, deserts, and oases, Journal of Theoretical Biology, 372, 65-73, (2015). (pdf)

81. N. Amini, S. Nowroozizadeh, N. Cirineo, S. Henry, T. Chang, Tom Chou, A. L. Coleman, J. Caprioli, and K. Nouri-Mahdavi, Influence of The Disc-Fovea Angle on Limits of RNFL Variability and Glaucoma Discrimination, Investigative Ophthalmology & Visual Science, 55, 7332-7342, (2014). (pdf)

80. K. Chikere, N. E. Webb, Tom Chou, K. Borm, J. Sterjovski, P. R. Gorry and B. Lee, Distinct HIV-1 entry phenotypes are associated with transmission, subtype specificity, and resistance to broadly neutralizing antibodies, Retrovirology, 11, 48, (2014). (pdf)

79. Maria R. D'Orsogna, Qi Lei, and Tom Chou, First assembly times and equilibration in stochastic coagulation-fragmentation, Journal of Chemical Physics, 143, 014112, (2015). (pdf)

78. S. Nowroozizadeh, N. Cirineo, N. Amini, S. Knipping, T. Chang, Tom Chou, J. Caprioli, and K. Nouri-Mahdavi, Influence of Correction of Ocular Magnification on Performance of Spectral-Domain Retinal Nerve Fiber Layer Measurements, Investigative Ophthalmology & Visual Science, 55, 3439-3446, (2014). (pdf)

77. Joshua C. Chang, Van M. Savage, and Tom Chou, A path integral approach to Bayesian inference for inverse problems using the semiclassical approach, Journal of Statistical Physics, 157, 582-602, (2014). (pdf)

76. Bijan Berenji, Tom Chou, and M. R. D'Orsogna, Recidivism and rehabilitation of criminal offenders: a carrot and stick evolutionary game, PLoS One, 9, e85531, (2014). (pdf)

75. Tom Chou and M. R. D'Orsogna, First Passage Problems in Biology, in First-Passage Phenomena and Their Applications, eds. R. Metzler, G. Oshanin and S. Redner (World Scientific, 2014), pp. 306-345. (pdf)

74. Joshua C. Chang and Tom Chou, Iterative graph cuts for image segmentation with a nonlinear statistical shape prior, Journal of Mathematical Imaging and Vision, 49, 87-97, (2014). (pdf)

73. Hamid Hosseini, Nariman Nassiri, Parham Azarbod, JoAnn Giaconi, Tom Chou, Joseph Caprioli, and Kouros Nouri-Mahdavi, Measurement of the Optic Disc Vertical Tilt Angle With Spectral-Domain Optical Coherence Tomography and Influencing Factors, American Journal of Ophthalmology, 156, 737-744, (2013). (pdf)

72. M. R. D'Orsogna, Bingyu Zhao, Bijan Berenji, and Tom Chou, Combinatoric analysis of heterogeneous stochastic self-assembly, Journal of Chemical Physics, 139, 121918, (2013). (pdf)

71. Pak-Wing Fok and Tom Chou, Identifiability of age-dependent branching processes from extinction probabilities and number distributions, Journal of Statistical Physics, 152, 769–786, (2013). (pdf)

70. Pak-Wing Fok, Qunhui Han, Tom Chou, Reconstruction of persistent random walks from exit time distributions, The IMA Journal of Applied Mathematics, 80, 1-23, (2013). (pdf)

69. Kelechi Chikere, Tom Chou, Paul R. Gorry, and Benhur Lee, Affinofile Profiling: How efficiency of CD4/CCR5 usage impacts the biological and pathogenic phenotype of HIV, Virology, 435, 81-91, (2013). (pdf)

68. Romain Yvenic, M. R. D'Orsogna, and Tom Chou, First passage times in stochastic self-assembly, Journal of Chemical Physics, 137, 244107, (2012). (pdf)

67. Tom Chou and Michael Siegel, The mechanics of retinal detachment, Physical Biology, 9, 046001, (2012). (pdf)

66. Tom Chou, K. Mallick, and R. K. P. Zia, Non-equilibrium statistical mechanics: Fundamental issues, a paradigmatic model, and applications to biological transport, Reports on Progess in Physics, 74, 116601, (2011). (pdf)

65. M. R. D'Orsogna, G. Lakatos, and Tom Chou, Stochastic nucleation of incommensurate clusters, Journal of Chemical Physics, 136, 084110, (2012). (pdf)

64. J. Chang, K. C. Brennan, and T. Chou, Tracking monotonically advancing boundaries in image sequences using graph cuts and recursive kernel shape priors, IEEE Transactions on Medical Imaging, 31, 1008-1020, (2012). (pdf)

63. Tom Chou and M. R. D'Orsogna, Coarsening and accelerated equilibration in mass-conserving heterogeneous nucleation, Phys. Rev. E, 84, 011608, (2011). (pdf)

62. Melissa Gibbons, Tom Chou and M. R. D'Orsogna, Diffusion-dependent mechanisms of receptor engagement and viral entry, J. Phys. Chem. B, 114, 15403-15412, (2010). (pdf)

61. B. Hertz Shargel, M. R. D'Orsogna, and Tom Chou, Arrival times in a Zero-Range Process with injection and decay, J. Phys. A, 43, 305003, (2010). (pdf)

60. Pak-Wing Fok and Tom Chou, Reconstruction of bond energy profiles from multiple first passage time distributions, Proc. Royal Soc. A, 466, 3479-3499, (2010). (pdf)

59. Filippo Posta and Tom Chou, A mathematical model for intercellular signaling during epithelial wound healing, Journal of Theoretical Biology, 266, 70-78, (2010). (pdf)

58. Sarah A. Nowak, Buddhapriya Chakrabarti, Tom Chou, and Ajay Gopinathan, Frequency-dependent Chemotactic Target Selection, Physical Biology, 7, 026003, (2010). (pdf)

57. Sarah A. Nowak and Tom Chou, Models of dynamic extraction of lipid tethers from cell membranes, Physical Biology, 7, 026002, (2010). (pdf)

56. Benjamin H. Shargel and Tom Chou, Fluctuation Theorems for Entropy Production and Heat Dissipation in Periodically Driven Markov Chains, J. Stat. Phys., 137, 165-188, (2009). (pdf)

55. M. D'Orsogna, and Tom Chou, Optimal cytoplasmic transport in viral infections, PLoS One, 4, e8165, (2009). (pdf)

54. F. Posta, M. D'Orsogna, and Tom Chou, Enhancement of cargo processivity by cooperating molecular motors, Physical Chemistry and Chemical Physics, 11, 4851-4869, (2009). PMID:19506760 (pdf)

53. Tom Chou, Enhancement of charged macromolecule capture by nanopores in a salt gradient, J. Chem. Phys., 131, 034703, (2009). PMID:19624217 (pdf)

52. K. G. Lassen, et al., Elite suppressor-derived HIV-1 envelope glycoproteins exhibit reduced entry efficiency and kinetics, PLoS Pathogens , 5, e1000377, (2009). PMCID:PMC2661022 (pdf)

51. Pak-Wing Fok and Tom Chou, Accelerated search kinetics mediated by redox reactions of DNA repair enzymes, Biophys. J., 96,3949-3958, (2009). PMID:19450467 (pdf)

50. Pak-Wing Fok, Chin-Lin Guo,and Tom Chou, Charge-transport-mediated recruitment of DNA repair enzymes, J. Chem. Phys., 129, 235101, (2008). PMID:19102557 (pdf)

49. Sarah A. Nowak and Tom Chou, Mechanisms of receptor/coreceptor-mediated entry of enveloped viruses, Biophysical Journal, 96, 2624-2636, (2009). PMID:19348746 (pdf)

48. S. H. Johnston, M. A. Lobritz, S. Nguyen, K. Lassen, S. Delair, F. Posta, Y. J. Bryson, E. J. Arts, Tom Chou, and Benhur Lee, A quantitative metric reveals differential CD4/CCR5 usage patterns amongst HIV-1 and SIV strains, J. Virology, 83, 11016-11026, (2009). PMID:19692480

47. Sarah A. Nowak and Tom Chou, Membrane Lipid Segregation in Endocytosis, Phys. Rev. E,78, 021908, (2008). (pdf)

46. Pak-Wing Fok, and Tom Chou, Interface Growth Driven by Surface Kinetics and Convection, SIAM Appl. Math., 70, 24-39, (2009). (pdf)

45. K. S. Kim, Tom Chou, and Joseph Rudnick, Degenerate ground-state lattices of membrane inclusions, Phys. Rev. E, 78, 011401, (2008). PMID:18763950 (pdf)

44. Amit Lakhanpal and Tom Chou, Brownian ratchets driven by asymmetric nucleation of hydrolysis waves, Phys. Rev. Lett., 99, 248302, (2007). PMID:18233496 (pdf)

43. Sarah A. Nowak, Pak-Wing Fok, and Tom Chou, Dynamic Boundaries in Asymmetric Exclusion Processes, Phys. Rev. E, 76, 031135, (2007). PMID:17930227 (pdf)

42. Tom Chou, Stochastic entry of enveloped viruses: Fusion vs. endocytosis, Biophys. J., 93, 1116-1123, (2007). PMCID:PMC1929032 (pdf)

41. Tom Chou, Peeling and Sliding in Nucleosome Repositioning, Phys. Rev. Lett., 99, 058105, (2007). PMID:17930799 (pdf)

40. Tom Chou and M. R. D'Orsogna, Multistage adsorption of diffusing macromolecules and viruses, J. Chem. Phys., 127, 105101, (2007). PMID:17867780 (pdf)

39. M. R. D'Orsogna, Tom Chou, and Tibor Antal, Exact steady-states for translocation ratchets driven by random sequential adsorption, J. Phys. A, 40, 5575-5584, (2007). PMCID:PMC2600482 (pdf)

38. Tom Chou, Band gaps and the Kelvin-Helmholtz instability, Physical Rev. E, 75, 016315, (2007). PMID:17358261 (pdf)

37. Greg Lakatos, J. D. O'Brien, Tom Chou, Hydrodynamic solutions of 1D exclusion processes with spatially varying hopping rates, J. Phys. A, 39, 2253-2264, (2006). (pdf)

36. Greg Lakatos, Tom Chou, Birger Bergersen, and Gren N. Patey, First passage times of driven DNA hairpin unzipping. Physical Biology, 2, 166-174, (2005). PMID:16224122 (pdf)

35. Maria R. D'Orsogna and Tom Chou, First passage and cooperativity of queueing kinetics, Physical Review Letters, 95, 170603, (2005). PMID:16383812 (pdf)

34. Greg Lakatos, Tom Chou, and Anatoly Kolomeisky, Steady-state properties of a totally asymmetric exclusion process with periodic structure, Phys. Rev. E, 71 , 011103, (2005). PMID:15697576 (pdf)

33. Maria R. D'Orsogna and Tom Chou, Interparticle gap distributions on one-dimensional lattices. Journal of Physics A, 38, 531-542, (2005). (pdf)

32. Sally M. Blower and Tom Chou, Modelling the emergence of the "Hot Zones:" tuberculosis and the amplification dynamics of drug resistance, Nature Medicine, 10, 1111-1116, (2004). PMID:15378053 (pdf)

31. Tom Chou, Water alignment, dipolar interactions, and multiple proton occupancy during water-wire proton transport, Biophys. J., 86, 2827-2836, (2004). PMCID:PMC1304152 (pdf)

30. Tom Chou and Greg Lakatos, Clustered Bottlenecks in mRNA translation and protein synthesis, Phys. Rev. Lett. 93, 198101, (2004). PMID:15600884 (pdf)

29. William J. Foster and Tom Chou, Physical mechanisms of gas and perfluron retinopexy and sub-retinal fluid displacement, Physics in Medicine and Biology, 49, 2989-2997, (2004). PMID:15285260 (pdf)

28. Maria D'Orsogna and Tom Chou, Chiral molecule adsorption on helical polymers, Phys. Rev. E 69, 021805, (2004). PMID:14995481 (eps)

27. Kevin Klapstein, Tom Chou, and Robijn Bruinsma, Physics of RecA-mediated homologous recognition, Biophysical Journal, 87, 1466-1477, (2004). PMCID:PMC1304555 (pdf)

26. Maria D'Orsogna, M. Suchard, and Tom Chou, Interplay of chemotaxis and chemokinesis mechanisms in bacterial dynamics, Phys. Rev. E 68, 021925, (2003). PMID:14525024 (pdf)

25. Guillaume Bal and Tom Chou, On the reconstruction of diffusions using a single first-exit time distribution, Inverse Problems, 20, 1053-1065, (2003). (pdf)

24. Tom Chou, Ribosome recycling, diffusion, and mRNA loop formation in translational regulation, Biophysical Journal, 85, 755-773, (2003). PMCID: PMC1303200 (pdf)

23. Tom Chou, An exact theory of histone-DNA adsorption and wrapping, Europhysics Letters, 62, 753-759, (2003). (pdf)

22. G. Lakatos and Tom Chou, Totally asymmetric exclusion processes with particles of arbitrary size, J. Phys. A: Math. Gen., 36, 2027-2041, (2003). (pdf)

21. Tom Chou, An interacting spin-flip model for one-dimensional proton conduction, J. Phys. A: Math. Gen., 35, 4515-4526, (2002). (pdf)

20. Tom Chou, Geometry-Dependent Electrostatics near Contact Lines, Phys. Rev. Lett., 87(10), 106101, (2001). PMID:11531488 (pdf)

19. M. P. McGee and Tom Chou, Surface-dependent Coagulation Enzymes: Flow Kinetics of Factor Xa Generation on Live Cell Membranes, J. Biol. Chem., 276, 7827-7835, (2001). PMID:11108710 (pdf)

18. Tom Chou, K. Kim, and G. Oster , Statistical thermodynamics of membrane bending mediated protein-protein attractions, Biophys. J., 80, 1075-1087, (2001). PMCID:PMC1301305 (pdf)

17. Guillaume Bal and Tom Chou, Capillary-gravity wave transport over spatially random drift, Wave Motion 35, 107-124, (2002). (postscript, pdf)

16. Tom Chou and Detlef Lohse, Entropy-driven pumping in zeolites and ion channels, Physical Review Letters, 82(17), 3552-3555, (1999). (postscript, pdf)

15. Tom Chou, Kinetics and thermodynamics across single-file pores: solute permeability and rectified osmosis, Journal of Chemical Physics, 110, 606-615, (1999). (postscript, pdf)

14. Tom Chou, Band Structure of Periodically Surface-Scattered Flexural-Gravity Waves, Journal of Fluid Mechanics, 369, 333-350, (1998). (pdf)

13. Tom Chou, How Fast do Fluids Squeeze Through Microscopic Single-File Channels? Physical Review Letters, 80(1), 85-88, (1998). (postscript, pdf)

12. Tom Chou, Liquid Surface Wave Band Structure Instabilities, Physical Review Letters, 79(24), 4802-4805, (1997). (postscript, pdf)

11. E. G. Blackman and Tom Chou, Coupled Vorticity-Magnetic Field Dynamo Instability, Astrophysical Journal, 489, L95-L98, (1997). PMID:10061751 (postscript)

10. Tom Chou, Marko Jaric, and E. D. Siggia, Electrostatics of Lipid Bilayer Bending, Biophysical Journal, 72, 2042-2055, (1997). PMCID:PMC1184399

9. R. V. E. Lovelace and Tom Chou, Counter-rotating accretion disks, Astrophysical Journal, 468, L25-L28, (1996). (postscript)

8. Tom Chou and E. G. Blackman, Magnetic Field Diagnostic for Sonoluminescence, Physical Review Letters, 76(7), (1996). (postscript, pdf)

7. Tom Chou and D. R. Nelson, Dislocation Mediated Melting Near Isostructural Critical Points, Physical Review E, 52(9), (1996). PMID:9964542

6. Tom Chou, S. K. Lucas, and H. A. Stone, Capillary Wave Scattering from a Surfactant Domain, Physics of Fluids, 7(8), 1872, (1995).

5. Tom Chou and D. R. Nelson, Surface Wave Scattering from Nonuniform Interfaces, Journal of Chemical Physics, 101(10), 9022, (1994).

4. Tom Chou and D. R. Nelson, Buckling Instabilities of a Confined Colloid Crystal Layer, Physical Review E 48(6), 4611, (1993). PMID:9961143

3. K.Y. Lee, T. Chou, D.S. Chung, and E. Mazur, Direct Measurement of the Spatial Damping of Capillary Waves at Liquid-Vapor Interfaces, Journal of Physical Chemistry, 97, 12876 (1993).

2. Tom Chou and D. R. Nelson, Buckling of a Confined Colloidal Crystal, in Evolution of Surface and Thin Film Microstructure: Materials Research Society Symposium, 305, Nov. 30-Dec. 4, 1992, Boston, MA.

1. K. Q. Lao, M. D. Person, T. Chou, and L. J. Butler, Emission Spectroscopy of the Predissociative Rydberg B State of CH3I and CD3I at 193.3 nm, Journal of Chemical Physics, 89(6) 3463, (1988).


  Contact Info:

 

Mail:

Dept. of Biomathematics
University of California Los Angeles
LS 5209
Los Angeles
CA 90095-1766

 

Phone:

email : tomchou (at) ucla (dot) edu
Lab    : (310)-206-2787
Fax    : (310)-825-8685