Publications in Chronological Order

Manuscripts under review

  1. Network models for characterization of trabecular bone. A. Mondal, C. Nguyen, X. Ma, A. E. Elbanna, and J. M. Carlson. 2018. arXiv:1811.00092


Publications

  1. Microbiome interactions shape host fitness. A. L. Gould, V. Zhang, L. Lamberti, E. W. Jones, B. Obadia, N. Korasidis, A. Gavryushkin, J. M. Carlson, N. Beerenwinkel, and W. B. Ludington. PNAS doi:10.1073/pnas.1809349115 (advance online publication), 2018.


  2. Modeling individual and group evacuation decisions during wildfires. C. Nguyen, K. J. Schlesinger, F. Han, I. Gur, J. M. Carlson. Fire Technology doi:10.1007/s10694-018-0770-7 (advance online publication), 2018.


  3. Novel magnetic resonance technique for characterizing mesoscale structure of trabecular bone. C. Nguyen, K. J. Schlesinger, T. W. James, K. M. James, R. L. Sah, K. Masuda, and J. M. Carlson. Royal Soc Open Sci 5(8):180563, 2018.


  4. In silico analysis of antibiotic-induced Clostridium difficile infection: Remediation techniques and biological adaptations. E. W. Jones and J. M. Carlson. PLOS Comput Bio 14(2):e1006001, 2018.


  5. Improving resolution of dynamic communities in human brain networks through targeted node removal. K. J. Schlesinger, B. O. Turner, S. T. Grafton, M. B. Miller, and J. M. Carlson PLOS ONE 12(12):e0187715, 2017.


  6. Sensitivity analysis of human brain structural network construction. K. Wei, M. Cieslak, C. Greene, S. T. Grafton, and J. M. Carlson. Network Neuroscience 1(0):1–37, 2017.


  7. Data-driven models for individual and group decision making. C. Nguyen, K. J. Schlesinger, and J. M. Carlson. In the Proceedings of the 2017 IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining. doi:10.1145/3110025.3116204, 2017.


  8. Age-dependent changes in task-based modular organization of the human brain. K. J. Schlesinger, B. O. Turner, B. Lopez, M. B. Miller, and J. M. Carlson. Neuroimage 146:741-762, 2017.


  9. Collective decision dynamics in group evacuation. C. Nguyen, K. J. Schlesinger, and J. M. Carlson. In the Proceedings of the Summer Computer Simulation Conference 2017. doi:10.22360/SummerSim.2017.SCSC.002, 2017.


  10. Optimizing real time vaccine allocation in a stochastic SIR model. C. Nguyen and J. M. Carlson. PLOS ONE 11(4):e0152950, 2016.


  11. Individual differences in dynamic functional brain connectivity across the human lifespan. E. N. Davison, B. O. Turner, K. J. Schlesinger, M. B. Miller, S. T. Grafton, D. S. Bassett, and J. M. Carlson. PLOS Comput Biol 12(11):e1005178, 2016.


  12. Dynamic friction in sheared fault gouge: Implications of acoustic vibration on triggering and slow slip. C. K. C. Lieou, A. E. Elbanna, and J. M. Carlson. J Geophys Res Solid Earth 121:1483–1496, 2016.


  13. Optimal vaccination in a stochastic epidemic model of two non-interacting populations. E. C. Yuan, D. L. Alderson, S. Stromberg, and J. M. Carlson. PLOS ONE 10(2):e0115826, 2015.


  14. Brain network adaptability across task states. E. N. Davison, K. J. Schlesinger, D. S. Bassett, M.-E. Lynall, M. B. Miller, S. T. Grafton, and J. M. Carlson. PLoS Comput Biol 11(1):e1004029, 2015.


  15. Stick-slip instabilities in sheared granular flow: The role of friction and acoustic vibrations. C. K. C. Lieou, A. E. Elbanna, J. S. Langer, and J. M. Carlson. Phys Rev E 92:022209, 2015.


  16. A two-scale model for sheared fault gouge: Competition between macroscopic disorder and local viscoplasticity. A. E. Elbanna and J. M. Carlson. J Geophys Res Solid Earth 119:4841–4859, 2014.


  17. Shear flow of angular grains: Acoustic effects and nonmonotonic rate dependence of volume. C. K. C. Lieou, A. E. Elbanna, J. S. Langer, and J. M. Carlson. Phys Rev E 90:032204, 2014.


  18. Grain fragmentation in sheared granular flow: Weakening effects, energy dissipation, and strain localization. C. K. C. Lieou, A. E. Elbanna, and J. M. Carlson. Phys Rev E 89:022203, 2014.


  19. Measuring and modeling behavioral decision dynamics in collective evacuation. J. M. Carlson, D. L. Alderson, S. P. Stromberg, D. S. Bassett, E. M. Craparo, F. Guiterrez-Villareal, and T. Otani. PLOS ONE 9(2): e87380, 2014.


  20. Structurally-constrained relationships between cognitive states in the human brain. A. M. Hermundstad, K. S. Brown, D. S. Bassett, E. M. Aminoff, A. Frithsen, A. Johnson, C. M. Tipper, M. B. Miller, S. T. Grafton, and J. M. Carlson. PLOS Comput Biol 10(5): e1003591, 2014.


  21. Co-evolutionary immune system dynamics driving pathogen speciation. K. J. Schlesinger, S. P. Stromberg, and J. M. Carlson. PLOS ONE 9(7): e102821, 2014.


  22. Resolving structural variability in network models and the brain. F. Klimm, D.S. Bassett, J. M. Carlson, and P. J. Mucha. PLOS Comput Biol 10(3): e1003491, 2014.


  23. Resolving anatomical and functional structure in human brain organization: Identifying mesoscale organization in weighted network representations. C. Lohse, D. S. Bassett, K. O. Lim, and J. M. Carlson. PLOS Comput Biol 10(10): e1003712, 2014.


  24. Sacrificial bonds and hidden length in biomaterials -- a kinetic, constitutive description of strength and toughness in bone. C. K. C. Lieou, A. E. Elbanna, and J. M. Carlson. Phys Rev E 88:012703, 2013.


  25. Reproducible paired sources from concurrent EEG-fMRI data using BICAR. K. S. Brown, R. Kasper, B. Giesbrecht, J. M. Carlson, and S. T. Grafton. J Neurosci Methods 219(2):205–219, 2013.


  26. Dynamics of polymer molecules with sacrificial bond and hidden length systems: Towards a physically-based mesoscopic constitutive law. A. E. Elbanna and J. M. Carlson. PLOS ONE8(4): e56118, 2013.


  27. Diversity of T-cell responses. S. P. Stromberg and J. M. Carlson. Phys Biol 10(2):025002, 2013.


  28. Robust detection of dynamic community structure in networks. D. S. Bassett, M. A. Porter, N. F. Wymbs, S. T. Grafton, J. M. Carlson, and P. J. Mucha. Chaos 23:013142, 2013.


  29. Structural foundations of resting-state and task-based functional connectivity in the human brain. A. M. Hermundstad, D. S. Bassett, K. S. Brown, E. M. Aminoff, D. Clewett, S. Freeman, A. Frithsen, A. Johnson, C. Tipper, M. B. Miller, S. T. Grafton, and J. M. Carlson. PNAS 110(15):6169-74, 2013.


  30. A decision making framework for wildfire suppression. N. Petrovic and J. M. Carlson, International Journal of Wildland Fire doi.org/10.1071/WF11140, 2012.


  31. BICAR: A new algorithm for multiresolution spatiotemporal data fusion. K. S. Brown, S. T. Grafton, and J. M. Carlson, PLOS ONE 7(11):e50268, 2012.


  32. Collective decision dynamics in the presence of external drivers. D. S. Bassett, D. L. Alderson, and J. M. Carlson Phys Rev E 86:036105, 2012.


  33. Dynamic resource allocation in disaster response: Tradeoffs in wildfire suppression. N. Petrovic, D. L. Alderson, and Jean M. Carlson. PLOS ONE 7(4): e33285, 2012.


  34. Structural drivers of function in information processing networks. A. M. Hermundstad, K. S. Brown, D. S. Bassett, and J. M. Carlson. In the Proceedings of the Forty-Fifth Asilomar Conference on Signals, Systems, and Computers, 837-841, 2011.


  35. Architectural constraints on learning and memory function. A. M. Hermundstad, K. S. Brown, D. S. Bassett, and J. M. Carlson. BMC Neuroscience 12(Suppl. 1):P31, 2011.


  36. Dynamic reconfiguration of human brain networks during learning. D. S. Bassett, N. Wymbs, M. A. Porter, P. J. Mucha, J. M. Carlson, S. T. Grafton. PNAS 108(18):7641-7646, 2011


  37. Learning, memory, and the role of neural network architecture. A. M. Hermundstad, K. S. Brown, D. S. Bassett, and J. M. Carlson. PLOS Comput Biol 7:e1002063, 2011.


  38. Pupillometric evidence for decoupling of attention from perceptual input during offline thought. J. Smallwood, K. S. Brown, C. Tipper, B. Giesbrecht, M. S. Franklin, M. D. Mrazek, J. M. Carlson, and J. W. Schooler. PLOS ONE 6: e18298, 2011.


  39. Dynamic reconfiguration of human brain networks during learning, Bassett, D. S., Wymbs, N., Porter, M. A., Mucha, P., Carlson, J. M., and S. A. Grafton, Proc. Nat. Acad. Sci. 108, 7645 (2011).


  40. Conserved and variable architecture of human white matter connectivity, Bassett, D. S., Brown, J. A., Deshpande, V., Carlson, J. M., and S. A. Grafton, Neuroimage, 54(2):1262-1279, (2011).


  41. Modeling long-term fire regimes of southern California shrublands, Peterson S. H., Moritz M. A., Morais M. E., Dennison P. E., and Carlson J. M., International Journal of Wildland Fire, 20, 1-16, (2011).


  42. Friction, Fracture, and Earthquakes, Daub, E. G., and J. M. Carlson, Ann. Rev. of Cond. Matt. Phys. Vol. 1: 397-418, (doi:10.1146/annurev-conmatphys-070909-104025), August 2010.


  43. Energetics of strain localization in a model of seismic slip, Hermundstad, A. M., Daub, E. G., and J. M. Carlson, Journal of Geophysical Research, 115:B06320-1-9, (2010).


  44. Pulse-like, crack-like, and supershear earthquake ruptures with shear strain localization, Daub, E. G., Manning, M. L., and Carlson, J. M., J. Geophys. Res., 115, B05311, doi:10.1029/2009JB006388 (2010).


  45. The Suppression of Immune System Disorders by Passive Attrition, Stromberg, S. P. and Carlson, J. M., PLoS One 5(3):e9648, (2010).


  46. Improving human brain mapping via joint inversion of brain electrodynamics and the BOLD signal, Brown, K. S., Ortigue, S., Grafton, S. T., and J. M. Carlson, Neuroimage, 49, 2401-2415, (2010).


  47. Deformation and Localization in Earthquake Ruptures and Stick-Slip Instabilities 
    abstract  pdf
    Daub, E. G., thesis (2009).

  48. Stick-slip instabilities and shear strain localization in amorphous materials 
    abstract  pdf
    E. G. Daub and J. M. Carlson, Phys. Rev. E. 80, 066113 (2009).

  49. Dynamics of Immune System Vulnerabilities 
    abstract  pdf
    Sean P. Stromberg, thesis (2009).

  50. Fire in the Earth System 
    abstract  pdf
    David M. J. S. Bowman, J. K. Balch, P. A., William, J. Bond, J. M. Carlson, M. A. Cochrane, C. M. D’Antonio, R. S. DeFries, J. C. Doyle, S. P. Harrison, F. H. Johnston, J. E. Keeley, M. A. Krawchuk, C. A. Kull, J. B. Marston, M. A. Moritz, I. C. Prentice, C. I. Roos, A. C. Scott, T. W. Swetnam, G. R. van der Werf, S. J. Pyne, Science, Vol. 324. no. 5926, pp. 481 - 484 DOI: 10.1126/science.1163886, (2009).

  51. Seismicity in a Model Governed by Competing Frictional Weakening and Healing Mechanisms 
    abstract pdf
    G. Hillers, J. M. Carlson, and R. J. Archuleta, Geophysical Journal International, Volume 178, Number 3, 1363-1383(21), (2009).

  52. Using ICA and realistic BOLD models to obtain joint EEG/fMRI solutions to the problem of source localization 
    abstract pdf
    T. Brookings, S. Ortigue, S. Grafton, and J. Carlson, NeuroImage, 15;44(2):411-20,(2009).

  53. Rate dependent shear bands in a shear transformation zone model of amorphous solids 
    abstract pdf
    M. L. Manning, E. G. Daub, J. S. Langer, and J. M. Carlson, Phys Rev E, 79, 016110 (2009).

  54. Constraining Earthquake Source Inversions with GPS Data 1: Resolution Based Removal of Artifacts  
    abstract pdf
    Page, Morgan T., Susana Custódio, Ralph J. Archuleta, and J. M. Carlson, submitted to JGR - Solid Earth.(2009).

  55. Mapping live fuel moisture with MODIS data: A multiple regression approach 
    abstract  pdf
    Seth H. Peterson, Dar A. Roberts, and Philip E. Dennison, Remote Sensing of Evironment, Volume 112, Issue 12, Pages 4272-4284, doi:10.1016/j.rse.2008.07.012, (2008).

  56. What grid cells convey about rat location 
    abstract  pdf
    I. R. Fiete, Y. Burak, T. Brookings, The Journal of Neuroscience, 28(27):6858-6871; doi:10.1523/JNEUROSCI.5684-07.2008, (2008).

  57. Shear strain localization in elastodynamic rupture simulations 
    abstract pdf
    E.G. Daub, M.L. Manning, and J.M. Carlson, Geophysical Research Letters, 35, L12310, doi:10.1029/2008GL033835 (2008).

  58. A constitutive model for fault gouge deformation in dynamic rupture simulations 
    abstract pdf
    E.G. Daub and J.M. Carlson, Journal of Geophysical Research, 113, B12309, doi:10.1029/2007JB003577 (2008).

  59. Momentum transport in granular flows  
    abstract pdf
    Lois, G., Lemaitre, A., and Carlson, J.M., Computers and Mathematics with Applications 55, 175-183 (2008).

  60. Strain localization in a shear transformation zone model for amorphous solids 
    abstract pdf
    M.L. Manning, J.S. Langer, and J.M. Carlson, Phys. Rev. E 76 056106 (2007).

  61. Descriptor approach for eliminating spurious eigenvalues in hydrodynamic equations 
    abstract pdf
    M.L. Manning, B. Bamieh, and J.M. Carlson, Journal of Computational Physics, arXiv:0705.1542v2 [physics.comp-ph] (2007).

  62. Steady-state, effective-temperature dynamics in a glassy material.
    abstract pdf
    J. S. Langer and M. L. Manning. Phys. Rev. E 76 056107 (2007).

  63. Force networks and the dynamic approach to jamming in sheared granular media
     abstract pdf 
    Lois, G., and Carlson, J.M., Europhys. Lett.80, 58001 (2007)

  64. Spatial force correlations in granular shear flow I: numerical evidence  
    abstract pdf 
    Lois, G., Lemaitre, A., and Carlson, J. M., Phys. Rev. E.76, 021302 (2007)

  65. Spatial force correlations in granular shear flow II: theoretical implications
    abstract  pdf 
    Lois, G., Lemaitre, A., and Carlson, J. M., Phys. Rev. E.76, 021303 (2007)

  66. Microstructure and Modeling of Granular Materials
    abstract  pdf
    G. Lois, thesis (2006)

  67. Emergence of multi-contact interactions in contact dynamics simulations of granular shear flows 
    abstract   pdf
    G. Lois, A. Lemaitre and J. M. Carlson, Europhysics Letters 76, 318 (2006)

  68. Methodologies for Earthquake Hazard Assessment: Model Uncertainty and the WGCEP-2002 Forecast
    abstract  pdf
    Page, M. T. and J. M. Carlson (2006) Bull. Seism. Soc. Am. 96, 5, doi: 10.1785/0120050195

  69. Robustness and Fragility in Immunosenescence
    abstract  Small pdf  Large pdf
    Stromberg SP, Carlson J (2006) PLoS Comput Biol 2(11): e160. doi:10.1371/journal.pcbi.002016

  70. Numerical Tests of Constitutive Laws for Dense Granular Flows
    abstract  pdf
    G. Lois, A. Lemaitre and J. M. Carlson, Physical Review E 72, 051303 (2005).

  71. Distinguishing Barriers and Asperities in Near-Source Ground Motion
    abstract  pdf
    Page, M. T., E. M. Dunham, and J. M. Carlson (2005) J. Geophys. Res. - Solid Earth.  110, B11302, doi:10.1029/2005JB003736.

  72. Highly optimized tolerance and power laws in dense and sparse resource regimes
    abstract ps pdf
    Manning, M, Carlson, JM & Doyle, J (2005) Phys. Rev. E 72, article 016108.

  73. Three mechanisms for power laws on the Cayley tree
    abstract ps pdf
    Brookings, T, Carlson, JM & Doyle, J (2005) Phys. Rev. E 72, article 056120.

  74. Robustness and the Internet: Theoretical Foundations abstract 
    pdf 
    Doyle, J.C. S. Low, S., Carlson, J.M., Paganini, F., Vinnicombe, G., Willinger, W., and Parillo, P. (2005) Robust Design: A Repertoire of Biological, Ecological, and Engineering Case Studies (Santa Fe Institute Studies on the Sciences of Complexity) , Eric Jen, Editor, Oxford University Press.

  75. Wildfires, Complexity and Highly Optimized Tolerance
    abstract pdf
    Moritz, M., Morias, M., Summerell, L., Carlson, J.M., and J. Doyle (2005) Proc. Nat. Acad. Sci.102, 17912-17917.

  76. Evolutionary Dynamics and Highly Optimized Tolerance  
    abstract pdf 
    Zhou, T., Carlson, J.M., and Doyle, J. (2005) J. Theor. Bio. 236 , 438-447.

  77. Boundary lubrication with a glassy interface abstract
    pdf
    A. Lemaitre and J. M. Carlson, Physical Review E 69, 61611 (2004)

  78. Near-source Ground Motion from Steady State Dynamic Rupture Pulses
    abstract pdf  supplement-pdf
    Dunham, E & Archuleta, R (2004) Geophys. Res. Lett. 32, L03302, doi:10.1029/2004GL021793.

  79. Dissipative interface waves and the transient response of a three dimensional sliding interface with Coulomb friction
    abstract  pdf
    Dunham, E (2004) J. Mech. Phys. Solids. 53,327-357.

  80. Evidence for a supershear transient during the 2002 Denali earthquake
    abstract   pdf
    Dunham, E & Archuleta, R (2004) Bull. Seism. Soc. Am. 94, S256-S268.

  81. Coarse graining and control theory model reduction
    ps  pdf
    Reynolds, D.E. (submitted to J. Stat. Phys., 2003).

  82. A Supershear Transition Mechanism for Cracks
    abstract  pdf
    Dunham, E, Favreau, P, & Carlson, JM (2003) Science 299, 1557-1559.

  83. Complexity and robustness
    abstract ps pdf
    Carlson, JM & Doyle, J (2002) Proc. Nat. Acad. Sci. 99 , 2538-2545.

  84. Mutation, specialization, and hypersensitivity in HOT
    abstract ps pdf
    Zhou, T, Carlson, JM & Doyle, J (2002) Proc. Nat. Acad. Sci. 99 , 2049-2054.

  85. Design degrees of freedom and mechanisms for complexity
    abstract ps pdf
    Reynolds, D, Carlson, JM & Doyle, J (2002) Phys. Rev. E 66, article 016108.

  86. Dynamics and changing environments in HOT
    abstract ps pdf
    Zhou, T & Carlson, JM (2001) Phys. Rev. E 62, 3197-3204.

  87. Highly Optimized Tolerance in epidemic models incorporating local optimization and regrowth
    abstract ps pdf
    Robert, C, Carlson, JM & Doyle, J (2001) Phys. Rev. E 63 , article 056122.

  88. Rupture pulse characterization: Self-healing, self-similar, expanding solutions in a continuum model of fault dynamics
    abstract  ps  pdf
    Nielson, SB & Carlson, JM (2000) Bull. Seismol. Soc. Amer. 90,1480-1497.

  89. Influence of friction and fault geometry on earthquake rupture
    abstract   ps   pdf
    Nielson, SB, Carlson, JM & Olsen, KB (2000) J. Geophys. Res.-Solid Earth 105, 6069-6088.

  90. HOT: Robustness and design in complex systems
    abstract ps pdf
    Carlson, JM & Doyle, J (2000) Phys. Rev. Lett. 84, 2529-2532.

  91. Power laws, HOT, and generalized source coding
    abstract ps pdf
    Doyle, J & Carlson, JM (2000) Phys. Rev. Lett. 84, 5656-5659.

  92. HOT: A mechanism for power laws in designed systems
    abstract ps pdf
    Carlson, JM & Doyle, J (1999) Phys. Rev. E 60, 1412-1427.

  93. Bifurcations from steady sliding to slip in boundary lubrication
    abstract  ps   pdf
    Batista, AA & Carlson, JM (1998) Phys. Rev. E 57, 4986-4996.

  94. Constitutive relation for the friction between lubricated surfaces
    abstract  ps   pdf
    Carlson, JM & Batista, AA (1996) Phys. Rev. E 53, 4153-4165.