Publication List by Topic

Theoretical immunology

An overview of the work on theoretical immunology.

Earthquakes: simulations and hazards

An overview of the work on analyzing earthquake ruptures and hazards.

  • Seismicity in a Model Governed by Competing Frictional Weakening and Healing Mechanisms 
    abstract pdf
    G. Hillers, J. M. Carlson, and R. J. Archuleta, submitted to Geophysical Journal International.

  • 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.

  • 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.

  • A constitutive model for fault gouge deformation in dynamic rupture simulations 
    abstract pdf
    E.G. Daub and J.M. Carlson, Journal of Geophysical Research, in press.

  • 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

  • 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.

  • 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.

  • 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.

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

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

  • 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.

  • 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.

Neuroscience

  • 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, submitted



Econophysics

  • No papers yet.

Constitutive models for friction

An overview of the work on constitutive equations, rate-and-state friction and continuum models.

  • 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.

  • A constitutive model for fault gouge deformation in dynamic rupture simulations 
    abstract pdf
    E.G. Daub and J.M. Carlson, Journal of Geophysical Research, in press.

  • 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)

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

  • 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).

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

  • 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.

  • 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.

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

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

Deformation in granular/amorphous materials

An overview of the work on granular materials and amorphous solids.

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

  • 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)

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

  • 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)

  • 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)

  • 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)

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

  • 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)

  • 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).

Highly Optimized Tolerance

An overview of the work on HOT.

  • 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

  • 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.

  • 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.

  • 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.

  • 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.

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

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

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

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

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

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

  • 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.

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

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

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

Ecology, Evolution, and Forest Fires

An overview of the work on ecology and forest fires.

An overview of the work on evolution.

  • Spatial modeling of fire in shrublands using HFire: I. Model description and event simulation 
    abstract pdf 
    Peterson, S.E., Morais, M.E., Carlson, J.M., Dennison, P.E., Roberts, D.A., Moritz, M.A., and Weise, D.R. International Journal of Wildland Fire, submitted

  • Spatial modeling of fire in shrublands using HFire: II. Fire regime sensitivities 
    abstract pdf 
    Moritz, M.A., Morais, M.E., Dennison, P.E., Summerell, L.A. and Carlson, J.M. International Journal of Wildland Fire, submitted

  • 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.

  • 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.

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

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

  • 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.

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