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.

  • Friction, Fracture, and Earthquakes 
    abstract pdf
    Daub, E. G., and J. M. Carlson, Ann. Rev. of Cond. Matt. Phys., in press.

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

  • Energetics of strain localization in a model of seismic slip 
    abstract pdf
    A. M. Hermundstad, E. G. Daub, and J. M. Carlson, J. Geophys. Res., accepted, in press.

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

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

  • 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, 113, B12309, doi:10.1029/2007JB003577.

  • 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

  • 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).

  • 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, (2009).

  • Improving Human Brain Mapping via Joint Inversion of Brain Electrodynamics and the BOLD Signal
    abstract  pdf
    Brown, K., Ortigue, S., Grafton, S., and Carlson, J.M., in revision, NeuroImage, (2009).

  • Conserved and variable architecture of human white matter connectivity

    Danielle S. Bassett, Jesse A. Brown, Vibhas Deshpande, Jean M. Carlson, Scott T. Grafton, in preparation.

Econophysics

  • A Fast Mean-Reverting Correction to Heston Stochastic Volatility Model 
    abstract
    Fouque, J-P. and Lorig, M. J., submitted.

Constitutive models for friction

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

  • 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).

  • 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
    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.

  • How simple can a fire regime model be while still approximating reality? 
    abstract  
    Peterson S. H., Doyle J., and Carlson J. M., in preparation.

  • Wildfire resource allocations in conditions involving multiple threats 
    abstract  
    Petrovic, Nada and J. M. Carlson, in preparation.

  • Fire in the Earth System 
    abstract pdf 
    David M. J. S. Bowman, Jennifer K. Balch, Paulo Artaxo, William J. Bond, Jean M. Carlson, Mark A. Cochrane, Carla M. D’Antonio, Ruth S. DeFries, John C. Doyle, Sandy P. Harrison, Fay H. Johnston, Jon E. Keeley, Meg A. Krawchuk, Christian A. Kull, J. Brad Marston, Max A. Moritz, I. Colin Prentice, Christopher I. Roos, Andrew C. Scott, Thomas W. Swetnam, Guido R. van der Werf, Stephen J. Pyne, Science 24 April 2009: Vol. 324. no. 5926, pp. 481 - 484 DOI: 10.1126/science.1163886 , (2009)

  • 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)

  • Using HFire for Spatial Modeling of Fire in Shrublands 
    abstract pdf 
    Peterson, Seth H.; Morais, Marco E.; Carlson, Jean M.; Dennison, Philip E.; Roberts, Dar A.; Moritz, Max A.; Weise, David R. Res. Pap. PSW-RP-259, Albany, CA: U.S. Department of Agriculture, Forest Service, Pacific Southwest Research Station. 44 p.

  • Modeling Long-term Fire Regimes of Southern California Shrublands 
    abstract pdf 
    Peterson, Seth H., Moritz, M.A., Morais, M.E., Dennison, P.E. and Carlson, J.M. International Journal of Wildland Fire, accepted.

  • 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.