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Publications, 2006

LEGEND: boldfaced names are CNLS postdocs, students, directors and deputies, Ulam scholars, visitors and affiliates.

1.              Ahluwalia, R., Lookman, T. & Saxena, A. (2006). Dynamic strain loading of cubic to tetragonal martensites. Acta Materialia 54, 2109-2120.

2.              Altmann, E. G., Motter, A. E. & Kantz, H. (2006). Stickiness in Hamiltonian systems: From sharply divided to hierarchical phase space. Physical Review E 73, 026207.

3.              Amoruso, C., Hartmann, A. K., Hastings, M. B. & Moore, M. A. (2006). Conformal invariance and stochastic loewner evolution processes in two-dimensional Ising spin glasses. Physical Review Letters 97, 267202.

4.              Balatsky, A. V., Fransson, J., Mozyrsky, D. & Manassen, Y. (2006). STM NMR and nuclear spin noise. Physical Review B 73, 184429-1.

5.              Bandi, M. M., Goldburg, W. I. & Cressman, J. R. (2006). Measurement of entropy production rate in compressible turbulence. Europhysics Letters 76, 595-601.

6.              Barre, J., Bishop, A. R., Lookman, T. & Saxena, A. (2006). Oscillating elastic defects: Competition and frustration. Physical Review B 74, 024104.

7.              Ben-Naim, E., Kahng, B. & Kim, J. S. (2006). Dynamics of multi-player games. Journal of Statistical Mechanics: Theory and Experiment 2006, 15p.

8.              Ben-Naim, E. & Krapivsky, P. L. (2006). Weak disorder in Fibonacci sequences. Journal of Physics A (Mathematical and General) 39, L301-7.

9.              Ben-Naim, E. & Krapivsky, P. L. (2006). Alignment of rods and partition of integers. Physical Review E 73, 31109-1.

10.           Ben-Naim, E., Vazquez, F. & Redner, S. (2006). On the structure of competitive societies. European Physical Journal B 49, 531-8.

11.           Ben-Naim, E., Vazquez, F. & Redner, S. (2006). Parity and Predictability of Competitions, J. Quant. Anal. Sports 2, Article 1.

12.           Berman, G. P., Borgonovi, F., Gorshkov, V. N. & Tsifrinovich, V. I. (2006). Magnetic resonance force microscopy and a single-spin measurement, World Scientific.

13.           Berman, G. P. & Chumak, A. A. (2006). Photon distribution function for long-distance propagation of partially coherent beams through the turbulent atmosphere. Physical Review A (Atomic, Molecular, and Optical Physics) 74, 13805-1.

14.           Borzsonyi, T. & Ecke, R. E. (2006). Rapid granular flows on a rough incline: Phase diagram, gas transition, and effects of air drag. Physical Review E 74.

15.           Bravyi, S., Hastings, M. B. & Verstraete, F. (2006). Lieb-robinson bounds and the generation of correlations and topological quantum order. Physical Review Letters 97, 050401.

16.           Celardo, G. L., Barre, J., Borgonovi, F. & Ruffo, S. (2006). Time scale for magnetic reversal and the topological nonconnectivity threshold. Physical Review E 73, 011108.

17.           Chen, J., Odier, P., Rivera, M. & Ecke, R. (2006). Measurement of turbulent mixing along slope in stratified flow. Proceedings of ASME Fluids Engineering Division Summer Meeting 2006, FEDSM2006 2 FORUMS, 27-34.

18.           Chen, Q., Levin, K. & Stajic, J. (2006). Applying BCS-BEC crossover theory to high-temperature superconductors and ultracold atomic Fermi gases. Low Temperature Physics 32, 406-423.

19.           Chen, S. Y., Ecke, R. E., Eyink, G. L., Rivera, M., Wan, M. P. & Xiao, Z. L. (2006). Physical mechanism of the two-dimensional inverse energy cascade. Physical Review Letters 96, 084502.

20.           Chen, S. Y., Eyink, G. L., Wan, M. P. & Xiao, Z. L. (2006). Is the Kelvin theorem valid for high Reynolds number turbulence? Physical Review Letters 97, 144505.

21.           Chen, Y., Lopez, E., Havlin, S. & Stanley, H. E. (2006). Universal behavior of optimal paths in weighted networks with general disorder. Physical Review Letters  96, 068702.

22.           Chernyak, V. Y., Chertkov, M. & Jarzynski, C. (2006). Path-integral analysis of fluctuation theorems for general Langevin processes. Journal of Statistical Mechanics-Theory and Experiment, P08001.

23.           Chertkov, M. & Chernyak, V. Y. (2006). Loop calculus in statistical physics and information science. Physical Review E 73.

24.           Chertkov, M. & Chernyak, V. Y. (2006). Loop series for discrete statistical models on graphs. Journal of Statistical Mechanics: Theory and Experiment 2006, 28p.

25.           Choi, C. H., Usheva, A., Kalosakas, G., Rasmussen, K. O. & Bishop, A. R. (2006). Comment on "Can one predict DNA transcription start sites by studying bubbles?" Physical Review Letters 96, 239801.

36.           Chowell, G., Ammon, C. E., Hengartner, N. W. & Hyman, J. M. (2006). Transmission dynamics of the great influenza pandemic of 1918 in Geneva, Switzerland: Assessing the effects of hypothetical interventions. Journal of Theoretical Biology 241, 193-204.

37.           Chowell, G., Ammon, C. E., Hengartner, N. W. & Hyman, J. M. (2006). Estimation of the reproductive number of the Spanish flu epidemic in Geneva, Switzerland. Vaccine 24, 6747-6750.

38.           Chowell, G., Cintron-Arias, A., Del Valle, S., Sanchez, F., Song, B. J., Hyman, J. M., Hethcote, H. W. & Castillo-Chavez, C. (2006). Mathematical applications associated with the deliberate release of infectious agents. Contemporary Mathematics Series 410, 51-71.

39.           Chowell, G., Diaz-Duenas, P., Bustos-Saldana, R., Mireles, A. A. & Fet, V. (2006). Epidemiological and clinical characteristics of scorpionism in Colima, Mexico (2000-2001). Toxicon 47, 753-758.

43.           Chowell, G., Rivas, A. L., Hengartner, N. W., Hyman, J. M. & Castillo-Chavez, C. (2006). The role of spatial mixing in the spread of foot-and-mouth disease. Preventive Veterinary Medicine 73, 297-314.

44.           Chowell, G., Rivas, A. L., Hengartner, N. W., Hyman, J. M. & Castillo-Chavez, C. (2006). Critical response to post-outbreak vaccination against foot-and-mouth disease. Contemporary Mathematics Series 410, 73-87.

45.           Chowell, G., Rivas, A. L., Smith, S. D. & Hyman, J. M. (2006). Identification of case clusters and counties with high infective connectivity in the 2001 epidemic of foot-and-mouth disease in Uruguay. American Journal of Veterinary Research 67, 102-113.

46.           Chowell, G., Shim, E., Brauer, F., Diaz-Duenas, P., Hyman, J. M. & Castillo-Chavez, C. (2006). Modelling the transmission dynamics of acute haemorrhagic conjunctivitis: Application to the 2003 outbreak in Mexico. Statistics in Medicine 25, 1840-1857.

26.           Chumakov, S. G. (2006). Statistics of subgrid-scale stress states in homogeneous isotropic turbulence. Journal of Fluid Mechanics 562, 405-14.

27.           Connaughton, C., Rajesh, R. & Zaboronski, O. (2006). Cluster-cluster aggregation as an analogue of a turbulent cascade: Kolmogorov phenomenology, scaling laws and the breakdown of self-similarity. Physica D 222, 97-115.

28.           Cooper, F., Khare, A. & Saxena, A. (2006). Exact elliptic compactons in genepalized Kopteweg-De Pies equations. Complexity 11, 30-34.

29.           Cuevas, J., Kevrekidis, P. G., Frantzeskakis, D. J. & Bishop, A. R. (2006). Existence of bound states of a polaron with a breather in soft potentials. Physical Review B 74, 064304.

30.           Dahal, H. P., Joglekar, Y. N., Bedell, K. S. & Balatsky, A. V. (2006). Absence of Wigner crystallization in graphene. Physical Review B 74, 233405.

31.           Dandoloff, R. & Saxena, A. (2006). XY-model on planar and space curves. Physics Letters A 358, 421-425.

32.           Danila, B., Yong, Y., Earl, S., Marsh, J. A., Toroczkai, Z. & Bassler, K. E. (2006). Congestion-gradient driven transport on complex networks. Physical Review E 74, 046114.

33.           Daya, Z. A., Ben-Naim, E. & Ecke, R. E. (2006). Experimental characterization of vibrated granular rings. European Physical Journal E 21, 1-10.

34.           Doorn, S. K., Goupalov, S., Satishkumar, B. C., Shreve, A. P., Haroz, E. H., Bachilo, S. M. & Weisman, R. B. (2006). Raman studies of electron-phonon coupling in single walled carbon nanotubes. Physica Status Solidi B 243, 3171-5.

35.           Ercsey-Ravasz, M., Roska, T. & Neda, Z. (2006). Stochastic simulations on the cellular wave computers. European Physical Journal B 51, 407-11.

36.           Eyink, G. L. (2006). Cascade of circulations in fluid turbulence. Physical Review E 74, 066302.

37.           Eyink, G. L. (2006). Turbulent cascade of circulations. Academie des Sciences. Comptes Rendus, Physique 7, 449-55.

38.           Eyink, G. L. & Aluie, H. (2006). The breakdown of Alfven's theorem in ideal plasma flows: Necessary conditions and physical conjectures. Physica D 223, 82-92.

39.           Fransson, J. & Balatsky, A. V. (2006). Exchange interaction and Fano resonances.

40.           Fransson, J. & Zhu, J.-X. (2006). Spin dynamics in a tunnel junction between ferromagnets.

41.           Frauenfelder, H., Fenimore, P.W., Chen, G. & McMahon, B.H. (2006). Protein folding is slaved to solvent motions. Proc. Natl. Acad. Sci. USA 103, 15469-15472.

42.           Gambetta, A., Manzoni, C., Menna, E., Meneghetti, M., Cerullo, G., Lanzani, G., Tretiak, S., Piryatinski, A., Saxena, A., Martin, R. L. & Bishop, A. R. (2006). Real-time observation of nonlinear coherent phonon dynamics in single-walled carbon nanotubes. Nature Physics 2, 515-20.

43.           Goh, K. I., Eom, Y. H., Jeong, H., Kahng, B. & Kim, D. (2006). Structure and evolution of online social relationships: Heterogeneity in unrestricted discussions. Physical Review E 73, 066123.

44.           Gomez-Gardenes, J., Floria, L. M. & Bishop, A. R. (2006). Discrete breathers in two-dimensional anisotropic nonlinear Schrodinger lattices. Physica D 216, 31-43.

45.           Gomez-Gardenes, J., Malomed, B. A., Floria, L. M. & Bishop, A. R. (2006). Solitons in the Salerno model with competing nonlinearities. Physical Review E 73, 036608.

46.           Gomez-Gardenes, J., Malomed, B. A., Floria, L. M. & Bishop, A. R. (2006). Discrete solitons and vortices in the two-dimensional Salerno model with competing nonlinearities. Physical Review E 74, 036607.

47.           Goupalov, S. V., Satishkumar, B. C. & Doorn, S. K. (2006). Excitation and chirality dependence of the exciton-phonon coupling in carbon nanotubes. Physical Review B 73, 115401-1.

48.           Guclu, H., Korniss, G., Novotny, M. A., Toroczkai, Z. & Racz, Z. (2006). Synchronization landscapes in small-world-connected computer networks. Physical Review E 73.

49.           Gulbahce, N., Bishop, A. R. & Johnson, G. (2006). Statistical mechanics of histories: a cluster Monte Carlo algorithm. Phys Rev E Stat Nonlin Soft Matter Phys 73, 026701.

50.           Hastings, M. B. (2006). Community detection as an inference problem. Physical Review E 74, 35102-1.

51.           Hastings, M. B. (2006). Systematic series expansions for processes on networks. Physical Review Letters 96, 1-4.

52.           Hastings, M. B. (2006). Solving gapped Hamiltonians locally. Physical Review B 73, 85115-1.

53.           Hastings, M. B. & Koma, T. (2006). Spectral gap and exponential decay of correlations. Communications in Mathematical Physics 265, 781-804.

54.           Hastings, M. B. & Mudry, C. (2006). Universal scaling relations in strongly anisotropic materials. Physical Review Letters 96, 027215-4.

55.           Hlavacek, W. S., Faeder, J. R., Blinov, M. L., Posner, R. G., Hucka, M. & Fontana, W. (2006). Rules for modeling signal-transduction systems. Sci STKE 2006, re6.

56.           Hohenadler, M., Wellein, G., Bishop, A. R., Alvermann, A. & Fehske, H. (2006). Spectral signatures of the Luttinger liquid to the charge-density-wave transition. Physical Review B 73, 245120.

57.           Hurtado, P. I. & Redner, S. (2006). Simplest piston problem. I. Elastic collisions. Physical Review E 73, 016136.

58.           Hurtado, P. I. & Redner, S. (2006). Simplest piston problem. II. Inelastic collisions. Physical Review E 73, 016137.

59.           Hyman, J. M. & Li, J. (2006). Differential susceptibility and infectivity epidemic models. Mathematical Biosciences and Engineering 3, 89-100.

60.           Ianeselli, S., Menotti, C. & Smerzi, A. (2006). Beyond the Landau criterion for superfluidity. Journal of Physics B (Atomic, Molecular and Optical Physics) 39, S135-42.

61.           Jun, C., Odier, P., Rivera, M. & Ecke, R. (2006). Measurement of turbulent mixing along slope in stratified flow. 2006 ASME Joint U.S.-European Fluids Engineering Summer Meeting, FEDSM 2006 2006.

62.           Kalosakas, G., Rasmussen, K. O. & Bishop, A. R. (2006). Non-exponential decay of base-pair opening fluctuations in DNA. Chemical Physics Letters 432, 291-5.

63.           Kamenev, D. I., Berman, G. P. & Tsifrinovich, V. I. (2006). Creation of entanglement in a scalable spin quantum computer with long-range dipole-dipole interaction between qubits. Physical Review A - Atomic, Molecular, and Optical Physics 73.

64.           Kamisaka, H., Kilina, S. V., Yamashita, K. & Prezhdo, O. V. (2006). Ultrafast vibrationally-induced dephasing of electronic excitations in PbSe quantum dots. Nano Letters 6, 2295-2300.

65.           Kauffman, J. F., Turner, J. M., Alabugin, I. V., Breiner, B., Kovalenko, S. V., Badaeva, E. A., Masunov, A. & Tretiak, S. (2006). Two-photon excitation of substituted enediynes. Journal of Physical Chemistry A 110, 241-51.

66.           Khare, A., Rasmussen, K. O., Salerno, M., Samuelsen, M. R. & Saxena, A. (2006). Discrete nonlinear Schrodinger equations with arbitrarily high-order nonlinearities. Physical Review E 74, 016607.

67.           Khare, A. & Saxena, A. (2006). Domain wall and periodic solutions of coupled phi(4) models in an external field. Journal of Mathematical Physics 47, 092902-1.

68.           Korniss, G., Hastings, M. B., Bassler, K. E., Berryman, M. J., Kozma, B. & Abbott, D. (2006). Scaling in small-world resistor networks. Physics Letters A 350, 324-30.

69.           Libal, A., Reichhardt, C., Janko, B. & Reichhardt, C. J. O. (2006). Dynamics, rectification, and fractionation for colloids on flashing substrates. Physical Review Letters 96, 188301-4.

70.           Libal, A., Reichhardt, C. & Reichhardt, C. J. O. (2006). Realizing colloidal artificial ice on arrays of optical traps. Physical Review Letters 97, 228302-4.

71.           Lin, J. X., Reichhardt, C., Nussinov, Z., Pryadko, L. P. & Olson Reichhardt, C. J. (2006). Heterogeneities and topological defects in two-dimensional pinned liquids. Physical Review E 73.

72.           Lookman, T., Ahluwalia, R. & Saxena, A. (2006). Dynamic strain loading of cubic to tetragonal martensites. Acta Materialia 54, 2109-20.

73.           Machacek, D. L., Foreman, E. A., Hoq, Q. E., Kevrekidis, P. G., Saxena, A., Frantzeskakis, D. J. & Bishop, A. R. (2006). Statics and dynamics of an inhomogeneously nonlinear lattice. Physical Review E 74, 036602.

74.           Martinsen-Burrell, N., Julien, K., Petersen, M. R. & Weiss, J. B. (2006). Merger and alignment in a reduced model for three-dimensional quasigeostrophic ellipsoidal vortices. Physics of Fluids 18.

75.           Mertens, F. G., Morales-Molina, L., Bishop, A. R., Sanchez, A. & Muller, P. (2006). Optimization of soliton ratchets in inhomogeneous sine-Gordon systems. Physical Review E 74, 066602.

76.           Mu, F. P., Unkefer, P. J., Unkefer, C. J. & Hlavacek, W. S. (2006). Prediction of oxidoreductase-catalyzed reactions based on atomic properties of metabolites. Bioinformatics (Oxford) 22, 3082-3088.

77.           Naso, A., Chertkov, M. & Pumir, A. (2006). Scale dependence of the coarse-grained velocity derivative tensor: Influence of large-scale shear on small-scale turbulence. Journal of Turbulence 7, 1-11.

78.           Nishikawa, T. & Motter, A. E. (2006). Synchronization is optimal in nondiagonalizable networks. Physical Review E 73, 065106.

79.           Peters, O. & Christensen, K. (2006). Rain viewed as relaxational events. Journal of Hydrology 328, 46-55.

80.           Peters, O. & Neelin, J. D. (2006). Critical phenomena in atmospheric precipitation. Nature Physics 2, 393-6.

81.           Petersen, M. R., Julien, K. & Weiss, J. B. (2006). Vortex cores, strain cells, and filaments in quasigeostrophic turbulence. Physics of Fluids 18.

82.           Pezze, L. & Smerzi, A. (2006). Phase sensitivity of a Mach-Zehnder interferometer. Physical Review A - Atomic, Molecular, and Optical Physics 73.

83.           Piryatinski, A., Stepanov, M., Tretiak, S. & Chernyak, V. (2006). Photoexcited wavepacket scattering on conical intersections: Semiclassical expansion. Abstracts of Papers of the American Chemical Society 231, U98-U99.

84.           Pruessner, G. & Peters, O. (2006). Self-organized criticality and absorbing states: Lessons from the Ising model. Physical Review E 73, 025106.

85.           Redner, S. & Petersen, M. R. (2006). Role of global warming on the statistics of record-breaking temperatures. Physical Review E 74, 061114.

86.           Ramaprabhu, P., Dimonte, G., Young, Y. N., Calder, A. C. & Fryxell, B. (2006). Limits of the potential flow approach to the single-mode Rayleigh-Taylor problem. Physical Review E 74, 066308.

87.           Rapti, Z., Smerzi, A., Rasmussen, K. O., Bishop, A. R., Choi, C. H. & Usheva, A. (2006). Healing length and bubble formation in DNA. Physical Review E 73.

88.           Rapti, Z., Smerzi, A., Rasmussen, K. O., Bishop, A. R., Choi, C. H. & Usheva, A. (2006). Lengthscales and cooperativity in DNA bubble formation. Europhysics Letters 74, 540-546.

89.           Reichhardt, C. J. O., Libal, A. & Reichhardt, C. (2006). Vortex configurations and dynamics in elliptical pinning sites for high matching fields. Physical Review B 73, 184519-1.

90.           Reichhardt, C. & Reichhardt, C. J. O. (2006). Crossover from intermittent to continuum dynamics for locally driven colloids. Physical Review Letters 96, 028301-4.

91.           Reichhardt, C. & Reichhardt, C. J. O. (2006). Statics and dynamics of two-dimensional vortex liquid crystals. Europhysics Letters 75, 489-95.

92.           Reichhardt, C. & Reichhardt, C. J. O. (2006). Cooperative behavior and pattern formation in mixtures of driven and nondriven colloidal assemblies. Physical Review E 74, 11403-1.

93.           Reichhardt, C. & Reichhardt, C. J. O. (2006). Coarsening of topological defects in oscillating systems with quenched disorder. Physical Review E 73, 46122-1.

94.           Reichhardt, C. & Reichhardt, C. J. O. (2006). Ratchet effect and nonlinear transport for particles on random substrates with crossed ac drives. Physical Review E 73, 11102-1.

95.           Reichhardt, C. J. O. & Reichhardt, C. (2006). Electrophoresis of DNA on a disordered two-dimensional substrate. Physical Review E 74, 51908-1.

96.           Reichhardt, C. J. O. & Reichhardt, C. (2006). Ratchet cellular automata for colloids in dynamic traps. Europhysics Letters 74, 792-798.

97.           Rivas, A. L., Kunsberg, B., Chowell, G., Smith, S. D., Hyman, J. M. & Schwager, S. J. (2006). Human-mediated foot-and-mouth disease epidemic dispersal: Disease and vector clusters. Journal of Veterinary Medicine Series B 53, 1-10.

98.           Satishkumar, B. C., Goupalov, S. V., Haroz, E. H. & Doorn, S. K. (2006). Transition level dependence of Raman intensities in carbon nanotubes: role of exciton decay. Physical Review B 74, 155409-1.104.

99.           Saxena, A. & Dandoloff, R. (2006). XY-model on planar and space curves. Physics Letters A 358, 421-5.

100.        Voulgarakis, N. K., Redondo, A., Bishop, A. R. & Rasmussen, K. O. (2006). Probing the mechanical unzipping of DNA. Physical Review Letters 96, 248101-4.

101.        Voulgarakis, N. K., Redondo, A., Bishop, A. R. & Rasmussen, K. O. (2006). Sequencing DNA by dynamic force spectroscopy: Limitations and prospects. Nano Letters 6, 1483-1486.

102.        Wellein, G., Bishop, A. R., Hohenadler, M., Schubert, G. & Fehske, H. (2006). Optical response of many-polaron systems. Physica B 378/380, 281-2.

103.        Wingate, B. A. & Taylor, M. A. (2006). Measuring characteristic length scales of eigenfunctions of Sturm-Liouville equations in one and two dimensions. Journal of Engineering Mathematics 56, 237-245.

104.        Wu, C., Malinin, S. V., Tretiak, S. & Chernyak, V. Y. (2006). Exciton scattering and localization in branched dendrimeric structures. Nature Physics 2, 631-635.

105.        Yang, I., Oh, E. & Kahng, B. (2006). Network analysis of online bidding activity. Physical Review E 74, 016121.

106.        Zhou, C. S., Motter, A. E. & Kurths, J. (2006). Universality in the synchronization of weighted random networks. Physical Review Letters 96, 034101.

107.        Zhu, J. X. & Fransson, J. (2006). Electric field control of spin dynamics in a magnetically active tunnel junction. Journal of Physics Condensed Matter 18, 9929-9936.

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