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Publications, 2005

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

1.              Altmann, E. G., Motter, A. E. & Kantz, H. (2005). Stickiness in mushroom billiards. Chaos 15, 033105.

2.              Antal, T., Krapivsky, P. L. & Redner, S. (2005). Dynamics of social balance on networks. Physical Review E 72, 036121.

3.              Antal, T. & Redner, S. (2005). The excited random walk in one dimension. Journal of Physics A (Mathematical and General) 38, 2555-77.

4.              Ares, S., Voulgarakis, N. K., Rasmussen, K. O. & Bishop, A. R. (2005). Bubble nucleation and Cooperativity in DNA melting. Physical Review Letters 94, 035504-4.

5.              Badaeva, E. A., Timofeeva, T. V., Masunov, A. M. & Tretiak, S. (2005). Role of donor-acceptor strengths and separation on the two-photon absorption response of cytotoxic dyes: a TD-DFT study. Journal of Physical Chemistry A 109, 7276-84.

6.              Barre, J., Bishop, A. R., Lookman, T. & Saxena, A. (2005). The cavity method for the rigidity transition. Journal of Statistical Physics 118, 1057-71.

7.              Barre, J., Bishop, A. R., Lookman, T. & Saxena, A. (2005). Adaptability and "intermediate phase" in randomly connected networks. Physical Review Letters 94, 208701-4.

8.              Barre, J., Bouchet, F., Dauxois, T. & Ruffo, S. (2005). Large deviation techniques applied to systems with long-range interactions. Journal of Statistical Physics 119, 677-713.

9.              Beleva, V., Rasmussen, K. & Garcia, A. (2005). Modeling DNA bubble formation at the atomic scale. Biophysical Journal 88, 60A-61A.

10.           Ben-Naim, E. (2005). Opinion dynamics: rise and fall of political parties. Europhysics Letters 69, 671-7.

11.           Ben-Naim, E. & Krapivsky, P. L. (2005). Chronological rank in biological evolution. Journal of Statistical Mechanics: Theory and Experiment 2005, 8p.

12.           Ben-Naim, E. & Krapivsky, P. L. (2005). Kinetic theory of random graphs: From paths to cycles. Physical Review E 71, 1-11.

13.           Ben-Naim, E. & Krapivsky, P. L. (2005). Percolation with multiple giant clusters. Journal of Physics A-Mathematical and General 38, L417-L423.

14.           Ben-Naim, E. & Krapivsky, P. L. (2005). Polymerization with freezing. Journal of Physics: Condensed Matter 17, S4249-62.

15.           Ben-Naim, E., Machta, B. & Machta, J. (2005). Power-law velocity distributions in granular gases. Physical Review E 72, 1-10.

16.           Ben-Naim, E. & Machta, J. (2005). Stationary states and energy cascades in inelastic gases. Physical Review Letters 94, 138001-4.

17.           Ben-Naim, E. & Redner, S. (2005). Dynamics of social diversity. Journal of Statistical Mechanics: Theory and Experiment 2005, 8p.

18.           Benczik, I. J., Neufeld, Z. & Tel, T. (2005). Multifractal spectra of chemical fields in fluid flows. Physical Review E 71, 016208.

19.           Berman, G. P., Borgonovi, F. & Tsifrinovich, V. I. (2005). A model for quantum jumps in magnetic resonance force microscopy. Physics Letters A 337, 161-5.

20.           Berman, G. P., Borgonovi, F. & Tsifrinovich, V. I. (2005). Theory of frequency shifts in the oscillating cantilever-driven adiabatic reversals technique as a function of the spin location. Physical Review B 72, 224406.

21.           Berman, G. P. & Izrailev, F. M. (2005). The Fermi-Pasta-Ulam problem: fifty years of progress. Chaos 15, 15104-1.

22.           Berman, G. P., Kamenev, D. I. & Tsifrinovich, V. I. (2005). Collective decoherence of the superpositional entangled states in the quantum Shor algorithm. Physical Review A 71, 032346.

23.           Bonca, J., Batista, C. D., Gubernatis, J. E. & Lin, H. Q. (2005). Electronically driven ferroelectricity in the extended Falicov-Kimball model. International Journal of Modern Physics B 19, 525-527.

24.           Borgonovi, F., Celardo, G. L. & Berman, G. P. (2005). Quantum signatures of the classical topological nonconnectivity threshold. Physical Review B 72, 224416.

25.           Borzsonyi, T., Halsey, T. C. & Ecke, R. E. (2005). Two scenarios for avalanche dynamics in inclined granular layers. Physical Review Letters 94, 208001-4.

26.           Bouchet, F. & Barre, J. (2005). Classification of phase transitions and ensemble inequivalence, in systems with long range interactions. Journal of Statistical Physics 118, 1073-105.

27.           Celani, A., Puliafito, A. & Turitsyn, K. (2005). Polymers in linear shear flow: a numerical study. Europhysics Letters 70, 464-70.

28.           Chen, P. & Redner, S. (2005). Consensus formation in multi-state majority and plurality models. Journal of Physics A (Mathematical and General) 38, 7239-52.

29.           Chen, Q. N., Chen, S. Y., Eyink, G. L. & Holm, D. D. (2005). Resonant interactions in rotating homogeneous three-dimensional turbulence. Journal of Fluid Mechanics 542, 139-164.

30.           Chen, S. Y., Dhruva, B., Kurien, S., Sreenivasan, K. R. & Taylor, M. A. (2005). Anomalous scaling of low-order structure functions of turbulent velocity. Journal of Fluid Mechanics 533, 183-92.

31.           Chernyak, V., Chertkov, M. & Jarzynski, C. (2005). Dynamical generalization of nonequilibrium work relation. Physical Review E 71, 025102.

32.           Chertkov, M., Kolokolov, I. & Lebedev, V. (2005). Effects of surface tension on immiscible Rayleigh-Taylor turbulence. Physical Review E 71, 055301.

33.           Chertkov, M., Kolokolov, I., Lebedev, V. & Turitsyn, K. (2005). Polymer statistics in a random flow with mean shear. Journal of Fluid Mechanics 531, 251-60.

34.           Cheskidov, A., Holm, D. D., Olson, E. & Titi, E. S. (2005). On a Leray- alpha model of turbulence. Proceedings of the Royal Society of London, Series A (Mathematical, Physical and Engineering Sciences) 461, 629-49.

40.           Chowell, G., Diaz-Duenas, P. & Chowell, D. (2005). The dynamics of pulmonary tuberculosis in Colima, Mexico (1999-2002). Scandinavian Journal of Infectious Diseases 37, 858-862.

41.           Chowell, G., Hyman, J. M., Diaz-Duenas, P. & Hengartner, N. W. (2005). Predicting scorpion sting incidence in an endemic region using climatological variables. International Journal of Environmental Health Research 15, 425-435.

47.           Chung, Y. J. & Peleg, A. (2005). Strongly non-Gaussian statistics of optical soliton parameters due to collisions in the presence of delayed Raman response. Nonlinearity 18, 1555-1574.

48.           Del Valle, S., Hethcote, H., Hyman, J. M. & Castillo-Chavez, C. (2005). Effects of behavioral changes in a smallpox attack model. Mathematical Biosciences 195, 228-251.

49.           Dimonte, G., Ramaprabhu, P., Youngs, D. L., Andrews, M. J. & Rosner, R. (2005). Recent advances in the turbulent Rayleigh-Taylor instability. Physics of Plasmas 12, 56301-1.

50.           Drocco, J. A., Hastings, M. B., Reichhardt, C. J. O. & Reichhardt, C. (2005). Multiscaling at point J: Jamming is a critical phenomenon. Physical Review Letters 95, 088001-4.

51.           Ernst, M. H. (2005). Universal power law tails of time correlation functions. Physical Review E 71, 030101.

52.           Fenimore, P. W., Frauenfelder, H., McMahon, B. H. & Young, R. D. (2005). Proteins are paradigms of stochastic complexity. Physica A 351, 1-13.

53.           Goncalves, S., Fusco, C., Bishop, A. R. & Kenkre, V. M. (2005). Bistability and hysteresis in the sliding friction of a dimer. Physical Review B 72.

54.           Goupalov, S. V. (2005). Chirality dependence of the Raman cross section of carbon nanotubes. Physical Review B 71, 153404-1.

55.           Goupalov, S. V. (2005). Continuum model for long-wavelength phonons in two-dimensional graphite and carbon nanotubes. Physical Review B 71, 085420.

56.           Goupalov, S. V. (2005). Optical transitions in carbon nanotubes. Physical Review B 72, 195403.

57.           Goupalov, S. V. (2005). Nonradiative multiphonon transitions in semiconductor quantum dots. Physical Review B 72, 073301.

58.           Goupalov, S. V. (2005). Chirality dependence of Raman cross-section in carbon nanotubes. Quantum Electronics and Laser Science Conference (QELS) 1, 208-210.

59.           Gurvitz, S. A., Mozyrsky, D. & Berman, G. P. (2005). Coherent effects in magnetotransport through Zeeman-split levels. Physical Review B 72, 205341.

60.           Hastings, M. B. (2005). Sufficient conditions for topological order in insulators. Europhysics Letters 70, 824-30.

61.           Hastings, M. B. (2005). Statistical mechanics of interfering links. Physical Review E 72, 1-4.

62.           Hastings, M. B. & Wen, X. G. (2005). Quasiadiabatic continuation of quantum states: The stability of topological ground-state degeneracy and emergent gauge invariance. Physical Review B 72, 045141.

63.           Hastings, M. B. & Xiao-Gang, W. (2005). Quasiadiabatic continuation of quantum states: the stability of topological ground-state degeneracy and emergent gauge invariance. Physical Review B 72, 45141-1.

64.           Herring, G., Kevrekidis, P. G., Carretero-Gonzalez, R., Malomed, B. A., Frantzeskakis, D. J. & Bishop, A. R. (2005). Trapped bright matter-wave solitons in the presence of localized inhomogeneities. Physics Letters A 345, 144-153.

65.           Holm, D. D. & Wingate, B. I. (2005). Baroclinic instabilities of the two-layer quasigeostrophic alpha model. Journal of Physical Oceanography 35, 1287-96.

66.           Huang, C.-F. & Rocha, L. M. (2005). Tracking extreme in dynamic environments using a coevolutlonery agent-based model of genotype edition. GECCO 2005 - Genetic and Evolutionary Computation Conference, 545-552.

67.           Huang, C.-F., Wolpert, D. H., Bieniawski, S. & Strauss, C. E. M. (2005). A comparative study of probability collectives based multi-agent systems and genetic algorithms. GECCO 2005 - Genetic and Evolutionary Computation Conference, 751-752.

68.           Hyman, J. A. & Li, J. (2005). The reproductive number for an HIV model with differential infectivity and staged progression. Linear Algebra and Its Applications 398, 101-116.

69.           Hyman, J. M. & Li, J. (2005). Differential susceptibility epidemic models. Journal of Mathematical Biology 50, 626-644.

70.           Joglekar, Y. N., Balatsky, A. V. & Lilly, M. P. (2005). Excitonic condensate and quasiparticle transport in electron-hole bilayer systems. Physical Review B 72, 205313-1.

71.           Kalosakas, G. & Bezel, I. (2005). Electron dynamics in two-dimensions: a hunt for the ground-state polarons. Chemical Physics Letters 403, 89-94.

72.           Karolyi, G., Neufeld, Z. & Scheuring, I. (2005). Rock-scissors-paper game in a chaotic flow: The effect of dispersion on the cyclic competition of microorganisms. Journal of Theoretical Biology 236, 12-20.

73.           Kenzelmann, M., Batista, C. D., Chen, Y., Broholm, C., Reich, D. H., Park, S. & Qiu, Y. (2005). S=1/2 chain in a staggered field: High-energy hound-spinon state and the effects of a discrete lattice. Physical Review B 71, 094411.

74.           Kevrekidis, P. G., Frantzeskakis, D. J., Carretero-Gonzalez, R., Malomed, B. A. & Bishop, A. R. (2005). Discrete solitons and vortices on anisotropic lattices. Physical Review E 72, 046613.

75.           Kevrekidis, P. G., Frantzeskakis, D. J., Carretero-Gonzalez, R., Malomed, B. A., Herring, G. & Bishop, A. R. (2005). Statics, dynamics, and manipulations of bright matter-wave solitons in optical lattices. Physical Review A 71, 023614.

76.           Kevrekidis, P. G., Malomed, B. A., Frantzeskakis, D. J., Bishop, A. R., Nistazakis, H. E. & Carretero-Gonzalez, R. (2005). Domain walls of single-component Bose-Einstein condensates in external potentials. Mathematics and Computers in Simulation 69, 334-45.

77.           Kohlstedt, K., Snezhko, A., Sapozhnikov, M. V., Aranson, I. S., Olafsen, J. S. & Ben-Naim, E. (2005). Velocity distributions of granular gases with drag and with long-range interactions. Physical Review Letters 95, 068001-4.

78.           Kozma, B., Hastings, M. B. & Korniss, G. (2005). Diffusion processes on power-law small-world networks. Physical Review Letters 95, 018701-4.

79.           Krapivsky, P. L. & Redner, S. (2005). Network growth by copying. Physical Review E 71, 036118.

80.           Magyar, R. J., Tretiak, S., Gao, Y., Wang, H. L. & Shreve, A. P. (2005). A joint theoretical and experimental study of phenylene-acetylene molecular wires. Chemical Physics Letters 401, 149-56.

81.           Maniadis, P., Kalosakas, G., Rasmussen, K. O. & Bishop, A. R. (2005). ac conductivity in a DNA charge transport model. Physical Review E 72, 021912.

82.           Masunov, A., Tretiak, S., Hong, J. W., Liu, B. & Bazan, G. C. (2005). Theoretical study of the effects of solvent environment on photophysical properties and electronic structure of paracyclophane chromophores. Journal of Chemical Physics 122, 224505-1.

83.           Mertens, F. G., Arevalo, E. & Bishop, A. R. (2005). Nondissipative diffusion of lattice solitons out of thermal equilibrium. Physical Review E 72, 036617.

84.           Paschek, D., Gnanakaran, S. & Garcia, A. E. (2005). Simulations of the pressure and temperature unfolding of an alpha -helical peptide. Proceedings of the National Academy of Sciences of the United States of America 102, 6765-70.

85.           Pezze, L., Collins, L. A., Smerzi, A., Berman, G. P. & Bishop, A. R. (2005). Sub-shot-noise phase sensitivity with a Bose-Einstein condensate Mach-Zehnder interferometer. Physical Review A - Atomic, Molecular, and Optical Physics 72, 1-8.

86.           Piryatinski, A., Stepanov, M., Tretiak, S. & Chernyak, V. (2005). Semiclassical scattering on conical intersections. Physical Review Letters 95, 223001-4.

87.           Puliafito, A. & Turitsyn, K. (2005). Numerical study of polymer tumbling in linear shear flows. Physica D 211, 9-22.

88.           Ramaprabhu, P., Dimonte, G. & Andrews, M. J. (2005). A numerical study of the influence of initial perturbations on the turbulent Rayleigh-Taylor instability. Journal of Fluid Mechanics 536, 285-319.

89.           Redner, S. (2005). Citation statistics from 110 years of Physical Review. Physics Today 58, 49-54.

90.           Reichhardt, C. & Olson Reichhardt, C. J. (2005). Pinning and dynamics of colloids on one-dimensional periodic potentials. Physical Review E 72, 1-4.

91.           Reichhardt, C. & Reichhardt, C. J. O. (2005). Ordering and melting in colloidal molecular crystal mixtures. Physical Review E 71, 1-4.

92.           Reichhardt, C., Reichhardt, C. J. O. & Bishop, A. R. (2005). Hysteresis and noise in stripe- and clump-forming systems. Europhysics Letters 72, 444-50.

93.           Reichhardt, C., Reichhardt, C. J. O. & Hastings, M. B. (2005). Glassy ratchets for collectively interacting particles. Physics Letters A 342, 162-7.

94.           Reichhardt, C. J. O. & Reichhardt, C. (2005). Rectification and flux reversals for vortices interacting with triangular traps. Physica C 432, 125-32.

95.           Ripoll, M. & Ernst, M. H. (2005). Model system for classical fluids out of equilibrium. Physical Review E 71, 041104.

96.           Ripoll, M. & Ernst, M. H. (2005). Power law tails of time correlations in a mesoscopic fluid model. Physical Review E 72, 011101.

97.           Rivera, M. K. & Ecke, R. E. (2005). Lagrangian dynamics in two-dimensional turbulence. Chaos 15, 41108-1.

98.           Rivera, M. K. & Ecke, R. E. (2005). Pair dispersion and doubling time statistics in two-dimensional turbulence. Physical Review Letters 95, 194503-4.

99.           Rybin, A. V., Vadeiko, I. P. & Bishop, A. R. (2005). Driving slow-light solitons by a controlling laser field. Journal of Physics A-Mathematical and General 38, L357-L362.

100.        Rybin, A. V., Vadeiko, I. P. & Bishop, A. R. (2005). Theory of slow-light solitons. Physical Review E 72, 026613.

101.        Rybin, A. V., Vadeiko, I. P. & Bishop, A. R. (2005). Stopping a slow-light soliton: An exact solution. Journal of Physics A (Mathematical and General) 38, L177-82.

102.        Rybin, A. V., Vadeiko, I. P. & Bishop, A. R. (2005). Non-adiabatic manipulation of slow-light solitons. New Journal of Physics 7, 146.

103.        Schaller, R. D., Pietryga, J. M., Goupalov, S. V., Petruska, M. A., Ivanov, S. A. & Klimov, V. I. (2005). Breaking the phonon bottleneck in semiconductor nanocrystals via multiphonon emission induced by intrinsic nonadiabatic interactions. Physical Review Letters 95, 196401-4.

104.        Sood, V. & Redner, S. (2005). Voter model on heterogeneous graphs. Physical Review Letters 94, 178701-4.

105.        Sood, V., Redner, S. & ben-Avraham, D. (2005). First-passage properties of the Erdos-Renyi random graph. Journal of Physics A (Mathematical and General) 38, 109-23.

106.        Stepanov, M. G., Chernyak, V., Chertkov, M. & Vasic, B. (2005). Diagnosis of weaknesses in modern error correction codes: A physics approach. Physical Review Letters 95, 1-4.

107.        Stajic, J. & Elezovic-Hadzic, S. (2005). Hamiltonian walks on Sierpinski and n-simplex fractals. Journal of Physics A (Mathematical and General) 38, 5677-95.

108.        Takeno, S., Dmitriev, S. V., Kevrekidis, P. G. & Bishop, A. R. (2005). Nonlinear lattices generated from harmonic lattices with geometric constraints. Physical Review B 71, 014304.

109.        Theocharis, G., Kevrekidis, P. G., Nistazakis, H. E., Frantzeskakis, D. J. & Bishop, A. R. (2005). Generation of dark solitons in oscillating Bose-Einstein condensates. Physics Letters A 337, 441-8.

110.        Tretiak, S., Igumenshchev, K. & Chernyak, V. (2005). Exciton sizes of conducting polymers predicted by time-dependent density functional theory. Physical Review B 71, 33201-1.

111.        Vorontsov, A. B., Sauls, J. A. & Graf, M. J. (2005). Phase diagram and spectroscopy of Fulde-Ferrell-Larkin-Ovchinnikov states of two-dimensional d-wave superconductors. Physical Review B 72, 184501.

112.        Weronski, P. (2005). Application of the extended RSA models in studies of particle deposition at partially covered surfaces. Advances in Colloid and Interface Science 118, 1-24.

113.        Zhang, J. S., Li, N., Chen, Y. T. & Rusanov, A. E. (2005). Corrosion behaviors of US steels in flowing lead-bismuth eutectic (LBE). Journal of Nuclear Materials 336, 1-10.

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