When microbes compete for limited resources, they often engage in chemical warfare using bacterial toxins. This competition can be understood in terms of evolutionary game theory ({EGT).} We study the predictions of {EGT} for the bacterial “suicide bomber” game in terms of the phase portraits of population dynamics, for parameter combinations that cover all interesting games for two-players, and seven of the 38 possible phase portraits of the three-player game. We compare these predictions to simulations of these competitions in finite well-mixed populations, but also allowing for probabilistic rather than pure strategies, as well as Darwinian adaptation over tens of thousands of generations. We find that Darwinian evolution of probabilistic strategies stabilizes games of the rock-paper-scissors type that emerge for parameters describing realistic bacterial populations, and point to ways in which the population fixed point can be selected by changing those parameters.

VL - 85 UR - http://link.aps.org/doi/10.1103/PhysRevE.85.011914 ER - TY - JOUR T1 - Expression profiling of Cucumis sativus in response to infection by Pseudoperonospora cubensis JF - PLoS ONE, in press Y1 - 2012 A1 - C. R. Buell A1 - Adhikari, B. A1 - Savory, E. A1 - Vaillancourt, B. A1 - Childs, K. L. A1 - Hamilton, J. P. A1 - B. Day ER - TY - JOUR T1 - Mass Measurements of the Neutron-Deficient 41Ti, 45Cr, 49Fe, and 53Ni Nuclides: ￼First Test of the Isobaric Multiplet Mass Equation in fp-Shell Nuclei JF - PHYSICAL REVIEW LETTERS Y1 - 2012 A1 - Y.H. Zhang A1 - H.S. Xu A1 - Yu. A. Litvinov A1 - X.L. Tu A1 - X.L. Yan A1 - S. Typel A1 - K. Blaum A1 - M. Wang A1 - X.H. Zhou A1 - Y. Sun A1 - B. A. Brown A1 - Y.J. Yuan A1 - J.W. Xia A1 - J.C. Yang A1 - G. Audi A1 - X.C. Chen A1 - G.B. Jia A1 - Z.G. Hu A1 - X.W. Ma A1 - R.S. Mao A1 - B. Mei A1 - P. Shuai A1 - Z.Y. Sun A1 - S.T. Wang A1 - G.Q. Xiao A1 - X. Xu A1 - T. Yamaguchi A1 - Y. Yamaguchi A1 - Y.D. Zang A1 - H.W. Zhao A1 - T.C. Zhao A1 - W. Zhang A1 - W.L. Zhan VL - 109 UR - http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.109.102501 ER - TY - Generic T1 - Methylmercury (MeHg) disrupts fluo4 fluorescence in cerebellar slices from GABAA receptor alpha6 (-/-) mice Y1 - 2012 A1 - A B Bradford A1 - W D Atchison PB - Society of Toxicology 2012 CY - San Francisco, CA ER - TY - JOUR T1 - mRNA-Seq analysis of the Pseudoperonospora cubensis transcriptome during cucumber (Cucumis sativus L.) infection JF - PLoS ONE, in press Y1 - 2012 A1 - Savory, E. A1 - Adhikari, B. A1 - Hamilton, J. P. A1 - Vaillancourt, B. A1 - C. R. Buell A1 - B. Day ER - TY - Generic T1 - The role of standing genetic variation in adaptation of digital organisms to a new environment T2 - Proceedings of the 13th International Conference on Artificial Life Y1 - 2012 A1 - Anderson, CJR JF - Proceedings of the 13th International Conference on Artificial Life VL - 13: 3-10 ER - TY - JOUR T1 - The Comprehensive Phytopathogen Genomics Resource: An electronic resource for data-mining plant pathogen genomes JF - Database, doi: 10.1093/database/bar053. Y1 - 2011 A1 - Hamilton, J. P. A1 - Neeno-Eckwall, E. A1 - Adhikari, B. A1 - Perna, N. A1 - Tisserat, N. A1 - Leach, J.E. A1 - Lévesque, C. A. A1 - C. R. Buell ER - TY - JOUR T1 - East African Food Security as Influenced by Future Climate Change and Land Use Change at Local to Regional Scales JF - Climatic Change Y1 - 2011 A1 - Moore, Nathan A1 - Alagarswamy, Gopal A1 - Pijanowski, Bryan A1 - Thornton, Phil A1 - Lofgren, Brent A1 - Olson, Jennifer A1 - Yanda, Pius A1 - Qi, Jiaguo VL - 107 ER - TY - JOUR T1 - Information Content of Colored Motifs in Complex Networks JF - Artificial Life Y1 - 2011 A1 - Adami, Christoph A1 - Qian, Jifeng A1 - Rupp, Matthew A1 - Hintze, Arend AB -We study complex networks in which the nodes are tagged with different colors depending on their function (colored graphs), using information theory applied to the distribution of motifs in such networks. We find that colored motifs can be viewed as the building blocks of the networks (much more than the uncolored structural motifs can be) and that the relative frequency with which these motifs appear in the network can be used to define its information content. This information is defined in such a way that a network with random coloration (but keeping the relative number of nodes with different colors the same) has zero color information content. Thus, colored motif information captures the exceptionality of coloring in the motifs that is maintained via selection. We study the motif information content of the C. elegans brain as well as the evolution of colored motif information in networks that reflect the interaction between instructions in genomes of digital life organisms. While we find that colored motif information appears to capture essential functionality in the C. elegans brain (where the color assignment of nodes is straightforward), it is not obvious whether the colored motif information content always increases during evolution, as would be expected from a measure that captures network complexity. For a single choice of color assignment of instructions in the digital life form Avida, we find rather that colored motif information content increases or decreases during evolution, depending on how the genomes are organized, and therefore could be an interesting tool to dissect genomic rearrangements.

VL - 17 UR - http://dx.doi.org/10.1162/artl_a_00045 ER - TY - JOUR T1 - Adapting MODIS-derived LAI and fractional cover into the RAMS model for East Africa JF - International Journal of Climatology Y1 - 2010 A1 - Moore, Nathan A1 - Torbick, Nathan A1 - Pijanowski, Bryan A1 - Lofrgren, Brent A1 - Wang, Jing A1 - Kim, Dong-Yun A1 - Andresen, Jeffrey A1 - Olson, Jennifer VL - 30 IS - 13 ER - TY - JOUR T1 - Thermodynamic modeling of transcription: sensitivity analysis differentiates biological mechanism from mathematical model-induced effects JF - BMC Systems Biology Y1 - 2010 A1 - Dresch, J.M. A1 - Liu, X. A1 - Arnosti, D.N. A1 - Ay, A. PB - BioMed Central Ltd VL - 4 ER - TY - JOUR T1 - The Formation of Population III Binaries from Cosmological Initial Conditions JF - Science Y1 - 2009 A1 - Turk, M. J. A1 - Abel, T. A1 - O'Shea, B. W. VL - 325 ER - TY - JOUR T1 - Protecting the Amazon with Protected Areas JF - PNAS Y1 - 2009 A1 - Robert Walker A1 - Moore, Nathan A1 - Arima, Eugenio A1 - Perz, Stephen A1 - Simmons, Cynthia A1 - Caldas, Marcellus A1 - Vergara, Dante A1 - Bohrer, Claudio VL - 106 ER - TY - CONF T1 - Large Eddy Simulations of Turbulent Flows in IC Engines T2 - ASME 2008 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference (IDETC/CIE2008) Y1 - 2008 A1 - Banaeizadeh, A. A1 - Afshari, A. A1 - Jaberi, F.A. A1 - H. Schock AB -A new computational methodology is developed and tested for large eddy simulation (LES) of turbulent flows in internal combustion (IC) engines. In this methodology, the filtered compressible Navier-Stokes equations in curvilinear coordinate systems are solved via a generalized, high-order, multi-block, compact differencing scheme and various subgrid-scale (SGS) stress closures. Both reacting and nonreacting flows with and without spray are considered. The LES models have been applied to a piston-cylinder assembly with a stationary open valve and harmonically moving flat piston. The flow in a direct-injection spark-ignition (DISI) engine is also considered. It is observed that during the intake stroke of the engine operation, large-scale unsteady turbulent flow motions are developed behind the intake valves. The physical features of these turbulent motions and the ability of LES to capture them are studied and tested by simulating the flow in a simple configuration involving a stationary valve. The flow statistics predicted by LES are shown to compare well with the available experimental data. The DISI configuration includes all the complexities involved in a realistic single-cylinder IC engine, such as the complex geometry, moving valves, moving piston, spray and combustion. The spray combustion is simulated with the recently developed two-phase filtered mass density (FMDF) model.

JF - ASME 2008 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference (IDETC/CIE2008) PB - ASME CY - Brooklyn, New York SN - 978-0-7918-4327-7 ER - TY - JOUR T1 - Large-Eddy Simulation of a Dispersed Particle-Laden Turbulent Round Jet JF - International Journal of Heat and Mass Transfer Y1 - 2008 A1 - Almeida, T. A1 - Jaberi, F.A. KW - Particle-laden jet; dilute KW - two-phase flows; turbulent jet; LES AB -The numerical results obtained by large-eddy simulation (LES) of a particle-laden axisymmetric turbulent jet are compared with the available experimental data. The results indicate that with a new stochastic subgrid-scale (SGS) closure, the effects of the particles on the carrier gas and those of the carrier gas on the particles are correctly captured by the LES. Additional numerical experiments are conducted and used to investigate the effects of particle size, mass-loading ratio, and other flow/particle parameters on the statistics of both the carrier gas phase and the particle dispersed phase.

VL - 51 IS - 3-4 ER - TY - JOUR T1 - Large-Eddy Simulation of Turbulent Flow in an Axisymmetric Dump Combustor JF - AIAA Journal Y1 - 2008 A1 - Afshari, A. A1 - Jaberi, F.A. KW - combustion KW - Gas turbine; modeling; combustion chamber; Monte Carlo method; Lagragian Method; turbulent flow; large eddy simulation AB -A hybrid Eulerian–Lagrangian, mathematical/computational methodology is developed and evaluated for large- eddy simulations of turbulent combustion in complex geometries. The formulation for turbulence is based on the standard subgrid-scale stress models. The formulation for subgrid-scale combustion is based on the filtered mass density function and its equivalent stochastic Lagrangian equations. An algorithm based on high-order compact differencing on generalized multiblock grids is developed for numerical solution of the coupled Eulerian–Lagrangian equations. The results obtained by large-eddy simulations/filtered mass density function show the computational method to be more efficient than existing methods for similar hybrid systems. The consistency, convergence, and accuracy of the filtered mass density function and its Lagrangian–Monte Carlo solver is established for both reacting and nonreacting flows in a dump combustor. The results show that the finite difference and the Monte Carlo numerical methods employed are both accurate and consistent. The results for a reacting premixed dump combustor also agree well with available experimental data. Additionally, the results obtained for other nonreacting turbulent flows are found to be in good agreement with the experimental and high-order numerical data. Filtered mass density function simulations are performed to examine the effects of boundary conditions, subgrid-scale models, as well as physical and geometrical parameters on dump-combustor flows. The results generated for combustors with and without an inlet nozzle are found to be similar as long as appropriate boundary conditions are employed.

VL - 46 IS - 7 ER - TY - CONF T1 - LES/FMDF of Turbulent Combustion in Complex Flow Systems T2 - 45th AIAA Aerospace Sciences Meeting and Exhibit Y1 - 2007 A1 - Afshari, A. A1 - Jaberi, F.A. A1 - Shih, T. I-P. AB -A high-order Lagrangian/Eulerian method based on the the filtered mass density func- tion (FMDF) for subgrid-scale (SGS) combustion closure was developed to perform large eddy simulation (LES) of turbulent reacting flows in complex geometrical configurations in multi-block structured grids. In particular, an efficient algorithm has been developed to search and locate particles in multi-block, hexahedral-structured grid system. Also, the consistency, convergence, and accuracy of the FMDF and the Monte Carlo solution of its equivalent stochastic differential equations were assessed. The consistency between Eulerian and Lagrangian fields were established for a reacting flow in a dump combustor. The results obtained for a reacting flow in an axisymmetric, premixed dump-combustor, were found to compare favorably with measured experimental data.

JF - 45th AIAA Aerospace Sciences Meeting and Exhibit PB - AIAA CY - Reno, Nevada ER - TY - JOUR T1 - Shape and Structure of N = Z 64Ge: Electromagnetic Transition Rates from the Application ￼of the Recoil Distance Method to a Knockout Reaction JF - PHYSICAL REVIEW LETTERS Y1 - 2007 A1 - K. Starosta A1 - A. Dewald A1 - A. Dunomes A1 - P. Adrich A1 - A.M. Amthor A1 - T. Baumann A1 - D. Bazin A1 - M. Bowen A1 - B. A. Brown A1 - A. Chester A1 - A. Gade A1 - D. Galaviz A1 - T. Glasmacher A1 - T. Ginter A1 - M. Hausmann A1 - M. Horoi A1 - J. Jolie A1 - B. Melon A1 - D. Miller A1 - V. Moeller A1 - R.P. Norris A1 - T. Pissulla A1 - M. Portillo A1 - W. Rother A1 - Y. Shimbara A1 - A. Stolz A1 - C. Vaman A1 - P. Voss A1 - D. Weisshaar A1 - V. Zelevinsky VL - 99 UR - http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.99.042503 ER - TY - JOUR T1 - Uncertainty and the changing hydroclimatology of the Amazon JF - Geophysical Research Letters Y1 - 2007 A1 - Moore, Nathan A1 - Robert Walker A1 - Arima, Eugenio A1 - Ramos da Silva, Renato VL - 34 ER - TY - JOUR T1 - Z = 0 Shell Gap near 100Sn from Intermediate-Energy Coulomb Excitations ￼in Even-Mass 106-112Sn Isotopes JF - PHYSICAL REVIEW LETTERS Y1 - 2007 A1 - C. Vaman A1 - C. Andreoiu A1 - D. Bazin A1 - A. Beccerril A1 - B. A. Brown A1 - C.M. Campbell A1 - A. Chester A1 - J.M. Cook A1 - D.C. Dinca A1 - A. Gade A1 - D. Galaviz A1 - T. Glasmacher A1 - M. {Hjorth-Jensen} A1 - M. Horoi A1 - D. Miller A1 - V. Moeller A1 - W. F. Mueller A1 - A. Schiller A1 - K. Starosta A1 - A. Stolz A1 - J.R. Terry A1 - A. Volya A1 - V. Zelevinsky A1 - H. Zwahlen VL - 99 UR - http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.99.162501 ER - TY - JOUR T1 - Ab initio studies of the electronic structure of defects in {PbTe} JF - Physical Review B Y1 - 2006 A1 - Salameh Ahmad A1 - S. D. Mahanti A1 - Khang Hoang A1 - M. G. Kanatzidis AB -Understanding the detailed electronic structure of deep defect states in narrow band-gap semiconductors has been a challenging problem. Recently, self-consistent ab initio calculations within density functional theory using supercell models have been successful in tackling this problem. In this paper, we carry out such calculations in {PbTe,} a well-known narrow band-gap semiconductor, for a large class of defects: cationic and anionic substitutional impurities of different valence, and cationic and anionic vacancies. For the cationic defects, we study the chemical trends in the position of defect levels by looking at series of compounds {RPb2n−1Te2n,} where R is vacancy or monovalent, divalent, or trivalent atom. Similarly, for anionic defects, we study compounds {MPb2nTe2n−1,} where M is vacancy, S, Se or I. We find that the density of states near the top of the valence band and the bottom of the conduction band get significantly modified for most of these defects. This suggests that the transport properties of {PbTe} in the presence of impurities may not always be interpreted by simple carrier doping (from bound impurity states in the gap) concepts, confirming such ideas developed from qualitative and semiquantitative arguments.

VL - 74 IS - 15 N1 - Copyright {(C)} 2010 The American Physical Society; Please report any problems to prola@aps.org ER - TY - JOUR T1 - Direct Numerical Simulations of a Planar Jet Laden with Evaporating Droplets JF - International Journal of Heat and Mass Transfer Y1 - 2006 A1 - Almeida, T. A1 - Jaberi, F.A. KW - droplet-laden turbulent jet; two-phase planar jet; droplet evaporation; DNS AB -A direct numerical simulation (DNS) study is conducted on the various aspects of phase interactions in a planar turbulent gas-jet laden with non-evaporative and evaporative liquid droplets. A compressible computational model utilizing a finite difference scheme for the carrier gas and a Lagrangian solver for the droplet phase is used to conduct the numerical experiments. The effects of droplet time constant, mass-loading and mass/momentum/energy coupling between phases on droplet and gas-jet fields are investigated. Significant changes in velocity, temperature, density and turbulence production on account of the coupling between the liquid and gas phases are observed in non-isothermal jets with evaporating droplets. Most of these changes are attributed to the density stratification in the carrier gas that is caused by droplet momentum and heat transfer.

VL - 49 IS - 13-14 ER -