Order Parameter Equations for Front Transitions: Nonuniformly Curved Fronts

Kinematic equations for the motion of slowly propagating, weakly curved fronts in bistable media are derived. The equations generalize earlier derivations where algebraic relations between the normal front velocity and its curvature are assumed. Such relations do not capture the dynamics near nonequilibrium Ising-Bloch (NIB) bifurcations, where transitions between counterpropagating Bloch fronts may spontaneously occur. The kinematic equations consist of coupled integro-differential equations for the front curvature and the front velocity, the order parameter associated with the NIB bifurcation. They capture the NIB bifurcation, the instabilities of Ising and Bloch fronts to transverse perturbations, the core structure of a spiral wave, and the dynamic process of spiral wave nucleation.Comment: 20 pages. Aric Hagberg: http://cnls.lanl.gov/~aric; Ehud Meron:http://www.bgu.ac.il/BIDR/research/staff/meron.htm

Interdependent security experiments

This paper analyzes the behavior of subjects in interdependent security experiments which exhibit strategic complementarity. In these experiments, subjects decide whether to pay to mitigate the risk of a loss, but the exact risk depends on the actions of other subjects. Two ranked equilibria exist, and the efficient equilibrium is for all agents to pay for the mitigation. Subjects in the interdependent security experiments rarely coordinate on the efficient equilibrium. Coordination is slightly more common in similar coordination games without the risk mitigation decision. The experiments also compare the effectiveness of two policies at inducing higher levels of mitigation.experiments, coordination game, risk mitigation, interdependent security

Optimal Interdiction of Unreactive Markovian Evaders

The interdiction problem arises in a variety of areas including military logistics, infectious disease control, and counter-terrorism. In the typical formulation of network interdiction, the task of the interdictor is to find a set of edges in a weighted network such that the removal of those edges would maximally increase the cost to an evader of traveling on a path through the network. Our work is motivated by cases in which the evader has incomplete information about the network or lacks planning time or computational power, e.g. when authorities set up roadblocks to catch bank robbers, the criminals do not know all the roadblock locations or the best path to use for their escape. We introduce a model of network interdiction in which the motion of one or more evaders is described by Markov processes and the evaders are assumed not to react to interdiction decisions. The interdiction objective is to find an edge set of size B, that maximizes the probability of capturing the evaders. We prove that similar to the standard least-cost formulation for deterministic motion this interdiction problem is also NP-hard. But unlike that problem our interdiction problem is submodular and the optimal solution can be approximated within 1-1/e using a greedy algorithm. Additionally, we exploit submodularity through a priority evaluation strategy that eliminates the linear complexity scaling in the number of network edges and speeds up the solution by orders of magnitude. Taken together the results bring closer the goal of finding realistic solutions to the interdiction problem on global-scale networks.Comment: Accepted at the Sixth International Conference on integration of AI and OR Techniques in Constraint Programming for Combinatorial Optimization Problems (CPAIOR 2009

Caenorhabditis nomenclature

Genetic nomenclature allows the genetic features of an organism to be structured and described in a uniform and systematicway. Genetic features, including genes, variations (both natural and induced), and gene products, are assigned descriptorsthat inform on the nature of the feature. These nomenclature designations facilitate communication among researchers (in publications,presentations, and databases) to advance understanding of the biology of the genetic feature and the experimental utilizationof organisms that contain the genetic feature. The nomenclature system that is used for C. elegans was first employed by Sydney Brenner (1974) in his landmark description of the genetics of this model organism, and then substantially extended and modified in Horvitz et al., 1979. The gene, allele, and chromosome rearrangement nomenclature, described below, is an amalgamation of that from bacteria andyeast, with the rearrangement types from Drosophila. The nomenclature avoids standard words, subscripts, superscripts, and Greek letters and includes a hyphen (-) to separatethe gene name from gene number (distinct genes with similar phenotypes or molecular properties). As described by Jonathan Hodgkin, ‘the hyphen is about 1 mm in length in printed text and therefore symbolizes the 1 mm long worm’. These nomenclature propertiesmake C. elegans publications highly suitable for informatic text mining, as there is minimal ambiguity. From the founding of the CaenorhabditisGenetics Center (CGC) in 1979 until 1992, Don Riddle and Mark Edgley acted as the central repository for genetic nomenclature. Jonathan Hodgkin was nomenclature czar from 1992 through 2013; this was a pivotal period with the elucidation of the genome sequence of C. elegans, and later that of related nematodes, and the inception of WormBase. Thus, under the guidance of Hodgkin, the nomenclature system became a central feature of WormBase and the number and types of genetic features significantly expanded. The nomenclature system remains dynamic, with recentadditions including guidelines related to genome engineering, and continued reliance on the community for input. WormBase assigns specific identifying codes to each laboratory engaged in dedicated long-term genetic research on C. elegans. Each laboratory is assigned a laboratory/strain code for naming strains, and an allele code for naming genetic variation(e.g., mutations) and transgenes. These designations are assigned to the laboratory head/PI who is charged with supervisingtheir organization in laboratory databases and their associated biological reagents that are described on WormBase, in publications, and distributed to the scientific community on request. The laboratory/strain code is used: a) to identifythe originator of community-supplied information on WormBase, which, in addition to attribution, facilitates communicationbetween the community/curators and the originator if an issue related to the information should arise at a later date; andb) to provide a tracking code for activities at the CGC. The laboratory/strain designation consists of 2-3 uppercase letters while the allele designation has 1-3 lowercase letters.The final letter of a laboratory code should not be an “O” or an “I” so as not to be mistaken for the numbers “0” or “1” respectively.Additionally, allele designations should also not end with the letter “l” which could also be mistaken for the number “1.” These codes are listed at the CGC and in WormBase. Investigators generating strains, alleles, transgenes, and/or defining genes require these designations and should applyfor them at [email protected]. Information for several other nematode species, in addition to C. elegans, is curated at WormBase. All species are referred to by their Linnean binomial names (e.g,. Caenorhabditis elegans or C. elegans). Details of all the genomes available at WormBase and the degree of their curation can be found at www.wormbase.org/species/al

Crossing Patterns in Nonplanar Road Networks

We define the crossing graph of a given embedded graph (such as a road network) to be a graph with a vertex for each edge of the embedding, with two crossing graph vertices adjacent when the corresponding two edges of the embedding cross each other. In this paper, we study the sparsity properties of crossing graphs of real-world road networks. We show that, in large road networks (the Urban Road Network Dataset), the crossing graphs have connected components that are primarily trees, and that the remaining non-tree components are typically sparse (technically, that they have bounded degeneracy). We prove theoretically that when an embedded graph has a sparse crossing graph, it has other desirable properties that lead to fast algorithms for shortest paths and other algorithms important in geographic information systems. Notably, these graphs have polynomial expansion, meaning that they and all their subgraphs have small separators.Comment: 9 pages, 4 figures. To appear at the 25th ACM SIGSPATIAL International Conference on Advances in Geographic Information Systems(ACM SIGSPATIAL 2017