An Empirical Analysis of Search in GSAT

We describe an extensive study of search in GSAT, an approximation procedure for propositional satisfiability. GSAT performs greedy hill-climbing on the number of satisfied clauses in a truth assignment. Our experiments provide a more complete picture of GSAT's search than previous accounts. We describe in detail the two phases of search: rapid hill-climbing followed by a long plateau search. We demonstrate that when applied to randomly generated 3SAT problems, there is a very simple scaling with problem size for both the mean number of satisfied clauses and the mean branching rate. Our results allow us to make detailed numerical conjectures about the length of the hill-climbing phase, the average gradient of this phase, and to conjecture that both the average score and average branching rate decay exponentially during plateau search. We end by showing how these results can be used to direct future theoretical analysis. This work provides a case study of how computer experiments can be used to improve understanding of the theoretical properties of algorithms.Comment: See http://www.jair.org/ for any accompanying file

Differential introgression and the maintenance of species boundaries in an advanced generation avian hybrid zone

Background: Evolutionary processes, including selection and differential fitness, shape the introgression of genetic material across a hybrid zone, resulting in the exchange of some genes but not others. Differential introgression of molecular or phenotypic markers can thus provide insight into factors contributing to reproductive isolation. We characterized patterns of genetic variation across a hybrid zone between two tidal marsh birds, Saltmarsh (Ammodramus caudacutus) and Nelson’s (A. nelsoni) sparrows (n = 286), and compared patterns of introgression among multiple genetic markers and phenotypic traits. Results: Geographic and genomic cline analyses revealed variable patterns of introgression among marker types. Most markers exhibited gradual clines and indicated that introgression exceeds the spatial extent of the previously documented hybrid zone. We found steeper clines, indicating strong selection for loci associated with traits related to tidal marsh adaptations, including for a marker linked to a gene region associated with metabolic functions, including an osmotic regulatory pathway, as well as for a marker related to melanin-based pigmentation, supporting an adaptive role of darker plumage (salt marsh melanism) in tidal marshes. Narrow clines at mitochondrial and sex-linked markers also offer support for Haldane’s rule. We detected patterns of asymmetrical introgression toward A. caudacutus, which may be driven by differences in mating strategy or differences in population density between the two species. Conclusions: Our findings offer insight into the dynamics of a hybrid zone traversing a unique environmental gradient and provide evidence for a role of ecological divergence in the maintenance of pure species boundaries despite ongoing gene flow

Differential introgression and the maintenance of species boundaries in an advanced generation avian hybrid zone

Background: Evolutionary processes, including selection and differential fitness, shape the introgression of genetic material across a hybrid zone, resulting in the exchange of some genes but not others. Differential introgression of molecular or phenotypic markers can thus provide insight into factors contributing to reproductive isolation. We characterized patterns of genetic variation across a hybrid zone between two tidal marsh birds, Saltmarsh (Ammodramus caudacutus) and Nelson’s (A. nelsoni) sparrows (n = 286), and compared patterns of introgression among multiple genetic markers and phenotypic traits. Results: Geographic and genomic cline analyses revealed variable patterns of introgression among marker types. Most markers exhibited gradual clines and indicated that introgression exceeds the spatial extent of the previously documented hybrid zone. We found steeper clines, indicating strong selection for loci associated with traits related to tidal marsh adaptations, including for a marker linked to a gene region associated with metabolic functions, including an osmotic regulatory pathway, as well as for a marker related to melanin-based pigmentation, supporting an adaptive role of darker plumage (salt marsh melanism) in tidal marshes. Narrow clines at mitochondrial and sex-linked markers also offer support for Haldane’s rule. We detected patterns of asymmetrical introgression toward A. caudacutus, which may be driven by differences in mating strategy or differences in population density between the two species. Conclusions: Our findings offer insight into the dynamics of a hybrid zone traversing a unique environmental gradient and provide evidence for a role of ecological divergence in the maintenance of pure species boundaries despite ongoing gene flow

Recent advances in multidisciplinary optimization of rotorcraft

A joint activity involving NASA and Army researchers at NASA LaRC to develop optimization procedures to improve the rotor blade design process by integrating appropriate disciplines and accounting for all of the important interactions among the disciplines is described. The disciplines involved include rotor aerodynamics, rotor dynamics, rotor structures, airframe dynamics, and acoustics. The work is focused on combining these five key disciplines in an optimization procedure capable of designing a rotor system to satisfy multidisciplinary design requirements. Fundamental to the plan is a three-phased approach. In phase 1, the disciplines of blade dynamics, blade aerodynamics, and blade structure are closely coupled while acoustics and airframe dynamics are decoupled and are accounted for as effective constraints on the design for the first three disciplines. In phase 2, acoustics is integrated with the first three disciplines. Finally, in phase 3, airframe dynamics is integrated with the other four disciplines. Representative results from work performed to date are described. These include optimal placement of tuning masses for reduction of blade vibratory shear forces, integrated aerodynamic/dynamic optimization, and integrated aerodynamic/dynamic/structural optimization. Examples of validating procedures are described

On The Complexity and Completeness of Static Constraints for Breaking Row and Column Symmetry

We consider a common type of symmetry where we have a matrix of decision variables with interchangeable rows and columns. A simple and efficient method to deal with such row and column symmetry is to post symmetry breaking constraints like DOUBLELEX and SNAKELEX. We provide a number of positive and negative results on posting such symmetry breaking constraints. On the positive side, we prove that we can compute in polynomial time a unique representative of an equivalence class in a matrix model with row and column symmetry if the number of rows (or of columns) is bounded and in a number of other special cases. On the negative side, we show that whilst DOUBLELEX and SNAKELEX are often effective in practice, they can leave a large number of symmetric solutions in the worst case. In addition, we prove that propagating DOUBLELEX completely is NP-hard. Finally we consider how to break row, column and value symmetry, correcting a result in the literature about the safeness of combining different symmetry breaking constraints. We end with the first experimental study on how much symmetry is left by DOUBLELEX and SNAKELEX on some benchmark problems.Comment: To appear in the Proceedings of the 16th International Conference on Principles and Practice of Constraint Programming (CP 2010

Fine-scale population structure and asymmetrical dispersal in an obligate salt-marsh passerine, the Saltmarsh Sparrow (Ammodramus Caudacutus)

Understanding the spatial scale of gene flow can yield valuable insight into the ecology of an organism and guide conservation strategies. Fine-scale genetic structure is uncommon in migratory passerines because of their high vagility and presumed high dispersal abilities. Aspects of the behavior and ecology of some migratory species, however, may promote structure on a finer scale in comparison to their mobility. We investigated population genetic structure in the Saltmarsh Sparrow (Ammodramus caudacutus), a migratory passerine that breeds along the northeastern coast of the United States, where it is restricted exclusively to a narrow strip of patchily distributed tidal marsh habitat. Using genotyping with 10 microsatellite loci, we detected weak but significant population structure among Saltmarsh Sparrows from nine marshes on the breeding grounds between Scarborough, Maine, and Oceanside, New York. Genetic variation among marshes was largely consistent with a pattern of isolation by distance, with some exceptions. One inland marsh was genetically divergent despite its proximity to other sampled marshes, which suggests that mechanisms besides geographic distance influence population genetic structure. Bayesian clustering, multivariate analyses, and assignment tests supported a population structure consisting of five groups. Estimates of migration rates indicated variation in gene flow among marshes, which suggests asymmetrical dispersal and possible source-sink population dynamics. The genetic structure that we found in Saltmarsh Sparrows may result from natal philopatry and breeding-site fidelity, combined with restricted dispersal due to obligate dependence on a patchy habitat. Our findings suggest that fine-scale population structure may be important in some migratory passerines. Received 12 July 2011, accepted 1 February 2012

The Milky Way Heart: Investigating molecular gas and gamma-ray morphologies in the Central Molecular Zone

Since the discovery of a broad distribution of very high energy (VHE; >0.1 TeV) gamma-rays in the Central Molecular Zone (CMZ) of the Galaxy in 2006 by the HESS collaboration, the correlation of this emission with the integrated intensity of the CS(1-0) molecular line emission has inferred a hadronic origin for the gamma-rays. Here we describe the beginning of our investigation into the strength of this correlation utilising new multi-line millimeter data from the Mopra CMZ and HOP surveys and multi-wavelength GBT radio continuum observations towards the CMZ and compare these in detail with the diffuse TeV gamma-ray emission from HESS. The benefit of these new data is that they allow us to simultaneously observe and analyse correlations using a large number (>10) of molecular species, some of which contain their isotopologue pairs. The use of isotopologue pairs is especially powerful, since it allows one to analyse the optical depth of a number of different molecular species, thus investigating the nature of the correlation over a range of different physical conditions. Here we begin by comparing the integrated line emission and continuum radio emission with the diffuse gamma-ray emission, and, by using isotopologue pairs such as HCN/H$^{13}$CN, obtain optical depths throughout the CMZ corresponding to regions of both strong and weak gamma-ray emission. We find that the radio continuum better matches the peak of the gamma-ray emission, which corresponds to the more compact -- compared to the relatively coarse resolution of the gamma-ray images -- sources in the CMZ. Using the isotopologue pairs, we find that the optical depth at all positions and velocities within the CMZ are about 2--4. This is similar to that found for the CS(1--0) line and would underestimate the mass of the CMZ, potentially explaining why molecular line emission peaks appear offset from the gamma-ray peaks.Comment: 8 pages, 5 figures. Accepted to the Proceedings of the 25th Texas Symposium on Relativistic Astrophysics (Heidelberg, 2010

Atomistic origins of the phase transition mechanism in Ge2Sb2Te5

Combined static and molecular dynamics first-principles calculations are used to identify a direct structural link between the metastable crystalline and amorphous phases of Ge2Sb2Te5. We find that the phase transition is driven by the displacement of Ge atoms along the rocksalt [111] direction from the stable-octahedron to high-energy-unstable tetrahedron sites close to the intrinsic vacancy regions, which give rise to the formation of local 4-fold coordinated motifs. Our analyses suggest that the high figures of merit of Ge2Sb2Te5 are achieved from the optimal combination of intrinsic vacancies provided by Sb2Te3 and the instability of the tetrahedron sites provided by GeTe

Genotype-environment associations support a mosaic hybrid zone between two tidal marsh birds

Local environmental features can shape hybrid zone dynamics when hybrids are bounded by ecotones or when patchily distributed habitat types lead to a corresponding mosaic of genotypes. We investigated the role of marsh-level characteristics in shaping a hybrid zone between two recently diverged avian taxa – Saltmarsh (Ammodramus caudacutus) and Nelson\u27s (A. nelsoni) sparrows. These species occupy different niches where allopatric, with caudacutus restricted to coastal marshes and nelsoni found in a broader array of wetland and grassland habitats and co-occur in tidal marshes in sympatry. We determined the influence of habitat types on the distribution of pure and hybrid sparrows and assessed the degree of overlap in the ecological niche of each taxon. To do this, we sampled and genotyped 305 sparrows from 34 marshes across the hybrid zone and from adjacent regions. We used linear regression to test for associations between marsh characteristics and the distribution of pure and admixed sparrows. We found a positive correlation between genotype and environmental variables with a patchy distribution of genotypes and habitats across the hybrid zone. Ecological niche models suggest that the hybrid niche was more similar to that of A. nelsoni and habitat suitability was influenced strongly by distance from coastline. Our results support a mosaic model of hybrid zone maintenance, suggesting a role for local environmental features in shaping the distribution and frequency of pure species and hybrids across space