Global Optimization by Energy Landscape Paving

We introduce a novel heuristic global optimization method, energy landscape paving (ELP), which combines core ideas from energy surface deformation and tabu search. In appropriate limits, ELP reduces to existing techniques. The approach is very general and flexible and is illustrated here on two protein folding problems. For these examples, the technique gives faster convergence to the global minimum than previous approaches.Comment: to appear in Phys. Rev. Lett. (2002

Regional hydrology controls stream microbial biofilms: evidence from a glacial catchment

International audienceGlaciers are highly responsive to global warming and important agents of landscape heterogeneity. While it is well established that glacial ablation and snowmelt regulate stream discharge, linkage among streams and streamwater hydrogeochemistry, the controls of these factors on stream microbial biofilms remain insufficiently understood. We investigated glacial (metakryal, hypokryal), groundwater-fed (krenal) and snow-fed (rhithral) streams ? all of them representative for alpine stream networks ? and present evidence that these hydrologic and hydrogeochemical factors differentially affect sediment microbial biofilms. Average microbial biomass and bacterial carbon production were low in the glacial streams, whereas bacterial cell size, biomass, and carbon production were higher in the tributaries, most notably in the krenal stream. Whole-cell in situ fluorescence hybridization revealed reduced detection rates of the Eubacteria and higher abundance of ?-Proteobacteria in the glacial stream, a pattern that most probably reflects the trophic status of this ecosystem. Our data suggest low flow during the onset of snowmelt and autumn as a short period (hot moment) of favorable environmental conditions with pulsed inputs of allochthonous nitrate and dissolved organic carbon, and with disproportional high microbial growth. Krenal and rhithral streams with more constant and favorable environments serve as possible sources of microbes and organic matter to the main glacial channel during periods (e.g. snowmelt) of elevated hydrologic linkage among streams. Ice and snow dynamics have a crucial impact on microbial biofilms, and we thus need better understanding of the microbial ecology and enhanced consideration of critical hydrological episodes in future models predicting alpine stream communities

Efficient GPU Offloading with OpenMP for a Hyperbolic Finite Volume Solver on Dynamically Adaptive Meshes

We identify and show how to overcome an OpenMP bottleneck in the administration of GPU memory. It arises for a wave equation solver on dynamically adaptive block-structured Cartesian meshes, which keeps all CPU threads busy and allows all of them to offload sets of patches to the GPU. Our studies show that multithreaded, concurrent, non-deterministic access to the GPU leads to performance breakdowns, since the GPU memory bookkeeping as offered through OpenMP’s map clause, i.e., the allocation and freeing, becomes another runtime challenge besides expensive data transfer and actual computation. We, therefore, propose to retain the memory management responsibility on the host: A caching mechanism acquires memory on the accelerator for all CPU threads, keeps hold of this memory and hands it out to the offloading threads upon demand. We show that this user-managed, CPU-based memory administration helps us to overcome the GPU memory bookkeeping bottleneck and speeds up the time-to-solution of Finite Volume kernels by more than an order of magnitude

Clones in Graphs

Finding structural similarities in graph data, like social networks, is a far-ranging task in data mining and knowledge discovery. A (conceptually) simple reduction would be to compute the automorphism group of a graph. However, this approach is ineffective in data mining since real world data does not exhibit enough structural regularity. Here we step in with a novel approach based on mappings that preserve the maximal cliques. For this we exploit the well known correspondence between bipartite graphs and the data structure formal context $(G,M,I)$ from Formal Concept Analysis. From there we utilize the notion of clone items. The investigation of these is still an open problem to which we add new insights with this work. Furthermore, we produce a substantial experimental investigation of real world data. We conclude with demonstrating the generalization of clone items to permutations.Comment: 11 pages, 2 figures, 1 tabl

Barrier-controlled carrier transport in microcrystalline semiconducting materials: Description within a unified model

A recently developed model that unifies the ballistic and diffusive transport mechanisms is applied in a theoretical study of carrier transport across potential barriers at grain boundaries in microcrystalline semiconducting materials. In the unified model, the conductance depends on the detailed structure of the band edge profile and in a nonlinear way on the carrier mean free path. Equilibrium band edge profiles are calculated within the trapping model for samples made up of a linear chain of identical grains. Quantum corrections allowing for tunneling are included in the calculation of electron mobilities. The dependence of the mobilities on carrier mean free path, grain length, number of grains, and temperature is examined, and appreciable departures from the results of the thermionic-field-emission model are found. Specifically, the unified model is applied in an analysis of Hall mobility data for n-type microcrystalline Si thin films in the range of thermally activated transport. Owing mainly to the effect of tunneling, potential barrier heights derived from the data are substantially larger than the activation energies of the Hall mobilities. The specific features of the unified model, however, cannot be resolved within the rather large uncertainties of the analysis.Comment: REVTex, 19 pages, 9 figures; to appear in J. Appl. Phy

Hector, a fast simulator for the transport of particles in beamlines

Computing the trajectories of particles in generic beamlines is an important ingredient of experimental particle physics, in particular regarding near-beam detectors. A new tool, Hector, has been built for such calculations, using the transfer matrix approach and energy corrections. The limiting aperture effects are also taken into account. As an illustration, the tool was used to simulate the LHC beamlines, in particular around the high luminosity interaction points (IPs), and validated with results of the Mad-X simulator. The LHC beam profiles, trajectories and beta functions are presented. Assuming certain forward proton detector scenarios around the IP5, acceptance plots, irradiation doses and chromaticity grids are produced. Furthermore, the reconstruction of proton kinematic variables at the IP (energy and angle) is studied as well as the impact of the misalignment of beamline elements.Comment: 40 pages, 20 figures; added references, corrected typos ; submitted to JINS

Ab initio and nuclear inelastic scattering studies of Fe3_3Si/GaAs heterostructures

The structure and dynamical properties of the Fe$_3$Si/GaAs(001) interface are investigated by density functional theory and nuclear inelastic scattering measurements. The stability of four different atomic configurations of the Fe$_3$Si/GaAs multilayers is analyzed by calculating the formation energies and phonon dispersion curves. The differences in charge density, magnetization, and electronic density of states between the configurations are examined. Our calculations unveil that magnetic moments of the Fe atoms tend to align in a plane parallel to the interface, along the [110] direction of the Fe$_3$Si crystallographic unit cell. In some configurations, the spin polarization of interface layers is larger than that of bulk Fe$_3$Si. The effect of the interface on element-specific and layer-resolved phonon density of states is discussed. The Fe-partial phonon density of states measured for the Fe$_3$Si layer thickness of three monolayers is compared with theoretical results obtained for each interface atomic configuration. The best agreement is found for one of the configurations with a mixed Fe-Si interface layer, which reproduces the anomalous enhancement of the phonon density of states below 10 meVComment: 14 pages, 9 figures, 4 table