A parallel edge orientation algorithm for quadrilateral meshes

One approach to achieving correct finite element assembly is to ensure that the local orientation of facets relative to each cell in the mesh is consistent with the global orientation of that facet. Rognes et al. have shown how to achieve this for any mesh composed of simplex elements, and deal.II contains a serial algorithm to construct a consistent orientation of any quadrilateral mesh of an orientable manifold. The core contribution of this paper is the extension of this algorithm for distributed memory parallel computers, which facilitates its seamless application as part of a parallel simulation system. Furthermore, our analysis establishes a link between the well-known Union-Find algorithm and the construction of a consistent orientation of a quadrilateral mesh. As a result, existing work on the parallelisation of the Union-Find algorithm can be easily adapted to construct further parallel algorithms for mesh orientations.Comment: Second revision: minor change

Voids in cosmological simulations over cosmic time

We study evolution of voids in cosmological simulations using a new method for tracing voids over cosmic time. The method is based on tracking watershed basins (contiguous regions around density minima) of well developed voids at low redshift, on a regular grid of density field. It enables us to construct a robust and continuous mapping between voids at different redshifts, from initial conditions to the present time. We discuss how the new approach eliminates strong spurious effects of numerical origin when voids evolution is traced by matching voids between successive snapshots (by analogy to halo merger trees). We apply the new method to a cosmological simulation of a standard LambdaCDM cosmological model and study evolution of basic properties of typical voids (with effective radii between 6Mpc/h and 20Mpc/h at redshift z=0) such as volumes, shapes, matter density distributions and relative alignments. The final voids at low redshifts appear to retain a significant part of the configuration acquired in initial conditions. Shapes of voids evolve in a collective way which barely modifies the overall distribution of the axial ratios. The evolution appears to have a weak impact on mutual alignments of voids implying that the present state is in large part set up by the primordial density field. We present evolution of dark matter density profiles computed on iso-density surfaces which comply with the actual shapes of voids. Unlike spherical density profiles, this approach enables us to demonstrate development of theoretically predicted bucket-like shape of the final density profiles indicating a wide flat core and a sharp transition to high-density void walls.Comment: 13 pages, 13 figures; accepted for publication in MNRA

An Examination of Demographics, Personal Values, and Philosophical Orientations of College Students from Multiple University Campuses

The purpose of this study is to identify what current students value today and to determine whether there is a link between personal values and student demographics. A brief demographic survey of fourteen questions was developed and distributed, along with a twenty-question survey which is used determine participant’s values, or philosophical orientation (McKee, Boyatzis, & Johnston, 2008). There were two hundred and forty-two subjects who volunteered over a two-week time period for this research project. Analysis was completed comparing various demographics (such as age, gender, nationality, first generation students) to determine if certain demographics strongly correlated with a particular philosophical orientation, such as pragmatic, human or intellectual. This manuscript further describes some of the current research within the field, the method in which the data was collected and analyzed, as well as the results

Numerical study of the thermoelectric power factor in ultra-thin Si nanowires

Low dimensional structures have demonstrated improved thermoelectric (TE) performance because of a drastic reduction in their thermal conductivity, {\kappa}l. This has been observed for a variety of materials, even for traditionally poor thermoelectrics such as silicon. Other than the reduction in {\kappa}l, further improvements in the TE figure of merit ZT could potentially originate from the thermoelectric power factor. In this work, we couple the ballistic (Landauer) and diffusive linearized Boltzmann electron transport theory to the atomistic sp3d5s*-spin-orbit-coupled tight-binding (TB) electronic structure model. We calculate the room temperature electrical conductivity, Seebeck coefficient, and power factor of narrow 1D Si nanowires (NWs). We describe the numerical formulation of coupling TB to those transport formalisms, the approximations involved, and explain the differences in the conclusions obtained from each model. We investigate the effects of cross section size, transport orientation and confinement orientation, and the influence of the different scattering mechanisms. We show that such methodology can provide robust results for structures including thousands of atoms in the simulation domain and extending to length scales beyond 10nm, and point towards insightful design directions using the length scale and geometry as a design degree of freedom. We find that the effect of low dimensionality on the thermoelectric power factor of Si NWs can be observed at diameters below ~7nm, and that quantum confinement and different transport orientations offer the possibility for power factor optimization.Comment: 42 pages, 14 figures; Journal of Computational Electronics, 201

BioEM: GPU-accelerated computing of Bayesian inference of electron microscopy images

In cryo-electron microscopy (EM), molecular structures are determined from large numbers of projection images of individual particles. To harness the full power of this single-molecule information, we use the Bayesian inference of EM (BioEM) formalism. By ranking structural models using posterior probabilities calculated for individual images, BioEM in principle addresses the challenge of working with highly dynamic or heterogeneous systems not easily handled in traditional EM reconstruction. However, the calculation of these posteriors for large numbers of particles and models is computationally demanding. Here we present highly parallelized, GPU-accelerated computer software that performs this task efficiently. Our flexible formulation employs CUDA, OpenMP, and MPI parallelization combined with both CPU and GPU computing. The resulting BioEM software scales nearly ideally both on pure CPU and on CPU+GPU architectures, thus enabling Bayesian analysis of tens of thousands of images in a reasonable time. The general mathematical framework and robust algorithms are not limited to cryo-electron microscopy but can be generalized for electron tomography and other imaging experiments

Coherent open-loop optimal control of light-harvesting dynamics

We apply theoretically open-loop quantum optimal control techniques to provide methods for the verification of various quantum coherent transport mechanisms in natural and artificial light-harvesting complexes under realistic experimental constraints. We demonstrate that optimally shaped laser pulses allow to faithfully prepare the photosystem in specified initial states (such as localized excitation or coherent superposition, i.e. propagating and non-propagating states) and to probe efficiently the dynamics. These results provide a path towards the discrimination of the different transport pathways and to the characterization of environmental properties, enhancing our understanding of the role that coherent processes may play in biological complexes.Comment: 12 pages, 15 figure