Three-dimensional low Reynolds number flows near biological filtering and protective layers

Mesoscale filtering and protective layers are replete throughout the natural world. Within the body, arrays of extracellular proteins, microvilli, and cilia can act as both protective layers and mechanosensors. For example, blood flow profiles through the endothelial surface layer determine the amount of shear stress felt by the endothelial cells and may alter the rates at which molecules enter and exit the cells. Characterizing the flow profiles through such layers is therefore critical towards understanding the function of such arrays in cell signaling and molecular filtering. External filtering layers are also important to many animals and plants. Trichomes (the hairs or fine outgrowths on plants) can drastically alter both the average wind speed and profile near the leaf's surface, affecting the rates of nutrient and heat exchange. In this paper, dynamically scaled physical models are used to study the flow profiles outside of arrays of cylinders that represent such filtering and protective layers. In addition, numerical simulations using the Immersed Boundary Method are used to resolve the 3D flows within the layers. The experimental and computational results are compared to analytical results obtained by modeling the layer as a homogeneous porous medium with free flow above the layer. The experimental results show that the bulk flow is well described by simple analytical models. The numerical results show that the spatially averaged flow within the layer is well described by the Brinkman model. The numerical results also demonstrate that the flow can be highly 3D with fluid moving into and out of the layer. These effects are not described by the Brinkman model and may be significant for biologically relevant volume fractions. The results of this paper can be used to understand how variations in density and height of such structures can alter shear stresses and bulk flows.Comment: 28 pages, 10 figure

Throughput Optimized Implementations of QUAD

We present several software and hardware implementations of QUAD, a recently introduced stream cipher designed to be provably secure and practical to implement. The software implementations target both a personal computer and an ARM microprocessor. The hardware implementations target field programmable gate arrays. The purpose of our work was to first find the baseline performance of QUAD implementations, then to optimize our implementations for throughput. Our software implementations perform comparably to prior work. Our hardware implementations are the first known implementations to use random coefficients, in agreement with QUAD’s security argument, and achieve much higher throughput than prior implementations

SILAC-based quantitative proteomic analysis of Drosophila gastrula stage embryos mutant for fibroblast growth factor signalling

Quantitative proteomic analyses in combination with genetics provide powerful tools in developmental cell signalling research. Drosophila melanogaster is one of the most widely used genetic models for studying development and disease. Here we combined quantitative proteomics with genetic selection to determine changes in the proteome upon depletion of Heartless (Htl) Fibroblast-Growth Factor (FGF) receptor signalling in Drosophila embryos at the gastrula stage. We present a robust, single generation SILAC (stable isotope labelling with amino acids in cell culture) protocol for labelling proteins in early embryos. For the selection of homozygously mutant embryos at the pre-gastrula stage, we developed an independent genetic marker. Our analyses detected quantitative changes in the global proteome of htl mutant embryos during gastrulation. We identified distinct classes of downregulated and upregulated proteins, and network analyses indicate functionally related groups of proteins in each class. In addition, we identified changes in the abundance of phosphopeptides. In summary, our quantitative proteomic analysis reveals global changes in metabolic, nucleoplasmic, cytoskeletal and transport proteins in htl mutant embryos

Preparing for Climatic Change: The Water, Salmon, and Forests of the Pacific Northwest

The impacts of year-to-year and decade-to-decade climatic variations on some of the Pacific Northwest’s key natural resources can be quantified to estimate sensitivity to regional climatic changes expected as part of anthropogenic global climatic change. Warmer, drier years, often associated with El Niño events and/or the warm phase of the Pacific Decadal Oscillation, tend to be associated with below-average snowpack, streamflow, and flood risk, below-average salmon survival, below-average forest growth, and above-average risk of forest fire. During the 20th century, the region experienced a warming of 0.8 ◦C. Using output from eight climate models, we project a further warming of 0.5–2.5 ◦C (central estimate 1.5 ◦C) by the 2020s, 1.5–3.2 ◦C (2.3◦C) by the 2040s, and an increase in precipitation except in summer. The foremost impact of a warming climate will be the reduction of regional snowpack, which presently supplies water for ecosystems and human uses during the dry summers. Our understanding of past climate also illustrates the responses of human management systems to climatic stresses, and suggests that a warming of the rate projected would pose significant challenges to the management of natural resources. Resource managers and planners currently have few plans for adapting to or mitigating the ecological and economic effects of climatic change

Preparing for Climatic Change: The Water, Salmon, and Forests of the Pacific Northwest

The impacts of year-to-year and decade-to-decade climatic variations on some of the Pacific Northwest’s key natural resources can be quantified to estimate sensitivity to regional climatic changes expected as part of anthropogenic global climatic change. Warmer, drier years, often associated with El Niño events and/or the warm phase of the Pacific Decadal Oscillation, tend to be associated with below-average snowpack, streamflow, and flood risk, below-average salmon survival, below-average forest growth, and above-average risk of forest fire. During the 20th century, the region experienced a warming of 0.8 ◦C. Using output from eight climate models, we project a further warming of 0.5–2.5 ◦C (central estimate 1.5 ◦C) by the 2020s, 1.5–3.2 ◦C (2.3◦C) by the 2040s, and an increase in precipitation except in summer. The foremost impact of a warming climate will be the reduction of regional snowpack, which presently supplies water for ecosystems and human uses during the dry summers. Our understanding of past climate also illustrates the responses of human management systems to climatic stresses, and suggests that a warming of the rate projected would pose significant challenges to the management of natural resources. Resource managers and planners currently have few plans for adapting to or mitigating the ecological and economic effects of climatic change

Towards Symbolic Model-Based Mutation Testing: Combining Reachability and Refinement Checking

Model-based mutation testing uses altered test models to derive test cases that are able to reveal whether a modelled fault has been implemented. This requires conformance checking between the original and the mutated model. This paper presents an approach for symbolic conformance checking of action systems, which are well-suited to specify reactive systems. We also consider nondeterminism in our models. Hence, we do not check for equivalence, but for refinement. We encode the transition relation as well as the conformance relation as a constraint satisfaction problem and use a constraint solver in our reachability and refinement checking algorithms. Explicit conformance checking techniques often face state space explosion. First experimental evaluations show that our approach has potential to outperform explicit conformance checkers.Comment: In Proceedings MBT 2012, arXiv:1202.582

Topological Color Codes and Two-Body Quantum Lattice Hamiltonians

Topological color codes are among the stabilizer codes with remarkable properties from quantum information perspective. In this paper we construct a four-valent lattice, the so called ruby lattice, governed by a 2-body Hamiltonian. In a particular regime of coupling constants, degenerate perturbation theory implies that the low energy spectrum of the model can be described by a many-body effective Hamiltonian, which encodes the color code as its ground state subspace. The gauge symmetry $\mathbf{Z}_{2}\times\mathbf{Z}_{2}$ of color code could already be realized by identifying three distinct plaquette operators on the lattice. Plaquettes are extended to closed strings or string-net structures. Non-contractible closed strings winding the space commute with Hamiltonian but not always with each other giving rise to exact topological degeneracy of the model. Connection to 2-colexes can be established at the non-perturbative level. The particular structure of the 2-body Hamiltonian provides a fruitful interpretation in terms of mapping to bosons coupled to effective spins. We show that high energy excitations of the model have fermionic statistics. They form three families of high energy excitations each of one color. Furthermore, we show that they belong to a particular family of topological charges. Also, we use Jordan-Wigner transformation in order to test the integrability of the model via introducing of Majorana fermions. The four-valent structure of the lattice prevents to reduce the fermionized Hamiltonian into a quadratic form due to interacting gauge fields. We also propose another construction for 2-body Hamiltonian based on the connection between color codes and cluster states. We discuss this latter approach along the construction based on the ruby lattice.Comment: 56 pages, 16 figures, published version

Climate change and mountain water resources: overview and recommendations for research, management and policy

Mountains are essential sources of freshwater for our world, but their role in global water resources could well be significantly altered by climate change. How well do we understand these potential changes today, and what are implications for water resources management, climate change adaptation, and evolving water policy? To answer above questions, we have examined 11 case study regions with the goal of providing a global overview, identifying research gaps and formulating recommendations for research, management and policy. <br><br> After setting the scene regarding water stress, water management capacity and scientific capacity in our case study regions, we examine the state of knowledge in water resources from a highland-lowland viewpoint, focusing on mountain areas on the one hand and the adjacent lowland areas on the other hand. Based on this review, research priorities are identified, including precipitation, snow water equivalent, soil parameters, evapotranspiration and sublimation, groundwater as well as enhanced warming and feedback mechanisms. In addition, the importance of environmental monitoring at high altitudes is highlighted. We then make recommendations how advancements in the management of mountain water resources under climate change could be achieved in the fields of research, water resources management and policy as well as through better interaction between these fields. <br><br> We conclude that effective management of mountain water resources urgently requires more detailed regional studies and more reliable scenario projections, and that research on mountain water resources must become more integrative by linking relevant disciplines. In addition, the knowledge exchange between managers and researchers must be improved and oriented towards long-term continuous interaction