A Passive Micromixer for Bioanalytical Applications

This paper was presented at the 4th Micro and Nano Flows Conference (MNF2014), which was held at University College, London, UK. The conference was organised by Brunel University and supported by the Italian Union of Thermofluiddynamics, IPEM, the Process Intensification Network, the Institution of Mechanical Engineers, the Heat Transfer Society, HEXAG - the Heat Exchange Action Group, and the Energy Institute, ASME Press, LCN London Centre for Nanotechnology, UCL University College London, UCL Engineering, the International NanoScience Community, www.nanopaprika.eu.Three passive micromixers with different geometries, i.e. zigzag, spiral, and split and merge (SaM) with labyrinthine channels, are compared with respect to their mixing efficiency by means of a computational study. The specifications are imposed from flexible printed circuit (FPC) technology which is used for their fabrication and from the applications to be implemented, i.e. the mixing of biochemical reagents. The computations include the numerical solution of continuity, Navier-Stokes, and mass conservation equations in 3d by ANSYS Fluent. The highest mixing efficiency is calculated for the SaM micromixer with the labyrinthine channel. Compared to a linear micromixer, the spiral micromixer improves the mixing efficiency by 8%, the zigzag by 11%, and the SaM by 92%; the diffusion coefficient of the biomolecule is 10-10 m2/s, the Reynolds number is 0.5, and the volume of each micromixer is 2.54 μl. The best of the three designs is realized by FPC technology and is experimentally evaluated by fluorescence microscopy

A Distributed Merge and Split Algorithm for Fair Cooperation in Wireless Networks

This paper introduces a novel concept from coalitional game theory which allows the dynamic formation of coalitions among wireless nodes. A simple and distributed merge and split algorithm for coalition formation is constructed. This algorithm is applied to study the gains resulting from the cooperation among single antenna transmitters for virtual MIMO formation. The aim is to find an ultimate transmitters coalition structure that allows cooperating users to maximize their utilities while accounting for the cost of coalition formation. Through this novel game theoretical framework, the wireless network transmitters are able to self-organize and form a structured network composed of disjoint stable coalitions. Simulation results show that the proposed algorithm can improve the average individual user utility by 26.4% as well as cope with the mobility of the distributed users.Comment: This paper is accepted for publication at the IEEE ICC Workshop on Cooperative Communications and Networkin

Hardware-aware block size tailoring on adaptive spacetree grids for shallow water waves.

Spacetrees are a popular formalism to describe dynamically adaptive Cartesian grids. Though they directly yield an adaptive spatial discretisation, i.e. a mesh, it is often more efficient to augment them by regular Cartesian blocks embedded into the spacetree leaves. This facilitates stencil kernels working efficiently on homogeneous data chunks. The choice of a proper block size, however, is delicate. While large block sizes foster simple loop parallelism, vectorisation, and lead to branch-free compute kernels, they bring along disadvantages. Large blocks restrict the granularity of adaptivity and hence increase the memory footprint and lower the numerical-accuracy-per-byte efficiency. Large block sizes also reduce the block-level concurrency that can be used for dynamic load balancing. In the present paper, we therefore propose a spacetree-block coupling that can dynamically tailor the block size to the compute characteristics. For that purpose, we allow different block sizes per spacetree node. Groups of blocks of the same size are identied automatically throughout the simulation iterations, and a predictor function triggers the replacement of these blocks by one huge, regularly rened block. This predictor can pick up hardware characteristics while the dynamic adaptivity of the fine grid mesh is not constrained. We study such characteristics with a state-of-the-art shallow water solver and examine proper block size choices on AMD Bulldozer and Intel Sandy Bridge processors

Inference of single-cell phylogenies from lineage tracing data using Cassiopeia.

The pairing of CRISPR/Cas9-based gene editing with massively parallel single-cell readouts now enables large-scale lineage tracing. However, the rapid growth in complexity of data from these assays has outpaced our ability to accurately infer phylogenetic relationships. First, we introduce Cassiopeia-a suite of scalable maximum parsimony approaches for tree reconstruction. Second, we provide a simulation framework for evaluating algorithms and exploring lineage tracer design principles. Finally, we generate the most complex experimental lineage tracing dataset to date, 34,557 human cells continuously traced over 15 generations, and use it for benchmarking phylogenetic inference approaches. We show that Cassiopeia outperforms traditional methods by several metrics and under a wide variety of parameter regimes, and provide insight into the principles for the design of improved Cas9-enabled recorders. Together, these should broadly enable large-scale mammalian lineage tracing efforts. Cassiopeia and its benchmarking resources are publicly available at www.github.com/YosefLab/Cassiopeia

How organized is deep convection over Germany?

Deep moist convection shows a tendency to organize into mesoscale structures. To be able to understand the potential effect of convective organization on the climate, one needs first to characterize organization. In this study, we systematically characterize the organizational state of convection over Germany based on two years of cloud-top observations derived from the Meteosat Second Generation satellite and of precipitation cores detected by the German C-band radar network. The organizational state of convection is characterized by commonly employed organization indices, which are mostly based on the object numbers, sizes and nearest-neighbour distances. According to the organization index Iorg, cloud tops and precipitation cores are found to be in an organized state for 69% and 92% of the time, respectively. There is an increase in rainfall when the number of objects and their sizes increase, independently of the organizational state. Case-studies of specific days suggest that convectively organized states correspond to either local multi-cell clusters, with less numerous, larger objects close to each other, or to scattered clusters, with more numerous, smaller organized objects spread out over the domain. For those days, simulations are performed with the large-eddy model ICON with grid spacings of 625, 312 and 156?m. Although the model underestimates rainfall and shows a too large cold cloud coverage, the organizational state is reasonably well represented without significant differences between the grid spacings