Bridging the computational gap between mesoscopic and continuum modeling of red blood cells for fully resolved blood flow

We present a computational framework for the simulation of blood flow with fully resolved red blood cells (RBCs) using a modular approach that consists of a lattice Boltzmann solver for the blood plasma, a novel finite element based solver for the deformable bodies and an immersed boundary method for the fluid-solid interaction. For the RBCs, we propose a nodal projective FEM (npFEM) solver which has theoretical advantages over the more commonly used mass-spring systems (mesoscopic modeling), such as an unconditional stability, versatile material expressivity, and one set of parameters to fully describe the behavior of the body at any mesh resolution. At the same time, the method is substantially faster than other FEM solvers proposed in this field, and has an efficiency that is comparable to the one of mesoscopic models. At its core, the solver uses specially defined potential energies, and builds upon them a fast iterative procedure based on quasi-Newton techniques. For a known material, our solver has only one free parameter that demands tuning, related to the body viscoelasticity. In contrast, state-of-the-art solvers for deformable bodies have more free parameters, and the calibration of the models demands special assumptions regarding the mesh topology, which restrict their generality and mesh independence. We propose as well a modification to the potential energy proposed by Skalak et al. 1973 for the red blood cell membrane, which enhances the strain hardening behavior at higher deformations. Our viscoelastic model for the red blood cell, while simple enough and applicable to any kind of solver as a post-convergence step, can capture accurately the characteristic recovery time and tank-treading frequencies. The framework is validated using experimental data, and it proves to be scalable for multiple deformable bodies

Middleware’s message : the financial technics of codata

In this paper, I will argue for the relevance of certain distinctive features of messaging systems, namely those in which data (a) can be sent and received asynchronously, (b) can be sent to multiple simultaneous recipients and (c) is received as a “potentially infinite” flow of unpredictable events. I will describe the social technology of the stock ticker, a telegraphic device introduced at the New York Stock Exchange in the 1860s, with reference to early twentieth century philosophers of synchronous experience (Bergson), simultaneous sign interpretations (Mead and Peirce), and flows of discrete events (Bachelard). Then, I will show how the ticker’s data flows developed into the 1990s-era technologies of message queues and message brokers, which distinguished themselves through their asynchronous implementation of ticker-like message feeds sent between otherwise incompatible computers and terminals. These latter systems’ characteristic “publish/subscribe” communication pattern was one in which conceptually centralized (if logically distributed) flows of messages would be “published,” and for which “subscribers” would be spontaneously notified when events of interest occurred. This paradigm—common to the so-called “message-oriented middleware” systems of the late 1990s—would re-emerge in different asynchronous distributed system contexts over the following decades, from “push media” to Twitter to the Internet of Things

A Framework for Spatio-Temporal Data Analysis and Hypothesis Exploration

We present a general framework for pattern discovery and hypothesis exploration in spatio-temporal data sets that is based on delay-embedding. This is a remarkable method of nonlinear time-series analysis that allows the full phase-space behaviour of a system to be reconstructed from only a single observable (accessible variable). Recent extensions to the theory that focus on a probabilistic interpretation extend its scope and allow practical application to noisy, uncertain and high-dimensional systems. The framework uses these extensions to aid alignment of spatio-temporal sub-models (hypotheses) to empirical data - for example satellite images plus remote-sensing - and to explore modifications consistent with this alignment. The novel aspect of the work is a mechanism for linking global and local dynamics using a holistic spatio-temporal feedback loop. An example framework is devised for an urban based application, transit centric developments, and its utility is demonstrated with real data

The Drosophila Inhibitor of Apoptosis (IAP) DIAP2 Is Dispensable for Cell Survival, Required for the Innate Immune Response to Gram-negative Bacterial Infection, and Can Be Negatively Regulated by the Reaper/Hid/Grim Family of IAP-binding Apoptosis Inducers

Many inhibitor of apoptosis (IAP) family proteins inhibit apoptosis. IAPs contain N-terminal baculovirus IAP repeat domains and a C-terminal RING ubiquitin ligase domain. Drosophila IAP DIAP1 is essential for the survival of many cells, protecting them from apoptosis by inhibiting active caspases. Apoptosis initiates when proteins such as Reaper, Hid, and Grim bind a surface groove in DIAP1 baculovirus IAP repeat domains via an N-terminal IAP-binding motif. This evolutionarily conserved interaction disrupts DIAP1-caspase interactions, unleashing apoptosis-inducing caspase activity. A second Drosophila IAP, DIAP2, also binds Rpr and Hid and inhibits apoptosis in multiple contexts when overexpressed. However, due to a lack of mutants, little is known about the normal functions of DIAP2. We report the generation of diap2 null mutants. These flies are viable and show no defects in developmental or stress-induced apoptosis. Instead, DIAP2 is required for the innate immune response to Gram-negative bacterial infection. DIAP2 promotes cytoplasmic cleavage and nuclear translocation of the NF-{kappa}B homolog Relish, and this requires the DIAP2 RING domain. Increasing the genetic dose of diap2 results in an increased immune response, whereas expression of Rpr or Hid results in down-regulation of DIAP2 protein levels. Together these observations suggest that DIAP2 can regulate immune signaling in a dose-dependent manner, and this can be regulated by IBM-containing proteins. Therefore, diap2 may identify a point of convergence between apoptosis and immune signaling pathways

Redundant Arrays of IDE Drives

The next generation of high-energy physics experiments is expected to gather prodigious amounts of data. New methods must be developed to handle this data and make analysis at universities possible. We examine some techniques that use recent developments in commodity hardware. We test redundant arrays of integrated drive electronics (IDE) disk drives for use in offline high-energy physics data analysis. IDE redundant array of inexpensive disks (RAID) prices now equal the cost per terabyte of million-dollar tape robots! The arrays can be scaled to sizes affordable to institutions without robots and used when fast random access at low cost is important. We also explore three methods of moving data between sites; internet transfers, hot pluggable IDE disks in FireWire cases, and writable digital video disks (DVD-R).Comment: Submitted to IEEE Transactions On Nuclear Science, for the 2001 IEEE Nuclear Science Symposium and Medical Imaging Conference, 8 pages, 1 figure, uses IEEEtran.cls. Revised March 19, 2002 and published August 200