Solving the Boltzmann equation on GPU’s

This paper was presented at the 2nd Micro and Nano Flows Conference (MNF2009), which was held at Brunel University, West London, UK. The conference was organised by Brunel University and supported by the Institution of Mechanical Engineers, IPEM, the Italian Union of Thermofluid dynamics, the Process Intensification Network, HEXAG - the Heat Exchange Action Group and the Institute of Mathematics and its Applications.We present algorithms specifically tailored for solving kinetic equations onto graphics processing units. Unlike particle methods, the proposed methods of solution are ideally suited for solving the unsteady low speed flows which typically occur inMEMS containing oscillating components. The efficiency of the algorithms is demonstrated by solving the two-dimensional low Mach number driven cavity flow of a monatomic gas. Computational results show that it is possible to cut down the computing time of the sequential codes up to two order of magnitudes. The algorithms can easily be extended to three-dimensional flows and to non-equilibrium flows of mixtures

Solving the Boltzmann Equation on GPU

We show how to accelerate the direct solution of the Boltzmann equation using Graphics Processing Units (GPUs). In order to fully exploit the computational power of the GPU, we choose a method of solution which combines a finite difference discretization of the free-streaming term with a Monte Carlo evaluation of the collision integral. The efficiency of the code is demonstrated by solving the two-dimensional driven cavity flow. Computational results show that it is possible to cut down the computing time of the sequential code of two order of magnitudes. This makes the proposed method of solution a viable alternative to particle simulations for studying unsteady low Mach number flows.Comment: 18 pages, 3 pseudo-codes, 6 figures, 1 tabl

Work memories in super 8: the dawn of paper recycling in Brescia

This paper describes the digital acquisition and restoration of a documentary in Super 8 of the origins of citizen\u2019s awareness on paper recycling in Brescia, a city of Lombardy, northern Italy. This short movie has been shot in 1980 by ASM the public company which used to provide all the city supply (gas, water, electricity, district heating) and city transport. Now this film is part of the Fondazione ASM archive and its acquisition is part of a larger project of preservation of industrial memories in Italy. Here we describe the tools used for the acquisition and the technical choices done, together with the restoration test made. As well, we discuss the problems that one must face in trying to preserve a visual document of this kind from the unavoidable damage of time

Regenerating the human heart : direct reprogramming strategies and their current limitations

Cardiovascular diseases are the leading cause of death in the Western world. Unfortunately, current therapies are often only palliative, consequently essentially making heart transplantation necessary for many patients. However, several novel therapeutic approaches in the past two decades have yielded quite encouraging results. The generation of induced pluripotent stem cells, through the forced expression of stem cell-specific transcription factors, has inspired the most promising strategies for heart regeneration by direct reprogramming of cardiac fibroblasts into functional cardiomyocytes. Initial attempts at this reprogramming were conducted using a similar approach to the one used with transcription factors, but during years, novel strategies have been tested, e.g., miRNAs, recombinant proteins and chemical molecules. Although preliminary results on animal models are promising, the low reprogramming efficiency, as well as the incomplete maturation of the cardiomyocytes, still represents important obstacles. This review covers direct transdifferentiation strategies that have been proposed and developed and illustrates the pros and cons of each approach. Indeed, as described in the manuscript, there are still many unanswered questions and drawbacks that require a better understanding of the basic signaling pathways and transcription factor networks before functional cells, suitable for cardiac regeneration and safe for the patients, can be generated and used for human therapies

Genotype-Phenotype Correlation in a Family with Brugada Syndrome Harboring the Novel p.Gln371* Nonsense Variant in the SCN5A Gene

Brugada syndrome (BrS) is marked by coved ST-segment elevation and increased risk of sudden cardiac death. The genetics of this syndrome are elusive in over half of the cases. Variants in the SCN5A gene are the single most common known genetic unifier, accounting for about a third of cases. Research models, such as animal models and cell lines, are limited. In the present study, we report the novel NM_198056.2:c.1111C>T (p.Gln371*) heterozygous variant in the SCN5A gene, as well as its segregation with BrS in a large family. The results herein suggest a pathogenic effect of this variant. Functional studies are certainly warranted to characterize the molecular effects of this variant

NEU3 sialidase role in activating HIF-1α in response to chronic hypoxia in cyanotic congenital heart patients

Background Hypoxia is a common feature of many congenital heart defects (CHDs) and significantly contributes to their pathophysiology. Thus, understanding the mechanism underlying cell response to hypoxia is vital for the development of novel therapeutic strategies. Certainly, the hypoxia inducible factor (HIF) has been extensively investigated and it is now recognized as the master regulator of cell defense machinery counteracting hypoxic stress. Along this line, we recently discovered and reported a novel mechanism of HIF activation, which is mediated by sialidase NEU3. Thus, aim of this study was to test whether NEU3 played any role in the cardiac cell response to chronic hypoxia in congenital cyanotic patients. Methods Right atrial appendage biopsies were obtained from pediatric patients with cyanotic/non-cyanotic CHDs and processed to obtain mRNA and proteins. Real-Time PCR and Western Blot were performed to analyze HIF-1\uce\ub1 and its downstream targets expression, NEU3 expression, and the NEU3 mediated effects on the EGFR signaling cascade. Results Cyanotic patients showed increased levels of HIF-1\uce\ub1, NEU3, EGFR and their downstream targets, as compared to acyanotic controls. The same patients were also characterized by increased phosphorylation of the EGFR signaling cascade proteins. Moreover, we found that HIF-1\uce\ub1 expression levels positively correlated with those recorded for NEU3 in both cyanotic and control patients. Conclusions Sialidase NEU3 plays a central role in activating cell response to chronic hypoxia inducing the up-regulation of HIF-1\uce\ub1, and this represent a possible novel tool to treat several CHD pathologies

GM1 Ganglioside Promotes Osteogenic Differentiation of Human Tendon Stem Cells

Gangliosides, the sialic acid-conjugated glycosphingolipids present in the lipid rafts, have been recognized as important regulators of cell proliferation, migration, and apoptosis. Due to their peculiar localization in the cell membrane, they modulate the activity of several key cell receptors, and increasing evidence supports their involvement also in stem cell differentiation. In this context, herein we report the role played by the ganglioside GM1 in the osteogenic differentiation of human tendon stem cells ( hTSCs). In particular, we found an increase of GM1 levels during osteogenesis that is instrumental for driving the process. In fact, supplementation of the ganglioside in the medium significantly increased the osteogenic differentiation capability of hTSCs. Mechanistically, we found that GM1 supplementation caused a reduction in the phosphorylation of the platelet-derived growth factor receptor-ss ( PDGFR-ss), which is a known inhibitor of osteogenic commitment. These results were further corroborated by the observation that GM1 supplementation was able to revert the inhibitory effects on osteogenesis when the process was inhibited with exogenous PDGF

GPU ACCELERATED SIMULATIONS OF RAREFIED GASESMICROFLOWS

Kinetic equations represent the natural theoretical and computational tool for the investigation of rarefaction effects in gaseous flows. Their complex mathematical structure leads to numerical schemes of various complexity whose common feature is the considerable demand of computing resources. In the case of a dilute gas, the most complex term, i.e. the collision term, has a spatially local structure. Hence, its time consuming numerical evaluation or simulation can be concurrently performed on multi-processor hardware platforms. Recent developments of hardware and software tools have made the massively parallel architecture of graphic processing units (GPUs) available for low cost scientific computing. The paper aims at showing that a particular class of numerical schemes, based on finite difference discretization of the distribution function combined with Monte Carlo evaluation of the collision integral, is very well adapted to the single instruction multiple data (SIMD) structure of GPUs, allowing a two orders of magnitude reduction of the computing time required by the single threaded version of the same code. The numerical scheme implementation is discussed and its application is illustrated by solving the full nonlinear unsteady Boltzmann equation in two dimensional planar geometry and by solving a system of coupled Boltzmann equations to investigate the sound propagation in a binary mixture. The strategies to correct the scheme main drawbacks and further improvements of its performances are discussed