Hardware acceleration of reaction-diffusion systems:a guide to optimisation of pattern formation algorithms using OpenACC

Reaction Diffusion Systems (RDS) have widespread applications in computational ecology, biology, computer graphics and the visual arts. For the former applications a major barrier to the development of effective simulation models is their computational complexity - it takes a great deal of processing power to simulate enough replicates such that reliable conclusions can be drawn. Optimizing the computation is thus highly desirable in order to obtain more results with less resources. Existing optimizations of RDS tend to be low-level and GPGPU based. Here we apply the higher-level OpenACC framework to two case studies: a simple RDS to learn the ‘workings’ of OpenACC and a more realistic and complex example. Our results show that simple parallelization directives and minimal data transfer can produce a useful performance improvement. The relative simplicity of porting OpenACC code between heterogeneous hardware is a key benefit to the scientific computing community in terms of speed-up and portability

Emergent behavior of soil fungal dynamics:influence of soil architecture and water distribution

Macroscopic measurements and observations in two-dimensional soil-thin sections indicate that fungal hyphae invade preferentially the larger, air-filled pores in soils. This suggests that the architecture of soils and the microscale distribution of water are likely to influence significantly the dynamics of fungal growth. Unfortunately, techniques are lacking at present to verify this hypothesis experimentally, and as a result, factors that control fungal growth in soils remain poorly understood. Nevertheless, to design appropriate experiments later on, it is useful to indirectly obtain estimates of the effects involved. Such estimates can be obtained via simulation, based on detailed micron-scale X-ray computed tomography information about the soil pore geometry. In this context, this article reports on a series of simulations resulting from the combination of an individual-based fungal growth model, describing in detail the physiological processes involved in fungal growth, and of a Lattice Boltzmann model used to predict the distribution of air-liquid interfaces in soils. Three soil samples with contrasting properties were used as test cases. Several quantitative parameters, including Minkowski functionals, were used to characterize the geometry of pores, air-water interfaces, and fungal hyphae. Simulation results show that the water distribution in the soils is affected more by the pore size distribution than by the porosity of the soils. The presence of water decreased the colonization efficiency of the fungi, as evinced by a decline in the magnitude of all fungal biomass functional measures, in all three samples. The architecture of the soils and water distribution had an effect on the general morphology of the hyphal network, with a "looped" configuration in one soil, due to growing around water droplets. These morphologic differences are satisfactorily discriminated by the Minkowski functionals, applied to the fungal biomass

Simulating microbial degradation of organic matter in a simple porous system using the 3-D diffusion-based model MOSAIC

This paper deals with the simulation of microbial degradation of organic matter in soil within the pore space at a microscopic scale. Pore space was analysed with micro-computed tomography and described using a sphere network coming from a geometrical modelling algorithm. The biological model was improved regarding previous work in order to include the transformation of dissolved organic compounds and diffusion processes. We tested our model using experimental results of a simple substrate decomposition experiment (fructose) within a simple medium (sand) in the presence of different bacterial strains. Separate incubations were carried out in microcosms using five different bacterial communities at two different water potentials of −10 and −100 cm of water. We calibrated the biological parameters by means of experimental data obtained at high water content, and we tested the model without changing any parameters at low water content. Same as for the experimental data, our simulation results showed that the decrease in water content caused a decrease of mineralization rate. The model was able to simulate the decrease of connectivity between substrate and microorganism due the decrease of water content

Passive anterior tibia translation in anterior cruciate ligament-injured, anterior cruciate ligament-reconstructed and healthy knees:A systematic review

Anterior tibia translation (ATT) is mainly prevented by the anterior cruciate ligament. Passive ATT tests are commonly used to diagnose an anterior cruciate ligament (ACL) injury, to select patients for an ACL reconstruction (ACLR), and as an outcome measure after an ACLR. The aim of this review was to present an overview of possible factors determining ATT. A second purpose was to give a summary of the ATT measured in the literature in healthy, ACL-injured and ACLR knees and a comparison between those groups. A literature search was conducted with PubMed. Inclusion criteria were full-text primary studies published in English between January 2006 and October 2016. Studies included reported ATT in explicit data in healthy as well as ACL-injured or ACLR knees or in ACL-injured as well as ACLR knees. Sixty-one articles met inclusion criteria. Two articles measured the ATT in healthy as well as ACL-injured knees, 51 in ACL-injured as well as in ACLR knees, three in ACLR as well as in healthy knees and three in healthy, ACL-injured and ACLR knees. A difference in ATT is found between healthy, contralateral, ACLR and ACL-injured knees and between chronic and acute ACL injury. Graft choices and intra-articular injuries are factors which could affect the ATT. The mean ATT was lowest to highest in ACLR knees using a bone-patella tendon-bone autograft, ACLR knees using a hamstring autograft, contralateral healthy knees, healthy knees, ACLR knees with an allograft and ACL-injured knees. Factors which could affect the ATT are graft choice, ACL injury or reconstruction, intra-articular injuries and whether an ACL injury is chronic or acute. Comparison of ATT between studies should be taken with caution as a high number of different measurement methods are used. To be able to compare studies, more consistency in measuring devices used should be introduced to measuring ATT. The clinical relevance is that an autograft ACLR might give better results than an allograft ACLR as knee laxity is greater when using an allograft tendon. LEVEL OF EVIDENCE: III

Prominent effect of soil network heterogeneity on microbial invasion

Using a network representation for real soil samples and mathematical models for microbial spread, we show that the structural heterogeneity of the soil habitat may have a very significant influence on the size of microbial invasions of the soil pore space. In particular, neglecting the soil structural heterogeneity may lead to a substantial underestimation of microbial invasion. Such effects are explained in terms of a crucial interplay between heterogeneity in microbial spread and heterogeneity in the topology of soil networks. The main influence of network topology on invasion is linked to the existence of long channels in soil networks that may act as bridges for transmission of microorganisms between distant parts of soil

A design flow for performance planning : new paradigms for iteration free synthesis

In conventional design, higher levels of synthesis produce a netlist, from which layout synthesis builds a mask specification for manufacturing. Timing anal ysis is built into a feedback loop to detect timing violations which are then used to update specifications to synthesis. Such iteration is undesirable, and for very high performance designs, infeasible. The problem is likely to become much worse with future generations of technology. To achieve a non-iterative design flow, early synthesis stages should use wire planning to distribute delays over the functional elements and interconnect, and layout synthesis should use its degrees of freedom to realize those delays

Electromechanical tuning of vertically-coupled photonic crystal nanobeams

We present the design, the fabrication and the characterization of a tunable one-dimensional (1D) photonic crystal cavity (PCC) etched on two vertically-coupled GaAs nanobeams. A novel fabrication method which prevents their adhesion under capillary forces is introduced. We discuss a design to increase the flexibility of the structure and we demonstrate a large reversible and controllable electromechanical wavelength tuning (> 15 nm) of the cavity modes.Comment: 11 pages, 4 figure

Wavelength controlled multilayer-stacked linear InAs quantum dot arrays on InGaAsP/InP(100) by self-organized anisotropic strain engineering : a self-ordered quantum dot crystal

Multilayer-stacked linear InAs quantum dot (QD) arrays are created on InAs/InGaAsP superlattice templates formed by self-organized anisotropic strain engineering on InP (100) substrates in chemical beam epitaxy. Stacking of the QD arrays with identical emission wavelength in the 1.55 µm region at room temperature is achieved through the insertion of ultrathin GaAs interlayers beneath the QDs with increasing interlayer thickness in successive layers. The increment in the GaAs interlayer thickness compensates the QD size/wavelength increase during strain correlated stacking. This is the demonstration of a three-dimensionally self-ordered QD crystal with fully controlled structural and optical properties

The effect of heterogeneity on invasion in spatial epidemics: from theory to experimental evidence in a model system

Heterogeneity in host populations is an important factor affecting the ability of a pathogen to invade, yet the quantitative investigation of its effects on epidemic spread is still an open problem. In this paper, we test recent theoretical results, which extend the established “percolation paradigm” to the spread of a pathogen in discrete heterogeneous host populations. In particular, we test the hypothesis that the probability of epidemic invasion decreases when host heterogeneity is increased. We use replicated experimental microcosms, in which the ubiquitous pathogenic fungus Rhizoctonia solani grows through a population of discrete nutrient sites on a lattice, with nutrient sites representing hosts. The degree of host heterogeneity within different populations is adjusted by changing the proportion and the nutrient concentration of nutrient sites. The experimental data are analysed via Bayesian inference methods, estimating pathogen transmission parameters for each individual population. We find a significant, negative correlation between heterogeneity and the probability of pathogen invasion, thereby validating the theory. The value of the correlation is also in remarkably good agreement with the theoretical predictions. We briefly discuss how our results can be exploited in the design and implementation of disease control strategies