•Algebra-based simulation approach for incompressible turbulent flows with heat transfer.•Efficient heterogeneous execution of computing kernels with halo update on CPU+GPU.•Overlap of computations ...and communications, multithreaded data exchange processing.•NUMA-aware OpenMP parallelization for computing on manycore CPUs and managing devices.•Detailed performance study of the SpMV kernel on various supercomputer architectures.
The quest for new portable implementations of simulation algorithms is motivated by the increasing variety of computing architectures. Moreover, the hybridization of high-performance computing systems imposes additional constraints, since heterogeneous computations are needed to efficiently engage processors and massively-parallel accelerators. This, in turn, involves different parallel paradigms and computing frameworks and requires complex data exchanges between computing units. Typically, simulation codes rely on sophisticated data structures and computing subroutines, so-called kernels, which makes portability terribly cumbersome. Thus, a natural way to achieve portability is to dramatically reduce the complexity of both data structures and computing kernels. In our algebra-based approach, the scale-resolving simulation of incompressible turbulent flows on unstructured meshes relies on three fundamental kernels: the sparse matrix-vector product, the linear combination of vectors and the dot product. It is noteworthy that this approach is not limited to a particular kind of numerical method or a set of governing equations. In our code, an auto-balanced multilevel partitioning distributes workload among computing devices of various architectures. The overlap of computations and multistage communications efficiently hides the data exchanges overhead in large-scale supercomputer simulations. In addition to computing on accelerators, special attention is paid at efficiency on manycore processors in multiprocessor nodes with significant non-uniform memory access factor. Parallel efficiency and performance are studied in detail for different execution modes on various supercomputers using up to 9,600 processor cores and up to 256 graphics processor units. The heterogeneous implementation model described in this work is a general-purpose approach that is well suited for various subroutines in numerical simulation codes.
Understanding nanoscale thermal transport is of substantial importance for designing contemporary semiconductor technologies. Heat removal from small sources is well established to be severely ...impeded compared to diffusive predictions due to the ballistic nature of the dominant heat carriers. Experimental observations are commonly interpreted through a reduction of effective thermal conductivity, even though most measurements only probe a single aggregate thermal metric. Here, we employ thermoreflectance thermal imaging to directly visualise the 2D temperature field produced by localised heat sources on InGaAs with characteristic widths down to 100 nm. Besides displaying effective thermal performance reductions up to 50% at the active junctions in agreement with prior studies, our steady-state thermal images reveal that, remarkably, 1-3 μm adjacent to submicron devices the crosstalk is actually reduced by up to fourfold. Submicrosecond transient imaging additionally shows responses to be faster than conventionally predicted. A possible explanation based on hydrodynamic heat transport, and some open questions, are discussed.
Premise
The interfertile species Anacyclus clavatus, A. homogamos, and A. valentinus represent a plant complex coexisting in large anthropic areas of the western Mediterranean Basin with ...phenotypically mixed populations exhibiting a great floral variation. The goal of this study was to estimate the genetic identity of each species, to infer the role of hybridization in the observed phenotypic diversity, and to explore the effect of climate on the geographic distribution of species and genetic clusters.
Methods
We used eight nuclear microsatellites to genotype 585 individuals from 31 populations of three Anacyclus species for population genetic analyses by using clustering algorithms based on Bayesian models and ordination methods. In addition, we used ecological niche models and niche overlap analyses for both the species and genetic clusters. We used an expanded data set, including 721 individuals from 129 populations for ecological niche models of the genetic clusters.
Results
We found a clear correspondence between species and genetic clusters, except for A. clavatus that included up to three genetic clusters. We detected individuals with admixed genetic ancestry in A. clavatus and in mixed populations. Ecological niche models predicted similar distributions for species and genetic clusters. For the two specific genetic clusters of A. clavatus, ecological niche models predicted remarkably different areas.
Conclusions
Gene flow between Anacyclus species likely explains phenotypic diversity in contact areas. In addition, we suggest that introgression could be involved in the origin of one of the two A. clavatus genetic clusters, which also showed ecological differentiation.
3D interconnected nanowire scaffoldings are shown to increase the thermoelectric efficiency in comparison to similar diameter 1D nanowires and films grown under similar electrodeposition conditions. ...Bi2Te3 3D nanonetworks offer a reduction in thermal conductivity (κT) while preserving the high electrical conductivity of the films. The reduction in κT is modeled using the hydrodynamic heat transport equation, and it can be understood as a heat viscosity effect due to the 3D nanostructuration. In addition, the Seebeck coefficient is twice that of nanowires and films, and up to 50% higher than in a single crystal. This increase is interpreted as a nonequilibrium effect that the geometry of the structure induces on the distribution function of the phonons, producing an enhanced phonon drag. These thermoelectric metamaterials have higher performance and are fabricated with large areas by a cost-effective method, which makes them suitable for up-scale production.
We present a formalism to solve the phonon Boltzmann transport equation (BTE) for finite Knudsen numbers that supplies a hydrodynamic heat transport equation similar to the Navier-Stokes equation for ...general semiconductors. This generalization of Fourier's law applies in general cases, from systems dominated by momentum-preserving normal collisions, as is well known, to kinetic materials dominated by resistive collisions, where it captures nonlocal effects. The key feature of our framework is that the macrostate is described in terms of the heat flux and its first derivatives. We obtain explicit expressions for the nonequilibrium phonon distribution and for the geometry-independent macroscopic parameters as a function of phonon properties that can be calculated from first principles. Ab initio model predictions are found to agree with a wide range of experiments in silicon. In contrast to approaches directly based on the BTE, the hydrodynamic equation can be solved in arbitrary geometries, thus providing a powerful tool for nanoscale heat modeling at a low computational cost.
Heat management is crucial in the design of nanoscale devices as the operating temperature determines their efficiency and lifetime. Past experimental and theoretical works exploring nanoscale heat ...transport in semiconductors addressed known deviations from Fourier’s law modeling by including effective parameters, such as a size-dependent thermal conductivity. However, recent experiments have qualitatively shown behavior that cannot be modeled in this way. Here, we combine advanced experiment and theory to show that the cooling of 1D- and 2D-confined nanoscale hot spots on silicon can be described using a general hydrodynamic heat transport model, contrary to previous understanding of heat flow in bulk silicon. We use a comprehensive set of extreme ultraviolet scatterometry measurements of nondiffusive transport from transiently heated nanolines and nanodots to validate and generalize our ab initio model, that does not need any geometry-dependent fitting parameters. This allows us to uncover the existence of two distinct time scales and heat transport mechanisms: an interface resistance regime that dominates on short time scales and a hydrodynamic-like phonon transport regime that dominates on longer time scales. Moreover, our model can predict the full thermomechanical response on nanometer length scales and picosecond time scales for arbitrary geometries, providing an advanced practical tool for thermal management of nanoscale technologies. Furthermore, we derive analytical expressions for the transport time scales, valid for a subset of geometries, supplying a route for optimizing heat dissipation.
The use of flux limiters is widespread within the scientific computing community to capture shock discontinuities and are of paramount importance for the temporal integration of high-speed ...aerodynamics, multiphase flows and hyperbolic equations in general.
Meanwhile, the breakthrough of new computing architectures and the hybridization of supercomputer systems pose a huge portability challenge, particularly for legacy codes, since the computing subroutines that form the algorithms, the so-called kernels, must be adapted to various complex parallel programming paradigms. From this perspective, the development of innovative implementations relying on a minimalist set of kernels simplifies the deployment of scientific computing software on state-of-the-art supercomputers, while it requires the reformulation of algorithms, such as the aforementioned flux limiters.
Equipped with basic algebraic topology and graph theory underlying the classical mesh concept, a new flux limiter formulation is presented based on the adoption of algebraic data structures and kernels. As a result, traditional flux limiters are cast into a stream of only two types of computing kernels: sparse matrix-vector multiplication and generalized pointwise binary operators. The newly proposed formulation eases the deployment of such a numerical technique in massively parallel, potentially hybrid, computing systems and is demonstrated for a canonical advection problem.
Conventional models for predicting thermal conductivity of alloys usually assume a pure kinetic regime as alloy scattering dominates normal processes. However, some discrepancies between these models ...and experiments at very small alloy concentrations have been reported. In this work, we use the full first principles kinetic collective model (KCM) to calculate the thermal conductivity of Si
1−
x
Ge
x
and In
x
Ga
1−
x
As alloys. The calculated thermal conductivities match well with the experimental data for all alloy concentrations. The model shows that the collective contribution must be taken into account at very low impurity concentrations. For higher concentrations, the collective contribution is suppressed, but normal collisions have the effect of significantly reducing the kinetic contribution. The study thus shows the importance of the proper inclusion of normal processes even for alloys for accurate modeling of thermal transport. Furthermore, the phonon spectral distribution of the thermal conductivity is studied in the framework of KCM, providing insights to interpret the superdiffusive regime introduced in the truncated Lévy flight framework.
Suppressing collective effects from momentum-conserving phonon collisions cause fast drop in thermal conductivity at small semiconductor alloy impurity concentrations.
AKR1B10 is a human aldo-keto reductase (AKR) found to be elevated in several cancer types and in precancerous lesions. In vitro, AKR1B10 exhibits a much higher retinaldehyde reductase activity than ...any other human AKR, including AKR1B1 (aldose reductase). We here demonstrate that AKR1B10 also acts as a retinaldehyde reductase in vivo. This activity may be relevant in controlling the first step of retinoic acid synthesis. Up-regulation of AKR1B10, resulting in retinoic acid depletion, may lead to cellular proliferation. Both in vitro and in vivo activities of AKR1B10 were inhibited by tolrestat, an AKR1B1 inhibitor developed for diabetes treatment. The crystal structure of the ternary complex AKR1B10-NADP⁺-tolrestat was determined at 1.25-Å resolution. Molecular dynamics models of AKR1B10 and AKR1B1 with retinaldehyde isomers and site-directed mutagenesis show that subtle differences at the entrance of the retinoid-binding site, especially at position 125, are determinant for the all-trans-retinaldehyde specificity of AKR1B10. Substitutions in the retinaldehyde cyclohexene ring also influence the specificity. These structural features should facilitate the design of specific inhibitors, with potential use in cancer and diabetes treatments.
Non-uniform self-heating and temperature hotspots are major concerns compromising the performance and reliability of submicron electronic and optoelectronic devices. At deep submicron scales where ...effects such as contact-related artifacts and diffraction limits accurate measurements of temperature hotspots, non-contact thermal characterization can be extremely valuable. In this work, we use a Bayesian optimization framework with generalized Gaussian Markov random field (GGMRF) prior model to obtain accurate full-field temperature distribution of self-heated metal interconnects from their thermoreflectance thermal images (TRI) with spatial resolution 2.5 times below Rayleigh limit for 530nm illumination. Finite element simulations along with TRI experimental data were used to characterize the point spread function of the optical imaging system. In addition, unlike iterative reconstruction algorithms that use ad hoc regularization parameters in their prior models to obtain the best quality image, we used numerical experiments and finite element modeling to estimate the regularization parameter for solving a real experimental inverse problem.
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