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At least 1,081 records · Page 60

Position Papers for the ASCR Workshop on the Science of Scientific-Software Development and Use

Software is an increasingly important component in the pursuit of scientific discovery. Both its development and use are essential activities for many scientific teams. At the same time, very little scientific study has been conducted to understand, characterize, and improve the development and use of software for science. Computational science teams have diversified over time to include contributions from domain scientists who provide expertise in scientific and engineering disciplines, applied mathematicians and computer scientists who provide optimal algorithms and data structures, and software and data engineers who provide methodologies and tools adapted and adopted from other software domains. These diverse contributions have enabled tremendous advances in the pursuit of scientific discovery, even as models, computer architectures, and software environments have become more complicated. With this increasing diversity, we believe the next opportunity for qualitative improvement comes from applying the scientific method to understanding, characterizing, and improving how scientific software is developed and used. We believe that this pursuit requires expertise from computational scientists themselves, and from the cognitive and social sciences as well as the software engineering research community. As we look to increase the productivity and sustainability of the scientific-software-development-and-use cycle, a more systematic application of the scientific method to understand processes for software development and use will be a valuable tool to guide future work and result in more usable and sustainable software. This workshop will bring together computer scientists, software engineering researchers, computational scientists, applied mathematicians, social scientists, cognitive scientists, and others, to explore how we can conduct such systematic investigations, what can be learned, and how doing so will benefit the scientific enterprise. The workshop will be structured around a set of breakout sessions, with every attendee expected to participate actively in the discussions. Afterward, workshop attendees — from DOE, industry, and academia — will produce a report for ASCR that summarizes the findings of the workshop.

42 ENGINEERING↗

RedThreads: An Interface for Application-Level Fault Detection/Correction Through Adaptive Redundant Multithreading

In the presence of accelerated fault rates, which are projected to be the norm on future exascale systems, it will become increasingly difficult for high-performance computing (HPC) applications to accomplish useful computation. Due to the fault-oblivious nature of current HPC programming paradigms and execution environments, HPC applications are insufficiently equipped to deal with errors. We believe that HPC applications should be enabled with capabilities to actively search for and correct errors in their computations. The redundant multithreading (RMT) approach offers lightweight replicated execution streams of program instructions within the context of a single application process. Furthermore, the use of complete redundancy incurs significant overhead to the application performance.

97 MATHEMATICS AND COMPUTING↗

Cannabis monoterpene synthases: evaluating structure–function relationships

Terpene synthases catalyze the first committed step in the biosynthesis of terpenes, a structurally diverse class of natural products that also encompasses volatiles derived from precursors in the C10 to C15 range (termed monoterpenes and sesquiterpenes, respectively). In the review section of this article, we are providing information about all functionally characterized monoterpene synthases (MTSs) and sesquiterpene synthases (STSs) of Cannabis sativa L. We are also exploring the locations of MTSs and STSs in the chromosome-level assembly of the reference chemovar CBDRx. A follow-up computational structure–function analysis focuses on MTSs, as there is already a rich literature available on the topic. More specifically, by employing sequence comparisons and homology structural modeling, we infer which amino acid residues are likely to constrain the available space in the active site of cannabis MTSs. The emphasis of these studies was to investigate why some MTSs accept only a C10 diphosphate as substrate, while mixed MTS/STS enzymes also accommodate a C15 diphosphate. Here, by combining a literature review and computational analyses in a hybrid format, we are laying the foundation for future studies to better understand the determinants of substrate and product specificity in these fascinating enzymes.

59 BASIC BIOLOGICAL SCIENCES↗

Laboratory Study of Collisionless Magnetic Reconnection

A concise review is given on the past two decades’ results from laboratory experiments on collisionless magnetic reconnection in direct relation with space measurements, especially by the Magnetospheric Multiscale (MMS) mission. Highlights include spatial structures of electromagnetic fields in ion and electron diffusion regions as a function of upstream symmetry and guide field strength, energy conversion and partitioning from magnetic field to ions and electrons including particle acceleration, electrostatic and electromagnetic kinetic plasma waves with various wavelengths, and plasmoid-mediated multiscale reconnection. Combined with the progress in theoretical, numerical, and observational studies, the physics foundation of fast reconnection in collisionless plasmas has been largely established, at least within the parameter ranges and spatial scales that were studied. Immediate and long-term future opportunities based on multiscale experiments and space missions supported by exascale computation are discussed, including dissipation by kinetic plasma waves, particle heating and acceleration, and multiscale physics across fluid and kinetic scales.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

An investigation of the multi-mode Richtmyer-Meshkov instability at a gas/HE interface using Pagosa

Here, in this work, we present a hydrocode Pagosa and explore the Richtmyer-Meshkov Instability (RMI) at an air/high explosive (HE) interface for the first time that is important but has not received much attention yet in the high explosive safety field. Thus, the presented Pagosa can be expected to predict the whole deflagration-to-detonation transition (DDT) process in future. In Pagosa, spatial discretization is implemented on cubic staggered grids by computing different variables at the vertex and the cell center, respectively, a special operator-splitting technique is employed to reduce the computational cost, and an artificial viscosity is added to handle the discontinuous shock waves in our simulations. To quantitatively evaluate the capability of Pagosa to solve these kinds of instabilities, the single mode Rayleigh-Taylor instability (RTI) and the multimode RMI at an air/SF 6 interface are first performed, respectively. The Pagosa results are compared with the related numerical solutions in the existing references and the experimental result. Moreover, a theoretical derivation of growth of RTI is also provided based on our numerical method. Subsequently, we explore the multi-mode RMI at an air/HE interface as well as the effects of several factors using Pagosa. Numerical results show that Pagosa is a powerful toolset to generate the right structures and the amplitude of RTI and RMI at an air/SF 6 interface. The solid HE can be penetrated by a strong shock wave and forms RMI deformations. The RMI at an air/HE interface behaves very different than at an air/SF 6 interface, periodic, decreased oscillation is observed due to material character, and is very sensitive to the initial simulation settings, that is, a tiny change in physical quantities will lead to a remarkable RMI structure, which is also observed in a shock bubble interaction. The findings in this work are significant, and will present a new insight for the high explosive field.

97 MATHEMATICS AND COMPUTING↗

Graphic statics and their potential for digital design and fabrication with concrete

The paper describes the influence of the lower bound theorem of theory of plasticity on the design of structures during the last 70 years. Starting with the fundamental theorems developed in the middle of the last century, the influence of rigid plastic (discontinuous) stress fields on the design of reinforced beam, wall, slab and shell structures is worked out. The potential of graphic statics for digital design and fabrication is illustrated by the results of several research projects on form finding and design of reinforced concrete structures carried out during the last decade. It is shown that the design methods allow for simultaneous considerations about structure and architecture. This leads to leaner structure and reduced material consumption. However, while a current limitation of manufacturing objects in these ''nonstandard'' shapes is presently cost limiting, digital fabrication may change this and open a much greater scope for the use and application of graphic statics in a near future.

36 MATERIALS SCIENCE↗

Rafting and elastoplastic deformation of superalloys studied by neutron diffraction

The rafting of monocrystalline Ni- and Co-based superalloys has been studied by neutron diffractometry. Lattice parameter misfit values and the difference in phase stiffnesses at room temperature, 650 °C, and 900 °C are presented. These microstructural parameters should assist in refining computer models that aim to predict precipitate evolution in superalloys and aid future alloy design. The nature of rafting is shown experimentally to be dependent upon the lattice parameter misfit. The 900 °C yield strength of the γ-phase of the Co-based superalloy with a rafted microstructure occurs at ~100 MPa, when loaded at a low strain rate.

36 MATERIALS SCIENCE↗

Bridging Scales in Bioenergy and Catalysis: A Review of Mesoscale Modeling Applications, Methods, and Future Directions

Between the molecular and reactor scales, which are familiar to the chemical engineering community, lies an intermediate regime, here termed the “mesoscale,” where transport phenomena and reaction kinetics compete on similar time scales. Bioenergy and catalytic processes offer particularly important examples of mesoscale phenomena owing to their multiphase nature and the complex, highly variable porosity characteristic of biomass and many structured catalysts. In this review, we overview applications and methods central to mesoscale modeling as they apply to reaction engineering of biomass conversion and catalytic processing. A brief historical perspective is offered to put recent advances in context. Applications of mesoscale modeling are described, and several specific examples from biomass pyrolysis and catalytic upgrading of bioderived intermediates are highlighted. Methods including reduced order modeling, finite element and finite volume approaches, geometry construction and import, and visualization of simulation results are described; in each category, recent advances, current limitations, and areas for future development are presented. Owing to improved access to high-performance computational resources, advances in algorithm development, and sustained interest in reaction engineering to sustainably meet societal needs, we conclude that a significant upsurge in mesoscale modeling capabilities is on the horizon that will accelerate design, deployment, and optimization of new bioenergy and catalytic technologies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Constructing the Mechanism of Dinoflagellate Luciferin Bioluminescence Using Computation

Dinoflagellate luciferin bioluminescence is unique since it does not rely on decarboxylation but is poorly understood compared to that of firefly, bacteria, and coelenterata luciferins. Here, in this work, we computationally investigate possible protonation states, stereoisomers, a chemical mechanism, and the dynamics of the bioluminescence intermediate that is responsible for chemiexcitation. Using semiempirical dynamics, time-dependent density functional theory static calculations, and a correlation diagram, we find that the intermediate’s functional group that is likely responsible for chemiexcitation is a 4-member ring, a dioxetanol, that undergoes [2π + 2π] cycloreversion and the biolumiphore is the cleaved structure. The simulated emission spectra and luciferase-dependent absorbance spectra agree with the experimental data, giving support to our proposed mechanism and biolumiphore. We also compute circular dichroism spectra of the intermediate’s four stereoisomers to guide future experiments in differentiating them.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Strain release by 3D atomic misfit in fivefold twinned icosahedral nanoparticles with amorphization and dislocations

Multiple twinning to form fivefold twinned nanoparticles in crystal growth is common and has attracted broad attention ranging from crystallography research to physical chemistry and materials science. Lattice-misfit strain and defects in multiple twinned nanoparticles (MTP) are key to understand and tailor their electronic properties. However, the structural defects and related strain distributions in MTPs are poorly understood in three dimensions (3D). Here, we show the 3D atomic misfit and strain relief mechanism in fivefold twinned icosahedral nanoparticles with amorphization and dislocations by using atomic resolution electron tomography. We discover a two-sided heterogeneity in variety of structural characteristics. A nearly ideal crystallographic fivefold face is always found opposite to a less ordered face, forming Janus-like icosahedral nanoparticles with two distinct hemispheres. The disordered amorphous domains release a large amount of strain. Molecular dynamics simulations further reveal the Janus-like icosahedral nanoparticles are prevalent in the MTPs formed in liquid-solid phase transition. This work provides insights on the atomistic models for the modelling of formation mechanisms of fivefold twinned structures and computational simulations of lattice distortions and defects. We anticipate it will inspire future studies on fundamental problems such as twin boundary migration and kinetics of structures in 3D at atomic level.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Matrix product operators, matrix product states, and ab initio density matrix renormalization group algorithms

Current descriptions of the ab initio density matrix renormalization group (DMRG) algorithm use two superficially different languages: an older language of the renormalization group and renormalized operators, and a more recent language of matrix product states and matrix product operators. The same algorithm can appear dramatically different when written in the two different vocabularies. Here, we carefully describe the translation between the two languages in several contexts. First, we describe how to efficiently implement the ab initio DMRG sweep using a matrix product operator based code, and the equivalence to the original renormalized operator implementation. Next we describe how to implement the general matrix product operator/matrix product state algebra within a pure renormalized operator-based DMRG code. Finally, we discuss two improvements of the ab initio DMRG sweep algorithm motivated by matrix product operator language: Hamiltonian compression, and a sum over operators representation that allows for perfect computational parallelism. The connections and correspondences described here serve to link the future developments with the past and are important in the efficient implementation of continuing advances in ab initio DMRG and related algorithms.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Exploring solvation structure and transport behavior for rational design of advanced electrolytes for next generation of lithium batteries

The efficacy of electrolytes significantly affects battery performance, leading to the development of several strategies to enhance them. Despite this, the understanding of solvation structure remains inadequate. It is imperative to understand the structure–property–performance relationship of electrolytes using diverse techniques. Here, this review explores the recent advancements in electrolyte design strategies for high capacity, high-voltage, wide-temperature, fast-charging, and safe applications. To begin, the current state-of-the-art electrolyte design directions are comprehensively reviewed. Subsequently, advanced techniques and computational methods used to understand the solvation structure are discussed. Additionally, the importance of high-throughput screening and advanced computation of electrolytes with the help of machine learning is emphasized. Finally, future horizons for studying electrolytes are proposed, aimed at improving battery performance and promoting their application in various fields by enhancing the microscopic understanding of electrolytes.

25 ENERGY STORAGE↗

Multiphysics Running-In Simulations for Pebble-Bed Reactors with Griffin

Griffin, a Multiphysics Object-Oriented Simulation Environment (MOOSE)–based application targeting transient modeling of advanced reactors, has been used recently to model pebble-bed reactors (PBRs). The modeling effort has focused thus far on equilibrium core calculations. A new capability to simulate the running-in phase of PBR operation has been added to Griffin. This work demonstrates the new capability with a coupled multiphysics running-in simulation. Griffin computes power densities in the core at each time step of the running-in simulation and passes these to Pronghorn, which models fluid flow and heat transfer to calculate pebble surface temperatures. These surface temperatures are used along with the power densities in a heat conduction model to compute average fuel and moderator temperatures, which are passed back to Griffin and accounted for with temperature-dependent cross sections. This work also describes a novel methodology for determining appropriate pebble feed rates and control rod positioning during the running-in simulation. Furthermore, the RZ-geometry model used in this work requires minimal computational resources and can be used for optimization and uncertainty studies in future works.

Griffin↗

A SEMI-ANALYTICAL MODEL OF VISIBLE-WAVELENGTH PHASE CURVES OF EXOPLANETS AND APPLICATIONS TO KEPLER- 7 B AND KEPLER- 10 B

Kepler has detected numerous exoplanet transits by measuring stellar light in a single visible-wavelength band. In addition to detection, the precise photometry provides phase curves of exoplanets, which can be used to study the dynamic processes on these planets. However, the interpretation of these observations can be complicated by the fact that visible-wavelength phase curves can represent both thermal emission and scattering from the planets. Here we present a semi-analytical model framework that can be applied to study Kepler and future visible-wavelength phase curve observations of exoplanets. The model efficiently computes reflection and thermal emission components for both rocky and gaseous planets, considering both homogeneous and inhomogeneous surfaces or atmospheres. We analyze the phase curves of the gaseous planet Kepler- 7 b and the rocky planet Kepler- 10 b using the model. In general, we find that a hot exoplanet’s visible-wavelength phase curve having a significant phase offset can usually be explained by two classes of solutions: one class requires a thermal hot spot shifted to one side of the substellar point, and the other class requires reflective clouds concentrated on the same side of the substellar point. Particularly for Kepler- 7 b, reflective clouds located on the west side of the substellar point can best explain its phase curve. The reflectivity of the clear part of the atmosphere should be less than 7% and that of the cloudy part should be greater than 80%, and the cloud boundary should be located at 11° ± 3° to the west of the substellar point. We suggest single-band photometry surveys could yield valuable information on exoplanet atmospheres and surfaces.

79 ASTRONOMY AND ASTROPHYSICS↗

Fourth level MSSM inflation from new flat directions

We propose a model of inflation driven by minimal extension of SUSY, commonly known as MSSM. Starting from gauge invariant flat directions in the n = 4 level comprising of QQQL,QuQd,QuLe and uude, we construct the inflaton potential and employ it to investigate for its consequences around the saddle point arising from the non-vanishing fourth derivative of the original potential. To this end, we derive the expressions for the important parameters in MSSM inflation using the loop corrected potential. We further estimate the observable parameters and find them to fit well with recent observational data from WMAP7 by using the code CAMB. We also explore the possibility of primordial black hole formation from our model. Finally, we analyze one loop RGE and compute different phenomenological parameters which could be precisely determined in LHC or future Linear Colliders.

79 ASTRONOMY AND ASTROPHYSICS↗

The mechanics of brittle granular materials with coevolving grain size and shape

The influence of particle shape on the mechanics of sand is widely recognized, especially in mineral processing and geomechanics. However, most existing continuum theories for engineering applications do not encompass the morphology of the grains and its evolution during comminution. Similarly, the relatively few engineering models accounting for grain-scale processes tend to idealize particles as spheres, with their diameters considered as the primary and sole geometric descriptor. This paper inspires a new generation of constitutive laws for crushable granular continua with arbitrary, yet evolving, particle morphology. We explore the idea of introducing multiple grain shape descriptors into Continuum Breakage Mechanics (CBM), a theory originally designed to track changes in particle size distributions during confined comminution. We incorporate the influence of these descriptors on the elastic strain energy potential and treat them as dissipative state variables. In analogy with the original CBM, and in light of evidence from extreme fragmentation in nature, the evolution of the additional shape descriptors is postulated to converge towards an attractor. Comparisons with laboratory experiments, discrete element analyses and particle-scale fracture models illustrate the encouraging performance of the theory. The theory provides insights into the feedback among particle shape, compressive yielding and inelastic deformation in crushable granular continua. These results inspire new questions that should guide future research into crushable granular systems using particle-scale imaging and computations.

36 MATERIALS SCIENCE↗

Coupled-channel scattering on a torus

Based on the Hamiltonian formalism approach, a generalized Luscher's formula for two particle scattering in both the elastic and coupled-channel cases in moving frames is derived from a relativistic Lippmann-Schwinger equation. Some strategies for extracting scattering amplitudes for a coupled-channel system from the discrete finite-volume spectrum are discussed and illustrated with a toy model of two-channel resonant scattering. This formalism will, in the near future, be used to extract information about hadron scattering from lattice QCD computations.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Scaling Graph Community Detection on the Tilera Many-core Architecture

In an era when power constraints and data movement are proving to be significant barriers for the application of high-end computing, the Tilera many-core architecture offers a low-power platform exhibiting many important characteristics of future systems, including a large number of simple cores, a sophisticated network-on-chip, and fine-grained control over memory and caching policies. While this emerging architecture has been previously studied for structured compute-intensive kernels, benchmarking the platform for data-bound, irregular applications present significant challenges that have remained unexplored. Community detection is an advanced prototypical graph-theoretic operation with applications in numerous scientific domains including life sciences, cyber security, and power systems. In this work, we explore multiple design strategies toward developing a scalable tool for community detection on the Tilera platform. Using several memory layout and work scheduling techniques we demonstrate speedups of up to 46x on 36 cores of the Tilera TileGX36 platform over the best serial implementation, and also show results that have comparable quality and performance to mainstream x86 platforms. To the best of our knowledge this is the first work addressing graph algorithms on the Tilera platform. This study demonstrates that through careful design space exploration, low-power many-core platforms like Tilera can be effectively exploited for graph algorithms that that embody all the essential characteristics of an irregular application.

community detection↗