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At least 685 records · Page 38

Yet another method for triangulation and contouring for automated cartography

An algorithm is presented for hierarchical subdivision of a set of three-dimensional surface observations. The data structure used for obtaining the desired triangulation is also singularly appropriate for extracting contours. Some examples are presented, and the results obtained are compared with those given by Delaunay triangulation. The data points selected by the algorithm provide a better approximation to the desired surface than do randomly selected points.

De Floriani, L.↗

MBX V1.2: Accelerating Data-Driven Many-Body Molecular Dynamics Simulations

The MBX software provides an advanced platform for molecular dynamics simulations, leveraging state-of-the-art MB-pol and MB-nrg data-driven many-body potential energy functions. Developed over the past decade, these potential energy functions integrate physics-based and machine-learned many-body terms trained on electronic structure data calculated at the "gold standard" coupled-cluster level of theory. Recent advancements in MBX have focused on optimizing its performance, resulting in the release of MBX v1.2. While the inherently many-body nature of MB-pol and MB-nrg ensures high accuracy, it poses computational challenges. MBX v1.2 addresses these challenges with significant performance improvements, including enhanced parallelism that fully harnesses the power of modern multicore CPUs. In conclusion, these advancements enable simulations on nanosecond time scales for condensed-phase systems, significantly expanding the scope of high-accuracy, predictive simulations of complex molecular systems powered by data-driven many-body potential energy functions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Binding site for coenzyme A revealed in the structure of pyruvate:ferredoxin oxidoreductase from Moorella thermoacetica

Pyruvate:ferredoxin oxidoreductase (PFOR) is a microbial enzyme that uses thiamine pyrophosphate (TPP), three [4Fe-4S] clusters, and coenzyme A (CoA) in the reversible oxidation of pyruvate to generate acetyl-CoA and carbon dioxide. The two electrons that are generated as a result of pyruvate decarboxylation are used in the reduction of low potential ferredoxins, which provide reducing equivalents for central metabolism, including the Wood–Ljungdahl pathway. PFOR is a member of the 2-oxoacid:ferredoxin oxidoreductase (OFOR) superfamily, which plays major roles in both microbial redox reactions and carbon dioxide fixation. Here, we present a set of crystallographic snapshots of the best-studied member of this superfamily, the PFOR from Moorella thermoacetica ( Mt PFOR). These snapshots include the native structure, those of lactyl-TPP and acetyl-TPP reaction intermediates, and the first of an OFOR with CoA bound. These structural data reveal the binding site of CoA as domain III, the function of which in OFORs was previously unknown, and establish sequence motifs for CoA binding in the OFOR superfamily. Mt PFOR structures further show that domain III undergoes a conformational change upon CoA binding that seals off the active site and positions the thiolate of CoA directly adjacent to the TPP cofactor. Finally, these structural findings provide a molecular basis for the experimental observation that CoA binding accelerates catalysis by 10 5 -fold.

59 BASIC BIOLOGICAL SCIENCES↗

Deep Hierarchical Super Resolution for Scientific Data

We present a novel technique for hierarchical super resolution (SR) with neural networks (NNs), which upscales volumetric data represented with an octree data structure to a high-resolution uniform gridwith minimal seam artifacts on octree node boundaries. Our method uses existing state-of-the-art SR models and adds flexibility to upscale input data with varying levels of detail across the domain, instead of only uniform grid data that are supported in previous approaches.The key is to use a hierarchy of SR NNs, each trained to perform 2x SR between two levels of detail, with a hierarchical SR algorithm that minimizes seam artifacts by starting from the coarsest level of detail and working up.We show that our hierarchical approach outperforms baseline interpolation and hierarchical upscaling methods, and demonstrate the usefulness of our proposed approach across three use cases including data reduction using hierarchical downsampling+SR instead of uniform downsampling+SR, computation savings for hierarchical finite-time Lyapunov exponent field calculation, and super-resolving low-resolution simulation results for a high-resolution approximation visualization.

97 MATHEMATICS AND COMPUTING↗

Coupling fine-scale root and canopy structure using ground-based remote sensing

Ecosystem physical structure, defined by the quantity and spatial distribution of biomass, influences a range of ecosystem functions. Remote sensing tools permit the non-destructive characterization of canopy and root features, potentially providing opportunities to link above- and belowground structure at fine spatial resolution in functionally meaningful ways. To test this possibility, we employed ground-based portable canopy LiDAR (PCL) and ground penetrating radar (GPR) along co-located transects in forested sites spanning multiple stages of ecosystem development and, consequently, of structural complexity. We examined canopy and root structural data for coherence (i.e., correlation in the frequency of spatial variation) at multiple spatial scales 10 m within each site using wavelet analysis. Forest sites varied substantially in vertical canopy and root structure, with leaf area index and root mass more becoming even vertically as forests aged. In all sites, above- and belowground structure, characterized as mean maximum canopy height and root mass, exhibited significant coherence at a scale of 3.5–4 m, and results suggest that the scale of coherence may increase with stand age. Our findings demonstrate that canopy and root structure are linked at characteristic spatial scales, which provides the basis to optimize scales of observation. Lastly, our study highlights the potential, and limitations, for fusing LiDAR and radar technologies to quantitatively couple above- and belowground ecosystem structure.

09 BIOMASS FUELS↗

SharP

The pre-exascale systems are expected to have a significant amount of hierarchical and heterogeneous on-node memory, and this trend of system architecture in extreme-scale systems is expected to continue into the exascale era. along with hierarchical-heterogeneous memory, the system typically has a high-performing network ad a compute accelerator. This system architecture is not only effective for running traditional High Performance Computing (HPC) applications (Big-Compute), but also for running data-intensive HPC applications and Big-Data applications. As a consequence, there is a growing desire to have a single system serve the needs of both Big-Compute and Big-Data applications. Though the system architecture supports the convergence of the Big-Compute and Big-Data, the programming models and software layer have yet to evolve to support either hierarchical-heterogeneous memory systems or the convergence. A programming abstraction to address this problem. The programming abstraction is implemented as a software library and runs on pre-exascale and exascale systems supporting current and emerging system architecture. Using distributed data-structures as a central concept, it provides (1) a simple, usable, and portable abstraction for hierarchical-heterogeneous memory and (2) a unified programming abstraction for Big-Compute and Big-Data applications.

Venkata, Manjunath Gorentla↗

DRoP: Automated detection of conserved solvent‐binding sites on proteins

Abstract Water and ligand binding play critical roles in the structure and function of proteins, yet their binding sites and significance are difficult to predict a priori. Multiple solvent crystal structures (MSCS) is a method where several X‐ray crystal structures are solved, each in a unique solvent environment, with organic molecules that serve as probes of the protein surface for sites evolved to bind ligands, while the first hydration shell is essentially maintained. When superimposed, these structures contain a vast amount of information regarding hot spots of protein‐protein or protein‐ligand interactions, as well as conserved water‐binding sites retained with the change in solvent properties. Optimized mining of this information requires reliable structural data and a consistent, objective analysis tool. Detection of related solvent positions (DRoP) was developed to automatically organize and rank the water or small organic molecule binding sites within a given set of structures. It is a flexible tool that can also be used in conserved water analysis given multiple structures of any protein independent of the MSCS method. The DRoP output is an HTML format list of the solvent sites ordered by conservation rank in its population within the set of structures, along with renumbered and recolored PDB files for visualization and facile analysis. Here, we present a previously unpublished set of MSCS structures of bovine pancreatic ribonuclease A (RNase A) and use it together with published structures to illustrate the capabilities of DRoP.

Kearney, Bradley M.↗

The UPC++ PGAS library for exascale computing. Extended Abstract

We describe UPC++ V1.0, a C++11 library that supports APGAS programming. UPC++ targets distributed data structures where communication is irregular or fine-grained. The key abstractions are global pointers, asynchronous programming via RPC, and futures. Global pointers incorporate ownership information useful in optimizing for locality. Futures capture data readiness state, are useful for scheduling and also enable the programmer to chain operations to execute asynchronously as high-latency dependencies become satisfied, via continuations. The interfaces for moving non-contiguous data and handling memories with different optimal access methods are composable and closely resemble those used in modern C++. Communication in UPC++ runs at close to hardware speeds by utilizing the low-overhead GASNet-EX communication library.

97 MATHEMATICS AND COMPUTING↗

Effect of crash pulse shape on seat stroke requirements for limiting loads on occupants of aircraft

An analytical study was made to provide comparative information on various crash pulse shapes that potentially could be used to test seats under conditions included in Federal Regulations Part 23 Paragraph 23.562(b)(1) for dynamic testing of general aviation seats, show the effects that crash pulse shape can have on the seat stroke requirements necessary to maintain a specified limit loading on the seat/occupant during crash pulse loadings, compare results from certain analytical model pulses with approximations of actual crash pulses, and compare analytical seat results with experimental airplace crash data. Structural and seat/occupant displacement equations in terms of the maximum deceleration, velocity change, limit seat pan load, and pulse time for five potentially useful pulse shapes were derived; from these, analytical seat stroke data were obtained for conditions as specified in Federal Regulations Part 23 Paragraph 23.562(b)(1) for dynamic testing of general aviation seats.

Carden, Huey D.↗

TPSAS-NF1676L-12354-DND

This work deals with performance properties of a dynamic traffic model, the Air Traffic Monotonic Lagrangian Grid (ATMLG), which can be used to evaluate new control strategies for conflict avoidance, separation assurance, and traffic management. The model is based on an algorithm and data structure called the Monotonic Lagrangian Grid (MLG), originally developed at NRL in the mid 1980s and since then used as an underpinning for various particle dynamics simulations. The MLG stores positions and other data needed to describe N moving objects, where N can be very large. The MLG algorithm involves sorting and ordering objects. A stationary grid is an alternative to the dynamic grid of MLG. Stationary grids can be attractive in that they do not require sorting. We investigate and report on the relative performances of air traffic simulations based on dynamic (MLG) and static (lat-long) grids.

C Kaplan↗

TPSAS-NF1676L-12301-DND

This work deals with performance properties of a dynamic traffic model, the Air Traffic Monotonic Lagrangian Grid (ATMLG), which can be used to evaluate new control strategies for conflict avoidance, separation assurance, and traffic management. The model is based on an algorithm and data structure called the Monotonic Lagrangian Grid (MLG), originally developed at NRL in the mid 1980s and since then used as an underpinning for various particle dynamics simulations. The MLG stores positions and other data needed to describe N moving objects, where N can be very large. The MLG algorithm involves sorting and ordering objects. A stationary grid is an alternative to the dynamic grid of MLG. Stationary grids can be attractive in that they do not require sorting. We investigate and report on the relative performances of air traffic simulations based on dynamic (MLG) and static (lat-long) grids.

Carolyn Kaplan↗

Synthesis and structural characterization of the vividly colored first row transition metal-containing oxyfluoride antiperovskites Sr3-xMnxMO4F and Sr3-xMnxMO4-αF1-δ (M = Al, Ga)

Highlights: • Substitution of Mn{sup 2+} demonstrates Sr{sub 3-x}A{sub x}MO{sub 4}F can tolerate divalent first row transition metals. • The colors of these materials vary from green to purple depending on anion stoichiometry. • Intense colors are likely due to small amounts of Mn{sup 3+} on the tetrahedral Al site. • Structural data is consistent with preferential occupation of eight-coordinate Sr(2) site by Mn{sup 2+}. • Large off-center displacements are observed on the underbonded ten-coordinate Sr(1) site. - Abstract: Incorporation of dopant amounts of the divalent transition metal cation Mn{sup 2+} into the oxyfluoride material Sr{sub 3-x}Mn{sub x}MO{sub 4}F (M = Al, Ga; 0 ≤ x ≤ 0.1) yields green powders which vary in hue depending on the identity of M. Treatment of these phases with post-synthesis annealing under reducing conditions produces anion deficient phases according to Sr{sub 3-x}Mn{sub x}MO{sub 4-α}F{sub 1-δ} displaying vivid purple coloration. Intense colors are likely due to small amounts of Mn{sup 3+} on the tetrahedral M site. Full structural characterization based upon powder X-ray diffraction (PXRD), neutron powder diffraction (NPD), and thermogravimetric analysis (TGA) data are presented herein, demonstrating that the Sr{sub 3-x}A{sub x}MO{sub 4}F (A = Ca, Sr, Ba; M = Al, Ga) anti-perovskite structure can readily accommodate first row transition metals.

36 MATERIALS SCIENCE↗

Determination of airplane model structure from flight data using splines and stepwise regression

A procedure for the determination of airplane model structure from flight data is presented. The model is based on a polynomial spline representation of the aerodynamic coefficients, and the procedure is implemented by use of a stepwise regression. First, a form of the aerodynamic force and moment coefficients amenable to the utilization of splines is developed. Next, expressions for the splines in one and two variables are introduced. Then the steps in the determination of an aerodynamic model structure and the estimation of parameters are discussed briefly. The focus is on the application to flight data of the techniques developed.

Klein, V.↗

Implementing efficient data compression and encryption in a persistent key-value store for HPC

Recently, persistent data structures, like key-value stores (KVSs), which are stored in a high-performance computing (HPC) system’s nonvolatile memory, provide an attractive solution for a number of emerging challenges like limited I/O performance. Data compression and encryption are two well-known techniques for improving several properties of such data-oriented systems. This article investigates how to efficiently integrate data compression and encryption into persistent KVSs for HPC with the ultimate goal of hiding their costs and complexity in terms of performance and ease of use. Our compression technique exploits deep memory hierarchy in an HPC system to achieve both storage reduction and performance improvement. Our encryption technique provides a practical level of security and enables sharing of sensitive data securely in complex scientific workflows with nearly imperceptible cost. We implement the proposed techniques on top of a distributed embedded KVS to evaluate the benefits and costs of incorporating these capabilities along different points in the dataflow path, illustrating differences in effective bandwidth, latency, and additional computational expense on Swiss National Supercomputing Centre’s Grand Tavé and National Energy Research Scientific Computing Center’s Cori.

97 MATHEMATICS AND COMPUTING↗

Flight test results for the Daedalus and Light Eagle human powered aircraft

The results of the flight test program of the Daedalus and Light Eagle human powered aircraft in the winter of 1987/88 are given. The results from experiments exploring the Light Eagle's rigid body and structural dynamics are presented. The interactions of these dynamics with the autopilot design are investigated. Estimates of the power required to fly the Daedalus aircraft are detailed. The system of sensors, signal conditioning boards, and data acquisition equipment used to record the flight data is also described. In order to investigate the dynamics of the aircraft, flight test maneuvers were developed to yield maximum data quality from the point of view of estimating lateral and longitudinal stability derivatives. From this data, structural flexibility and unsteady aerodynamics have been modeled in an ad hoc manner and are used to augment the equations of motion with flexibility effects. Results of maneuvers that were flown are compared with the predictions from the flexibility model. To extend the ad hoc flexibility model, a fully flexible aeroelastic model has been developed. The model is unusual in the approximate equality of many structural natural frequencies and the importance of unsteady aerodynamic effects. the Gossamer Albatross. It is hypothesized that this inverse ground effect is caused by turbulence in the Earth's boundary layer. The diameters of the largest boundary layer eddies (which represent most of the turbulent kinetic energy) are proportional to altitude; thus, closer to the ground, the energy in the boundary layer becomes concentrated in eddies of smaller and smaller diameter. Eventually the eddies become sufficiently small (approximately 0.5 cm) that they trip the laminar boundary layer on the wing. As a result, a greater percentage of the wing area is covered with turbulent flow. Consequently the aircraft's drag and the pow er required both increase as the aircraft flies closer to the ground. The results of the flight test program are examined critically, especially with respect to future applications. Maneuvers that allow the observation of stability derivatives for flexible aircraft are detailed. Considerations for the design of autopilots for future human power aircraft and high-altitude RPV's are discussed. Techniques useful in estimating the power required to fly aircraft of very high lift to drag ratio are described.

Sullivan, R. Bryan↗

Developing a Standard Method for Link-Layer Security of CCSDS Space Communications

Communications security for space systems has been a specialized field generally far removed from considerations of mission interoperability and cross-support in fact, these considerations often have been viewed as intrinsically opposed to security objectives. The space communications protocols defined by the Consultative Committee for Space Data Systems (CCSDS) have a twenty-five year history of successful use in over 400 missions. While the CCSDS Telemetry, Telecommand, and Advancing Orbiting Systems protocols for use at OSI Layer 2 are operationally mature, there has been no direct support within these protocols for communications security techniques. Link-layer communications security has been successfully implemented in the past using mission-unique methods, but never before with an objective of facilitating cross-support and interoperability. This paper discusses the design of a standard method for cryptographic authentication, encryption, and replay protection at the data link layer that can be integrated into existing CCSDS protocols without disruption to legacy communications services. Integrating cryptographic operations into existing data structures and processing sequences requires a careful assessment of the potential impediments within spacecraft, ground stations, and operations centers. The objective of this work is to provide a sound method for cryptographic encapsulation of frame data that also facilitates Layer 2 virtual channel switching, such that a mission may procure data transport services as needed without involving third parties in the cryptographic processing, or split independent data streams for separate cryptographic processing.

Biggerstaff, Craig↗

Database Design Strategies for Coordinated Simulation and Testing in Additive Manufacturing

The qualification and certification (Q&C) process presents a significant challenge for widespread adoption of additive manufacturing (AM) materials and processes for aerospace applications. A relational database framework will be presented as a tool for data curation of coordinated experimental and computational materials modeling research activities. A comparison of relational and hierarchical data structures in this domain will be emphasized through the evolution of a database design strategy. This framework’s mission is to support the advancement of computational materials-informed Q&C by providing the necessary data infrastructure to trace reliability and reproducibility measures through unified AM materials simulation and experimental testing. FAIR (findable, accessible, interoperable, and reusable) data will be highlighted as a necessary precursor for automation of specific actions, which ultimately reduces the time and expense burden for Q&C. The discussion will be mostly limited to back-end design elements, though a few front-end user experience examples will also be shared.

Qualification↗

Requirements and principles for the implementation and construction of large-scale geographic information systems

This paper provides a brief survey of the history, structure and functions of 'traditional' geographic information systems (GIS), and then suggests a set of requirements that large-scale GIS should satisfy, together with a set of principles for their satisfaction. These principles, which include the systematic application of techniques from several subfields of computer science to the design and implementation of GIS and the integration of techniques from computer vision and image processing into standard GIS technology, are discussed in some detail. In particular, the paper provides a detailed discussion of questions relating to appropriate data models, data structures and computational procedures for the efficient storage, retrieval and analysis of spatially-indexed data.

Smith, Terence R.↗