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At least 235 records · Page 13

Model Exploration of an Information-Based Healthcare Intervention Using Parallelization and Active Learning

This paper describes the application of a large-scale active learning method to characterize the parameter space of a computational agent-based model developed to investigate the impact of CommunityRx, a clinical information-based health intervention that provides patients with personalized information about local community resources to meet basic and self-care needs. Additionally, the diffusion of information about community resources and their use is modeled via networked interactions and their subsequent effect on agents' use of community resources across an urban population. A random forest model is iteratively fitted to model evaluations to characterize the model parameter space with respect to observed empirical data. We demonstrate the feasibility of using high-performance computing and active learning model exploration techniques to characterize large parameter spaces; by partitioning the parameter space into potentially viable and non-viable regions, we rule out regions of space where simulation output is implausible to observed empirical data. We argue that such methods are necessary to enable model exploration in complex computational models that incorporate increasingly available micro-level behavior data. We provide public access to the model and high-performance computing experimentation code.

97 MATHEMATICS AND COMPUTING↗

Localization of proteins involved in the biogenesis and repair of the photosynthetic apparatus to thylakoid subdomains in Arabidopsis

Abstract Thylakoid membranes in chloroplasts and cyanobacteria harbor the multisubunit protein complexes that catalyze the light reactions of photosynthesis. In plant chloroplasts, the thylakoid membrane system comprises a highly organized network with several subcompartments that differ in composition and morphology: grana stacks, unstacked stromal lamellae, and grana margins at the interface between stacked and unstacked regions. The localization of components of the photosynthetic apparatus among these subcompartments has been well characterized. However, less is known about the localization of proteins involved in the biogenesis and repair of the photosynthetic apparatus, the partitioning of proteins between two recently resolved components of the traditional margin fraction (refined margins and curvature), and the effects of light on these features. In this study, we analyzed the partitioning of numerous thylakoid biogenesis and repair factors among grana, curvature, refined margin, and stromal lamellae fractions of Arabidopsis thylakoid membranes, comparing the results from illuminated and dark‐adapted plants. Several proteins previously shown to localize to a margin fraction partitioned in varying ways among the resolved curvature and refined margin fractions. For example, the ALB3 insertase and FtsH protease involved in photosystem II (PSII) repair were concentrated in the refined margin fraction, whereas TAT translocon subunits and proteins involved in early steps in photosystem assembly were concentrated in the curvature fraction. By contrast, two photosystem assembly factors that facilitate late assembly steps were depleted from the curvature fraction. The enrichment of the PSII subunit OE23/PsbP in the curvature fraction set it apart from other PSII subunits, supporting the previous conjecture that OE23/PsbP assists in PSII biogenesis and/or repair. The PSII assembly factor PAM68 partitioned differently among thylakoid fractions from dark‐adapted plants and illuminated plants and was the only analyzed protein to convincingly do so. These results demonstrate an unanticipated spatial heterogeneity of photosystem biogenesis and repair functions in thylakoid membranes and reveal the curvature fraction to be a focal point of early photosystem biogenesis.

Chotewutmontri, Prakitchai↗

Solubilities of nitrogen and noble gases in basalt melt

Nitrogen and noble gases are important tracers in geochemistry and chosmochemistry. Compared to noble gases, however, physicochemical properties of nitrogen, such as solubility in melt or melt/silicate partition, are not well known. Solubility of nitrogen in basalt melt depends on redox condition of the atmosphere. For example, solubility of nitrogen in E chondrite melt under reducing conditions is as high as 2 mol percent at 1500 C, suggesting that nitrogen is chemically dissolved in silicate melts, i.e., being dissolved as free anions or replacing oxygen sites in silicate network. However, the solubility and the dissolution mechanism of nitrogen under oxidizing conditions are not well investigated. To obtain nitrogen solubility in silicate melts under various redox conditions and to understand its mechanism, we are conducting experiments by using (15)N(15)N-labeled nitrogen gas. This makes it easy to distinguish dissolved nitrogen from later contamination of atmospheric nitrogen, and hence enables us to measure the nitrogen solubility accurately. As a preliminary experiment, we have measured solubility of nitrogen in basalt melt under the atmospheric oxygen pressure.

Miyazaki, A.↗

Aggregate data‐driven dynamic modeling of active distribution networks with DERs for voltage stability studies

Abstract Electric distribution networks increasingly host distributed energy resources based on power electronic converter (PEC) toward active distribution networks (ADN). Despite advances in computational capabilities, electromagnetic transient models are limited in scalability because of their reliance on exact data about the distribution system and each of its components. Similarly, the use of the DER_A model, which is intended to examine the combined dynamic behavior of many DERs, is limited by the difficulty in parameterization. There is a need for improved dynamic models of DERs for use in large power system simulations for stability analysis. This paper proposes an aggregate model‐free, data‐driven approach for deriving a dynamic partitioned model (DPM) of ADNs. Detailed residential distribution feeders were first developed, including PEC‐based DERs and composite load models (CMLDs), from which the aggregated DPM was derived. The performance was evaluated through various case studies and validated against the detailed ADN model and state‐of‐the‐art DER_A model with CMLD. The data‐driven DPM achieved a of over 90%, accurately representing the aggregated dynamic behavior of ADNs. Furthermore, the DPM significantly accelerated the simulation process with a computational speedup of 68 times compared to the detailed ADN and a 3.5 times speedup compared to the DER_A CMLD model.

42 ENGINEERING↗

Method of up-front load balancing for local memory parallel processors

In a parallel processing computer system with multiple processing units and shared memory, a method is disclosed for uniformly balancing the aggregate computational load in, and utilizing minimal memory by, a network having identical computations to be executed at each connection therein. Read-only and read-write memory are subdivided into a plurality of process sets, which function like artificial processing units. Said plurality of process sets is iteratively merged and reduced to the number of processing units without exceeding the balance load. Said merger is based upon the value of a partition threshold, which is a measure of the memory utilization. The turnaround time and memory savings of the instant method are functions of the number of processing units available and the number of partitions into which the memory is subdivided. Typical results of the preferred embodiment yielded memory savings of from sixty to seventy five percent.

Baffes, Paul Thomas↗

Methodologies and systems for heterogeneous concurrent computing

Heterogeneous concurrent computing is gaining increasing acceptance as an alternative or complementary paradigm to multiprocessor-based parallel processing as well as to conventional supercomputing. While algorithmic and programming aspects of heterogeneous concurrent computing are similar to their parallel processing counterparts, system issues, partitioning and scheduling, and performance aspects are significantly different. In this paper, we discuss critical design and implementation issues in heterogeneous concurrent computing, and describe techniques for enhancing its effectiveness. In particular, we highlight the system level infrastructures that are required, aspects of parallel algorithm development that most affect performance, system capabilities and limitations, and tools and methodologies for effective computing in heterogeneous networked environments. We also present recent developments and experiences in the context of the PVM system and comment on ongoing and future work.

Sunderam, V. S.↗

Dynamic conformational switching underlies TFIIH function in transcription and DNA repair and impacts genetic diseases

Transcription factor IIH (TFIIH) is a protein assembly essential for transcription initiation and nucleotide excision repair (NER). Yet, understanding of the conformational switching underpinning these diverse TFIIH functions remains fragmentary. TFIIH mechanisms critically depend on two translocase subunits, XPB and XPD. To unravel their functions and regulation, we build cryo-EM based TFIIH models in transcription- and NER-competent states. Using simulations and graph-theoretical analysis methods, we reveal TFIIH’s global motions, define TFIIH partitioning into dynamic communities and show how TFIIH reshapes itself and self-regulates depending on functional context. Our study uncovers an internal regulatory mechanism that switches XPB and XPD activities making them mutually exclusive between NER and transcription initiation. By sequentially coordinating the XPB and XPD DNA-unwinding activities, the switch ensures precise DNA incision in NER. Mapping TFIIH disease mutations onto network models reveals clustering into distinct mechanistic classes, affecting translocase functions, protein interactions and interface dynamics.

59 BASIC BIOLOGICAL SCIENCES↗

A Fast and Scalable Genetic Algorithm-Based Approach for Planning of Microgrids in Distribution Networks: Preprint

As a result of climate change, extreme weather events are occurring more frequently and with increasing impact. This trend poses a significant challenge for distribution utilities and system operators to ensure that there is uninterrupted power supply to critical loads in their networks; thus, the level of proactive preparation of the distribution system to be able to handle severe impacts of extreme weather events represents the system's resilience. One method that distribution systems use to prepare for extreme events is to form multiple microgrids and thereby isolate themselves from the grid supply by using local generation as much as possible to supply critical loads. But partitioning an existing system into multiple feasible islands capable of supporting critical loads is still challenging for distribution systems - first, because of the size of the graph partitioning problem and, second, because of the difficulty in properly formulating the desired attributes of such islands or microgrids. Therefore, this paper presents a genetic algorithmbased approach that facilitates incorporating multiple objectives for grid partitioning by formulating two types of problems - node allocation and edge elimination - and it considers multiple topological and resilience-enhancing objectives. The performance of the proposed genetic algorithm-based approach is numerically evaluated on multiple test systems as well as on a real distribution feeder in Colorado, USA.

edge elimination↗

Impact of Surface Roughness and Soil Texture on Mineral Dust Emission Fluxes Modeling

Dust production models (DPM) used to estimate vertical fluxes of mineral dust aerosols over arid regions need accurate data on soil and surface properties. The Laboratoire Inter-Universitaire des Systemes Atmospheriques (LISA) data set was developed for Northern Africa, the Middle East, and East Asia. This regional data set was built through dedicated field campaigns and include, among others, the aerodynamic roughness length, the smooth roughness length of the erodible fraction of the surface, and the dry (undisturbed) soil size distribution. Recently, satellite-derived roughness length and high-resolution soil texture data sets at the global scale have emerged and provide the opportunity for the use of advanced schemes in global models. This paper analyzes the behavior of the ERS satellite-derived global roughness length and the State Soil Geographic data base-Food and Agriculture Organization of the United Nations (STATSGO-FAO) soil texture data set (based on wet techniques) using an advanced DPM in comparison to the LISA data set over Northern Africa and the Middle East. We explore the sensitivity of the drag partition scheme (a critical component of the DPM) and of the dust vertical fluxes (intensity and spatial patterns) to the roughness length and soil texture data sets. We also compare the use of the drag partition scheme to a widely used preferential source approach in global models. Idealized experiments with prescribed wind speeds show that the ERS and STATSGO-FAO data sets provide realistic spatial patterns of dust emission and friction velocity thresholds in the region. Finally, we evaluate a dust transport model for the period of March to July 2011 with observed aerosol optical depths from Aerosol Robotic Network sites. Results show that ERS and STATSGO-FAO provide realistic simulations in the region.

textures↗

Structure and Sulfur: Tuning the Viscoelastic and Surface Properties of Natural Keratin Fibers

Natural keratin fibers, such as wool, possess a complex hierarchical structure that governs their mechanical properties and surface energy. However, the extent to which these characteristics are influenced by combined contributions of structural variations (e.g., fiber diameter, intermediate filament (IF) packing) and chemical composition (e.g., disulfide bond density) remains poorly understood. In this study, we investigate wool fibers from five sheep breeds (Merino, Polwarth, Cheviot, Eider, and Devon) to elucidate how these factors influence viscoelasticity and surface interactions. Using a multimodal approach integrating interfacial and bulk characterization methods, including inverse gas chromatography (IGC), atomic force microscopy-infrared spectroscopy (AFM-IR), X-ray photoelectron spectroscopy (XPS), uniaxial tensile testing, and synchrotron small-angle X-ray scattering (SAXS), we show that the nanometer-thick 18-methyleicosanoic acid (18-MEA) layer is consistently present across all wool types and plays a key role in governing hydrophobicity and surface heterogeneity. A controlled isothermal treatment at 200 °C, designed to cleave disulfide bonds, results in a nearly 40% reduction in specific surface area across all fiber types, accompanied by a significant decrease in tensile strength and 80% reduction in elongation at break for Merino and Devon wool, but limited influence on the mechanical properties of Eider fibers. Furthermore, rate-dependent tensile testing within the elastic regime reveals distinct viscoelastic responses among the fiber types, suggesting that the sulfur-rich protein matrix surrounding IFs and its structure contribute actively to stress partitioning. Altogether, when combined with conclusions from SAXS measurements of IF spacing, our work offers compelling insights into the role of the keratin-associated protein (KAP) matrix in shaping wool fiber mechanics. Differences in mechanical behavior among wool types, despite similar IF spacing or sulfur content, highlight the importance of matrix composition and cross-linking density, suggesting that the molecular architecture of the KAP network may be a dominant factor in determining fiber performance.

X-ray scattering↗

Advanced systems engineering and network planning support

The objective of this task was to take a fresh look at the NASA Space Network Control (SNC) element for the Advanced Tracking and Data Relay Satellite System (ATDRSS) such that it can be made more efficient and responsive to the user by introducing new concepts and technologies appropriate for the 1997 timeframe. In particular, it was desired to investigate the technologies and concepts employed in similar systems that may be applicable to the SNC. The recommendations resulting from this study include resource partitioning, on-line access to subsets of the SN schedule, fluid scheduling, increased use of demand access on the MA service, automating Inter-System Control functions using monitor by exception, increase automation for distributed data management and distributed work management, viewing SN operational control in terms of the OSI Management framework, and the introduction of automated interface management.

Walters, David H.↗

Optimizing tertiary storage organization and access for spatio-temporal datasets

We address in this paper data management techniques for efficiently retrieving requested subsets of large datasets stored on mass storage devices. This problem represents a major bottleneck that can negate the benefits of fast networks, because the time to access a subset from a large dataset stored on a mass storage system is much greater that the time to transmit that subset over a network. This paper focuses on very large spatial and temporal datasets generated by simulation programs in the area of climate modeling, but the techniques developed can be applied to other applications that deal with large multidimensional datasets. The main requirement we have addressed is the efficient access of subsets of information contained within much larger datasets, for the purpose of analysis and interactive visualization. We have developed data partitioning techniques that partition datasets into 'clusters' based on analysis of data access patterns and storage device characteristics. The goal is to minimize the number of clusters read from mass storage systems when subsets are requested. We emphasize in this paper proposed enhancements to current storage server protocols to permit control over physical placement of data on storage devices. We also discuss in some detail the aspects of the interface between the application programs and the mass storage system, as well as a workbench to help scientists to design the best reorganization of a dataset for anticipated access patterns.

Chen, Ling Tony↗

Spacecraft On-Board Information Extraction Computer (SOBIEC)

The Jet Propulsion Laboratory is the Technical Monitor on an SBIR Program issued for Irvine Sensors Corporation to develop a highly compact, dual use massively parallel processing node known as SOBIEC. SOBIEC couples 3D memory stacking technology provided by nCUBE. The node contains sufficient network Input/Output to implement up to an order-13 binary hypercube. The benefit of this network, is that it scales linearly as more processors are added, and it is a superset of other commonly used interconnect topologies such as: meshes, rings, toroids, and trees. In this manner, a distributed processing network can be easily devised and supported. The SOBIEC node has sufficient memory for most multi-computer applications, and also supports external memory expansion and DMA interfaces. The SOBIEC node is supported by a mature set of software development tools from nCUBE. The nCUBE operating system (OS) provides configuration and operational support for up to 8000 SOBIEC processors in an order-13 binary hypercube or any subset or partition(s) thereof. The OS is UNIX (USL SVR4) compatible, with C, C++, and FORTRAN compilers readily available. A stand-alone development system is also available to support SOBIEC test and integration.

Eisenman, David↗

Global Magni4icence, or: 4G Networks

The global magnificent four theory is the homological version of a maximally supersymmetric $(8+1)$-dimensional gauge theory on a Calabi-Yau fourfold fibered over a circle. In the case of a toric fourfold we conjecture the formula for its twisted Witten index. String-theoretically we count the BPS states of a system of $D0$-$D2$-$D4$-$D6$-$D8$-branes on the Calabi-Yau fourfold in the presence of a large Neveu-Schwarz $B$-field. Mathematically, we develop the equivariant $K$-theoretic DT4 theory, by constructing the four-valent vertex with generic plane partition asymptotics. Physically, the vertex is a supersymmetric localization of a non-commutative gauge theory in $8+1$ dimensions.

Mathematics↗

Graph-Based Representations and Applications to Process Simulation

Rapid and robust convergence of a process flowsheet is critical to enable large-scale simulations that address core scientific questions related to process design, optimization, and sustainability. However, due to the highly coupled and nonlinear nature of chemical processes, efficiently solving a flowsheet remains a challenge. In this work, we show that graph representations of the underlying physical phenomena in unit operations may help identify potential avenues to systematically reformulate the network of equations and enable more robust topology-based convergence of flowsheets. To this end, we developed graph abstractions of the governing equations of vapor-liquid and liquid-liquid equilibrium separation equipment. These graph abstractions consist of a mesh of interconnected variable nodes and equation nodes that are systematically generated through PhenomeNode, a new open-source library in Python developed in this study. We show that partitioning the graph into separate mass, energy, and equilibrium subgraphs can help decouple nonlinearities and guide decomposition algorithms. By employing the graph abstraction on an industrial separation process for separating glacial acetic acid from water, we implemented a new block decomposition scheme in BioSTEAM and demonstrated that this can accelerate convergence over a traditional sequential modular approach.

Distillation↗

'Electrically-Hot' Convection and Tropical Cyclone Development in the Eastern Atlantic

The depth and intensity of convective-scale "hot" towers in intensifying tropical disturbances has been hypothesized to play a role in tropical cyclogenesis via dynamic and thermodynamic feedbacks on the larger meso-to-synoptic scale circulation. In this investigation we investigate the role that widespread and/or intense lightning-producing convection (i.e., "electrically-hot towers") resident in African Easterly Waves (AEW) may play in tropical cyclogenesis over the eastern Atlantic Ocean. NCEP reanalysis data for the months of July to November for the years 2004, 2006, and 2007 are analyzed for the domain of 5 N - 15 N and 500W - 300 E. Specifically, NCEP data for individual AEWs are partitioned into northerly, southerly, trough, and ridge phases using the 700 hPa meridional winds. Subsequently, information from National Hurricane Center storm reports were divided up into developing and non-developing waves (i.e. tropical cyclogenesis). Finally, composites were created of developing and non-developing waves using the NCEP variables, but with the inclusion of lightning flash count and infrared brightness temperature information. The Zeus and World Wide Lightning Location Network lightning data were used for the lightning information, and the IR brightness temperature data was extracted from the NASA global-merged infrared brightness temperature dataset.

Leppert, Kenneth, II↗

Multitask graph neural networks for elastoplastic response prediction in dual-phase polycrystals

Microstructure-sensitive prediction of elastoplastic response remains a recurring bottleneck in multiscale damage and fatigue modeling, where large ensembles of statistically distinct polycrystals are required to quantify variability and extreme-value behavior. In this work, we develop a multitask graph neural network (GNN) surrogate that maps dual-phase ferrite–martensite polycrystal microstructures to Statistical Volume Element (SVE)-level elastoplastic Quantities of Interest (QoIs). Each SVE is represented as a grain-adjacency graph, with node features encoding phase, geometry, and crystallographic orientation, and edge features encoding relative misorientation. A message-passing graph convolution generates node embeddings, which are pooled into a graph representation and passed to a multitask regression head that jointly predicts 10 scalar QoIs and vector-valued stress–strain responses in orthogonal loading directions across multiple martensite volume fractions and SVE sizes. Results show high accuracy for scalar QoIs and strong agreement for full stress–strain trajectories, with population envelopes reproducing both median behavior and finite-SVE variability across compositions and partition scales. A unified model trained on pooled volume-fraction data preserves most within-regime accuracy relative to regime-specific models while also capturing the broader cross-regime variation reflected in the pooled test set. Distributional comparisons further demonstrate that the surrogate preserves heterogeneity under SVE partitioning, enabling statistically consistent block-wise random-field construction for mesoscale analyses. Overall, the proposed grain-graph surrogate provides a practical pathway to accelerate ensemble-based studies of SVE-level constitutive variability in dual-phase polycrystals.

Crystal plasticity↗

The Urban Fabric of the City as Its Affects Thermal Energy Responses Derived from Remote Sensing Data

The physical geography of the city affects numerous aspects of its interlinked biophysical, social, and land-atmosphere characteristics - those attributes that come together to form the total urban environment. One approach to studying the multitude of interactions that occur as a result of urbanization is to view the city from a systems ecology perspective, where energy and material cycle into and out of the urban milieu. Thus, the urban ecosystem is synergistic in linking land, air, water, and living organisms in a vast network of interrelated physical, human, and biological process. Given the number and the shear complexity of the exchanges and, ultimately, their effects, that occur within the urban environment, we are focusing our research on looking at how the morphology or urban fabric of the city, drives thermal energy exchanges across the urban landscape. The study of thermal energy attributes for different cities provides insight into how thermal fluxes and characteristics are partitioned across the city landscape in response to each city's morphology. We are using thermal infrared remote sensing data obtained at a high spatial resolution from aircraft, along with satellite data, to identify and quantify thermal energy characteristics for 4 U.S. cities: Atlanta, GA, Baton Rouge, LA, Salt Lake City, UT, and Sacramento, CA. Analysis of how thermal energy is spatially distributed across the urban landscapes for these cities provides a unique perspective for understanding how the differing morphology of cities forces land-atmosphere exchanges, such as the urban heat island effect, as well as related meteorological and air quality interactions. Keyword: urban ecosystems, remote sensing, urban heat island

Quattrochi, Dale A.↗