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At least 91 records · Page 5

Rapid Computational Identification of Therapeutic Targets for Pathogens

Biological threats continue to persist and evolve as an important challenge to national security. There are multiple ways in which novel viral pathogens could emerge to pose a serious threat to human health. This project developed a pathogen target identification tool that can rapidly respond to a novel or emerging viral biological threat. A set of computational tools were developed that provide detailed information on the newly sequenced genes, their protein products and the drug target sites for the proteins that are best suited for biological countermeasure development. Three key innovations were developed in the project. 1) Development of a new extensive database of protein pocket structures with structure-based search algorithms to rapidly link novel protein targets with the complete collection of previously experimentally solved protein structures. 2) A novel clustering pipeline was introduced to group matching structures and associated small-molecule binding ligands into a consensus protein pocket with the associated small-molecule chemotypes predicted to fit in the pocket site. The matching experimentally solved structures were used to inform the value of different target sites. 3) Where there are viral protein targets with pockets structurally matched to similar human proteins, a biological knowledge graph, which links molecular interactions with human disease, was used to further assess the potential negative impact of a viral protein target with similarities to human proteins that could have important off target side effects. In total, the project produced a new resource for rapid and detailed assessment of promising targets for countermeasures, reflecting the ongoing wet lab, clinical, and computational data being collected. These capabilities will improve the ability to respond to a biological threat in multiple domains.

59 BASIC BIOLOGICAL SCIENCES↗

A Blockchain and PKI-Based Secure Vehicle-to-Vehicle Energy-Trading Protocol

With the increasing awareness for sustainable future and green energy, the demand for electric vehicles (EVs) is growing rapidly, thus placing immense pressure on the energy grid. To alleviate this, local trading between EVs should be encouraged. In this paper, we propose a blockchain and public key infrastructure (PKI)-based secure vehicle-to-vehicle (V2V) energy-trading protocol. A permissioned blockchain utilizing the proof of authority (PoA) consensus and smart contracts is used to securely store data. Encrypted communication is ensured through transport layer security (TLS), with PKI managing the necessary digital certificates and keys. A multi-leader, multi-follower Stackelberg game-based trade algorithm is formulated to determine the optimal energy demands, supplies, and prices. Finally, we propose a detailed communication protocol that ties all the components together, enabling smooth interaction between them. Key findings, such as system behavior and performance, scalability of the trade algorithm and the blockchain, smart contract execution costs, etc., are presented through numerical results by implementing and simulating the protocol in various scenarios. This work not only enhances local energy trading among EVs, encouraging efficient energy usage and reducing burden on the power grid, but also paves a way for future research in sustainable energy management.

Stackelberg game↗

Generalized Ocean Color Inversion Model for Retrieving Marine Inherent Optical Properties

Ocean color measured from satellites provides daily, global estimates of marine inherent optical properties (IOPs). Semi-analytical algorithms (SAAs) provide one mechanism for inverting the color of the water observed by the satellite into IOPs. While numerous SAAs exist, most are similarly constructed and few are appropriately parameterized for all water masses for all seasons. To initiate community-wide discussion of these limitations, NASA organized two workshops that deconstructed SAAs to identify similarities and uniqueness and to progress toward consensus on a unified SAA. This effort resulted in the development of the generalized IOP (GIOP) model software that allows for the construction of different SAAs at runtime by selection from an assortment of model parameterizations. As such, GIOP permits isolation and evaluation of specific modeling assumptions, construction of SAAs, development of regionally tuned SAAs, and execution of ensemble inversion modeling. Working groups associated with the workshops proposed a preliminary default configuration for GIOP (GIOP-DC), with alternative model parameterizations and features defined for subsequent evaluation. In this paper, we: (1) describe the theoretical basis of GIOP; (2) present GIOP-DC and verify its comparable performance to other popular SAAs using both in situ and synthetic data sets; and, (3) quantify the sensitivities of their output to their parameterization. We use the latter to develop a hierarchical sensitivity of SAAs to various model parameterizations, to identify components of SAAs that merit focus in future research, and to provide material for discussion on algorithm uncertainties and future ensemble applications.

Werdell, P. Jeremy↗

Continual coordination of shared activities

Interacting agents that interleave planning and execution must reach consensus on their commitments to each other. For domains with varying degrees of interaction and different constraints on communication and computation, agents will require different coordination protocols in order to efficiently achieve their goals. ShAC (Shared Activity Coordination) is a framework for designing coordination protocols and an algorithm for continually coordinating agents using these protocols during execution. We show how a variety of protocols can be constructed using this framework and describe how ShAC coordinates two rovers and an orbiter in a simulated Mars scenario.

multiple agents coordination planning scheduling M↗

Local Estimators for Spacecraft Formation Flying

A formation estimation architecture for formation flying builds upon the local information exchange among multiple local estimators. Spacecraft formation flying involves the coordination of states among multiple spacecraft through relative sensing, inter-spacecraft communication, and control. Most existing formation flying estimation algorithms can only be supported via highly centralized, all-to-all, static relative sensing. New algorithms are needed that are scalable, modular, and robust to variations in the topology and link characteristics of the formation exchange network. These distributed algorithms should rely on a local information-exchange network, relaxing the assumptions on existing algorithms. In this research, it was shown that only local observability is required to design a formation estimator and control law. The approach relies on breaking up the overall information-exchange network into sequence of local subnetworks, and invoking an agreement-type filter to reach consensus among local estimators within each local network. State estimates were obtained by a set of local measurements that were passed through a set of communicating Kalman filters to reach an overall state estimation for the formation. An optimization approach was also presented by means of which diffused estimates over the network can be incorporated in the local estimates obtained by each estimator via local measurements. This approach compares favorably with that obtained by a centralized Kalman filter, which requires complete knowledge of the raw measurement available to each estimator.

Fathpour, Nanaz↗

The DESI DR1 peculiar velocity survey: growth rate measurements from the maximum likelihood fields method

We present the constraint on the growth rate of structure from the combination of DESI DR1 BGS sample, Fundamental Plane, and Tully-Fisher peculiar velocity catalogues using the maximum likelihood fields method. The combined catalogue contains 415,523 galaxy redshifts and 76,616 peculiar velocity measurements. To handle the large amount of data in the DESI DR1 peculiar velocity catalogue, we significantly improve the computational efficiency by rewriting the algorithm with JAX. After removing outliers and Tully-Fisher galaxies that are affected by systematics, we find fσ 8 = 0.483 -0.043 +0.080 (stat) ± 0.018(sys), consistent within 1σ with the power spectrum and correlation function analysis using the same dataset. Combining all three measurements with appropriate correlations, the consensus measurement is fσ 8 (z eff = 0.07) = 0.450±0.055, consistent with Planck +ΛCDM cosmology (fσ 8 = 0.449±0.008). Combining with the high redshift growth rate of structure measurements from DESI ShapeFit, the constraint on the growth index is γ = 0.58±0.11, consistent with GR.

cosmic flows↗

Graph Analytics on Jellyfish topology

Because large unstructured datasets is important for many science domains, distributed graph analytics is critical to many scientists. Unfortunately, obtaining scaling and performance for irregular communication is challenging because contemporary network interconnects are primarily designed to maximize bandwidths of fixed-neighborhoods large-message exchanges (e.g., stencils). Although there is no consensus on the “best” network topologies for irregular communication, unstructured graph-based interconnects can be more suitable. We analyze three popular graph workloads – clustering, pattern enumeration, and traversal — on comparable networks (in terms of resources and costs) constructed from Jellyfish Random Regular, Dragonfly and Fat tree topologies, varying the routing algorithms. Using packet-level simulations, we demonstrate up to 60% improvement in communication time with Jellyfish due to diversity of the short paths between arbitrary endpoints, which can reduce overall network stalls and congestion.

Graph Analytics, network topology, interconnect, H↗

Robust Decentralized Learning Using ADMM With Unreliable Agents

Many signal processing and machine learning problems can be formulated as consensus optimization problems which can be solved efficiently via a cooperative multi-agent system. However, the agents in the system can be unreliable due to a variety of reasons: noise, faults and attacks. Providing erroneous updates leads the optimization process in a wrong direction, and degrades the performance of distributed machine learning algorithms. This paper considers the problem of decentralized learning using ADMM in the presence of unreliable agents. First, we rigorously analyze the effect of erroneous updates (in ADMM learning iterations) on the convergence behavior of the multi-agent system. We show that the algorithm linearly converges to a neighborhood of the optimal solution under certain conditions and characterize the neighborhood size analytically. Next, we provide guidelines for network design to achieve a faster convergence to the neighborhood. Here, we also provide conditions on the erroneous updates for exact convergence to the optimal solution. Finally, to mitigate the influence of unreliable agents, we propose ROAD , a robust variant of ADMM, and show its resilience to unreliable agents with an exact convergence to the optimum.

97 MATHEMATICS AND COMPUTING↗

A Proposed Clock Synchronization Method for the Solar System Internet

Networked communications in space are necessary to achieve scalability in terms of the number of communicating nodes but also in terms of the overall system complexity. A key component to such a system is the ability to synchronize clocks, which is the focus of this paper. The so-called Solar System Internet (SSI) will be built upon Delay Tolerant Networking (DTN), which, in analogy to the Internet Protocol (IP), can be considered a suite of protocols necessary for networking in the space domain. Therefore, our goal is to extend this suite to include a DTN clock synchronization capability, analogous to the Network Time Protocol (NTP) used in the Internet. A motivating example of a network in space is NASA’s LunaNet, a vision for a multi-hop multi-path network extending to the moon wherein not all nodes will have direct connections to an authoritative reference clock. In this paper, we propose a general clock synchronization methodology and algorithm that could be used for LunaNet as well as more elaborate time-varying networks. In recent years, DTN has benefited from modeling efforts founded on the mathematical tool of sheaves. Here we continue this work to provide an approach to clock synchronization. Due to the time-varying nature of space networks, absolute consensus is not possible. However, the sheaf Laplacian provides a practical, distributed approach to approximating consensus by allowing data to diffuse through the network. In particular, the sheaf Laplacian is readily computable, lending our approach to implementation. Our approach is well suited to handle the difficulties of space networks. For instance, differences in clock accuracy mean certain nodes are more authoritative than others; we can account for these differences through hierarchies in the network, generalizing the strata in NTP. Furthermore, just as error estimation is an integral part of NTP, we are able to give concrete error bounds for our approach. Indeed, different applications (e.g., communications schedules, pointing, navigation, distributed science) will have different requirements, hence it is necessary to maintain clocks within a given tolerance. We outline some of the necessary steps to turn our approach into a practical network protocol that could be used in DTN, and we conclude the paper with suggestions for future research.

Michael Moy↗

Integrating multimodal data through interpretable heterogeneous ensembles

Motivation: Integrating multimodal data represents an effective approach to predicting biomedical characteristics, such as protein functions and disease outcomes. However, existing data integration approaches do not sufficiently address the heterogeneous semantics of multimodal data. In particular, early and intermediate approaches that rely on a uniform integrated representation reinforce the consensus among the modalities but may lose exclusive local information. The alternative late integration approach that can address this challenge has not been systematically studied for biomedical problems. Results: We propose Ensemble Integration (EI) as a novel systematic implementation of the late integration approach. EI infers local predictive models from the individual data modalities using appropriate algorithms and uses heterogeneous ensemble algorithms to integrate these local models into a global predictive model. We also propose a novel interpretation method for EI models. We tested EI on the problems of predicting protein function from multimodal STRING data and mortality due to coronavirus disease 2019 (COVID-19) from multimodal data in electronic health records. We found that EI accomplished its goal of producing significantly more accurate predictions than each individual modality. It also performed better than several established early integration methods for each of these problems. The interpretation of a representative EI model for COVID-19 mortality prediction identified several disease-relevant features, such as laboratory test (blood urea nitrogen and calcium) and vital sign measurements (minimum oxygen saturation) and demographics (age). These results demonstrated the effectiveness of the EI framework for biomedical data integration and predictive modeling.

59 BASIC BIOLOGICAL SCIENCES↗

Evaluating the Application of Multi-Satellite Observations in Hydrologic Modeling

When monitoring local or regional hydrosphere dynamics for applications such as agricultural productivity or drought and flooding events, it is necessary to have accurate, high-resolution estimates of terrestrial water and energy storages. Though in-situ observations provide reliable estimates of hydrologic states and fluxes, they are only capable of accurately capturing the dynamics at relatively discrete points in space and time, which makes them inadequate for characterizing the variability of the water budget across scales. In contrast, satellite-based remote sensing is ideal for providing observations of hydrological states and fluxes because it provides spatially-distributed observations at spatial and temporal scales required for regional land surface process modeling. Due to the continued progress in algorithm development and emerging satellite technology, we now have near-real time monitoring of several components of the water cycle including precipitation, soil moisture, lake and river height, terrestrial water storage, snow cover, and evapotranspiration. As these data become more readily available, their application to hydrologic modeling is becoming more common, however there remains little consensus on the most appropriate method for optimal integration and evaluation in regard to hydrological applications. Here we present two case studies operationally applying several remotely sensed products from AMSR-E, GRACE, and MODIS and discuss assimilation strategies, ease of integration and interpretation, and methods for quantifying the success of the application methodology.

Bolten, John↗

Quantification of geologic lineaments by manual and machine processing techniques

A study was conducted to investigate the effect of operator variability and subjectivity in lineament mapping and to examine methods to minimize or eliminate these problems by use of several machine preprocessing methods. LANDSAT scenes from the Anadarko Basin of Oklahoma and the Colorado Plateau were analyzed as test cases. Four geologists mapped lineaments on an Anadarko Basin scene, using transparencies of MSS bands 4-7, and their results are compared statistically. The total number of fractures mapped by the operators and their average lengths varied considerably, although comparison of lineament directions revealed some consensus. A summary map (785 linears) produced by overlaying the maps generated by the four operators showed that only 0.4% were recognized by all four operators, 4.7% by three, 17.8% by two and 77% by one operator. Two methods of machine aided mapping were tested, both simulating directional filters. One consists of computer (digital) processing of CCTs using edge enhancement algorithms, the other employs a television (analog) scanning of an image transparency which superimposes the original image and one offset in the direction of the scan line.

Podwysocki, M. H.↗

NASA's SnowEx Campaign and Measuring Global Snow from Space

Snow blankets 30% of Earth's land surface (60% of northern hemisphere land) in midwinter, dramatically changing our planet's land surface and affecting our weather for months. Seasonal snow is critically important to society for the management of water resources, natural hazards, water security, and in many economic sectors. The only practical way to estimate the quantity of snow on a global scale is through satellites. Despite 4 decades of satellite observations, the highly variable nature of snow still presents significant challenges toward achieving this goal. For example, current space-based techniques underestimate snow water equivalent (SWE) by as much as 50%, and model-based estimates can differ greatly versus estimates based on remotely-sensed observations. Snow community consensus is that a multi-sensor approach is needed to adequately address global snow, combined with modeling and data assimilation to fill the gaps in space and time. What remains, then, is how best to combine and use the various sensors under different types of snow conditions and confounding factors. NASA's multi-year SnowEx airborne campaign is designed to collect measurements needed to enable algorithm development and to guide those mission trade studies. Year 1 (2017) focused on the distribution of snow-water equivalent (SWE) and the snow energy balance in a forested environment. This paper will discuss the various remote sensing options for snow, the challenging factors, and describe the recently-completed first year of SnowEx in Colorado, USA. Ground-based remote sensing and in situ data collection involved nearly 100 participants over three weeks. The airborne campaign included nine sensors on five aircraft. We will conclude by discussing options for a future snow satellite mission.

campaign↗

Smallsat 2024 - Starling Cubesat Swarm Technology Demonstration Flight Results

The Starling swarm of four 6U CubeSats launched in July 2023 to test four key technologies to enable future swarm missions: 1) Mobile Ad-Hoc Networking (MANET) over a crosslink radio network 2) Autonomous onboard decision-making for operations 3) Optical-based absolute and relative navigation 4) Autonomous maneuver planning and execution The Starling team implemented the Better Approach to Mobile Ad-hoc Networking (B.A.T.M.A.N.) protocol to automatically manage the crosslink network of four satellites. The B.A.T.M.A.N. protocol uses a decentralized approach to managing a multi-hop mesh network of devices, in this case, a satellite swarm. The four satellites were able to successfully establish a network at multiple data rates and demonstrate file transfer and command issuance between spacecraft over the network. Starling incorporated Distributed Spacecraft Autonomy's (DSA) software to demonstrate onboard decision-making. The DSA software takes L1/L2 band GPS measurements and uses them to estimate the relative Total Electron Count (TEC) in the ionosphere. The onboard software then determines if there are any features of interest and provides that information to the other satellites over the crosslink network. The swarm of satellites then reaches a consensus on the optimal TEC observation strategy and adjusts its measurement collection tactics autonomously. The Starling Formation-Flying Optical Experiment (StarFOX), produced by Stanford's Space Rendezvous Laboratory, uses the onboard star trackers to collect images of the other swarm spacecraft and produce angles-only navigation estimates. This system is envisioned to be valuable in applications in which Global Navigation Satellite Systems (GNSS) are not available, such as in cis-lunar or deep space. StarFOX successfully applied its algorithms to multiple simultaneous spacecraft targets using the star tracker imagery. Finally, Starling used Emergent Space's Cluster Flight Application (CFA) software suite for the Reconfiguration and Orbit Maintenance Experiments Onboard (ROMEO) demonstration of autonomously planning and executing propulsive maneuvers. Large swarms will need to be able to maintain formation requirements with minimal operator involvement, especially as the size of the swarm scales up. Results from the ROMEO experiment are presented. Starling is funded by the Small Spacecraft Technology (SST) program out of NASA's Space Technology Mission Directorate (STMD).

distributed systems↗

Onward to Petaflops Computing

With the recent demonstration of a computing rate of one Tflop/s at Sandia National Lab, one might ask what lies ahead for high-end computing. The next major milestone is a sustained rate of one Pflop/s (also written one petaflops, or 10(exp 15) floating-point operations per second). It should be emphasized that we could just as well use the term "peta-ops", since it appears that large scientific systems will be required to perform intensive integer and logical computation in addition to floating-point operations, and completely non- floating-point applications are likely to be important as well. In addition to prodigiously high computational performance, such systems must of necessity feature very large main memories, between ten Tbyte (10(exp 13) byte) and one Pbyte (10 (exp 15) byte) depending on application, as well as commensurate I/O bandwidth and huge mass storage facilities. The current consensus of scientists who have performed initial studies in this field is that "affordable" petaflops systems may be feasible by the year 2010, assuming that certain key technologies continue to progress at current rates. A sustained petaflops computing capability however is a daunting challenge; it appears significantly more challenging from today's state-of-the-art than achieving one Tflop/s has been from the level of one Gflop/s about 12 years ago. Challenges are faced in the arena of device technology, system architecture, system software, algorithms and applications. This talk will give an overview of some of these challenges, and describe some of the recent initiatives to address them.

Bailey, David H.↗

Challenges of Future High-End Computing

The next major milestone in high performance computing is a sustained rate of one Pflop/s (also written one petaflops, or 10(circumflex)15 floating-point operations per second). In addition to prodigiously high computational performance, such systems must of necessity feature very large main memories, as well as comparably high I/O bandwidth and huge mass storage facilities. The current consensus of scientists who have studied these issues is that "affordable" petaflops systems may be feasible by the year 2010, assuming that certain key technologies continue to progress at current rates. One important question is whether applications can be structured to perform efficiently on such systems, which are expected to incorporate many thousands of processors and deeply hierarchical memory systems. To answer these questions, advanced performance modeling techniques, including simulation of future architectures and applications, may be required. It may also be necessary to formulate "latency tolerant algorithms" and other completely new algorithmic approaches for certain applications. This talk will give an overview of these challenges.

Bailey, David↗

Fidelity-preserving enhancement of ptychography with foundational text-to-image models

Ptychographic phase retrieval enables high-resolution imaging of complex samples but often suffers from artifacts such as grid pathology and multislice crosstalk, which degrade reconstructed images. We propose a plug-and-play (PnP) framework that integrates physics model-based phase retrieval with text-guided image editing using foundational diffusion models. By employing the alternating direction method of multipliers, our approach ensures consensus between data fidelity and artifact removal subproblems, maintaining physical consistency while enhancing image quality. Artifact removal is achieved using a text-guided diffusion image editing method (LEDITS++) with a pre-trained foundational diffusion model, allowing users to specify artifacts for removal in natural language. Demonstrations on simulated and experimental datasets show significant improvements in artifact suppression and structural fidelity, validated by metrics such as peak signal-to-noise ratio and diffraction pattern consistency. This work highlights the combination of text-guided generative models and model-based phase retrieval algorithms as a transferable and fidelity-preserving method for high-quality diffraction imaging.

image editing↗

Key predictors of soil organic matter vulnerability to mineralization differ with depth at a continental scale

Abstract Soil organic matter (SOM) is the largest terrestrial pool of organic carbon, and potential carbon-climate feedbacks involving SOM decomposition could exacerbate anthropogenic climate change. However, our understanding of the controls on SOM mineralization is still incomplete, and as such, our ability to predict carbon-climate feedbacks is limited. To improve our understanding of controls on SOM decomposition, A and upper B horizon soil samples from 26 National Ecological Observatory Network (NEON) sites spanning the conterminous U.S. were incubated for 52 weeks under conditions representing site-specific mean summer temperature and sample-specific field capacity (−33 kPa) water potential. Cumulative carbon dioxide respired was periodically measured and normalized by soil organic C content to calculate cumulative specific respiration (CSR), a metric of SOM vulnerability to mineralization. The Boruta algorithm, a feature selection algorithm, was used to select important predictors of CSR from 159 variables. A diverse suite of predictors was selected (12 for A horizons, 7 for B horizons) with predictors falling into three categories corresponding to SOM chemistry, reactive Fe and Al phases, and site moisture availability. The relationship between SOM chemistry predictors and CSR was complex, while sites that had greater concentrations of reactive Fe and Al phases or were wetter had lower CSR. Only three predictors were selected for both horizon types, suggesting dominant controls on SOM decomposition differ by horizon. Our findings contribute to the emerging consensus that a broad array of controls regulates SOM decomposition at large scales and highlight the need to consider changing controls with depth.

59 BASIC BIOLOGICAL SCIENCES↗