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At least 19 records

Protein conformational switch discerned via network centrality properties

Network analysis has emerged as a powerful tool for examining structural biology systems. The spatial organization of the components of a biomolecular structure has been rendered as a graph representation and analyses have been performed to deduce the biophysical and mechanistic properties of these components. For proteins, the analysis of protein structure networks (PSNs), especially via network centrality measurements and cluster coefficients, has led to identifying amino acid residues that play key functional roles and classifying amino acid residues in general. Whether these network properties examined in various studies are sensitive to subtle (yet biologically significant) conformational changes remained to be addressed. Here, we focused on four types of network centrality properties (betweenness, closeness, degree, and eigenvector centralities) for conformational changes upon ligand binding of a sensor protein (constitutive androstane receptor) and an allosteric enzyme (ribonucleotide reductase). We found that eigenvector centrality is sensitive and can distinguish salient structural features between protein conformational states while other centrality measures, especially closeness centrality, are less sensitive and rather generic with respect to the structural specificity. We also demonstrated that an ensembleinformed, modified PSN with static edges removed (which we term PSN*) has enhanced sensitivity at discerning structural changes.

59 BASIC BIOLOGICAL SCIENCES↗

Gene network centrality analysis identifies key regulators coordinating day-night metabolic transitions in Synechococcus elongatus PCC 7942 despite limited accuracy in predicting direct regulator-gene interactions

Synechococcus elongatus PCC 7942 is a model organism for studying circadian regulation and bioproduction, where precise temporal control of metabolism significantly impacts photosynthetic efficiency and CO 2 -to-bioproduct conversion. Despite extensive research on core clock components, our understanding of the broader regulatory network orchestrating genome-wide metabolic transitions remains incomplete. We address this gap by applying machine learning tools and network analysis to investigate the transcriptional architecture governing circadian-controlled gene expression. While our approach showed moderate accuracy in predicting individual transcription factor-gene interactions - a common challenge with real expression data - network-level topological analysis successfully revealed the organizational principles of circadian regulation. Our analysis identified distinct regulatory modules coordinating day-night metabolic transitions, with photosynthesis and carbon/nitrogen metabolism controlled by day-phase regulators, while nighttime modules orchestrate glycogen mobilization and redox metabolism. Through network centrality analysis, we identified potentially significant but previously understudied transcriptional regulators: HimA as a putative DNA architecture regulator, and TetR and SrrB as potential coordinators of nighttime metabolism, working alongside established global regulators RpaA and RpaB. This work demonstrates how network-level analysis can extract biologically meaningful insights despite limitations in predicting direct regulatory interactions. The regulatory principles uncovered here advance our understanding of how cyanobacteria coordinate complex metabolic transitions and may inform metabolic engineering strategies for enhanced photosynthetic bioproduction from CO 2 .

59 BASIC BIOLOGICAL SCIENCES↗

Mapping Critical Vulnerabilities in Natural Gas Pipeline Systems through Network Centrality and GIS Analytics

Natural gas plays a central role in the US energy landscape, providing 43% of electricity generation in 2023. Its exclusive recovery ability on pipelines for transmission underscores the importance of understanding the disruption recovery ability of this infrastructure. This study employs a network-based analytical framework integrating geographic information systems (GIS) with multiple centrality measures—betweenness, closeness, degree, and eigenvector—to pinpoint key segments and evaluate the structural robustness of the national pipeline network. Pipelines are grouped by System ID and Operator ID to capture variations across organizational and physical structures. The analysis reveals uneven patterns of network influence, where certain pipelines function as critical connectors or dominant hubs. Spatial mapping highlights geographic dependencies and potential chokepoints, offering a clear view of where targeted risk prevention measures would be most effective. The findings provide practical guidance for prioritizing maintenance, enhancing system robustness, and mitigating risks to ensure a stable and secure energy supply. Future research will expand the framework to incorporate dynamic operational data and real-time network behavior.

Peterson, Steven [ORNL] (ORCID:0000000287672998)↗

Event Detection in Aerospace Systems using Centralized Sensor Networks: A Comparative Study of Several Methodologies

Recent advances in micro electromechanical systems technology, digital electronics, and wireless communications have enabled development of low-cost, low-power, multifunctional miniature smart sensors. These sensors can be deployed throughout a region in an aerospace vehicle to build a network for measurement, detection and surveillance applications. Event detection using such centralized sensor networks is often regarded as one of the most promising health management technologies in aerospace applications where timely detection of local anomalies has a great impact on the safety of the mission. In this paper, we propose to conduct a qualitative comparison of several local event detection algorithms for centralized redundant sensor networks. The algorithms are compared with respect to their ability to locate and evaluate an event in the presence of noise and sensor failures for various node geometries and densities.

Mehr, Ali Farhang↗

Comparison of Event Detection Methods for Centralized Sensor Networks

The development of an Integrated Vehicle Health Management (IVHM) for space vehicles has become a great concern. Smart Sensor Networks is one of the promising technologies that are catching a lot of attention. In this paper, we propose to a qualitative comparison of several local event (hot spot) detection algorithms in centralized redundant sensor networks. The algorithms are compared regarding their ability to locate and evaluate the event under noise and sensor failures. The purpose of this study is to check if the ratio performance/computational power of the Mote Fuzzy Validation and Fusion algorithm is relevant compare to simpler methods.

Sauvageon, Julien↗

A Distributed Trust Model Simulator for Energy Grid of Things Distributed Energy Resource Management System

The evolution of networks into more distributed, self-reliant nodes has mitigated single-point failures that plagued traditional centralized networks. Applied to power grids, distributed systems can increase the integrity and availability of grid services while also offering a power management solution. However, while distributed networks provide scalability, security, and sustainability compared to centralized networks, their distributed nature makes them harder for anomaly detection and prevention. Incorporating a Distributed Trust Model (DTM) System into an Energy Grid of Things Distributed Energy Resource Management System (EGOT DERMS) allows grid participants to be characterized and their communication to be analyzed for possible attacks. A Trust Model simulator is needed to evaluate and improve the DTM System.Trustworthiness is calculated using a Trust Model. While many trust models exist, most only consider 2-3 matrices to evaluate trust. The TM proposed in this thesis uses a Metric Vector of Trust (MVoT) monitoring 17 parameters when assessing trust. Moreover, unlike standard trust models, the proposed trust model establishes a method to test the trust between various actors within the network and probe the trust model itself. Using a Trust Model Simulator, MVoT calaculations, initial values, and parameters are fine-tuned to achieve high-confidence message classifications and minimize false positives. The DTM System and Trust Mode Simulation Suite allow for distributed trust evaluation with a real-time classification of EGOT DERMS actors, providing additional security for distributed systems.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Biology-inspired Architecture for Situation Management

Situation Management is a rapidly developing science combining new techniques for data collection with advanced methods of data fusion to facilitate the process leading to correct decisions prescribing action. Current research focuses on reducing increasing amounts of diverse data to knowledge used by decision makers and on reducing time between observations, decisions and actions. No new technology is more promising for increasing the diversity and fidelity of observations than sensor networks. However, current research on sensor networks concentrates on a centralized network architecture. We believe this trend will not realize the full potential of situation management. We propose a new architecture modeled after biological ecosystems where motes are autonomous and intelligent, yet cooperate with local neighborhoods. Providing a layered approach, they sense and act independently when possible, and cooperate with neighborhoods when necessary. The combination of their local actions results in global effects. While situation management research is currently dominated by military applications, advances envisioned for industrial and business applications have similar requirements. NASA has requirements for intelligent and autonomous systems in future missions that can benefit from advances in situation management. We describe requirements for the Integrated Vehicle Health Management program where our biology-inspired architecture provides a layered approach and decisions can be made at the proper level to improve safety, reduce costs, and improve efficiency in making diagnostic and prognostic assessments of the structural integrity, aerodynamic characteristics, and operation of aircraft.

Jones, Kennie H.↗

Wireless Sensing and Communication Capability from In-Core to a Monitoring Center

Significant cost savings can be made if electrical cables can be replaced by wireless technology in current Nuclear Power Plants (NPP) and in advance reactor designs. Wireless technology can also provide in-core opportunities by significantly reducing the number of penetrations in the pressure vessel, cost and complexity of sensor installation and by increasing the efficiency of current and advanced reactors. Unlike other deployment scenarios for an industrial environment, operators need to have centralized control over all the networks. Centralized control will reduce implementation costs, provide single point control and enable monitoring of network devices, improve security, and enhance connectivity. Micro-sensors that can simultaneously monitor temperature and pressure within a fuel rod inside nuclear reactors will enable preventative actions during abnormal operating conditions. This ability could avert accidents and enable the expedient development of accident tolerant fuels. A novel micro-sensor suite (~ mm) to simultaneously measure multiple parameters such as temperature, strain, pressure, and neutron/gamma flux inside a fuel rod is being developed for use in reactors. The necessary communication architecture is also being developed to transmit measurement signals from the core to the plant's data cloud or control room. A three three-tier strategy has been developed to support wireless transmission of in-core measurements to the control room or to a secure cloud platform for control, analytics, and decision-making purposes. 1. In-core: data signal from in-core to outside of the pressure vessel within the containment building 2. Containment building: data signal from inside to the outside of the containment building and into the balance of the plant network 3. Balance of the plant network: information transmitted to the data cloud and control room This plan presents a wireless sensing and communication system for use within a reactor core and elsewhere. The communication technology is advantageous to compensate for network equipment failures and adverse data transmission conditions. Wireless technology will significantly increase the resiliency of the plants network system. The wireless system naturally provides multiple transmission path capability and data redundancy.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Developing stable, simplified, functional consortia from Brachypodium rhizosphere for microbial application in sustainable agriculture

The rhizosphere microbiome plays a crucial role in supporting plant productivity and ecosystem functioning by regulating nutrient cycling, soil integrity, and carbon storage. However, deciphering the intricate interplay between microbial relationships within the rhizosphere is challenging due to the overwhelming taxonomic and functional diversity. Here we present our systematic design framework built on microbial colocalization and microbial interaction, toward successful assembly of multiple rhizosphere-derived Reduced Complexity Consortia (RCC). We enriched co-localized microbes from Brachypodium roots grown in field soil with carbon substrates mimicking Brachypodium root exudates, generating 768 enrichments. By transferring the enrichments every 3 or 7 days for 10 generations, we developed both fast and slow-growing reduced complexity microbial communities. Most carbon substrates led to highly stable RCC just after a few transfers. 16S rRNA gene amplicon analysis revealed distinct community compositions based on inoculum and carbon source, with complex carbon enriching slow growing yet functionally important soil taxa like Acidobacteria and Verrucomicrobia. Network analysis showed that microbial consortia, whether differentiated by growth rate (fast vs. slow) or by succession (across generations), had significantly different network centralities. Besides, the keystone taxa identified within these networks belong to genera with plant growth-promoting traits, underscoring their critical function in shaping rhizospheric microbiome networks. Furthermore, tested consortia demonstrated high stability and reproducibility, assuring successful revival from glycerol stocks for long-term viability and use. Our study represents a significant step toward developing a framework for assembling rhizosphere consortia based on microbial colocalization and interaction, with future implications for sustainable agriculture and environmental management.

59 BASIC BIOLOGICAL SCIENCES↗

Dynamic Network Analysis of Nuclear Science Literature for Research Influence Assessment

Analyzing nuclear science literature via data-driven methods is a critical step for assessing research influence and technology advancements. Indicators of scholarly activities may be buried in large volumes of nuclear research publications and collaboration networks over time. Mining for relevant scholarly influence trends in large volumes of text can be computationally challenging; however, open-source information on research collaborations over time can offer opportunities to extract meaningful insights. While network centrality analysis of scholarly research provides topology-based insights, additional emphasis on dynamics associated with the diffusion of information through these networks is important. Here this paper represents a step in that direction through the development of a novel dynamic network analysis framework and computational engine to identify key entities and capabilities over time within global scholarly nuclear science collaboration networks. Network theoretic, stochastic simulation, and optimization methods are leveraged to address variability in scholarly interactions, influence propagation, and collaboration patterns via network connections. A topic-aware influence maximization algorithm is developed to address the goal of identifying key influential authors in diverse research topics over time. Efficient parallelized implementation of the algorithm is applied to reduce computational costs. A proof-of-concept case study using open-source Scopus data with 33,517 published nuclear research papers from 2000-2019 is presented and representative analytic insights are generated. Broad implications of these insights are discussed and future research directions are also identified.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗

Finalizing Transition to the New Data Center at BNL

Computational science, data management and analysis have been key factors in the success of Brookhaven National Laboratory's scientific programs at the Relativistic Heavy Ion Collider (RHIC), the National Synchrotron Light Source (NSLS-II), the Center for Functional Nanomaterials (CFN), and in biological, atmospheric, and energy systems science, Lattice Quantum Chromodynamics (LQCD) and Materials Science, as well as our participation in international research collaborations, such as the ATLAS Experiment at Europe's Large Hadron Collider (LHC) at CERN (Switzerland) and the Belle II Experiment at KEK (Japan). The construction of a new data center is an acknowledgement of the increasing demand for computing and storage services at BNL in the near term and enable the Lab to address the needs of the future experiments at the High-Luminosity LHC at CERN and the Electron-Ion Collider (EIC) at BNL in the long term. The Computing Facility Revitalization (CFR) project is aimed at repurposing the former National Synchrotron Light Source (NSLS-I) building as the new data center for BNL. The construction of the new data center was finished in 2021Q3, and it was delivered for production in early FY2022 for all collaborations supported by the Scientific Data and Computing Center (SDCC), including STAR, PHENIX and sPHENIX experiments at RHIC collider at BNL, the Belle II Experiment at KEK (Japan), and the Computational Science Initiative at BNL (CSI). This paper highlights the key mechanical, electrical, and networking components of the new data center in its final configuration as used in production since 2021Q4 and gives an overview for the extension of the central network systems into the new data center and the migration of a significant portion of IT load and services from the old data center to the new data center carried out in 20212023, with expected completion of the main phase of the gradual IT equipment replacement and migration from the old data center into the new one set to the end of FY2023 (Sep 30, 2023).

99 GENERAL AND MISCELLANEOUS↗

A glimpse into the fungal metabolomic abyss: Novel network analysis reveals relationships between exogenous compounds and their outputs

Fungal specialized metabolites are a major source of beneficial compounds that are routinely isolated, characterized, and manufactured as pharmaceuticals, agrochemical agents, and industrial chemicals. The production of these metabolites is encoded by biosynthetic gene clusters that are often silent under standard growth conditions. There are limited resources for characterizing the direct link between abiotic stimuli and metabolite production. Herein, we introduce a network analysis-based, data-driven algorithm comprising two routes to characterize the production of specialized fungal metabolites triggered by different exogenous compounds: the direct route and the auxiliary route. Both routes elucidate the influence of treatments on the production of specialized metabolites from experimental data. The direct route determines known and putative metabolites induced by treatments and provides additional insight over traditional comparison methods. The auxiliary route is specific for discovering unknown analytes, and further identification can be curated through online bioinformatic resources. We validated our algorithm by applying chitooligosaccharides and lipids at two different temperatures to the fungal pathogen Aspergillus fumigatus. After liquid chromatography–mass spectrometry quantification of significantly produced analytes, we used network centrality measures to rank the treatments’ ability to elucidate these analytes and confirmed their identity through fragmentation patterns or in silico spiking with commercially available standards. Later, we examined the transcriptional regulation of these metabolites through real-time quantitative polymerase chain reaction. Our data-driven techniques can complement existing metabolomic network analysis by providing an approach to track the influence of any exogenous stimuli on metabolite production. Our experimental-based algorithm can overcome the bottlenecks in elucidating novel fungal compounds used in drug discovery.

59 BASIC BIOLOGICAL SCIENCES↗

Navigation Architecture for a Space Mobile Network

The Tracking and Data Relay Satellite System (TDRSS) Augmentation Service for Satellites (TASS) is a proposed beacon service to provide a global, space based GPS augmentation service based on the NASA Global Differential GPS (GDGPS) System. The TASS signal will be tied to the GPS time system and usable as an additional ranging and Doppler radiometric source. Additionally, it will provide data vital to autonomous navigation in the near Earth regime, including space weather information, TDRS ephemerides, Earth Orientation Parameters (EOP), and forward commanding capability. TASS benefits include enhancing situational awareness, enabling increased autonomy, and providing near real-time command access for user platforms. As NASA Headquarters' Space Communication and Navigation Office (SCaN) begins to move away from a centralized network architecture and towards a Space Mobile Network (SMN) that allows for user initiated services, autonomous navigation will be a key part of such a system. This paper explores how a TASS beacon service enables the Space Mobile Networking paradigm, what a typical user platform would require, and provides an in-depth analysis of several navigation scenarios and operations concepts. This paper provides an overview of the TASS beacon and its role within the SMN and user community. Supporting navigation analysis is presented for two user mission scenarios: an Earth observing spacecraft in low earth orbit (LEO), and a highly elliptical spacecraft in a lunar resonance orbit. These diverse flight scenarios indicate the breadth of applicability of the TASS beacon for upcoming users within the current network architecture and in the SMN.

Data Relay↗

Navigation Architecture For A Space Mobile Network

The Tracking and Data Relay Satellite System (TDRSS) Augmentation Service for Satellites (TASS) is a proposed beacon service to provide a global, space-based GPS augmentation service based on the NASA Global Differential GPS (GDGPS) System. The TASS signal will be tied to the GPS time system and usable as an additional ranging and Doppler radiometric source. Additionally, it will provide data vital to autonomous navigation in the near Earth regime, including space weather information, TDRS ephemerides, Earth Orientation Parameters (EOP), and forward commanding capability. TASS benefits include enhancing situational awareness, enabling increased autonomy, and providing near real-time command access for user platforms. As NASA Headquarters Space Communication and Navigation Office (SCaN) begins to move away from a centralized network architecture and towards a Space Mobile Network (SMN) that allows for user initiated services, autonomous navigation will be a key part of such a system. This paper explores how a TASS beacon service enables the Space Mobile Networking paradigm, what a typical user platform would require, and provides an in-depth analysis of several navigation scenarios and operations concepts.

Satellite↗

Personal communications via ACTS satellite HBR transponders

The concept of a fully meshed network of briefcase-sized terminals is presented for personal communications over Ka-band satellite transponders. In this concept, undesirable double-hop delays are avoided for voice communications. The bandwidth and power resources of the transponder are efficiently shared by users in a simple demand-assigned manner via code-division multiple access (CDMA). Voice, data, and facsimile are statistically multiplexed at each terminal. In order to minimize terminal costs, frequency-precorrected, and level-preadjusted continuous-wave tones are sent from the central network control station in each beam so that the terminals in each down-link beam can use these pilots as references for antenna acquisition and tracking, as reliable frequency sources, and as indicators of signal fade for up-link power control (ULPC). The potential CDMA 'near-far' problem due to up-link fades is mitigated by using ULPC. Quasi-burst mode transmission is employed to minimize the potential clock and pseudorandom number code synchronization.

Fang, Russell J. F.↗

A Case Study of Tunable White LED Lighting with Networked Lighting Controls (Emory University Cognitive Empowerment Program)

Emory University and Georgia Institute of Technology (Georgia Tech) partnered to create the Charlie and Harriet Schaffer Cognitive Empowerment Program (CEP) facility in northeast Atlanta. Together with the funders they are building a program to help individuals experiencing mild cognitive impairment (MCI) to maintain their physical and cognitive health, and independence as long as possible. In addition to applying effective strategies and therapies, the two research groups are investigating the responses of the MCI members to treatments that involve acoustical conditions, exercise and movement, and lighting changes that may support retention or relearning of skills. Care partners and family members receive support and instruction to improve home and work life, promoting joy, purpose, and wellness in the family groups. The lighting system uses tunable-white LEDs, employing luminaires with both warm and cool-color emitters that can be dimmed separately to produce any white correlated color temperature (CCT) between 2700 K and 6500 K. All luminaires were dimmable to achieve subdued or lively surroundings for different treatments, time-of-day, and mood. A central networked digital control system was employed to allow tuning of multiple spaces together (for example, bright, cool morning light could be programmed for extra stimulation, or lighting in all spaces at the end of the day could be reduced in both light output and CCT to promote relaxation and not interfere with the melatonin cycle of occupants). Almost all spaces were equipped with individual room control of dimming and color temperature with touch screens to allow users to tune the lighting as desired, but each room’s controls could also be specially programmed through the server in case the research staff were investigating lighting settings on learning, for example. The server incorporates a timeclock, and it is able to send signals to switch off all lighting after occupancy hours, or enable occupancy sensors to control the lighting. The bulk of the construction work was completed in January 2020. It was clear from an initial walk-through that although the lighting system produced the expected high light level with low-glare qualities of light, that there were issues and inconsistencies to be resolved. These were noted in an initial punchlist visit and expected to be resolved when the tech representatives from the agency visited with the electrical contractor in the following few weeks. What followed was 2.5 years of identifying unexpected lighting performance in terms of light output, color, scheduling, and occupancy. This report documents the issues encountered in the effort to get the lighting and controls systems to operate as intended. It concludes with guidance for design professionals and manufacturers to help avoid problematic complexity in future projects.

42 ENGINEERING↗