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DOE OSTI2024

A Simple Comparison of Biochemical Systems Theory and Metabolic Control Analysis

This paper explores some basic concepts of Biochemical Systems Theory (BST) and Metabolic Control Analysis (MCA), two frameworks developed to understand the behavior of biochemical networks. Initially introduced by Savageau, BST focuses on system stability and employs power laws in modeling biochemical systems. On the other hand, MCA, pioneered by authors such as Kacser and Burns and Heinrich and Rapoport, emphasizes linearization of the governing equations and describes relationships (known as theorems) between different measures. Despite apparent differences, both frameworks are shown to be equivalent in many respects. Through a simple example of a linear chain, the paper demonstrates how BST and MCA yield identical results when analyzing steady-state behavior and logarithmic gains within biochemical pathways. This comparative analysis highlights the interchangeability of concepts such as kinetic orders, elasticities and other logarithmic gains.

FOS: Biological sciences↗

DOE OSTI2021

The Impact of Behind-the-Meter Heterogeneous Distributed Energy Resources on Distribution Grids

behind-the-meter↗

DOE OSTI2023

Advanced Reactor Cyber Analysis and Development Environment (ARCADE) for System-Level Design Analysis

Cybersecurity is a persistent concern to the safety and security of Nuclear Power Plants (NPPs), but has lacked data-driven, evidence-based research. Rigorous cybersecurity analysis is critical for the licensing of advanced reactors using a performance-based approach. One tool that enables cybersecurity analysis is modeling and simulation. The nuclear industry makes extensive use of modeling and simulation throughout the decision process but lacks a method to incorporate cybersecurity analysis with existing models. To meet this need, the Advanced Reactor Cyber Analysis and Development Environment (ARCADE) was developed. ARCADE is a suite of publicly available tools that can be used to develop emulations of industrial control system devices and networks and integrate those emulations with physics simulators. This integration of cyber emulations and physics models enables rigorous cyber-physical analysis of cyber-attacks on NPP systems. This report provides an overview of key considerations for using ARCADE with existing physics models and demonstrates ARCADE’s capabilities for cybersecurity analysis. Using a model of the Small Modular Advanced High Temperature Reactor (SmAHTR), ARCADE was able to determine the sensitivity of the primary heat exchangers (PHX) to coordinated cyber-attacks. The analysis determined that while the PHX’s failures cause disruption to the reactor, they did not cause any safety limits to be exceeded because of the plant design, including passive safety features. Further development of ARCADE will enable rigorous, repeatable, and automated cyber-physical analysis of advanced reactor control systems. These efforts will also help reduce regulatory uncertainty by presenting similar types of cybersecurity analyses in a common format, driving standard approaches and reporting.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2022

A backward SDE method for uncertainty quantification in deep learning

Here, we develop a backward stochastic differential equation based probabilistic machine learning method, which formulates a class of stochastic neural networks as a stochastic optimal control problem. An efficient stochastic gradient descent algorithm is introduced with the gradient computed through a backward stochastic differential equation. Convergence analysis for stochastic gradient descent optimization and numerical experiments for applications of stochastic neural networks are carried out to validate our methodology in both theory and performance.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Network analysis of memristive device circuits: dynamics, stability and correlations

Abstract Networks with memristive devices are a potential basis for the next generation of computing devices. They are also an important model system for basic science, from modeling nanoscale conductivity to providing insight into the information-processing of neurons. The resistance in a memristive device depends on the history of the applied bias and thus displays a type of memory. The interplay of this memory with the dynamic properties of the network can give rise to new behavior, offering many fascinating theoretical challenges. But methods to analyze general memristive circuits are not well described in the literature. In this paper we develop a general circuit analysis for networks that combine memristive devices alongside resistors, capacitors and inductors and under various types of control. We derive equations of motion for the memory parameters of these circuits and describe the conditions for which a network should display properties characteristic of a resonator system. For the case of a purely memresistive network, we derive Lyapunov functions, which can be used to study the stability of the network dynamics. Surprisingly, analysis of the Lyapunov functions show that these circuits do not always have a stable equilibrium in the case of nonlinear resistance and window functions. The Lyapunov function allows us to study circuit invariances, wherein different circuits give rise to similar equations of motion, which manifest through a gauge freedom and node permutations. Finally, we identify the relation between the graph Laplacian and the operators governing the dynamics of memristor networks operators, and we use these tools to study the correlations between distant memristive devices through the effective resistance.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Disentangling direct from indirect relationships in association networks

Networks are vital tools for understanding and modeling interactions in complex systems in science and engineering, and direct and indirect interactions are pervasive in all types of networks. However, quantitatively disentangling direct and indirect relationships in networks remains a formidable task. Here, we present a framework, called iDIRECT (Inference of Direct and Indirect Relationships with Effective Copula-based Transitivity), for quantitatively inferring direct dependencies in association networks. Using copula-based transitivity, iDIRECT eliminates/ameliorates several challenging mathematical problems, including ill-conditioning, self-looping, and interaction strength overflow. With simulation data as benchmark examples, iDIRECT showed high prediction accuracies. Application of iDIRECT to reconstruct gene regulatory networks in Escherichia coli also revealed considerably higher prediction power than the best-performing approaches in the DREAM5 (Dialogue on Reverse Engineering Assessment and Methods project, #5) Network Inference Challenge. In addition, applying iDIRECT to highly diverse grassland soil microbial communities in response to climate warming showed that the iDIRECT-processed networks were significantly different from the original networks, with considerably fewer nodes, links, and connectivity, but higher relative modularity. Further analysis revealed that the iDIRECT-processed network was more complex under warming than the control and more robust to both random and target species removal ( P < 0.001). As a general approach, iDIRECT has great advantages for network inference, and it should be widely applicable to infer direct relationships in association networks across diverse disciplines in science and engineering.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Ultraviolet Superradiance from Mega-Networks of Tryptophan in Biological Architectures

Networks of tryptophan (Trp)–an aromatic amino acid with strong fluorescence response–are ubiquitous in biological systems, forming diverse architectures in transmembrane proteins, cytoskeletal filaments, subneuronal elements, photoreceptor complexes, virion capsids, and other cellular structures. We analyze the cooperative effects induced by ultraviolet (UV) excitation of several biologically relevant Trp mega-networks, thus giving insights into novel mechanisms for cellular signaling and control. Our theoretical analysis in the single-excitation manifold predicts the formation of strongly superradiant states due to collective interactions among organized arrangements of up to >10 5 Trp UV-excited transition dipoles in microtubule architectures, which leads to an enhancement of the fluorescence quantum yield (QY) that is confirmed by our experiments. We demonstrate the observed consequences of this superradiant behavior in the fluorescence QY for hierarchically organized tubulin structures, which increases in different geometric regimes at thermal equilibrium before saturation, highlighting the effect’s persistence in the presence of disorder. Our work thus showcases the many orders of magnitude across which the brightest (hundreds of femtoseconds) and darkest (tens of seconds) states can coexist in these Trp lattices.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Evaluating the limitations of Bayesian metabolic control analysis

AbstractBayesian Metabolic Control Analysis (BMCA) has emerged as a promising framework for inferring metabolic control coefficients in data-limited scenarios by integrating Bayesian inference with linlog rate laws. However, its predictive accuracy and limitations remain underexplored. This study systematically evaluates BMCA’s ability to infer elasticity values, flux control coefficients (FCCs), and concentration control coefficients (CCCs) under varying data availability conditions using three synthetic metabolic network models. Our findings highlight the strengths and weaknesses of BMCA, guiding its application in metabolic engineering and emphasizing the need for methodological refinements.Author summaryUnderstanding how enzymes control metabolic pathways is crucial for optimizing biomanufacturing and synthetic biology applications. Bayesian Metabolic Control Analysis (BMCA) is a promising computational method that integrates Bayesian inference with metabolic control analysis to estimate key control parameters, even in cases with limited experimental data. However, the accuracy and limitations of BMCA remain unclear. In this study, we systematically evaluate BMCA using three synthetic metabolic networks to determine how different types of physiological data impact its predictive performance. We find that BMCA requires flux and enzyme concentration data for accurate predictions, while external metabolite concentrations contribute little. Additionally, BMCA fails to predict elasticity values beyond a magnitude of 1.5 and reliably infer allosteric regulation, even when strong regulatory interactions exist. In addition, BMCA does not accurately rank metabolic control points, which may limit its utility in identifying key enzymes in engineered pathways. Our work provides practical insights into when and how BMCA can be applied, guiding future research in metabolic modeling and control analysis.

Shin, Janis (ORCID:0000000216572455)↗

DOE OSTI2022

Epistemology of voltage control in DER-rich power system

Despite the recent development of several scalable, robust, and resilient control approaches with superior convergence properties considering an increasing penetration of distributed energy resources (DERs), cognitive oversights often simplify several aspects of the cyber–physical power system in the controller development. Here, following the identification of the limitations of classical controller definitions, we justify alternative definitions of voltage control approaches classifiers considering three inter-disciplinary domains: (i) power system, (ii) optimization and decision-making, and (iii) networking and cyber-security, to develop a taxonomy for helping in real-world comparative performance analysis and deployability of these controllers. We observe that classical and introduced domain-based definitions together can better classify the control algorithms.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2022

Data from the Development Evolution of a Vehicle for Custom Control

In order to develop custom controllers intended to operate vehicles on a live highway, a series of data collection-focused tests were performed at increasing stages of complexity. Modern vehicles with features like Adaptive Cruise Control (ACC) feature a rich set of sensors and drive-by-wire mechanisms. The presented stages of data collection begins with the analysis of raw data provided by various vehicles, and eventually results in spoofing Controller Area Network (CAN) protocols for sending control commands to operate a vehicle. This paper covers the data and technical efforts needed at various stages. The raw data and tools to plot the data are also publicly available.

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2020

Performance Prediction of Big Data Transfer Through Experimental Analysis and Machine Learning

Big data transfer in next-generation scientific applications is now commonly carried out over connections with guaranteed bandwidth provisioned in High-performance Networks (HPNs) through advance bandwidth reservation. To use HPN resources efficiently, provisioning agents need to carefully schedule data transfer requests and allocate appropriate bandwidths. Such reserved bandwidths, if not fully utilized by the requesting user, could be simply wasted or cause extra overhead and complexity in management due to exclusive access. This calls for the capability of performance prediction to reserve bandwidth resources that match actual needs. Towards this goal, we employ machine learning algorithms to predict big data transfer performance based on extensive performance measurements, which are collected over a span of several years from a large number of data transfer tests using different protocols and toolkits between various end sites on several real-life physical or emulated HPN testbeds. We first identify a comprehensive list of attributes involved in a typical big data transfer process, including end host system configurations, network connection properties, and control parameters of data transfer methods. We then conduct an in-depth exploratory analysis of their impacts on application-level throughput, which provides insights into big data transfer performance and motivates the use of machine learning. We also investigate the applicability of machine learning algorithms and derive their general performance bounds for performance prediction of big data transfer in HPNs. Experimental results show that, with appropriate data preprocessing, the proposed machine learning-based approach achieves 95% or higher prediction accuracy in up to 90% of the cases with very noisy real-life performance measurements.

Yun, Daqing↗

DOE OSTI2021

Cyber-Power Co-Simulation for End-to-End Synchrophasor Network Analysis and Applications

The resiliency, reliability and security of the next generation cyber-power smart grid depend upon efficiently leveraging advanced communication and computing technologies. Also, developing real-time data-driven applications is critical to enable wide-area monitoring and control of the cyber-power grid given high-resolution data from Phasor Measurement Units (PMUs). North American Synchrophasor Initiative Network (NASPlnet) provides guidance for PMU data exchanges. With the advancement in networking and grid operation, it is necessary to evaluate the performance of different data flow architectures suggested by NASPInet and analyze the impact on applications. Therefore, we need a cyber-power co-simulation framework that supports very large-scale co-simulation capable of running in parallel, high-performance computing platforms and capturing real-life network behavior. This work presents an end-to-end automated and user-driven cyber-power co-simulation using NS3 to model communication networks, GridPACK to model the power grid, and HELICS as a co-simulation engine. Comparative analysis of latency in synchrophasor networks and a performance evaluation of a power system stabilizer application utilizing PMU data in an IEEE 39 bus test system is presented using this cosimulation testbed.

Mustafa, Hussain M.↗

DOE OSTI2020

My vehicle is a data mine

In this talk we explore how analysis of vehicle data provides information of individual vehicle behaviors, information of other vehicles in the flow of traffic, and insights into the behavior of drivers. Over the last two decades traditional passenger vehicles have been transformed from integrated two-port electrical nodes to cyber-physical systems of communicating computational nodes whose individual state and control variables are shared on a standard controller area network (CAN) bus. As driver assistance systems have crept into vehicles as safety features, driver behaviors can be observed through analysis of the data streams on the CAN bus as these new nodes communicate with one another. The properties of these data streams, as well as architectures and approaches to gather the data, are important to consider when drawing conclusions on the relevance of the data in making decisions at varying levels of the information hierarchy. We will demonstrate several technical challenges associated with these data collection processes, as well as preliminary results that demonstrate application relevance of the data to behavior, traffic, and systems domains.

42 ENGINEERING↗

DOE OSTI2023

Reinforcement learning for real-time process control in high-temperature superconductor manufacturing

With high efficiency and low energy loss, high-temperature superconductors (HTS) have demonstrated their profound applications in various fields, such as medical imaging, transportation, accelerators, microwave devices, and power systems. The high-field applications of HTS tapes have raised the demand for producing cost-effective tapes with long lengths in superconductor manufacturing. However, achieving the uniform and enhanced performance of a long HTS tape is challenging due to the unstable growth conditions in the manufacturing process. Although it is confirmed that the process parameters during the advanced metal organic chemical vapor deposition (A-MOCVD) process influence the uniformity of the produced HTS tapes, the high-dimensional process parameter signals and their complicated interactions make it difficult to develop an effective control policy. In this paper, we propose a local measure for the uniformity of HTS tapes to provide instant feedback for our control policy. Then, we model the manufacturing of HTS tapes as a Markov decision process (MDP) with continuous state and action spaces to assess the instant reward in real time in our feedback control model. As our MDP involves continuous and high-dimensional state and action spaces, a neural fitted Q-iteration (NFQ) algorithm is adopted to solve the MDP with artificial neural network (ANN) function approximation. The collinearity of process parameters can restrict our capability of adjusting the process parameters, which is addressed by the principal component analysis (PCA) in our method. The control policy adjusts the PCA of process parameters using the NFQ algorithm. In conclusion, based on our case studies on real A-MOCVD dataset, the obtained control policy increases the average uniformity of tapes by 5.6% and performs especially well on sample HTS tapes with a low uniformity.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2026

QProR: An Efficient Framework for Quantity-of-Interest Based Progressive Retrieval with Guaranteed Error Control

Scientific applications generate an unprecedented volume of data, overwhelming the network and file systems’ bandwidth and posing challenges for efficient and scalable data retrieval and analysis. Progressive data compression offers a promising solution by enabling on-demand retrieval at reduced size. However, existing progressive methods either fail to bound the errors in essential quantities of interest (QoIs) derived from raw data or suffer from suboptimal retrieval efficiency. In this work, we propose QProR, an efficient QoI-based progressive framework that optimizes progressive retrieval for target QoIs. Our key contributions include: (1) a systematic framework that integrates error-controlled lossy compressors with bitplane encoding while decoupling the two processes for high flexibility and adaptability; (2) a novel weighted bitplane encoding method which incorperates QoI knowledge into data refactoring to enhance retrieval efficiency; (3) an optimized retrieval strategy that accounts for the varying impacts of different variables on multivariate QoIs; (4) comprehensive evaluations using six real-world datasets from multiple scientific applications and thorough comparisons against state of the arts. Experimental results demonstrate that QProR achieves up to 80.38% reduction in the retrieval size under the same requested QoI error tolerance, when compared with the best-performing existing methods. When transferring 384 GB of scientific data to remote sites, QProR delivers up to 1.68 × speedup in the end-to-end data transfer performance.

Li, Wenbo [University of Kentucky]↗

DOE OSTI2020

DC Microgrids Under Denial of Service Attacks: Feasibility and Stability Issues

Distributed control has been extensively studied for a DC microgrid to coordinate multiple grid assets where each asset can generate its own control decisions based on communications within its neighborhood. Nevertheless, such a control strategy usually has a strong dependence on active information exchange and needs to always maintain a pre-determined communication graph. This makes it vulnerable to cyber attacks, especially denial of service (DoS) attacks that block communication channels that effectively change the communication graph. In this paper, we study two potential impacts of DoS attacks: the inability to maintain steady-state and dynamical generation-demand balance, i.e. the feasibility and stability issues. We develop a mathematical model to describe the cyber-induced system steady-state and dynamical performance. The model reveals the impacts of DoS attacks and enables formal analysis. Case studies are shown to verify the proposed work.

41 EE - Solar Energy Technologies Office (EE-4S)↗

DOE OSTI2020

The Impact of Behind-the-Meter Heterogeneous Distributed Energy Resources on Distribution Grids: Preprint

The increasing integration of distributed energy resources (DERs) on the electric grid brings new challenges and opportunities for utility grid operations. With the rapid deployment of DERs, there is emerging interest in integrating these controllable devices with utility operations at all levels for monitoring and management. Different types of DERs such as Photovoltaics (PV), energy storage, electric vehicles (EVs), etc. have varying effects on the grid based on how and where they are deployed. Again, the DER deployment and its impact are network-dependent, while the traditional electric grids were not designed to host DERs. To understand the challenges with increasing behind-the-meter (BTM) DERs and to identify the needs in deploying advanced controls, a comprehensive grid impact study is indispensable. This paper investigates the impacts of integrating a mix of DERs in the utility distribution network in Colorado, U.S. Firstly, BTM DERs at the residential scale including distributed PV; battery energy storage systems (BESS); heating, ventilation, and air-conditioning (HVAC) load; electric water heater (EWH) load; and EVs are modeled. The impacts of integrating these resources on the distribution network are evaluated by conducting time-series simulations for different scenarios considering different days to capture the worst-case conditions. Monte Carlo simulations are conducted to generate the realistic EV charging profile. The voltage issues, substation transformer loadings, and critical nodes in the network are identified with the incorporation of uncoordinated EV charging loads and other DER in the network. This analysis helps visualize the DER impact on the grid, identify the challenges, and provides an insight into the new distribution management and control needs to enable reliable and resilient distribution grid operations. Additionally, further analysis is performed to estimate the daily residential electricity cost with the inclusion of DERs under time-of-use tariffs. The result shows the daily residential electricity cost reduced by 20:7% on average with DERs compared to the case without DERs.

27 ARPA - Advanced Research Projects Agency-Energy↗

DOE OSTI2025

Developing ML/AI Methods for High-Throughput Characterization of Multiple-Sensor Streams of Tokamak Dynamics for High-Speed Control (Final Report)

This project evaluated and developed new mathematical and algorithmic techniques capable of handling (in real-time) the growing amounts of data generated by modern fusion research. While existing numerical linear algebra (NLA) methods provide the backbone to classical data analysis and algorithms, these methods fundamentally do not port to distributed architectures nor do they allow low-latency data reduction for control. Motivated by the needs for modern fusion reactors, this project explored and implemented new numerical methods to characterize plasma dynamics, respond in real-time to discharge evolution, and to process massive-scale data accurately and rapidly more fully. This project links expertise in multiple-sensor diagnostics of tokamak plasma dynamics from Columbia University’s Plasma Physics Laboratory with expertise in massive-scale data reduction and extreme data control algorithms at Columbia University’s Data Science Institute. This interdisciplinary project (i) applied machine learning methods, (ii) implemented a properly-trained neural-network for very fast processing of high-speed plasma videography, and (ii) developed the applied mathematical methods, based on randomized-NLA (rNLA) routines, for data analysis, reduction, and real-time control. The Columbia University High Beta Tokamak-Extended Pulse (HBT-EP) facility provided data to test new algorithms and partnership with Columbia University's Data Sciences Institute evaluated the broader use of new algorithms for many challenging control applications.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗