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At least 415 records · Page 23

CMIP5 model selection for ISMIP6 ice sheet model forcing: Greenland and Antarctica

Abstract. The ice sheet model intercomparison project for CMIP6 (ISMIP6) effort brings together the ice sheet and climate modeling communities to gain understanding of the ice sheet contribution to sea level rise. ISMIP6 conducts stand-alone ice sheet experiments that use space- and time-varying forcing derived from atmosphere–ocean coupled global climate models (AOGCMs) to reflect plausible trajectories for climate projections. The goal of this study is to recommend a subset of CMIP5 AOGCMs (three core and three targeted) to produce forcing for ISMIP6 stand-alone ice sheet simulations, based on (i) their representation of current climate near Antarctica and Greenland relative to observations and (ii) their ability to sample a diversity of projected atmosphere and ocean changes over the 21st century. The selection is performed separately for Greenland and Antarctica. Model evaluation over the historical period focuses on variables used to generate ice sheet forcing. For stage (i), we combine metrics of atmosphere and surface ocean state (annual- and seasonal-mean variables over large spatial domains) with metrics of time-mean subsurface ocean temperature biases averaged over sectors of the continental shelf. For stage (ii), we maximize the diversity of climate projections among the best-performing models. Model selection is also constrained by technical limitations, such as availability of required data from RCP2.6 and RCP8.5 projections. The selected top three CMIP5 climate models are CCSM4, MIROC-ESM-CHEM, and NorESM1-M for Antarctica and HadGEM2-ES, MIROC5, and NorESM1-M for Greenland. This model selection was designed specifically for ISMIP6 but can be adapted for other applications.

54 ENVIRONMENTAL SCIENCES↗

Critical Roles of Information, Analysis, Research, and Operations in the Cyber Realm

PNNL has developed an adaptive cyber integration framework (ACIF) to facilitate the timely sharing of cyber threat information along with the advancement of situational awareness tools to enhance protection against and respond to critical infrastructure cybersecurity threats. The ACIF comprises components implemented iteratively to achieve research and mission goals. The ACIF components include data generation technologies, analytic tools development and maturation, data enrichment and fusion, trust building with stakeholders, investigative research, analytic rigor, production, and dissemination. Each component, its importance to the ACIF, and how they can be adopted and applied across other information-sharing sectors and domains are discussed in this paper.

Cyber Threat Intelligence, Cyber Security, Data En↗

Control Algorithms for Dual-wavefront Sensor Single-conjugate Adaptive Optics

High-contrast imaging systems using active control with adaptive optics (AO) are often limited by non-common path (NCP) aberrations that are seen only at the final science image. AO systems employing focal-plane wavefront sensors (FP-WFSs) are able to simultaneously correct NCP aberrations and measure science images, but they typically require a second stage of control that adds system cost and complexity. We present control algorithms to augment AO systems with FP-WFSs within their existing control setup. We demonstrate inter-arm NCP aberration transfer can be mitigated through temporal filtering, present frequency- and time-domain validation of controller stability and performance, and discuss the optimality of the chosen controllers. This work will enable the development, testing, and installation of FP-WFS technologies for direct imaging of exoplanets.

79 ASTRONOMY AND ASTROPHYSICS↗

Explainable AI (XAI)-driven vibration sensing scheme for surface quality monitoring in a smart surface grinding process

Local Interpretable and Model-agnostic Explanation (LIME), an explainable artificial intelligence (XAI) approach is adapted to identify the globally important time-frequency bands for predicting average surface roughness (Ra) in a smart grinding process. The smart grinding setup consisted of a Supertech CNC precision surface grinding machine, instrumented with a Dytran piezoelectric accelerometer attached to the tailstock quill along the tangential direction (Y-axis). For every grinding pass, vibration signatures were captured, and the ground truth surface roughness values were recorded using a Mahr Marsurf M300C portable surface roughness profilometer. The roughness values ranged from 0.06 to 0.14 microns over the complete set of experiments. Time-frequency domain spectrogram frames were extracted for each of the vibration signals collected during the grinding process. Convolutional Neural Networks (CNNs) were modeled to predict the surface roughness based on these spectrogram frames and their image augmentations. The best CNN model was able to predict the roughness values with an overall R2-score of 0.95, training R2-score of 0.99, and testing R2-score of 0.81 with only 80 sets of vibration signals corresponding to 4 experiments with 20 trials each. Although the data size is not large enough to guarantee such performance metrics in real-world scenarios, one can extract statistically consistent explanations underlying the relationships these complex deep learning models capture. Further, the LIME methodology was implemented on the developed surface roughness CNN model to identify the important time-frequency bands (i.e., the superpixels of a spectrogram) influencing the predictions. Based on the identified important regions on the spectrogram frames, the corresponding frequency characteristics were determined that influence the surface roughness predictions. The important frequency range based on LIME results was approximately 11.7 to 19.1 kHz. The power of XAI was demonstrated by cutting down the sampling rate from 160 kHz to 30, 20, 10, and 5 kHz based on the important frequency range and considering Nyquist criteria. Separate CNN models were developed for these ranges by only extracting time-frequency contents below their corresponding Nyquist cut-offs. A proper data acquisition strategy is proposed by comparing the model performances to argue the selection of a sufficient sampling rate to capture the grinding process successfully and robustly.

42 ENGINEERING↗

Reprint of: Explainable AI (XAI)-driven vibration sensing scheme for surface quality monitoring in a smart surface grinding process

Local Interpretable and Model-agnostic Explanation (LIME), an explainable artificial intelligence (XAI) approach is adapted to identify the globally important time-frequency bands for predicting average surface roughness (Ra) in a smart grinding process. The smart grinding setup consisted of a Supertech CNC precision surface grinding machine, instrumented with a Dytran piezoelectric accelerometer attached to the tailstock quill along the tangential direction (Y-axis). For every grinding pass, vibration signatures were captured, and the ground truth surface roughness values were recorded using a Mahr Marsurf M300C portable surface roughness profilometer. The roughness values ranged from 0.06 to 0.14 microns over the complete set of experiments. Time-frequency domain spectrogram frames were extracted for each of the vibration signals collected during the grinding process. Convolutional Neural Networks (CNNs) were modeled to predict the surface roughness based on these spectrogram frames and their image augmentations. The best CNN model was able to predict the roughness values with an overall R2-score of 0.95, training R2-score of 0.99, and testing R2-score of 0.81 with only 80 sets of vibration signals corresponding to 4 experiments with 20 trials each. Although the data size is not large enough to guarantee such performance metrics in real-world scenarios, one can extract statistically consistent explanations underlying the relationships these complex deep learning models capture. Further, the LIME methodology was implemented on the developed surface roughness CNN model to identify the important time-frequency bands (i.e., the superpixels of a spectrogram) influencing the predictions. Based on the identified important regions on the spectrogram frames, the corresponding frequency characteristics were determined that influence the surface roughness predictions. The important frequency range based on LIME results was approximately 11.7 to 19.1 kHz. The power of XAI was demonstrated by cutting down the sampling rate from 160 kHz to 30, 20, 10, and 5 kHz based on the important frequency range and considering Nyquist criteria. Separate CNN models were developed for these ranges by only extracting time-frequency contents below their corresponding Nyquist cut-offs. A proper data acquisition strategy is proposed by comparing the model performances to argue the selection of a sufficient sampling rate to capture the grinding process successfully and robustly.

47 OTHER INSTRUMENTATION↗

MARBLES (Multi-scale Adaptively Refined Boltzmann LatticE Solver) [SWR-23-37]

MARBLES (Multi-scale Adaptively Refined Boltzmann LatticE Solver) is an open-source computational fluid dynamics package powered by the lattice Boltzmann equations and built on AMReX. In the lattice Boltzmann method, local collisions between meso-scale fictitious particles drive the governing equations which enables MARBLES to easily simulate flow around complex and/or moving geometry without the generation of a body-conforming mesh. Using AMReX data structures and operations ensures a high level of computational performance and parallel scaling on heterogenous architectures while also naturally supporting locally enhanced grid resolution and fidelity through automatic mesh refinement. New domains and problem definitions are easily specified through an input file with examples and guidance on all options and variables provided in the MARBLES documentation.

Henry de Frahan, Marc↗

An entropy-based debiasing approach to quantifying experimental coverage for novel applications of interest in the nuclear community

This manuscript proposes a novel information-theoretic approach to the quantification of experimental relevance, i.e., coverage, to achieve optimal data assimilation results for nuclear engineering applications. Specifically, this work posits the need for a new metric, called coverage (q C ) of an application’s quantity of interest, i.e., eigenvalue or power peaking for an advanced reactor concept, defined herein as the theoretically maximum achievable reduction in the quantity’s uncertainty given measurements from a pool of experiments in a manner that is independent of the data assimilation procedure employed. Currently, reduction in a quantity’s uncertainty is strongly biased by the underlying assumptions of the assimilation procedure to account for the under-determined nature of such problems and the similarity criterion employed to identify relevant experiments. To address this challenge, this work has developed a coverage metric, q C , based on mutual information, which establishes a new conceptual framework for assessing coverage, one that is independent of the model parameters and responses degree of variations in both the experimental and application domains, i.e., linear vs non-linear, and their prior uncertainty distributions, i.e., Gaussian vs. non-Gaussian. The q C is an entropic measure capable of addressing coverage for general nonlinear problems with non-Gaussian uncertainties and inclusive of the measurement uncertainties from multiple experiments. Numerical experiments from manufactured analytical problems as well as a set of benchmarks from the ICSBEP handbook are employed to demonstrate its theoretical and practical performance as compared to the c k -based experiment selection methodology, commonly employed in the neutronic community. The manuscript then employs other well-known adaptations to existing data assimilation methodologies for nonlinear and non-Gaussian problems capable of achieving the coverage posited by q C .

Bayesian data assimilation↗

Structural coordination between active sites of a CRISPR reverse transcriptase-integrase complex

CRISPR-Cas systems provide adaptive immunity in bacteria and archaea, beginning with integration of foreign sequences into the host CRISPR genomic locus and followed by transcription and maturation of CRISPR RNAs (crRNAs). In some CRISPR systems, a reverse transcriptase (RT) fusion to the Cas1 integrase and Cas6 maturase creates a single protein that enables concerted sequence integration and crRNA production. To elucidate how the RT-integrase organizes distinct enzymatic activities, we present the cryo-EM structure of a Cas6-RT-Cas1—Cas2 CRISPR integrase complex. The structure reveals a heterohexamer in which the RT directly contacts the integrase and maturase domains, suggesting functional coordination between all three active sites. Together with biochemical experiments, our data support a model of sequential enzymatic activities that enable CRISPR sequence acquisition from RNA and DNA substrates. These findings highlight an expanded capacity of some CRISPR systems to acquire diverse sequences that direct CRISPR-mediated interference.

59 BASIC BIOLOGICAL SCIENCES↗

Full wave modeling of radio-frequency beams in tokamaks in the electron cyclotron frequency range

Simulation of full wave, without paraxial approximation, high-resolution solution of wave equations in frequency domain in the electron cyclotron resonance (ECR) frequency range for realistic Tokamak plasma parameters became possible by using recently formulated hybrid iterative algorithm [Svidzinski et al., Phys. Plasmas 25, 082509 (2018)] for numerically solving discretized wave equations. This approach combines time evolution and iterative relaxation techniques into iteration cycles. This algorithm is implemented in 2D code FullWave, solving wave equations in Tokamaks in cold and hot plasma models, and it has been tested in 3D full wave iterative RF beams simulation tool, which is presently being developed to model 3D ECRH RF beams in fusion devices using dynamic grid adaptation. The results of 2D full wave modeling, assuming specified toroidal mode number, of ECRH RF beams in DIII-D plasma, performed in the cold and hot plasma models for outboard and top launch scenarios using FullWave are presented. Nonlocal hot plasma response model, based on accurate numerical solution of linearized Vlasov equation, is used to model beam propagation and absorption in the 2nd electron cyclotron harmonic region. Demonstration of capability of the hybrid iterative algorithm to model ECRH RF beams in 3D is made by simulating a substantial part of realistic beam in DIII-D, launched from outboard side of the machine. All relevant physics of RF beam propagation, most of which is not captured in paraxial approximation, such as beam's divergence, interference between the X and O modes in the beam, X-O mode conversion, beam splitting into the X and O mode beams, transformation of beam's cross section, and absorption at the 2nd electron cyclotron harmonic, is captured in the simulations. A numerical technique to find an optimal beam polarization at the launcher to launch a nearly pure X or O mode beam in plasma is developed and tested.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Computational prediction of the effect of amino acid changes on the binding affinity between SARS-CoV-2 spike RBD and human ACE2

The association of the receptor binding domain (RBD) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein with human angiotensin-converting enzyme 2 (hACE2) represents the first required step for cellular entry. SARS-CoV-2 has continued to evolve with the emergence of several novel variants, and amino acid changes in the RBD have been implicated with increased fitness and potential for immune evasion. Reliably predicting the effect of amino acid changes on the ability of the RBD to interact more strongly with the hACE2 can help assess the implications for public health and the potential for spillover and adaptation into other animals. Here, we introduce a two-step framework that first relies on 48 independent 4-ns molecular dynamics (MD) trajectories of RBD-hACE2 variants to collect binding energy terms decomposed into Coulombic, covalent, van der Waals, lipophilic, generalized Born solvation, hydrogen bonding, π-π packing, and self-contact correction terms. The second step implements a neural network to classify and quantitatively predict binding affinity changes using the decomposed energy terms as descriptors. The computational base achieves a validation accuracy of 82.8% for classifying single–amino acid substitution variants of the RBD as worsening or improving binding affinity for hACE2 and a correlation coefficient of 0.73 between predicted and experimentally calculated changes in binding affinities. Both metrics are calculated using a fivefold cross-validation test. Our method thus sets up a framework for screening binding affinity changes caused by unknown single– and multiple–amino acid changes offering a valuable tool to predict host adaptation of SARS-CoV-2 variants toward tighter hACE2 binding.

60 APPLIED LIFE SCIENCES↗

Structure-guided discovery of ancestral CRISPR-Cas13 ribonucleases

The RNA-guided ribonuclease CRISPR-Cas13 enables adaptive immunity in bacteria and programmable RNA manipulation in heterologous systems. Cas13s share limited sequence similarity, hindering discovery of related or ancestral systems. Here, to address this, we developed an automated structural-search pipeline to identify an ancestral clade of Cas13 (Cas13an) and further trace Cas13 origins to defense-associated ribonucleases. Despite being one-third the size of other Cas13s, Cas13an mediates robust programmable RNA depletion and defense against diverse bacteriophages. However, unlike its larger counterparts, Cas13an uses a single active site for both CRISPR RNA processing and RNA-guided cleavage, revealing that the ancestral nuclease domain has two modes of activity. Discovery of Cas13an deepens our understanding of CRISPR-Cas evolution and expands opportunities for precision RNA editing, showcasing the promise of structure-guided genome mining.

59 BASIC BIOLOGICAL SCIENCES↗

Smart Mobility in the Cloud: Enabling Real-Time Situational Awareness and Cyber-Physical Control Through a Digital Twin for Traffic

This article presents the design, implementation, and use cases of the Chattanooga Digital Twin (CTwin) towards the vision for next-generation smart city applications for urban mobility management. CTwin is an end-to-end web-based platform that incorporates various aspects of the decision-making process for optimizing urban transportation systems in Chattanooga, Tennessee, to reduce traffic congestion, incidents, and vehicle fuel consumption. The platform serves as a cyberinfrastructure to collect and integrate multi-domain urban mobility data from various online repositories and Internet of Things (IoT) sensors, covering multiple urban aspects (e.g., traffic, natural hazards, weather, and safety) that are relevant to urban mobility management. The platform enables advanced capabilities for: (a) real-time situational awareness on traffic and infrastructure conditions on highways and urban roads, (b) cyber-physical control for optimizing traffic signal timing, and (c) interactive visual analytics on big urban mobility data and various metrics for traffic prediction and transportation performance evaluation. The platform is designed using a multi-level componentization paradigm and is implemented using modular and adaptive architecture, rendering it as a generalizable and extendable prototype for other urban management applications. We present several use cases to demonstrate CTwin's core capabilities for supporting decision-making in smart urban mobility management.

33 ADVANCED PROPULSION SYSTEMS↗

Applying Time-Parallelization to Turbulent Flows

Parallelization of the temporal domain is explored for the solution of turbulent flows. Multigrid reduction-in-time (MGRIT) is used to advance the large-scale fluid dynamics in time sequentially on the coarsest space-time grid but propagate the information in time parallel on all other levels. The goal of this process is to accurately and efficiently resolve the coarse-scale turbulence structure and use that to drive the fine-scales of the turbulent flow. The extra forcing from nonlinear multigrid facilitates the coupling and interaction between fine and coarse scales, through which the multiscale nonlinear physics is properly captured. Adaptive mesh refinement is employed to finely resolve only the regions with strong gradients, which provides further computational efficiency. The underlying computational fluid dynamics solver is a fourth-order finite-volume scheme with the standard 4-stage Runge-Kutta method. An advanced approach is devised and implemented to enable MGRIT to solve highly turbulent flows successfully. Furthermore, the method is applied to solve a Taylor-Green vortex problem and a doubleshear-layer turbulent mixing flow. Results are promising, validating that MGRIT with the filtering approach has the potential to efficiently solve general turbulent flows.

Computational Fluid Dynamics↗

In Situ High-Pressure Synthesis of New Outstanding Light-Element Materials under Industrial P-T Range

High-pressure synthesis (which refers to pressure synthesis in the range of 1 to several GPa) adds a promising additional dimension for exploration of compounds that are inaccessible to traditional chemical methods and can lead to new industrially outstanding materials. It is nowadays a vast exciting field of industrial and academic research opening up new frontiers. In this context, an emerging and important methodology for the rapid exploration of composition-pressure-temperature-time space is the in situ method by synchrotron X-ray diffraction. This review introduces the latest advances of high-pressure devices that are adapted to X-ray diffraction in synchrotrons. It focuses particularly on the “large volume” presses (able to compress the volume above several mm3 to pressure higher than several GPa) designed for in situ exploration and that are suitable for discovering and scaling the stable or metastable compounds under “traditional” industrial pressure range (3–8 GPa). We illustrated the power of such methodology by (i) two classical examples of “reference” superhard high-pressure materials, diamond and cubic boron nitride c-BN; and (ii) recent successful in situ high-pressure syntheses of light-element compounds that allowed expanding the domain of possible application high-pressure materials toward solar optoelectronic and infra-red photonics. Finally, in the last section, we summarize some perspectives regarding the current challenges and future directions in which the field of in situ high-pressure synthesis in industrial pressure scale may have great breakthroughs in the next years.

36 MATERIALS SCIENCE↗

Experimental and Computational Insights into the Structural Dynamics of the Fc Fragment of IgG1 Subtype from Biosimilar VEGF‐Trap

The constant fragment (Fc) of the immunoglobulin G1 (IgG1) subtype is increasingly recognized as a crucial scaffold in the development of advanced therapeutics due to its enhanced specificity, efficacy, and extended half‐life. A prime example is VEGF‐Trap (Aflibercept), a recombinant fusion protein that merges the Fc region of the IgG1 subtype with the binding domains of vascular endothelial growth factor receptors (VEGFR)‐1 and VEGFR‐2. The Fc region's role in N‐glycosylation is particularly important, as it significantly influences protein stability. Herein, the first near‐physiological temperature structures of the N‐glycan‐bound Fc fragment of IgG1 subtype from a biosimilar VEGF‐Trap are presented, determined using the SPring‐8 Angstrom Compact free electron LAser (SACLA) and the Turkish Light Source (Turkish DeLight). Comparative analysis with cryogenic structures, including existing data, reveals alternate conformations within the glycan‐binding pocket. Furthermore, molecular dynamics simulations indicate the presence of a high degree of structural plasticity, explaining how the protein adapts its structure through conformational changes. The observed structural fluctuations/conformational changes demonstrate the effect of N‐glycans on protein stability. These findings offer new insights into the molecular basis of Fc‐mediated functions and provide valuable information for the design of next‐generation therapeutics.

60 APPLIED LIFE SCIENCES↗

MarK, a Novosphingobium aromaticivorans kinase required for catabolism of multiple aromatic monomers

The aromatic compounds used in a variety of industrial products are currently obtained from nonrenewable petroleum sources. Alternatively, the plant polymer lignin is an abundant renewable source of aromatics, and its depolymerization generates a variety of products that can include acetovanillone, a vanillin derivative containing an acetyl side chain. The Alphaproteobacterium Novosphingobium aromaticivorans DSM12444 can metabolize several chemically modified aromatics in deconstructed lignin, but not acetovanillone. In this work, adaptive laboratory evolution identified a single amino acid change in the previously uncharacterized gene product Saro_1862 that is necessary and sufficient for N. aromaticivorans growth with acetovanillone as a sole growth substrate, as well as other aromatic monomers not metabolized by wild-type cells. We show that a glutamate (E) to lysine (K) substitution at amino acid residue 16 of Saro_1862 results in a ~1600-fold increase in the rate of ATP-dependent acetovanillone phosphorylation. We also find that recombinant Saro_1862 E16K phosphorylates several other aromatic compounds in vitro , defining the first reported catalytic activity for the widespread UPF0261 protein domain contained in Saro_1862. Thus, we propose naming Saro_1862 MarK, for multiple aromatic kinase. A 1.57 Å crystal structure of MarK E16K predicts that the E16K substitution lies in a potential ATP binding site, suggesting how this amino acid change increased catalytic activity. A search for homologs of MarK and other proteins required for acetovanillone degradation predicts that this pathway for aromatic metabolism exists throughout the bacterial phylogeny.

Novosphingobium↗

Isoform-specific functions of synaptopodin-2 variants in cytoskeleton stabilization and autophagy regulation in muscle under mechanical stress

Highlights: • Muscle cells express different synaptopodin-2 isoforms with individual functions. • Reduced SYNPO2 expression results in enhanced vulnerability of myofibrils. • SYNPO2e recruites BAG3 to mechanically stressed myofibrillar areas. • SYNPO2 is an organizer and regulator of BAG3-containing proteostasis systems. • BAG3 forms functionally distinct protein complexes with different SYNPO2 isoforms. Protein homeostasis (proteostasis) in multicellular organisms depends on the maintenance of force-bearing and force-generating cellular structures. Within myofibrillar Z-discs of striated muscle, isoforms of synaptopodin-2 (SYNPO2/myopodin) act as adapter proteins that are engaged in proteostasis of the actin-crosslinking protein filamin C (FLNc) under mechanical stress. SYNPO2 directly binds F-actin, FLNc and α-actinin and thus contributes to the architectural features of the actin cytoskeleton. By its association with autophagy mediating proteins, i.e. BAG3 and VPS18, SYNPO2 is also engaged in protein quality control and helps to target mechanical unfolded and damaged FLNc for degradation. Here we show that deficiency of all SYNPO2-isoforms in myotubes leads to decreased myofibrillar stability and deregulated autophagy under mechanical stress. In addition, isoform-specific proteostasis functions were revealed. The PDZ-domain containing variant SYNPO2b and the shorter, PDZ-less isoform SYNPO2e both localize to Z-discs. Yet, SYNPO2e is less stably associated with the Z-disc than SYNPO2b, and is dynamically transferred into FLNc-containing myofibrillar lesions under mechanical stress. SYNPO2e also recruits BAG3 into these lesions via interaction with the WW domain of BAG3. Our data provide evidence for a role of myofibrillar lesions as a transient quality control compartment essential to prevent and repair contraction-induced myofibril damage in muscle and indicate an important coordinating activity for SYNPO2 therein.

60 APPLIED LIFE SCIENCES↗

Evaluating Resilience of Water Distribution Networks to Operational Failures from Cyber-Physical Attacks

Water cyber-physical systems (CPSs) have gained increasing interest to improve operational efficiency and reliability. However, due to growing exposure to cyber-physical attacks, cybersecurity and resilience against the attacks have become significant concerns. There have been efforts to improve cybersecurity in water CPSs, yet few attempts to investigate resilience against cyber-physical attacks. This study contributes to characterizing resilience of a water CPS and investigating potential resilience strategies. An advanced resilience measure integrating withstanding, absorptive, adaptive, and restorative capability of a system is proposed and applied to the C-town water distribution network (WDN) for 15 failure set scenarios with a pressure-driven hydraulic simulation. The results provide identification of failure sets and unfavorable operational conditions that make the system more vulnerable to the cyber-physical attacks and in turn produce low resilience and capabilities. It is also found that, after recovery of a disrupted component, adjustment of overall operational interactions across system components is needed for complete restoration of disrupted functionality. The findings provide insights on infrastructure investment with resilience strategies in cyber and physical water system domains.

Shin, Sangmin↗