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At least 37 records · Page 2

CRISPR-COPIES: an in silico platform for discovery of neutral integration sites for CRISPR/Cas-facilitated gene integration

Abstract The CRISPR/Cas system has emerged as a powerful tool for genome editing in metabolic engineering and human gene therapy. However, locating the optimal site on the chromosome to integrate heterologous genes using the CRISPR/Cas system remains an open question. Selecting a suitable site for gene integration involves considering multiple complex criteria, including factors related to CRISPR/Cas-mediated integration, genetic stability, and gene expression. Consequently, identifying such sites on specific or different chromosomal locations typically requires extensive characterization efforts. To address these challenges, we have developed CRISPR-COPIES, a COmputational Pipeline for the Identification of CRISPR/Cas-facilitated intEgration Sites. This tool leverages ScaNN, a state-of-the-art model on the embedding-based nearest neighbor search for fast and accurate off-target search, and can identify genome-wide intergenic sites for most bacterial and fungal genomes within minutes. As a proof of concept, we utilized CRISPR-COPIES to characterize neutral integration sites in three diverse species: Saccharomyces cerevisiae, Cupriavidus necator, and HEK293T cells. In addition, we developed a user-friendly web interface for CRISPR-COPIES (https://biofoundry.web.illinois.edu/copies/). We anticipate that CRISPR-COPIES will serve as a valuable tool for targeted DNA integration and aid in the characterization of synthetic biology toolkits, enable rapid strain construction to produce valuable biochemicals, and support human gene and cell therapy applications.

59 BASIC BIOLOGICAL SCIENCES↗

On Distribution Grid Optimal Power Flow Development and Integration

Due to changes in electric distribution grid operation, new operation regimes have been recommended. Distribution grid optimal power flow (DOPF) has received tremendous attention in the research community, yet it has not been fully adopted across the utility industry. Our paper recognizes this problem and suggests a development and integration procedure for DOPF. We propose development of DOPF as a three step procedure of 1) processing the grid, 2) obtaining a tractable solution, and 3) implementing multiple solution algorithms and benchmarking them to improve application reliability. For the integration of DOPF, we demonstrate how a DOPF federate may be developed that can be integrated in a co-simulation environment to mimic the real-world conditions and hence improve its practicality to be deployed in the field. To demonstrate the efficacy of the proposed methods, tests on IEEE 123 bus system are performed where the usage of tractable formulation in DOPF algorithm development and its comparison to the benchmark solution are demonstrated.

Hanif, Sarmad↗

Integrating 5G Technology for Improved Process Monitoring and Network Slicing in ICS

Industrial Control Systems (ICS) are crucial for monitoring physical processes that support essential cyber-enabled services like power generation. The use of proprietary communication and lack of effective intrusion detection mechanisms pose constraints for efficient operation. Therefore, there is a need to modernize these systems with decentralized technologies like Edge Computing and 5G. However, integrating 5G and Edge Computing into large-scale ICS networks presents implementation and performance challenges. To address these challenges, this paper proposes an integrated ICS architecture that combines 5G and Edge Computing technologies with traditional ICS protocols. The objective is to minimize implementation and operational difficulties while improving the monitoring of physical processes and enabling robust intrusion detection. The proposed architecture outlines the necessary components, services, and communication protocols required for the integration of 5G and Edge Computing.

Aguayo, Jared M.↗

Data for "Discovery, Characterization, and Application of Chromosomal Integration Sites in the Hyperthermophilic Archaeon Sulfolobus islandicus"

Sulfolobus islandicus , an emerging archaeal model organism, offers unique advantages for metabolic engineering and synthetic biology applications owing to its ability to thrive in extreme environments. Although several genetic tools have been established for this organism, the lack of well-characterized chromosomal integration sites has limited its potential as a cellular factory. Here, we systematically identified and characterized 13 artificial CRISPR RNAs targeting eight integration sites in S. islandicus using the CRISPR-COPIES pipeline and a multi-omics-informed computational workflow. We leveraged the endogenous CRISPR-Cas system to integrate the reporter gene lacS and validated heterologous expression through a β-galactosidase assay, revealing significant positional effects. As a proof of concept, we utilized these sites to genetically manipulate lipid ether composition by overexpressing glycerol dibiphytanyl glycerol tetraether (GDGT) ring synthase B (GrsB). This study expands the genetic toolbox for S. islandicus and advances its potential as a robust platform for archaeal synthetic biology and industrial biotechnology.

AI/ML↗

High-density integrated delay line using extreme skin-depth subwavelength grating waveguides

Optical delay lines control the flow of light in time, introducing phase and group delays for engineering interferences and ultrashort pulses. Photonic integration of such optical delay lines is essential for chip-scale lightwave signal processing and pulse control. However, typical photonic delay lines based on long spiral waveguides require extensively large chip footprints, ranging from mm 2 to cm 2 scales. Here we present a scalable, high-density integrated delay line using a skin-depth engineered subwavelength grating waveguide, i.e., an extreme skin-depth (eskid) waveguide. The eskid waveguide suppresses the crosstalk between closely spaced waveguides, significantly saving the chip footprint area. Our eskid-based photonic delay line is easily scalable by increasing the number of turns and should improve the photonic chip integration density.

Ahmed, Ishtiaque↗

Energy Systems Integration Facility (ESIF): World-Class Systems Integration Capabilities and Research

The Energy Systems Integration Facility (ESIF), located at the National Renewable Energy Laboratory (NREL) South Table Mountain campus, is a world-renowned user facility for research and development of modern, advanced, and clean energy technologies. ESIF is distinguished by its continuously evolving, highly integrated systems that span throughout the building, connecting research capabilities across multiple laboratories and test areas. The primary ESIF research systems include: [1] data, cyber, and control networks, [2] research electrical distribution buses (REDB), [3] thermal integration infrastructure, and [4] hydrogen systems. The data, cyber, and control networks provide monitoring, control, communication, automation, visualization, and time series data storage and tagging capabilities for research projects and ESIF systems, including facility safety functions. The REDB system consists of four dedicated AC and DC electrical power networks that can connect devices located across the facility through versatile, automatic circuit configuration to support complex power electronics experiments up to the megawatt-scale. The thermal integration infrastructure consists of three temperature-conditioned water loops that provide heating and cooling interfaces and capabilities for thermal energy research. The hydrogen systems provide megawatt-scale hydrogen production, drying, compression, high-pressure storage, and delivery to laboratory end uses, including hydrogen fuel cell vehicle fueling. The ESIF research systems interconnect and extend throughout the various lab areas of the facility to create elaborate networks composed of diverse technologies for cutting-edge research. The ESIF capabilities are operated and stewarded by the ESIF Research Operations group, who also actively upgrade and advance the systems to ensure they remain ahead of anticipated research - enabling the success of many pioneering energy integration projects. The poster, created by members of the ESIF Research Operations team, highlights and summarizes the four core integrated systems at ESIF. The poster was first presented at the internal NREL Energize Forum on May 13th, 2024, and received the "Best Poster" award.

capabilities↗

Integrated Thermal Energy Storage and Brayton Cycle Equipment Demonstration (Integrated TESTBED) Project Design Basis

The Integrated Thermal Energy Storage and Brayton cycle Equipment Demonstration (Integrated TESTBED) project seeks to retire commercial-scale risks associated with the design, integration,and operation of a supercritical carbon dioxide (sCO2) power cycle and concentrating solar power (CSP) thermal energy storage (TES) system. This requires an understanding of commercial-scale collector system transient impacts on the TES system, the dynamics of heat exchange from theTES to the power cycle, and the control and operation of the power cycle to accommodate various dispatch strategies. In order to retire these risks, Heliogen has proposed to construct a 5 MWe CSP demonstration facility based on directly heated particle and sCO2 technology. The receivers, primary heat exchanger, and power cycle will be deployed at a full commercial scale based on Heliogen’s modular plant architecture to ensure actual system integration risks are validated during design, construction, and operation. This work summarizes the design basis for the Integrated TESTBED project demonstration facility including a design target for capacity factor to support test operations, hours of storage, particle silo arrangement, centrifugal article receivers, a diffusion bonded particle-sCO2 heat exchanger, and a 5 MWe (net) integrally geared sCO2 recompression Brayton cycle.

14 SOLAR ENERGY↗

Path-Integrated X-Ray Images for Multi-Surface Digital Image Correlation (PI-DIC)

X-ray imaging offers unique possibilities for Digital Image Correlation (DIC), opening the door for full-field deformation measurements of a test article in complex environments where optical DIC suffers severe biases or is impossible. While X-ray DIC has been performed in the past with standard DIC codes designed for optical images, the path-integrated nature of X-ray images places constraints on the experimental setup, predominantly that only a single surface of interest moves/deforms. These requirements are difficult to realize for many practical situations and limit the amount of information that can be garnered in a single test. Other X-ray based diagnostics such as Digital Volume Correlation (DVC) and Projection DVC (P-DVC) overcome these obstacles, but DVC is limited to quasi-static tests, and both DVC and P-DVC necessitate high-resolution computed tomography (CT) scan(s) and often require a potentially invasive pattern throughout the volume of the specimen. Here this work presents a novel approach to measure time-resolved displacements and strains on multiple surfaces from a single series of 2D, path-integrated (PI) X-ray images, called PI-DIC. The principle of optical flow or conservation of intensity—the foundation of DIC—was reframed for path-integrated images, for an exemplar setup comprised of two plates moving and deforming independently. Synthetic images were generated for rigid translations, rigid rotations, and uniform stretches, where each plate underwent a unique motion/deformation. Experimental specimens were fabricated (either an aluminum plate with tantalum features or a plastic plate with steel features) and the two specimens were independently translated. PI-DIC was successfully demonstrated with the synthetic images and validated with the experimental images. Prescribed displacements were recovered for each plate from the single set of path-integrated, deformed images. Errors were approximately 0.02 px for the synthetic images with 1.5% image noise, and 0.05 px for the experimental images. These results provide the foundation for PI-DIC to measure motion and deformation of multiple, independent surfaces with subpixel accuracy from a single series of path-integrated X-ray images.

47 OTHER INSTRUMENTATION↗

Engineering integration in elementary science classrooms: Effects of disciplinary language scaffolds on English learners' content learning and engineering identity

Abstract Background Limited research examines the effects of integrated science and engineering (SE) instruction emphasizing disciplinary literacy and language activities on engineering identity and content understanding. Far fewer studies target English learners (ELs). Purpose The impact of an SE intervention on the development of science, engineering, and technology knowledge as well as engineering identity was examined. To address ELs' learning needs, the curricular design was built on a validated SE model by integrating (1) developmental, (2) language scaffolds, and (3) culturally based accommodations. Design/Method Separate analysis of variance examined the effects of the intervention on science, engineering, and technology knowledge as well as engineering identity. The relationship among engineering identity and content outcomes was also examined. ELs from kindergarten to second grade classrooms were randomly assigned to the integrated SE group or control group. Results Integrated SE instruction significantly increased ELs' science, engineering, and technology knowledge as well as a substantially developed engineering identity. Overall, ELs' engineering identity is associated with an increase in science, engineering, and technology content knowledge. However, second grade girls' identity development was not associated with learning measures. These correlations suggest the context of the engineering activity may have reinforced gendered stereotypes and reduced the effects for girls' engineering attitudes. Conclusions Integrated SE instruction emphasizing disciplinary literacy and cultural accommodations increases early elementary ELs' learning and engineering identity. Future studies should examine the unique effects of language scaffolds and cultural modifications on student learning and the impact of gender stereotypes on girls' engineering attitudes.

Aguirre‐Muñoz, Zenaida↗

Efficiently evaluating loop integrals in the EFTofLSS using QFT integrals with massive propagators

We develop a new way to analytically calculate loop integrals in the Effective Field Theory of Large Scale-Structure. Previous available methods show severe limitations beyond the one-loop power spectrum due to analytical challenges and computational and memory costs. Our new method is based on fitting the linear power spectrum with cosmology-independent functions that resemble integer powers of quantum field theory massive propagators with complex masses. A remarkably small number of them is sufficient to reach enough accuracy. Similarly to former approaches, the cosmology dependence is encoded in the coordinate vector of the expansion of the linear power spectrum in our basis. We first produce cosmology-independent tensors where each entry is the loop integral evaluated on a given combination of basis vectors. For each cosmology, the evaluation of a loop integral amounts to contracting this tensor with the coordinate vector of the linear power spectrum. The 3-dimensional loop integrals for our basis functions can be evaluated using techniques familiar to particle physics, such as recursion relations and Feynman parametrization. We apply our formalism to evaluate the one-loop bispectrum of galaxies in redshift space. The final analytical expressions are quite simple and can be evaluated with little computational and memory cost. We show that the same expressions resolve the integration of all one-loop N-point function in the EFTofLSS. This method, which is originally presented here, has already been applied in the first one-loop bispectrum analysis of the BOSS data to constraint ΛCDM parameters and primordial non-Gaussianities [1, 2].

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

An integrated integral projection model ( IPM 2 ) to disentangle size‐structured harvest and natural mortality

Abstract Body size is one of the most important traits governing individual‐level demographic rates and modulating population‐level processes. Multiple size‐dependent demographic rates can simultaneously change population structure, so distinguishing their individual contributions to overall population dynamics remains a challenge. Disentangling size‐dependent harvest rates from other demographic rates is critical for assessing the impact of removal on populations of invasive species. Inference about invasive populations can be difficult, however, as observations are often collected opportunistically as part of removal programs, rather than experimentally designed. Yet accurate inference is essential for understanding the feasibility of population suppression and optimising management decisions. We develop an integrated integral projection model (IPM 2 ) that leverages the strengths of the integrated population model and integral projection model to enable inference about complex, size‐structured demographic rates from imperfect observations. We apply the IPM 2 in the context of invasive European green crab ( Carcinus maenas ), a species for which individual body size strongly regulates both the observation‐generating process and latent, population dynamics. The IPM 2 facilitates the distinct estimation of green crab size‐structured harvest and natural mortality rates, parameters for which no explicit data is collected and that are unidentifiable in component datasets of the integrated population model. The model represents how the green crab population changes over time, providing the first estimates of size‐structured abundance of this high‐priority species. By forecasting the stable size distribution and equilibrium population size under varying removal efforts, we demonstrate that extremely high levels of removal effort can reduce the equilibrium green crab population size. Yet these high mortality rates also shift the stable size distribution and increase the equilibrium abundance of smaller crabs, since size‐selective removal alters intraspecific interactions. The ecological outcome of this shift in size structure will be variable, as green crab size modulates only some of its interactions with other species. These results highlight the value of the IPM 2 framework for inferring complex population dynamics with information needs that outpace information in individual observational datasets, providing a path forward for accurate assessment of conservation programs.

Keller, Abigail G. [Department of Environment Scie↗

Overview of System Integration Analysis Activities for Integrated Waste Management

Spent nuclear fuel (SNF) generated by the current fleet of commercial nuclear reactors is being stored at the reactor sites in spent fuel pools (SFPs) and in dry independent spent fuel storage installations (ISFSIs). The US Department of Energy Office of Nuclear Energy (DOE-NE) is developing an Integrated Waste Management Program (IWMP) comprising a suite of options and supporting analyses to enable future informed choices. The IWMP is organized into the following five major areas: 1) Consent-Based Siting, 2) IWM Facilities and Equipment Concepts and Development, 3) Transportation Capability Analysis and Support, 4) Information Technology Solutions and Support, and 5) System Integration Analysis and Support. This paper discusses the activities ongoing in the IWMP System Integration Analysis and Support area. Two main areas of research in system integration are data and tools development, as well as system analysis assessments. One of the tools being developed in the system integration area is the Used Nuclear Fuel-Storage, Transportation & Disposal Analysis Resource and Data System (UNF-ST&DARDS) tool. It is being developed as a foundational resource for DOE-NE to manage SNF data, along with several compatible analysis tools for time-dependent characterization of SNF and related systems. UNF-ST&DARDS has the unparalleled ability to track SNF through the entire back end of the fuel cycle—from the time the fuel is discharged from a reactor through its disposal in a geological repository. UNF ST&DARDS interfaces with the SCALE code system for nuclear analysis and COBRA-SFS for thermal analysis. Another main tool being developed is the Next Generation System Analysis Model (NGSAM). NGSAM is an agent-based simulation software tool expressly designed to be capable of modeling the waste management system. NGSAM has been developed to enable informed decision-making by providing the capability of analyzing various potential system options for the management of SNF and HLW. Using NGSAM, system architecture analyses are being conducted to support the future deployment of a comprehensive nuclear waste management system that considers all major back-end aspects of the nuclear fuel cycle (i.e., transportation, storage, and disposal). System analysis assessments may investigate the implications of various strategies such as different acceptance rates, acceptance queues, facility capacities and options, standardized canisters, and different assumed system operation start dates. Recently, some system analysis effort has begun to look at how the waste management system might operate for advanced reactor fuel cycles.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Experimental Covariance Determination for Critical Integral Experiments

Integral benchmarks for criticality safety and nuclear data validation require expensive uncertainty quantification studies. In general, uncertainty quantification techniques ignore correlations between experiments and shared parts. Experiments, such as the TEX (Thermal/Epithermal eXperiments) campaigns, consist of many shared parts, such as the ‘Jemima’ HEU fuel plates, which create a strong correlation in their uncertainties. While these correlations are known to exist, they are often not estimated due to the complexity of such calculations. This paper describes an intuitive method of determining the covariance for each of the experimental components, providing a correlation for each family of parts across the multiple cases examined within a benchmark. A proof-of-principle study using the TEX-HEU experimental campaign was performed and verified that the correlations can be calculated with information commonly found in the ICSBEP (International Criticality Safety Benchmark Evaluation Project) benchmarks. This study showed that the introduction of model and experimental covariances reduces the χ 2 per degree of freedom from 2.203 to 1.179, indicating that the omission causes overly pessimistic bias quantifications. This technique can be seamlessly integrated to current benchmark evaluations as well as reevaluations of legacy benchmarks.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Engineering-Scale Integrated Energy System Data Projection Demonstration via the Dynamic Energy Transport and Integration Laboratory

The objective of this study is to demonstrate and validate the Dynamic Energy Transport and Integration Laboratory (DETAIL) preliminary scaling analysis using Modelica language system-code Dymola. The DETAIL preliminary scaling analysis includes a multisystem integral scaling package between thermal-storage and hydrogen-electrolysis systems. To construct the system of scaled equations, dynamical system scaling (DSS) was applied to all governing laws and closure relations associated with the selected integral system. The existing Dymola thermal-energy distribution system (TEDS) facility and high-temperature steam electrolysis (HTSE) facility models in the Idaho National Laboratory HYBRID repository were used to simulate a test case and a corresponding scaled case for integrated system HYBRID demonstration and validation. The DSS projected data based on the test-case simulations and determined scaling ratios were generated and compared with scaled case simulations. The preliminary scaling analysis performance was evaluated, and scaling distortions were investigated based on data magnitude, sequence, and similarity. The results indicated a necessity to change the normalization method for thermal storage generating optimal operating conditions of 261 kW power and mass flow rate of 6.42 kg/s and the possibility of reselecting governing laws for hydrogen electrolysis to improve scaling predictive properties. To enhance system-scaling similarity for TEDS and HTSE, the requirement for scaling validation via physical-facility demonstration was identified.

08 HYDROGEN↗

An Integrated Traction Drive with a High Speed Surface Permanent Magnet External Rotor Motor for Electric Vehicles

This work presents the detailed design of an outer rotor motor and integrated drive for passenger electric vehicles. The motor uses non-heavy rare earth permanent magnets and operates at a top speed of 20,000rpm. In-slot ceramic heat exchangers are utilized for the cooling of the windings. The external rotor configuration of the motor leaves a significant amount of space in the stator bore, which is leveraged for the integration of the power electronics. A high speed external rotor motor creates a number of mechanical, thermal and assembly challenges and this work presents detailed thermal, mechanical and rotordynamics analysis.

ADVANCED PROPULSION SYSTEMS↗

A Blockchain Based Co-Simulation Framework for Integrating DERs to Wholesale Electricity Markets

As the number of distributed energy resources (DERs) continue to increase across energy-delivery systems, there remains a need for integrating their capabilities into traditional grid operations. In this paper, a blockchain-based solution is proposed to facilitate FERC's Order No. 2222 implementations. The presented use-case enables small-scale DERs to participate in wholesale market operations through DER aggregators, while also enabling local distribution system operators to enforce distribution system constraints in a secure and traceable manner. The presented use case is built around the Unified Testing Platform (UTP) being developed as a part of the Blockchain for Optimized Security and Energy Management (BLOSEM) project. This is a multi-lab effort intended to simplify the deployment of blockchain-powered grid solutions by enabling the integration of simulation tools, and blockchain technologies through the use of system-agnostic interfaces that provide a modular, interoperable, and reusable connectivity layer.

blockchain interoperability↗

Evaluating Probability of Containment Effectiveness at a GCS Sites using integrated assessment modeling approach with Bayesian decision Networks

Improved scientific and engineering understanding of the behavior of geologic CO2 storage together with established regulatory framework and incentive structures raise the prospects for accelerated, large-scale deployment of this greenhouse gas emissions reduction approach. Incentive structures call for the establishment of appropriate verification and accounting approaches to support claims of the integrity of a geologic storage complex and to justify taking credit for long-term storage. In this study, we present a framework for assessing the probability of containment effectiveness over the lifetime of a geologic carbon storage site (e.g., after 70 years of injection and post-injection site performance) using forward stochastic model realizations based on site characterization data and using a monitoring-informed Bayesian network based on hypothetical detectability from surface seismic surveys over the site injection and post-injection phases. The National Risk Assessment Partnership’s open-source Integrated Assessment Model (NRAP-Open-IAM) was utilized to develop an ensemble of 10,000 a priori stochastic forecasts of CO2 containment. Those simulations were used to train the Bayesian network model to estimate the prior probabilities of the CO2 leakage mass into overlying, monitorable aquifers considering the uncertainties in the reservoir properties, permeability of potentially leaky wells and the overlying aquifers. The conditional probabilities in the Bayesian network were either learned from the NRAP-Open-IAM simulations or derived from the predefined detection thresholds for the monitoring method. Observations obtained from monitoring, over time during the site operation phases were then used to generate updated posterior probabilities of containment (and any loss from containment) in the Bayesian network by propagating the prior probabilities through the conditional probabilities. We demonstrate how to construct and use the Bayesian network for verifying the long-term storage complex effectiveness informed by monitoring based on the NRAP-Open-IAM simulations previously developed for the FutureGen 2.0 site. This approach may have relevance for stake holders to demonstrate secure geologic storage, provide a defensible, probabilistic approach to claim credit for geologic storage, and to estimate the likelihood that any fraction of the claimed credit may need to be refunded to the creditor based on available monitoring information.

Bayesian network, Risk assessment, Monitoring, car↗

Mocking the u-plane integral

Abstract The u -plane integral is the contribution of the Coulomb branch to correlation functions of $${\mathcal {N}}=2$$ N = 2 gauge theory on a compact four-manifold. We consider the u -plane integral for correlators of point and surface observables of topologically twisted theories with gauge group $$\mathrm{SU}(2)$$ SU ( 2 ) , for an arbitrary four-manifold with $$(b_1,b_2^+)=(0,1)$$ ( b 1 , b 2 + ) = ( 0 , 1 ) . The u -plane contribution equals the full correlator in the absence of Seiberg–Witten contributions at strong coupling, and coincides with the mathematically defined Donaldson invariants in such cases. We demonstrate that the u -plane correlators are efficiently determined using mock modular forms for point observables, and Appell–Lerch sums for surface observables. We use these results to discuss the asymptotic behavior of correlators as function of the number of observables. Our findings suggest that the vev of exponentiated point and surface observables is an entire function of the fugacities.

Mathematics↗