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At least 145 records · Page 8

COMPILE: a GWAS computational pipeline for gene discovery in complex genomes

Abstract Background Genome-Wide Association Studies (GWAS) are used to identify genes and alleles that contribute to quantitative traits in large and genetically diverse populations. However, traits with complex genetic architectures create an enormous computational load for discovery of candidate genes with acceptable statistical certainty. We developed a streamlined computational pipeline for GWAS (COMPILE) to accelerate identification and annotation of candidate maize genes associated with a quantitative trait, and then matches maize genes to their closest rice and Arabidopsis homologs by sequence similarity. Results COMPILE executed GWAS using a Mixed Linear Model that incorporated, without compression, recent advancements in population structure control, then linked significant Quantitative Trait Loci (QTL) to candidate genes and RNA regulatory elements contained in any genome. COMPILE was validated using published data to identify QTL associated with the traits of α-tocopherol biosynthesis and flowering time, and identified published candidate genes as well as additional genes and non-coding RNAs. We then applied COMPILE to 274 genotypes of the maize Goodman Association Panel to identify candidate loci contributing to resistance of maize stems to penetration by larvae of the European Corn Borer ( Ostrinia nubilalis ). Candidate genes included those that encode a gene of unknown function, WRKY and MYB-like transcriptional factors, receptor-kinase signaling, riboflavin synthesis, nucleotide-sugar interconversion, and prolyl hydroxylation. Expression of the gene of unknown function has been associated with pathogen stress in maize and in rice homologs closest in sequence identity. Conclusions The relative speed of data analysis using COMPILE allowed comparison of population size and compression. Limitations in population size and diversity are major constraints for a trait and are not overcome by increasing marker density. COMPILE is customizable and is readily adaptable for application to species with robust genomic and proteome databases.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A Conceptual Framework to Describe Energy Efficiency and Demand Response Interactions

Energy efficiency (EE) and demand response (DR) resources provide important utility systems and ratepayer benefits. At the same time, the rapid change in the amount and type of variable renewable energy, like solar and wind, is reshaping the role and economic value of EE and DR, and will likely affect the time-dependent valuation of EE and DR measures. Utilities are increasingly interested in integrating EE and DR measures as a strategic approach to improve their collective cost-effectiveness and performance. We develop a framework to identify the EE and DR attributes, system conditions, and technological factors that are likely to drive interactions between EE and DR. We apply the framework to example measures with different technology specifics in the context of different utility system conditions. We find that EE and DR interactions are likely driven by changes in discretionary load, the addition of controls or other capabilities to shift loads, and the coincidence of savings with system peak or load building periods. Our analysis suggests increasing complexity in evaluating EE and DR interactions when moving from standalone equipment to integrated systems. The framework can be applied to research on integrated building systems by grouping measures into portfolios with different likely implications for EE and DR interactions.

Satchwell, Andrew J. (ORCID:0000000244053599)↗

Propagation of Cryogenic Thermal Fractures from Unconfined PMMA Boreholes

In cryogenic fracturing, a rock surface exposed to cryogenic fluids undergoes a large thermal gradient, and the resultant local tensile stress overcomes rock strength and initiates fractures. This study investigates the development of cracks generated from the cryogenic treatment of a borehole under no external confining stress on specimens. The experiments were performed on transparent PMMA specimens to observe fracture proliferation around boreholes. Liquid nitrogen was flowed through the boreholes to cool the borehole surface. The results show that initial fracture growth is characterized by abrupt starts and stops, and as the fracture propagates outward, the growth appears more continuous. In an early stage, horizontal/radial fractures and vertical fractures are the defining patterns. Horizontal fractures tend to be separated by a specific exclusion distance (i.e., spacing between cracks). While distinct horizontal/vertical fractures and exclusion distance manifest themselves at an early stage, fractures resulting from fracture interactions and curvatures can develop into complex shapes at later stages. Cryogenic thermal loading induces distinctively curved fractures. The tendency of curvature may prevent greater penetration. An increase in the borehole pressure during liquid nitrogen flow, however, can lessen fracture tortuosity and facilitate radial propagation. A high flow pressure and rate are also advantageous in that they accelerate cooling and fracture propagation.

42 ENGINEERING↗

Applying Quantum Computing to Simulate Power System Dynamics

Power system dynamics are generally modeled by high dimensional nonlinear differential-algebraic equations due to a large number of generators, loads, and transmission lines. Thus, its computational complexity grows exponentially with the system size. This paper demonstrates the potential use of quantum computing algorithms to model the power system dynamics. Leveraging a symbolic programming framework, we equivalently convert the power system dynamics’ differential algebraic equations (DAEs) into ordinary differential equations (ODEs), where the data of the state vector can be encoded into quantum computers via amplitude encoding. The system's nonlinearity is captured by Taylor polynomial expansion, the quantum state tensor, and Hamiltonian simulation, whereas state variables can be updated by a quantum linear equation solver. Our results show that quantum computing can simulate the dynamics of the power system with high accuracy, whereas its complexity is polynomial in the logarithm of the system dimension. Our work also illustrates the use of scientific machine learning tools for implementing scientific computing concepts, e.g., Taylor expansion, DAEs/ODEs transform, and quantum computing solver, in the field of power engineering.

Tran, Huynh↗

From Resilient and Ready to Used and Useful: Managing Temporal and Locational Uncertainty in Electrification, DER Adoption, and Climate Adaptation

Grid planning decisions involve weighing risks against benefits. The best decisions will facilitate development of electrical infrastructure that minimizes risk and maximizes benefits. With the rapidly evolving energy landscape, today's planner must discern new loads and demand cycles; embrace the operational complexity of climate risk; revise settled standards; and anticipate and manage the system impacts of distributed energy resource (DER) adoption. Only by managing the combined uncertainty of these dynamic processes can a planner hope to make effective decisions. Our analysis focuses on the management of temporal and locational uncertainty, and particularly on the risks presented to customers by the mismanagement of the factors that are the sources of these uncertainties.

climate↗

Coupled Aerodynamic and Hydrodynamic Hybrid Simulation of Floating Offshore Wind Turbines

The development and innovation of floating offshore wind energy in the U.S. requires detailed high-fidelity observations and measurements of turbine and platform loading due to wind, waves, and currents. However, full-scale and quasi-full-scale experiments require significant financial and temporal investments for construction, experimental testing, and long-term field campaigns. To support the commercial advancement of the offshore wind energy industry, specialized wind tunnel and wave basin experimental facilities are critical to be able to test FOWT designs at small scale under controlled conditions prior to full-scale deployment. Oregon State University (OSU) is internationally known as a leader in water and energy research, development, and testing. The O.H. Hinsdale Wave Research Laboratory (HWRL) and the Wallace Energy Systems and Renewables Facility (WESRF) at OSU have extensive experience building, modeling, monitoring, controlling, and actuating scaled systems. Experiments on wave-structure interaction have been performed at the HWRL since its establishment in 1972. Studies have included the interaction of waves with coastal structures (breakwaters, seawalls, buildings, cylinders, bridges, fixed foundations of offshore wind turbines, etc.) and with floating structures (e.g., wave energy converters, maneuvering of vessels, etc.). Hinsdale is actively used by marine energy technology developers, both for private testing and OSU-collaborative research projects. However, despite the availability of several large-scale facilities for hydrodynamic testing (at OSU and elsewhere in the U.S.), existing experimental laboratories are generally limited in their ability to accurately generate combined wind and wave conditions. The simulation of both wind and waves in experimental testing is complicated due to a number of constraints, including: [i] incompatible similitude laws governing the wind and waves for scaled experiments, [ii] producing accurate wind over a large enough control volume via fans, and [iii] generating wind that reasonably represents the atmospheric boundary layer in existing wave basins/flumes. Hence, physical test data providing insight into the simultaneous wave- and wind-structure response of floating offshore wind components can be difficult to generate. Given the aforementioned challenges in classic hydrodynamic experiments, the motivation of this project is to establish a real-time hybrid simulation (RTHS) approach that can apply aero- and hydro-dynamic loading by augmenting wave-only experimental facilities with virtual aerodynamic forces through numerical models representing the remaining dynamic forces. RTHS is a physical-numerical approach that partitions a prototype system into physical and numerical sub-assemblies that interact with each other through actuators and sensors in real time. In coupling physical and numerical models, the hybrid simulation approach applied herein is ideal for problems with: (1) structures subjected to different scaling laws, such as floating offshore wind turbines subjected to combined aero/hydro-dynamic loading, (2) structures that are too large or complex to be tested entirely in a laboratory setting, such as deep-water mooring applications, and (3) component testing, where the behavior of a portion of the assembly is uncertain but still interacts with other portions of the structure, such as testing the fatigue life of turbine blades. Few U.S. experimental facilities are able to test simultaneous aero- and hydro-dynamic loading and none can accurately produce aero/hydro-dynamic response on scaled FOWT models due to conflicting similitude laws between the wind (commonly Reynolds) and the waves (commonly Froude). To aid in accelerating the development of the U.S. floating offshore industry, there is a significant need to develop a flexible, modular framework that can expand the capacities of existing wave-only laboratories. The project goal is to demonstrate a hydrodynamic real-time hybrid simulation (hydro-RTHS) framework that couples numerical wind and physical waves acting on a FOWT, thus representing simultaneous aero/hydro-dynamic loading. The FOWT is partitioned into a full-scale numerical sub-assembly associated with the aerodynamics and a model-scale physical sub-assembly associated with the hydrodynamics. The numerical-physical partition associated with hydro-RTHS mitigates scaling constraints by supplying different scaling laws to the physical and numerical sub-assemblies. Herein, length, force, and time are scaled and exchanged between the sub-assemblies using Froude scaling to represent the open-channel flow in the physical sub-assembly. Other similitude laws could also be utilized depending on the problem definition. It is envisioned that the ability to model FOWTs under waves and wind, with mitigation of similitude distortions, would result in reduced development costs (currently, FOWT concept development is performed with full-size pro- totypes at enormous expense and risk) and increase the reliability of the FOWT industry (since extreme wave and wind conditions and contingency events can be tested safely in a controlled environment).

16 TIDAL AND WAVE POWER↗

Structural mechanism of helicase loading onto replication origin DNA by ORC-Cdc6

Significance The loading of the core Mcm2-7 helicase onto origin DNA is essential for the formation of replication forks and genomic stability. Here, we report two cryo-electron microscopy (cryo-EM) structures that capture helicase loader–helicase complexes just prior to DNA insertion. These pre-loading structures, combined with a computational simulation of the dynamic transition from the pre-loading state to the loaded state, provide crucial insights into the mechanism required for topologically linking the helicase to DNA. The helicase loading system is highly conserved from yeast to human, which means that the molecular principles described here for the yeast system are likely applicable to the human system.

59 BASIC BIOLOGICAL SCIENCES↗

Managing Increased Electric Vehicle Shares on Bulk Power Systems

The convergence of transportation electrification, other load growth, and the integration of many power sector technologies presents a complex planning problem requiring realistic, region-specific modeling and analysis to ensure the power system can support new loads quickly and affordably.

33 ADVANCED PROPULSION SYSTEMS↗

Tailored Fiber Placement for Complex Preforms

Tailored Fiber Placement (TFP) offers a novel approach to optimize fiber architecture for the fabrication of complex, structural parts not traditionally suitable for advanced composites. This technology not only offers new routes for weight reduction via metal substitution, it also offers cost reduction through minimization of material scrap and reduced labor. This reduction in component weight leads to increased fuel efficiency, and reduced production energy consumption, thereby, helping to achieve the stated IACMI technical goals. This technology leverages centuries of manufacturing development in support of the textile and embroidery industry. One major drawback to this technology is the lack of commercial or non- proprietary structural performance data and robust analytical tools used to optimize fiber architecture and predict performance. This project was structured to utilize common sub-element features to validate analytical performance tools, generate performance data, and gather cost and performance data on components of interest. This project was designed to give industry sponsors the confidence and ability to take full advantage of TFP to fabricate primary, highly loaded structure and integrate features such as metallic fasteners. The project focused principally on the use of high strength carbon fiber, such as T700, and the use of aerospace epoxy resin matrix to primarily support development of new composite applications in vehicle, aerospace, and industrial markets. This project applied previously developed analytical tools to predict the performance of TFP produced parts. This work focused on developing the pipeline to characterize material in order to accurately predict component performance when modifying the TFP print paths and stitch density. This focused on experimental characterization via standardized ASTM testing, alongside experimental testing of more representative service components by testing curved beam strength, beam shear performance, a large scale TFP lug, and ultimately designing a fully TFP clip bracket that reduced weight and cost compared to a traditional metallic component. The new knowledge gained from this program included: 1) development and demonstration of novel analytical tools applied to analysis of TFP preforms; 2) development and demonstration of a building block approach using coupons and sub-elements to optimize the design of a more complex component; 3) demonstration that optimized fiber orientation using TFP can exceed performance of conventional textile composite materials and can open new applications currently limited to metallic components; 4) Demonstration of performance and cost benefits of the TFP process as compared to metallic and conventional textile composites. Recommendations for follow-on work include development of design allowables to assess the impact of high temperature/moisture exposure or saturation during loading, tracking the impact of stitching needle wear on the performance of parts and ability to stitch thicker preforms, using TFP preforms as local reinforcement at areas of bearing or complex loading, and topology optimization of components by tow steering. The expertise developed during the course of this project can be leveraged to provide commercial engineering design and fabrication services using TFP. UDRI is in the process of formalizing their partnership with Spintech, who will serve as the commercialization partner for this technology and provide molding services and deliver finished components to the end user. UDRI will continue to produce the preforms until the economics allow Spintech to procure its own TFP equipment or lease UDRI equipment, at which point UDRI will step away from manufacture and serve as the engineering and design lead on product development.

36 MATERIALS SCIENCE↗

Dual-Bed Radioiodine Capture from Complex Gas Streams with Zeolites: Regeneration and Reuse of Primary Sorbent Beds for Sustainable Waste Management

Dual-sorbent systems are proposed for radioiodine management with a regenerated primary bed for multiple cycles of use in complex conditions and a secondary bed for disposal with higher waste loadings. Sorbent approaches for the effective capture of gaseous radioiodine (isotopes 129 I and 131 I) produced from a range of nuclear processes have been studied for over half a century. (1−5) Whether or not a sorbent (e.g., molecular sieve) is required to physically screen/trap or chemically bind a radionuclide of interest through chemisorption, the complexity of the gas stream has a large impact on the performance (e.g., loading capacity, selectivity) and active life of a sorbent bed. (3) Silver mordenite (AgZ), the U.S. Department of Energy baseline sorbent for radioiodine capture from nuclear processes, performs well within acidic conditions and at elevated temperatures (6) and can be consolidated into a chemically durable waste form for long-term disposal. (7,8) However, new sorbents are being sought because optimal capture performance of AgZ significantly decreases in dynamic oxidizing environments with competing species, and it is expensive and it contains Ag (a toxic metal). (9) Until a new sorbent is found to replace AgZ, the regeneration and reuse of AgZ is an attractive alternative to a single-use primary sorbent bed. In this regard, a primary sorbent could be designed for enhanced capture in complex gas streams and the ability to be regenerated for reuse. Here, a secondary sorbent could then be tailored for maximum iodine loading in the gas stream and chemical durability within a disposal facility.

chemisorption↗

On the Feasibility of Market Manipulation and Energy Storage Arbitrage via Load-Altering Attacks

Around the globe, electric power networks are transforming into complex cyber–physical energy systems (CPES) due to the accelerating integration of both information and communication technologies (ICT) and distributed energy resources. While this integration improves power grid operations, the growing number of Internet-of-Things (IoT) controllers and high-wattage appliances being connected to the electric grid is creating new attack vectors, largely inherited from the IoT ecosystem, that could lead to disruptions and potentially energy market manipulation via coordinated load-altering attacks (LAAs). In this article, we explore the feasibility and effects of a realistic LAA targeted at IoT high-wattage loads connected at the distribution system level, designed to manipulate local energy markets and perform energy storage (ES) arbitrage. Realistic integrated transmission and distribution (T&D) systems are used to demonstrate the effects that LAAs have on locational marginal prices at the transmission level and in distribution systems adjacent to the targeted network.

25 ENERGY STORAGE↗

High-Fidelity Large-Signal Order Reduction Approach for Composite Load Model

With the increasing penetration of electronic loads and distributed energy resources, conventional load models cannot capture their dynamics. Therefore, a new comprehensive composite load model is developed by Western Electricity Coordinating Council (WECC). However, this model is a complex high-order non-linear system with multi-time-scale property, which poses challenges on power system studies with heavy computational burden. In order to reduce the model complexity, the authors firstly develop a large-signal order reduction (LSOR) method using singular perturbation theory. In this method, the fast dynamics are integrated into the slow ones to preserve transient characteristics of the former. Then, accuracy assessment conditions are proposed and embedded into the LSOR to improve and guarantee the accuracy of reduced-order model. Finally, the reduced-order WECC composite load model is derived by using the proposed algorithm. Overall, simulation results show that the reduced-order large-signal model significantly alleviates the computational burden while maintaining similar dynamic responses as the original composite load model.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Cryo-EM structure of AAV2 Rep68 bound to integration site AAVS1: insights into the mechanism of DNA melting

Abstract The Rep68 protein from Adeno-Associated Virus (AAV) is a multifunctional SF3 helicase that performs most of the DNA transactions necessary for the viral life cycle. During AAV DNA replication, Rep68 assembles at the origin of replication, catalyzing the DNA melting and nicking reactions during the hairpin rolling replication process to complete the second-strand synthesis of the AAV genome. We report the cryo-electron microscopy structures of Rep68 bound to the adeno-associated virus integration site 1 in different nucleotide-bound states. In the nucleotide-free state, Rep68 forms a heptameric complex around DNA, with three origin-binding domains (OBDs) bound to the Rep-binding element sequence, while three remaining OBDs form transient dimers with them. The AAA+ domains form an open ring without interactions between subunits and DNA. We hypothesize that the heptameric structure is crucial for loading Rep68 onto double-stranded DNA. The ATPγS complex shows that only three subunits associate with the nucleotide, leading to a conformational change that promotes the formation of both intersubunit and DNA interactions. Moreover, three phenylalanine residues in the AAA+ domain induce a steric distortion in the DNA. Our study provides insights into how an SF3 helicase assembles on DNA and provides insights into the DNA melting process.

Jaiswal, Rahul↗

Levelized cost of charging of extreme fast charging with stationary LMO/LTO batteries

Extreme DC fast charging for electric vehicles (EVs) could be competitive with the internal combustion engine refueling experience and enable longer-distance travel, which could help with EV adoption and decarbonization, but these systems have high capital costs and extremely variable high-power demands. Behind-the-meter systems (BTMS) could support extreme-fast-charging (XFC) stations to increase nationwide adoption of EVs. Here, this study examines the optimal break-even levelized cost of charging (LCOC) across 96 BTMS scenarios to enable low-wait XFC stations providing 200 miles of charge in 10 min. This research simulates LCOC via synthetic XFC-capable EV loads, machine-learned battery life models from testing data, and nonlinear optimal controls, co-minimizing complex utility costs and battery replacements. An aggregate optimal BTMS design treating each EV load as equal likely gives an optimal LCOC per utility rate, the average of which is $\$$0.59/kWh. In addition, the sensitivity of optimal and off-optimal design factors, the long-life LMO/LTO chemistry, and optimized controls are analyzed. The battery control model, based on battery stressors to compare chemistries, optimizes LMO/LTO resting state of charge and cycle depth without compromising cost reduction, which enables greater flexibility in operation. The LCOC savings due to replacement reduction are small, up to $\$$0.035/kWh (6%), with an average of $\$$0.02/kWh (3.5%). Compared with gasoline stations, the aggregate XFC station design achieves comparable speed, experience of service, and cost at $\$$3.81/gal gasoline, showing that EVs can replace gasoline vehicles even for longer-distance travel.

25 ENERGY STORAGE↗

SPE-CZE-MS Quantifies Zeptomole Amounts of Phosphorylated Peptides

Capillary zone electrophoresis (CZE) is gaining attention in the field of single-cell proteomics for its ultralow-flow and high-resolution separation abilities. Even more sample-limited yet rich in biological information are phosphoproteomics experiments, as the phosphoproteome composes only a fraction of the whole cellular proteome. Rapid analysis, high sensitivity, and maximization of sample utilization are paramount for single-cell analysis. Some challenges of coupling CZE analysis with mass spectrometry analysis (MS) of complex mixtures include 1. sensitivity due to volume loading limitations of CZE and 2. incompatibility of MS duty cycles with electropherographic time scales. Here, we address these two challenges as applied to singlecell- equivalent phosphoproteomics experiments by interfacing a microchip-based CZE device integrated with a solid-phaseextraction (SPE) bed with the Orbitrap Astral mass spectrometer. Using 225 phosphorylated peptide standards and phosphorylated peptide-enriched mouse brain tissue, we investigate microchip-based SPE-CZE functionality, quantitative performance, and complementarity to nano-LC-MS (nLC-MS) analysis. We highlight unique SPE-CZE separation mechanisms that can empower fitfor- purpose applications in single-cell-equivalent phosphoproteomics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

An intelligent energy router for managing behind-the-meter resources and assets

With increase in distributed energy resources (DERs) and smart loads, each energy resource and load need a separate power conversion system leading to complex coordination and interaction, reduced energy conversion efficiency, coordinating compliance to grid standards (IEEE 1547) from multiple sources, reduced security. Also, multiple vendors with legacy system designs and proprietary communications interfaces result in redundancy and increase in cost of power electronics systems. This paper presents an energy router concept for buildings applications which provides autonomous power flow between sources and loads with a novel agent-based software interface.

Chinthavali, Madhu Sudhan↗

The heterogeneous nature of mechanically accelerated grain growth

Abstract While grain growth is traditionally viewed as a purely thermally driven process, nanocrystalline metals can undergo grain growth under mechanical loads, even at room temperature. We performed a detailed atomistic study of the heterogeneous nature of mechanically accelerated grain growth in a polycrystalline Pt nanowire. Using molecular dynamics simulations, we compared the grain-growth behavior of individual grains during tensile and shear cyclic loading, for three different equivalent strain levels, and at two temperatures. Pure thermal grain growth with no mechanical loading provided a baseline reference case. On average, grains that were already susceptible to thermal grain growth were stimulated to grow faster with mechanical loading, as expected. However, when analyzed on a grain-by-grain basis, the results were far more complex: grains that grew fastest under one stimuli were less accelerated under other stimuli. Even when the magnitude of loading changed, the relative growth of individual grains was distorted. We interpret this complexity from the perspective of superimposed growth mechanisms.

Chen, Elton Y.↗

Virtual diffraction simulations using the quasi-coarse-grained dynamics method to understand and interpret plasticity contributions during in situ shock experiments

The dynamic deformation response of metallic materials has contributions from dislocations, deformation twinning, and plastic deformation. The current state-of-art techniques can detail the complex mechanistic history of deformation modes under shock loading in real-time using in situ X-ray diffraction (XRD). However, the capability of these experiments to unravel plasticity contributions is challenging due to limitations in interpreting results and the lack of validation from atomistic simulations. Molecular dynamics (MD) simulations can successfully capture various deformation modes in metals and complement experiments using simulated diffractograms at various stages of evolution. However, the difference in length and time scales of MD simulations and experiments is a substantial obstacle in completing and interpreting in situ diffractograms. Therefore, the existing modeling methods require various approximations to model defect evolution and interaction at the mesoscales. However, while using approximations to correlate the peak broadening behavior to the density of dislocations or the shifts/splitting due to the presence of twins, the interpretations of the plasticity contributions from diffractograms are non-trivial, especially when multiple modes of deformation may be operating. This viewpoint discusses combining a mesoscale modeling method called quasi-coarse-grained dynamics and virtual XRD to characterize the plasticity contributions in BCC metals from slip, twinning, and phase transformation behavior. Furthermore, the combined approach shows promise in bridging the mesoscale gap between the capabilities of atomic-scale simulations and in situ experiments to characterize the dynamic deformation of materials.

36 MATERIALS SCIENCE↗