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Structures of the substrate-binding protein YfeA in apo and zinc-reconstituted holo forms
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Core Design of the Holos-Quad Microreactor
The Holos-Quad micro-reactor concept, developed by HolosGen LLC, is equipped with a 22 MWt (Mega-Watt thermal) core and an integral power conversion system converting the core thermal energy into approximately 10 MWe (Mega-Watt electric). This design can be configured to support a wide range of applications. It is a very innovative high-temperature gas-cooled reactor concept using TRI-structural ISOtropic particle fuel (TRISO) distributed in graphite hexagonal blocks, cooled with helium in a direct Brayton cycle independently executed by four Subcritical Power Modules (SPMs) fitted into a hardened 40-foot container whose dimensions are in compliance with ISO shipping containers requirements. In FY2019 HolosGen LLC was awarded by the Department of Energy Advanced Research Project Agency-Energy (DOE ARPA-E) under the MEITNER funding program. As part of the MEITNER award, the Argonne National Laboratory (ANL) contributed expertise through two specialized teams: The “Design Team” and the “Resource Team”. The Design Team was dedicated to validate feasibility of the Holos-Quad core and to optimize its core design through neutronics analyses. The Resource Team was dedicated to feasibility verification via high-fidelity codes of Holos-Quad thermal-hydraulic, heat transfer, shielding, and structural aspects. This report summarizes the activities conducted by ANL Design Team. A rigorous design approach based on multi-criteria optimization and code-to-code comparison involving stochastic and high-fidelity deterministic solutions was developed and employed at several evolutionary stages of the Holos-Quad design. Several generations of the Holos-Quad core were designed within this project before converging to the current full-scale Gen 2+ design that is detailed in this report. Figure EA-1 illustrates a cross-sectional view of Gen 2+ Holos-Quad core configuration, and Figure EA-2 provides a simplified perspective view of 1-of-4 SPMs. The Holos-Quad uses four thermal-hydraulically independent SPMs locked into stationary positions during power operation, surrounded by BeO reflector and structural component fully comprised within the dimensional constraints represented by traditional ISO containers. One of the benefits of this approach is to enable transportation of each SPM promptly after irradiation in shielded containers. The core is designed to operate for approximately 8 full-power years while the reactivity controls and power conversion system enable load-following operations. The reactivity controls are represented by independent, diversified, and redundant reactivity control systems based on control drums and redundant sets of shutdown rods. The high-fidelity simulation tools were used to assess detailed power and flux distributions of the three-dimensional full-core or quarter-core of the Gen 2+ configuration. Single-physics and multi-physics simulations of the neutronics code PROTEUS and the thermal-hydraulic code System Analysis Module (SAM) were performed to analyze the Holos design configurations with detailed high-fidelity solutions. The design work performed confirmed feasibility of the Holos-Quad concept, provided realistic design description for detailed design of the operational system, and identified several core design improvements to be further considered for future reactor development activities.
Neutronic Design and Analysis of the Holos-Quad Concept
HolosGen, LLC is proposing a highly innovative micro-reactor concept targeting both civilian and military applications. It consists of an advanced helium-cooled gas reactor using a turbojet-type turbine and compressor to achieve a highly condensed reactor that fits into a commercial ISO container. The Holos-Quad concept being considered for civilian applications will generate 22MWt, using four Subcritical Power Modules (SPMs) that fit into one 40-foot ISO container. It is a high-temperature gas-cooled reactor concept using TRISO fuel distributed in graphite hexagonal blocks, cooled with helium gas at 7MPa and a high outlet temperature. In FY2019, HolosGen, LLC received an ARPA-E MEITNER grant to team up with the Argonne National Laboratory (ANL) design team to demonstrate the feasibility of the Holos-Quad concept in terms of neutronics. In particular, the evaluation study of the Holos design features and alternative options for reactivity control was considered. Through these tasks, the ANL design team has been working on demonstrating the feasibility of the Holos-Quad concept in terms of neutronics to help advance the core design of the Holos-Quad. A rigorous design approach was employed for the Holos-Quad in order to ensure that the input space is fully investigated, and that the best solutions are considered. The first step of this approach consisted of properly defining the Holos-Quad design problem by identifying the competitive design objectives: its economic performance is maximized with longer lifetime and its transportability to remote locations is maximized with reduced weight. The design problem also required to identify the operational constraints (in terms of thermal hydraulics, reactivity feedback and shutdown margins) and the input parameters that could be varied. In the second step, a sensitivity analysis was performed to enable preliminary investigation of the input space to identify the correlations among input and output variables. It allowed, for instance, to find input parameters that have relatively poor impact on the core performance and that could be removed from the optimization problem to accelerate its convergence. This sensitivity analysis showed that the design problem defined is highly constrained since only 117 solutions out of 1,000 simulated cores met all the design constraints. The design optimization was performed in the third step employing a genetic algorithm to effectively explore this highly constrained input space and find global optimal solutions. More than 2,500 cores were fully evaluated to converge to a Pareto Frontier of optimum solutions providing best compromise between the life-time target and the total core weight, as shown in Figure 1. The main benefit of this approach was to reduce the human effort and to be able to automatically re-run the optimization problem when changing the design problem. The multi-objective optimization identified various core solutions that would be optimum solutions for different types of applications.
Ligand-Binding-Site Refinement to Generate Reliable Holo Protein Structure Conformations from Apo Structures
The first important step in a structure-based virtual screening is the judicious selection of a receptor protein. In cases where the holo protein receptor structure is unavailable, significant reduction in virtual screening performance has been reported. In this work, we present a robust method to generate reliable holo protein structure conformations from apo structures using molecular dynamics (MD) simulation with restraints derived from holo structure binding-site templates. We perform benchmark tests on two different datasets: 40 structures from a directory of useful decoy-enhanced (DUD-E) and 84 structures from the Gunasekaran dataset. Our results show successful refinement of apo binding-site structures toward holo conformations in 82% of the test cases. In addition, virtual screening performance of 40 DUD-E structures is significantly improved using our MD-refined structures as receptors with an average enrichment factor (EF), an EF1% value of 6.2 compared to apo structures with 3.5. Docking of native ligands to the refined structures shows an average ligand root mean square deviation (RMSD) of 1.97 Å (DUD-E dataset and Gunasekaran dataset) relative to ligands in the holo crystal structures, which is comparable to the self-docking (i.e., docking of the native ligand back to its crystal structure receptor) average, 1.34 Å (DUD-E dataset) and 1.36 Å (Gunasekaran dataset). On the other hand, docking to the apo structures yields an average ligand RMSD of 3.65 Å (DUD-E) and 2.90 Å (Gunasekaran). These results indicate that our method is robust and can be useful to improve virtual screening performance of apo structures.
Holo-omics for deciphering plant-microbiome interactions
Host-microbiome interactions are recognized for their importance to host health. An improved understanding of the molecular underpinnings of host-microbiome relationships will advance our capacity to accurately predict host fitness and manipulate interaction outcomes. Within the plant microbiome research field, unlocking the functional relationships between plants and their microbial partners is the next step to effectively using the microbiome to improve plant fitness. We propose that strategies that pair host and microbial datasets—referred to here as holo-omics—provide a powerful approach for hypothesis development and advancement in this area. We discuss several experimental design considerations and present a case study to highlight the potential for holo-omics to generate a more holistic perspective of molecular networks within the plant microbiome system. In addition, we discuss the biggest challenges for conducting holo-omics studies; specifically, the lack of vetted analytical frameworks, publicly available tools, and required technical expertise to process and integrate heterogeneous data. Finally, we conclude with a perspective on appropriate use-cases for holo-omics studies, the need for downstream validation, and new experimental techniques that hold promise for the plant microbiome research field. We argue that utilizing a holo-omics approach to characterize host-microbiome interactions can provide important opportunities for broadening system-level understandings and significantly inform microbial approaches to improving host health and fitness.
Preliminary Thermal-hydraulics and Selected Safety Analysis for Holos-Quad Reactor Design
This report presents thermal hydraulics and safety analyses of the 10 MWe Holos-Quad micro-reactor design developed by HolosGen LLC. These analyses were executed under steady-state and station black-out (SBO) transient conditions using the System Analysis Module (SAM), with a focus on ensuring peak fuel temperatures do not exceed the safety thresholds of 1,250°C for steady state normal operating conditions and 1,600°C for transient conditions. For steady-state temperature predictions, a coupled 1D fluid-to-3D solid heat conduction methodology was used. The steady-state simulations included a model of the central core region where power peaking occurs to predict the maximum steady-state fuel temperature, and a coarse-mesh full-core model to provide the initial condition for the consequent transient SBO decay heat removal simulation. The maximum fuel temperature predicted from the central core region simulations under the normal operating condition was 1,222°C, which is below the design limit 1,250°C. To simulate a SBO transient, a full core model was necessary because of the non-axial symmetric core design and heat loss from the outer core structures to the environment. To reduce the required computational costs, a novel scaled subassembly approach was used to model the full core domain. With the full core steady-state temperature distribution provided as the initial condition, the passive decay heat removal of the core was simulated with the scaled subassembly full core model under SBO transient conditions. This analysis showed that the peak fuel temperatures of the Holos-Quad core remained below their steady-state values during the transient, therefore much lower than the safety limit 1,600°C. This is mainly due to the large thermal inertia of the graphite matrix, relatively low power density, and the large surface-to-volume-ratio of the core. The preliminary analyses presented in this report confirm the inherent safety of the Holos-Quad micro-reactor thermal-hydraulics design, as the peak fuel temperatures under both normal and off-normal operational conditions remain within design and safety limits.
MEITNER Resource Team Modeling and Simulation Support to Holos-Quad Reactor Development (Final CRADA Report)
The main objective of this CRADA is to provide Argonne National Laboratory (ANL)’s modeling and simulation capabilities via ARPA-E's MEITNER (Modeling-Enhanced Innovations Trailblazing Nuclear Energy Reinvigoration) Resource Team (RT) arrangement to support the demonstration of the viability of HolosGen’s Holos-Quad reactor design. The Holos-Quad reactor design is an advanced reactor concept that incorporates many new design features, such as the neutron-coupled Subcritical Power Modules (SPMs) in its core design, elimination of balance of plant (BOP) by direct integration of a helium Brayton cycle power conversion system with each SPM, among many other innovative features. The demonstration of the viability of such an innovative reactor design warrants iterations of modeling and simulation and testing. The purpose of this project is to utilize ANL’s modeling and simulation capabilities in nuclear reactor analysis and power conversion system analysis to inform HolosGen and the Design Team (DT) in the design and optimization of the Holos-Quad concept. The major work scopes of this project include: to investigate conceptual designs and materials for radiation shielding to protect personnel and internal components such as turbomachinery; Assess the the helium Brayton cycle power conversion system performance in both nominal and load following conditions; Investigate power conversion components and overall system performance; Identify control strategies to enable load following; Perform simulations of HolosGen’s subscale simulator and using available test data for code validation/benchmark purpose; Perform core thermal-hydraulics, safety analysis, and structural analysis.
Load Following Analysis of the Holos-Quad 10MWe Micro-Reactor with Plant Dynamics Code
This report presents the load following analysis of the “Holos-Quad” 10MWe micro-reactor design developed by HolosGen LLC. This analysis is focused on the Holos-Quad micro-reactor ability to match the changing grid demand at 10%/min rate. The control mechanisms for the plant are identified, simulated, and compared. Based on the comparison results, control strategy for load following of the Holos-Quad micro-reactor is developed. The control strategy and load following capabilities are demonstrated in a full-range down-and-up reactor power transient from 100% to 0% and back to 100% load at 10%/min rate. All calculations are carried out with Argonne’s Plant Dynamics Code.
What Is in Umbilicaria pustulata? A Metagenomic Approach to Reconstruct the Holo-Genome of a Lichen
Lichens are valuable models in symbiosis research and promising sources of biosynthetic genes for biotechnological applications. Most lichenized fungi grow slowly, resist aposymbiotic cultivation, and are poor candidates for experimentation. Obtaining contiguous, high-quality genomes for such symbiotic communities is technically challenging. Here, we present the first assembly of a lichen holo-genome from metagenomic whole-genome shotgun data comprising both PacBio long reads and Illumina short reads. The nuclear genomes of the two primary components of the lichen symbiosis—the fungus Umbilicaria pustulata (33 Mb) and the green alga Trebouxia sp. (53 Mb)—were assembled at contiguities comparable to single-species assemblies. The analysis of the read coverage pattern revealed a relative abundance of fungal to algal nuclei of ~20:1. Gap-free, circular sequences for all organellar genomes were obtained. The bacterial community is dominated by Acidobacteriaceae and encompasses strains closely related to bacteria isolated from other lichens. Gene set analyses showed no evidence of horizontal gene transfer from algae or bacteria into the fungal genome. Our data suggest a lineage-specific loss of a putative gibberellin-20-oxidase in the fungus, a gene fusion in the fungal mitochondrion, and a relocation of an algal chloroplast gene to the algal nucleus. Major technical obstacles during reconstruction of the holo-genome were coverage differences among individual genomes surpassing three orders of magnitude. Moreover, we show that GC-rich inverted repeats paired with nonrandom sequencing error in PacBio data can result in missing gene predictions. This likely poses a general problem for genome assemblies based on long reads.
Holo-Omics disentangle drought response and biotic interactions among plant, endophyte and pathogen
Holo-omics provide a novel opportunity to study the interactions among fungi from different functional guilds in host plants in field conditions. We address the entangled responses of plant pathogenic and endophytic fungi associated with sorghum when droughted through the assembly of the most abundant fungal, endophyte genome from rhizospheric metagenomic sequences followed by a comparison of its metatranscriptome with the host plant metabolome and transcriptome. The rise in relative abundance of endophytic Acremonium persicinum (operational taxonomic unit 5 (OTU5)) in drought co-occurs with a rise in fungal membrane dynamics and plant metabolites, led by ethanolamine, a key phospholipid membrane component. The negative association between endophytic A. persicinum (OTU5) and plant pathogenic fungi co-occurs with a rise in expression of the endophyte's biosynthetic gene clusters coding for secondary compounds. Endophytic A. persicinum (OTU5) and plant pathogenic fungi are negatively associated under preflowering drought but not under postflowering drought, likely a consequence of variation in fungal fitness responses to changes in the availability of water and niche space caused by plant maturation over the growing season. Our findings suggest that the dynamic biotic interactions among host, beneficial and harmful microbiota in a changing environment can be disentangled by a blending of field observation, laboratory validation, holo-omics and ecological modelling.
X-ray Characterization of Conformational Changes of Human Apo- and Holo-Transferrin
Human serum transferrin (Tf) is a bilobed glycoprotein whose function is to transport iron through receptor-mediated endocytosis. The mechanism for iron release is pH-dependent and involves conformational changes in the protein, thus making it an attractive system for possible biomedical applications. In this contribution, two powerful X-ray techniques, namely Macromolecular X-ray Crystallography (MX) and Small Angle X-ray Scattering (SAXS), were used to study the conformational changes of iron-free (apo) and iron-loaded (holo) transferrin in crystal and solution states, respectively, at three different pH values of physiological relevance. A crystallographic model of glycosylated apo-Tf was obtained at 3.0 Å resolution, which did not resolve further despite many efforts to improve crystal quality. In the solution, apo-Tf remained mostly globular in all the pH conditions tested; however, the co-existence of closed, partially open, and open conformations was observed for holo-Tf, which showed a more elongated and flexible shape overall.
Preliminary Study of Model Predictive Control for Load Follow Operation of Holos Reactor
This paper derives a state-space model for model predictive control of a high temperature gas micro-reactor based on the Holos-Quad Design.
Stability margin analysis of the Holos-quad microreactor design
A simplified point model of the Holos-Quad microreactor is introduced. The model is based on the point kinetics equations coupled to three heat balance equations, representing the mean temperatures of the fuel particles, the graphite moderator and the helium coolant. The differential equations are converted to the frequency domain, enabling the construction of the closed-loop reactor transfer function. Using this function the stability margins of the core design is analyzed for various power levels. It is shown that the gain margins approaches infinity, demonstrating the stability of the reactor for all power levels. The phase margin at nominal power is about 60 degrees, however it shows a non-monotonous dependence on power, with minimal value obtained for about 10% of nominal power. As power level is further increased, the phase margin also increases, demonstrating the reactor becomes more stable. This behavior may be of high importance in load-follow scenarios, where the power level of the reactor changes with time. (authors)
A perturbation-based hybrid methodology for control drum worth prediction applied to the HOLOS-Quad microreactor concept
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Catalytically active holo Homo sapiens adenosine deaminase I adopts a closed conformation
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Analysis of HolosGen Sub-Scale Simulator with Plant Dynamics Code
The Subcritical Power Module Sub-scale Simulator (SPM-SS) has been designed and constructed by HolosGen LLC under the ARPA-E MEITNER program to simulate the thermal-hydraulic and heat transfer behavior of the full-scale Holos-Quad Subcritical Power Modules (SPMs). Four coupled SPMs, each rated at 5.5MW, form the Holos-Quad gas-cooled microreactor design. The SPM-SS represents a substantially scaled-down system with a power rating less than 40 kW, equipped with an electrically heated fuel cartridge heat exchanger, an electrically heated compressor heat exchanger, and a valve actuated turbine heat exchanger, in addition to a recuperator and a cooler heat exchanger. The fuel cartridge represents a portion of the full-scale SPM core, the compressor heat exchanger mimics the temperature changes resulting from the compressor’s turbomachinery inefficiencies, the turbine heat exchanger mimics the expansion process normally occurring through the turbine, while the recuperator and cooler heat exchangers complete the subscale simulator loop. The heaters equipping the fuel cartridge and the compressor heat exchangers are electronically controlled to simulate normal and off-normal SPM operating conditions. The full-scale Holos-Quad SPM design eliminates the traditional balance of plant and executes thermal-to-electric energy conversion by means of an intercooled Brayton cycle with decoupled compressor-turbine turbomachinery. The Holos-Quad full-scale design is equipped with a multi-stage axial Low- and High-Pressure compressor, and a multistage axial turbine. The SPM-SS is designed for testing and validation of selected components which are instead coupled by a traditional balance of plant. The SPMSS is not equipped with turbo-machinery (compressor and turbine) as the development of these components were excluded from the scope of work under the ARPA-E MEITNER funding program. The SPM-SS balance of plant enables modifications, replacement and testing of individual components with different working fluids and is designed to include the turbo-machinery components that will be developed in future research . The SPM-SS can be operated with different gases, variable mass-flow-rates, pressures, and temperatures to obtain test data for selected components, whose performance can be scaled to validate the computer model of the full-scale SPM at various conditions (e.g., start-up, transients conditions). The SPM-SS can operate at the maximum Holos-Quad design pressure of 7 MPa, and a maximum temperature limited to 650 °C by the electrical heaters. Several SPM-SS tests have been conducted and analyzed with the Plant Dynamics Code (PDC) developed at the Argonne National Laboratory (ANL). These tests aimed at validating the PDC modeled predictions of the full-scale Holos-Quad design with data from selected SPM-SS components. In order to address SPM-SS specific characteristics, such as components heat losses and absence of turbomachinery components, some modifications to the PDC have been implemented to factor the design differences from the full-scale Holos-Quad SPM to the SPM-SS. As the PDC offers capabilities to analyze systems with different working fluids, air, nitrogen, and helium were utilized as the SPM-SS working fluids. Air was utilized to fine-tune the SPM-SS Systems Structures and Components (SSCs), nitrogen was utilized to pressure test the SPM-SS loop at the SPMs design maximum pressure of 7MPa. Helium was utilized as the working fluid circulating through the SPM-SS SSCs for specific tests to validate the PDC predictions of the fuel cartridge heat exchanger. SPM-SS tests data were also analyzed with both the steady-state and transient analysis capabilities offered by the PDC. This report describes the PDC analysis of the SPM-SS tests data, including the necessary code modifications and comparison of the code results with the experimental data. Based on the results, a discussion is presented on how the analysis supports design and transient calculations of the full-scale Holos-Quad microreactor. Also based on the results of this work, recommendations are made for future optimizations of the SPM-SS components and PDC model development needs.
On High-Order/Low-Order and Micro-Macro Methods for Implicit Time-Stepping of the BGK Model
In this paper, a high-order/low-order (HOLO) method is combined with a micro-macro (MM) decomposition to accelerate iterative solvers in fully implicit time-stepping of the Bhatnagar–Gross–Krook (BGK) equation for gas dynamics. The MM formulation represents a kinetic distribution as the sum of a local Maxwellian and a perturbation. In highly collisional regimes, the perturbation away from initial and boundary layers is small and can be compressed to reduce the overall storage cost of the distribution. The convergence behavior of the MM methods, the usual HOLO method, and the standard source iteration method is analyzed on a linear BGK model. Both the HOLO and MM methods are implemented using a discontinuous Galerkin (DG) discretization in phase space, which naturally preserves the consistency between high- and low-order models required by the HOLO approach. Furthermore, the accuracy and performance of these methods are compared on the Sod shock tube problem and a sudden wall heating boundary layer problem. Overall, the results demonstrate the robustness of the MM and HOLO approaches and illustrate the compression benefits enabled by the MM formulation when the kinetic distribution is near equilibrium.