Structural Studies and Structure Activity Relationships for Novel Computationally Designed Non-nucle
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Frey, Kathleen M.↗
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An Ab Initio Molecular Dynamics Study of Key Thermodynamic Input Parameters for Computer Simulation of U-6Nb Solidification
The key to metallic fuel development is the fabrication of uranium metal and alloys into fuel forms. U-Nb alloys are one of the best candidates for a metallic fuel alloy with high-temperature strength sufficient to support the core, acceptable nuclear properties, good fabricability, and compatibility with usable coolant media. Melt processing has been a key component of the metallic fuel cycle, and process models require thermophysical parameters at elevated temperatures, particularly above the melting temperatures, regarding which experimental data are scarce, for accurate simulations and process development. By means of ab initio density-functional theory (DFT) quantum molecular dynamics (QMD), we have calculated the main thermophysical parameters—the density, thermal expansion coefficient, specific heat, thermal conductivity, melting temperature, latent heat of fusion, and viscosity—used in the modeling of the U-6 wt.% Nb alloy casting. The melting temperature of the U-6 wt.% Nb alloy at ambient pressure is obtained by means of QMD simulations using the Z-method. The ambient volume change and latent heat of melting of U-6 wt.% Nb are also derived from QMD simulations in conjunction with analytical fitting for the energy and pressure. The thermal conductivity for the solid U-Nb alloy is calculated from the semi-classical Boltzmann transport equation combined with an estimate of the electron relaxation time obtained from DFT simulations.
11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
The Challenge of Disproportionate Importance of Temporal Features in Predicting HPC Power Consumption
In this work, we demonstrate the challenges in predicting HPC cluster power consumption in the face of significant temporal skew in power consumption behavioral patterns. Predicting large power swings that extend several megawatts has significant operational value for HPC centers, however, prediction is challenging due to the relative rarity of such events and also due to the abrupt or disjoint deviation from the average power consumption levels. To study the impact of this challenge, we have trained a recurrent neural network (RNN) as a reasonably sophisticated model to predict power consumption of the one-year worth of node power consumption data from the Summit supercomputer located in the Oak Ridge Leadership Computing Facility. By studying the prediction results, we have found that although simple usage of RNN models can provide good results on average power consumption levels, it would fail at predicting the power swings that have more operational value. With such results, we discuss potential next steps in addressing such issues aiming towards a robust usage of power prediction techniques in HPC operations.
Li, Chengcheng↗
Neutron spin echo shows pHLIP is capable of retarding membrane thickness fluctuations
In this study, cell membranes are responsible for a range of biological processes that require interactions between lipids and proteins. While the effects of lipids on proteins are becoming better understood, our knowledge of how protein conformational changes influence membrane dynamics remains rudimentary. Here, we performed experiments and computer simulations to study the dynamic response of a lipid membrane to changes in the conformational state of pH-low insertion peptide (pHLIP), which transitions from a surface-associated (SA) state at neutral or basic pH to a transmembrane (TM) α-helix under acidic conditions. Our results show that TM-pHLIP significantly slows down membrane thickness fluctuations due to an increase in effective membrane viscosity. Our findings suggest a possible membrane regulatory mechanism, where the TM helix affects lipid chain conformations, and subsequently alters membrane fluctuations and viscosity.
59 BASIC BIOLOGICAL SCIENCES↗
Risk-averse optimization for resilience enhancement of complex engineering systems under uncertainties
With the growth of complexity and extent, large scale interconnected network systems, e.g., transportation networks or infrastructure networks, become more vulnerable to external disturbances. Hence, managing potential disruptive events during the design, operating, and recovery phase of an engineered system and therefore improving the system’s resilience is an important yet challenging task. Here, to ensure system resilience after the occurrence of failure events, this study proposes a mixed-integer linear programming (MILP) based restoration framework using heterogeneous dispatchable agents. The scenario-based stochastic optimization (SO) technique is adopted to deal with the inherent uncertainties imposed on the recovery process from nature. Moreover, different from conventional SO using deterministic equivalent formulations, the CVaR risk measure is implemented for this study because of the temporal sparsity of the decision making in applications such as the recovery from extreme events. The resulting restoration framework involves a large-scale MILP problem and thus an adequate decomposition technique i.e. modified Lagrangian dual decomposition, is also employed to achieve tractable computational complexity. Case study results based on the IEEE 37-bus test feeder demonstrate the benefits of using the proposed framework for resilience improvement as well as the advantages of adopting SO formulations.
42 ENGINEERING↗
High temperature superconductivity in the candidate phases of solid hydrogen
As the simplest element in nature, unraveling the phase diagram of hydrogen is a primary task for condensed matter physics. As conjectured many decades ago, in the low-temperature and high-pressure part of the phase diagram, solid hydrogen is expected to become metallic with a high superconducting transition temperature. The metallization may occur via band gap closure in the molecular solid or via a transition to the atomic solid. Recently, a few experimental studies pushed the achievable pressures into the 400–500 GPa range. There are strong indications that at some pressure in this range metallization via either of these mechanisms occurs, although there are disagreements between experimental reports. Furthermore, there are multiple good candidate crystal phases that have emerged from recent computational and experimental studies which may be realized in upcoming experiments. Therefore, it is crucial to determine the superconducting properties of these candidate phases. In a recent study, we reported the superconducting properties of the C2/c-24 phase, which we believe to be a strong candidate for metallization via band gap closure. Here, we report the superconducting properties of the Cmca-12, Cmca-4 and I4 1 /amd-2 phases including the anharmonic effects using a Wannier function-based dense k-point and q-point sampling. Here we find that the Cmca-12 phase has a superconducting transition temperature that rises from 86 K at 400 GPa to 212 K at 500 GPa, whereas the Cmca-4 and I4 1 /amd-2 phases show a less pressure-dependent behavior with their T c in the 74–94 K and 307–343 K ranges, respectively. These properties can be used to distinguish between crystal phases in future experiments. Understanding superconductivity in pure hydrogen is also important in the study of high-T c hydrides.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Understanding Proton Movement in [Fe-Fe] Hydrogenases
Nature uses specialized metalloenzymes to carry out small molecule activation reactions, including CO 2 fixation, O 2 activation, and proton reduction, with unparalleled efficiency, rates, and selectivity. The latter reactions are performed by hydrogenases, protein metallo-complexes that interconverts H 2 to protons and electrons (H 2 oxidation) and the reverse reaction (H 2 production) with incredibly low energy input and amazingly fast kinetics. Reproducing both the activity and efficiency of metalloenzymes in sustainable anthropogenic systems remains one of the “holy grails” of inorganic chemistry. However, identifying the precise molecular components responsible for these desirable properties has been challenging in the natural metalloenzymes, hindering efforts to develop analogous processes in synthetic compounds. Considering the inherent complexity of a metalloenzyme and the many interactions, both strong and weak, that contribute to the function of an enzyme, we have elected to model natural metalloenzymes on a biochemical platform. Towards this end, we have a developed structural, functional, and mechanistic mimic of the [Ni-Fe] hydrogenases within a robust protein scaffold, rubredoxin, to understand the influence of the secondary coordination environment on the metal center. This involved preparing a series of three rubredoxin constructs containing a single point mutation at Val positions and making the NMR chemical shift assignments for the paramagnetic (nickel-substituted) and non-paramagnetic (zinc-substituted) form. These physical studies were complemented with in silico molecular dynamic studies on proteins with [Fe-S] clusters to engineer new proton channels to test in vitro . To assist our search for new natural metalloprotein scaffolds within the vast number of sequenced genomes, we created a neural network-based program to identify proteins with specific metal-binding sites. These computational and physical studies with metalloenzymes provide direct insight into the fundamental chemical principles driving the natural systems and offer design principles for developing catalysts that utilize analogous principles.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Optimization of Fairing Geometry for ORPC Modular RivGen Power System: Cooperative Research and Development (Final Report)
The work will optimize the hydrodynamic performance and flow augmentation of Ocean Renewable Power Company's (ORPC) modular fairing for their cross-flow marine hydrokinetic (MHK) turbine, using a computational fluid dynamics study. The influence of the fairing cross-sectional shape and rotor-fairing spacing will be assessed, to maximize power production and minimize structural loads.
16 TIDAL AND WAVE POWER↗
2 H -Thiopyran-2-thione sulfine, a compound for converting H 2 S to HSOH/H 2 S 2 and increasing intracellular sulfane sulfur levels
Reactive sulfane sulfur species such as persulfides (RSSH) and H 2 S 2 are important redox regulators and closely linked to H 2 S signaling. However, the study of these species is still challenging due to their instability, high reactivity, and the lack of suitable donors to produce them. Herein we report a unique compound, 2H-thiopyran-2-thione sulfine (TTS), which can specifically convert H 2 S to HSOH, and then to H 2 S 2 in the presence of excess H 2 S. Meanwhile, the reaction product 2H-thiopyran-2-thione (TT) can be oxidized to reform TTS by biological oxidants. The reaction mechanism of TTS is studied experimentally and computationally. TTS can be conjugated to proteins to achieve specific delivery, and the combination of TTS and H 2 S leads to highly efficient protein persulfidation. When TTS is applied in conjunction with established H 2 S donors, the corresponding donors of H 2 S 2 (or its equivalents) are obtained. Cell-based studies reveal that TTS can effectively increase intracellular sulfane sulfur levels and compensate for certain aspects of sulfide:quinone oxidoreductase (SQR) deficiency. These properties make TTS a conceptually new strategy for the design of donors of reactive sulfane sulfur species.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Simulated Adhesive Response to Aging (CRADA 453 Final Report)
The goal of this project was to develop a suite of molecular models to investigate adhesive performance as a result of the presence of different levels of moisture. These different levels of moisture are accepted in the adhesives community to represent different states of aging. First, our team modeled the adhesive’s crosslinked structure. Next, we modeled adding water to the crosslinked structure and used high performance computing resources to simulate water diffusion through the bulk adhesive and possible sites for chain scission. Finally, we modeled the response of the simulated adhesive to tensile loads at various levels of moisture content. These simulations were validated by experimental characterization by the industry partner. We found that the Young’s modulus of the adhesive decreased by about 30% when the water content increased to 3 wt.%. Our simulations also identified the likely site where the polymer chain could break. Our integration of molecular level simulations and mechanical property predictions using high performance computing with experimental studies of a hydrated epoxy system has yielded fundamental insights that will help industry advance lightweight joining technologies.
36 MATERIALS SCIENCE↗
Silver diamine fluoride differentially affects dentin and hypomineralized enamel permeabilities
OBJECTIVES: To investigate the physicochemical effect of silver diamine fluoride (SDF) by correlating permeability with mineral density and elemental composition of hypomineralized enamel and carious dentin. METHODS: Enamel and dentin from human carious primary teeth with and without SDF treatment in-vivo, and hypomineralized enamel from permanent molars with and without SDF treatment in-vitro were scanned using micro X-ray computed tomography. Spatial maps of biometals (calcium, zinc), phosphorus, and silver were generated using X-ray fluorescence microprobe. Permeabilities were computed using Porous Microstructure Analysis software. RESULTS: The intrinsic permeability of SDF-treated carious dentin was 14.3 % lower than untreated sound dentin (6.39e-15 ± 3.01e-15 m² vs 7.46e-15 ± 1.82e-15 m²; P < 0.0001), while untreated carious dentin was 98.4 % higher (1.48e-14 ± 7.11e-15 m²; P < 0.0001). SDF-treated and untreated transparent dentin showed similar reduced permeabilities (75.6 % and 78.4 % lower than untreated sound dentin, respectively; P = 0.93). Severely hypomineralized enamel showed permeability reaching 108.1 % of adjacent sound dentin (5.71e-15 ± 2.04e-15 m² vs 5.28e-15 ± 1.30e-15 m²; P = 0.1409) and was significantly higher than mildly hypomineralized enamel (1.39e-15 ± 1.04e-15 m²; P < 0.0001). SDF treatment did not significantly impact the permeability of severely hypomineralized enamel (12.4 % reduction; P = 0.07). Principal component regression identified Zn level as a significant effector of tissue permeabilities in carious primary teeth (P < 0.0001). SIGNIFICANCE: This study introduces a computational method to measure dental tissue permeability, and demonstrates that SDF significantly reduces permeability in carious dentin but not intact hypomineralized enamel. The study reveals biometal Zn localization can alter dentin and enamel permeabilities, providing new insights into pathobiological mechanisms underlying caries and hypomineralization.
Chou, Conrad↗
The Computational Capacity of Mem-LRC Reservoirs
Reservoir computing has a emerged as a powerful tool in data-driven time series analysis. The possibility of utilizing hardware reservoirs as specialized co-processors has generated interest in the properties of electronic reservoirs, especially those based on memristors as the nonlinearity of these devices should translate to an improved nonlinear computational capacity of the reservoir. However, designing these reservoirs requires a detailed understanding of how memristive networks process information which has thus far been lacking. In this work, we derive an equation for general memristor-inductor-resistor-capacitor (MEM-LRC) reservoirs that includes all network and dynamical constraints explicitly. Utilizing this we undertake a study of the computational capacity of these reservoirs. We demonstrate that hardware reservoirs may be constructed with extensive memory capacity and that the presence of memristors enacts a tradeoff between memory capacity and nonlinear computational capacity. Here, using these principles, we design reservoirs to tackle problems in signal processing, paving the way for applying hardware reservoirs to high-dimensional spatiotemporal systems.
Circuits with memory↗
Comparative Analysis of DNA LLM Classification Techniques Using Intra-Layer Feature Extraction with Autoencoder Stacks [Poster]
This project conducts a comparative analysis of DNA LLM classification techniques using Evo2, Grover, and UTRML, focusing on intra-layer feature extraction in Evo2. By extracting features from multiple layers of Evo2 and integrating them into an autoencoder stack with a binary classification head, we evaluate its effectiveness in classifying genomic sequences compared to smaller DNA language models. My findings demonstrate that Evo2 outperforms Grover and UTRML in classification accuracy on a dataset provided by department 08625, CAO2021, while UTRML offers competitive performance with lower computational costs. This study highlights the potential of advanced embedding techniques in enhancing genomic data analysis and informs future research in bioinformatics.
59 BASIC BIOLOGICAL SCIENCES↗
CFD modeling of turbulent air flow in self-heated gyroid TPMS structures: Thermal-hydraulic performance and validation
The application of mathematically derived geometries, such as triply periodic minimal surface (TPMS) lattices, has garnered significant interest across various fields, including the nuclear sector, due to their superior thermal-hydraulic characteristics for heat transfer compared to traditional plain or finned tubes. Here, this study validates a computational fluid dynamics (CFD) model, evaluates different turbulence models and CFD model settings, and performs uncertainty quantification to provide a comprehensive analysis. Despite extensive research on CFD modeling of TPMS lattices, such as gyroid and diamond geometries, there is a notable lack of publicly available literature providing comprehensive details on numerical analysis aspects, including convergence and methodological best practices. This study embarks on a benchmark analysis of a gyroid geometry to evaluate its thermal-hydraulic performance under turbulent flow conditions and scrutinize various CFD model configurations. The main contributions of this work include validating the CFD model, assessing and comparing different turbulence models, and enhancing pressure drop and temperature prediction capabilities. The results aim to support the development of methodologies needed to benchmark and enhance numerical analysis techniques for TPMS lattices. This work seeks to complement the existing body of knowledge, support the development of TPMS reactor concepts, and improve best practices for CFD modeling of TPMS lattices, ultimately advancing methodologies to support future applications in this domain.
22 - GENERAL STUDIES OF NUCLEAR REACTORS↗
Conceptual study of a two-layer silicon pixel detector to tag the passage of muons from cosmic sources through quantum processors
Abstract Recent studies in quantum computing have shown that quantum error correction with large numbers of physical qubits are limited by ionizing radiation from high-energy particles. Depending on the physical setup of the quantum processor, the contribution of muons from cosmic sources can constitute a significant fraction of these interactions. As most of these muons are difficult to stop, we perform a conceptual study of a two-layer silicon pixel detector to tag their hits on a solid-state quantum processor instead. With a typical dilution refrigerator geometry model, we find that efficiencies greater than 50% are most likely to be achieved if at least one of the layers is operated at the deep-cryogenic (<1 K) flanges of the refrigerator. Following this finding, we further propose a novel research program that could allow the development of silicon pixel detectors that are fast enough to provide input to quantum error correction algorithms, can operate at deep-cryogenic temperatures, and have very low power consumption.
Instruments & Instrumentation↗
Synergistic Solvent-Surface Interactions Enable Alkyne Semihydrogenation at Palladium
Enabling higher yield and better selectivity for fine-chemical synthesis through heterogeneous catalysis is intricately linked to the interplay of active sites, reaction conditions, and mass transfer influence provided by the catalyst. Alkyne semihydrogenation is ubiquitous in the production of bulk chemicals in the pharmaceutical, polymer, or fine-chemical industries, but product selectivity remains a major challenge. Here, in this study, we demonstrate that the design of catalysts encompassing nickel (Ni) foams as contiguous monolith supports, decorated with ultralow loading of Pd/PdO x nanoparticles on a carbonized polydopamine interface and tuned with a thin layer of Al 2 O 3 , in conjunction with an optimized reaction environment leads to highly selective alkyne semihydrogenation. The reactions demonstrate good functional group tolerance and applicability to flow reactor systems. Combined computational and experimental studies are presented to describe the synergistic effect between the solvent-surface interaction and the degree of Pd surface reduction that are necessary to promote this selectivity. The system highlights the opportunity for catalyst-solvent codesign as a benign alternative to more complex reactants featuring extrinsic poisons or less-favored dopants.
atomic layer deposition↗
Fully implicit crystal plasticity models representing orientations with modified Rodrigues parameters
Here, this work describes a crystal plasticity formulation combining several mathematical, numerical, and implementation choices to produce a highly efficient model. Specifically, the key choices in the implementation are (1) representing orientations with modified Rodrigues parameters, (2) implementing a fully coupled implicit time integration for the elastic stretch, the crystal orientations, and the model internal variables, (3) implementing the model in the NEML2 constitutive modeling framework, based on PyTorch, to vectorize the calculations and port the computation to GPUs and other hardware accelerators, and (4) an exact implementation of the consistent tangent matrix, even for arbitrary coupling to other field variables beyond the displacements, like temperature, neutron fluence, etc. The first two features of the model are, to our knowledge, novel. The paper considers each of these choices individually as well as the final model as a whole. This includes a full description of modified Rodrigues parameters, their advantages over other representations of orientations, the mathematical formulae and tools required to implement a model with modified Rodrigues parameters, and a detailed description of the geometry of the space of modified Rodrigues parameters (in an appendix). It also includes a description of a fully implicit time integration scheme for the orientations and the advantages in representing orientations with modified Rodrigues parameters in implementing such a model. The work then assess, via numerical examples, the advantages of fully coupled implicit time integration versus more common decoupled and explicit time integration schemes. These studies demonstrate the computational advantages of fully coupled integration versus other time integration algorithms, though the performance of the competing models depends on the complexity of the underlying single crystal model. The study concludes by demonstrating that the choice of time integration method affects the sharpness of the predicted texture, with explicit methods for integrating the orientations overestimating texture sharpness and implicit methods underestimating texture sharpness.
Crystal plasticity↗
Comparison between explicit and implicit discretization strategies for a dissipative thermal environment
We investigate strategies for simulating open quantum systems coupled to dissipative baths by comparing explicit wave function-based discretization [via multi-layer multi-configuration time-dependent Hartree (ML-MCTDH)] and the implicit density matrix-based master equation method [via tree tensor network hierarchical equations of motion (TTN-HEOM)]. For dissipative baths characterized by exponentially decaying bath correlation functions, the implicit discretization approach of HEOM—rooted in bath correlation function decompositions—proves significantly more efficient than explicit discretization of the bath into discrete harmonic modes. Explicit methods, like ML-MCTDH, require extensive mode discretization to approximate continuum baths, leading to computational bottlenecks. Case studies for two-level systems and a Fenna–Matthews–Olson complex model highlight TTN-HEOM’s superiority in capturing dissipative dynamics with relaxations with a minimal number of auxiliary modes, while the explicit methods are as exact as the HEOM in pure dephasing regimes. This comparison is enabled by the TENSO package, which has both ML-MCTDH and TTN-HEOM implemented using the same computational structure and propagation strategy.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗