Base editing HbS to HbG-Makassar improves hemoglobin function supporting its use in sickle cell disease
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Phase Transitions in Protein Solutions and Kinetics of HbS Polymerization
No abstract available
Vekilov, Peter G.↗
Hydrogen Bonding Inside Anionic Polymeric Brush Layer: Machine Learning-Driven Exploration of the Relative Roles of the Polymer Steric Effect, Charging, and Type of Screening Counterions
This paper employs a combination of all-atom molecular dynamics (MD) simulations and unsupervised machine learning (ML) for studying the water-water hydrogen bonds (HBs) inside the anionic poly-acrylic acid (PAA) brushes modeled using all-atom MD simulations. PAA brush layer with different charge fraction (f), namely f=0, f=0.25, and f=1, is considered. Water-water interactions, both inside and outside the brush layer, are represented through distinct clusters of tupules of variables representing distances associated with the interacting water molecules. While clusters representing the HBs are present for water inside and outside the brushes, several clusters representing the long-range water-water interactions are missing for the water molecules inside the highly charged (f=1) PAA brushes. More importantly, inside highly charged brushes, the edge of the clusters representing the water-water HBs is progressively shortened, as compared to that in the bulk. Both these results stem from the presence of the PAA brushes imparting the steric effect and the charge effect, or the effect associated with enhanced interactions of water molecules with PE charges and counterions, thereby disrupting the water connectivity. This water-charged-species interaction also increases the water-water HB angle, i.e., makes the water-water HBs less stable inside the highly charged PAA brush layer. The narrowing of the clusters representing the HBs and the alteration of the angle characterizing the HBs confirm that the conditions defining the water-water HBs change inside the PAA brush layer as a function of the charges on the PAA brush layer. Furthermore, we show that the use of the generic definition of HBs, as compared to using our simulation-motivated modified definition of water-water HBs, overpredict the number of water-water HBs inside the PAA brush layer. Finally, we employ this all-atom-MD-ML framework to quantify the effect of other types of screening counterions (Li + , Ca 2+ , and Y 3+ ions) in determining the water-water interactions and water-water HB properties inside the PAA brush layer. Furthermore, the findings of the present study, confirming the weakening of water-water HBs inside the PAA brush layer, points to the possibility that the water molecules will be more available for hydrating the brush layer and counterions, thereby leading to a more pronounced wetting of the PAA brush layer.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Machine learning enabled quantification of the hydrogen bonds inside the polyelectrolyte brush layer probed using all-atom molecular dynamics simulations
The configuration of densely grafted charged polyelectrolyte (PE) brushes is strongly dictated by the properties and behavior of the counterions that screen the PE brush charges and the solvent molecules (typically water) that solvate the brush molecules and these screening counterions. Only recently, efforts have been made to study the PE brushes atomistically, thereby shedding light on the properties of brush-supported ions and water molecules. However, even for such efforts, there are limitations associated with using a generic definition to estimate certain properties of water and ions inside the brush layer. For example, water–water hydrogen bonds (HBs) will behave differently for locations outside and inside the brush layer, given the fact that the densely closely grafted PE brush molecules create a soft nanoconfinement where the water connectivity becomes highly disrupted: therefore, using the same definition to quantify the HBs inside and outside the brush layer will be unwise. In this paper, we address this limitation by employing an unsupervised machine learning (ML) approach to predict the water–water hydrogen bonding inside a cationic PE brush layer modeled using all-atom molecular dynamics (MD) simulations. Here, the ML method, which relies on a clustering approach and uses the equilibrium coordinates of the water molecules (obtained from the all-atom MD simulations) as the input, is capable of identifying the structural modification of water–water HBs (revealed through appropriate clustering of the data) inside the PE brush layer induced soft nanoconfinement. Such capabilities would not have been possible by using a generic definition of the HBs. Our calculations lead to four key findings: (1) the clusters formed inside and outside the brush layer are structurally similar; (2) the margin of the cluster is shorter inside the PE brush layer confirming the possible disruption of the HBs inside the PE brush layer; (3) the average “hydrogen–acceptor-oxygen–donor-oxygen” angle that defines the HB is reduced for the HBs formed inside the brush layer; (4) the use of the generic definition (definition usable for characterizing the HBs in brush-free bulk) leads to an overprediction of the number of HBs formed inside the PE brush layer.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
In situ irradiation of spent nuclear fuels
To improve the economics of commercial nuclear reactors, nuclear vendors and utilities are seeking approval for increased burnup usage of the existing nuclear fleet. This is especially critical for meeting the clean energy initiative by the United States Government, Department of Energy (DOE). However, one of the key challenges the nuclear industry faces in this regard is that the regions exposed to high burnup and low temperatures exhibit a fine-grained microstructure with large bubbles known as high-burnup structure (HBS) [1]. The formation of HBS has been correlated to the diminished performance of the reactor, as well as fuel fragmentation and pulverization during transient and accidental conditions [2]. Therefore, it is paramount to understand the mechanisms for HBS formation along with its impact on the properties and performance of nuclear fuels. While existing programs, such as Nuclear Energy Advanced Modeling and Simulation (NEAMS) and Advanced Fuel Campaign (AFC) are focusing on evaluating the performance impact of HBS, the physical mechanisms contributing to HBS formation are still not fully understood. In addition, having predictive capabilities and sound understanding of the microstructural evolution of nuclear fuel is essential for accelerated development, qualification, and deployment of new nuclear materials and novel reactor designs for advanced nuclear reactors. There is a lack of consensus among researchers regarding the mechanisms leading to such restructuring observed in HBS. Grain subdivision due to polygonization versus recrystallization, continuous versus discrete recrystallization occurring in tandem or conjunction, etc., have been proposed and debated. In general, it is hypothesized that defect accumulation and dislocation interaction within the grains cause the realignment of dislocations into grain boundaries, leading to the new subgrain formation, which over time transforms into new grains. However, due to the lack of transient data, the importance of fission rate, irradiation, thermal, and stress history of the fuel on the restructuring could not be assessed. In situ microstructural evolution under various irradiation conditions is desired to bridge this gap. Alternatively, phase-field-based models have been developed to capture HBS formation via discrete recrystallization utilizing the classical nucleation approach [3–5]. However, in these models, the grain nucleation criteria are often defined based on empirical relations for burnup and fission gas density leading to dislocation density change. A mechanistic approach to capture the dislocation interaction with the microstructural features leading to grain subdivision is lacking.
11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
BISON microstructure-based pulverization criterion in high burnup structure
To improve the economics of commercial nuclear power production, utilities are seeking to increase the allowable burnup limit of UO$_2$ fuel. One of the main factors that contributes to the current burnup limit of 62 GWd/MTU in commercial light water reactors (LWRs) is the risk of fine fragmentation or pulverization during a loss of coolant accident (LOCA). Pulverization primarily occurs at high burnups, especially when the high burnup structure (HBS) has formed. To allow the industry to pursue increased burnup and develop mitigation strategies, it is essential to have improved capability to predict the onset of pulverization. However, the mechanism of pulverization is not well understood, and the existing predictive capabilities implemented in the BISON fuel performance code are empirical in nature. In this report, mesoscale simulations are used to improve understanding of the formation mechanism of the HBS and how it responds during a LOCA transient, and inform development of a BISON pulverization criterion. A phase-field model was used to simulate the evolution of bubble pressure as a result of HBS formation. The simulations showed that gas atoms diffuse from grain interiors to the new grain boundaries created during HBS formation, and diffuse rapidly along these grain boundaries to reach existing bubbles. This causes an increase in bubble pressure in existing bubbles, leading to bubble growth during steady-state operation. To simulate the response of HBS bubbles to a LOCA transient, a newly developed phase-field model was used; in agreement with preliminary results from FY20, bubble size did not change significantly during the duration of the transient. A phase-field fracture model was used to study fragmentation patterns in the HBS, including using input from the phase-field model as initial conditions. Phase-field fracture simulations were used to determine a pulverization criterion for BISON. A function for the critical pressure for pulverization to occur was fit to data from the phase-field fracture simulations, and this function was implemented as a material property in BISON. For comparison, an analytical criterion for pulverization was developed and implemented within the same material property.
11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
Implementation and testing of physics-based pulverization model in BISON
This report summarizes lower length scale computational research conducted to improve the pulverization criterion for high-burnup UO 2 fuel in the BISON fuel performance code. This research was sponsored by the NEAMS program during FY22. Efforts to improve the model primarily focus on calculating the current pressure of bubbles in the high-burnup structure (HBS) region, as well as the critical bubble pressure at which pulverization occurs in the HBS. The phase-field model for predicting initial bubble pressure in the HBS was improved by implementing a more realistic model for defect production, and by coupling the phase-field model for inter-granular bubble evolution with the spatially-resolved cluster dynamics code Xolotl to simulate intra-granular fission gas evolution. An evolution equation for current bubble pressure was added to BISON, an improvement over the previous model that assumed that bubble pressure was static following HBS formation. To improve calculations of critical bubble pressure for pulverization, 3-D phase-field fracture simulations were performed, and a function for critical bubble pressure was fit—based on the simulation results—to replace the previous function, which had been determined using 2-D simulations. The impacts of these modifications to the existing pulverization assessment cases will be reported in the forthcoming engineering scale milestone on high-burnup UO 2 pulverization. A poromechanics-based approach was used to include the effect of bubble over pressurization on the stress state of the pellet at the engineering scale, and the initial strategy for integration of the pulverization criterion with pellet-scale mechanical degradation using a smeared cracking model was developed. This report also describes the initial research that was conducted to inform a forthcoming transient fission gas release (tFGR) model in BISON. Focusing on the fission gas release caused by pulverization of the outer pellet rim, a model for the amount of fission gas release was developed as a function of fuel porosity, bubble size, and fragment size. Implementation of this model in BISON and its impact of engineering-scale predictions will also be described in the aforementioned engineering-scale milestone on high-burnup UO 2 pulverization.
11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
Extending TOUGH + HYDRATE with a parallel particle transport simulator: numerical investigation of sand production during gas production from hydrate deposits
A new parallel code for simulating particle transport in porous media is integrated with the TOUGH + HYDRATE simulator to investigate sand production associated with gas production from unconsolidated gas hydrate-bearing sediments (HBS). Here, the parallel coupled simulator is named THMPT and uses the integral finite difference method to describe the Darcian and non-Darcian flow of fluids and heat transport, the finite element method to describe the associated geomechanical changes, and the discrete element method to track the trajectory of individual sand particles within the HBS. The THMPT simulator is written in Fortran, incorporates multiple optimized algorithms, and can comprehensively address the coupled flow, thermal, chemical, geomechanical, and particle transport processes that characterize the system behaviors during gas production from HBS. The simulator can capture all processes involved in sand particle transport in porous media, including sand detachment, collision, clogging (i.e., bridging), and migration. A benchmark case study of sand production in the course of depressurization-induced gas production from a representative HBS reveals various distinct microscopic particle migration mechanisms and the adverse impact of sand particle detachment, transport, and clogging. The numerical investigation also examines the effect of bottomhole pressure on mitigating sand production. The simulation results indicate that sand clogging near the wellbore significantly reduces permeability, decreasing gas production by at least 50%. Lastly, the efficiency of gravel packing in mitigating sand production is numerically evaluated, revealing that the structure of the porous media appears to profoundly influence the macroscopic motion behavior of sand particles and sand clogging characteristics.
discrete element method↗
An Initial Microstructurally Informed Model of High Burnup Structure Formation in UO 2 Fuel
The microstructure of a UO 2 fuel pellet changes as burnup increases, impacting fuel performance. Predicting and characterizing high burnup structure (HBS) and dark zone formation is a key part of supporting burnup limit extensions for light water reactors. This paper describes a model developed through fitting radially resolved pellet data obtained from recently published microstructural characterization data. The model predicts grain size and grain character, in addition to pore density and size, with fitting dependencies on power history variables. Separately fitting power history variables to microstructural parameters allows for insight into the underlying physical phenomena for future model development. Additionally, experimental data have been correlated to an HBS fraction to facilitate the development of a model capable of predicting a total fuel restructured fraction at the engineering scale. In conclusion, this two-step approach provides a coupling from reactor power history to microstructural data to fractional HBS and creates a basis to model HBS-dependent parameters in a fuel performance code.
High burnup structure↗
Characterization of the radial microstructural evolution in LWR UO 2 using electron backscatter diffraction
Studies on high burnup UO 2 subjected to loss-of-coolant accident conditions have shown that restructured regions of the fuel are susceptible to pulverization and eventual dispersal. Due to a lack of pre-test characterization, the distinct microstructural features rendering the fuel prone to fragmentation remain ambiguous. Four samples of commercially irradiated light-water reactor UO 2 have been characterized utilizing electron backscatter diffraction to assess the susceptible microstructure. The microscopy focused on determining the burnup and temperature conditions responsible for the formation of the different microstructural regions where the regions were denoted as the high-burnup structure (HBS), HBS transition, mid-radial, restructured central, and central region. Previous works have outlined the specific conditions required for the restructuring of the microstructure into the HBS, but the conditions responsible for the restructuring in the central region of the fuel are not well understood. The four analyzed samples confirm a burnup threshold of 61 GWd/tU, and an unknown temperature range is needed to facilitate the formation of the restructured central region. In conclusion, additional fuel performance evaluations are needed to quantify the temperature range promoting restructuring in the central region.
11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
Contributions to the mechanistic understanding of the microstructural evolution in irradiated U-Mo dispersion fuel
Here, advanced microstructural characterization techniques, such as scanning electron microscopy (SEM) and scanning transmission electron microscopy - energy dispersive x-ray spectroscopy (STEM-EDS), were used to interpret the fuel microstructure evolution and fission products behavior in U-Mo dispersion fuel irradiated in the Advanced Test Reactor (ATR) as part of the European Mini-Plate Irradiation Experiment (EMPIrE) test. The larger as-fabricated fuel grain size achieved by heat-treating the U-Mo powder resulted in slower high burnup structure (HBS) development and reduced fission gas porosity. Slower HBS kinetics was observed at the fuel kernels’ periphery, which contained smaller and less fission gas bubbles at all fission densities (FDs) investigated and was attributed to a locally reduced damage density and fission products concentration, as corroborated with Monte Carlo simulations. The non-refined grains at the fuel kernel periphery hosted a perfectly ordered fission Gas Bubble Superlattice (GBS) up to 6.3 × 10 21 fissions/cm 3 . Nano-scale STEM-EDS analysis presented in this study provided useful information on the GBS characteristic morphology and evolution in U-Mo fuel. The concentration of fission gas in the GBS progressively increased with FD, pointing to an evolution of the nanobubble pressure status with irradiation. A possible connection between the GBS collapse and HBS onset is proposed for which there exists a threshold in the misorientation of the refined sub-grains above which the GBS stability during irradiation is no longer preserved, resulting in the GBS collapse.
11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
Phase-stabilized 2D/3D hetero-bilayers via lattice matching for efficient and stable inverted solar cells
2D-on-3D (2D/3D) perovskite heterostructures with engineered energy landscapes offer the potential to realize efficient and stable inverted solar cells. However, managing the energy landscape using 2D perovskites with thicker inorganic layers n > 1 necessitates the usage of the chemically unstable methylammonium MA + . Here, we synthesized formamidinium (FA)-rich and pure-FA n = 3 Ruddlesden-Popper (RPP) and Dion-Jacobson perovskite (DJP) single crystals by identifying ligands with suitably lattice-matched organic and inorganic components of the 2D lattice. These crystals were translated onto 3D perovskites as capping layers, forming 2D/3D hetero-bilayers (HBs). Degradation studies revealed that HBs with butylammonium-based RPPs as capping layers rapidly phase segregate into non-perovskites under combined extrinsic stressors, compromising the underlying 3D layer, whereas FA-rich DJPs based on 3-aminomethylpiperidine retain their phase stability. The DJP HBs also possess a favorable energy landscape and electron transport at the 2D/3D interface, enabling inverted solar cells with a champion PCE of 25.33% and remarkable stability.
77 NANOSCIENCE AND NANOTECHNOLOGY↗
Structures of glass-forming liquids by x-ray scattering: Glycerol, xylitol, and D-sorbitol
In this work, synchrotron X-ray scattering has been used to investigate three liquid polyalcohols of different sizes (glycerol, xylitol and D-sorbitol) from above the glass transition temperatures $T_g$ to below. We focus on two structural orders: the association of the polar OH groups by hydrogen bonds (HBs) and the packing of the non-polar hydrocarbon groups. We find that the two structural orders evolve very differently reflecting the different natures of bonding. Upon cooling from 400 K, the O$\cdots$O correlation at 2.8 Å increases significantly in all three systems, indicating more HBs, until kinetic arrest at $T_g$; the increase is well described by an equilibrium between bonded and non-bonded OH with ΔH = 9.1 kJ/mol and ΔS = 13.4 J/mol/K. When heated above $T_g$, glycerol loses the fewest HBs per OH, followed by xylitol and by D-sorbitol, in the same order the number of OH groups per molecule increases (3, 5, and 6). The pair correlation functions of all three liquids show exponentially damped density modulations of wavelength 4.5 Å, which are associated with the main scattering peak and with the intermolecular C$\cdots$C correlation. In this respect, glycerol is the most ordered with the most persistent density ripples, followed by D-sorbitol and by xylitol. Heating above $T_g$ causes faster damping of the density ripples with the rate of change being the slowest in xylitol, followed by glycerol and by D-sorbitol. Given the different dynamic fragility of the three liquids (glycerol being the strongest and D-sorbitol the most fragile), we relate our results to the current theories of the structural origin for the difference. We find that the fragility difference is better understood on the basis of the thermal stability of HB clusters than that of the structure associated with the main scattering peak.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Deployment of BISON models of fuel restructuring at high burnup and related fission gas behavior in UO 2
This milestone report details the advancements made in fiscal year 2024 under the Nuclear Energy Advanced Modeling and Simulation (NEAMS) program to improve the modeling of fission gas behavior in high burnup UO 2 nuclear fuel in the BISON fuel performance code. As nuclear fuel is pushed to higher burnups, significant microstructural changes occur within the fuel, including the formation of a high burnup structure (HBS) on the pellet rim and a dark zone deeper within the pellet. These regions, characterized by subgrain formation and increased pore densities, have critical implications for fission gas behavior and release, which are not well understood. The modeling capabilities in BISON did not adequately predict these phenomena, leading to an underestimation of fuel restructuring and - potentially - of fission gas release. To address these gaps, this milestone focused on three key objectives: (1) reviewing and assessing Sifgrs's capabilities for low burnup fuel, on which high burnup capabilities rely, (2) validating and expanding HBS fission gas modeling capabilities, including investigating mechanisms for fission gas release from HBS, and (3) expanding Sifgrs to enable modeling of dark zone formation and its effects on fission gas behavior. These objectives were achieved and are described herein. The achievements of this NEAMS milestone are significant for the industry's goal of burnup extension. The improved predictive modeling capabilities for both low- and high-burnup conditions enhance our understanding of fuel performance under both normal operations and transient scenarios. Although goals were reached, future work is necessary to validate these models against experimental data and quantify their accuracy in different conditions. In parallel, mechanistic modeling efforts should continue to extend and refine these capabilities to increase accuracy while reducing reliance on empirical models. This will ensure robust performance across a broader range of conditions.
11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
The Sound Parameter Effect in Metal-Rich Globular Clusters
Recent Hubble Space Telescope observations have found that the horizontal branches (HBs) in the metal-rich globular clusters NGC 6388 and NGC 6441 slope upward with decreasing B - V. Such a slope is not predicted by canonical HB models and cannot be produced by either a greater cluster age or enhanced mass loss along the red giant branch (RGB). The peculiar HB morphology in these clusters may provide an important clue for understanding the second-parameter effect. We have carried out extensive evolutionary calculations and numerical simulations in order to explore three noncanonical scenarios for explaining the sloped HBs in NGC 6388 and NGC 6441: (1) a high cluster helium abundance scenario, in which the HB evolution is characterized by long blue loops; (2) a rotation scenario, in which internal rotation during the RGB phase increases the HB core mass; and (3) a helium-mixing scenario, in which deep mixing on the RGB enhances the envelope helium abundance. All of these scenarios predict sloped HBs with anomalously bright RR Lyrae variables. We compare this prediction with the properties of the two known RR Lyrae variables in NGC 6388. Additional observational tests of these scenarios are suggested.
Hall, D. K↗
Effects of ZrN Coating and Heat Treatment on U-Mo Dispersion Fuel under Irradiation
The stability of U-Mo fuel particles in Al matrix can be improved using ZrN coating and heat treatment. This study investigated irradiation behaviors of fuel plates containing U-Mo fuel particles fabricated with different conditions including heat treatment and the thickness of ZrN coating. Additionally, different fission densities were applied to each fuel plate to understand how varying fission densities affect its irradiation behaviors. This study showed that more recrystallization of grains and development of high burnup structure (HBS) occurred in irradiated fuel particles with higher fission densities. Heat treatment reduced the accumulation of fission gas bubbles in the fuel particles by coarsening their grains. The fuel particles with a ZrN coating thickness of 1.2-1.8 µm showed less significant development of U-Mo/Al interaction layers than the particles with a coating thickness of 0.5 µm after irradiation. This might indicate the existence of a critical thickness of ZrN coating to minimize the formation of the interaction layers. Fission gas bubbles were observed at grain boundaries of irradiated U-Mo fuel particles at low fission densities, and the formation of dendritic features with a darker contrast was identified in backscattered electron images. These features stemmed from grain boundaries with fission gas bubbles or HBS, and some of them contained the bubbles, indicating that they might represent an early stage of HBS propagation in the fuel particles.
11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
Macrocyclic β‐Sheets Stabilized by Hydrogen Bond Surrogates
Abstract Mimics of protein secondary and tertiary structure offer rationally‐designed inhibitors of biomolecular interactions. β‐Sheet mimics have a storied history in bioorganic chemistry and are typically designed with synthetic or natural turn segments. We hypothesized that replacement of terminal inter‐β‐strand hydrogen bonds with hydrogen bond surrogates (HBS) may lead to conformationally‐defined macrocyclic β‐sheets without the requirement for natural or synthetic β‐turns, thereby providing a minimal mimic of a protein β‐sheet. To access turn‐less antiparallel β‐sheet mimics, we developed a facile solid phase synthesis protocol. We surveyed a dataset of protein β‐sheets for naturally observed interstrand side chain interactions. This bioinformatics survey highlighted an over‐abundance of aromatic–aromatic, cation‐π and ionic interactions in β‐sheets. In correspondence with natural β‐sheets, we find that minimal HBS mimics show robust β‐sheet formation when specific amino acid residue pairings are incorporated. In isolated β‐sheets, aromatic interactions endow superior conformational stability over ionic or cation‐π interactions. Circular dichroism and NMR spectroscopies, along with high‐resolution X‐ray crystallography, support our design principles.
Chemistry↗