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Results for “Nuclear binding”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 289 records · Page 16
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Genetic circuit design automation for yeast

Cells can be programmed to monitor and react to their environment using genetic circuits. Design automation software maps a desired circuit function to a DNA sequence, a process that requires units of gene regulation (gates) that are simple to connect and behave predictably. This poses a challenge for eukaryotes due to their complex mechanisms of transcription and translation. To this end, we have developed gates for yeast (Saccharomyces cerevisiae) that are connected using RNA polymerase flux as the signal carrier and are insulated from each other and host regulation. They are based on minimal constitutive promoters (~120 base pairs), for which rules are developed to insert operators for DNA-binding proteins. Using this approach, in this work we constructed nine NOT/NOR gates with nearly identical response functions and 400-fold dynamic range. In circuits, they are transcriptionally insulated from each other by placing ribozymes downstream of terminators to block nuclear export of messenger RNAs resulting from RNA polymerase readthrough. Based on these gates, Cello 2.0 was used to build circuits with up to 11 regulatory proteins. A simple dynamic model predicts the circuit response over days. Genetic circuit design automation for eukaryotes simplifies the construction of regulatory networks as part of cellular engineering projects, whether it be to stage processes during bioproduction, serve as environmental sentinels or guide living therapeutics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Atomistic modeling of lanthanide diffusion in refractory body-centered cubic molybdenum

Lanthanide fission products can strongly interact with candidate cladding alloys, but their transport properties in refractory metals remain poorly understood. Here, in this work, we investigate the atomic-scale diffusion behavior of La, Ce, Pr, and Nd in body-centered cubic (bcc) molybdenum, a potential candidate for advanced nuclear cladding. Self-consistent mean-field transport modeling is performed to evaluate the fission product transport and vacancy mobility, informed by first-principles and nudged elastic band calculations of vacancy formation energies, migration barriers, and solute–vacancy binding characteristics. Compared with bcc Fe, lanthanide solutes in bcc Mo exhibit slower tracer diffusion due to higher vacancy formation and migration energies. Furthermore, the calculations reveal that the influence of fission products on migration barriers in bcc Mo are not as extensive in range compared to bcc Fe. Among the studied lanthanides, La exhibits the strongest vacancy binding while also being the fastest diffuser in Mo. These findings highlight how refractory bcc alloys can reduce fission product infiltration, offering valuable insight into the development of durable cladding systems for advanced reactors.

36 - MATERIALS SCIENCE↗
DOE OSTI2023

Towards the understanding of the genuine three-body interaction for p–p–p and p–p–Λ

Three-body nuclear forces play an important role in the structure of nuclei and hypernuclei and are also incorporated in models to describe the dynamics of dense baryonic matter, such as in neutron stars. So far, only indirect measurements anchored to the binding energies of nuclei can be used to constrain the three-nucleon force, and if hyperons are considered, the scarce data on hypernuclei impose only weak constraints on the three-body forces. In this work, we present the first direct measurement of the p–p–p and p–p–Λ systems in terms of three-particle correlation functions carried out for pp collisions at $\sqrt{s}$=13 TeV. Three-particle cumulants are extracted from the correlation functions by applying the Kubo formalism, where the three-particle interaction contribution to these correlations can be isolated after subtracting the known two-body interaction terms. A negative cumulant is found for the p–p–p system, hinting to the presence of a residual three-body effect while for p–p–Λ the cumulant is consistent with zero. This measurement demonstrates the accessibility of three-baryon correlations at the LHC.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

Direct Observation of Ammonia Storage in UiO-66 Incorporating Cu(II) Binding Sites

The presence of active sites in metal–organic framework (MOF) materials can control and affect their performance significantly in adsorption and catalysis. However, revealing the interactions between the substrate and active sites in MOFs at atomic precision remains a challenging task. Here, we report the direct observation of binding of NH 3 in a series of UiO-66 materials containing atomically dispersed defects and open Cu(I) and Cu(II) sites. While all MOFs in this series exhibit similar surface areas (1111–1135 m 2 g –1 ), decoration of the -OH site in UiO-66-defect with Cu(II) results in a 43% enhancement of the isothermal uptake of NH 3 at 273 K and 1.0 bar from 11.8 in UiO-66-defect to 16.9 mmol g –1 in UiO-66-Cu II . A 100% enhancement of dynamic adsorption of NH 3 at a concentration level of 630 ppm from 2.07 mmol g –1 in UiO-66-defect to 4.15 mmol g –1 in UiO-66-Cu II at 298 K is observed. In situ neutron powder diffraction, inelastic neutron scattering, and electron paramagnetic resonance, solid-state nuclear magnetic resonance, and infrared spectroscopies, coupled with modeling reveal that the enhanced NH 3 uptake in UiO-66-Cu II originates from a {Cu(II)···NH 3 } interaction, with a reversible change in geometry at Cu(II) from near-linear to trigonal coordination. This work represents the first example of structural elucidation of NH 3 binding in MOFs containing open metal sites and will inform the design of new efficient MOF sorbents by targeted control of active sites for NH 3 capture and storage.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Mitigating Green's function Monte Carlo signal-to-noise problems using contour deformations

The Green's function Monte Carlo (GFMC) method provides accurate solutions to the nuclear many-body problem and predicts properties of light nuclei starting from realistic two- and three-body interactions. Controlling the GFMC fermion sign problem is crucial, as the signal-to-noise ratio decreases exponentially with imaginary time, requiring significant computing resources. Inspired by similar scenarios in lattice quantum field theory and spin systems, in this work, we employ integration contour deformations to improve the GFMC signal-to-noise ratio. Machine learning techniques are used to select optimal contours with minimal variance from parametrized families of deformations. As a proof of principle, we consider the deuteron binding energies and Euclidean density response functions. Here, we only observe mild signal-to-noise improvement for the binding energy case. On the other hand, we achieve an order of magnitude reduction of the variance for Euclidean density response functions, paving the way for computing electron- and neutrino-nucleus cross sections of larger nuclei.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2021

Effective interactions between nuclear clusters

In this work, the effective interactions between two nuclear clusters, d + d, t + t, and α + α, are investigated within a cluster model using local nucleon-nucleon (NN) forces. It is shown that the interaction in the spin-aligned d + d system is repulsive for all intercluster distances, whereas the α + α and spin-aligned t + t systems are attractive at intermediate distances. The Pauli blocking between identical-nucleon pairs is responsible for the cluster-cluster repulsion and becomes dominant in the shallow binding limit. We demonstrate that two d clusters could be bound if the NN force has nonzero range and is strong enough to form a deeply bound d cluster, or if the NN force has both even-parity and odd-parity attraction. Effective dimer-dimer interactions for general quantum systems of two-component fermions are also discussed in heavy-light mass limit, where one component is much heavier than the other, and their relation to intercluster interactions in nuclear systems are discussed. Our findings provide a conceptual foundation for conclusions obtained numerically in the literature, that increasing the range or strength of the local part of the attractive nucleon-nucleon interaction results in a more attractive cluster-cluster interaction.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2024

Microscale Thermophoresis (MST) as a Tool to Study Binding Interactions of Oxygen-Sensitive Biohybrids

Microscale thermophoresis (MST) is a technique used to measure the strength of molecular interactions. MST is a thermophoretic-based technique that monitors the change in fluorescence associated with the movement of fluorescent-labeled molecules in response to a temperature gradient triggered by an IR LASER. MST has advantages over other approaches for examining molecular interactions, such as isothermal titration calorimetry, nuclear magnetic resonance, biolayer interferometry, and surface plasmon resonance, requiring a small sample size that does not need to be immobilized and a high-sensitivity fluorescence detection. In addition, since the approach involves the loading of samples into capillaries that can be easily sealed, it can be adapted to analyze oxygen-sensitive samples. In this Bio-protocol, we describe the troubleshooting and optimization we have done to enable the use of MST to examine protein–protein interactions, protein–ligand interactions, and protein–nanocrystal interactions. The salient elements in the developed procedures include 1) loading and sealing capabilities in an anaerobic chamber for analysis using a NanoTemper MST located on the benchtop in air, 2) identification of the optimal reducing agents compatible with data acquisition with effective protection against trace oxygen, and 3) the optimization of data acquisition and analysis procedures. The procedures lay the groundwork to define the determinants of molecular interactions in these technically demanding systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

A nanobody suite for yeast scaffold nucleoporins provides details of the nuclear pore complex structure

Nuclear pore complexes (NPCs) are the main conduits for molecular exchange across the nuclear envelope. The NPC is a modular assembly of ~500 individual proteins, called nucleoporins or nups. Most scaffolding nups are organized in two multimeric subcomplexes, the Nup84 or Y complex and the Nic96 or inner ring complex. Working in S. cerevisiae, and to study the assembly of these two essential subcomplexes, we here develop a set of twelve nanobodies that recognize seven constituent nucleoporins of the Y and Nic96 complexes. These nanobodies all bind specifically and with high affinity. We present structures of several nup-nanobody complexes, revealing their binding sites. Additionally, constitutive expression of the nanobody suite in S. cerevisiae detect accessible and obstructed surfaces of the Y complex and Nic96 within the NPC. Overall, this suite of nanobodies provides a unique and versatile toolkit for the study of the NPC.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Modulation of Uptake and Reactivity of Nitrogen Dioxide in Metal-Organic Framework Materials

We report the modulation of reactivity of nitrogen dioxide (NO 2 ) in a charged metal–organic framework (MOF) material, MFM-305-CH 3 in which unbound N-centres are methylated and the cationic charge counter-balanced by Cl - ions in the pores. Uptake of NO 2 into MFM-305-CH 3 leads to reaction between NO 2 and Cl - to give nitrosyl chloride (NOCl) and NO 3 - anions. A high dynamic uptake of 6.58 mmol g -1 at 298 K is observed for MFM-305-CH 3 as measured using a flow of 500 ppm NO 2 in He. In contrast, the analogous neutral material, MFM-305, shows a much lower uptake of 2.38 mmol g -1 . The binding domains and reactivity of adsorbed NO 2 molecules within MFM-305-CH 3 and MFM-305 have been probed using in situ synchrotron X-ray diffraction, inelastic neutron scattering and by electron paramagnetic resonance, high-field solid-state nuclear magnetic resonance and UV/Vis spectroscopies. The design of charged porous sorbents provides a new platform to control the reactivity of corrosive air pollutants.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Hexagonal boron nitride: Epitaxial growth and device applications

As a newest family member of the III-nitrides, BN is considered amongst the remaining frontiers in wide energy bandgap semiconductors with potentials for technologically significant applications in deep UV (DUV) optoelectronics, solid-state neutron detectors, electron emitters, single photon emitters, switching/memory devices, and super-capacitors. It was shown that it is possible to produce h-BN epilayers with high hexagonal phase purity, UV transparency, and film stoichiometry by employing nitrogen-rich growth conditions. The quasi-2D nature of h-BN supports unusually strong optical transitions near the band edge and a large exciton binding energy on the order of 0.7 eV. Since the isotope of B-10 has a large capture cross-section for thermal neutrons, h-BN is an ideal material for the fabrication of solid-state neutron detectors for special nuclear materials detection, well and geothermal logging, and medical imaging applications. Freestanding B-10 enriched h-BN (h- 10 BN) epilayers with varying thicknesses up to 200 μm have been successfully synthesized by metal organic chemical vapor deposition (MOCVD) as of this writing. By utilizing the conductivity anisotropy nature of h-BN, 1 cm 2 lateral detectors fabricated from 100 μm thick h-10BN epilayers have demonstrated a detection efficiency of 59% for thermal neutrons, which is the highest on record among all solid-state neutron detectors as of today. It was noted that high growth temperatures, long growth times and the use of sapphire substrate tend to incorporate oxygen related impurities into h- 10 BN epilayers, which strongly impacted the carrier mobility-lifetime (μτ) products and charge collection efficiencies of h- 10 BN neutron detectors. As the h-BN material technology further develops, improved carrier mobilities and μτ products will allow the fabrication of h-BN devices with enhanced performance.

42 ENGINEERING↗
DOE OSTI2023

A bromodomain-independent mechanism of gene regulation by the BET inhibitor JQ1: direct activation of nuclear receptor PXR

Abstract Bromodomain and extraterminal (BET) proteins are extensively studied in multiple pathologies, including cancer. BET proteins modulate transcription of various genes, including those synonymous with cancer, such as MYC. Thus, BET inhibitors are a major area of drug development efforts. (+)-JQ1 (JQ1) is the prototype inhibitor and is a common tool to probe BET functions. While showing therapeutic promise, JQ1 is not clinically usable, partly due to metabolic instability. Here, we show that JQ1 and the BET-inactive (−)-JQ1 are agonists of pregnane X receptor (PXR), a nuclear receptor that transcriptionally regulates genes encoding drug-metabolizing enzymes such as CYP3A4, which was previously shown to oxidize JQ1. A PXR-JQ1 co-crystal structure identified JQ1′s tert-butyl moiety as a PXR anchor and explains binding by (−)-JQ1. Analogs differing at the tert-butyl lost PXR binding, validating our structural findings. Evaluation in liver cell models revealed both PXR-dependent and PXR-independent modulation of CYP3A4 expression by BET inhibitors. We have characterized a non-BET JQ1 target, a mechanism of physiological JQ1 instability, a biological function of (−)-JQ1, and BET-dependent transcriptional regulation of drug metabolism genes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Current Needs in Radiochemistry

There are a number of current needs in the development of the Pu and Am separations that underpin larger interest areas including nuclear waste issues, nuclear weapons, nuclear forensics, nuclear fuels and similarly related fields. In the large areas of interest, there are a number of sub-fields that include corrosion chemistry, pyrochemistry, solution-phase chemistry, rapid separations, environmental speciation, and other similar efforts. However, in all of the these fields it is important to realize that the underlying chemistry that underpins these efforts is similar in that Pu and Am are bound to ligands that can be in the solid, aqueous, or gas phase and separations occurs due to the preferential binding of the ligand to Pu or Am based on a number of factors that include pH, concentration, oxidation state, etc. In the past, most of the Pu and Am chemistry has occurred in limited scope within universities where micro-scale and bench-top scale chemistry are the dominate investigative theme. At US national laboratory and their international counterparts, larger scale reactions have been attempted such that industrial scale chemistry has been completed. Some of this technology has been harnessed in radiopharmaceuticals and nuclear fuel reprocessing. However, such bench-top research is expensive to due to the safety and security that is concerned when dealing with Pu, and scale-up of reactions is even more resource intensive. In an effort to offset this expensive, it would be of interest to explore the ability to predict selectivity based on the computational modeling of actinide chemistry. This has historically been limited by the abilities of large supercomputers, but with the emphasis on developing exascale computers within the US and similar efforts by other countries this predictive modeling has potential to produce significant results that would yield improved understanding of actinide chemistry.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2025

Strontium Speciation in Relevant Tank Waste Components Examined by Electrospray Ionization Mass Spectrometry

The identification of chemical species formed in complex nuclear waste is crucial for the development and employment of advanced separations technologies to remediate the Hanford site by processing tank waste. The current Tank Side Cesium Removal (TSCR) process deployed at Hanford utilizes crystalline silicotitanate (CST) ion exchange (IX) media to aid in the separation of low-activity waste for proper treatment and disposal. The inorganic IX media is highly selective for Cs but has been shown to also remove Sr from caustic simulants and small-scale IX processing of Hanford tank waste.(Fiskum, Rovira et al. 2019, Fiskum, Campbell et al. 2021, Westesen, Campbell et al. 2022) Quantitative Sr removal has not been observed in all tank waste supernates tested; thus, to better understand Sr removal and effectively predict processing behavior through TSCR, it is necessary to first investigate Sr speciation in tank waste. This work utilized electrospray ionization mass spectrometry (ESI-MS) to identify ionic Sr complexes that form in the presence of NO 3 –, NO 2 –, OH–, and Cl–. Although our results show that NO 3 –, NO 2 –, and OH– are competitive for Sr 2+ binding, previous data from IX studies indicate that [SrOH] + is not the dominant species of concern in tank waste processing schemes.(Fiskum, Campbell and Trang-Le 2020) Our results show that the [Sr(NO3)]+ species and the [Sr(NO2)] + species form in considerable abundances, which may affect the ability to separate Sr using CST in nuclear waste separation processes.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2021

Unlocking the secret of lignin-enzyme interactions: Recent advances in developing state-of-the-art analytical techniques

Bioconversion of renewable lignocellulosics to produce liquid fuels and chemicals is one of the most effective ways to solve the problem of fossil resource shortage, energy security, and environmental challenges. Among the many biorefinery pathways, hydrolysis of lignocellulosics to fermentable monosaccharides by cellulase is arguably the most critical step of lignocellulose bioconversion. In the process of enzymatic hydrolysis, the direct physical contact between enzymes and cellulose is an essential prerequisite for the hydrolysis to occur. However, lignin is considered one of the most recalcitrant factors hindering the accessibility of cellulose by binding to cellulase unproductively, which reduces the saccharification rate and yield of sugars. This results in high costs for the saccharification of carbohydrates. The various interactions between enzymes and lignin have been explored from different perspectives in literature, and a basic lignin inhibition mechanism has been proposed. However, the exact interaction between lignin and enzyme as well as the recently reported promotion of some types of lignin on enzymatic hydrolysis is still unclear at the molecular level. Multiple analytical techniques have been developed, and fully unlocking the secret of lignin-enzyme interactions would require a continuous improvement of the currently available analytical techniques. This review summarizes the current commonly used advanced research analytical techniques for investigating the interaction between lignin and enzyme, including quartz crystal microbalance with dissipation (QCM-D), surface plasmon resonance (SPR), attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy, atomic force microscopy (AFM), nuclear magnetic resonance (NMR) spectroscopy, fluorescence spectroscopy (FLS), and molecular dynamics (MD) simulations. Interdisciplinary integration of these analytical methods is pursued to provide new insight into the interactions between lignin and enzymes. Finally, this review will serve as a resource for future research seeking to develop new methodologies for a better understanding of the basic mechanism of lignin-enzyme binding during the critical hydrolysis process.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Diffusion behavior of lanthanide fission products in bcc Fe cladding: A first-principles study

Fuel-cladding chemical interaction poses significant challenges in nuclear reactors, where fission products generated from nuclear fuel interact with Fe-based cladding materials, potentially compromising their structural integrity. This study investigates the diffusion behavior of lanthanide fission products, Lanthanum (La), Cerium (Ce), Praseodymium (Pr), and Neodymium (Nd), within body-centered cubic (bcc) Fe cladding using the density functional theory, nudged elastic band method, and self-consistent mean field theory. Our results reveal significant vacancy binding energies, particularly with the 1st and 2nd nearest neighbors, which diminish beyond the 5th nearest neighbor, with La exhibiting the strongest binding affinity, followed by Nd, Ce, and Pr. The nudged elastic band calculations indicate significant high barriers for the dissociation of 1st nearest neighbor vacancy-solute pairs for all fission products. The tracer diffusion coefficients of these fission products were derived in an Arrhenius form, with a magnetic correction that accounts for the high-temperature paramagnetic state. The significant trapping effect of vacancies caused by a very dilute concentration of fission products reduces vacancy mobility, potentially leading to modifications in point defect supersaturation, void nucleation, and swelling under irradiation. These represent critical challenges for irradiated cladding materials. The tracer diffusion coefficients indicate that Nd diffuses the fastest, followed by La, Ce, and Pr. Furthermore, this study provides essential insights for understanding fission product transport in cladding materials and informs future design strategies to mitigate fuel-cladding chemical interaction, ultimately enhancing nuclear reactor safety and performance.

Diffusion↗
DOE OSTI2023

Examining Interactions of Uranyl(VI) Ions with Amino Acids in the Gas Phase

Gas-phase experiments, using electrospray ionization quadrupole ion trap mass spectrometry (ESI-QIT/MS), were conducted to probe basic interactions of the uranyl(VI) ion, UO 2 2+ , with selected natural amino acids, namely, L-cysteine (Cys), L-histidine (His), and L-aspartic acid (Asp), which strongly bind to metal ions. The simplest amino acid, glycine (Gly), was also studied for comparison. Cys, His, and Asp have additional potentially coordinating groups beyond the amino and carboxylic acid functional groups, specifically thiol in Cys, imidazole in His, and a second carboxylate in Asp. Gas-phase experiments comprised collision-induced dissociation (CID) of uranyl–amino acid complexes and competitive CID to assess the relative binding strength of different amino acids in the same uranyl complex. Reactivity of selected uranyl–amino acid complexes with water provided further insights into relative stabilities. In positive ion mode, CID and ensuing reactions with water suggested that uranyl–neutral AA binding strength decreased in the order His > Asp > Cys > Gly, which is similar to amino acid proton affinities. In negative ion mode, CID revealed a decreasing dissociation tendency in the order Gly >> His ≈ Cys > Asp, presumably reflecting a reverse enhanced binding to uranyl of the doubly deprotonated amino acids formed in CID.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2023

Mitigating Green's function Monte Carlo signal-to-noise problems using contour deformations

The Green's function Monte Carlo (GFMC) method provides accurate solutions to the nuclear many-body problem and predicts properties of light nuclei starting from realistic two- and three-body interactions. Controlling the GFMC fermion-sign problem is crucial, as the signal-to-noise ratio decreases exponentially with Euclidean time, requiring significant computing resources. Inspired by similar scenarios in lattice quantum field theory and spin systems, in this work, we employ integration contour deformations to improve the GFMC signal-to-noise ratio. Machine learning techniques are used to select optimal contours with minimal variance from parameterized families of deformations. As a proof of principle, we consider the deuteron binding energies and Euclidean density response functions. We only observe mild signal-to-noise improvement for the binding energy case. On the other hand, we achieve an order of magnitude reduction of the variance for Euclidean density response functions, paving the way for computing electron- and neutrino-nucleus cross-sections of larger nuclei.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗