Engineering Papers⌕ Search

SEARCH · Engineering Papers

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 181 records · Page 10
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Nucleon-pair coupling scheme in Elliott's SU(3) model

Elliott's SU(3) model is at the basis of the shell-model description of rotational motion in atomic nuclei. Here we demonstrate that SU(3) symmetry can be realized in a truncated shell-model space if constructed in terms of a sufficient number of collective S, D, G,...pairs (i.e., with angular momentum zero, two, four,...) and if the structure of the pairs is optimally determined either by a conjugate-gradient minimization method or from a Hartree-Fock intrinsic state. We illustrate the procedure for six protons and six neutrons in the pf (sdg) shell and exactly reproduce the level energies and electric quadrupole properties of the ground-state rotational band with SDG (SDGI) pairs. The SD-pair approximation without significant renormalization, on the other hand, cannot describe the full SU(3) collectivity. A mapping from Elliott's fermionic SU(3) model to systems with s, d, g,... bosons provides insight into the existence of a decoupled collective subspace in terms of S, D, G,... pairs.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2025

An evolutionarily conserved tryptophan cage promotes folding of the extended RNA recognition motif in the hnRNPR ‐like protein family

Abstract The heterogeneous nuclear ribonucleoprotein (hnRNP) R‐like family is a class of RNA binding proteins in the hnRNP superfamily with diverse functions in RNA processing. Here, we present the 1.90 Å X‐ray crystal structure and solution NMR studies of the first RNA recognition motif (RRM) of human hnRNPR. We find that this domain adopts an extended RRM (eRRM1) featuring a canonical RRM with a structured N‐terminal extension (N ext ) motif that docks against the RRM and extends the β‐sheet surface. The adjoining loop is structured and forms a tryptophan cage motif to position the N ext motif for docking to the RRM. Combining mutagenesis, solution NMR spectroscopy, and thermal denaturation studies, we evaluate the importance of residues in the N ext –RRM interface and adjoining loop on eRRM folding and conformational dynamics. We find that these sites are essential for protein solubility, conformational ordering, and thermal stability. Consistent with their importance, mutations in the N ext –RRM interface and loop are associated with several cancers in a survey of somatic mutations in cancer studies. Sequence and structure comparison of the human hnRNPR eRRM1 to experimentally verified and predicted hnRNPR‐like proteins reveals conserved features in the eRRM.

Biochemistry & Molecular Biology↗
DOE OSTI2022

Angular momentum eigenstates of the isotropic 3-D harmonic oscillator: Phase-space distributions and coalescence probabilities

The isotropic 3-dimensional harmonic oscillator potential can serve as an approximate description of many systems in atomic, solid state, nuclear, and particle physics. In particular, the question of 2 particles binding (or coalescing) into angular momentum eigenstates in such a potential has interesting applications. Here we compute the probabilities for coalescence of two distinguishable, non-relativistic particles into such a bound state, where the initial particles are represented by generic wave packets of given average positions and momenta. We use a phase-space formulation and hence need the Wigner distribution functions of angular momentum eigenstates in isotropic 3-dimensional harmonic oscillators. These distribution functions have been discussed in the literature before but we utilize an alternative approach to obtain these functions. Along the way, we derive a general formula that expands angular momentum eigenstates in terms of products of 1-dimensional harmonic oscillator eigenstates.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2025

Defining the Antitumor Mechanism of Action of a Clinical-stage Compound as a Selective Degrader of the Nuclear Pore Complex

Cancer cells are acutely dependent on nuclear transport due to elevated transcriptional activity, suggesting an unrealized opportunity for selective therapeutic inhibition of the nuclear pore complex (NPC). Through large-scale phenotypic profiling of cancer cell lines, genome-scale functional genomic modifier screens, and mass spectrometry–based proteomics, we discovered that the clinical drug PRLX-93936 is a molecular glue that binds and reprograms the TRIM21 ubiquitin ligase to degrade the NPC. Upon compound-induced TRIM21 recruitment, the nuclear pore is ubiquitylated and degraded, resulting in the loss of short-lived cytoplasmic mRNA transcripts and the induction of cancer cell apoptosis. Direct compound binding to TRIM21 was confirmed via surface plasmon resonance and X-ray crystallography, whereas compound-induced TRIM21–nucleoporin complex formation was demonstrated through multiple orthogonal approaches in cells and in vitro. Phenotype-guided optimization yielded compounds with 10-fold greater potency and drug-like properties, along with robust pharmacokinetics and efficacy against pancreatic cancer xenografts and patient-derived organoids.

Yuan, Linjie [Stanford School of Medicine, CA (Uni↗
DOE OSTI2022

Characterization of Heparin’s Conformational Ensemble by Molecular Dynamics Simulations and Nuclear Magnetic Resonance Spectroscopy

Heparin is a highly charged, polysulfated polysaccharide and serves as an anticoagulant. Heparin binds to multiple proteins throughout the body, suggesting a large range of potential therapeutic applications. Although its function has been characterized in multiple physiological contexts, heparin’s solution conformational dynamics and structure–function relationships are not fully understood. Molecular dynamics (MD) simulations facilitate the analysis of a molecule’s underlying conformational ensemble, which then provides important information necessary for understanding structure–function relationships. However, for MD simulations to afford meaningful results, they must both provide adequate sampling and accurately represent the energy properties of a molecule. The aim of this study is to compare heparin’s conformational ensemble using two well-developed force fields for carbohydrates, known as GLYCAM06 and CHARMM36, using replica exchange molecular dynamics (REMD) simulations, and to validate these results with NMR experiments. In this work, the anticoagulant sequence, an ultra-low-molecular-weight heparin, known as Arixtra (fondaparinux, sodium), was simulated with both parameter sets. The results suggest that GLYCAM06 matches experimental nuclear magnetic resonance three-bond J-coupling values measured for Arixtra better than CHARMM36. In addition, NOESY and ROESY experiments suggest that Arixtra is very flexible in the sub-millisecond time scale and does not adopt a unique structure at 25 C. Moreover, GLYCAM06 affords a much more dynamic conformational ensemble for Arixtra than CHARMM36.

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

A phage nucleus-associated RNA-binding protein is required for jumbo phage infection

Abstract Large-genome bacteriophages (jumbo phages) of the proposed family Chimalliviridae assemble a nucleus-like compartment bounded by a protein shell that protects the replicating phage genome from host-encoded restriction enzymes and DNA-targeting CRISPR-Cas nucleases. While the nuclear shell provides broad protection against host nucleases, it necessitates transport of mRNA out of the nucleus-like compartment for translation by host ribosomes, and transport of specific proteins into the nucleus-like compartment to support DNA replication and mRNA transcription. Here, we identify a conserved phage nuclear shell-associated protein that we term Chimallin C (ChmC), which adopts a nucleic acid-binding fold, binds RNA with high affinity in vitro, and binds phage mRNAs in infected cells. ChmC also forms phase-separated condensates with RNA in vitro. Targeted knockdown of ChmC using mRNA-targeting dCas13d results in accumulation of phage-encoded mRNAs in the phage nucleus, reduces phage protein production, and compromises virion assembly. Taken together, our data show that the conserved ChmC protein plays crucial roles in the viral life cycle, potentially by facilitating phage mRNA translocation through the nuclear shell to promote protein production and virion development.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Spatial Engineering Direct Cooperativity between Binding Sites for Uranium Sequestration

Preorganization is a basic design principle used by nature that allows for synergistic pathways to be expressed. Herein, a full account of the conceptual and experimental development from randomly distributed functionalities to a convergent arrangement that facilitates cooperative binding is given, thus conferring exceptional affinity toward the analyte of interest. The resulting material with chelating groups populated adjacently in a spatially locked manner displays up to two orders of magnitude improvement compared to a random and isolated manner using uranium sequestration as a model application. This adsorbent shows exceptional extraction efficiencies, capable of reducing the uranium concentration from 5 ppm to less than 1 ppb within 10 min, even though the system is permeated with high concentrations of competing ions. The efficiency is further supported by its ability to extract uranium from seawater with an uptake capability of 5.01 mg g -1 , placing it among the highest-capacity seawater uranium extraction materials described to date. The concept presented here uncovers a new paradigm in the design of efficient sorbent materials by manipulating the spatial distribution to amplify the cooperation of functions.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2020

Quantified limits of the nuclear landscape

The chart of the nuclides is limited by particle drip lines beyond which nuclear stability to proton or neutron emission is lost. Predicting the range of particle-bound isotopes poses an appreciable challenge for nuclear theory as it involves extreme extrapolations of nuclear masses well beyond the regions where experimental information is available. Still, quantified extrapolations are crucial for a wide variety of applications, including the modeling of stellar nucleosynthesis. We use microscopic nuclear global mass models, current mass data, and Bayesian methodology to provide quantified predictions of proton and neutron separation energies as well as Bayesian probabilities of existence throughout the nuclear landscape all the way to the particle drip lines. Here, we apply nuclear density functional theory with several energy density functionals. We also consider two global mass models often used in astrophysical nucleosynthesis simulations. To account for uncertainties, Bayesian Gaussian processes are trained on the separation-energy residuals for each individual model, and the resulting predictions are combined via Bayesian model averaging. This framework allows to account for systematic and statistical uncertainties and propagate them to extrapolative predictions. We establish and characterize the drip-line regions where the probability that the nucleus is particle- bound decreases from 1 to 0. In these regions, we provide quantified predictions for one- and two-nucleon separation energies. According to our Bayesian model averaging analysis, 7759 nuclei with Z ≤ 119 have a probability of existence ≥ 0.5. The extrapolation results obtained in this study will be put through stringent tests when new experimental information on existence and masses of exotic nuclei becomes available. In this respect, the quantified landscape of nuclear existence obtained in this study should be viewed as a dynamical prediction that will be fine-tuned when new experimental information and improved global mass models become available.

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

Structural and biochemical analyses of the nuclear IκBζ protein in complex with the NF-κB p50 homodimer

As part of the efforts to understand nuclear IκB function in NF-κB-dependent gene expression, we report an X-ray crystal structure of the IκBζ ankyrin repeat domain in complex with the dimerization domain of the NF-κB p50 homodimer. IκBζ possesses an N-terminal α helix that conveys domain folding stability. Affinity and specificity of the complex depend on a small portion of p50 at the nuclear localization signal. The model suggests that only one p50 subunit supports binding with IκBζ, and biochemical experiments confirm that IκBζ associates with DNA-bound NF-κB p50:RelA heterodimers. Comparisons of IκBζ:p50 and p50:κB DNA complex crystallographic models indicate that structural rearrangement is necessary for ternary complex formation of IκBζ and p50 with DNA.

Cell Biology↗
DOE OSTI2022

Defining the HIV Capsid Binding Site of Nucleoporin 153

The human immunodeficiency virus (HIV) can infect nondividing cells by interacting with the host nuclear pore complex. The host nuclear pore protein NUP153 directly interacts with the HIV capsid to promote viral nuclear entry.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Perturbative Quantum Monte Carlo Method for Nuclear Physics

While first order perturbation theory is routinely used in quantum Monte Carlo (QMC) calculations, higher-order terms present significant numerical challenges. We present a new approach for computing perturbative corrections in projection QMC calculations. Here we demonstrate the method by computing nuclear ground state energies up to second order for a realistic chiral interaction. We calculate the binding energies of several light nuclei up to 16 O by expanding the Hamiltonian around the Wigner SU(4) limit and find good agreement with data. In contrast to the natural ordering of the perturbative series, we find remarkably large second-order energy corrections. This occurs because the perturbing interactions break the symmetries of the unperturbed Hamiltonian. Our method is free from the sign problem and can be applied to QMC calculations for many-body systems in nuclear physics, condensed matter physics, ultracold atoms, and quantum chemistry.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2021

Rigorous constraints on three-nucleon forces in chiral effective field theory from fast and accurate calculations of few-body observables

We explore the constraints on the three-nucleon force (3NF) of chiral effective field theory (χ EFT) that are provided by bound-state observables in the A = 3 and A = 4 sectors. Our statistically rigorous analysis incorporates experimental error, computational method uncertainty, and the uncertainty due to truncation of the χ EFT expansion at next-to-next-to-leading order. A consistent solution for the 3 H binding energy, the 4 He binding energy and radius, and the 3 H β-decay rate can only be obtained if χ EFT truncation errors are included in the analysis. Here, the β-decay rate is the only one of these that yields a nondegenerate constraint on the 3NF low-energy constants, which makes it crucial for the parameter estimation. We use eigenvector continuation for fast and accurate emulation of no-core shell model calculations of the few-nucleon observables. This facilitates sampling of the posterior probability distribution, allowing us to also determine the distributions of the parameters that quantify the truncation error. We find a χ EFT expansion parameter of Q = 0.33 ± 0.06 for these observables.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2021

HNRNPUL1 inhibits cisplatin sensitivity of esophageal squamous cell carcinoma through regulating the formation of circMAN1A2

Highlights: • HNRNPUL1 is an independent prognostic factor of ESCC patients receiving platinum-based chemotherapy. • Knockdown of HNRNPUL1 enhances cisplatin sensitivity of ESCC cells. • HNRNPUL1 inhibits the cisplatin sensitivity of ESCC cells by regulating the formation of circMAN1A2. Cisplatin (CDDP) is widely used for chemotherapy of esophageal squamous cell carcinoma (ESCC) but the drug resistance limits its therapeutic benefit. Heterogeneous nuclear ribonucleoprotein U-like 1 (HNRNPUL1) belongs to the family of RNA-binding proteins (RBPs) and is involved in DNA damage repair. To investigate whether and how HNRNPUL1 affects CDDP resistance of ESCC, we evaluated the expression of HNRNPUL1 and found that it was associated with recurrence in ESCC patients receiving postoperative platinum-based chemotherapy and was an independent prognostic factor for disease-free survival (DFS). Besides, we showed that the reduced expression of HNRNPUL1 enhanced the CDDP sensitivity of ESCC cells. Furthermore, RNA immunoprecipitation coupled with high-throughput sequencing (RIP-seq) were performed and a range of HNRNPUL1-binding RNAs influenced by CDDP treatment were identified followed by bioinformatics analysis. In terms of mechanism, we found that HNRNPUL1 inhibited CDDP sensitivity of ESCC cells by regulating the CDDP sensitivity-inhibited circular RNA (circRNA) MAN1A2 formation. Taken together, our results first demonstrated the role of HNRNPUL1 in CDDP resistance of ESCC and suggested that HNRNPUL1 may be a potential target of ESCC chemotherapy.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Improved naive Bayesian probability classifier in predictions of nuclear mass

Recently, novel statistical methods such as neural networks and Bayesian learning methods are implemented to describe the nuclear masses. Based on previous studies, an improved naive Bayesian probability (iNBP) classifier is proposed to study the nuclear masses by refining the results of sophisticated nuclear models. In the iNBP method, the prediction for nuclear masses is treated as a classification problem. The residuals are classified into several groups to generate prior and conditional probabilities, and the posterior probabilities are further determined by the Bayesian formula. We choose the expectation with maximum probability as the final prediction. Reliability of the iNBP method is assessed by analyzing the global optimizations and the extrapolating capabilities. Here, the iNBP method exhibits impressive improvements on global descriptions for different mass models. Moreover, the method shows robust extrapolating capabilities. Results demonstrate the iNBP method can be applied to predict the nuclear masses of unknown regions. Considering the local mass relations, the iNBP method can offer considerable fine-tuning of the mass descriptions from nuclear models. The methodology proposed in this paper can also be applied to other model-based extrapolations of nuclear observables.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

Bayesian averaging for ground state masses of atomic nuclei in a Machine Learning approach

We present global predictions of the ground state mass of atomic nuclei based on a novel Machine Learning algorithm. We combine precision nuclear experimental measurements together with theoretical predictions of unmeasured nuclei. This hybrid data set is used to train a probabilistic neural network. In addition to training on this data, a physics-based loss function is employed to help refine the solutions. The resultant Bayesian averaged predictions have excellent performance compared to the testing set and come with well-quantified uncertainties which are critical for contemporary scientific applications. We assess extrapolations of the model’s predictions and estimate the growth of uncertainties in the region far from measurements.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2023

Evaluation of polyanionic cyclodextrins as high affinity binding scaffolds for fentanyl

Abstract Cyclodextrins (CDs) have been previously shown to display modest equilibrium binding affinities ( K a ~ 100–200 M -1 ) for the synthetic opioid analgesic fentanyl. In this work, we describe the synthesis of new CDs possessing extended thioalkylcarboxyl or thioalkylhydroxyl moieties and assess their binding affinity towards fentanyl hydrochloride. The optimal CD studied displays a remarkable affinity for the opioid of K a = 66,500 M −1 , the largest value reported for such an inclusion complex to date. One dimensional 1 H Nuclear Magnetic Resonance (NMR) as well as Rotational Frame Overhauser Spectroscopy (2D-ROESY) experiments supported by molecular dynamics (MD) simulations suggest an unexpected binding behavior, with fentanyl able to bind the CD interior in one of two distinct orientations. Binding energies derived from the MD simulations work correlate strongly with NMR-derived affinities highlighting its utility as a predictive tool for CD candidate optimization. The performance of these host molecules portends their utility as platforms for medical countermeasures for opioid exposure, as biosensors, and in other forensic science applications.

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

Dirac oscillator: An alternative basis for nuclear structure calculations

The isotropic harmonic oscillator supplemented by a strong spin-orbit interaction has been the cornerstone of nuclear structure since its inception more than seven decades ago. In this paper we introduce—or rather re-introduce—the “Dirac oscillator,” a fully relativistic basis that has all the desired attributes of the ordinary harmonic oscillator while naturally incorporating a strong spin-orbit coupling. To assess the power and flexibility of the Dirac oscillator basis in the solution of nuclear structure problems within the framework of covariant density-functional theory. Here, self-consistent calculations of binding energies and ground-state densities for a selected set of doubly magic nuclei are performed using the Dirac oscillator basis and are then compared against results obtained with the often-used Runge-Kutta method. Results obtained using the Dirac oscillator basis reproduce with high accuracy those derived using the Runge-Kutta method and suggest a clear path for a generalization to systems with axial symmetry. Although the harmonic oscillator with spin-orbit corrections has been the staple of the nuclear shell model since the beginning, the Dirac oscillator is practically unknown among the nuclear physics community. In this paper we illustrate the power and flexibility of the Dirac oscillator and suggest extensions to the study of systems without spherical symmetry, as required in constrained calculations of nuclear excitations.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2025

Ligand‐Directed Actinide Oxo‐Bond Manipulation in Actinyl Thiacalix[4]arene Complexes

Abstract Understanding the chemistry of the inert actinide oxo bond in actinyl ions AnO 2 2+ is important for controlling actinide behavior in the environment, during separations, and in nuclear waste (An=U, Np, Pu). The thioether calixarene TC4A (4‐ tert ‐butyltetrathiacalix[4]arene) binds equatorially to the actinyl cation forming a conical pocket that differentiates the two trans‐ oxo groups. The ‘ate’ complexes, [A] 2 [UO 2 (TC4A)] (A=[Li(DME) 2 ], HNEt 3 ) and [HNEt 3 ] 2 [AnO 2 (TC4A)] (An=U, Np, Pu), enable selective oxo chemistry. Silylation of the U VI oxo groups by bis(trimethylsilyl)pyrazine occurs first at only the unencapsulated exo oxo and only one silylation is needed to enable migration of the endo oxo out of the cone, whereupon a second silylation affords the stable U IV cis‐ bis(siloxide) [A] 2 [U(OSiMe 3 ) 2 (TC4A)]. Calculations confirm that only one silylation event is needed to initiate oxo rearrangement, and that the putative cis dioxo isomer of [UO 2 (TC4A)] 2− would be stable if it could be accessed synthetically, at only 23 kcal.mol −1 in energy above the classical trans dioxo. Calculations for the transuranic cis [AnO 2 (TC4A)] 2− (An=Np, Pu) are at higher energies, 30–35 kcal.mol −1 , retaining the U complexes as the more obvious target for a cis ‐dioxo actinyl ion. The aryloxide (OAr) groups of the macrocycle are essential in stabilizing this as‐yet unseen uranyl geometry as further bonding in the TC4A U‐O Ar groups stabilizes the U=O ‘yl’ bonds, explaining the stability of the putative cis [UO 2 (TC4A)] 2− in this ligand framework.

Pyrch, Mikaela M. [College of Chemistry University↗