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At least 217 records · Page 12

Engineered U7 snRNA mediates sustained splicing correction in erythroid cells from β-thalassemia/HbE patients

Highlights: • Defect of β{sup E}-globin pre-mRNA splicing was repaired by engineered splice-switching U7 snRNA. • Splice-switching oligonucleotide sequence was identified by a two-step tiling approach. • The engineered U7 snRNA improve pathology of erythroid cells from thalassemia patients. Repair of a splicing defect of β-globin pre-mRNA harboring hemoglobin E (HbE) mutation was successfully accomplished in erythroid cells from patients with β-thalassemia/HbE disorder by a synthetic splice-switching oligonucleotide (SSO). However, its application is limited by short-term effectiveness and requirement of lifelong periodic administration of SSO, especially for chronic diseases like thalassemias. Here, we engineered lentiviral vectors that stably express U7 small nuclear RNA (U7 snRNA) carrying the splice-switching sequence of the SSO that restores correct splicing of β{sup E}-globin pre-mRNA and achieves a long-term therapeutic effect. Using a two-step tiling approach, we systematically screened U7 snRNAs carrying splice-switching SSO sequences targeted to the cryptic 5′ splice site created by HbE mutation. We tested this approach and identified the most responsive element for mediating splicing correction in engineered U7 snRNAs in HeLa-β{sup E} cell model cell line. Remarkably, the U7 snRNA lentiviral vector (U7 βE4+1) targeted to this region effectively restored the correctly-spliced β{sup E}-globin mRNA for at least 5 months. Moreover, the effects of the U7 βE4+1 snRNA lentiviral vector were also evident as upregulation of the correctly-spliced β{sup E}-globin mRNA in erythroid progenitor cells from β-thalassemia/HbE patients treated with the vector, which led to improvements of pathologies in erythroid progenitor cells from thalassemia patients. These results suggest that the splicing correction of β{sup E}-globin pre-mRNA by the engineered U7 snRNA lentiviral vector provides a promising, long-term treatment for β-thalassemia/HbE.

60 APPLIED LIFE SCIENCES↗

Using Density-Corrected DFT to Understand Density-Driven and Functional-Dependent Errors in Ab Initio Simulations of the Hydrated Electron

The hydrated electron, an excess electron in liquid water, plays a crucial role in a plethora of chemical processes, motivating extensive research efforts to characterize its structure, dynamics, and reactivity in solution. Recent theoretical approaches to understanding this intriguing object have involved ab initio simulations based on density functional theory (DFT). Although DFT allows for the study of hydrated electron reactivity and quantum mechanical behavior, it is well-known that anionic systems can suffer from significant density-driven errors (DDEs). Density-corrected DFT (DC-DFT) provides a framework to mitigate such errors; the method reduces DDEs by replacing the self-consistent (SC) density associated with a given density functional with the Hartree–Fock (HF) density. Since HF densities tend to be more localized than DFT SC densities, the DC-DFT scheme significantly improves errors in calculations where the SC density is spuriously delocalized. Here, we investigate how the use of density correction affects the calculated properties of the DFT-simulated (PBEh) hydrated electron, a particularly challenging diffuse anionic system to simulate. First, we analyze charge delocalization in a system consisting of a model octahedral hydrated electron water cluster (the so-called Kevan structure) along with a spatially separated sulfur atom. We show that the use of density correction indeed reduces DDEs in comparison to a standard DFT global hybrid functional. We then propagate molecular dynamics trajectories of the hydrated electron using DC-DFT, where we find that DC further localizes electron density in the cavity region, a signature of reduced charge delocalization. Unfortunately, the decreased radius of gyration of the spin density and corresponding tightening of the local solvation structure from density correction causes predicted observables to deviate further from experimental measurements than when density correction is not employed. Here, we argue that DC’s worse agreement with experiment results from the removal of a fortuitous cancellation of errors that is intrinsic to the PBEh functional. This indicates that the difficulties with DFT to simulate hydrated electrons are primarily due to the inherent approximations in DFT rather than to density-driven errors.

Density functional theory↗

A Simple Correction for Nonadditive Dispersion within Extended Symmetry-Adapted Perturbation Theory (XSAPT)

Extended symmetry-adapted perturbation theory (XSAPT), in conjunction with empirical “+aiD” potentials fit to ab initio dispersion data, is a low-scaling approach to compute intermolecular interaction energies in noncovalent clusters. One shortcoming is that the aiD atom–atom dispersion potentials are independent of the chemical environment of the atoms in question and therefore neglect nonadditive dispersion effects. These can be significant in large systems, so to account for them we test a simple correction to XSAPT(KS)+aiD, where “KS” indicates the use of Kohn–Sham orbitals. This correction, which can be evaluated at fourth-order cost using double-ζ basis sets, is based on comparing second-order SAPT dispersion with and without a self-consistent charge embedding for the monomer wave functions. The correction amounts to ~1.4 kcal/mol in (H 2 O) 6 but ~5.5 kcal/mol in (H 2 O) 20 . With the nonadditive dispersion correction, XSAPT(KS)+aiD affords errors of ~1 kcal/mol for isomers of F–(H 2 O) 10 and (H 2 O) 20 , where the benchmarks are complete-basis CCSD(T) energies, as well as for ion–water clusters X(H 2 O)n where n ≤ 6 and X = F – , Cl – , SO 4 2– , Li + , Na + , or K + . We also test the MP2 method and a variety of density-functional methods that have been specifically recommended for noncovalent interactions. Among the latter, only ωB97X-V and ωB97M-V can be recommended for ion–water clusters, as mean errors for other popular approaches (including ωB97X-D3 and several Minnesota functionals) exceed 1 kcal/mol. Lastly, we examine clathrate-hydrate host/guest complexes whose mixture of hydrogen bonding and dispersion make them challenging tests for noncovalent quantum chemistry. Although the B97-D2 functional performs best for clathrate hydrates and has been previously recommended in other studies of these inclusion complexes, its performance for other systems examined here is quite poor. We are unable to find a functional whose accuracy is ≲1 kcal/mol accuracy for both clathrate hydrates and ion–water clusters. However, the XSAPT(KS)+aiD method with the nonadditive dispersion correction can achieve this, with a mean error for the clathrate hydrates of 0.3 kcal/mol.

74 ATOMIC AND MOLECULAR PHYSICS↗

Innovative dead-time correction and background subtraction for neutron multiplicity measurements using neural networks

Abstract The number of neutrons emitted from a nuclear reaction plays a crucial role in various fields, including nuclear theory, nuclear nonproliferation, nuclear energy and nuclear criticality safety. Accurate determination of neutron multiplicities requires the application of several corrections, with dead-time correction and background subtraction being particularly significant. These corrections become more challenging for neutron detectors with time-dependent neutron capture. In this work, we perform a comprehensive study of three existing methods used for dead-time correction and background subtraction in neutron detectors with time-dependent neutron capture. The methods were tested for dead-times in the range from 0 to 1 μs using a Monte Carlo model simulating the dead-time and background effects in the standard neutron multiplicity probability distribution of $$^{252}$$ 252 Cf. The previous methods showed larger than desired uncertainty or systematic trade off. Those uncertainties prompted the development of a novel approach using neural networks trained with data from Monte Carlo simulations. The Neural Network method enabled the correction of neutron multiplicity probabilities more accurately than the other methods with fractional errors smaller than 3% for multiplicities around the peak of $$^{252}$$ 252 Cf. A similar approach using neural networks could be applied to problems where the system being studied can be accurately simulated without having an accurate analytical description available. The neural network method presented in this paper can be easily expanded if multiplicities greater than 10 are expected.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

AutoLabs: cognitive multi-agent systems with self-correction for autonomous chemical experimentation

The automation of chemical research through self-driving laboratories (SDLs) promises to accelerate scientific discovery, yet the reliability and granular performance of the underlying AI agents remain critical, under-examined challenges. In this work, we introduce AutoLabs, a self-correcting, multi-agent architecture designed to autonomously translate natural-language instructions into executable protocols for a high-throughput liquid handler. The system engages users in dialogue, decomposes experimental goals into discrete tasks for specialized agents, performs tool-assisted stoichiometric calculations, and iteratively self-corrects its output before generating a hardware-ready file. We present a comprehensive evaluation framework featuring five benchmark experiments of increasing complexity, from simple sample preparation to multi-plate timed syntheses. Through a systematic ablation study of 20 agent configurations, we assess the impact of reasoning capacity, architectural design (single- vs. multi-agent), tool use, and self-correction mechanisms. Our results demonstrate that agent reasoning capacity is the most critical factor for success, reducing quantitative errors in chemical amounts (nRMSE) by over 85% in complex tasks. When combined with a multi-agent architecture and iterative self-correction, AutoLabs approaches expert-authored reference procedures on the benchmark (F1-score > 0.89) on challenging multi-plate syntheses. These findings establish a clear blueprint for developing robust and trustworthy AI partners for autonomous laboratories, highlighting the synergistic effects of modular design, advanced reasoning, and self-correction to ensure both performance and reliability in high-stakes scientific applications. Code: https://github.com/pnnl/autolabs

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Density-related properties from self-interaction corrected density functional theory calculations

The Perdew–Zunger self-interaction correction (PZ-SIC) removes unphysical electron self-interaction from calculations employing standard density functional approximations. Doing so improves many computed properties, bringing them into better agreement with experimental observations or with results from high-level quantum chemistry calculations. However, while PZ-SIC generally corrects in the right direction relative to the corresponding reference values, in many cases, it over-corrects. For this reason, scaled-down versions of PZ-SIC have been proposed and investigated. These approaches have mostly employed exterior scaling in which SIC correction terms are scaled in the same way at every point in space. Recently, a new local, or interior, scaling SIC method was proposed on non-empirical grounds to restore a property of the exact, but unknown, density functional that is broken in PZ-SIC. Here, the scaling at each point depends on the character of the charge density at that point. However, the local scaling can be done in various ways while still restoring the behavior of the exact functional. In this work, we compare and contrast the performance of various interior scaling approaches for addressing over-corrections of calculated molecular dipole moments and atomic polarizabilities and properties that reflect the nature of the electronic charge density.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Static dipole polarizabilities of polyacenes using self-interaction-corrected density functional approximations

Density functional approximations are known to significantly overestimate the polarizabilities of long chain-like molecules. We study the static electric dipole polarizabilities and the vertical ionization potentials of polyacenes from benzene to pentacene using the Fermi-L\"owdin orbital based self-interaction corrected (FLOSIC) density functional method. The orbital-by-orbital self-interaction correction corrects for the overestimation tendency of density functional approximations. The polarizabilities calculated with FLOSIC-DFA are however overly corrected. We also tested the recently developed locally-scaled self-interaction correction (LSIC) method on the polyacenes. The local-scaling method applies full SIC in the one-electron regions and restores the proper behavior of the SIC exchange-correlation functionals in the uniform density limit. The results show that LSIC removes the overcorrection tendency of the FLOSIC-DFA and produces results that are in excellent agreement with reference CCSD values. The vertical ionization potentials with LSIC also show good agreement with available experimental values.

74 ATOMIC AND MOLECULAR PHYSICS↗

Influence of fourth-order vibrational corrections on semi-experimental (reSE) structures of linear molecules

Semi-experimental structures (reSE) are derived from experimental ground state rotational constants combined with theoretical vibrational corrections. They permit a meaningful comparison with equilibrium structures based on high-level ab initio calculations. Typically, the vibrational corrections are evaluated with second-order vibrational perturbation theory (VPT2). The amount of error introduced by this approximation is generally thought to be small; however, it has not been thoroughly quantified. Herein, we assess the accuracy of theoretical vibrational corrections by extending the treatment to fourth order (VPT4) for a series of small linear molecules. Typical corrections to bond distances are on the order of 10−5 Å. Larger corrections, nearly 0.0002 Å, are obtained to the bond lengths of NCCN and CNCN. A borderline case is CCCO, which will likely require variational computations for a satisfactory answer. Treatment of vibrational effects beyond VPT2 will thus be important when one wishes to know bond distances confidently to four decimal places (10−4 Å). Certain molecules with shallow bending potentials, e.g., HOC+, are not amenable to a VPT2 description and are not improved by VPT4.

Chemistry↗

Toward the “platinum standard” of quantum chemistry on quantum computers: Perturbative quadruple corrections in unitary coupled cluster theory

We propose a non-iterative, post-hoc correction to the unitary coupled cluster theory with the single, double, and triple excitations (UCCSDT) Ansatz, which considers the leading-order effects of neglected quadruple excitations. We present two ways to derive this correction, henceforth referred to as [Q-6], which leads to an improvement in the correlation energy shown to be truncated to sixth-order in many-body perturbation theory. Furthermore, a comparison between the UCC-based [Q-6] correction proposed in this work and analogous, “platinum standard” quadruple corrections proposed in conventional coupled cluster theory recognizes that [Q-6] is distinct from prior corrections since it is constructed entirely from internally connected components. Although trotterized (t) and full operator variants of UCCSDT exhibit errors in scans of small molecule potential energy surfaces that routinely exceed 1.6 mH, we find that t/UCCSDT[Q-6] is, nevertheless, able to achieve chemical accuracy as measured by the mean unsigned error.

Correlation energy↗

Less than the sum of its parts: the dust-corrected H α luminosity of star-forming galaxies explored at different spatial resolutions with MaNGA and MUSE

ABSTRACT The H α and H β emission-line luminosities measured in a single integrated spectrum are affected in non-trivial ways by point-to-point variations in dust attenuation in a galaxy. This work investigates the impact of this variation when estimating global H α luminosities corrected for the presence of dust by a global Balmer decrement. Analytical arguments show that the dust-corrected H α luminosity is always underestimated when using the global H α/H β flux ratio to correct for dust attenuation. We measure this effect on 156 face-on star-forming galaxies from the Mapping Nearby Galaxies at APO (MaNGA) survey. At 1–2 kpc spatial resolution, the effect is small but systematic, with the integrated dust-corrected H α luminosity underestimated by 2–4 per cent (and typically not more than by 10 per cent), and depends on the specific star formation rate of the galaxy. Given the spatial resolution of MaNGA, these are lower limits for the effect. From Multi Unit Spectroscopic Explorer (MUSE) observations of NGC 628 with a resolution of 36 pc, we find the discrepancy between the globally and the point-by-point dust-corrected H α luminosity to be 14 ± 1 per cent, which may still underestimate the true effect. We use toy models and simulations to show that the true difference depends strongly on the spatial variance of the H α/H β flux ratio, and on the slope of the relation between H αluminosity and dust attenuation within a galaxy. Larger samples of higher spatial resolution observations are required to quantify the dependence of this effect as a function of galaxy properties.

Vale Asari, N.↗

Magnetic frame-dragging correction to the electromagnetic solution of a compact neutron star

ABSTRACT Neutron stars are usually modelled as spherical, rotating perfect conductors with a predominant intrinsic dipolar magnetic field anchored to their stellar crust. Due to their compactness, General Relativity corrections must be accounted for in Maxwell’s equations, leading to modified interior and exterior electromagnetic solutions. We present analytical solutions for slowly rotating magnetized neutron stars, taking into account the magnetic frame-dragging correction. For typical compactness values, i.e. Rs ∼ 0.5 [R*], we show that the new terms lead to a per cent order correction in the magnetic field orientation and strength compared to the case, with no magnetic frame-dragging correction. Also, we obtain a self-consistent redistribution of the surface azimuthal current. We verify the validity of the derived solution through two-dimensional particle-in-cell simulations of an isolated neutron star. Defining the azimuthal electric and magnetic field amplitudes during the transient phase as observables, we prove that the magnetic frame-dragging correction reduces the transient wave amplitude, as expected from the analytical solution. We show that simulations are more accurate and stable, when we include all first-order terms. The increased accuracy at lower spatiotemporal resolutions translates into a reduction in simulation runtimes.

Torres, R. (ORCID:0000000291820228)↗

Analytical noise bias correction for precise weak lensing shear inference

Noise bias is a significant source of systematic error in weak gravitational lensing measurements that must be corrected to satisfy the stringent standards of modern imaging surveys in the era of precision cosmology. This paper reviews the analytical noise bias correction method and provides analytical derivations demonstrating that we can recover shear to its second order using the ‘renoising’ noise bias correction approach introduced by METACALIBRATION. We implement this analytical noise bias correction within the AnaCal shear estimation framework and propose several enhancements to the noise bias correction algorithm. We evaluate the improved AnaCal using simulations designed to replicate Rubin Legacy Survey of Space and Time (LSST) imaging data. These simulations feature semi-realistic galaxies and stars, complete with representative distributions of magnitudes and Galactic spatial density. We conduct tests under various observational challenges, including cosmic rays, defective CCD columns, bright star saturation, bleed trails, and spatially variable point spread functions. Our results indicate a multiplicative bias in weak lensing shear recovery of less than a few tenths of a per cent, meeting LSST Dark Energy Science Collaboration requirements without requiring calibration from external image simulations. Additionally, our algorithm achieves rapid processing, handling one galaxy in less than a millisecond.

79 ASTRONOMY AND ASTROPHYSICS↗

Numerical calculation of Coulomb corrections in forward elastic 𝑝↑⁢𝑝 and 𝑝↑⁢𝐴 scattering

The analysis of RHIC hydrogen gas jet target polarimeter measurements of transverse analyzing powers 𝐴 N ⁡(𝑡) in proton-nucleus scattering requires accurate Coulomb corrections to both spin-flip and nonflip amplitudes. These corrections must cover a wide range of nuclear charges 𝑍 and form factor slopes, with flexibility to vary form factors during data fitting. To avoid technically challenging calculations involving a small but finite fictitious photon mass, the Coulomb correction to the nonflip electromagnetic amplitude with an exponential form factor was related to the corresponding correction for the spin-flip amplitude. This approach allows soft photon contributions to all amplitudes, including those with nonexponential form factors, to be calculated in the massless photon limit using only analytical expressions and numerically stable integrals with nonsingular integrands and finite integration limits. In addition, an absorptive correction to the spin-flip electromagnetic amplitude, which plays a critical role in spin effects in forward polarized proton-nucleus scattering, was accurately evaluated.

43 PARTICLE ACCELERATORS↗

Z α 2 correction to superallowed beta decays in effective field theory and implications for | V u d |

Superallowed ( 0 + → 0 + ) beta decays currently provide the most precise extraction of quark mixing in the Standard Model. Their interpretation as a measurement of | V u d | relies on a reliable first-principles computation of QED radiative corrections expressed as a series in Z α and α . In this work, we provide the first model-independent result for two-loop, O ( Z α 2 ) , long-distance radiative corrections where the nuclei are treated as heavy pointlike particles. We use renormalization group analysis to obtain new results at O ( Z α 3 ) for the coefficient of double logarithms in the ratio of the maximal beta energy to the inverse nuclear size, E m / R - 1 . We use the Kinoshita-Lee-Nauenberg theorem to obtain new results at O ( Z 2 α 3 ) for the coefficient of logarithms in the ratio of maximal beta energy to the electron mass, log ( 2 E m / m ) . We identify a structure-dependent, and, therefore, short-distance, contribution to the traditional Z α 2 correction that should be revisited. We provide the first comprehensive update to the long-distance corrections in almost 40 years and comment on the impact of our findings for extractions of | V u d | . We find that shifts in the long-distance corrections are 2.5 × larger than past estimates of their uncertainty, 1.5 × larger than the statistical uncertainty from the combined fit of superallowed decays, and about 1 / 2 the size of estimated systematic error, which stems dominantly from nuclear structure effects.

Cao, Zehua [Kentucky U.] (ORCID:0009000354256423)↗

Full versus quasiparticle self-consistency in vertex-corrected GW approaches

Here, using seven semiconductors/insulators with band gaps covering the range from 1 eV to 10 eV we systematically explore the performance of two different variants of self-consistency associated with famous Hedin's system of equations: the full self-consistency and the so called quasi-particle approximation to it. The pros and cons of these two variants of self-consistency are sufficiently well documented in literature for the simplest GW approximation to the Hedin's equations. Our study, therefore, aims primarily at the level of theory beyond GW approximation, i.e. at the level of theory which includes vertex corrections. Whereas quasi-particle self-consistency has certain advantages at GW level (well known fact), the situation becomes quite different when vertex corrections are included. In the variant with full self-consistency, vertex corrections (both for polarizability and for self energy) systematically reduce the calculated band gaps making them closer to the experimental values. In the variant with quasi-particle self-consistency, however, an inclusion of the same diagrams has considerably larger effect and calculated band gaps become severely underestimated. Different effect of vertex corrections in two variants of self-consistency can be related to the Z-factor cancellation which plays positive role in quasi-particle self-consistency at GW level of theory but appears to be destructive for the quasi-particle approximation when higher order diagrams are included. Second result of our study is that we were able to reproduce the results obtained with the Questaal code using our FlapwMBPT code when the same variant of self-consistency (quasi-particle) and the same level of vertex corrections (for polarizability only, static approximation for screened interaction, and Tamm-Dancoff approximation for the Bethe-Salpeter equation) are used.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Nonfactorizable corrections to Higgs boson production in weak boson fusion

We discuss the nonfactorizable corrections to Higgs boson production in weak boson fusion at the Large Hadron Collider. Such corrections depend on the finite part of the two-loop virtual amplitude q Q → q ′ Q ′ + H which, up to now, has only been computed in the eikonal approximation. We combine this contribution with real-virtual and double-real nonfactorizable QCD corrections and study their impact on the various observables in weak boson fusion. We find that the nonfactorizable corrections are strongly dominated by the two-loop virtual contributions, while all other contributions play a very minor role. This striking imbalance between real and virtual contributions is caused by a process-specific kinematic suppression of the former and a particular enhancement of the virtual corrections related to a Glauber phase. Published by the American Physical Society 2024

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Renormalons and power corrections in pseudo- and quasi-GPDs

High-order behavior of the perturbative expansion for short-distance observables in QCD is intimately related to the contributions of small momenta in the corresponding Feynman diagrams and this correspondence provides one with a useful tool to investigate power-suppressed nonperturbative corrections. We use this technique to study the structure of power corrections to parton quasi- and pseudo-GPDs which are used in lattice calculations of generalized parton distributions. As the main result, we predict the functional dependence of the leading power corrections to quasi(pseudo)-GPDs on x variable for nonzero skewedness parameter ξ . The kinematic point x = ± ξ turns out to be special. We find that the nonperturbative corrections to quasi-GPDs at this point are suppressed by the first power of the hard scale only. These contributions come from soft momenta and have nothing to do with the known UV renormalon in the Wilson line. We also show that power corrections can be strongly suppressed by the normalization procedure. Published by the American Physical Society 2024

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Quasiprobabilistic Readout Correction of Midcircuit Measurements for Adaptive Feedback via Measurement Randomized Compiling

Quantum measurements are a fundamental component of quantum computing. However, on present-day quantum computers, measurements can be more error prone than quantum gates and are susceptible to nonunital errors as well as nonlocal correlations due to measurement crosstalk. While readout errors can be mitigated in postprocessing, this is inefficient in the number of qubits due to a combinatorially large number of possible states that need to be characterized. In this work, we show that measurement errors can be tailored into a simple stochastic error model using randomized compiling, enabling the efficient mitigation of readout errors via quasiprobability distributions reconstructed from the measurement of a single preparation state in an exponentially large confusion matrix. We demonstrate the scalability and power of this approach by correcting readout errors without matrix inversion on a large number of different preparation states applied to a register of eight superconducting transmon qubits. Moreover, we show that this method can be extended to midcircuit measurements used for active feedback via quasiprobabilistic error cancellation, and we demonstrate the correction of measurement errors on an ancilla qubit used to detect and actively correct bit-flip errors on an entangled memory qubit. Our approach enables the correction of readout errors on large numbers of qubits and offers a strategy for correcting readout errors in adaptive circuits in which the results of midcircuit measurements are used to perform conditional operations on nonlocal qubits in real time.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗