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At least 1,279 records · Page 71

Ideal conductor/dielectric model (ICDM): A generalized technique to correct for finite-size effects in molecular simulations of hindered ion transport

Molecular simulations serve as indispensable tools for investigating the kinetics and elucidating the mechanism of hindered ion transport across nanoporous membranes. In particular, recent advancements in advanced sampling techniques have made it possible to access translocation timescales spanning several orders of magnitude. In our prior study [Shoemaker et al., J. Chem. Theory Comput. 18, 7142 (2022)], we identified significant finite size artifacts in simulations of pressure-driven hindered ion transport through nanoporous graphitic membranes. We introduced the ideal conductor model, which effectively corrects for such artifacts by assuming the feed to be an ideal conductor. In the present work, we introduce the ideal conductor dielectric model (Icdm), a generalization of our earlier model, which accounts for the dielectric properties of both the membrane and the filtrate. Using the Icdm model substantially enhances the agreement among corrected free energy profiles obtained from systems of varying sizes, with notable improvements observed in regions proximate to the pore exit. Moreover, the model has the capability to consider secondary ion passage events, including the transport of a co-ion subsequent to the traversal of a counter-ion, a feature that is absent in our original model. We also investigate the sensitivity of the new model to various implementation details. The Icdm model offers a universally applicable framework for addressing finite size artifacts in molecular simulations of ion transport. It stands as a significant advancement in our quest to use molecular simulations to comprehensively understand and manipulate ion transport processes through nanoporous membranes.

Chemistry↗

Diagonalizing the Born–Oppenheimer Hamiltonian via Moyal perturbation theory, nonadiabatic corrections, and translational degrees of freedom

This article describes a method for calculating higher order or nonadiabatic corrections in Born–Oppenheimer theory and its interaction with the translational degrees of freedom. The method uses the Wigner–Weyl correspondence to map nuclear operators into functions on the classical phase space and the Moyal star product to represent operator multiplication on those functions. These are explained in the body of the paper. The result is a power series in κ 2 , where κ = (m/M)1/4 is the usual Born–Oppenheimer parameter. The lowest order term is the usual Born–Oppenheimer approximation, while higher order terms are nonadiabatic corrections. These are needed in calculations of electronic currents, momenta, and densities. The separation of nuclear and electronic degrees of freedom takes place in the context of the exact symmetries (for an isolated molecule) of translations and rotations, and these, especially translations, are explicitly incorporated into our discussion. This article presents an independent derivation of the Moyal expansion in molecular Born–Oppenheimer theory. Here, we show how electronic currents and momenta can be calculated within the framework of Moyal perturbation theory; we derive the transformation laws of the electronic Hamiltonian, the electronic eigenstates, and the derivative couplings under translations; we discuss in detail the rectilinear motion of the molecular center of mass in the Born–Oppenheimer representation; and we show how the elimination of the translational components of the derivative couplings leads to a unitary transformation that has the effect of exactly separating the translational degrees of freedom.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Development of improved higher-order correction for the NIF opacity spectrometer

X-ray opacity measurements on the National Ignition Facility (NIF) are in the process of reproducing earlier measurements from the Sandia Z Facility, in particular for oxygen and iron plasmas. These measurements have the potential to revise our understanding of the “solar problem” and of the hot degenerate Q class white dwarf structure by probing plasma conditions near the base of their convection zones. Accurate opacity measurements using soft x-ray Bragg crystal spectrometers require correction for higher-order diffraction effects. Extending prior work in this area [Dutra et al., Review of Scientific Instruments 93, 113527 (2022)], we have developed a new method to remove higher-order spectral components from NIF opacity spectrometer data. Furthermore, by modeling absorption and backlighting continuum spectra and subtracting the second- and third-order components from the measured data, we are able to perform this correction while avoiding imprinting first-order model line features onto the data.

79 ASTRONOMY AND ASTROPHYSICS↗

An algebraic convolution formulation for multiple-scattering correction in small-angle neutron scattering

Multiple scattering in small-angle neutron scattering (SANS) redistributes spectral weight and distorts structural interpretation, particularly for thick or strongly scattering samples. We develop a finite-dimensional spectral desmearing framework that corrects multiple scattering without resorting to integral transforms or model-dependent extrapolation. The primary intensity is expanded in an orthonormal basis adapted to the isotropic transverse-momentum measure, under which convolution reduces to a recursive tensor contraction, allowing the Poisson-weighted multiple-scattering series to be evaluated directly in a finite-dimensional basis representation. This formulation yields a stable forward–inverse mapping between apparent and primary spectra. Numerical tests demonstrate convergence under repeated convolution and accurate recovery of the single-scattering intensity. Application to SANS measurements collected at multiple neutron facilities, including the Spallation Neutron Source, the High Flux Isotope Reactor, and the Institut Laue-Langevin, shows the quantitative reconstruction of the underlying primary spectrum across a wide range of transmission conditions, including strongly attenuating samples. Here, the method provides a stable, model-agnostic framework for multiple-scattering correction in SANS and enables consistent structural interpretation across instruments and scattering regimes.

Tung, Chi-Huan [Oak Ridge National Laboratory (ORN↗

Atomic ionization: sd energy imbalance and Perdew–Zunger self-interaction correction energy penalty in 3d atoms

To accurately describe the energetics of transition metal systems, density functional approximations (DFAs) must provide a balanced description of s- and d- electrons. One measure of this is the sd transfer error, which has previously been defined as E ( 3 d n − 1 4 s 1 ) − E ( 3 d n − 2 4 s 2 ) . Theoretical concerns have been raised about this definition due to its evaluation of excited-state energies using ground-state DFAs. A more serious concern appears to be strong correlation in the 4s 2 configuration. Here, we define a ground-state measure of the sd energy imbalance, based on the errors of s- and d-electron second ionization energies of the 3d atoms, that effectively circumvents the aforementioned problems. We find an improved performance as we move from the local spin density approximation (LSDA) to the Perdew-Burke-Ernzerhof (PBE) generalized gradient approximation (GGA) to the regularized and restored Strongly Constrained and Appropriately Normed (r 2 SCAN) meta-GGA for first-row transition metal atoms. However, we find large (∼2 eV) ground-state sd energy imbalances when applying a Perdew–Zunger 1981 self-interaction correction. This is attributed to an “energy penalty” associated with the noded 3d orbitals. A local scaling of the self-interaction correction to LSDA results in a balance of s- and d-errors.

Science & Technology - Other Topics↗

Active Thermochemical Tables: the thermophysical and thermochemical properties of methyl, CH 3 , and methylene, CH 2 , corrected for nonrigid rotor and anharmonic oscillator effects

The thermophysical properties (isobaric heat capacity, entropy, enthalpy increment) of two prominent radicals, methyl, CH 3 , and methylene, CH 2 , were computed using the Nonrigid Rotor Anharmonic Oscillator (NRRAO) approach and compared to their RRHO counterparts, demonstrating significant differences between the results from the two approaches. Methylene presents a typical case in which the NRRAO thermophysical properties have significantly higher values than their RRHO counterparts at higher temperatures. In the case of methyl, the positive anharmonicity of the umbrella motion causes an opposite effect, and the NRRAO corrected thermophysical properties have lower values than their RRHO counterparts. The NRRAO corrected thermophysical properties, in turn, affect the resulting thermochemical properties. Here, two reactions important in combustion modelling were tested: the recombination of methyl radical with hydrogen atoms to form methane, and the recombination of two methyl radicals to form ethane. The related NRRAO equilibrium constants differ significantly from their RRHO analogs, and the consequences for chemical modelling are discussed. Also reported are the most current ATcT enthalpies of formation for CH n (n = 4-0) species and for C 2 H 6 , together with the tightly related sequential bond dissociation enthalpies along with the CHn series.

74 ATOMIC AND MOLECULAR PHYSICS↗

Bayesian analysis of nuclear polarizability corrections to the Lamb shift of muonic H-atoms and He-ions

The extraction of nuclear charge radii from spectroscopy experiments in muonic atoms is currently limited by the large uncertainties associated with the theoretical evaluation of the nuclear polarizability effects. To facilitate calculations, these polarizability corrections are conventionally expressed as an expansion in a dimensionless parameter η, which has been argued in previous literature to hold an approximate value of 0.33 in light-nuclear systems. In this work, we check this claim by doing a Bayesian analysis of the nuclear-polarizability corrections to the Lamb shift in µ 2 H and µ 3 H atoms and in µ 3 He + and µ 4 He + ions at various orders in the η-expansion. As presented here, our analysis supports the claim that η $\ll$ 1 in these systems and finds truncation uncertainties that are similar to the previous estimate, the only exception being the truncation uncertainties in the µ 3 He + ion, which are found to be larger.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Error field measurements and correction on MUSE permanent magnet stellarator

The magnetic field topology and error fields are measured in the MUSE permanent magnet stellarator with an electron beam and fluorescent rod. The effective magnetization of the magnets is determined by measuring rational flux surface locations. Electron magnetic drift effects must be considered self-consistently due to the small magnetic shear on MUSE. Error fields are characterized by flux surface shape deviation and magnetic island chain width and phase. Error fields are then corrected by adjusting the permanent magnet (PM) holders as rigid bodies. Resonant error fields are on the order of or smaller than 3 x 10 -6 of the toroidal field after correction and surface shape matches well with the design. Resonant components of the quasi-symmetry deviation are estimated, using a novel magnetic drift measurement, to be in the 10 −4 range. The PM approach is validated as a low-cost and precise way to build optimized stellarators.

electron beam mapping↗

Distributed quantum sensing enhanced by continuous-variable error correction

Abstract A distributed sensing protocol uses a network of local sensing nodes to estimate a global feature of the network, such as a weighted average of locally detectable parameters. In the noiseless case, continuous-variable (CV) multipartite entanglement shared by the nodes can improve the precision of parameter estimation relative to the precision attainable by a network without shared entanglement; for an entangled protocol, the root mean square estimation error scales like 1/ M with the number M of sensing nodes, the so-called Heisenberg scaling, while for protocols without entanglement, the error scales like 1 / M . However, in the presence of loss and other noise sources, although multipartite entanglement still has some advantages for sensing displacements and phases, the scaling of the precision with M is less favorable. In this paper, we show that using CV error correction codes can enhance the robustness of sensing protocols against imperfections and reinstate Heisenberg scaling up to moderate values of M . Furthermore, while previous distributed sensing protocols could measure only a single quadrature, we construct a protocol in which both quadratures can be sensed simultaneously. Our work demonstrates the value of CV error correction codes in realistic sensing scenarios.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Error field detection and correction studies towards ITER operation

In magnetic fusion devices, error field (EF) sources, spurious magnetic field perturbations, need to be identified and corrected for safe and stable (disruption-free) tokamak operation. Within Work Package Tokamak Exploitation RT04, a series of studies have been carried out to test the portability of the novel non-disruptive method, designed and tested in DIII-D (Paz-Soldan et al 2022 Nucl. Fusion62 126007), and to perform an assessment of model-based EF control strategies towards their applicability in ITER. In this paper, the lessons learned, the physical mechanism behind the magnetic island healing, which relies on enhanced viscous torque that acts against the static electro-magnetic torque, and the main control achievements are reported, together with the first design of the asynchronous EF correction current/density controller for ITER.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Impact of error fields and error field correction on heat fluxes in SPARC

Using a single toroidal array of coils to reduce the m,n = 2,1 resonant error field (EF) produced by the misalignment of the axisymmetric coils in SPARC can result in the enhancement of the local divertor heat fluxes. Managing high divertor heat fluxes (q ∥ $\simeq$ 10 GW m -2 ) poses a challenge for compact tokamak devices such as SPARC. The presence of non-axisymmetric magnetic field perturbations adds complexity to the problem by generating intricate 3D edge magnetic topologies that alter the heat flux distributions on the target plates. The aim of this work is to investigate the impact of the EF correction (EFC) on the heat fluxes at the divertor plates in SPARC. The MHD code M3DC1 has been used to simulate the 3D magnetic perturbations generated by the shift and tilt of several axisymmetric coils within specified tolerances, as well as from the array of EFC coils located at the midplane. Using a heuristic model that extends the concept of an axisymmetric heat flux layer to 3D plasmas, the resultant heat flux distributions is derived from magnetic footprints calculated with the MAFOT code. The results show that the EFC could either decrease or further enhance the local heat flux when used to correct the m,n = 2,1 resonant EF to enhance the core plasma performance.

3D fields↗

Demonstration of improvement in 2D tomographic reconstructions of filtered cameras in the JET ITER-like wall divertor due to corrected interpretation of reflections

Improved localization of emission and reduction of artefacts have been achieved in tomographic reconstructions of the tangentially viewing spectroscopic divertor cameras in JET by introducing the contribution of reflections from the metallic wall surfaces in the geometry definition of the tomography process. The reconstructions thus describe the plasma emission only without features arising from misinterpreted reflected light. Benchmarks with synthetic emission distributions showed accurate reproduction within 10% and 1–2% of the reference emission distributions and camera images, respectively, when the reflection correction was applied. Without the correction, the reconstructed emission was observed to concentrate from the divertor volume towards the wall surfaces together with bright emission artefacts appearing in front of the surfaces to reproduce the reflections seen in the camera images.

Karhunen, Juuso↗

More exact results in the Wilson loop defect CFT: bulk-defect OPE, nonplanar corrections and quantum spectral curve

We perform here exact computations of correlation functions of 1/2-BPS local operators and protected operator insertions on the 1/8-BPS Wilson loop in $\mathcal{N}=4$ SYM. This generalizes the results of our previous paper arXiv:1802.05201, which employs supersymmetric localization, OPE and the Gram-Schmidt process. In particular, we conduct a detailed analysis for the 1/2-BPS circular (or straight) Wilson loop in the planar limit, which defines an interesting nontrivial defect CFT. We compute its bulk-defect structure constants at finite 't Hooft coupling, and present simple integral expressions in terms of the $Q$-functions that appear in the Quantum Spectral Curve---a formalism originally introduced for the computation of the operator spectrum. The results at strong coupling are found to be in precise agreement with the holographic calculation based on perturbation theory around the AdS$_2$ string worldsheet, where they correspond to correlation functions of open string fluctuations and closed string vertex operators inserted on the worldsheet. Along the way, we clarify several aspects of the Gram-Schmidt analysis which were not addressed in the previous paper. Specifically, we clarify the role played by the multi-trace operators at the non-planar level, and confirm its importance by computing the non-planar correction to the defect two-point function. We also provide a formula for the first non-planar correction to the defect correlators in terms of the Quantum Spectral Curve, which suggests the potential applicability of the formalism to the non-planar correlation functions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

VIRULIGN: fast codon-correct alignment and annotation of viral genomes

Abstract Summary Virus sequence data are an essential resource for reconstructing spatiotemporal dynamics of viral spread as well as to inform treatment and prevention strategies. However, the potential benefit of these applications critically depends on accurate and correctly annotated alignments of genetically heterogeneous data. VIRULIGN was built for fast codon-correct alignments of large datasets, with standardized and formalized genome annotation and various alignment export formats. Availability and implementation VIRULIGN is freely available at https://github.com/rega-cev/virulign as an open source software project. Supplementary information Supplementary data is available at Bioinformatics online.

Libin, Pieter J. K. (ORCID:000000033906758X)↗

Automating STEM Aberration Correction via Bayesian Optimization

Multipole aberration correctors have given scanning transmission electron microscopes (STEM) the ability to produce high-quality, atomic-resolution images, enabling STEM to be a key tool in material sciences for characterizing the structure and composition of materials. However, the process of correcting these aberrations typically requires human input and is accomplished using scanned STEM or Ronchigram images at different focii and beam tilts. In this work, we demonstrate an automated on-sample aberration correction system using Bayesian Optimization. We have developed a Python-based server able to communicate with the CEOS DCOR aberration corrector and the Thermo Fischer microscope scripting interface. This server allows us to change aberrations, acquire images and perform basic image analysis.

47 OTHER INSTRUMENTATION↗

Correcting for fibre assignment incompleteness in the DESI Bright Galaxy Survey

The Dark Energy Spectroscopic Instrument (DESI) Bright Galaxy Survey (BGS) will be a survey of bright, low-redshift galaxies, which is planned to cover an area of ~14000 square degrees in three passes. Each pass will cover the survey area with ~2000 pointings, each of area ~8 square degrees. The BGS is currently proposed to consist of a bright high priority sample to an r-band magnitude limit r ~ 19.5, with a fainter low priority sample to r ~ 20. The geometry of the DESI fibre positioners in the focal plane of the telescope affects the completeness of the survey and has a non-trivial impact on clustering measurements. Using a BGS mock catalogue, we demonstrate that completeness due to fibre assignment primarily depends on the surface density of galaxies. Completeness is high (>95 per cent) in low-density regions, but very low (<10 per cent) in the centre of massive clusters. We apply the pair inverse probability (PIP) weighting correction to clustering measurements from a BGS mock which has been through the fibre assignment algorithm. This method is only unbiased if it is possible to observe every galaxy pair. To expedite this, we randomly promote a small fraction of the fainter sample to be high priority, and dither the set of tile positions by a small angle. We show that inverse pair weighting combined with angular upweighting provides an unbiased correction to galaxy clustering measurements for the complete three pass survey, and also after one pass, which is highly incomplete.

79 ASTRONOMY AND ASTROPHYSICS↗

Coulomb corrections for the nonflip and spin-flip electromagnetic 𝑝 ↑⁢ 𝐴 amplitudes

It is demonstrated that, within the eikonal approach, the Coulomb corrections to the elastic electromagnetic nonflip and spin-flip proton-nucleus amplitudes are identical when the two amplitudes share the same exponential form factors. This result allows Coulomb corrections to be computed numerically, and with high precision, for both electromagnetic and hadronic elastic 𝑝 ↑⁢ 𝐴 amplitudes in the massless-photon limit, including the effects of soft magnetic photon exchange. The method relies on analytical expressions and numerical integrations over a finite impact-parameter range with nonsingular integrands, providing a practical and systematically controlled framework for phenomenological applications.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Error-correcting Bacon-Shor code with continuous measurement of noncommuting operators

We analyze the continuous operation of the nine-qubit error correcting Bacon-Shor code with all noncommuting gauge operators measured at the same time. The error syndromes are continuously monitored using cross-correlations of sets of three measurement signals. We calculate the logical error rates due to $X$, $Y$ and $Z$ errors in the physical qubits and compare the continuous implementation with the discrete operation of the code. We find that both modes of operation exhibit similar performances when the measurement strength from continuous measurements is sufficiently strong. Here, we also estimate the value of the crossover error rate of the physical qubits, below which continuous error correction gives smaller logical error rates. Continuous operation has the advantage of passive monitoring of errors and avoids the need for additional circuits involving ancilla qubits.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗