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At least 1,099 records · Page 61

Unveiling the microbial realm with VEBA 2.0: a modular bioinformatics suite for end-to-end genome-resolved prokaryotic, (micro)eukaryotic and viral multi-omics from either short- or long-read sequencing

Abstract The microbiome is a complex community of microorganisms, encompassing prokaryotic (bacterial and archaeal), eukaryotic, and viral entities. This microbial ensemble plays a pivotal role in influencing the health and productivity of diverse ecosystems while shaping the web of life. However, many software suites developed to study microbiomes analyze only the prokaryotic community and provide limited to no support for viruses and microeukaryotes. Previously, we introduced the Viral Eukaryotic Bacterial Archaeal (VEBA) open-source software suite to address this critical gap in microbiome research by extending genome-resolved analysis beyond prokaryotes to encompass the understudied realms of eukaryotes and viruses. Here we present VEBA 2.0 with key updates including a comprehensive clustered microeukaryotic protein database, rapid genome/protein-level clustering, bioprospecting, non-coding/organelle gene modeling, genome-resolved taxonomic/pathway profiling, long-read support, and containerization. We demonstrate VEBA’s versatile application through the analysis of diverse case studies including marine water, Siberian permafrost, and white-tailed deer lung tissues with the latter showcasing how to identify integrated viruses. VEBA represents a crucial advancement in microbiome research, offering a powerful and accessible software suite that bridges the gap between genomics and biotechnological solutions.

59 BASIC BIOLOGICAL SCIENCES↗

Intrinsically Quantum Effects of Axion Dark Matter Are Undetectable

Is the usual treatment of axion dark matter as a classical field reliable? We show that the answer is subtle: the axion field could well be in a quantum state that has no complete classical description, but realistic detectors cannot tell the difference. To see this, we solve a fully quantum model of axion detection using quantum optics techniques. We show that intrinsically quantum effects are washed out by mode averaging or small amounts of noise, and significantly suppressed by the weakness of the axion coupling. Our Letter exemplifies that there should always be a classical analog for axion dark matter effects, extends to other wave (ultralight) dark-matter candidates, and gives a general method to compute the effects of exotic dark-matter states.

Bao, Yunjia [University of Chicago, IL (United Sta↗

Fixed-point quantum circuits for quantum field theories

Renormalization group ideas and effective operators are introduced to efficiently prepare ground states of massive lattice field theories on digital quantum devices. This is accomplished with a systematic approximation through localized unitaries that removes an exponentially costly barrier in the spatial volume of the quantum simulation. With these methods, classically computed ground states in a spatial volume L, containing a few Compton wavelengths, can be used to determine operators for preparing the ground state toward the thermodynamic limit with a precision improving as e –mL on beyond-classical quantum registers. Here, due to the exponential spatial decay of correlations in massive theories and the double exponential suppression of digitization artifacts in the number of qubits representing the scalar field, the derived fixed-point quantum circuits are expected to be relevant for simulations of quantum field theories throughout the evolution from small-scale near-term quantum devices to large-scale fault-tolerant quantum computers.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Preparing angular momentum eigenstates using engineered quantum walks

Coupled angular-momentum eigenstates are widely used in atomic and nuclear physics calculations and are building blocks for spin networks and the Schur transform. To combine two angular momenta J 1 and J 2 , forming eigenstates of their total angular momentum J=J 1 +J 2 , we develop a quantum-walk scheme that does not require inputting O(j 3 ) nonzero Clebsch–Gordan (CG) coefficients classically. In fact, our scheme may be regarded as a unitary method for computing CG coefficients on quantum computers with a typical complexity of O⁡(j) and a worst-case complexity of O⁡(j 3 ). Equivalently, our scheme provides decompositions of the dense CG unitary into sparser unitary operations. Our scheme prepares angular-momentum eigenstates using a sequence of Hamiltonians to move an initial state deterministically to desired final states, which are usually highly entangled states in the computational basis. In contrast with usual quantum walks, whose Hamiltonians are prescribed, we engineer the Hamiltonians in su⁡(2)×su⁡(2), which are inspired by, but different from, Hamiltonians that govern magnetic resonances and dipole interactions. To achieve a deterministic preparation of both ket and bra states, we use projection and destructive interference to double pinch the quantum walks, such that each step is a unit-probability population transfer within a two-level system. We test our state preparation scheme on classical computers, reproducing tables of CG coefficients. Finally, we also implement small test problems on current quantum hardware.

97 MATHEMATICS AND COMPUTING↗

Sensor-Assisted Fault Mitigation in Quantum Computation

We propose a method for assisting fault mitigation in quantum computation through the use of sensors, co-located near physical qubits. Specifically, we consider using transition edge sensors co-located on silicon substrates hosting superconducting qubits to monitor for energy injection from ionizing radiation that has been demonstrated to increase decoherence in transmon qubits. We generalize from these two physical device concepts and explore the potential advantages of co-located sensors to assist fault mitigation in quantum computation. In the simplest scheme, co-located sensors beneficially assist rejection of calculations potentially affected by environmental disturbances. Investigating the potential computational advantage further required development of an extension to the standard formulation of quantum error correction. In a specific case the standard three-qubit, bit flip quantum correction code, we show that given a 20% overall error probability per qubit, approximately 90% of repeated calculation attempts are correctable. However, when sensor-detectable errors account for 45% of overall error probability, the use of colocated sensors uniquely associated with independent qubits, boosts the fraction of correct final-state calculations to 96% at the cost of rejecting 7% of repeated calculation attempts.

Orrell, John L.↗

Excitons and trions in monolayer semiconductors with correlated electrons

We revisit low-temperature optical spectra of transition-metal dichalcogenide monolayers and point to a possible crystallization of electrons (or holes) at low to moderate charge densities. To calculate the excitonic spectra under such conditions, we introduce the recursion method and compute how the charge density affects the energies, linewidths, and oscillator strengths of exciton and trion complexes. Equally important, we study how excitons and trions in the monolayer evolve when the charge particles gradually transition to a periodic Wigner lattice. The results provide valuable information on the ability to detect whether the particles are ordered through the exciton spectrum. Finally, we calculate the change in exciton energy in cases where the added charge particles have similar and dissimilar quantum numbers (spin and valley) to those of the electron or hole in the exciton. Here, the results of this work shed new light on the important optical properties of monolayer semiconductors.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Modified Brink-Axel hypothesis for astrophysical Gamow-Teller transitions

Weak interaction charged current transition strengths from highly excited nuclear states are fundamental ingredients for accurate modeling of compact object composition and dynamics, but are difficult to obtain either from experiment or theory. For lack of alternatives, calculations have often fallen back upon a generalized Brink-Axel hypothesis, that is, assuming the strength function (transition probability) is independent of the initial nuclear state but depends only upon the transition energy and the weak interaction properties of the parent nucleus ground state. Here we present numerical evidence for a modified “local” Brink-Axel hypothesis for Gamow-Teller transitions for pf-shell nuclei relevant to astrophysical applications. Specifically, while the original Brink-Axel hypothesis does not hold globally, strength functions from initial states nearby in energy are similar within statistical fluctuations. This agrees with previous work on strength function moments. Using this modified hypothesis, we can tackle strength functions at previously intractable initial energies, using semiconverged initial states at arbitrary excitation energy. Our work provides a well-founded method for computing accurate thermal weak transition rates for medium-mass nuclei at temperatures occurring in stellar cores near collapse. We finish by comparing results to previous calculations of astrophysical rates.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Ab initio studies of the double–Gamow-Teller transition and its correlation with neutrinoless double- β decay

Here, we use chiral interactions and several ab initio methods to compute the nuclear matrix elements (NMEs) for ground-state-to-ground-state double Gamow-Teller transitions in a range of isotopes and explore the correlation of these NMEs with those for neutrinoless double beta decay produced by the exchange of a light Majorana neutrino. When all the NMEs of both isospin-conserving and isospin-changing transitions from the ab initio calculations are considered, the correlation is strong. For the experimentally relevant isospin-changing transitions by themselves, however, the correlation is weaker and may not be helpful for reducing the uncertainty in the NMEs for neutrinoless double beta decay.

20 ≤ A ≤ 38↗

Nuclear-level effective theory of 𝜇→𝑒 conversion: Formalism and applications

Over the next decade new 𝜇→𝑒 conversion searches at Fermilab (Mu2e) and J-PARC (COMET, DeeMe) are expected to advance limits on charged lepton flavor violation (CLFV) by more than four orders of magnitude. Here, by considering the consequence of 𝑃 and 𝐶⁢𝑃 on elastic 𝜇→𝑒 conversion and the structure of possible charge and current densities, we show that rates are governed by six nuclear responses and a single scale, 𝑞/𝑚 𝑁 , where 𝑞 ≈ 𝑚 𝜇 is the momentum transferred from the leptons to the nucleus. To relate this result to microscopic formulations of CLFV, we construct in nonrelativistic effective theory (NRET) the CLFV nucleon-level interaction, pointing out the relevance of the dimensionless scales 𝑦=($^{𝑞⁢𝑏}_2$) 2 ⁢ > |$\overrightarrow{𝑣}_N$⁢|>|$\overrightarrow{𝑣}_μ$⁢|>|$\overrightarrow{𝑣}_T$| , where 𝑏 is the nuclear size, $\overrightarrow{𝑣}_N$ and $\overrightarrow{𝑣}_μ$ are the nucleon and muon intrinsic velocities, and $\overrightarrow{𝑣}_T$ is the target recoil velocity. We discuss previous work, noting the lack of a systematic treatment of the various small parameters. Because the parameter 𝑦 is not small, a proper calculation of 𝜇→𝑒 conversion requires a full multipole expansion of the nuclear response functions, an apparently daunting task with Coulomb-distorted electron partial waves. We demonstrate that the multipole expansion can be carried out to high precision by introducing a simplifying local momentum 𝑞 eff for the electron. Previous work has been limited to simple charge or spin interactions, thereby treating the nucleus effectively as a point particle. We show that such formulations are not compatible with the general form of the 𝜇→𝑒 conversion rate, failing to generate three of the six allowed nuclear response functions. The inclusion of the nucleon velocity $\overrightarrow{𝑣}_N$ yields an NRET with 16 operators and a rate of the general form. Consequently, in the current discovery era for CLFV, it provides the most sensible starting point for experimental analysis, defining what can and cannot be determined about CLFV from the highly exclusive process of 𝜇→𝑒 conversion. Finally, we expand the NRET operator basis to account for the effects of $\overrightarrow{𝑣}_μ$, associated with the muon's lower component, generating corrections to the CLFV coefficients of the point-nucleus response functions. Using advanced shell-model methods, we compute 𝜇→𝑒 conversion rates for a series of experimental targets, deriving bounds on the coefficients of the CLFV operators. These calculations are the first to include a general basis of CLFV operators, full evaluation of the associated nuclear response functions, and an accurate treatment of electron and muon Coulomb effects. We discuss target selection as an experimental “knob” that can be turned to probe the microscopic origins of CLFV. We describe two types of coherence that enhance certain CLFV operators and selection rules that blind elastic 𝜇→𝑒 conversion to others. We discuss the matching of the NRET onto higher level effective field theories, such as those constructed at the light quark level, noting opportunities to build on existing work in direct detection of dark matter. We discuss the relation of 𝜇→𝑒 conversion to 𝜇→𝑒+𝛾 and 𝜇→3⁢𝑒, showing how MEG II and Mu3e results will complement those of Mu2e and COMET. Finally we describe a accompanying script—in Mathematica and Python versions—that can be used to compute 𝜇→𝑒 conversion rates in various nuclear targets for the full set of NRET operators.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Stochastic properties of ultralight scalar field gradients

Ultralight axion-like particles are well-motivated dark matter candidates that are the target of numerous direct detection efforts. In the vicinity of the Solar System, such particles can be treated as oscillating scalar fields. The velocity dispersion of the Milky Way determines a coherence time of about 10 6 oscillations, beyond which the amplitude of the axion field fluctuates stochastically. Any analysis of data from an axion direct detection experiment must carefully account for this stochastic behavior to properly interpret the results. This is especially true for experiments sensitive to the gradient of the axion field that are unable to collect data for many coherence times. Indeed, the direction, in addition to the amplitude, of the axion field gradient fluctuates stochastically. We present the first complete stochastic treatment for the gradient of the axion field, including multiple computationally efficient methods for performing likelihood-based data analysis, which can be applied to any axion signal, regardless of coherence time. Additionally, we demonstrate that ignoring the stochastic behavior of the gradient of the axion field can potentially result in failure to discover a true axion signal

79 ASTRONOMY AND ASTROPHYSICS↗

New method for detecting fast neutrino flavor conversions in core-collapse supernova models with two-moment neutrino transport

Fast-pairwise neutrino oscillations potentially affect many aspects of core-collapse supernovae (CCSNe): the explosion mechanism, neutrino signals, and nucleosynthesis in the ejecta. This particular mode of collective neutrino oscillations has a deep connection to the angular structure of neutrinos in momentum space; for instance, the appearance of electron-neutrino lepton number (ELN) angular crossings in momentum space is a good indicator of the occurrence of flavor conversions. However, many multidimensional CCSN simulations are carried out with approximate neutrino transport (such as two-moment methods), which limits access to the angular distributions of neutrinos, i.e., inhibits ELNcrossing searches. In this paper, we develop a new method of searching for ELN crossing in these CCSN simulations. The required data is the zeroth and first angular moments of neutrinos and the matter profile, all of which are available in CCSN models with the two-moment method. One of the novelties of our new method is the use of a ray-tracing neutrino transport to determine ELNs in the direction of the stellar center. It is designed to compensate for shortcomings of the crossing searches with only two angular moments. We assess the capability of the method by carrying out a detailed comparison with results of full Boltzmann neutrino transport in 1D and 2D CCSN models. In this work, we find that the ray-tracing neutrino transport improves the accuracy of crossing searches; indeed, the appearance/disappearance of the crossings is accurately detected even in the region of forward-peaked angular distributions. The new method is computationally cheap and has the benefit of efficient parallelization; hence, it will be useful for ELN-crossing searches in any CCSN models that employ two-moment neutrino transport.

79 ASTRONOMY AND ASTROPHYSICS↗

Stress inside the pion in holographic light-front QCD

In this work, we propose a method to compute the gravitational form factor D ( Q 2 ) in holographic QCD by exploiting the remarkable correspondence between semiclassical light-front QCD and semiclassical field theories in wrapped spacetime in five dimensions. The use of light-front holography bridges physics at large Q 2 as attained in light-front QCD and physics at small Q 2 where the coupling to scalar and tensor fields, e.g. glueballs, are dominant. As an application, we compute the D -term for the pion and compare the results with recent lattice simulations. Published by the American Physical Society 2024

Astronomy & Astrophysics↗

Tetraquarks made of sufficiently unequal-mass heavy quarks are bound in QCD

Tetraquarks, bound states composed of two quarks and two antiquarks, have been the subject of intense study but are challenging to understand from first principles. We apply variational and Green’s function Monte Carlo methods to compute tetraquark ground-state energies in potential nonrelativistic QCD using a wide range of color and spatial wave functions. We find no evidence for bound tetraquarks composed of equal-mass quarks and antiquarks. Conversely, we find clear evidence for the existence of bound tetraquarks for sufficiently unequal quark/antiquark mass ratios at all overall mass scales where our effective theory results are applicable. We predict the critical mass ratios for bound state formation and study tetraquark bound states’ spatial and color structure at leading order and next-to-leading order in potential nonrelativistic QCD. Published by the American Physical Society 2024

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Quantum closures for neutrino moment transport

A computationally efficient method for calculating the transport of neutrino flavor in simulations is to use angular moments of the neutrino one-body reduced density matrix, i.e., “quantum moments.” As with any moment-based radiation transport method, a closure is needed if the infinite tower of moment evolution equations is truncated. We derive a general parametrization of a quantum closure and the limits the parameters must satisfy in order for the closure to be physical. We then derive from multiangle calculations the evolution of the closure parameters in two test cases which we then progressively insert into a moment evolution code and show how the parameters affect the moment results until the full multiangle results are reproduced. This parametrization paves the way to setting prescriptions for genuine quantum closures adapted to neutrino transport in a range of situations.

79 ASTRONOMY AND ASTROPHYSICS↗

Competition between roughness and strength for scale-dependent surfaces

Rocks famously have scale-dependent strength, yet the actual dependence is notoriously hard to measure or incorporate into any theoretical framework. Natural rough surfaces present an opportunity to solve the problem. Surfaces sliding in shear evolve as protrusions collide. These asperities can deform or break, thus creating a new surface shape. In particular, natural surfaces have roughness at all scales as well as scale-dependent strength. Based on a scaling analysis, we have previously suggested that the scale-dependent aspect ratio of steady-state surfaces should be proportional to the scale-dependent shear strain at yield. If true, scale-dependent strength could easily be inferred from natural surfaces. Thus, moving beyond the scaling argument to a rigorous treatment of scale-dependent strength for multiscale rough surfaces in shear is important. However, analytic frameworks for analyzing multiscale problems are challenging, as conventional continuum mechanics typically involves a single value for a material property across scales. Here, in this work, we build on the formalism of Persson (2001) that presents a method to compute contact area for rough surfaces with a prescribed topographic spectrum using a stochastic differential equation. The Persson formalism allows for plastic yield under normal loading of otherwise elastic materials and leaves open the possibility of scale-dependent yield stress. In this study, we pursue this route to develop a theory and numerical results for the yielding of a rough, elastoplastic surface with scale-dependent yield stress. Here, we examine surfaces for which the power spectrum of the topography 𝐶 and yield stress 𝑌 follow power laws as a function of scale 𝜆, such that 𝐶∼𝜆 −𝑚 and 𝑌∼𝜆 −𝑛 , respectively. In this formal treatment of the problem, we focus on surfaces in contact and the resulting yield and do not impose shear. Numerical solutions show that the deviation from the elastic scaling solution is bounded as expected by the prior 1D heuristic scaling argument that anticipates the Hurst exponent as 1−𝑛. We also show that the plasticity is expected to erode the contacts if 𝑚 is lower than 𝑛−3, which corresponds to a Hurst exponent lower than 1−𝑛/2. This result is rigorously sound for 2D, i.e., realistic surfaces, and quantitatively different than the prior scaling argument. The theory now permits a correspondingly quantitative approach to interpreting natural surfaces.

elasticity↗

Eddy diffusivity operator in homogeneous isotropic turbulence

Here, we use the recently developed macroscopic forcing method to compute the scale-dependent eddy diffusivity characterizing ensemble-averaged scalar and momentum transport in incompressible homogeneous isotropic turbulence. For scales larger than the energy containing eddies, eddy diffusivity is found to be constant and consistent with the Boussinesq approximation. However, for small scales eddy diffusivity is found to vanish inversely proportional to the wave number. Behavior at all scales is reasonably captured by a nonlocal eddy diffusivity operator modeled as D/$\sqrt{I - l^2∇^2}$, where D is the eddy diffusivity in the Boussinesq limit, and l is a constant on the order of the large-eddy length. These results present a direct measurement of eddy diffusivity in turbulence with implications in turbulence modeling.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Embedding hard physical constraints in neural network coarse-graining of three-dimensional turbulence

In recent years, deep learning approaches have shown much promise in modeling complex systems in the physical sciences. A major challenge in deep learning of partial differential equations is enforcing physical constraints and boundary conditions. In this work, we propose a general framework to directly embed the notion of an incompressible fluid into convolutional neural networks, and apply this to coarse-graining of turbulent flow. These physics-embedded neural networks leverage interpretable strategies from numerical methods and computational fluid dynamics to enforce physical laws and boundary conditions by taking advantage the mathematical properties of the underlying equations. Here, we demonstrate results on three-dimensional fully developed turbulence, showing that this technique drastically improves local conservation of mass, without sacrificing performance according to several other metrics characterizing the fluid flow.

97 MATHEMATICS AND COMPUTING↗

Global Sensitivity Analysis of Bulk Properties of an Atomic Nucleus

We perform a global sensitivity analysis of the binding energy and the charge radius of the nucleus 16 O to identify the most influential low-energy constants in the next-to-next-to-leading order chiral Hamiltonian with two- and three-nucleon forces. For this purpose, we develop a subspace-projected coupled-cluster method using eigenvector continuation [Frame D. et al., Phys. Rev. Lett. 121, 032501 (2018)]. With this method, we compute the binding energy and charge radius of 16 O at more than 106 different values of the 16 low-energy constants in one hour on a standard laptop computer. For relatively small subspace projections, the root-mean-square error is about 1% compared to full-space coupled-cluster results. We find that 58(1)% of the variance in energy can be apportioned to a single contact term in the 3 S 1 wave, whereas the radius depends sensitively on several low-energy constants and their higher-order correlations. The results identify the most important parameters for describing nuclear saturation and help prioritize efforts for uncertainty reduction of theoretical predictions. The achieved acceleration opens up an array of computational statistics analyses of the underlying description of the strong nuclear interaction in nuclei across the Segrè chart.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗