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At least 37 records · Page 2

Information theory optimization of signals from small-angle scattering measurements

Small-angle X-ray scattering (SAXS) of particles in solution informs on the conformational states and assemblies of biological macromolecules (bioSAXS) outside of cryo- and solid-state conditions. In bioSAXS, the SAXS measurement under dilute conditions is resolution limited, and through an inverse Fourier transform, the measured SAXS intensities directly relate to the physical space occupied by the particles via the P (r)-distribution. Yet, this inverse transform of SAXS data has been historically cast as an ill-posed, ill-conditioned problem requiring an indirect approach. Here, we show that through the applications of matrix and information theories, the inverse transform of SAXS intensity data is a well-conditioned problem. The so-called ill-conditioning of the inverse problem is directly related to the Shannon number. By exploiting the oversampling enabled by modern detectors, a direct inverse Fourier transform of the SAXS data is possible, provided the recovered information does not exceed the Shannon number. The Shannon limit corresponds to the maximum number of significant singular values that can be recovered in a SAXS experiment, suggesting this relationship is a fundamental property of band-limited inverse integral transform problems. This correspondence reduces the complexity of the inverse problem to the Shannon limit and maximum dimension. We propose a hybrid scoring function using an information theory framework that assesses both the quality of the model-data fit as well as the quality of the recovered P (r)-distribution. The hybrid score utilizes the Akaike information criteria and Durbin-Watson statistic that considers parameter-model complexity, i.e., degrees of freedom, and the randomness of the model-data residuals. The described tests and findings extend the boundaries for bioSAXS by completing the information theory formalism initiated by Peter B. Moore to enable a quantitative measure of resolution in SAXS, robustly determine maximum dimension, and more precisely define the best parameter model appropriately representing the observed scattering data.

Rambo, Robert P. [Science and Technology Facilitie↗

$$ T\overline{T},J\overline{T},T\overline{J} $$ partition sums from string theory

We calculate the torus partition sum of a general CFT 2 with left and right moving conserved currents J and $ \overline{J} $ J ¯ , perturbed by a combination of the irrelevant operators $ T\overline{T},J\overline{T} $ T T ¯ , J T ¯ and $ T\overline{J} $ T J ¯ . We use string theory techniques to write it as an integral transform of the partition sum of the unperturbed CFT with chemical potentials for the left and right moving conserved charges. The resulting expression transforms in the right way under the modular group, and reproduces the known spectrum of these models. We also derive a formula for the partition function of deformed CFT 2 with non-vanishing chemical potentials.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Scattering amplitudes and N -body post-Minkowskian Hamiltonians in general relativity and beyond

We present a general framework for calculating post-Minskowskian, classical, conservative Hamiltonians for N non-spinning bodies in general relativity from relativistic scattering amplitudes. Novel features for N > 2 are described including the subtraction of tree-like iteration contributions and the calculation of non-trivial many-body Fourier transform integrals needed to construct position space potentials. A new approach to calculating these integrals as an expansion in the hierarchical limit is described based on the method of regions. As an explicit example, we present the O(G 2 ) 3-body momentum space potential in general relativity as well as for charged bodies in Einstein-Maxwell. The result is shown to be in perfect agreement with previous post-Newtonian calculations in general relativity up to O(G 2 v 4 ). Furthermore, in appropriate limits the result is shown to agree perfectly with relativistic probe scattering in multi-center extremal black hole backgrounds and with the scattering of slowly-moving extremal black holes in the moduli space approximation.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Thermal partition function of $$ {J}_3{\overline{J}}_3 $$ deformed AdS3

Abstract We derive a compact formula for the one-loop, bosonic string partition function of Euclideanized$$ {J}_3{\overline{J}}_3 $$ J 3 J ¯ 3 deformedAdS 3 with periodic Euclidean time as an integral transform of the partition function of the undeformed EuclideanizedAdS 3 . Such a deformation is interpretable as an irrelevant “single-trace$$ T\overline{T} $$ T T ¯ deformation” of the boundary. We will do this by first establishing a formal procedure to compute a worldsheet torus zero point function for an exactly marginal$$ J\overline{J} $$ J J ¯ deformation of a sigma model with U(1) L × U(1) R global symmetry. We then describe how this procedure is implemented on SL(2,R) sigma model and its Euclidean continuation. Finally, we describe the embedding of the deformed SL(2,R) torus amplitude into critical string theory and interpret the result as the leading perturbative contribution to the thermal partition function of the deformed theory.

Physics↗

Wormholes and black hole microstates in AdS/CFT

It has long been known that the coarse-grained approximation to the black hole density of states can be computed using classical Euclidean gravity. In this work we argue for another entry in the dictionary between Euclidean gravity and black hole physics, namely that Euclidean wormholes describe a coarse-grained approximation to the energy level statistics of black hole microstates. To do so we use the method of constrained instantons to obtain an integral representation of wormhole amplitudes in Einstein gravity and in full-fledged AdS/CFT. These amplitudes are non-perturbative corrections to the two-boundary problem in AdS quantum gravity. The full amplitude is likely UV sensitive, dominated by small wormholes, but we show it admits an integral transformation with a macroscopic, weakly curved saddle-point approximation. The saddle is the “double cone” geometry of Saad, Shenker, and Stanford, with fixed moduli. In the boundary description this saddle appears to dominate a smeared version of the connected two-point function of the black hole density of states, and suggests level repulsion in the microstate spectrum. Using these methods we further study Euclidean wormholes in pure Einstein gravity and in IIB supergravity on Euclidean AdS 5 × S 5 . We address the perturbative stability of these backgrounds and study brane nucleation instabilities in 10d supergravity. In particular, brane nucleation instabilities of the Euclidean wormholes are lifted by the analytic continuation required to obtain the Lorentzian spectral form factor from gravity. Our results indicate a factorization paradox in AdS/CFT.

79 ASTRONOMY AND ASTROPHYSICS↗

Photometric redshifts for the S-PLUS Survey: Is machine learning up to the task?

The Southern Photometric Local Universe Survey (S-PLUS) is a novel project that aims to map the Southern Hemisphere using a twelve filter system, comprising five broad-band SDSS-like filters and seven narrow-band filters optimized for important stellar features in the local universe. In this paper we use the photometry and morphological information from the first S-PLUS data release (S-PLUS DR1) cross-matched to unWISE data and spectroscopic redshifts from Sloan Digital Sky Survey DR15. We explore three different machine learning methods (Gaussian Processes with GPz and two Deep Learning models made with TensorFlow) and compare them with the currently used template-fitting method in the S-PLUS DR1 to address whether machine learning methods can take advantage of the twelve filter system for photometric redshift prediction. Using tests for accuracy for both single-point estimates such as the calculation of the scatter, bias, and outlier fraction, and probability distribution functions (PDFs) such as the Probability Integral Transform (PIT), the Continuous Ranked Probability Score (CRPS) and the Odds distribution, we conclude that a deep-learning method using a combination of a Bayesian Neural Network and a Mixture Density Network offers the most accurate photometric redshifts for the current test sample. In conclusion, it achieves single-point photometric redshifts with scatter (σ NMAD ) of 0.023, normalized bias of -0.001, and outlier fraction of 0.64% for galaxies with r_auto magnitudes between 16 and 21.

79 ASTRONOMY AND ASTROPHYSICS↗

Photometric redshifts probability density estimation from recurrent neural networks in the DECam local volume exploration survey data release 2

Photometric wide-field surveys are imaging the sky in unprecedented detail. These surveys face a significant challenge in efficiently estimating galactic photometric redshifts while accurately quantifying associated uncertainties. In this work, we address this challenge by exploring the estimation of Probability Density Functions (PDFs) for the photometric redshifts of galaxies across a vast area of 17,000 square degrees, encompassing objects with a median 5 σ point-source depth of g = 24.3, r = 23 . 9 , i = 23.5, and z = 22.8 mag. Our approach uses deep learning, specifically integrating a Recurrent Neural Network architecture with a Mixture Density Network, to leverage magnitudes and colors as input features for constructing photometric redshift PDFs across the whole DECam Local Volume Exploration (DELVE) survey sky footprint. Subsequently, we rigorously evaluate the reliability and robustness of our estimation methodology, gauging its performance against other well-established machine learning methods to ensure the quality of our redshift estimations. Our best results constrain photometric redshifts with the bias of − 0 . 0013 , a scatter of 0.0293, and an outlier fraction of 5.1%. These point estimates are accompanied by well-calibrated PDFs evaluated using diagnostic tools such as Probability Integral Transform and Odds distribution. We also address the problem of the accessibility of PDFs in terms of disk space storage and the time demand required to generate their corresponding parameters.We present a novel Autoencoder model that reduces the size of PDF parameter arrays to one-sixth of their original length, significantly decreasing the time required for PDF generation to one-eighth of the time needed when generating PDFs directly from the magnitudes.

79 ASTRONOMY AND ASTROPHYSICS↗

Smart culture medium optimization for recombinant protein production: Experimental, modeling, and AI/ML-driven strategies

Recombinant protein production (RPP) is central to biotechnology, where recombinant proteins are used as either end products or catalysts in the synthesis of chemicals, fuels, and materials. Among the major cost drivers, culture medium plays a pivotal role in determining protein yield and quality. This review presents a comprehensive perspective on the critical stages of “smart” culture medium optimization: planning, screening, modeling, optimization, and validation. In the planning stage, we examine the nutritional and energetic roles of medium components, including carbon, nitrogen, amino acids, salts, and trace metals, and their impacts on culture parameters such as pH, oxidative state, and osmolality. We highlight the variability in trace metal content due to water sources, culture vessels, and raw materials, which can substantially influence RPP. The screening stage covers Design of Experiments (DoE) approaches, assessing their theoretical basis, implementation, and limitations. For modeling, we describe methods that integrate experimental data to develop predictive models for smart medium formulation. Model-based optimization strategies can then be employed to select optimal media compositions for a given application. The validation stage aims to evaluate model predictions and provide feedback for model training and refinement. Finally, we survey mechanistic and artificial intelligence/machine learning (AI/ML)-driven models as integrated, transformational tools for predictive modeling of bioprocess conditions, nutrient availability, cellular metabolism, and protein quality, with the goal of optimizing culture media to enhance protein yields while reducing costs and environmental impact. We conclude by addressing the challenges of translating laboratory-scale medium optimization to industrial-scale settings and exploring future AI/ML-driven approaches that may overcome current bottlenecks and accelerate medium design for RPP. Overall, this review provides a unified framework for advancing smart medium design in RPP.

Artificial Intelligence/Machine Learning (AI/ML)↗

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↗

TreeSAPP: the Tree-based Sensitive and Accurate Phylogenetic Profiler

Microbial communities drive matter and energy transformations integral to global biogeochemical cycles, yet many taxonomic groups facilitating these processes remain poorly represented in biological sequence databases. Due to this missing information, taxonomic assignment of sequences from environmental genomes remains inaccurate. We present the Tree-based Sensitive and Accurate Phylogenetic Profiler (TreeSAPP) software for functionally and taxonomically classifying genes, reactions and pathways from genomes of cultivated and uncultivated microorganisms using reference packages representing coding sequences mediating multiple globally relevant biogeochemical cycles. TreeSAPP uses linear regression of evolutionary distance on taxonomic rank to improve classifications, assigning both closely related and divergent query sequences at the appropriate taxonomic rank. TreeSAPP is able to provide quantitative functional and taxonomic classifications for both assembled and unassembled sequences and files supporting interactive tree of life visualizations.

54 ENVIRONMENTAL SCIENCES↗

A machine learning approach to galaxy properties: joint redshift–stellar mass probability distributions with Random Forest

We demonstrate that highly accurate joint redshift–stellar mass probability distribution functions (PDFs) can be obtained using the Random Forest (RF) machine learning (ML) algorithm, even with few photometric bands available. As an example, we use the Dark Energy Survey (DES), combined with the COSMOS2015 catalogue for redshifts and stellar masses. We build two ML models: one containing deep photometry in the griz bands, and the second reflecting the photometric scatter present in the main DES survey, with carefully constructed representative training data in each case. We validate our joint PDFs for 10 699 test galaxies by utilizing the copula probability integral transform and the Kendall distribution function, and their univariate counterparts to validate the marginals. Benchmarked against a basic set-up of the template-fitting code bagpipes, our ML-based method outperforms template fitting on all of our predefined performance metrics. In addition to accuracy, the RF is extremely fast, able to compute joint PDFs for a million galaxies in just under 6 min with consumer computer hardware. Such speed enables PDFs to be derived in real time within analysis codes, solving potential storage issues. As part of this work we have developed galpro 1, a highly intuitive and efficient python package to rapidly generate multivariate PDFs on-the-fly. galpro is documented and available for researchers to use in their cosmology and galaxy evolution studies.

79 ASTRONOMY AND ASTROPHYSICS↗

Spectral function for 4 He using the Chebyshev expansion in coupled-cluster theory

Here, we compute spectral function for 4 He by combining coupled-cluster theory with an expansion of integral transforms into Chebyshev polynomials. Our method allows us to estimate the uncertainty of spectral reconstruction. The properties of the Chebyshev polynomials make the procedure numerically stable and considerably lower in memory usage than the typically employed Lanczos algorithm. We benchmark our predictions with other calculations in the literature and with electron-scattering data in the quasi-elastic peak. The spectral function formalism allows one to extend ab initio lepton-nucleus cross sections into the relativistic regime. This makes it a promising tool for modeling this process at higher-energy transfers. The results we present open the door for studies of heavier nuclei, important for the neutrino oscillation programs.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Uncertainty-quantification-enabled inversion of nuclear responses

Nuclear quantum many-body methods rely on integral transform techniques to infer properties of electroweak response functions from ground-state expectation values. Retrieving the energy dependence of these responses is highly nontrivial, especially for quantum Monte Carlo methods, as it requires inverting the Laplace transform, a notoriously ill-posed problem. Here, in this work, we propose an artificial neural network architecture suitable for accurate response function reconstruction with precise estimation of the uncertainty of the inversion. We demonstrate the capabilities of this new architecture benchmarking it against maximum entropy and previously developed neural network methods designed for a similar task, paying particular attention to its robustness noise in the Euclidean

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Electromagnetic observables of open-shell nuclei from coupled-cluster theory

Here we develop a new method to describe electromagnetic observables of open-shell nuclei with two nucleons outside a closed shell. This approach combines the equation-of-motion coupled-cluster method for such systems and the Lorentz integral transform technique, expanding the applicability of coupled-cluster theory for electromagnetic observables beyond closed-(sub)shell nuclei. To validate this new approach, we compute the non-energy-weighted dipole sum rule and the dipole polarizability of 16,24 ⁢O in both the closed-(sub)shell and the new equation-of-motion coupled-cluster frameworks, finding agreement within error bars. We then analyze the evolution of the dipole polarizability along the oxygen and calcium isotopic chains. Our predictions agree well with available experimental data and other available theoretical calculations for the closed-(sub)shell 16,22 ⁢O and the open-shell 18 O. In the calcium isotopes, we observe that our dipole polarizability predictions for open-shell nuclei are lower than those of closed-(sub)shell nuclei. We expect that our predictions for 24 O and 54,56 ⁢Ca will motivate future experimental studies at the drip line.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Spectral density reconstruction with Chebyshev polynomials

Accurate calculations of the spectral density in a strongly correlated quantum many-body system are of fundamental importance to study its dynamics in the linear response regime. Typical examples are the calculation of inclusive and semiexclusive scattering cross sections in atomic nuclei and transport properties of nuclear and neutron star matter. Integral transform techniques play an important role in accessing the spectral density in a variety of nuclear systems. However, their accuracy is in practice limited by the need to perform a numerical inversion which is often ill-conditioned. Here, in the present work we extend a recently proposed quantum algorithm which circumvents this problem. We show how to perform controllable reconstructions of the spectral density over a finite energy resolution with rigorous error estimates. An appropriate expansion in Chebyshev polynomials allows for efficient simulations also on classical computers. We apply our idea to obtain the local density of states for graphene in a magnetic field as a proof of principle. This paves the way for future applications in nuclear and condensed matter physics.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Ab Initio Computation of the Longitudinal Response Function in 40 Ca

In this work, we present a consistent ab initio computation of the longitudinal response function RL in 40 Ca using the coupled-cluster and Lorentz integral transform methods starting from chiral nucleon-nucleon and three-nucleon interactions. We validate our approach by comparing our results for R L in 4 He and the Coulomb sum rule in 40 Ca against experimental data and other calculations. For R L in 40 Ca we obtain a very good agreement with experiment in the quasielastic peak up to intermediate momentum transfers, and we find that final state interactions are essential for an accurate description of the data. This work presents a milestone towards ab initio computations of neutrino-nucleus cross sections relevant for experimental long-baseline neutrino programs.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

16 O Electroweak Response Functions from First Principles

We present calculations of various electroweak response functions for the 16 O nucleus obtained using coupled-cluster theory in conjunction with the Lorentz integral transform method. We employ nuclear forces derived at next-to-leading order and next-to-next-to-leading order in chiral effective field theory and perform a Bayesian analysis to assess uncertainties. Our results are in good agreement with available electron-scattering data at |𝐪|≈326 MeV/c. Additionally, we provide several predictions for the weak response functions in the quasielastic peak region at |𝐪| =300 and 400 MeV/c, which are critical for long-baseline neutrino experiments.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Nuclear Responses with Neural-Network Quantum States

We introduce a variational Monte Carlo framework that combines neural-network quantum states with the Lorentz integral transform technique to compute the dynamical properties of self-bound quantum many-body systems in continuous Hilbert spaces. While broadly applicable to various quantum systems, including atoms and molecules, in this initial application we focus on the photoabsorption cross section of light nuclei, where benchmarks against numerically exact techniques are available. Our accurate theoretical predictions are complemented by robust uncertainty quantification, enabling meaningful comparisons with experiments. Here, we demonstrate that a relatively simple nuclear Hamiltonian—based on a leading-order pionless EFT expansion and known to accurately reproduce ground-state energies of nuclei with 𝐴 ≤ 40—also provides a reliable description of the photoabsorption cross section.

Ab initio calculations↗