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All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

To bin or not to bin: Does binning in multiplicity reliably suppress unwanted volume fluctuations?

Here, in this study, we examine the effect of the so-called Centrality Bin Width Correction (CBWC) on the measurement of (net-)proton number cumulants in nucleus-nucleus collisions. We present an analytically tractable model, which includes correlations between multiplicity and proton number similar to those generated by the decay of baryon resonances. Within this model, we analyze the circumstances under which the CBWC method correctly removes the undesired effects of volume or impact parameter fluctuations. Additionally, we explore situations where the method fails and produces misleading results.

Critical point↗
DOE OSTI2023

Improved Tomographic Binning of 3 × 2 pt Lens Samples: Neural Network Classifiers and Optimal Bin Assignments

Abstract Large imaging surveys, such as the Legacy Survey of Space and Time, rely on photometric redshifts and tomographic binning for 3 × 2 pt analyses that combine galaxy clustering and weak lensing. In this paper, we propose a method for optimizing the tomographic binning choice for the lens sample of galaxies. We divide the CosmoDC2 and Buzzard simulated galaxy catalogs into a training set and an application set, where the training set is nonrepresentative in a realistic way, and then estimate photometric redshifts for the application sets. The galaxies are sorted into redshift bins covering equal intervals of redshift or comoving distance, or with an equal number of galaxies in each bin, and we consider a generalized extension of these approaches. We find that bins of equal comoving distance produce the highest dark energy figure of merit of the initial binning choices, but that the choice of bin edges can be further optimized. We then train a neural network classifier to identify galaxies that are either highly likely to have accurate photometric redshift estimates or highly likely to be sorted into the correct redshift bin. The neural network classifier is used to remove poor redshift estimates from the sample, and the results are compared to the case when none of the sample is removed. We find that the neural network classifiers are able to improve the figure of merit by ∼13% and are able to recover ∼25% of the loss in the figure of merit that occurs when a nonrepresentative training sample is used.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Integrating chromatin conformation information in a self-supervised learning model improves metagenome binning

Metagenome binning is a key step, downstream of metagenome assembly, to group scaffolds by their genome of origin. Although accurate binning has been achieved on datasets containing multiple samples from the same community, the completeness of binning is often low in datasets with a small number of samples due to a lack of robust species co-abundance information. In this study, we exploited the chromatin conformation information obtained from Hi-C sequencing and developed a new reference-independent algorithm, Metagenome Binning with Abundance and Tetra-nucleotide frequencies—Long Range (metaBAT-LR), to improve the binning completeness of these datasets. This self-supervised algorithm builds a model from a set of high-quality genome bins to predict scaffold pairs that are likely to be derived from the same genome. Then, it applies these predictions to merge incomplete genome bins, as well as recruit unbinned scaffolds. We validated metaBAT-LR’s ability to bin-merge and recruit scaffolds on both synthetic and real-world metagenome datasets of varying complexity. Benchmarking against similar software tools suggests that metaBAT-LR uncovers unique bins that were missed by all other methods.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

BinaRena: a dedicated interactive platform for human-guided exploration and binning of metagenomes

Background: Exploring metagenomic contigs and “binning” them into metagenome-assembled genomes (MAGs) are essential for the delineation of functional and evolutionary guilds within microbial communities. Despite the advances in automated binning algorithms, their capabilities in recovering MAGs with accuracy and biological relevance are so far limited. Researchers often find that human involvement is necessary to achieve representative binning results. This manual process however is expertise demanding and labor intensive, and it deserves to be supported by software infrastructure. Results: We present BinaRena, a comprehensive and versatile graphic interface dedicated to aiding human operators to explore metagenome assemblies via customizable visualization and to associate contigs with bins. Contigs are rendered as an interactive scatter plot based on various data types, including sequence metrics, coverage profiles, taxonomic assignments, and functional annotations. Various contig-level operations are permitted, such as selection, masking, highlighting, focusing, and searching. Binning plans can be conveniently edited, inspected, and compared visually or using metrics including silhouette coefficient and adjusted Rand index. Completeness and contamination of user-selected contigs can be calculated in real time. In demonstration of BinaRena’s usability, we show that it facilitated biological pattern discovery, hypothesis generation, and bin refinement in a complex tropical peatland metagenome. It enabled isolation of pathogenic genomes within closely related populations from the gut microbiota of diarrheal human subjects. It significantly improved overall binning quality after curating results of automated binners using a simulated marine dataset. Conclusions: BinaRena is an installation-free, dependency-free, client-end web application that operates directly in any modern web browser, facilitating ease of deployment and accessibility for researchers of all skill levels. The program is hosted at https://github.com/qiyunlab/binarena, together with documentation, tutorials, example data, and a live demo. It effectively supports human researchers in intuitive interpretation and fine tuning of metagenomic data.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Frequency-bin photonic quantum information

Discrete frequency modes, or bins, present a blend of opportunities and challenges for photonic quantum information processing. Frequency-bin-encoded photons are readily generated by integrated quantum light sources, naturally high-dimensional, stable in optical fiber, and massively parallelizable in a single spatial mode. Yet quantum operations on frequency-bin states require coherent and controllable multifrequency interference, making them significantly more challenging to manipulate than more traditional spatial degrees of freedom. In this mini-review, we describe recent developments that have transformed these challenges and propelled frequency bins forward. Focusing on sources, manipulation schemes, and detection approaches, we introduce the basics of frequency-bin encoding, summarize the state of the art, and speculate on the field’s next phases. Given the combined progress in integrated photonics, high-fidelity quantum gates, and proof-of-principle demonstrations, frequency-bin quantum information is poised to emerge from the lab and leave its mark on practical quantum information processing—particularly in networking where frequency bins offer unique tools for multiplexing, interconnects, and high-dimensional communications.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Binning is Sinning: Redemption for Hubble Diagram Using Photometrically Classified Type Ia Supernovae

Bayesian Estimation Applied to Multiple Species (BEAMS) is implemented in the BEAMS with Bias Corrections (BBC) framework to produce a redshift-binned Hubble diagram (HD) for Type Ia supernovae (SNe Ia). BBC corrects for selection effects and non–SN Ia contamination, and systematic uncertainties are described by a covariance matrix with dimension matching the number of BBC redshift bins. For spectroscopically confirmed SN Ia samples, a recent "Binning is Sinning" article showed that an unbinned HD and covariance matrix reduces the systematic uncertainty by a factor of ~1.5 compared to the binned approach. Here we extend their analysis to obtain an unbinned HD for a photometrically identified sample processed with BBC. To test this new method, we simulate and analyze 50 samples corresponding to the Dark Energy Survey (DES) with a low-redshift anchor; the simulation includes SNe Ia, and contaminants from core-collapse SNe and peculiar SNe Ia. The analysis includes systematic uncertainties for calibration and measures the dark energy equation of state parameter (w). Compared to a redshift-binned HD, the unbinned HD with nearly 2000 events results in a smaller systematic uncertainty, in qualitative agreement with BHS21, and averaging results among the 50 samples we find no evidence for a w-bias. To reduce computation time for fitting an unbinned HD with large samples, we propose an HD-rebinning method that defines the HD in bins of redshift, color, and stretch; the rebinned HD results in similar uncertainty as the unbinned case, and shows no evidence for a w-bias.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Cloud droplet diffusional growth in homogeneous isotropic turbulence: bin microphysics versus Lagrangian super-droplet simulations

The increase in the spectral width of an initially monodisperse population of cloud droplets in homogeneous isotropic turbulence is investigated by applying a finite-difference fluid flow model combined with either Eulerian bin microphysics or a Lagrangian particle-based scheme. The turbulence is forced applying a variant of the so-called linear forcing method that maintains the mean turbulent kinetic energy (TKE) and the TKE partitioning between velocity components. The latter is important for maintaining the quasi-steady forcing of the supersaturation fluctuations that drive the increase in the spectral width. We apply a large computational domain (64 3 m 3 ), one of the domains considered in Thomas et al. (2020). The simulations apply 1 m grid length and are in the spirit of the implicit large eddy simulation (ILES), that is, with small-scale dissipation provided by the model numerics. This is in contrast to the scaled-up direct numerical simulation (DNS) applied in Thomas et al. (2020). Two TKE intensities and three different droplet concentrations are considered. Analytic solutions derived in Sardina et al. (2015), valid for the case when the turbulence integral timescale is much larger than the droplet phase relaxation timescale, are used to guide the comparison between the two microphysics simulation techniques. The Lagrangian approach reproduces the scalings relatively well. Representing the spectral width increase in time is more challenging for the bin microphysics because appropriately high resolution in the bin space is needed. The bin width of 0.5 µm is only sufficient for the lowest droplet concentration (26 cm -3 ). For the highest droplet concentration (650 cm -3 ), an order of magnitude smaller bin size is barely sufficient. The scalings are not expected to be valid for the lowest droplet concentration and the high-TKE case, and the two microphysics schemes represent similar departures. Finally, because the fluid flow is the same for all simulations featuring either low or high TKE, one can compare point-by-point simulation results. Such a comparison shows very close temperature and water vapor point-by-point values across the computational domain and larger differences between simulated mean droplet radii and spectral width. The latter are explained by fundamental differences in the two simulation methodologies, numerical diffusion in the Eulerian bin approach and a relatively small number of Lagrangian particles that are used in the particle-based microphysics.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Large‐Eddy Simulations of a Convection Cloud Chamber: Sensitivity to Bin Microphysics and Advection

Abstract Bin microphysics schemes are useful tools for cloud simulations and are often considered to provide a benchmark for model intercomparison. However, they may experience issues with numerical diffusion, which are not well quantified, and the transport of hydrometeors depends on the choice of advection scheme, which can also change cloud simulation results. Here, an atmospheric large‐eddy simulation model is adapted to simulate a statistically steady‐state cloud in a convection cloud chamber under well‐constrained conditions. Two bin microphysics schemes, a spectral bin method and the method of moments, as well as several advection methods for the transport of the microphysical variables are employed for model intercomparison. Results show that different combinations of microphysics and advection schemes can lead to considerable differences in simulated cloud properties, such as cloud droplet number concentration. We find that simulations using the advection scheme that suffers more from numerical diffusion tends to have a smaller droplet number concentration and liquid water content, while simulation with the microphysics scheme that suffers more from numerical diffusion tends to have a broader size distribution and thus larger mean droplet sizes. Sensitivities of simulations to bin resolution, spatial resolution, and temporal resolution are also tested. We find that refining the microphysical bin resolution leads to a broader cloud droplet size distribution due to the advection of hydrometeors. Our results provide insight for using different advection and microphysics schemes in cloud chamber simulations, which might also help understand the uncertainties of the schemes used in atmospheric cloud simulations.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Zero-added-loss entanglement multiplexing using time-bin spectral shearing

High-quality quantum communications that enable important capabilities, such as distributed quantum computing and sensing, will require quantum repeaters for providing high-quality entanglement. To realize high-rate heralded entanglement for quantum repeaters, Chen et al . [Phys. Rev. Appl. 19 , 054029 (2023)] proposed a scheme for heralded-multiplexed generation of quasideterministic entangled photon pairs, called zero-added-loss multiplexing (ZALM). Here, we propose a design of the ZALM source using time-bin entanglement and spectral shearing. Additionally, we provide an analysis of experimentally relevant spectral-shearing parameters to optimize the spectral multiplexing. Moreover, we experimentally verify the compatibility of time-bin pulses and spectral shearing, as supported by observation of no appreciable phase shift when the same shearing is applied to both time bins. These results expand the benefits of applying a ZALM source to time-bin entanglement use cases. Moreover, more fully demonstrating time-bin and spectral shearing compatibility clears a path toward a broader use of spectral shearing that provides a deterministic frequency shift of high utility.

entanglement production↗
DOE OSTI2023

An Intercomparison of Large‐Eddy Simulations of a Convection Cloud Chamber Using Haze‐Capable Bin and Lagrangian Cloud Microphysics Schemes

Abstract Recent in situ observations show that haze particles exist in a convection cloud chamber. The microphysics schemes previously used for large‐eddy simulations of the cloud chamber could not fully resolve haze particles and the associated processes, including their activation and deactivation. Specifically, cloud droplet activation was modeled based on Twomey‐type parameterizations, wherein cloud droplets were formed when a critical supersaturation for the available cloud condensation nuclei (CCN) was exceeded and haze particles were not explicitly resolved. Here, we develop and adapt haze‐capable bin and Lagrangian microphysics schemes to properly resolve the activation and deactivation processes. Results are compared with the Twomey‐type CCN‐based bin microphysics scheme in which haze particles are not fully resolved. We find that results from the haze‐capable bin microphysics scheme agree well with those from the Lagrangian microphysics scheme. However, both schemes significantly differ from those from a CCN‐based bin microphysics scheme unless CCN recycling is considered. Haze particles from the recycling of deactivated cloud droplets can strongly enhance cloud droplet number concentration due to a positive feedback in haze‐cloud interactions in the cloud chamber. Haze particle size distributions are more realistic when considering solute and curvature effects that enable representing the complete physics of the activation process. Our study suggests that haze particles and their interactions with cloud droplets may have a strong impact on cloud properties when supersaturation fluctuations are comparable to mean supersaturation, as is the case in the cloud chamber and likely is the case in the atmosphere, especially in polluted conditions.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

On-chip frequency-bin quantum photonics

Abstract Frequency-bin encoding furnishes a compelling pathway for quantum information processing systems compatible with established lightwave infrastructures based on fiber-optic transmission and wavelength-division multiplexing. Yet although significant progress has been realized in proof-of-principle tabletop demonstrations, ranging from arbitrary single-qubit gates to controllable multiphoton interference, challenges in scaling frequency-bin processors to larger systems remain. In this Perspective, we highlight recent advances at the intersection of frequency-bin encoding and integrated photonics that are fundamentally transforming the outlook for scalable frequency-based quantum information. Focusing specifically on results on sources, state manipulation, and hyperentanglement, we envision a possible future in which on-chip frequency-bin circuits fulfill critical roles in quantum information processing, particularly in communications and networking.

electro-optic modulators↗
DOE OSTI2026

Optimal binning of correlated measurements

Experimental measurements are commonly represented on a discrete grid, requiring a balance between granularity and statistical noise. Two strategies have traditionally been used to improve such representations: selecting an appropriate bin width to control discretization error and applying kernel-based smoothing to suppress fluctuations. Despite their shared goal, these approaches have largely developed independently, without a unified statistical description of how discretization and correlation jointly determine measurement precision. Here, we extend the discussion of optimal interval averaging to a correlation-aware setting by Gaussian process regression, which explicitly accounts for correlations among neighboring bins. Starting from first principles, we derive the mean-squared error of discretized measurements and obtain closed-form asymptotic expressions for the optimal bin width and correlation length. When recast in reduced variables, the theory reveals distinct universal scaling laws governing the error in the correlation-free and correlation-controlled regimes. Characterized by intrinsically smooth intensity profiles and counting-based statistics, neutron scattering measurements are well suited for demonstrating the enhanced error contraction enabled by inter-bin correlations. We show that such improvement is achievable over the experimentally accessible Q-range and across multiple instruments and material systems. These results show that explicitly accounting for correlations systematically reshapes the limits of precision in discretized, noise-limited measurements. More broadly, the framework provides a transferable statistical foundation for optimizing data representation, inference, and experimental design across the physical and data sciences.

Tung, Chi-Huan [ORNL] (ORCID:0000000221972074)↗
DOE OSTI2023

Trimming and Decontamination of Metagenomic Data can Significantly Impact Assembly and Binning Metrics, Phylogenomic and Functional Analysis

Background: Investigators using metagenomic sequencing to study microbiomes often trim and decontaminate reads without knowing their effect on downstream analyses. Objective: This study was designed to evaluate the impacts JGI trimming and decontamination procedures have on assembly and binning metrics, placement of MAGs into species trees, and functional profiles of MAGs extracted from complex rhizosphere metagenomes, as well as how more aggressive trimming impacts these binning metrics. Methods: Twenty-three Miscanthus x giganteus rhizosphere metagenomes were subjected to different combinations and thresholds of force, kmer, and quality trimming and decontamination using BBDuk. Reads were assembled and binned in KBase. Phylogenomic and statistical analyses were applied to evaluate the effects of trimming and decontamination on downstream analyses. Results: We found that JGI trimmed and decontaminated reads had significant impacts on assembly and binning metrics compared to raw reads, including significantly higher total contig counts, more contigs greater than 10k bp in length, and larger total lengths of raw assemblies compared to QC assemblies, and 2.0% lower average contamination of QC MAGs compared to raw MAGs. We also found that differences in the placement of MAGs in species trees increased with decreasing completeness and contamination thresholds. Furthermore, aggressive trimming (Q20) was found to significantly reduce MAG counts. Conclusion: Trimming and decontamination of metagenomics reads prior to assembly can change an investigator’s answer to the questions, “Who is there and what are they doing?” However, mild trimming and decontamination of metagenomic reads with high-quality scores are recommended for removing sample processing and sequencing artifacts.

Whitham, Jason M.↗
DOE OSTI2022

Spanning the Gap From Bulk to Bin: A Novel Spectral Microphysics Method

Microphysics methods for climate models and numerical weather prediction typically track one, two, or three moments of a droplet size distribution for various categories of liquid, ice, and aerosol. Such methods rely on conversion parameters between these categories, which introduces uncertainty into predictions. While higher-fidelity options such as bin and Lagrangian schemes exist, they require too many degrees of freedom for climate modeling applications and introduce numerical challenges. Here we introduce a flexible spectral microphysics method based on collocation of basis functions. This method generalizes to a linear bulk scheme when using few basis functions and to a smoothed bin scheme with more degrees of freedom. Tested in an idealized box setting, the method improves spectral accuracy for droplet collision-coalescence and may eliminate the need for precipitation autoconversion rates required by bulk methods; furthermore, it generalizes well to multimodal distributions with less complexity than a bin method. The potential to extend this collocation representation to multiple hydrometeor classes suggests a path forward to unify liquid, ice, and aerosol microphysics in a single, flexible, computational framework for climate modeling.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

The impact of tomographic redshift bin width errors on cosmological probes

ABSTRACT Systematic errors in the galaxy redshift distribution n(z) can propagate to systematic errors in the derived cosmology. We characterize how the degenerate effects in tomographic bin widths and galaxy bias impart systematic errors on cosmology inference using observational data from the Deep Lens Survey. For this we use a combination of galaxy clustering and galaxy–galaxy lensing. We present two end-to-end analyses from the catalogue level to parameter estimation. We produce an initial cosmological inference using fiducial tomographic redshift bins derived from photometric redshifts, then compare this with a result where the redshift bins are empirically corrected using a set of spectroscopic redshifts. We find that the derived parameter S8 ≡ σ8(Ωm/.3)1/2 decreases from $0.841^{+0.062}_{-0.061}$ to $0.781^{0.061}_{0.054}$ upon correcting the n(z) errors in the second method.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Gamma-ray bursts, supernovae Ia, and baryon acoustic oscillations: A binned cosmological analysis

Abstract Cosmological probes at any redshift are necessary to reconstruct consistently the cosmic history. Studying properly the tension on the Hubble constant, H0, obtained by supernovae type Ia (SNe Ia) and the Planck measurements of the cosmic microwave background radiation would require complete samples of distance indicators at any epoch. Gamma-ray bursts (GRBs) are necessary for the aforementioned task because of their huge luminosity that allows us to extend the cosmic ladder to very high redshifts. However, using GRBs alone as standard candles is challenging, because their luminosity varies widely. To this end, we choose a reliable correlation for GRBs with a very small intrinsic scatter: the so-called fundamental plane correlation for GRB afterglows corrected for selection biases and redshift evolution. We choose a well defined sample: the platinum sample, composed of 50 long GRBs. To further constrain the cosmological parameters, we use baryon acoustic oscillations (BAOs) given their reliability as standard rulers. Thus, we have applied GRBs, SNe Ia, and BAOs in a binned analysis in redshifts so that the GRB contribution is fully included in the last redshift bin, which reaches z = 5. We use the fundamental plane correlation (also known as the 3D Dainotti relation), together with SNe Ia and BAOs, to constrain H0 and the density matter today, ΩM. This methodology allows us to assess the role of GRBs combined with SNe Ia and BAOs. We have obtained results for H0 and ΩM using GRBs+SNe Ia+BAOs with better precision than SNe Ia alone for every bin, thus confirming the beneficial role of BAOs and GRBs added together. In addition, consistent results between GRBs+SNe Ia+BAOs are obtained when compared with SNe Ia+BAOs, showing the importance of GRBs since the distance ladder is extended up to z = 5 with a similar precision obtained with other probes without including GRBs.

Dainotti, Maria Giovanna↗
DOE OSTI2026

Correlation-aware binning for small-angle neutron scattering via Gaussian-process inference

Binning in small-angle neutron scattering (SANS) is typically performed empirically, with fixed parameters chosen for convenience rather than statistical optimality. Such practices often fail to balance statistical precision and spatial resolution, leading to inconsistencies across instruments and datasets. Here we establish a correlation-aware framework that determines the optimal bin width from first principles by extending the classical Freedman–Diaconis (FD) rule to account for inter-bin correlations with a Gaussian process. In this formulation, the scattering intensity is treated as a smooth stochastic field whose statistical coherence is described by a covariance matrix. Analytical expressions of errors derived from this model yield closed-form criteria that separate the total deviation into contributions from counting noise, aliasing distortion and curvature-dependent correlation effects. Expressed in reduced variables, the resulting dimensionless error surface reveals a continuous transition from the uncorrelated FD regime to the correlation-dominated limit, providing a unified description of noise suppression and resolution control. Because the formulation depends only on the profile characteristics of scattering intensity I(Q), specifically its average intensity and first- and second-order derivatives, it applies generally to any SANS measurement regardless of sample, instrument or geometry. Experimental validation using small- and ultra-small-angle neutron scattering data confirms the predicted scaling behavior, demonstrating that correlation-aware inference systematically reduces mean-squared error and enables information-efficient reproducible data reduction across materials and instruments.

Tung, Chi-Huan [ORNL] (ORCID:0000000221972074)↗
DOE OSTI2026

Fidelity Comparison of Time-Bin and Fock State Encoding in Hybrid Quantum Systems Under Channel and Transduction Effects

Future quantum networks are expected to integrate a heterogeneous combination of quantum systems, owing to the diverse advantages offered by different physical platforms in terms of scalability, coherence times, and interfacing capabilities. Within the context of this emerging quantum communication paradigm, this paper presents an analytical comparison of two photonic encoding schemes—time-bin and Fock state (single rail)—in hybrid quantum systems where flying qubits are entangled with stationary matter qubits. We evaluate their resilience against fiber channel and quantum transduction effects by calculating the fidelity of the final states relative to their ideal forms. Employing the characteristic function approach, we derive analytical fidelity expressions and investigate their dependence on parameters such as transmissivity, noise levels, fiber length, and source generation success probability. Additionally, we simulate the scenario with a dedicated QuTiP software implementation to verify the validity of the theoretical models. Our findings reveal that due to its inherent single-mode structure, the Fock state encoding consistently outperforms time-bin encoding in fidelity, as this structure significantly minimizes susceptibility to losses compared to the two-mode nature of the time-bin scheme. This analysis offers valuable insights for future hybrid quantum communication and information processing applications.

Fiorini, Francesco [Pisa U.]↗