Biphoton Interference from Spectrally Overlapping Resonances in Nonlinear Metasurfaces
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Noh, Jiho [Sandia National Laboratories (SNL-NM), ↗
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Unexpected Overlaps in the Molecular Mechanisms Underlying Interactions Between Fungi and Bacteria
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59 BASIC BIOLOGICAL SCIENCES↗
In-vivo neuronal dysfunction by Aβ and tau overlaps with brain-wide inflammatory mechanisms in Alzheimer’s disease
The molecular mechanisms underlying neuronal dysfunction in Alzheimer’s disease (AD) remain uncharacterized. Here, we identify genes, molecular pathways and cellular components associated with whole-brain dysregulation caused by amyloid-beta (Aβ) and tau deposits in the living human brain. We obtained in-vivo resting-state functional MRI (rs-fMRI), Aβ- and tau-PET for 47 cognitively unimpaired and 16 AD participants from the Translational Biomarkers in Aging and Dementia cohort. Adverse neuronal activity impacts by Aβ and tau were quantified with personalized dynamical models by fitting pathology-mediated computational signals to the participant’s real rs-fMRIs. Then, we detected robust brain-wide associations between the spatial profiles of Aβ-tau impacts and gene expression in the neurotypical transcriptome (Allen Human Brain Atlas). Within the obtained distinctive signature of in-vivo neuronal dysfunction, several genes have prominent roles in microglial activation and in interactions with Aβ and tau. Moreover, cellular vulnerability estimations revealed strong association of microglial expression patterns with Aβ and tau’s synergistic impact on neuronal activity (q < 0.001). These results further support the central role of the immune system and neuroinflammatory pathways in AD pathogenesis. Neuronal dysregulation by AD pathologies also associated with neurotypical synaptic and developmental processes. In addition, we identified drug candidates from the vast LINCS library to halt or reduce the observed Aβ-tau effects on neuronal activity. Top-ranked pharmacological interventions target inflammatory, cancer and cardiovascular pathways, including specific medications undergoing clinical evaluation in AD. Our findings, based on the examination of molecular-pathological-functional interactions in humans, may accelerate the process of bringing effective therapies into clinical practice.
60 APPLIED LIFE SCIENCES↗
Impact of Heat Input and Step Over Distance on Part Geometry for Multi-Bead WAAM Components
Abstract This study investigates the impact of heat input and overlap ratio or stepover distance on part geometry in wire arc additive manufacturing (WAAM). In this work, an experimental approach was taken to quantify the variation in height and aspect ratio of walls at different combinations of overlap and heat input. Multi-bead walls were deposited with the overlap ratio varying from ½, ⅔, and 1 at a low, medium, and high-power set point on the welding power supply. A relationship between heat input, overlap ratio, and the resultant part geometry is established. Trials with an overlap ratio of one and low to medium heat input exhibited greater lack of fusion defects than the high heat input trials. At higher heat input levels, the as-deposited geometry was found to have less variation in height and an increase in aspect ratio compared to lower heat input trials. The aspect ratio of deposited walls ranged from approximately 1, for the low-power trial with an overlap ratio of ½, to approximately 7, for the high-power trial with an overlap ratio of 1. Additionally, the low and medium power trials with an overlap ratio of ⅔ exhibited the least height variation in the top surface for those heat input levels with an average range of 2.9 mm and 1.8 mm respectively. For the high heat input trials, an overlap ratio of 1 was observed to have the least variation in height with a standard deviation of 0.42 mm and an average range of 1.7 mm; however, lack of fusion defects were present in the top surface and the part cross section.
Hussein, Zaky↗
Optimizing aluminum oxide passivation layers—Laser-induced plasmas for layer formation, real-time diagnostics, and layer evaluation
Molten salts have beneficial thermophysical and electrolytic properties, but the aggressive nature of molten salts requires corrosion mitigation strategies, such as structural material surface treatment. In this study, a laser-induced breakdown spectroscopy (LIBS) system was used to simultaneously ablate and monitor de-excitation spectra to form and identify dense alumina passivation layers. Additionally, high-frequency (kHz) LIBS imaging allowed rapid elemental mapping and depth profiling for surface O/Al ratios via minimally destructive analysis. The paired t-test rejected the null hypothesis that air and Ar cover gases were equivalent (p = 0.00012), and the analysis of variance (ANOVA) showed that overlap between shots (p = 0.03112) and cover gas flow rate (p = 0.02729) were statistically significant. At 75% overlap, the O/Al ratio increased to 10% ± 2%, and 90% overlap rose further to 31% ± 2%. Regardless of overlap, tuning the gas flow from 0.5 to 2.5 L min −1 enhanced the O/Al ratio by 24% ± 4%. LIBS depth profiling showed a 3× increase in layer thickness from 75% to 90% overlap. Molecular band peaks of AlO, a precursor to Al 2 O 3 found during treatment, suggest that band intensity could be used for real-time Al 2 O 3 optimization. Ultimately, by adjusting laser spot overlap and cover gas flow rate, a 266 nm laser was shown to form Al 2 O 3 layers on an Al6061 sample, with cover gas flow rate primarily affecting the O/Al ratio and layer thickness correlating with laser spot overlap. This combination of molecular spectra collection, imaging, and depth profiling demonstrated the robust layer analysis capabilities of LIBS.
Corrosion↗
Rapid Initial-State Preparation for the Quantum Simulation of Strongly Correlated Molecules
Studies on quantum algorithms for ground-state energy estimation often assume perfect ground-state preparation; however, in reality the initial state will have imperfect overlap with the true ground state. Here, we address that problem in two ways: by faster preparation of matrix-product-state (MPS) approximations and by more efficient filtering of the prepared state to find the ground-state energy. We show how to achieve unitary synthesis with a Toffoli complexity about 7 × lower than that in prior work and use that to derive a more efficient MPS-preparation method. For filtering, we present two different approaches: sampling and binary search. For both, we use the theory of window functions to avoid large phase errors and minimize the complexity. We find that the binary-search approach provides better scaling with the overlap at the cost of a larger constant factor, such that it will be preferred for overlaps less than about 0.003 . Finally, we estimate the total resources to perform ground-state energy estimation of Fe - S cluster systems, including the Fe Mo cofactor by estimating the overlap of different MPS initial states with potential ground states of the Fe Mo cofactor using an extrapolation procedure. With a modest MPS bond dimension of 4000 , our procedure produces an estimate of approximately 0.9 overlap squared with a candidate ground state of the Fe Mo cofactor, producing a total resource estimate of 7.3 × 10 10 Toffoli gates; neglecting the search over candidates and assuming the accuracy of the extrapolation, this validates prior estimates that have used perfect ground-state overlap. This presents an example of a practical path to prepare states of high overlap in a challenging-to-compute chemical system. Published by the American Physical Society 2025
Berry, Dominic W. (ORCID:0000000334461449)↗
Seasonal changes in occupancy and activity patterns in native Collared Peccary and non-native wild pig and Common Warthog in southern Texas, the United States
Abstract Southern Texas, USA, is home to native collared peccaries (Dicotyles tajacu) and introduced populations of invasive wild pigs (generally Sus scrofa × domesticus hybrids) and non-native African warthogs (Phacochoerus africanus). Although these ecologically similar mammals co-occur in this region, the potential impacts of invasive suids on collared peccaries are poorly understood. We examined co-occupancy and activity pattern overlap of collared peccaries, wild pigs, and warthogs across 3 seasons (fall, winter, and spring) using remote camera data collected from Chaparral Wildlife Management Area, Cotulla, Texas (November 2020 to June 2021). Using activity pattern analyses and single and 2-species occupancy models incorporating habitat and climate characteristics, we found evidence of extensive spatial overlap between all species pairs and varying degrees of temporal overlap depending on species pairs and season. Collared peccaries and wild pigs displayed moderate temporal overlap across all seasons. Collared peccaries appeared to alter fall activity in the presence of wild pigs to be active earlier in the morning and less active during the day. Collared peccaries and warthogs had low-to-moderate temporal overlap (low in fall, winter; moderate in spring). Wild pigs and warthogs had low temporal overlap (fall, spring) and wild pigs appeared to alter activity in the presence of warthogs (fall), becoming less active during the day during peak warthog activity. Overall, our results suggest that peccary, wild pig, and warthog interactions and activity are dynamic and vary seasonally according to the ecology and preferred environmental conditions of each species. Given the potential for interspecific competition and disease transmission with Collared Peccary and other native wildlife, resource partitioning between wild pigs and warthogs needs to be further examined to aid in effective management strategies.
Kupferman, Caitlin A. (ORCID:0009000953554860)↗
Transportability of exogenous microbial community correlates with interwell connectivity in deep aquifers
Subsurface resource engineering operations often utilize continuous injection of externally-sourced water into geological reservoirs for formation pressure maintenance, resource recovery or energy/waste storage. Such injected water generally contains naturally occurring microbes. Little is known, however, about how the injectate microbes transport through geological media as a community, how such transportability is affected by injector-producer connectivity, and whether such knowledge can be utilized for flowpath characterization. In this study, we analyzed daily-to-weekly timeseries microbial community data from the injected- and produced-fluids of a ten-month flow test at a deep, well-characterized engineered aquifer. We found that the injectate microbial community was distinct from the indigenous community at the amplicon sequence variant (ASV) level, and that the transportability of injectate community towards a given producer, quantified by an “nASV-Overlap” metric we propose, had strong and significant positive correlation with known injector-producer connectivities at our site. This suggests that the better the connectivity, the higher the probability for more injectate species to flow through the interwell region and arrive at a producer. Because interwell connectivity is an important yet usually unknown parameter in subsurface resource engineering, such correlation in turn points to nASV-Overlap as a useful indicator of interwell connectivity for aquifer characterization and long-term monitoring. Based on our findings, an nASV-Overlap-based microbial tracing approach was developed for characterizing and monitoring the relative connectivities across multiple producers with a given injector. A side-by-side comparison between the new nASV-Overlap approach and traditional artificial tracer methods is presented, and their respective strengths and limitations are discussed.
Deep biosphere↗
Metrics and extrapolation of resonant magnetic perturbation thresholds for ELM suppression
This large database study of resonant magnetic perturbation (RMP) edge localized mode (ELM) suppression thresholds in the AUG, DIII-D, EAST, and KSTAR tokamaks details the key strengths and weaknesses of RMP metrics. The RMP ELM suppression database used for this work contains plasma information at the time of transition from ELMing to ELM suppressed states where a clear experimental threshold is identified. The experimental threshold distributions are compared for five metrics: (1) the island overlap width, (2) pedestal top Chirikov overlap, (3) peeling edge displacement, (4) pedestal top resonant drive, and (5) edge dominant mode overlap. The distributions, the regularity of the dependence on RMP coil currents, and the sensitivities of a given metric to equilibrium reconstruction details are compared. The overlap metric proves to be a good compromise between including the appropriate plasma response physics and maintaining a numerical robustness. This quantity does not exhibit clear power-law scalings for projection, but machine learning can assist in predicting thresholds within the existing parameter ranges and providing uncertainty quantification of those predictions. Two new first-principles models, one utilizing a threshold from the non-linear Modified Rutherford equation evaluated at the pedestal top and one utilizing the SLAYER code to calculate the linear tearing threshold from torque balance, offer possible paths to extrapolation beyond the existing database parameter space.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
GENTANGLE: integrated computational design of gene entanglements
The design of two overlapping genes in a microbial genome is an emerging technique for adding more reliable control mechanisms in engineered organisms for increased stability. The design of functional overlapping gene pairs is a challenging procedure, and computational design tools are used to improve the efficiency to deploy successful designs in genetically engineered systems. GENTANGLE (Gene Tuples ArraNGed in overLapping Elements) is a high-performance containerized pipeline for the computational design of two overlapping genes translated in different reading frames of the genome. This new software package can be used to design and test gene entanglements for microbial engineering projects using arbitrary sets of user-specified gene pairs.
59 BASIC BIOLOGICAL SCIENCES↗
Simplex‐based model for nanoparticle grain identification in four‐dimensional scanning transmission electron microscopy data
Grain identification in polycrystalline nanoparticles, for example, determining which crystal phases are present at each spatial location, is fundamental to materials characterisation. This is particularly challenging when grains overlap extensively, as commonly occurs in four-dimensional scanning transmission electron microscopy (4D-STEM) datasets. We propose a simplex-based model (SBM) in which each simplex vertex represents the diffraction pattern (DP) of a pure grain, and the simplex edges and interior represent overlapping grains. Our SBM grain identification algorithm operates on the Bragg disk (BD) data matrix distilled from the 4D-STEM data to identify the grain membership at each scan position, together with a BD feature matrix whose columns represent the DPs for each constituent grain, which is important for identifying the crystal structure of each grain. We solve the model using a two-stage algorithm. In Stage 1, we adapt a linear mixing algorithm to estimate an initial BD feature matrix whose columns represent DPs of potentially overlapping grains. Our Stage 2 algorithm incorporates sparsity considerations to transform the initial BD feature matrix so that its columns represent DPs of pure grains. Using simulated datasets with various grain configurations, we demonstrate that SBM recovers both the BD feature matrix and membership maps more accurately than existing methods, even when a grain lacks any pure region and completely overlaps with other grains.
4D-STEM segmentation↗
Mitigating Algorithmic Bias in Cancer Site Classification Models
Purpose Integrating artificial intelligence in cancer diagnostics has improved tumor classification beyond rule-based systems. Despite these advancements, these models may still encode demographic biases. We conducted a large-scale, applied bias-probing study of a deep learning–based cancer site classifier to quantify race information encoded in document embeddings. We then evaluated how performance changes when race-correlated embedding dimensions are removed in a post-training sensitivity analysis. Methods The cancer site classifier was trained using 3.5 million electronic cancer pathology reports from six of the National Cancer Institute's SEER registries. We trained a hierarchical self-attention network to generate 400-dimensional document embeddings. These embeddings were used to train two downstream, gradient-boosted decision tree classifiers: one to classify the cancer sites and another to predict racial categories. We identified overlapping features by intersecting the top 50 feature-importance rankings from the site and race models and computed their cumulative feature importance in each model. As a post hoc sensitivity analysis, we progressively pruned these overlapping dimensions, retrained the site model, and compared overall macro-F1 and accuracy, race-stratified macro-F1, and group fairness metrics on the basis of demographic parity and equalized odds before and after pruning. Results The analysis revealed minimal feature overlap between the cancer site and race prediction models, and the cumulative importance scores indicated a negligible influence of racial information on clinical predictions. Post-training pruning of overlapping features did not compromise the models' diagnostic accuracy, with a 0.07% loss in accuracy. Conclusion Our findings demonstrate that HiSAN-generated embeddings from SEER data can be used effectively in cancer site classification without significant demographic bias influencing the outcomes. Post-training pruning therefore functions as a practical audit and sensitivity check.
Shivanna, Abhishek [ORNL] (ORCID:0009000665228593)↗
Personalized, disease-stage specific, rapid identification of immunosuppression in sepsis
Introduction Data overlapping of different biological conditions prevents personalized medical decision-making. For example, when the neutrophil percentages of surviving septic patients overlap with those of non-survivors, no individualized assessment is possible. To ameliorate this problem, an immunological method was explored in the context of sepsis. Methods Blood leukocyte counts and relative percentages as well as the serum concentration of several proteins were investigated with 4072 longitudinal samples collected from 331 hospitalized patients classified as septic (n=286), non-septic (n=43), or not assigned (n=2). Two methodological approaches were evaluated: (i) a reductionist alternative, which analyzed variables in isolation; and (ii) a non-reductionist version, which examined interactions among six (leukocyte-, bacterial-, temporal-, personalized-, population-, and outcome-related) dimensions. Results The reductionist approach did not distinguish outcomes: the leukocyte and serum protein data of survivors and non-survivors overlapped. In contrast, the non-reductionist alternative differentiated several data groups, of which at least one was only composed of survivors (a finding observable since hospitalization day 1). Hence, the non-reductionist approach promoted personalized medical practices: every patient classified within a subset associated with 100% survival subset was likely to survive. The non-reductionist method also revealed five inflammatory or disease-related stages (provisionally named ‘early inflammation, early immunocompetence, intermediary immuno-suppression, late immuno-suppression, or other’). Mortality data validated these labels: both ‘suppression’ subsets revealed 100% mortality, the ‘immunocompetence’ group exhibited 100% survival, while the remaining sets reported two-digit mortality percentages. While the ‘intermediary’ suppression expressed an impaired monocyte-related function, the ‘late’ suppression displayed renal-related dysfunctions, as indicated by high concentrations of urea and creatinine. Discussion The data-driven differentiation of five data groups may foster early and non-overlapping biomedical decision-making, both upon admission and throughout their hospitalization. This approach could evaluate therapies, at personalized level, earlier. To ascertain repeatability and investigate the dynamics of the ‘other’ group, additional studies are recommended.
Immunology↗
Exact chiral symmetry with quantum signal processing
We give a quantum signal processing (QSP) algorithm for the overlap fermion Hamiltonian which preserves the Ginsparg-Wilson relation up to a controllable error $ε_e$. Quantum simulations of Dirac fermions with exact chiral symmetry are thus nearly free: applying the overlap Hamiltonian costs only a factor logarithmic in $ε_e$ more than the Wilson-Dirac Hamiltonian. Comparing to domain-wall fermions, a mild overhead is found in circuit complexity while reducing qubit costs. We show how QSP effectively constructs an extra dimension when simulating the overlap operator, illustrating that the scaling of quantum algorithms reflects the deeper physics of overlap fermions arising at the boundary of domain-wall fermions.
Lamm, Henry [Fermilab] (ORCID:0000000330330791)↗
Measuring Thread Timing to Assess the Feasibility of Early-Bird Message Delivery Across Systems and Scales
Early-bird communication is a communication/computation overlap technique that leverages fine-grained communication to improve application run-time. Communication is divided such that each individual thread can initiate transmission of its portion of the data upon completion rather than waiting for a dedicated communication phase. The benefit of early-bird communication depends on the completion timing of the individual threads: On the one hand, if all threads are complete at nearly the same time, the overheads of sending multiple messages will accumulate, leading to performance that is worse than if a single message had been sent. On the other hand, if thread completions are spread out in time, those that complete earlier can send data while others continue working, leading to performance that is better than if a single message had been sent. The challenge is that the completion times are currently unknown and can vary based on application, problem size, system software, and underlying hardware. In this paper, we address this lacuna by measuring and evaluating the potential overlap afforded by early-bird communication for a selection of proxy applications. These measurements help us understand whether a given application could benefit from early-bird communication. Here, we present our technique for gathering this data and evaluate data collected from three proxy applications: MiniFE, MiniMD, and MiniQMC. Each application is run on three systems with distinct CPU architectures and strong scales across three run sizes. To characterize the behavior of these workloads, we study the trends of thread timings at both a macro level, across all threads across all runs of an application, and a micro level, that is, within a single process of a single run. We observe that our tested applications exhibit significantly different thread arrival distributions. The machine used had a significant impact, with the window of potential overlap varying by as much as an order of magnitude.
97 MATHEMATICS AND COMPUTING↗
Strongly vs. weakly coupled in-medium showers: energy stopping in large-Nf QED
Abstract Inside a medium, showers originating from a very high-energy particle may develop via medium-induced splitting processes such as hard bremsstrahlung or pair production. During shower development, two consecutive splittings sometimes overlap quantum mechanically, so that they cannot be treated independently. Some of these effects can be absorbed into an effective value of a medium parameter known as$$ \hat{q} $$ q ̂ . Previous calculations (with certain simplifying assumptions) have found that, after adjusting the value of$$ \hat{q} $$ q ̂ , the leftover effect of overlapping splittings is quite small for purely gluonic large-N c showers but is very much larger for large-N f QED showers, at comparable values ofNα. Those works did not quite make for apples-to-apples comparisons: the gluon shower work investigated energy deposition from a gluon-initiated shower, whereas the QED work investigated charge-deposition from an electron-initiated shower. As a first step to tighten up the comparison, this paper investigates energy deposition in the QED case. Along the way, we develop a framework that should be useful in the future to explore whether the very small effect of overlapping splitting in purely gluonic showers is an artifact of having ignored quarks.
Physics↗
Cosmohedra
It has been a long-standing challenge to find a geometric object underlying the cosmological wavefunction for Tr(ϕ 3 ) theory, generalizing associahedra and surfacehedra for scattering amplitudes. In this note, we describe a new class of polytopes — “cosmohedra” — that provide a natural solution to this problem. The faces of associahedra capture the combinatorics of non-overlapping chords of the momentum polygon, reflecting all partial factorizations of amplitudes. Cosmohedra are far richer — instead of non-overlapping chords, their faces capture the “russian doll” structure of non-overlapping subpolygons that determine the wavefunction. We show that cosmohedra are intimately related to associahedra, obtained by “blowing up” faces of the associahedron in a simple way. We give a full combinatorial description of cosmohedron faces and their factorization properties, and provide an explicit realization in terms of facet inequalities that further “shave” the facet inequalities of the associahedron. We also discuss a novel way for computing the wavefunction from cosmohedron geometry that extends the usual connection with polytope canonical forms. We illustrate cosmohedra with examples at tree-level and one loop; the close connection to surfacehedra suggests the generalization to all loop orders. Moving beyond the wavefunction, we briefly describe “cosmological correlahedra” for full correlators, which are one higher-dimensional polytopes, interpolating between associahedra and cosmohedra on opposite facets in an extra direction associated with the total energy. We speculate on how the existence of cosmohedra might suggest a “stringy” formulation for the cosmological wavefunction/correlators, generalizing the way in which the Minkowski sum decomposition of associahedra naturally extend particle to string amplitudes.
Scattering Amplitudes↗
Accelerating Multivariate Functional Approximation Computation with Domain Decomposition Techniques⋆
Modeling large datasets through Multivariate Functional Approximations (MFA) provide an elegant way to handle many visualization and scientific analysis workflows. The process necessitates scalable data partitioning methods to compute MFA representations efficiently without compromising the accuracy or continuity of the reconstructed solution. We propose a domain -decomposed method for computing the MFA with B -spline bases, which reduces the total work per task and uses a restricted Additive Schwarz (RAS) method to converge the control point data degrees -of -freedom along subdomain boundaries. We provide an in-depth analysis of the parallel approach with domain decomposition solvers, aiming to minimize local subdomain error residuals and recover high -order continuity at subdomain interfaces with appropriate choices of knot overlaps. The communication cost, determined by the overlap regions in the RAS implementation, is optimized to recover the numerical error profile of the single subdomain case. Our proposed method stands in contrast to previous methods, which typically only recover either C 0 or at best C 1 continuity for arbitrary B -spline degree expansions, or those that require post -processing to blend discontinuities in the reconstructed data. We demonstrate the effectiveness of our approach using analytical and real -world datasets in 1D, 2D, and 3D through both strong and weak scaling studies. The performance results indicate that the overall cost of computing the approximation is directly proportional to the underlying nearest -neighbor communication implementation, and is only weakly dependent on the overlap region size that determines the size of the messages. This finding underscores the efficiency and scalability of our proposed method, making it a promising solution for handling large datasets in scientific workflows.
additive Schwarz solvers↗