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Many languages such as Lua, Haskell and MATLAB support the ability to create nested comments. My proposal is to add a nested comment pragma to BNFC which would allow it to support the parsing of code. In this proposal I will provide sample implementations of nested comments for each of the lexer generators used by BNFC and outline the extension points by which I will add the functionality to the codebase.
This paper discusses the microphysical simulation of interactions in liquid xenon, the active detector medium in many leading rare-event searches for new physics, and describes experimental observables useful for understanding detector performance. The scintillation and ionization yield distributions for signal and background are presented using the Noble Element Simulation Technique (NEST), a toolkit based on experimental data and simple empirical formulas, which mimic previous microphysics modeling but are guided by data. The NEST models for light and charge production as a function of the particle type, energy, and electric field are reviewed, along with models for energy resolution and final pulse areas. NEST is compared with other models or sets of models and validated against real data, with several specific examples drawn from XENON, ZEPLIN, LUX, LZ, PandaX, and table-top experiments used for calibrations.
We focus on the study of the photodetachment of bare, i.e., single-cage (CN)− as well as nested (multi-cage) (CN@CM@…)− singly charged fullerene anions. We calculate the attached electron’s wavefunctions, energies, oscillator strengths and photodetachment cross sections of the C60−, C240−, C540−, (C60@C240)−, (C60@C540)−, (C240@C540)− and (C60@C240@C540)− fullerene anions, where the attached electron is captured into the ground s-state by the resultant external field provided by all fullerene cages in the anion. The goal is to gain insight into the changes in behavior ofphotodetachment of this valence electron as a function of the different geometries and potentials of the various underlying fullerenes or nested fullerenes (fullerene onions) both due to their increasing size and due to “stuffing” of a larger bare fullerene with smaller fullerenes. To meet this goal, we opt for a simple semi-empirical approximation to this problem: we approximate each individual fullerene cage by a rigid potential sphere of a certain inner radius, thickness and potential depth, as in numerous other model studies performed to date. The results reveal a number of rather significant differences in the wavefunctions, oscillator strengths and photodetachment cross sections among these fullerene anions, some of which are completely counter-intuitive. The results obtained can serve as a “zeroth-order-touchstone” for future studies of single-cage and nested fullerene anions by more rigorous theories and/or experiments to build upon this work to assess the importance of interactions omitted in the present study.
The spin-fermion (SF) model postulates that the dominant coupling between low-energy fermions in near critical metals is mediated by collective spin fluctuations (paramagnons) peaked at the Néel wave vector, Q N , connecting hot spots on opposite sides of the Fermi surface. It has been argued that strong correlations at hot spots lead to a Fermi surface deformation (FSD) featuring flat regions and increased nesting. This conjecture was confirmed in the perturbative self-consistent calculations when the paramagnon propagator dependence on momentum deviation from Q N is given by χ − 1 ∝ | Δ q | . Using diagrammatic Monte Carlo (diagMC) technique we show that such a dependence holds only at temperatures orders of magnitude smaller than any other energy scale in the problem, indicating that a different mechanism may be at play. Instead, we find that a χ − 1 ∝ | Δ q | 2 dependence yields a robust finite- T scenario for achieving FSD. To link phenomenological and microscopic descriptions, we applied the connected determinant diagMC method to the ( t − t ′ ) Hubbard model and found that at large U / t > 5.5 before the formation of electron and hole pockets (i) the FSD defined as a maximum of the spectral function is not very pronounced; instead, it is the lines of zeros of the renormalized dispersion relation that deforms toward nesting, and (ii) the static spin susceptibility is well described by χ − 1 ∝ | Δ q | 2 . Flat FS regions yield a nontrivial scenario for realizing a non-Fermi liquid state. Published by the American Physical Society 2024
Here, we propose a new algorithm for the fast solution of large, sparse, symmetric positive-definite linear systems, spaND (sparsified Nested Dissection). It is based on nested dissection, sparsification, and low-rank compression. After eliminating all interiors at a given level of the elimination tree, the algorithm sparsifies all separators corresponding to the interiors. This operation reduces the size of the separators by eliminating some degrees of freedom but without introducing any fill-in. This is done at the expense of a small and controllable approximation error. The result is an approximate factorization that can be used as an efficient preconditioner. We then perform several numerical experiments to evaluate this algorithm. We demonstrate that a version using orthogonal factorization and block-diagonal scaling takes fewer CG iterations to converge than previous similar algorithms on various kinds of problems. Furthermore, this algorithm is provably guaranteed to never break down and the matrix stays symmetric positive-definite throughout the process. We evaluate the algorithm on some large problems show it exhibits near-linear scaling. The factorization time is roughly $\mathcal{O}$(N), and the number of iterations grows slowly with N.
Egg hatchability in birds is a critical component of individual reproductive success and is associated with eggshell integrity. Contaminants, such as DDT, can influence eggshell thickness and are known to cause population declines. Moisture content and temperature can also impact eggshell thickness, but the influence of environmental conditions on the natural variation in eggshell thickness in wild populations is not well understood. Our goal was to investigate the relationship between environmental conditions and eggshell thickness of Western Bluebird (Sialia mexicana) and Ash-throated Flycatcher (Myiarchus cinerascens) eggs from 1997 to 2013 on the Pajarito Plateau in northern New Mexico. We tested whether nesting elevation, temperature, precipitation, and drought conditions influenced eggshell thickness in these two secondary cavity-nesting species, while also looking at eggshell thickness over time. Over the 16 years, nonviable or abandoned eggs were collected, and the analyzed dataset included 330 bluebird eggs and 113 flycatcher eggs. There was a significant increase in eggshell thickness over time for both species. Flycatcher eggshells were correlated with higher temperatures, whereas bluebird eggshells were influenced by an interaction between temperature and drought severity. In drought conditions, bluebird eggshell thickness was positively correlated with temperature, whereas in wet conditions, eggshell thickness was negatively correlated with temperature. Thicker eggshells in drought conditions may be a way of reducing water loss from eggs, which occurs faster at higher temperatures. In the southwestern United States, frequent and severe drought, higher temperatures, and decreases in precipitation are all expected to continue. In conclusion, the structure of eggs will be important to consider regarding how species may or may not adapt to novel conditions or persist in new environments.
Amniotic eggs are multifunctional structures that enabled early tetrapods to colonize the land millions of years ago, and are now the reproductive mode of over 70% of all terrestrial amniotes. Eggshell morphology is at the core of animal survival, mediating the interactions between embryos and their environment, and has evolved into a massive diversity of forms and functions in modern reptiles. These functions are critical to embryonic survival and may serve as models for new antimicrobial and/or breathable membranes. However, we still lack critical data on the basic structural and functional properties of eggs, particularly of reptiles. Here, we first characterized egg shape, shell thickness, porosity, and mineralization of eggs from 91 reptile species using optical images, scanning electron microscopy, and micro computed tomography, and collected data on nesting ecology from the literature. We then used comparative analyses to test hypotheses on the selective pressures driving their evolution. We hypothesized that eggshell morphology has evolved to protect shells from physical damage and desiccation, and, in support, found a positive relationship between thickness and precipitation, and a negative relationship between porosity and temperature. Although mineralization varied extensively, it was not correlated with nesting ecology variables. Ancestral state reconstructions show thinning and increased porosity over evolutionary time in squamates, but the opposite in turtles and crocodilians. Egg shape, size, porosity and calcification were correlated, suggesting potential structural or developmental tradeoffs. This study provides new data and insights into the morphology and evolution of reptile eggs, and raises numerous questions for additional research.
Abstract Designing cost‐efffective electrocatalysts for the oxygen evolution reaction (OER) holds significant importance in the progression of clean energy generation and efficient energy storage technologies, such as water splitting and rechargeable metal–air batteries. In this work, an OER electrocatalyst is developed using Ni and Fe precursors in combination with different proportions of graphene oxide. The catalyst synthesis involved a rapid reduction process, facilitated by adding sodium borohydride, which successfully formed NiFe nanoparticle nests on graphene support (NiFe NNG). The incorporation of graphene support enhances the catalytic activity, electron transferability, and electrical conductivity of the NiFe‐based catalyst. The NiFe NNG catalyst exhibits outstanding performance, characterized by a low overpotential of 292.3 mV and a Tafel slope of 48 mV dec −1 , achieved at a current density of 10 mA cm − 2 . Moreover, the catalyst exhibits remarkable stability over extended durations. The OER performance of NiFe NNG is on par with that of commercial IrO 2 in alkaline media. Such superb OER catalytic performance can be attributed to the synergistic effect between the NiFe nanoparticle nests and graphene, which arises from their large surface area and outstanding intrinsic catalytic activity. The excellent electrochemical properties of NiFe NNG hold great promise for further applications in energy storage and conversion devices.
As a corollary of the rapid advances in computing, ab initio simulation is playing an increasingly important role in modeling materials at the atomic scale. Two strategies are possible, ab initio Monte Carlo (AIMC) and molecular dynamics (AIMD) simulation. The former benefits from exact sampling from the correct thermodynamic distribution, while the latter is typically more efficient with its collective all-atom coordinate updates. In this study, using a relatively simple test model comprised of helium and argon, we show that AIMC can be brought up to, and even above, the performance levels of AIMD via a hybrid nested sampling/machine learning (ML) strategy. Here, ML provides an accurate classical reference potential (up to three-body explicit interactions) that can pilot long collective Monte Carlo moves that are accepted or rejected in toto à la nested Monte Carlo (NMC); this is in contrast to the single move nature of a naive implementation. Our proposed method only requires a small up front expense from evaluating the ab initio energies and forces of (100) random configurations for training. Importantly, our method does not totally rely on the trained, assuredly imperfect, interaction. We show that high performance and exact sampling at the desired level of theory can be realized even when the trained interaction has appreciable differences from the ab initio potential. Remarkably, at the highest levels of performance realized via our approach, a pair of statistically uncorrelated atomic configurations can be generated with (1) ab initio calculations.
Abstract Global quantification of protein abundances in single cells could provide direct information on cellular phenotypes and complement transcriptomics measurements. However, single-cell proteomics is still immature and confronts many technical challenges. Herein we describe a nested nanoPOTS (N2) chip to improve protein recovery, operation robustness, and processing throughput for isobaric-labeling-based scProteomics workflow. The N2 chip reduces reaction volume to <30 nL and increases capacity to >240 single cells on a single microchip. The tandem mass tag (TMT) pooling step is simplified by adding a microliter droplet on the nested nanowells to combine labeled single-cell samples. In the analysis of ~100 individual cells from three different cell lines, we demonstrate that the N2 chip-based scProteomics platform can robustly quantify ~1500 proteins and reveal membrane protein markers. Our analyses also reveal low protein abundance variations, suggesting the single-cell proteome profiles are highly stable for the cells cultured under identical conditions.
To meet changing research demands, new scanning tunneling microscope (STM) features must constantly evolve. We describe the design, development, and performance of a modular plug-in STM, which is compact and stable. The STM head is equipped with a quick-connect socket that is matched to a universal connector plug, enabling it to be transferred between systems. This head can be introduced into a vacuum system via a load-lock and transferred to various sites equipped with the connector plug, permitting multi-site STM operation. Its design allows for reliable operation in a variety of experimental conditions, including a broad temperature range, ultra-high vacuum, high magnetic fields, and closed-cycle pulse-tube cooling. The STM’s compact size is achieved by a novel nested piezoelectric coarse walker design, which allows for large orthogonal travel in the X, Y, and Z directions, ideal for studying both bulk and thin film samples ranging in size from mm to μm. Its stability and noise tolerance are demonstrated by achieving atomic resolution under ambient conditions on a laboratory desktop with no vibrational or acoustic isolation. The operation of the nested coarse walkers is demonstrated by successful navigation to a μm-sized 2D sample.
ABSTRACT We introduce a novel approach to boost the efficiency of the importance nested sampling (INS) technique for Bayesian posterior and evidence estimation using deep learning. Unlike rejection-based sampling methods such as vanilla nested sampling (NS) or Markov chain Monte Carlo (MCMC) algorithms, importance sampling techniques can use all likelihood evaluations for posterior and evidence estimation. However, for efficient importance sampling, one needs proposal distributions that closely mimic the posterior distributions. We show how to combine INS with deep learning via neural network regression to accomplish this task. We also introduce nautilus, a reference open-source python implementation of this technique for Bayesian posterior and evidence estimation. We compare nautilus against popular NS and MCMC packages, including emcee, dynesty, ultranest, and pocomc, on a variety of challenging synthetic problems and real-world applications in exoplanet detection, galaxy SED fitting and cosmology. In all applications, the sampling efficiency of nautilus is substantially higher than that of all other samplers, often by more than an order of magnitude. Simultaneously, nautilus delivers highly accurate results and needs fewer likelihood evaluations than all other samplers tested. We also show that nautilus has good scaling with the dimensionality of the likelihood and is easily parallelizable to many CPUs.
ABSTRACT Dark matter as scalar particles consisting of multiple species is well motivated in string theory where axion fields are ubiquitous. A two-field fuzzy dark matter (FDM) model features two species of ultralight axion particles with different masses, m1 ≠ m2, which is extended from the standard one-field model with $m_a \sim 10^{-22} \, {\rm eV}$. Here we perform numerical simulations to explore the properties of two-field FDM haloes. We find that the central soliton has a nested structure when m2 ≫ m1, which is distinguishable from the generic flat-core soliton in one-field haloes. However, the formation of this nested soliton is subject to many factors, including the density fraction and mass ratio of the two fields. Finally, we study non-linear structure formation in two-field cosmological simulations with self-consistent initial conditions and find that the small-scale structure in two-field cosmology is also distinct from the one-field model in terms of DM halo counts and soliton formation time.
The search for dark matter, the missing mass of the Universe, is one of the most active fields of study within particle physics. The XENON1T experiment recently observed a 3.5𝜎 excess potentially consistent with dark matter, or with solar axions. Here, we will use the Noble Element Simulation Technique (NEST) software to simulate the XENON1T detector, reproducing the excess. We utilize different detector efficiency and energy reconstruction models, but they primarily impact sub-keV energies and cannot explain the XENON1T excess. However, using NEST, we can reproduce their excess in multiple, unique ways, most easily via the addition of 31 ± 11 37 Ar decays. Furthermore, this results in new, modified background models, reducing the significance of the excess to ≤2.2𝜎 at least using non-Profile Likelihood Ratio (PLR) methods. This is independent confirmation that the excess is a real effect, but potentially explicable by known physics. Many cross-checks of our 37 Ar hypothesis are presented.
Skyrmions in noncentrosymmetric materials are believed to occur due to the Dzyaloshinskii-Moriya interaction. By contrast, the skyrmion formation mechanism in centrosymmetric materials remains elusive. Here, in this work, we reveal the intrinsic electronic structure of the centrosymmetric GdRu 2 Si 2 by selectively measuring magnetic domains using angle-resolved photoemission spectroscopy (ARPES). We found robust Fermi surface (FS) nesting, consistent with the magnetic modulation q -vector detected by the previous resonant x-ray scattering measurements. The pseudogap opens at the nested FS portions, which vary for different magnetic domains. The anomalous pseudogap disconnects the FS to generate Fermi arcs with twofold symmetry. These results indicate that the Ruderman-Kittel-Kasuya-Yosida (RKKY) interaction plays a decisive role in generating the screw spin modulation responsible for the skyrmion formation in GdRu 2 Si 2 . Furthermore, we demonstrate the flexible nature of magnetism in GdRu 2 Si 2 by manipulating magnetic domains with magnetic field and temperature cyclings, providing potential future applications for data storage and processing devices.
Variational quantum algorithms (VQAs) have the potential to demonstrate quantum utility on near-term quantum computers. However, these algorithms often get executed on the highest-fidelity qubits and computers to achieve the best performance, causing low system throughput. Recent efforts have shown that VQAs can be run on low-fidelity qubits initially and high-fidelity qubits later on to still achieve good performance. We take this effort forward and show that carefully varying the qubit fidelity map of the VQA over its execution using our technique, Nest, does not just (1) improve performance (i.e., help achieve close to optimal results), but also (2) lead to faster convergence. We also use Nest to co-locate multiple VQAs concurrently on the same computer, thus (3) increasing the system throughput, and therefore, balancing and optimizing three conflicting metrics simultaneously.
There is increasing interest in the use of mechanism-based multi-scale computational models (such as agent-based models (ABMs)) to generate simulated clinical populations in order to discover and evaluate potential diagnostic and therapeutic modalities. The description of the environment in which a biomedical simulation operates (model context) and parameterization of internal model rules (model content) requires the optimization of a large number of free parameters. In this work, we utilize a nested active learning (AL) workflow to efficiently parameterize and contextualize an ABM of systemic inflammation used to examine sepsis. Contextual parameter space was examined using four parameters external to the model’s rule set. The model’s internal parameterization, which represents gene expression and associated cellular behaviors, was explored through the augmentation or inhibition of signaling pathways for 12 signaling mediators associated with inflammation and wound healing. We have implemented a nested AL approach in which the clinically relevant (CR) model environment space for a given internal model parameterization is mapped using a small Artificial Neural Network (ANN). The outer AL level workflow is a larger ANN that uses AL to efficiently regress the volume and centroid location of the CR space given by a single internal parameterization. We have reduced the number of simulations required to efficiently map the CR parameter space of this model by approximately 99%. In addition, we have shown that more complex models with a larger number of variables may expect further improvements in efficiency.
This data package is associated with the publication “Riverine dissolved organic matter transformations increase with watershed area, water residence time, and Damköhler numbers in nested watersheds” submitted to Biogeochemistry by Ryan et al., 2024 (DOI: https://doi.org/10.1007/s10533-024-01169-5). This study aims to investigate fundamental and transferable drivers of dissolved organic matter (DOM) diversity across five nested watersheds within the contiguous United States. DOM diversity was explored using ultrahigh-resolution Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS). The samples and the unprocessed FTICR-MS data used in this study are publicly available on the Environmental System Science Data Infrastructure for a Virtual Ecosystem (ESS-DIVE) data repository (see DOIs below). The data for the Willamette, Gunnison, Connecticut, and Deschutes basins were collected as part of a collaboration between the Watershed Rules of Life (WROL) project and Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems (WHONDRS). The data for the Yakima River basin (YRB) was collected by the PNNL River Corridor SFA. The raw, unprocessed FTICR-MS data with additional (meta)data can be found at doi:10.15485/1895159 for WROL samples and doi:10.15485/1898912 for YRB samples. This data package contains the processed data used in the associated manuscript. This package also contains ancillary geospatial, hydrological, and geochemical information that supports the interpretation of the FTICR-MS data within Ryan et al., 2024. This data package is associated with the GitHub repository found at https://github.com/WHONDRS-Hub/rcsfa-RC4-WROL-YRB_DOM_Diversity. This data package was originally published August 2024. It was updated January 2025 (modified files). See the change history in the readme more details. At the directory level, the data package is comprised of three folders: (1) data, (2) output, and (3) src; and five additional files including the data dictionary (file ending in "_dd.csv”) and file-level metadata (file ending in “_flmd.csv”). The “src” folder contains the scripts used to process the FTICR data, conduct the analyses, and produce the manuscript figures. The inputs for these scripts are in the “data” folder and the returned outputs in the “output” folder. Inputs include temporal and spatial metadata associated with the sampling efforts, processed FTICR data, and total and normalized putative biochemical transformations per sample. Outputs include cleaned and combined data presented as tables, descriptive statistics, and plots. The file-level metadata file lists all files contained in this data package and descriptions for each. The data dictionary describes the units and definitions for each tabular data column or row header.