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At least 1,567 records · Page 87

Noise Decoherence and Errors from Entanglement-function Theory for Quantum Computing

A significant problem in quantum computing is the development of physical realizations of algorithms that are robust against noise. One way to examine and mitigate noise would be to simulate large sets of qubits coupling to the external environment on classical computers. This is extremely challenging as quantum information processing is in some sense tied to computing resources that scale exponentially with the number of computing elements (qubits). In this LDRD, we set the foundation for a computational framework potentially allowing simulations of 1000s of qubits vs. 10s now possible. Exact wave-function-based methods demand exponentially increasing resources with system size. The method proposed, entanglement-functional theory (EFT), requires vastly fewer resources. The crucial step is to map the information contained in the wave-functions into a simpler object with associated 1.) auxiliary gate operations and 2.) entanglement functionals of this object. This is similar to the Time-dependent Density Functional Theory (TDDFT) approach that has revolutionized chemistry and materials science. Instead of dealing with the exponentially large wave-function, EFT works with a polynomially large set of projections (the density) that are easily manipulated through unitary operations. For a given set of quantum gates, an isomorphism exists that relates the sequence of events to the time-dependent density. A system of entangled qubits can be simulated at drastically reduced cost relative to existing state-of-the-art vector-state simulation codes.

97 MATHEMATICS AND COMPUTING↗

Density Functional Theory Applied to Transition Metal Elements and binaries: Development Application and Results of the V-DM/16 Test Set

Density functional theory (DFT) is undergoing a shift from a descriptive to a predictive tool in the field of solid state physics, heralded by a spike in “high-throughput” studies. However, methods to rigorously evaluate the validity and accuracy of these studies is lacking, raising serious questions when simulation and experiment disagree. In response, we have developed the V-DM/16 test set, designed to evaluate the experimental accuracy of DFT’s various implementations for pe riodic transition metal solids. Our test set evaluates 26 transition metal elements and 80 transition metal alloys across three physical observables: lattice constants, elastic coefficients, and formation energy of alloys. Whether or not a functional can accurately evaluate the formation energy offers key insights into whether the relevant physics are being captured in a simulation, an especially impor tant question in transition metals where active d-electrons can thwart the accuracy of an otherwise well-performing functional. Our test set captures a wide variety of cases where the unique physics present in transition metal binaries can undermine the effectiveness of “traditional” functionals. By application of the V/DM-16 test set, we aim to better characterize the performance of existing functionals on transition metals, and to offer a new tool to rigorously evaluate the performance of new functionals in the future.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

An Investigational Platform of the Human Brain for Understanding Complex Neural Function

In this project we focused on developing an experimental model of the human central nervous system that more accurately mirrors the function and physiology of the human brain. This in vitro brain-on-a-chip can provide critical insight into human brain function in response to chemical exposure and disease. To develop a more accurate experimental model, we evaluated and optimized key elements designed to more accurately recapitulate neuron function. We demonstrated that neuronal function was more robust when neurons were cultured with other neuronal cells as well as complex extracellular matrix molecules. We also designed a novel threedimensional multi-electrode array (3DMEA) that provides an unprecedented ability to noninvasively monitor and record neuronal function in 3D in a reproducible manner. We also optimized an experimental model of the blood-brain barrier, providing an important tool for understanding how this interface regulates the exchange of molecules from the blood to the brain. Underpinning all of these experimental efforts were novel data analytics and modeling approaches. The successful completion of this project has positioned LLNL to use our novel tools and expertise to understand human brain function in the context of the Lab’s national security mission.

59 BASIC BIOLOGICAL SCIENCES↗

Approximating and incorporating model uncertainty in an inversion for seismic source functions: Preliminary results

We present preliminary work on propagating model uncertainty into the estimation of the time domain source time functions of the seismic source. Our method is based on an estimated model covariance function, which we estimate from the data. The model covariance function is then used to construct a suite of surrogate Greens functions which we use in a Monte Carlo type inversion scheme. The result is a probability density function of the six independent source time functions, each of which corresponds to an individual component of the seismic moment tensor. We compare the results of our method with those obtained using a computationally expensive finite difference Monte Carlo method and find that our new method produces results that are deficient in low frequencies. The advantage of our new method, which we term the Karhunen-Loeve Monte Carlo (KLMC) method, is that is several orders of magnitude faster than our current method, which uses a finite difference scheme to produce the suite of forward models.

42 ENGINEERING↗

GaAs Neutron Response Functions and Radiation Damage Metrics

The radiation effects community needs clear, well-documented, neutron energy-dependent responses that can be used in assessing radiation-induced material damage to GaAs semiconductors and for correlating observed radiation-induced changes in the GaAs electronic properties with computed damage metrics. In support of the objective, this document provides: a) a clearly defined set of relevant neutron response functions for use in dosimetry applications; b) clear mathematical expressions for the defined response functions; and c) updated quantitative values for the energy- dependent response functions that reflect the best current nuclear data and modelling. This document recaps the legacy response functions. It then surveys the latest nuclear data and updates the recommended response function to support current GaAs damage studies. A detailed tabulation for six of the energy-dependent response functions is provided in an Appendix.

36 MATERIALS SCIENCE↗

Collinear Structure Functions of the Nucleon: Status and Future

While our ultimate goal is a complete three-dimensional picture of the nucleon in terms of its fundamental constituents, there are still important lessons to be learned about its “one?dimensional” collinear parton distribution functions (PDFs) like f1(x) and g1(x). There are rigorous proofs for factorization and universality (process independence) which make these PDFs fundamental. They also appear as limits of Generalized Parton Distributions (GPD) and as integrals of transverse momentum-dependent (TMD) parton distribution functions. Experimentally, the unpolarized structure functions F1(x,Q 2 ),F2(x,Q 2 ) have been studied over a huge kinematic range in both variables. Information on the polarized structure functions g1(x,Q 2 ),g2(x,Q 2 ) is somewhat more limited, both in kinematics and in statistical precision. In both cases, much less is known about the neutron than the proton, due to the absence of a free neutron target. Accessing these structure functions at large x (where valence quarks dominate) has been challenging due to the high luminosity and the high resolution required. Finally, much information can be extracted from studying higher twist contributions to these structure functions and the connection between the DIS limit and the region where nucleon resonance excitation dominates. I present an overview of recent experimental results (with special emphasis on the valence region and the transition from quark to hadronic degrees of freedom). I will also give an outlook on the next round of experiments coming online with the energy-upgraded Jefferson Lab electron beam, and future projects like the Electron Ion Collider.

Kuhn, Sebastian E.↗

Open library of g-functions for 34,321 configurations

Thermal response functions, known as g-functions, are commonly used in ground heat exchanger design tools and whole building energy simulation programs to simulate the ground heat exchanger performance. Calculation of g-functions can be quite computationally time-consuming, particularly as the number of boreholes gets large. However, once the g-function is computed, the actual simulation time can be quite short, particularly if a hybrid time-step (Cullin and Spitler 2011) approach is used. Because of this, pre-computed g-function libraries are commonly used in design tools and building simulation tools. This paper describes development of a new, publicly available library containing g-functions for 34,321 borehole field configurations; for each configuration, gfunctions are provided for 5 depths to allow interpolation between different borehole-to-height ratios. The available configurations include configurations in standard shapes: lines, rectangles, open rectangles, L-shapes, and U-shapes. It also includes new configurations: C-shapes, lopsided-U-shapes, and zoned rectangles, which are rectangular configurations with different interior and perimeter spacing of the boreholes.

Spitler, Jeffery↗

Influence functions for the Delaware Oil and Gas Basin Tower Network

This data consists of influence functions created for the Delaware tower network for the purpose of calculating methane enhancements in the region. Two different footprint models were used. The Lagrangian Particle Dispersion model (LPDM, Uliasz 1993) was run from March 2020-May 2023. The model uses in-house WRF simulations for the meteorological transport as described in Barkley et al., (2023). Nine hundred (900) particles were released during each hourly period and are traced back 72 hours backwards in time. A static binning height of 110 m AGL was used to calculate surface influence. After May 2023, the LPDM simulations were phased out and replaced with influence functions created using HYSPLIT under the STILT configuration (Lin et al., 2003). The STILT influence functions use HRRR for the meteorological transport (Dowell et al., 2022). Nine hundred (900) particles were released during each hourly period and are traced back 72 hours backwards in time. A binning height of half the boundary layer height was used to calculate surface influence. Footprints are currently available from Sept 2020-December 2024 and will be updated periodically as more are generated in time. No STILT influence functions were created for tower site Maljimar, which was decommissioned in March 2022. Lat/Lon grid information for the LPDM influence functions is contained in lpdm-lat-lon-grid.nc. STILT grid information is contained within the influence functions themselves. Tower coordinates and heights can be found in tower-info.csv

Barkley, Z. R.↗

Developing a media formulation to sustain ex vivo chloroplast function

Chloroplasts are critical organelles in plants and algae responsible for accumulating biomass through photosynthetic carbon fixation and cellular maintenance through metabolism in the cell. Chloroplasts are increasingly appreciated for their role in biomanufacturing, as they can produce many useful molecules, and a deeper understanding of chloroplast regulation and function would provide more insight for the biotechnological applications of these organelles. However, traditional genetic approaches to manipulate chloroplasts are slow, and generation of transgenic organisms to study their function can take weeks to months, significantly delaying the pace of research. To develop chloroplasts themselves as a quicker and more defined platform, we isolated chloroplasts from the green algae, Chlamydomonas reinhardtii, and examined their photosynthetic function after extraction. Combined with a metabolic modeling approach using flux-balance analysis, we identified key metabolic reactions essential to chloroplast function and leveraged this information into reagents that can be used in a “chloroplast media” capable of maintaining chloroplast photosynthetic function over time ex vivo compared to buffer alone. We envision this could serve as a model platform to enable more rapid design-build-test-learn cycles to study and improve chloroplast function in combination with genetic modifications and potentially as a starting point for the bottom-up design of a synthetic organelle-containing cell.

Chlamydomonas reinhardtii↗

Phylogeny and phylogeography of functional genes shared among seven terrestrial subsurface metagenomes reveal N-cycling and microbial evolutionary relationships

Comparative studies on community phylogenetics and phylogeography of microorganisms living in extreme environments are rare. Terrestrial subsurface habitats are valuable for studying microbial biogeographical patterns due to their isolation and the restricted dispersal mechanisms. Since the taxonomic identity of a microorganism does not always correspond well with its functional role in a particular community, the use of taxonomic assignments or patterns may give limited inference on how microbial functions are affected by historical, geographical and environmental factors. With seven metagenomic libraries generated from fracture water samples collected from five South African mines, this study was carried out to (1) screen for ubiquitous functions or pathways of biogeochemical cycling of CH 4 , S, and N; (2) to characterize the biodiversity represented by the common functional genes; (3) to investigate the subsurface biogeography as revealed by this subset of genes; and (4) to explore the possibility of using metagenomic data for evolutionary study. The ubiquitous functional genes are NarV, NPD, PAPS reductase, NifH, NifD, NifK, NifE, and NifN genes. Although these eight common functional genes were taxonomically and phylogenetically diverse and distinct from each other, the dissimilarity between samples did not correlate strongly with geographical or environmental parameters or residence time of the water. Por genes homologous to those of Thermodesulfovibrio yellowstonii detected in all metagenomes were deep lineages of Nitrospirae, suggesting that subsurface habitats have preserved ancestral genetic signatures that inform the study of the origin and evolution of prokaryotes.

59 BASIC BIOLOGICAL SCIENCES↗

Contrasting Community Assembly Forces Drive Microbial Structural and Potential Functional Responses to Precipitation in an Incipient Soil System

Microbial communities in incipient soil systems serve as the only biotic force shaping landscape evolution. However, the underlying ecological forces shaping microbial community structure and function are inadequately understood. We used amplicon sequencing to determine microbial taxonomic assembly and metagenome sequencing to evaluate microbial functional assembly in incipient basaltic soil subjected to precipitation. Community composition was stratified with soil depth in the pre-precipitation samples, with surficial communities maintaining their distinct structure and diversity after precipitation, while the deeper soil samples appeared to become more uniform. The structural community assembly remained deterministic in pre- and post-precipitation periods, with homogenous selection being dominant. Metagenome analysis revealed that carbon and nitrogen functional potential was assembled stochastically. Sub-populations putatively involved in the nitrogen cycle and carbon fixation experienced counteracting assembly pressures at the deepest depths, suggesting the communities may functionally assemble to respond to short-term environmental fluctuations and impact the landscape-scale response to perturbations. We propose that contrasting assembly forces impact microbial structure and potential function in an incipient landscape; in situ landscape characteristics (here homogenous parent material) drive community structure assembly, while short-term environmental fluctuations (here precipitation) shape environmental variations that are random in the soil depth profile and drive stochastic sub-population functional dynamics.

16S amplicon sequencing↗

SineKAN: Kolmogorov-Arnold Networks using sinusoidal activation functions

Recent work has established an alternative to traditional multi-layer perceptron neural networks in the form of Kolmogorov-Arnold Networks (KAN). The general KAN framework uses learnable activation functions on the edges of the computational graph followed by summation on nodes. The learnable edge activation functions in the original implementation are basis spline functions (B-Spline). Here, we present a model in which learnable grids of B-Spline activation functions are replaced by grids of re-weighted sine functions (SineKAN). We evaluate numerical performance of our model on a benchmark vision task. We show that our model can perform better than or comparable to B-Spline KAN models and an alternative KAN implementation based on periodic cosine and sine functions representing a Fourier Series. Further, we show that SineKAN has numerical accuracy that could scale comparably to dense neural networks (DNNs). Compared to the two baseline KAN models, SineKAN achieves a substantial speed increase at all hidden layer sizes, batch sizes, and depths. Current advantage of DNNs due to hardware and software optimizations are discussed along with theoretical scaling. Additionally, properties of SineKAN compared to other KAN implementations and current limitations are also discussed.

Reinhardt, Eric↗

Citric Acid Functionalized Natural Fibers to Enhance Thermal Stability and Moisture Resistance in Polylactic Acid Composites

Cellulosic fibers can impart many unique benefits into composite applications, such as reduced weight or structural reinforcement; however, these materials also increase hygroscopicity and decrease thermal stability, restricting broader applications. The present work adapted an experimental process for functionalizing the cellulose surface using citric acid (CA) for three fibers: a 100% cellulose bleached soft Kraft pulp (e.g., creafill) and two natural fibers with similar composition but different fiber morphology, flax fiber and banana fiber. The process uses CA with a sodium hypophosphite (SHP) catalyst to chemically functionalize fiber surfaces, and the reaction mechanism was investigated through Fourier Transform Infrared Spectroscopy (FTIR), which suggested a grafting mechanism rather than a surface-based crosslinking between neighboring sites. Functionalized fibers were compounded into polylactic acid (PLA) at 20 wt.% to better understand how this functionalization might impact critical performance properties like thermal stability, crystallization, thermal mechanical properties, and water uptake of these composites. The study demonstrated varying levels of efficacy for the functionalization of cellulosic fibers with CA/SHP and the fiber with the most open microstructure, e.g., banana fiber, exhibited the largest change in its properties with a 38% reduction in water uptake compared to untreated banana fiber composites. Parallel evaluation of the functionalization process for different fibers demonstrates the importance of fiber morphology on surface modification and can enable their use in composites by demonstrating the efficacy of this potentially low-cost, low-toxicity method for reducing hygroscopicity and improving thermal stability.

citric acid↗

Pre-Bleaching Coral Microbiome Is Enriched in Beneficial Taxa and Functions

Coral reef health is tightly connected to the coral holobiont, which is the association between the coral animal and a diverse microbiome functioning as a unit. The coral holobiont depends on key services such as nitrogen and sulfur cycling mediated by the associated bacteria. However, these microbial services may be impaired in response to environmental changes, such as thermal stress. A perturbed microbiome may lead to coral bleaching and disease outbreaks, which have caused an unprecedented loss in coral cover worldwide, particularly correlated to a warming ocean. The response mechanisms of the coral holobiont under high temperatures are not completely understood, but the associated microbial community is a potential source of acquired heat-tolerance. Here we investigate the effects of increased temperature on the taxonomic and functional profiles of coral surface mucous layer (SML) microbiomes in relationship to coral–algal physiology. We used shotgun metagenomics in an experimental setting to understand the dynamics of microbial taxa and genes in the SML microbiome of the coral Pseudodiploria strigosa under heat treatment. The metagenomes of corals exposed to heat showed high similarity at the level of bacterial genera and functional genes related to nitrogen and sulfur metabolism and stress response. The coral SML microbiome responded to heat with an increase in the relative abundance of taxa with probiotic potential, and functional genes for nitrogen and sulfur acquisition. Coral–algal physiology significantly explained the variation in the microbiome at taxonomic and functional levels. These consistent and specific microbial taxa and gene functions that significantly increased in proportional abundance in corals exposed to heat are potentially beneficial to coral health and thermal resistance.

59 BASIC BIOLOGICAL SCIENCES↗

Evolutionary Description of Giant Molecular Cloud Mass Functions on Galactic Disks

Recent radio observations show that giant molecular cloud (GMC) mass functions noticeably vary across galactic disks. High-resolution magnetohydrodynamics simulations show that multiple episodes of compression are required for creating a molecular cloud in the magnetized interstellar medium. In this article, we formulate the evolution equation for the GMC mass function to reproduce the observed profiles, for which multiple compressions are driven by a network of expanding shells due to H ii regions and supernova remnants. We introduce the cloud–cloud collision (CCC) terms in the evolution equation in contrast to previous work (Inutsuka et al.). The computed time evolution suggests that the GMC mass function slope is governed by the ratio of GMC formation timescale to its dispersal timescale, and that the CCC effect is limited only in the massive end of the mass function. In addition, we identify a gas resurrection channel that allows the gas dispersed by massive stars to regenerate GMC populations or to accrete onto pre-existing GMCs. Our results show that almost all of the dispersed gas contributes to the mass growth of pre-existing GMCs in arm regions whereas less than 60% contributes in inter-arm regions. Our results also predict that GMC mass functions have a single power-law exponent in the mass range <10{sup 5.5} M{sub ⊙} (where M{sub ⊙} represents the solar mass), which is well characterized by GMC self-growth and dispersal timescales. Measurement of the GMC mass function slope provides a powerful method to constrain those GMC timescales and the gas resurrecting factor in various environments across galactic disks.

79 ASTRONOMY AND ASTROPHYSICS↗

Panchromatic Hubble Andromeda Treasury. XVIII. The High-mass Truncation of the Star Cluster Mass Function

We measure the mass function for a sample of 840 young star clusters with ages between 10 and 300 Myr observed by the Panchromatic Hubble Andromeda Treasury (PHAT) survey in M31. The data show clear evidence of a high-mass truncation: only 15 clusters more massive than 10{sup 4} M{sub ⊙} are observed, compared to the ∼100 expected for a canonical M{sup −2} pure power-law mass function with the same total number of clusters above the catalog completeness limit. Adopting a Schechter function parameterization, we fit a characteristic truncation mass of M{sub c}=8.5{sub −1.8}{sup +2.8}×10{sup 3} M {sub ☉}. Although previous studies have measured cluster mass function truncations, the characteristic truncation mass we measure is the lowest ever reported. Combining this M31 measurement with previous results, we find that the cluster mass function truncation correlates strongly with the characteristic star formation rate surface density of the host galaxy, where M{sub c}∝〈Σ{sub SFR}〉{sup ∼1.1}. We also find evidence that suggests the observed M {sub c}–Σ{sub SFR} relation also applies to globular clusters, linking the two populations via a common formation pathway. If so, globular cluster mass functions could be useful tools for constraining the star formation properties of their progenitor host galaxies in the early universe.

79 ASTRONOMY AND ASTROPHYSICS↗

Stellar Mass Function of Active and Quiescent Galaxies via the Continuity Equation

The continuity equation is developed for the stellar mass content of galaxies and exploited to derive the stellar mass function of active and quiescent galaxies over the redshift range z∼0--8. The continuity equation requires two specific inputs gauged from observations: (i) the star formation rate functions determined on the basis of the latest UV+far-IR/submillimeter/radio measurements and (ii) average star formation histories for individual galaxies, with different prescriptions for disks and spheroids. The continuity equation also includes a source term taking into account (dry) mergers, based on recent numerical simulations and consistent with observations. The stellar mass function derived from the continuity equation is coupled with the halo mass function and with the SFR functions to derive the star formation efficiency and the main sequence of star-forming galaxies via the abundance-matching technique. A remarkable agreement of the resulting stellar mass functions for active and quiescent galaxies of the galaxy main sequence, and of the star formation efficiency with current observations is found; the comparison with data also allows the characteristic timescales for star formation and quiescence of massive galaxies, the star formation history of their progenitors, and the amount of stellar mass added by in situ star formation versus that contributed by external merger events to be robustly constrained. The continuity equation is shown to yield quantitative outcomes that detailed physical models must comply with, that can provide a basis for improving the (subgrid) physical recipes implemented in theoretical approaches and numerical simulations, and that can offer a benchmark for forecasts on future observations with multiband coverage, as will become routinely achievable in the era of JWST.

79 ASTRONOMY AND ASTROPHYSICS↗

Natively Periodic Fast Multipole Method: Approximating the Optimal Green’s Function

The fast multipole method (FMM) obeys periodic boundary conditions "natively" if it uses a periodic Green's function for computing the multipole expansion in the interaction zone of each FMM oct-tree node. One can define the "optimal" Green's function for such a method that results in the numerical solution that converges to the equivalent particle-mesh (PM) solution in the limit of sufficiently high order of multipoles. A discrete functional equation for the optimal Green's function can be derived, but is not practically useful as methods for its solution are not known. Instead, this paper presents an approximation for the optimal Green's function that is accurate to better than 10 -3 in ${L}_{\mathrm{MAX}}$ norm and 10 -4 in L 2 norm for practically useful multipole counts. Such an approximately optimal Green's function offers a practical way for implementing the FMM with periodic boundary conditions natively, without the need to compute lattice sums or to rely on hybrid FMM-PM approaches.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗