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At least 1,495 records · Page 83

In silico evidence for sequence-dependent nucleosome sliding

Significance The dynamic compaction of DNA into chromatin is essential for gene expression. Errors during compaction are associated with numerous diseases. Several molecular factors are known to affect chromatin dynamics, but their relative importance and the interplay between them are poorly understood. A detailed molecular model is used here to examine chromatin dynamics at the level of its most fundamental building block, namely the nucleosome. Nucleosome dynamics are demonstrated to be encoded in the DNA sequence itself, and key fundamental factors are uncovered that can significantly alter these dynamics at the molecular level. The results serve to complete a hitherto unavailable description of nucleosome dynamics by introducing previously unappreciated molecular processes, with the potential to influence macroscopic chromatin structure and genetics.

59 BASIC BIOLOGICAL SCIENCES↗

Spectral partitioning with blends of eigenvectors

We report many common methods for data analysis rely on linear algebra. We provide new results connecting data analysis error to numerical accuracy in the context of spectral graph partitioning. We provide pointwise convergence guarantees so that spectral blends (linear combinations of eigenvectors) can be employed to solve data analysis problems with confidence in their accuracy. We apply this theory to an accessible model problem, the ring of cliques, by deriving the relevant eigenpairs and finding necessary and sufficient solver tolerances. Analysis of the ring of cliques provides an upper bound on eigensolver tolerances for graph partitioning problems. These results bridge the gap between linear algebra based data analysis methods and the convergence theory of iterative approximation methods. These results explain how the combinatorial structure of a problem can be recovered much faster than numerically accurate solutions to the associated linear algebra problem.

97 MATHEMATICS AND COMPUTING↗

A General Spatiotemporal Imputation Framework for Missing Sensor Data

Many applications from precision agriculture, environmental monitoring and transportation networks rely on data collected across space and time over a large geographic area. Missing data poses a significant challenge for any data-driven inference and control tasks. Data imputation or the estimation of missing data can help fill these gaps by utilizing inherent spatial relationships and temporal patterns. A variety of spatiotemporal imputation models have been developed to address missing data in spatiotemporal datasets. However, these classical methods rely on the assumption that the underlying data follows a smooth trend and fail to provide accurate estimates when there is a large number of missing points in the data. Even though there are machine learning driven tensor completion approaches such as convolutional neural network based tensor completion (CoSTCo) that capture the non-linear relationships in the dataset, the transductive nature makes the algorithm less scalable. Thus, existing approaches for estimating the missing information do not effectively capture all dimensions of the spatiotemporal data structure, resulting in erroneous predictions and poor performance. The main contributions of this paper are: (1) We propose a novel inductive framework (G-LSTM) for missing data imputation that integrates a graph neural network with LSTMs to effectively capture both spatial and temporal dependencies. (2) Experimental results on a traffic dataset demonstrate that the proposed GNN integrated with an LSTM framework achieves improved imputation and maintains steady performance even when there are extreme missing conditions in comparison with the state-of-the-art imputation framework (i.e, CoSTCo). (3) The simulation results on a traffic network show up to 69% reduction in mean absolute error and 61% reduction in root mean square error when compared to CoSTCo.

Tharzeen, Aabila↗

Closed-Form Approximation of the Total Variation Proximal Operator

Total variation (TV) is a widely used function for regularizing imaging inverse problems that is particularly appropriate for images whose underlying structure is piecewise constant. TV regularized optimization problems are typically solved using proximal methods, but the way in which they are applied is constrained by the absence of a closed-form expression for the proximal operator of the TV function. A closed-form approximation of the TV proximal operator has previously been proposed, but its accuracy was not theoretically explored in detail. Here, we address this gap by making several new theoretical contributions, proving that the approximation leads to a proximal operator of some convex function, it is equivalent to a gradient descent step on a smoothed version of TV, and that its error can be fully characterized and controlled with its scaling parameter. We experimentally validate our theoretical results on image denoising and sparse-view computed tomography (CT) image reconstruction.

97 MATHEMATICS AND COMPUTING↗

Energy Frontier Research Centers: Center for the Computational Design of Functional Layered Materials (CCDM) August 1, 2014 - July 31, 2018; Center for Complex Materials from First Principles (CCM) August 1, 2018 - July 31, 2021 (Final Report)

The mission of the DOE Energy Frontier Research Centers CCDM (2014-2018) and CCM (2018-2021) was to theoretically develop, computationally apply, and experimentally validate electronic structure methods for all materials, with a focus on the complex materials, especially layered and two-dimensional materials, strongly-correlated materials, and liquid water. This was achieved by over 200 published journal articles authored by about 17 senior investigators from physics and chemistry and from theory, computation, and experiment, plus their collaborators. In particular, the Centers confirmed the predictive power of the SCAN (strongly constrained and appropriately normed) density functional, which was constructed to satisfy 17 known exact constraints and several appropriate norms. Without being fitted to real bonded systems, and at a modest computational cost, SCAN correctly predicted covalent, ionic, metallic, hydrogen, and van der Waals bonds in many challenging materials. SCAN gave an improved description of defects in semiconductors, surface properties of metals, seven phases of ice, liquid water, liquid and supercooled silicon, subtle structural distortions in ferroelectrics, formation energies and structural predictions for solids, and critical pressures for structural phase transitions. Perhaps most remarkably, SCAN correctly described some strongly-correlated materials that were previously believed to be beyond the reach of density-functional approximations. SCAN is the only density functional that correctly predicts the band gap closing under chemical doping of the cuprate high-temperature superconducting materials. SCAN also predicts a landscape of competing stripe and magnetic phases in the cuprates. For some materials with some codes, SCAN has convergence problems that are greatly reduced by the CCM-developed r 2 SCAN, without loss of accuracy or rigor. SCAN and r 2 SCAN still make some self-interaction error, which is greatly reduced by the CCDM/ CCM-developed local orbital scaling correction (LOSC). These Centers further proved that the fundamental energy gaps of a solid from an orbital energy difference and from total energy differences are the same for a large class of generalized Kohn-Sham (GKS) functionals, including SCAN and standard hybrid functionals, and that symmetry breaking arises when a dynamic density fluctuation drops to zero frequency. The Centers identified new mechanisms for catalysis in layered materials with ions intercalated between the layers, investigated charge density waves both in model systems and in real layered materials, studied changes of band gap with the number of layers, and explored topological ultrathin films, bent nanoribbons, and defects.

08 HYDROGEN↗

Production of magnetic biochar from waste-derived fungal biomass for phosphorus removal and recovery

This study presents a new bottom-up biofabrication method to produce highly porous magnetic biochar from waste-derived fungal biomass. Neurospora crassa was grown in iron containing coagulation backwash (BW) diluted with primary effluent (PE) wastewater in two ratios of 1:4 (PE-BW 1:4) and 3:4 (PE-BW 3:4). The fungi encapsulated iron directly into biomass hyphae and carbonization resulted in one-step biochar preparation and maghemite (Fe2O3) formation. The morphology and structure of the materials were investigated using a suite of characterization tools. Results indicated that the physiochemical properties of each char were dependent on the blend used for fungal cultivation. PE-BW 1:4 had much larger average pore diameters (13.2 nm vs. 6.1 nm), less elemental surface carbon (2.1% vs. 23.7%), and more expansive Fe2O3 formation. Batch phosphorus adsorption experiments were conducted in the range of 0-90 mg-P/L, and a maximum adsorption density of 23.9 mg/g was achieved. Langmuir, Freundlich and Temkin isotherms were used to describe the interactions of the phosphate on the absorbents and an in-depth error analysis was conducted. Further characterization of the P-loaded chars indicated adsorption primarily via P-OH bonding on the surface of the materials. This new biofabrication method showed great potential to magnetic biochar production with excellent phosphorus adsorption, which can be effectively used in wastewater resource recovery.

09 BIOMASS FUELS↗

Three dimensional cluster analysis for atom probe tomography using Ripley’s K-function and machine learning

The size and structure of spatial molecular and atomic clustering can significantly impact material properties and is therefore important to accurately quantify. Ripley’s K-function (K(r)), a measure of spatial correlation, can be used to perform such quantification when the material system of interest can be represented as a marked point pattern. This work demonstrates how machine learning models based on K (r)-derived metrics can accurately estimate cluster size and intra-cluster density in simulated three dimensional (3D) point patterns containing spherical clusters of varying size; over 90% of model estimates for cluster size and intra-cluster density fall within 11% and 18% error of the true values, respectively. These K (r)-based size and density estimates are then applied to an experimental APT reconstruction to characterize MgZn clusters in a 7000 series aluminum alloy. Here we find that the estimates are more accurate, consistent, and robust to user interaction than estimates from the popular maximum separation algorithm. Using K (r) and machine learning to measure clustering is an accurate and repeatable way to quantify this important material attribute.

36 MATERIALS SCIENCE↗

Predicting Excitation Energies of Twisted Intramolecular Charge-Transfer States with the Time-Dependent Density Functional Theory: Comparison with Experimental Measurements in the Gas Phase and Solvents Ranging from Hexanes to Acetonitrile

Electronically excited states characterized by intramolecular charge transfer play an essential role in many biological processes and optical devices. The ability to make quantitative ab initio predictions of the relative energetics involved is a challenging yet desirable goal, especially for large molecules in solution. In this work, we present a data set of 61 experimental measurements of absorption and emission processes, both in the gas phase and in solvents representing a broad range of polarities, which involve intramolecular charge transfer mediated by a nonzero, "twisted" dihedral angle between one or more donor and acceptor subunits. Among a variety of density functionals investigated within the framework of linear-response theory, the "optimally tuned" LRC-ωPBE functional, which utilizes a system-specific yet nonempirical procedure to specify the range-separation parameter, emerges as the preferred choice. For the entire set of excitation energies, involving changes in dipole moment ranging from 4 to >20 Debye, the mean signed and absolute errors are 0.02 and 0.18 eV, respectively (compared, e.g., to -0.30 and 0.30 for PBE0, 0.44 and 0.47 for LRC-ωPBEh, 0.83 and 0.83 for ωB97X-V). We analyze the performance of polarizable continuum solvation models available in Q-Chem that partition the solvent response into fast and slow time scales, and clear trends emerge when measurements corresponding to the four small 4-(dimethylamino)benzonitrile (DMABN)-like molecules and a charged species are excluded. We make the case that the large errors found only for small molecules in the gas phase and weak solvents cannot be expected to improve via the optimal tuning procedure, which enforces a condition that is exact only in the well-separated donor-acceptor limit, and present empirical evidence implicating the outsized importance for small donor-acceptor systems of relaxation effects that cannot be accounted for by the linear-response time-dependent density functional theory within the adiabatic approximation. Finally, we demonstrate the utility of the optimally tuned density functional approach by targeting the charge-transfer states of a large biomimetic model system for light-harvesting structures in Photosystem II.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

CH 4 Activation over Perovskite Catalysts: True Density and Reactivity of Active Sites

The high thermal stability of perovskites has drawn attention toward their applications for catalytic CH 4 activation and conversion, typically occurring at high temperatures. The reaction rates of perovskite catalysts for CH 4 combustion, however, trail behind those of noble metal catalysts. Ways to optimize the performance of perovskite catalysts are destined to trial-and-error approaches unless their complex reconstructed surfaces are correlated with fundamental kinetic parameters. Discerning the intrinsic activity of surface catalytic sites and the density of those sites is crucial to rationally envision complex metal oxides with enhanced catalytic performance. Here, the present work presents a detailed kinetic analysis of catalytic CH 4 combustion over a set of seven perovskites (SrTiO 3 , SrZrO 3 , SrFeO 3 , LaFeO 3 , LaInO 3 , LaCoO 3 , LaMnO 3 ) with various surface terminations. Steady-state isotopic transient kinetic analysis was employed to measure turnover frequency (TOF) and density of surface intermediates (N) under operando conditions. Top surface characterization elucidated performance-structure relationships between near-monolayer surface composition and intrinsic reactivity of the catalysts. By using a chemical etching procedure to expose Fe-sites at the top surface of LaFeO 3 (LaFeO 3 , HNO 3 ), its TOF was increased 4-fold, compared with the unmodified sample, although N on the surface of LaFeO 3 , HNO 3 decreased. Density functional theory simulations corroborated that surface Fe-termination and La-Fe termination offer lower energetic barriers for CH 4 activation when compared with La-termination. In general, surface reconstruction is shown as a tool to tune TOF and N to improve reaction rates. This work fills a gap in current kinetic studies of perovskites through a careful assessment and discussion of the density and intrinsic reactivity of active sites for methane combustion over well-characterized reconstructed perovskite surfaces.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Dark Energy Survey Year 3 Results: Galaxy mock catalogs for BAO analysis

The calibration and validation of scientific analysis in simulations is a fundamental tool to ensure unbiased and robust results in observational cosmology. In particular, mock galaxy catalogs are a crucial resource to achieve these goals in the measurement of baryon acoustic oscillation (BAO) in the clustering of galaxies. Here we present a set of 1952 galaxy mock catalogs designed to mimic the Dark Energy Survey Year 3 BAO sample over its full photometric redshift range 0.6 < zphoto < 1.1. The mocks are based upon 488 ICE-COLA fast N-body simulations of full-sky light cones and were created by populating halos with galaxies, using a hybrid halo occupation distribution – halo abundance matching model. This model has ten free parameters, which were determined, for the first time, using an automatic likelihood minimization procedure. We also introduced a novel technique to assign photometric redshift for simulated galaxies, following a two-dimensional probability distribution with VIMOS Public Extragalactic Redshift Survey data. The calibration was designed to match the observed abundance of galaxies as a function of photometric redshift, the distribution of photometric redshift errors, and the clustering amplitude on scales smaller than those used for BAO measurements. An exhaustive analysis was done to ensure that the mocks reproduce the input properties. Finally, mocks were tested by comparing the angular correlation function w(θ), angular power spectrum Cℓ, and projected clustering ξp(r⊥) to theoretical predictions and data. The impact of volume replication in the estimate of the covariance is also investigated. The success in accurately reproducing the photometric redshift uncertainties and the galaxy clustering as a function of redshift render this mock creation pipeline as a benchmark for future analyses of photometric galaxy surveys.Key words: catalogs / large-scale structure of Universe / galaxies: distances and redshifts / Galaxy: halo / methods: numerical

79 ASTRONOMY AND ASTROPHYSICS↗

Development and experimental evaluation of new building air leakage measurement methods: measurement of interior air leaks and comparison to conventional methods

Building air leaks (both through exterior and interior surfaces) can have a significant impact on energy consumption, indoor air quality, fire safety, and moisture accumulation affecting structural durability. Blower door testing has been used to measure leaks in buildings, but commonly used testing methods do not directly measure interior leaks. In this paper, new testing methods (guarded interior test and zonal multipoint pressure testing method) are presented that directly measure these interior leaks, utilizing common blower door equipment for both single and multi-point testing. Furthermore, these new methods are compared to conventional methods in terms of the information provided, limitations and time/effort needed. In addition, building leak measurement results are analyzed to reveal a) coupling between power law model values (exponent and coefficient) for an ensemble of buildings, b) the error in using single point testing when estimating low pressure leakage, and c) how building power law models vary from low to high pressure ranges.

99 GENERAL AND MISCELLANEOUS↗

Analysis of Structural Options for Bench Measurement of AGU Segment Prototype

Refer to Tech Note TN #257 for an introduction to the mechanics and structure for the proposed prototype of a multi-segment Adaptive-Gap Undulator (AGU). Here we investigate various proposed design options for a magnet structure intended to prototype the upper and lower halves of a single segment: A) Assembly SLS-15.55-004, the historic X9 platen (0.6m long, with integral strongback) and single large centric mechanical feed-through post; B) Initial assembly SR-ID-SAGU-4300 with three pairs of feed-throughs spaced along platen length (0.7m); C) That assembly SR-ID-SAGU-4300 with increased base plate thickness. All options have “base plate” affixed to the same actuated gap-drive system with single driven axis as was on NSLS X9 MGU. As shown in Figure 1, design criteria like Gap Tolerance, Taper Error, and the critical Planarity of the pole plane within the gap are used to evaluate performance. The error in planarity to be minimized is the differential in vertical displacement (Y direction) along the Platen length (beam Z direction). Applied loads are magnetic pressure and gravity.

36 MATERIALS SCIENCE↗

Mitigating baryonic effects with a theoretical error covariance

ABSTRACT One of the primary sources of uncertainties in modelling the cosmic-shear power spectrum on small scales is the effect of baryonic physics. Accurate cosmology for stage-IV surveys requires knowledge of the matter power spectrum deep in the non-linear regime at the per cent level. Therefore, it is important to develop reliable mitigation techniques to take into account baryonic uncertainties if information from small scales is to be considered in the cosmological analysis. In this work, we develop a new mitigation method for dealing with baryonic physics for the case of the shear angular power spectrum. The method is based on an augmented covariance matrix that incorporates baryonic uncertainties informed by hydrodynamical simulations. We use the results from 13 hydrodynamical simulations and the residual errors arising from a fit to a ΛCDM model using the extended halo model code HMCode to account for baryonic physics. These residual errors are used to model a so-called theoretical error covariance matrix that is added to the original covariance matrix. In order to assess the performance of the method, we use the 2D tomographic shear from four hydrodynamical simulations that have different extremes of baryonic parameters as mock data and run a likelihood analysis comparing the residual bias on Ωm and σ8 of our method and the HMCode for an LSST-like survey. We use different modelling of the theoretical error covariance matrix to test the robustness of the method. We show that it is possible to reduce the bias in the determination of the tested cosmological parameters at the price of a modest decrease in the precision.

79 ASTRONOMY AND ASTROPHYSICS↗

Moving lens effect: Simulations, forecasts, and foreground mitigation

The peculiar motion of massive objects across the line of sight imprints a dipolar temperature anisotropy pattern on the cosmic microwave background known as the moving lens effect. This effect provides a unique probe of the transverse components of the peculiar velocity field, but has not yet been detected due to its small size. We implement and validate a stacking estimator for the moving lens signal using a galaxy catalog as a tracer of massive haloes combined with reconstructed velocities from the galaxy number density field. Using simulations, we forecast detection prospects for the moving lens signal from current and upcoming microwave background and galaxy surveys. Here, we demonstrate a new foreground mitigation strategy likely sufficient for current datasets, and discuss various sources of systematic error and noise. Upcoming galaxy surveys will provide high-significance statistical detections of the moving lens effect.

Astrophysical & cosmological simulations↗

The Mira-Titan Universe. II. Matter Power Spectrum Emulation

We introduce a new cosmic emulator for the matter power spectrum covering eight cosmological parameters. Targeted at optical surveys, the emulator provides accurate predictions out to a wavenumber k ~ 5Mpc -1 and redshift z ≤ 2. Besides covering the standard set of CDM parameters, massive neutrinos and a dynamical dark energy of state are included. The emulator is built on a sample set of 36 cosmological models, carefully chosen to provide accurate predictions over the wide and large parameter space. For each model, we have performed a high-resolution simulation, augmented with sixteen medium-resolution simulations and TimeRG perturbation theory results to provide accurate coverage of a wide k-range; the dataset generated as part of this project is more than 1.2Pbyte. With the current set of simulated models, we achieve an accuracy of approximately 4%. Because the sampling approach used here has established convergence and error-control properties, follow-on results with more than a hundred cosmological models will soon achieve ~1% accuracy. We compare our approach with other prediction schemes that are based on halo model ideas and remapping approaches. The new emulator code is publicly available.

97 MATHEMATICS AND COMPUTING↗

Maximizing energy efficiency in wastewater treatment plants: A data-driven approach for waste heat recovery and an economic analysis using Organic Rankine Cycle and thermal energy storage

Maximizing energy efficiency through waste heat recovery (WHR) processes is crucial for sustainable and ecofriendly operations across multiple industries, notably in wastewater treatment plants (WWTPs). This work proposes a comprehensive approach for assessing the WHR feasibility in WWTPs, structured in two main objectives. Firstly, an Artificial Neural Network (ANN) model is developed to accurately predict WHR based on operational data, including biogas temperature, biogas pressure, daily production in kWh, and WHR values in kWh th . The second objective focuses on economically evaluating the WHR feasibility based on the estimated WHR values obtained by the ANN model, and then realistically assessing the economic feasibility of integrating the Organic Rankine Cycle (ORC) and Seasonal Thermal Energy Storage (STES) systems. With an application to the As-Samra WWTP located in Jordan, the developed ANN model demonstrates promising results in the validation phase, with a root mean square error (RMSE) of 2206 kWh/day, a mean absolute error (MAE) of 1674 kWh/day, and an R-squared (R 2 ) value of 68%. On the other hand, the economic analysis reveals that an optimal ORC system of 412.14 kW e capacity yields a Net Present Value (NPV) of 2.09 million US dollars, a Levelized Cost of Energy (LCOE) of 0.0749 USD/kWh, a Payback Period (PBP) of 4.8 years, and annual revenues of 428 kUSD. This work also investigates the techno-economic feasibility of integrating ORC-STES. Results indicate that the LCOE and PBP are highly affected by the ORC's capital cost, and integrating STES increases the LCOE to 0.0824 USD/kWh, rendering its integration with ORC infeasible. In conclusion, this study aims to advance the understanding and application of WHR in WWTPs, paving the way for more efficient and sustainable practices in the field.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Chirped-probe-pulse femtosecond CARS thermometry in turbulent spray flames

This paper presents temperature measurements in turbulent dilute and dense spray flames using single-laser-shot chirped-probe-pulse femtosecond coherent anti-Stokes Raman spectroscopy (CPP-fs-CARS). This ultrafast technique, with a repetition rate of 5 kHz, is applied to the piloted Sydney Needle Spray Burner (SYNSBURN TM ). The burner system features air-blast atomization of liquid injected from a needle that can be translated within a co-flowing air stream. The pilot-stabilized spray flames can range between the two extremes of dense and dilute by physically translating the needle tip relative to the burner's exit plane. The CPP-fs-CARS set-up has achieved integration times of 3 picoseconds (ps) as well as spatial resolution of approximately 800 µm along beam propagation and 60 µm in the transverse dimension. Brief details of the technique, calibration, correction of interferences, and spectral fitting processes are presented along with estimates of the associated error. The measurements are compared against well-established, line Raman–Rayleigh data for temperature collected in a turbulent CH 4 /air jet diffusion flame, which is largely non-sooting. At peak gaseous flame temperatures of up to 2512 K, the relative accuracy and precision were 2.8% and ±3.4%, respectively. Measurements in turbulent spray flames are shown after applying the relevant corrections based on non-resonant background (NRB) behavior and camera saturation effects on the shape of the CARS signal spectrum. Preliminary mapping of the temperature fields demonstrates the wealth of information available in this dataset which will provide insights into the spatio-temporal structure of spray flames once relevant statistical analysis is applied.

42 ENGINEERING↗

Improved Reanalysis and Prediction of Atmospheric Fields Over the Southern Ocean Using Campaign‐Based Radiosonde Observations

Abstract This study investigated the impact of radiosonde observations from the Southern Ocean obtained by the Australian R/V Aurora Australis on the ALERA2 experimental ensemble reanalysis data set and ensemble forecast experiment. An observing system experiment (OSE) that included additional ship‐launched radiosonde data captured the atmospheric structure over the Southern Ocean. ALERA2 without additional radiosondes had positive temperature biases exceeding 7 °C in the upper troposphere when low‐pressure cyclonic systems passed over the ship. The spread in the upper level was reduced by 15% in the OSE, which propagated downstream from the ship's position because of the sparse observing network over southern high latitudes. Comparison of two 63‐member ensemble forecast experiments initialized by ALERA2 and the OSE revealed that prediction of midlatitude cyclone tracks was improved by the realistic representation of upper‐level troughs in the OSE forecast. This confirms that additional radiosondes over the Southern Ocean reduce uncertainty and error in midlatitude cyclone forecasts.

54 ENVIRONMENTAL SCIENCES↗