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Big Data and Deep data in scanning and electron microscopies: functionality from multidimensional data sets

The development of electron, and scanning probe microscopies in the second half of the twentieth century have produced spectacular images of internal structure and composition of matter with, at nanometer, molecular, and atomic resolution. Largely, this progress was enabled by computer-assisted methods of microscope operation, data acquisition and analysis. The progress in imaging technologies in the beginning of the twenty first century has opened the proverbial floodgates of high-veracity information on structure and functionality. High resolution imaging now allows information on atomic positions with picometer precision, allowing for quantitative measurements of individual bond length and angles. Functional imaging often leads to multidimensional data sets containing partial or full information on properties of interest, acquired as a function of multiple parameters (time, temperature, or other external stimuli). Here, we review several recent applications of the big and deep data analysis methods to visualize, compress, and translate this data into physically and chemically relevant information from imaging data.

36 MATERIALS SCIENCE↗

Fractal analysis on Ag 2 O thin film using a data-driven approach

The synthesis of fractal Ag oxide (Ag 2 O) on the surface of Ag thin film has been achieved at room temperature by using Synchrotron X-ray irradiation. We have performed an automated quantitative analysis of a batch of 1879 fractal Ag 2 O patterns in a scanning electron microscopy (SEM) image within a radius of 2000 mm outward from the center of the X-ray beam. The morphology is similar to that of the diffusion-limited cluster aggregation (DLCA) model. The fractal dimension (D) of Ag 2 O is between 1.7 and 1.5 from the center to the edge. The area distribution density of fractal Ag 2 O follows a quadratic function with radius R. It is found that the branches’ number of fractal Ag 2 O is a key factor affecting the fractal dimension. The more branches the fractal has, the greater the D is. This is the first time that Ag fractal has been investigated by combining automated data analysis methods with batch experimental data. This data-driven approach provides a new research perspective for rationally regulating materials’ fractal morphology and performance.

36 MATERIALS SCIENCE↗

Final Scientific/Technical Report, Multi-Sensor Inspection and Robotic Systems for Dry Storage Casks

Once removed from service, fuel rod assemblies are cooled in a pool and then placed in dry storage until they can be transported to a repository for disposal. The extended duration that used nuclear fuel spends in dry storage makes it prudent to be able to nondestructively inspect the dry storage casks. The degradation mechanisms of most concern are chloride-induced stress corrosion cracking of the stainless steel canister that confines the spent fuel and distributed cracking of the concrete in the overpack structure. Multi-sensor inspection and robotic systems were researched, developed, built, and tested. One system operates completely outside the cask to inspect the concrete. The other system, known as the PRINSE system, for Proactive Robotic Inspection of Nuclear Storage Enclosures, enters the cask through an outlet vent and navigates around the outer surface of the stainless steel canister. The PRINSE system delivers sensors for: (i) real-time characterization of the canister surface in order to assess whether chlorides are present, (ii) detecting the presence of cracks using shear-horizontal ultrasonic guided waves, (iii) measuring the temperature of the canister surface, and (iv) a gamma radiation counter. The four sensing modalities are applicable to any cask containing a stainless steel canister, however the robotic delivery system is designed specifically for Holtec’s HI-STORM family of casks. Horizontal axis casks have exposed concrete surfaces. A fully contactless air-coupled scanning ultrasonic test platform and a frequency-wavenumber domain data analysis method are used for these concrete structures. Analysis, numerical simulation and experimental results demonstrate that distributed cracks in concrete can be detected and cracked regions localized within a scanned region of concrete. Vertical axis casks (like the HI-STORM family) have steel-clad concrete overpacks. In a separate effort, a semi-coupled test platform and a guided wave attenuation-based data analysis method are used for disbond detection. Analysis, numerical simulation and experimental results show that the bonding conditions of steel-concrete interfaces can be quantitatively characterized using the guided wave signal analysis scheme. The PRINSE system is designed for vertical axis dry storage casks, specifically the HI-STORM family. The double pulse laser-induced breakdown spectroscopy (LIBS) system takes advantage of an optical fiber to deliver intense light to the canister surface that enables surface composition characterization in-situ in real time. Chlorine concentrations as low as 10 mg/m2 were detected on stainless steel. Additionally, a simpler laser setup was created to detect sodium as a surrogate for chlorine, and sodium was detectable when the chlorine concentration was as low as 0.5 mg/m2. The electromagnetic acoustic transducers (EMATs) enable detection of stress corrosion cracks. The EMATs generate shear-horizontal waves that propagate around the canister and are reflected by cracks enabling 100% of the canister weld lines to be inspected. The EMAT-based crack detection system was tested at the Pacific Northwest National Laboratory on a canister containing blind defects and was shown to detect the crack sizes it was designed to detect. The PRINSE system is a novel marsupial robot. The command center and winch outside the cask control the delivery arm and train of cars that traverse the outside of the canister from the cask ventilation system. The sensors are housed in the cargo bays of three cars that comprise the train, which is lowered to the bottom of the canister by the winch. Encoders on the winch enable the sensors to be delivered to a prescribed location, e.g., for re-inspection of a problem area. The PRINSE system does not mar the canister surface, can be extracted manually in the case of a power failure, and is designed for an elevated temperature and gamma radiation environment, although not all components of the prototype are made from the final materials. The PRINSE system was tested on a full canister that was placed inside a HI-STORM cask at the Holtec Manufacturing Division. It was also demonstrated on a full-height mockup at Penn State to a live audience.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Detecting the undetected: Dealing with non-routine events using advanced M&V meter-based savings approaches

In a rapidly evolving energy industry, utilities are dealing with new challenges like integrating distributed energy resources and market saturation for advanced lighting retrofits. Demand-side management programs require new approaches to meet aggressive carbon reduction goals. Advanced measurement & verification (M&V) is an energy data analysis method using smart meter data in combination with analytics to quantify energy efficiency project savings. Advanced M&V shows great promise for supporting next generation commercial programs including retro commissioning, multi-measure retrofits, and behavior change programs. Advanced M&V captures real project impacts at the meter, but sometimes non-project events can also impact consumption (so-called “non-routine events” [NREs]). Accurately detecting and accounting for NREs is important for reducing uncertainty of savings estimates and helps manage investment risk for different stakeholders (e.g., utilities, building owners, ESCOs). Recent research has shown promise in establishing data-driven techniques to identify and adjust for NREs, but fundamental questions still remain, such as: how can you distinguish NREs from acceptable noise in energy consumption profiles? What is the frequency and magnitude of NREs? Can their detection and adjustment be automated and streamlined? This paper documents the state of the art in NRE quantification and analysis. The results of research to quantify the frequency, nature and direction of NREs, and methods and metrics for determining a trigger threshold for taking action on NREs are presented. The paper also documents the latest technical guidance on application of NRE detection and adjustment methods.

Fernandes, Samuel↗

Subnanogram proteomics: Impact of LC column selection, MS instrumentation and data analysis strategy on proteome coverage for trace samples

One of the greatest challenges for mass spectrometry (MS)-based proteomics is the limited ability to analyze small samples. Here we investigate the relative contributions of liquid chromatography (LC), MS instrumentation and data analysis methods with the aim of improving proteome coverage for sample sizes ranging from 0.5 ng to 50 ng. We show that the LC separations utilizing 30-µm-i.d. columns increase signal intensity by >3-fold relative to those using 75-µm-i.d. columns, leading to 32% increase in peptide identifications. The Orbitrap Fusion Lumos mass spectrometer significantly boosted both sensitivity and sequencing speed relative to earlier generation Orbitraps (e.g., LTQ-Orbitrap), leading to a ~3× increase in peptide identifications and 1.7× increase in identified protein groups for 2 ng tryptic digests of bacterial lysate. The Match Between Runs algorithm of open-source MaxQuant software further increased proteome coverage by ~ 95% for 0.5 ng samples and by ~42% for 2 ng samples. The present platform is capable of identifying >3000 protein groups from tryptic digestion of cell lysates equivalent to 50 HeLa cells and 100 THP-1 cells (~10 ng total proteins), respectively, and >950 proteins from subnanogram bacterial and archaeal cell lysates. The present ultrasensitive LC-MS platform is expected to enable deep proteome coverage for subnanogram samples, including single mammalian cells.

Environmental Molecular Sciences Laboratory↗

Uncertainty in Experimental Data Analysis [Slides]

The talk was presented virtually to the Institute of Fundamental Technological Research, Polish Academy of Sciences in Warsaw, Poland, December 21, 2020. Astronomical observations, unusual medical cases, physics experiments too costly to repeat, natural events like earthquakes, hurricanes – all of them are impossible to repeat yet produce important scientific information not achievable in other way. This data should not be treated as qualitative, anecdotal evidence only. It should be analyzed in a mathematically rigorous way to produce quantitative experimental data. Analysis method for one-of-a-kind event data differs from analysis of a repeated experiment data. For a repeated experiments the experimental error includes a range of true values generated by repetitions of the experiment, and measurement uncertainty caused by detectors. They are independent. Repetitions of any experiment, as similar as achievable, always have built-in differences resulting in a range of the true values rather than in a single true experimental value. Measurement uncertainty depends on the measurement system only. Modern digital measurements have very small uncertainty, frequently smaller than the range of true experimental values resulting from built-in differences in the experiment repetitions. When data from one-of-a-kind experiment are analyzed, only the measurement uncertainty can be reported.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

nautilus : boosting Bayesian importance nested sampling with deep learning

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.

97 MATHEMATICS AND COMPUTING↗

Hacking Limnology Workshop and DSOS22: Creating a Community of Practice for the Nexus of Data Science, Open Science, and the Aquatic Sciences

The 2nd Aquatic Ecosystem Modeling-Junior (AEMON-J) Hacking Limnology Workshop and 3rd Virtual Summit: Incorporating Data Science and Open Science in the Aquatic Sciences (DSOS) took place on 25–29 July 2022. These virtual events were developed to bring together researchers from diverse backgrounds to share developments in data-intensive research in the aquatic sciences and train participants in cutting-edge data analysis methods related to remote sensing, data pipelines, and modeling of aquatic ecosystems.

54 ENVIRONMENTAL SCIENCES↗

From Theory to Practice: Lessons Learned from an Advanced M&V Commercial Pilot

Advanced measurement & verification (M&V), or M&V 2.0, is an energy data analysis method using advanced metering infrastructure (AMI) data in combination with analytics to quantify energy efficiency project savings. Advanced M&V is viewed as an enabler for underutilized behavioral, retrocommissioning, and holistic multi-measure efficiency efforts, as quantifying savings for these programs with existing methods has typically been very challenging. Despite its promise, there are still several unanswered questions about the use of advanced M&V such as: How accurately can these tools quantify energy savings? How can advanced M&V satisfy regulatory requirements for rigorous savings estimates? Where and how does advanced M&V intersect with traditional impact evaluation and the principles of ‘embedded’ evaluation, measurement & verification (EM&V)? Pilots are being pursued in various regions and program contexts to address these research questions. However, results from these pilots are rarely made public, meaning that lessons may not be widely shared and the scope of analyses varies widely. The paper presents encouraging results from a recent advanced M&V pilot and discusses key process-related aspects such as managing AMI data and refining analysis methodologies. An approach to reviewing and classifying projects based on savings characteristics and magnitude is demonstrated, as a potential risk management tool. The authors also demonstrate how advanced M&V can identify underperforming projects and non-routine events in a timely manner. The paper also outlines lessons learned from this and other recent pilot activity and barriers to be overcome in moving toward the goal of widespread adoption of holistic meter-based programs.

Crowe, Eliot↗

Sample manipulation and data assembly for robust microcrystal synchrotron crystallography

With the recent developments in microcrystal handling, synchrotron microdiffraction beamline instrumentation and data analysis, microcrystal crystallography with crystal sizes of less than 10 µm is appealing at synchrotrons. However, challenges remain in sample manipulation and data assembly for robust microcrystal synchrotron crystallography. Here, the development of micro-sized polyimide well-mounts for the manipulation of microcrystals of a few micrometres in size and the implementation of a robust data-analysis method for the assembly of rotational microdiffraction data sets from many microcrystals are described. The method demonstrates that microcrystals may be routinely utilized for the acquisition and assembly of complete data sets from synchrotron microdiffraction beamlines.

59 BASIC BIOLOGICAL SCIENCES↗

New MOF based on lithium tetrahydrofuran-2,3,4,5-tetracarboxylate: Its structure and conductivity behavior

A novel metal–organic framework, [Li{sub 6}(HTFTA){sub 2}(H{sub 2}O){sub 3}]·3H{sub 2}O (LiTFTA, H{sub 4}TFTA is tetrahydrofuran-2,3,4,5-tetracarboxylic acid), has been synthesized under solvothermal conditions and its structure was determined by single-crystal X-ray diffraction studies. It has six different LiO{sub 4} tetrahedra which forms two kinds of tetranuclear clusters that are coordinated to the ligands and form an overall three-dimensional structure with channels running along the crystallographic a axis. Some of the carboxylate groups of the ligand moiety jut out into the channels and the channels are occupied by water molecules. The proton conductivity behavior of LiTFTA with respect to temperature and relative humidity was analyzed by our newly developed impedance data analysis method called a random-walk approach. The results were compared with the data obtained by an analysis using an equivalent electric circuit model. Based on the physical parameters obtained by the random-walk method and the known structure we suggested the mechanism of the proton conductivity in this material. The proton conduction proceeds most probably by a vehicle conduction mechanism which employs mainly water molecules of crystallization present in the channels of LiTFTA. The value of the diffusion coefficient increases with temperature whereas the number of charge carriers remains constant. On the other hand, both the number of charge carriers and diffusion coefficient increase with increasing relative humidity. - Graphical abstract: Structure of a new metal organic framework was determined and its ionic conductivity was evaluated using a random-walk approach. - Highlights: • Lithium tetrahydrofuran-2,3,4,5-tetracarboxylate is a MOF with water-filled pores. • The impedance spectra indicate that this material is ion conductive. • Conductivity was evaluated using a random walk approach. • The number of charge carriers and diffusion coefficient was determined.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

For your consideration: Distance Analysis for PDV Data

An analytical study that discusses photonic Doppler velocimetry data analysis methods. The author intends to share this study with experts in this field at National Laboratory partners, e.g., LLNL, LANL, and Sandia. There is no plan to submit this work to a professional (public) conference or a journal publisher.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Simplified Processing Method for Meter Data Analysis

Simple/Quick metered data processing method that can be used for Army Metered Data Management System (MDMS) and Logistics Innovation Agency data, but may also be useful for other large data sets. Intended for large data sets when analyst has little information about the buildings.

97 MATHEMATICS AND COMPUTING↗

A dark matter search using the final CDMS-II data and 100 mm SuperCDMS germanium detector ionization test

Astrophysical observations indicate that approximately 85% of the matter in the universe is nonluminous, nonbaryonic, and nonrelativistic (cold) dark matter. Weakly Interacting Massive Particles (WIMPs) are a particularly well motivated dark matter particle candidate. They would be thermally produced in the early universe and their relics account for the current dark matter abundance. WIMP candidate particles are naturally provided by extensions to the Standard Model of particle physics, such as supersymmetry. The Cryogenic Dark Matter Search (CDMS) experiment operates cryogenic germanium and silicon particle detectors in the low-background environment of the Soudan Underground Laboratory in northern Minnesota to search for WIMP-nucleus scatters while rejecting electron-recoil background. The detectors simultaneously measure the ionization and phonon energies of each scattering event. The difference in ionization yield (ratio of ionization energy to recoil energy) discriminates nuclear recoils from the electron-recoil background efficiently.More sensitive detectors are required to probe the WIMP parameter space with lower WIMP-nucleon scattering cross sections. To support the R&D effort especially the detector R&D and characterization of the SuperCDMS experiment, a new CDMS test facility has been developed on the University of Minnesota campus. This thesis documents the test facility and the work involved in its development. In the test facility, we performed the first ionization collection efficiency measurements of the ionization test devices. The test devices are fabricated with detector-grade germanium crystals that are 100 mm in diameter, which is the largest available, and 33 mm in thickness. The measured efficiencies are consistent with the earlier measurements conducted with smaller Ge crystals, demonstrating that these 100 mm crystals can be used for development of the next generation dark matter detectors.Improvements of data analysis methods can also potentially improve the sensitivity of an experiment. The data taken during the last four runs of CDMS II with total raw exposure 612 kg-day were reprocessed with improved ionization pulse reconstruction algorithm. We present the classic timing analysis with the reprocessed data in this thesis. For the four runs combined, this analysis resulted in a new WIMP-nucleon cross section 4.4×10 -44 cm 2 for a WIMP mass of 70 GeV, which is a factor of 1.6 improvement compared to the original c58 classic timing analysis.

79 ASTRONOMY AND ASTROPHYSICS↗

Determination of electron beam polarization using electron detector in Compton polarimeter with less than 1% statistical and systematic uncertainty

The Q-weak experiment aims to measure the weak charge of proton with a precision of 4.2%. The proposed precision on weak charge required a 2.5% measurement of the parity violating asymmetry in elastic electron - proton scattering. Polarimetry was the largest experimental contribution to this uncertainty and a new Compton polarimeter was installed in Hall C at Jefferson Lab to make the goal achievable. In this polarimeter the electron beam collides with green laser light in a low gain Fabry-Perot Cavity; the scattered electrons are detected in 4 planes of a novel diamond micro strip detector while the back scattered photons are detected in lead tungstate crystals. This diamond micro-strip detector is the first such device to be used as a tracking detector in a nuclear and particle physics experiment. The diamond detectors are read out using custom built electronic modules that include a preamplifier, a pulse shaping amplifier and a discriminator for each detector micro-strip. We use field programmable gate array based general purpose logic modules for event selection and histogramming. Extensive Monte Carlo simulations and data acquisition simulations were performed to estimate the systematic uncertainties. Additionally, the Moller and Compton polarimeters were cross calibrated at low electron beam currents using a series of interleaved measurements. In this dissertation, we describe all the subsystems of the Compton polarimeter with emphasis on the electron detector. We focus on the FPGA based data acquisition system built by the author and the data analysis methods implemented by the author. The simulations of the data acquisition and the polarimeter that helped rigorously establish the systematic uncertainties of the polarimeter are also elaborated, resulting in the first sub 1% measurement of low energy (?1 GeV) electron beam polarization with a Compton electron detector. We have demonstrated that diamond based micro-strip detectors can be used for tracking in a high radiation environment and it has enabled us to achieve the desired precision in the measurement of the electron beam polarization which in turn has allowed the most precise determination of the weak charge of the proton.

43 PARTICLE ACCELERATORS↗

Small-angle X-ray and neutron scattering

Small-angle scattering (SAS) is a technique that is able to probe the structural organization of matter and quantify its response to changes in external conditions. X-ray and neutron scattering profiles measured from bulk materials or materials deposited at surfaces arise from nanostructural inhomogeneities of electron or nuclear density. Furthermore, the analysis of SAS data from coherent scattering events provides information about the length scale distributions of material components. Samples for SAS studies may be prepared in situ or under near-native conditions and the measurements performed at various temperatures, pressures, flows, shears or stresses, and in a time-resolved fashion. In this Primer, we provide an overview of SAS, summarizing the types of instrument used, approaches for data collection and calibration, available data analysis methods, structural information that can be obtained using the method, and data depositories, standards and formats. Recent applications of SAS in structural biology and the soft-matter and hard-matter sciences are also discussed.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗