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DOE OSTI2013

Final Scientific/Technical Report for DE-FG02-07ER64500 Study of Lignocellulosic Material Degradation with CARS Microscopy

The program of research undertaken by our Harvard group, in collaboration with Dr. Ding at the National Renewable Energy Laboratory (NREL) in Golden, CO, seeks to introduce, validate and apply a new analytical technique to study the conversion of lignocellulosic biomass into ethanol. This conversion process has been the subject of intense interest over the past few years because of its potential to provide a clean, renewable source of energy to meet increasing global demand. During the funding period, we have clearly demonstrated visualization of lignin and cellulose using intrinsic vibrational contrast with simulated Raman scattering (SRS) microscopy, developed at Harvard. Our approach offers high spatial resolution and time resolution that is sufficient to capture the kinetics of a pre‐treatment process. This is reflected by the publications listed below, as well as the use of SRS microscopy at NREL as a routine analysis tool for research on lignocellulosic biomass. In our original proposal, we envisioned moving to near‐field CARS imaging in order to perform chemical mapping at the nanoscale. However, given the dramatic progress made by our group in SRS imaging, we concentrated our efforts on using multi‐component SRS (lignin, cellulose, lipid, water, protein, deuterated metabolites, etc.) to quantitatively understand the spatially dispersed kinetics in a variety of plant samples under a variety of conditions. In addition, we built a next generation laser system based on fiber laser technology that allowed rugged and portable instrumentation for SRS microscopy. We also pursued new imaging approaches to improve the acquisition speed of SRS imaging of lignocellulose without sacrificing signal‐to‐noise ratio. This allowed us to image larger volumes of tissue with higher time resolution to get a more comprehensive picture of the heterogeneity of this chemical process from the submicron up to the centimeter scale.

09 BIOMASS FUELS↗

DOE OSTI2023

Aquifer Injection Modeling (AIM) Toolbox User Guide

The Aquifer Injection Modeling Toolbox (“AIM Toolbox”) software was developed by the Pacific Northwest National Laboratory (PNNL) for the U.S. Environmental Protection Agency’s (EPA) to provide a collection of analytical solutions suitable for evaluating the potential extent of the area impacted by subsurface injection operations. Subsurface injection operations are regulated under the EPA’s Underground Injection Control (UIC) program and are typically related to oil/gas development, waste disposal, or subsurface mining or storage. The analytical algorithms provided in the AIM Toolbox each have different approaches/assumptions/focus with respect to the nature and processes in subsurface and the nature of the injection operations. Collectively the set of analysis algorithms provides a broader evaluation of the area that can potentially be impacted by an injection operation. By providing estimates for the injectate plume extent, the software supports technical aspects of planning, evaluation, and overseeing injection activities. That is, the results help assess when further regulatory controls (e.g., monitoring, reporting) may be required and, in the case of disposal into an underground source of drinking water, the extent of the impacted area would require exemption from protection under the Safe Drinking Water Act. The AIM Toolbox software is available as a single-page web application, providing an interface to provide the necessary inputs, and both chart and map panes for visualizing the results. This User Guide describes the AIM Toolbox software, information required, user interactions, and the underlying basis of the calculations.

58 GEOSCIENCES↗

DOE OSTI2013

Molecular radiotherapy: The NUKFIT software for calculating the time-integrated activity coefficient

Purpose: Calculation of the time-integrated activity coefficient (residence time) is a crucial step in dosimetry for molecular radiotherapy. However, available software is deficient in that it is either not tailored for the use in molecular radiotherapy and/or does not include all required estimation methods. The aim of this work was therefore the development and programming of an algorithm which allows for an objective and reproducible determination of the time-integrated activity coefficient and its standard error.Methods: The algorithm includes the selection of a set of fitting functions from predefined sums of exponentials and the choice of an error model for the used data. To estimate the values of the adjustable parameters an objective function, depending on the data, the parameters of the error model, the fitting function and (if required and available) Bayesian information, is minimized. To increase reproducibility and user-friendliness the starting values are automatically determined using a combination of curve stripping and random search. Visual inspection, the coefficient of determination, the standard error of the fitted parameters, and the correlation matrix are provided to evaluate the quality of the fit. The functions which are most supported by the data are determined using the corrected Akaike information criterion. The time-integrated activity coefficient is estimated by analytically integrating the fitted functions. Its standard error is determined assuming Gaussian error propagation. The software was implemented using MATLAB.Results: To validate the proper implementation of the objective function and the fit functions, the results of NUKFIT and SAAM numerical, a commercially available software tool, were compared. The automatic search for starting values was successfully tested for reproducibility. The quality criteria applied in conjunction with the Akaike information criterion allowed the selection of suitable functions. Function fit parameters and their standard error estimated by using SAAM numerical and NUKFIT showed differences of <1%. The differences for the time-integrated activity coefficients were also <1% (standard error between 0.4% and 3%). In general, the application of the software is user-friendly and the results are mathematically correct and reproducible. An application of NUKFIT is presented for three different clinical examples.Conclusions: The software tool with its underlying methodology can be employed to objectively and reproducibly estimate the time integrated activity coefficient and its standard error for most time activity data in molecular radiotherapy.

61 RADIATION PROTECTION AND DOSIMETRY↗

DOE OSTI2023

Solar water splitting Pt-nanoparticle photosystem I thylakoid systems: Catalyst identification, location and oligomeric structure

In this study, photosynthetic conversion of light energy into chemical energy occurs in sheet-like membrane-bound compartments called thylakoids and is mediated by large integral membrane protein-pigment complexes called reaction centers (RCs). Oxygenic photosynthesis of higher plants, cyanobacteria and algae requires the symbiotic linking of two RCs, photosystem II (PSII) and photosystem I (PSI), to split water and assimilate carbon dioxide. Worldwide there is a large research investment in developing RC-based hybrids that utilize the highly evolved solar energy conversion capabilities of RCs to power catalytic reactions for solar fuel generation. Of particular interest is the solar-powered production of H 2 , a clean and renewable energy source that can replace carbonbased fossil fuels and help provide for ever-increasing global energy demands. Recently, we developed thylakoid membrane hybrids with abiotic catalysts and demonstrated that photosynthetic Z-scheme electron flow from the light-driven water oxidation at PSII can drive H 2 production from PSI. One of these hybrid systems was created by self-assembling Pt-nanoparticles (PtNPs) with the stromal subunits of PSI that extend beyond the membrane plane in both spinach and cyanobacterial thylakoids. Using PtNPs as site-specific probe molecules, we report the electron microscopic (EM) imaging of oligomeric structure, location and organization of PSI in thylakoid membranes and provide the first direct visualization of photosynthetic Z-scheme solar water-splitting biohybrids for clean H 2 production.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2017

New insights into the shock tube ignition of H 2 /O 2 at low to moderate temperatures using high-speed end-wall imaging

In this study, the effects of pre-ignition energy releases on H 2 —O 2 mixtures were explored in a shock tube with the aid of high-speed imaging and conventional pressure and emission diagnostics. Ignition delay times and time-resolved camera image sequences were taken behind the reflected shockwaves for two hydrogen mixtures. High concentration experiments spanned temperatures between 858 and 1035 K and pressures between 2.74 and 3.91 atm for a 15% H 2 \18% O 2 \Ar mixture. Low concentration data were also taken at temperatures between 960 and 1131 K and pressures between 3.09 and 5.44 atm for a 4% H 2 \2% O 2 \Ar mixture. These two model mixtures were chosen as they were the focus of recent shock tube work conducted in the literature. Experiments were performed in both a clean and dirty shock tube facility; however, no deviations in ignition delay times between the two types of tests were apparent. The high-concentration mixture (15%H 2 \18%O 2 \Ar) experienced energy releases in the form of deflagration flames followed by local detonations at temperatures < 1000 K. Measured ignition delay times were compared to predictions by three chemical kinetic mechanisms: GRI-Mech 3.0, AramcoMech 2.0, and Burke's et al. (2012) mechanisms. It was found that when proper thermodynamic assumptions are used, all mechanisms were able to accurately predict the experiments with superior performance from the well-validated AramcoMech 2.0 and Burke et al. mechanisms. Current work provides better guidance in using available literature hydrogen shock tube measurements, which spanned more than 50 years but were conducted without the aid of high-speed visualization of the ignition process, and their modeling using combustion kinetic mechanisms.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Single-Filament Imaging Mass Spectrometry Lipidomics in Arthrospira platensis

Elucidating intra-organismal biochemical and lipid organization in photosynthetic biological cell factories of filamentous cyanobacteria, i.e., Arthrospira platensis (Spirulina), is important to track physiological response mechanisms during growth. Little is known about the filaments' biochemical organization and cellular structure and no label-free imaging techniques exist that provide molecular mapping. We applied ultra-high resolution mass spectrometry (7T FT-ICR-MS) matrix-assisted laser desorption ionization (MALDI) imaging to immobilized Spirulina filaments to investigate the localization of lipids across distinct physiological regions. We optimized matrix selection and deposition methods with the goal of facilitating high spatial, and intra-filament, resolution using untargeted multivariate statistical spectral deconvolution across MS pixels. Our results demonstrate an improved two step application with an optimized procedure for intra-organismal lipid profiling to improve analyte sensitivity and achieve higher spatial resolution, whereby we evaluate three conventional matrices 2,5-dihydroxybenzoic acid (DHB), a 9:1 ratio of DHB:superDHB (sDHB), 1,5- diaminonaphthalene (DAN) and a 50:50 mix of DHB:sDHB and compare delineation and pixel-based elucidation of intra-filament lipidomics. We identified a total of 1,626 features that could be putatively assigned a lipid-like formula based on database query and 46 unique features, with associated lipid assignments that were significantly distinct in their intra-filament location. MALDI- imaging MS with untargeted statistical spectral deconvolution was used to visualize intra-filament lipidomics organization in Spirulina filaments. Improvements in matrix deposition, including sequential sublimation and pneumatic spraying, increased signal abundance at high spatial resolution and allowed for identification of distinct lipid composition regions. Here in this work outlines a methodology that may be used for micro-ecological untargeted molecular phenotyping.

09 BIOMASS FUELS↗

DOE OSTI2019

Simulation of discrete cracks driven by nearly incompressible fluid via 2D combined finite-discrete element method

Here, we propose a novel hydraulic solver in order to simulate key mechanisms that control fluid-driven cracks in the framework of the combined finite-discrete element method (FDEM). The main innovative aspect of the present work is the independence of the fluid's critical time step size with the fracture opening. This advantage is extremely important because it means that very fine meshes can be used around areas of interest, such as boreholes, without penalizing the computational cost as fractures propagate (ie, open) and the fluid flows through them. This is a great advantage over other recently introduced approaches that exhibit a dependency of the time step in the form of Δt crit ∝ (l/a) 2 where l is the element size and a is the fracture aperture. This paper presents a series of benchmark cases for the proposed solver. The rationale adopted by the authors was to benchmark and validate the implementation of the hydraulic solver in an incremental fashion, starting from the simplest cases and building in complexity. The calculations shown in this work clearly demonstrate that the proposed approach is able to reproduce analytical results for fluid flow through a single crack. The results presented in this paper also demonstrate that the new approach is robust enough to deal with complex fracture patterns and complex geometries; the obtained fluid-driven fracture patterns in the vicinity of a borehole certainly stand to the scrutiny of human visual perception.

58 GEOSCIENCES↗

DOE OSTI2016

Real-time microstructure imaging by Laue microdiffraction: A sample application in laser 3D printed Ni-based superalloys

Synchrotron-based Laue microdiffraction has been widely applied to characterize the local crystal structure, orientation, and defects of inhomogeneous polycrystalline solids by raster scanning them under a micro/nano focused polychromatic X-ray probe. In a typical experiment, a large number of Laue diffraction patterns are collected, requiring novel data reduction and analysis approaches, especially for researchers who do not have access to fast parallel computing capabilities. In this article, a novel approach is developed by plotting the distributions of the average recorded intensity and the average filtered intensity of the Laue patterns. Visualization of the characteristic microstructural features is realized in real time during data collection. As an example, this method is applied to image key features such as microcracks, carbides, heat affected zone, and dendrites in a laser assisted 3D printed Ni-based superalloy, at a speed much faster than data collection. Such analytical approach remains valid for a wide range of crystalline solids, and therefore extends the application range of the Laue microdiffraction technique to problems where real-time decision-making during experiment is crucial (for instance time-resolved non-reversible experiments).

36 MATERIALS SCIENCE↗

DOE OSTI2020

FaceBase 3: analytical tools and FAIR resources for craniofacial and dental research

ABSTRACT The FaceBase Consortium was established by the National Institute of Dental and Craniofacial Research in 2009 as a ‘big data’ resource for the craniofacial research community. Over the past decade, researchers have deposited hundreds of annotated and curated datasets on both normal and disordered craniofacial development in FaceBase, all freely available to the research community on the FaceBase Hub website. The Hub has developed numerous visualization and analysis tools designed to promote integration of multidisciplinary data while remaining dedicated to the FAIR principles of data management (findability, accessibility, interoperability and reusability) and providing a faceted search infrastructure for locating desired data efficiently. Summaries of the datasets generated by the FaceBase projects from 2014 to 2019 are provided here. FaceBase 3 now welcomes contributions of data on craniofacial and dental development in humans, model organisms and cell lines. Collectively, the FaceBase Consortium, along with other NIH-supported data resources, provide a continuously growing, dynamic and current resource for the scientific community while improving data reproducibility and fulfilling data sharing requirements.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

Aquifer Injection Modeling (AIM) Toolbox User Guide

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

Visualizing Tetrahedral Oxyanion Bound in HIV-1 Protease Using Neutrons: Implications for the Catalytic Mechanism and Drug Design

Not Available

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2018

Automated Transformation of Lignin Topologies into Atomic Structures with LigninBuilder

Lignin is an abundant aromatic heteropolymer found in secondary plant cell walls and is a potential feedstock for conversion into bioderived fuels and chemicals. Lignin chemical diversity complicates traditional structural studies, and so, relatively little experimental evidence exists for how lignin structure exists in aqueous solution or how lignin polymers respond to changes in their chemical environment. Molecular modeling can address these concerns; however, prior computational structural lignin models typically did not capture lignin heterogeneity, as only a few polymers were considered. LigninBuilder creates a framework for building structural libraries for lignin from existing topological libraries, permitting significantly greater diversity of lignin structures to be sampled at atomic detail. As a demonstration of its capabilities, LigninBuilder was applied to three libraries of lignin from hardwood, softwood, and grass, and the resulting polymer structures were simulated in an aqueous environment. The lignins adopted compact globular structures, as would be expected for polymers in poor solvents. The differences between the libraries were largest when quantifying the packing of nonadjacent aromatic residues, with greater branching within the polymer resulting in poorer aromatic packing. Individual lignin polymers were also found to undergo rapid conformational changes, with the dwell time within a state growing as the square of the molecular weight. This first application of LigninBuilder demonstrates the potential for atomic-level insight into lignin interactions. LigninBuilder is distributed as a plugin to the visualization software VMD, lowering the barrier for modeling lignin structure in diverse environments.

09 BIOMASS FUELS↗

DOE OSTI2016

In-situ realtime monitoring of nanoscale gold electroplating using micro-electro-mechanical systems liquid cell operating in transmission electron microscopy

The dynamics of nanoscale electroplating between gold electrodes was investigated using a microfabricated liquid cell mounted on a scanning transmission electron microscope. The electroplating was recorded in-situ for 10 min with a spatial resolution higher than 6 nm. At the beginning of the electroplating, gold spike-like structures of about 50 nm in size grew from an electrode, connected gold nanoclusters around them, and form three dimensional nanoscale structures. We visualized the elementary process of the gold electroplating, and believe that the results lead to the deeper understanding of electroplating at the nanoscale.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

EDX ClaiMM: Digital Resources for the Critical Minerals and Materials Community

Securing critical mineral supply chains is essential for transitioning to a clean energy economy and for maintaining national security. Big-data analytics can serve as a cost-effective means of identifying new domestic critical mineral resources but only if data can be easily located and digested. Using ArcGIS Enterprise Sites, EDX ClaiMM was developed to increase the accessibility of critical minerals data, reducing time spent on data collection and integration. Hosted tools provide rapid visualization and exploration of key datasets, unlocking insights to support resource assessments.

Yesenchak, Rachel↗

DOE OSTI2023

Development of an accelerator-based neutron source to prototype Mo-99 production, part I: A liquid LBE windowless target

In this article, Molybdenum-99 (Mo-99)’s decay product, technetium-99 (Tc-99 m), is one of the most critical isotopes for medical diagnostics. To provide U.S. domestic supply of Mo-99 without using high-enriched uranium (HEU), a subcritical uranium target assembly (UTA) is irradiated by an accelerator-based neutron source to create Mo-99 through fission. This study discusses the development of the accelerator-based neutron source. The high-energy electrons from the accelerator irradiate a liquid lead-bismuth eutectic (LBE) target to produce neutrons. Part I of this work focuses on numerical and experimental analysis towards the development of a liquid LBE windowless target. Unlike the existing windowless targets in literature, the current design creates a vertical free surface for a beam to irradiate. First, a hydrodynamic analysis of the LBE windowless target is performed. Simplified analytical calculations are assisted by 2D computational fluid dynamics (CFD) simulations to design the target, with the focus on eliminating recirculation zones and avoiding cavitation. With the optimized geometry, the experimental study is performed to investigate the flow hydrodynamics using liquid LBE. The experiments (1) compare pressure drop in the system to correlation predictions; (2) visualize the free surface liquid LBE flow from the beam view; (3) validate the LBE flow profile using temperature sensitive paint from the side view; and (4) validate the liquid LBE film thickness using gamma densitometer measurements. Second, the power handling capability of the designed windowless target is investigated. The divider plate in the current design is susceptible to overheating due to the thin LBE film in front. As LBE erosion and corrosion is likely to occur at an LBE velocity of 2.0 m/s and temperature above 500 °C, a power limit of 10 kW of beam power was established to prevent this corrosion from occurring, which is calculated by a Nusselt number correlation. The divider plate surface temperature at 10 kW agrees well with the 3D CFD simulation results. Part I demonstrates the fundamental physics in liquid LBE windowless target design and associated testing. A companion paper, Part II will demonstrate how to couple this windowless target into the Mo-99 production system, including an accelerator system operating under an ultra-high vacuum and the UTA cooled by water at room temperature.

43 PARTICLE ACCELERATORS↗

DOE OSTI2021

Advances and challenges in CO2 foam technologies for enhanced oil recovery in carbonate reservoirs

Utilization of surfactants for generating foam has the potential for fluid-mobility control during CO2 flooding processes, leading to improved oil recovery. This manuscript is a review of the most important aspects for the design of CO2-foams with mobility control in carbonate reservoirs, including recent advances in novel surfactants and analytical techniques for analysis of surfactant adsorption on carbonate minerals and their thermal stability. Several key parameters and properties regarding foam transport in porous media are reviewed such as, the minimum pressure gradient required for foam generation, the effects of the partition coefficient of a CO2-soluble surfactant on foam transport in rock cores, visualization of foam flow by either microfluidic or PET/CT imaging processes in heterogeneous or fractured systems and the effect of oil on foam transport under reservoir conditions. Also are discussed the most recent advances of two major foam modeling methods, including the semi-empirical STARS foam model and the population balance model, as well as CO2 foam pilot tests and the factors governing their successes.

Jian, Guoqing↗

DOE OSTI2014

Mechanical Resonances of Helically Coiled Carbon Nanowires

Despite their wide spread applications, the mechanical behavior of helically coiled structures has evaded an accurate understanding at any length scale (nano to macro) mainly due to their geometrical complexity. The advent of helically coiled micro/nanoscale structures in nano-robotics, nano-inductors, and impact protection coatings has necessitated the development of new methodologies for determining their shear and tensile properties. Accordingly, we developed a synergistic protocol which (i) integrates analytical, numerical(i.e., finite element using COMSOL ® ) and experimental (harmonic detection of resonance; HDR) methods to obtain an empirically validated closed form expression for the shear modulus and resonance frequency of a singly clamped helically coiled carbon nanowire (HCNW), and (ii) circumvents the need for solving 12th order differential equations. From the experimental standpoint, a visual detection of resonances (using in situ scanning electron microscopy) combined with HDR revealed intriguing non-planar resonance modes at much lower driving forces relative to those needed for linear carbon nanotube cantilevers. Interestingly, despite the presence of mechanical and geometrical nonlinearities in the HCNW resonance behavior the ratio of the first two transverse modes $f_2/f_1$ was found to be similar to the ratio predicted by the Euler-Bernoulli theorem for linear cantilevers.

42 ENGINEERING↗

DOE OSTI2021

Assessment of Local Observation of Atomic Ordering in Alloys via the Radial Distribution Function: A Computational and Experimental Approach

As a powerful analytical technique, atom probe tomography (APT) has the capacity to acquire the spatial distribution of millions of atoms from a complex sample. However, extracting information at the Ångstrom-scale on atomic ordering remains a challenge due to the limits of the APT experiment and data analysis algorithms. The development of new computational tools enable visualization of the data and aid understanding of the physical phenomena such as disorder of complex crystalline structures. Here, we report progress towards this goal using two steps. We describe a computational approach to evaluate atomic ordering in the crystal structure by generating radial distribution functions (RDF). Atomic ordering is rendered as the Fractional Cumulative Radial Distribution Function (FCRDF) which allows for greater visibility of local compositions at short range in the structure. Further, we accommodate in the analysis additional parameters such as uncertainty in the atomic coordinates and the atomic abundance to ascertain short-range ordering in APT data sets. We applied the FCRDF analysis to synthetic and experimental APT data sets for Ni 3 Al. The ability to observe a signal of atomic ordering consistent with the known L1 2 crystal structure is heavily dependent on spatial uncertainty, irrespective of abundance. Detection of atomic ordering is subject to an upper limit of spatial uncertainty of atoms described with Gaussian distributions with a standard deviation of 1.3 Å. The FCRDF analysis was also applied to the APT data set for a six-component alloy, Al 1.3 CoCrCuFeNi. In this case, we are currently able to visualize elemental segregation at the nanoscale, though unambiguous identification of atomic ordering at the Ångstrom (nearest-neighbor) scale remains a goal.

36 MATERIALS SCIENCE↗