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At least 343 records · Page 19

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DOE OSTI2020

Potential for Applying Continuous Directed Evolution to Plant Enzymes: An Exploratory Study

Plant evolution has produced enzymes that may not be optimal for maximizing yield and quality in today’s agricultural environments and plant biotechnology applications. By improving enzyme performance, it should be possible to alleviate constraints on yield and quality currently imposed by kinetic properties or enzyme instability. Enzymes can be optimized more quickly than naturally possible by applying directed evolution, which entails mutating a target gene in vitro and screening or selecting the mutated gene products for the desired characteristics. Continuous directed evolution is a more efficient and scalable version that accomplishes the mutagenesis and selection steps simultaneously in vivo via error-prone replication of the target gene and coupling of the host cell’s growth rate to the target gene’s function. However, published continuous systems require custom plasmid assembly, and convenient multipurpose platforms are not available. We discuss two systems suitable for continuous directed evolution of enzymes, OrthoRep in Saccharomyces cerevisiae and EvolvR in Escherichia coli, and our pilot efforts to adapt each system for high-throughput plant enzyme engineering. To test our modified systems, we used the thiamin synthesis enzyme THI4, previously identified as a prime candidate for improvement. Our adapted OrthoRep system shows promise for efficient plant enzyme engineering.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Inverse design of equilibrium cluster fluids applied to a physically informed model

Inverse design strategies have proven highly useful for the discovery of interaction potentials that prompt self-assembly of a variety of interesting structures. However, often the optimized particle interactions do not have a direct relationship to experimental systems. In this work, we show that Relative Entropy minimization is able to discover physically meaningful parameter sets for a model interaction built from depletion attraction and electrostatic repulsion that yield self-assembly of size-specific clusters. Here, we then explore the sensitivity of the optimized interaction potentials with respect to deviations in the underlying physical quantities, showing that clustering behavior is largely preserved even as the optimized parameters are perturbed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Quasi‐2D Perovskite Crystalline Layers for Printable Direct Conversion X‐Ray Imaging

Abstract Polycrystalline perovskite film‐based X‐ray detector is an appealing technology for assembling large scale imager by printing methods. However, thick crystalline layer without trap and solvent residual is challenging to fabricate. Here, the authors report a solution method to produce high quality quasi‐2D perovskite crystalline layers and detectors that are suitable for X‐ray imaging. By introducing n ‐butylamine iodide into methylammonium lead iodide precursor and coating at elevated temperatures, compact and crystalline layers with exceptional uniformity are obtained on both rigid and flexible substrates. Photodiodes built with the quasi‐2D layers exhibit a low dark current and stable operation under constant electrical field over 96 h in dark, and over 15 h under X‐ray irradiation. The detector responds sensitively under X‐ray, delivering a high sensitivity of 1214 µC Gy air −1 cm −2 and a sensitivity gain is observed when operated under higher fields. Finally, high resolution images are demonstrated using a single pixel device that can resolve 80–200 µm features. This work paves the path for printable direct conversion X‐ray imager development.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Preserving Structurally Labile Peptide Nanosheets After Molecular Functionalization of the Self-Assembling Peptides

A significant challenge in creating supramolecular materials is that conjugating molecular functionalities to building blocks often results in dissociation or undesired morphological transformation of their assemblies. Here we present a facile strategy to preserve structurally labile peptide assemblies after molecular modification of the self-assembling peptides. Sheet-forming peptides are designed to afford a staggered alignment with the segments bearing chemical modification sites protruding from the sheet surfaces. The staggered assembly allows for simultaneous separation of attached molecules from each other and from the underlying assembly motifs. Strikingly, using PEGs as the external molecules, PEG 400 - and PEG 700 -peptide conjugates directly self-associate into nanosheets with the PEG chains localized on the sheet surfaces. In contrast, the sheet formation based on in-register lateral packing of peptides does not recur upon the peptide PEGylation. This strategy allows for fabrication of densely modified assemblies with a variety of molecules, as demonstrated using biotin (hydrophobic molecule), c(RGDfK) (cyclic pentapeptide), and nucleic acid aptamer (negatively charged ssDNA). The staggered co-assembly also enables extended tunability of the amount/density of surface molecules, as exemplified by screening ligand-appended assemblies for cell targeting. In conclusion, this study paves the way for functionalization of historically challenging fragile assemblies while maintaining their overall morphology.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Visualizing a viral genome with contrast variation small angle X-ray scattering

Despite the threat to human health posed by some single-stranded RNA viruses, little is understood about their assembly. The goal of this work is to introduce a new tool for watching an RNA genome direct its own packaging and encapsidation by proteins. Contrast variation small-angle X-ray scattering (CV-SAXS) is a powerful tool with the potential to monitor the changing structure of a viral RNA through this assembly process. The proteins, though present, do not contribute to the measured signal. As a first step in assessing the feasibility of viral genome studies, the structure of encapsidated MS2 RNA was exclusively detected with CV-SAXS and compared with a structure derived from asymmetric cryo-EM reconstructions. Additional comparisons with free RNA highlight the significant structural rearrangements induced by capsid proteins and invite the application of time-resolved CV-SAXS to reveal interactions that result in efficient viral assembly.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Smart Self-Assembly Amphiphilic Cyclopeptide-Dye for Near-Infrared Window-II Imaging

Not provided.

Chemistry↗

DOE OSTI2022

Thin film block copolymer self-assembly for nanophotonics

The nanophotonic engineering of light–matter interactions has profoundly changed research behind the design and fabrication of optical materials and devices. Metasurfaces—arrays of subwavelength nanostructures that interact resonantly with electromagnetic radiation—have emerged as an integral nanophotonic platform for a new generation of ultrathin lenses, displays, polarizers and other devices. Their success hinges on advances in lithography and nanofabrication in recent decades. While existing nanolithography techniques are suitable for basic research and prototyping, issues of cost, throughput, scalability, and substrate compatibility may preclude their use for many metasurface applications. Patterning via spontaneous self-assembly of block copolymer thin films offers an enticing alternative for nanophotonic manufacturing that is rapid, inexpensive, and applicable to large areas and diverse substrates. This review discusses the advantages and disadvantages of block copolymer-based nanopatterning and highlights recent progress in their use for broadband antireflection, surface enhanced Raman spectroscopy, and other nanophotonic applications. Here recent advances in diversification of self-assembled block copolymer nanopatterns and improved processes for enhanced scalability of self-assembled nanopatterning using block copolymers are also discussed, with a spotlight on directions for future research that would enable a wider array of nanophotonic applications.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2022

Next Generation System Analysis Model: Recently Added Features and Future Plans

To better enable informed decision-making regarding the back-end of the nuclear fuel cycle, the Integrated Waste Management System (IWMS) program within the U.S. Department of Energy, Office of Nuclear Energy (DOE-NE) has been sponsoring the development and application of system analysis tools capable of analyzing various system options for the management of spent nuclear fuel (SNF) and high-level radioactive waste (HLW).With these tools, IWMS architecture analyses are being conducted to support the future deployment of a comprehensive nuclear waste management system that considers all major back-end aspects of the nuclear fuel cycle (i.e., transportation, storage, and disposal). The Next Generation System Analysis Model (NGSAM) is an agent-based simulation software tool expressly designed to be capable of modeling features within various IWMS architectures. NGSAM imports data from Oak Ridge National Laboratory (ORNL)’s unified database (e.g., historic assembly information, thermal profiles for assembly heat, and at-reactor dry storage loadings) to ensure that each simulation initializes with a realistic representation of the state of commercial SNF in the U.S. Recent major enhancements implemented into NGSAM in the period since NGSAM was last presented at the WM2019 conference include: • Tracking of railroad escort car acquisition and buffer car acquisition • The addition of heavy haul truck (HHT) and barge routes for some sites, as well as support for user-defined inter-modal routes • Updates to the logic that checks the transportation cask thermal limit maps prior to package transport • An allocation method that predicts when reactor sites would pack assemblies from their spent fuel pools for dry storage, and prioritizes shipments directly from the pools of those reactor sites in the preceding periods (before the predicted loadings to dry storage), thus reducing the number of casks loaded into dry storage at reactor sites • The addition of “reactor site family” operational limits to restrict the number of loads of SNF taken from the pool and from dry storage at a given reactor site each year • Added support for multiple canister loading map options and packages with multiple compatible transportation overpacks • Updates to the handling of non-commercial SNF, including a new database that contains data to support the updates • Updates to allow analysis of hypothetical scenarios which include repackaging at reactor sites, e.g., for possible comparative analysis with other scenarios • Implementation of additional output reports, or modification of existing ones • The ability to generate and implement user edits via the NGSAM website • The ability to model loading SNF from pool storage at an interim storage facility (ISF) into dry storage at the ISF • The ability to model consolidating SNF from different existing storage containers at a DOE site into the same DOE standard canister • The ability to model transferring SNF casks from one transportation mode to another, e.g., from HHT to rail, referred to as transloading. These new features have improved NGSAM capabilities and users’ experience with the model. Preliminary NGSAM requirements for modeling advanced reactor fuels, reprocessing, treatment, and conditioning were considered, and this paper describes them at a high level. Other nuclear fuel cycle system analysis tools developed under sponsorship of DOE-NE, like the VISION code developed at Idaho National Laboratory, might be better suited for initial high-level analysis of those technologies and advanced fuel cycles. As technologies are developed and system concepts evolve, NGSAM could provide value by providing more detailed modeling of transport, storage, and disposal of spent fuel and wastes from advanced reactors and advanced fuel cycles at the fuel element and waste container level.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2022

Condensers and electronic assemblies

Provided is a condenser for use in an electronic assembly. The condenser includes a first vertical wall extending in a vertical direction, the first vertical wall defining a first plurality of vertical condensation channels within the first vertical wall, a second vertical wall extending in the vertical direction, the second vertical wall defining a second plurality of vertical condensation channels within the second vertical wall, and a first plurality of fins extending in the vertical direction, each of the first plurality of fins connected to the first vertical wall, the second vertical wall or both the first vertical wall and the second vertical wall.

Cousineau, Emily↗

DOE OSTI2023

Condensers and electronic assemblies

Cousineau, Emily↗

DOE OSTI2022

LLNL Macroscopic Anisotropic Explosives Research at INL National Security Test Range - Test Results

A select team of 23 engineers, scientists, and explosives specialists from LLNL, LANL, INL, and Marine Raiders from Marine Special Operations Command (MARSOC) and U.S. Special Operations Command (SOCOM) assembled during the second week of November at the INL National Security Test Range near Idaho Falls to investigate and demonstrate fundamental principles of explosives anisotropy. Today's explosives are isotropic in their detonation performance. That is, no matter what direction a detonation runs through bulk explosive, the performance is the same; whereas, anisotropic explosives exhibit different performance, depending on which direction the detonation wave moves through the explosive. The ANISO Team worked in subfreezing temperatures on the Snake River Plain, carrying out 55 experimental explosives shots in four days that lead to a clear understanding of the performance and behavior of an assembly of small, linerless, C4 shaped charges. These shots clearly demonstrated, for the first time, on a macroscopic scale, the principle of anisotropy in measured progression of the detonation through the explosive assembly. The outputs of nine piezo timing pins in the explosive assembly clearly showed detonation progressing through the assembly faster than nominal detonation velocity and moving slower than nominal detonation velocity in the opposite direction. Basic data from these experiments will be used to design and construct explosives assemblies that will be shot in the LLNL High Explosives Applications Facility's (HEAF). These experimental tests will provide refined basic data that will then be used by modelers to develop high explosives models. Computer simulations using these models will then be run to predict performance and design inhomogeneous, anisotropic bulk explosive charges that will be tested at LLNL.

33 ADVANCED PROPULSION SYSTEMS↗

DOE OSTI2024

MultiGreen: A multiplexing architecture for GreenGate cloning

Genetic modification of plants fundamentally relies upon customized vector designs. The ever-increasing complexity of transgenic constructs has led to increased adoption of modular cloning systems for their ease of use, cost effectiveness, and rapid prototyping. GreenGate is a modular cloning system catered specifically to designing bespoke, single transcriptional unit vectors for plant transformation—which is also its greatest flaw. MultiGreen seeks to address GreenGate’s limitations while maintaining the syntax of the original GreenGate kit. The primary limitations MultiGreen addresses are 1) multiplexing in series, 2) multiplexing in parallel, and 3) repeated cycling of transcriptional unit assembly through binary intermediates. MultiGreen efficiently concatenates bespoke transcriptional units using an additional suite of level 1acceptor vectors which serve as an assembly point for individual transcriptional units prior to final, level 2, condensation of multiple transcriptional units. Assembly with MultiGreen level 1 vectors scales at a maximal rate of 2*⌈ log 6 n ⌉+3 days per assembly, where n represents the number of transcriptional units. Further, MultiGreen level 1 acceptor vectors are binary vectors and can be used directly for plant transformation to further maximize prototyping speed. MultiGreen is a 1:1 expansion of the original GreenGate architecture’s grammar and has been demonstrated to efficiently assemble plasmids with multiple transcriptional units. MultiGreen has been validated by using a truncated violacein operon from Chromobacterium violaceum in bacteria and by deconstructing the RUBY reporter for in planta functional validation. MultiGreen currently supports many of our in-house multi transcriptional unit assemblies and will be a valuable strategy for more complex cloning projects.

Science & Technology - Other Topics↗

DOE OSTI2024

Self-Assembling Cell-Free Systems for Scalable Bioconversion

This project focused on developing cell-free systems to directly express multi-enzyme catalysts and perform CO2 bioconversions for industrial chemical production. The use of cell-free expression (CFE) systems derived from bacterial lysates is emerging as a promising approach for biomanufacturing. CFEs are genetically programmable, permit the expression of toxic enzymes, and allow for rapid prototyping of metabolic pathways. Research Contributions: 1. Understanding the Area Investigated: This research advances the understanding of cell-free systems by demonstrating their capability to perform complex multi-enzyme reactions. By directly expressing multi-gene systems, CFEs avoid the high costs and inefficiencies associated with producing and purifying enzymes for multi-step pathways. 2. Technical Effectiveness and Economic Feasibility: The project successfully engineered a CFE-based multienzyme biocatalyst for the de novo synthesis of serine and glycine from CO2 equivalents (formate and bicarbonate) and ammonia. This method achieved a 30% conversion rate of formate into these industrially important amino acids. Additionally, an 8-gene CFE biocatalyst was developed to produce malate, conserving 43% of carbon that would otherwise be lost as CO2. This approach has the potential to reach higher carbon efficiency than microbial production. 3. Public Benefit: The cell-free production of chemicals like serine, glycine, and malate using electrochemically generated formate could significantly reduce CO2 emissions. For example, satisfying the global malate market with this method could avoid approximately 400,000 tons of CO2 emissions annually. This work demonstrates the potential of CFE systems to produce platform chemicals, contributing to environmental sustainability and reducing reliance on petrochemicals. Future Prospects: The CFE-based biocatalyst process could be extended to produce a variety of chemicals, including other industrial di-acids, aromatics, terpenes, alcohols, and polymers. This project showcases the capabilities of cell-free expression systems for prototyping carbon-conserving pathways and sustainably bioproducing platform chemicals, marking a significant step towards economically-viable industrial processes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Layered structures of assembled imine-linked macrocycles and two-dimensional covalent organic frameworks give rise to prolonged exciton lifetimes

Ordered organic materials and assemblies have great potential to be tailored to have desirable properties for optoelectronic applications, such as long exciton lifetime and high directional exciton mobility. Framework materials, such as two-dimensional covalent organic frameworks (2D COFs), as well as their truncated macrocyclic analogues, are versatile platforms to organize functional aromatic systems into designed assemblies and robust materials. In this study we investigate the exciton dynamics in a 2D COF, its corresponding hexagonal macrocycle, and extended nanotubes comprised of stacked macrocycles. The excitonic behavior of these three systems provide an understanding of excitonic processes that occur in the plane of the covalently bonded 2D macromolecules and between layers of the nanotubes and 2D COF. The nanotube and analogous 2D COF exhibit longer excited-state lifetimes (~100 ps) compared to the individual, solvated macrocycles (<0.5 ps). These differences are attributed to the internal conversion facilitated by the internal motions of the imine linkages which are significantly reduced in the assembled macrocycles in the nanotube and 2D COF sheets in the layered structures. The exciton diffusion processes in the assembled nanotubes and 2D COF systems were characterized by the autocorrelations of the transition dipole moment of the excitons, giving the depolarization time constants for both systems to be ~1 ps. This work also reveals the anisotropic exciton dynamics related to the in-plane and inter-plane structural factors in these systems. These studies provide guidance for the design of future COF materials, where the longer excited state lifetimes imparted by assembly are beneficial for optoelectronic applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

One-Step Facile Synthesis of High-Activity Nitrogen-Doped PtNiN Oxygen Reduction Catalyst

PtM alloy electrocatalysts (M = Fe, Co, Ni) have been the subject of many investigations aimed at increasing their attractive properties, in particular oxygen reduction reaction (ORR) activity, while reducing total platinum-group-metal content and improving durability. Despite some success, these catalysts still have relatively high Pt content and lack the necessary durability as M metals leach out from the alloys during potential cycling. Previously, we synthesized nitrogen (N)-doped PtMN/C catalysts consisting of thin Pt shells on M nitride cores by a two-step method, which showed higher ORR activity and stability than their PtM counterparts. In the present work, we developed a facile one-step synthesis method, which comprises a single thermal annealing process of the N-doped PtNiN/C alloy. The ORR performance of the one-step synthesized PtNiN/C catalyst is much higher than that of the two-step synthesized PtNiN/C, as revealed by rotating disk electrode measurements. Membrane electrode assembly fuel cell testing demonstrated superb durability and high activity. Formation of Pt monolayer shells on the nitrided (Pt x Ni 1-x ) 4 N cores was confirmed by in situ X-ray absorption spectroscopy. The origins of the enhanced activity and stability of the one-step synthesized PtNiN/C catalyst are elucidated based on density functional theory calculations together with the experimental results.

30 DIRECT ENERGY CONVERSION↗

DOE OSTI2020

The NtrYX Two-Component System Regulates the Bacterial Cell Envelope

ABSTRACT Activity of the NtrYX two-component system has been associated with important processes in diverse bacteria, ranging from symbiosis to nitrogen and energy metabolism. In the facultative alphaproteobacterium Rhodobacter sphaeroides , loss of the two-component system NtrYX results in increased lipid production and sensitivity to some known cell envelope-active compounds. In this study, we show that NtrYX directly controls multiple properties of the cell envelope. We find that the response regulator NtrX binds upstream of cell envelope genes, including those involved in peptidoglycan biosynthesis and modification and in cell division. We show that loss of NtrYX impacts the cellular levels of peptidoglycan precursors and lipopolysaccharide and alters cell envelope structure, increasing cell length and the thickness of the periplasm. Cell envelope function is also disrupted in the absence of NtrYX, resulting in increased outer membrane permeability. Based on the properties of R. sphaeroides cells lacking NtrYX and the target genes under direct control of this two-component system, we propose that NtrYX plays a previously undescribed, and potentially conserved, role in the assembly, structure, and function of the cell envelope in a variety of bacteria. IMPORTANCE The bacterial cell envelope provides many important functions. It protects cells from harsh environments, serves as a selective permeability barrier, houses bioenergetic functions, defines sensitivity to antibacterial agents, and plays a crucial role in biofilm formation, symbiosis, and virulence. Despite the important roles of this cellular compartment, we lack a detailed understanding of the biosynthesis and remodeling of the cell envelope. Here, we report that the R. sphaeroides two-component signaling system NtrYX is a previously undescribed regulator of cell envelope processes, providing evidence that it is directly involved in controlling transcription of genes involved in cell envelope assembly, structure, and function in this and possibly other bacteria. Thus, our data report on a newly discovered process used by bacteria to assemble and remodel the cell envelope.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Photocatalytic Hydrogen Evolution Using Mesoporous Honeycomb Iron Titanate

Mesoporous honeycomb iron titanate using a sol-gel, evaporation-induced self-assembly method is synthesized. A triblock copolymer, F127, serves as a structure-directing agents, with iron chloride and titanium (IV) isopropoxide as inorganic precursors. The strong intermolecular force of attraction among urea, metal precursors, and polymer led to the formation of the mesoporous honeycomb structure. The study of physicochemical properties using different techniques reveals the formation of microstructures with a remarkable degree of porosity. The amorphous iron titanate outperforms the photochemical generation of H 2 due to its disorderly structural arrangement and incomplete crystal formation. The randomness on the structure provides more area for catalytic reaction by providing more contact with the reactant and superior light absorption capability. The high amount of hydrogen gas, 40.66 mmolg -1 h -1 , is observed in the investigation over 3 h of activity for the iron titanate honeycomb sample. This yield is a more significant amount compared to the obtained for the commercially available TiO 2 (23.78 mmolg -1 h -1 ). The iron titanate materials synthesized with low-cost materials and methods are very effective and have the potential for hydrogen generation.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2023

Multifidelity uncertainty quantification with models based on dissimilar parameters

Multifidelity uncertainty quantification (MF UQ) sampling approaches have been shown to significantly reduce the variance of statistical estimators while preserving the bias of the highest-fidelity model, provided that the low-fidelity models are well correlated. However, maintaining a high level of correlation can be challenging, especially when models depend on different input uncertain parameters, which drastically reduces the correlation. Existing MF UQ approaches do not adequately address this issue. In this work, we propose a new sampling strategy that exploits a shared space to improve the correlation among models with dissimilar parameterization. We achieve this by transforming the original coordinates onto an auxiliary manifold using the adaptive basis (AB) method (Tipireddy and Ghanem, 2014). The AB method has two main benefits: (1) it provides an effective tool to identify the low-dimensional manifold on which each model can be represented, and (2) it enables easy transformation of polynomial chaos representations from high- to low-dimensional spaces. This latter feature is used to identify a shared manifold among models without requiring additional evaluations. Here we present two algorithmic flavors of the new estimator to cover different analysis scenarios, including those with legacy and non-legacy high-fidelity (HF) data. We provide numerical results for analytical examples, a direct field acoustic test, and a finite element model of a nuclear fuel assembly. For all examples, we compare the proposed strategy against both single-fidelity and MF estimators based on the original model parameterization.

42 ENGINEERING↗