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At least 253 records · Page 14

In vitro investigation of protein assembly by combined microscopy and infrared spectroscopy at the nanometer scale

The nanoscale structure and dynamics of proteins on surfaces has been extensively studied using various imaging techniques, such as transmission electron microscopy and atomic force microscopy (AFM) in liquid environments. These powerful imaging techniques, however, can potentially damage or perturb delicate biological material and do not provide chemical information, which prevents a fundamental understanding of the dynamic processes underlying their evolution under physiological conditions. Here, we use a platform developed in our laboratory that enables acquisition of infrared (IR) spectroscopy and AFM images of biological material in physiological liquids with nanometer resolution in a cell closed by atomically thin graphene membranes transparent to IR photons. In this work, we studied the self-assembly process of S-layer proteins at the graphene-aqueous solution interface. The graphene acts also as the membrane separating the solution containing the proteins and Ca 2+ ions from the AFM tip, thus eliminating sample damage and contamination effects. The formation of S-layer protein lattices and their structural evolution was monitored by AFM and by recording the amide I and II IR absorption bands, which reveal the noncovalent interaction between proteins and their response to the environment, including ionic strength and solvation. Our measurement platform opens unique opportunities to study biological material and soft materials in general.

59 BASIC BIOLOGICAL SCIENCES↗

Developing a Digital Twin for SRF Cavity Assembly at Fermilab

When assembling Superconducting Radio Frequency (SRF) Cavities, maintaining an environment devoid of particulates like dust and other small particles is essential. If a single spec of dust enters the cavity a significant degradation of performance can occur. To avoid a cavity failure Fermilab assembles the SRF cavities within a ISO-4 (Class 10) environment. This environment though is still susceptible to foreign contaminants when technicians enter and new components are added to the cleanroom. To reduce the risk even more Fermilab has introduced a cobot manipulator into the cleanroom environment to speed up the assembly time which will reduce the time that the technicians operate in the cleanroom. But, this still leaves the potential of contaminants to enter the cleanroom if new components need to be tested within the cleanroom. This project aims to lay the groundwork to develop a Digital Twin environment of the cleanroom to aid in manufacturing processes and testing. In its simplest form, a digital twin is a bidirectional link between a physical system and its digital counterpart or twin. NVIDIA Isaac Sim is used as the digital twin foundation for the digital representation of the cleanroom, specifically for the UR16e assembly area. A simulated UR16e was used to validate the performance of Isaac Sim as a testing environment by comparing the tool center points (TCP) positional data between the simulated and digital representation of the UR16e. Due to a new vision based robotic assembly process being introduced to the cleanroom a digital representation of the physical camera was tested and validated to ensure that it will produce close to the same outcome as the physical environment. The TCP comparison results showed a peak translational error of approximately 0.1mm and rotational errors of up to 8 between the simulated and digital UR16es. While the camera validation performed with high repeatability across multiple runs, it still requires minor tuning before it can accurately replicate a physical camera.

Imburgia, Joseph [Northern Illinois U.]↗

Supramolecular Assembly of Lanthanide-Binding Tag Peptides for Aqueous Separation of Rare Earth Elements

Selective and eco-friendly separation and purification methods for rare earth elements (REEs) are necessary to meet the increasing demand for these valuable metals, which are extensively used in modern electronics and clean energy technologies. Mining feedstocks consist of REE mixtures as stable trivalent cations (Ln 3+ ) that are difficult to separate due to their identical charge and similar size. Lanthanide-binding tags (LBTs), peptide chelates that coordinate Ln 3+ in binding pockets, show promise as selective, high-affinity extractants. We demonstrate that the LBT variant LBTLLA 5– , designed for high selectivity for Tb 3+ , is an effective extractant, forming complexes with REEs in solution that subsequently organize into self-assembling structures rich in Ln 3+ . These structures condense into aggregates that can be separated, enabling an efficient, all-aqueous, eco-friendly separation process. The self-assembled structures are studied using dynamic light scattering, ζ-potential measurements, transmission electron microscopy, anomalous small-angle X-ray scattering, inductively coupled plasma optical emission spectroscopy, and ultraviolet–visible absorption spectroscopy, which confirm LBTLLA 5– peptide-REE ion binding and the further assembly of micron-scale structures rich in REEs. Molecular dynamics simulations reveal the interactions promoting aggregation as well as the integrity of the binding pocket upon self-assembly. We find that LBTLLA 5– :Ln 3+ complexes recruit excess cations within the macrostructures, and we demonstrate that aggregation and selective separation can be controlled by manipulating the metal-peptide ratio in solution. Furthermore, we demonstrate separation from equimolar mixtures of REE pairs Tb 3+ -Lu 3+ and Tb 3+ -La 3+ , supporting the application of LBT peptides as a platform for the selective separation of REEs.

LBT peptides↗

Systems and methods for assessing cable insulation

Methods for assessing cable insulation are provided that can include engaging a first tine gap interdigital capacitor assembly with the exterior of the cable jacket to determine a first capacitance and dissipation factor value of the insulation using the first tine gap interdigital capacitor assembly; engaging a second tine gap interdigital capacitor assembly with the exterior of the cable jacket to determine a second capacitance and dissipation factor value of the insulation using the second tine gap interdigital capacitor assembly.Systems for assessing cable insulation are also provided. The systems can include a cable jacket encompassing cable insulation and conductive material; at least two tine gap interdigital capacitor assemblies engaged with the cable jacket; and processing circuitry operatively engaged with the capacitor assemblies.

Glass, III, Samuel W.↗

Manipulating nanoscale structure to control functionality in printed organic photovoltaic, transistor and bioelectronic devices

Printed electronics is simultaneously one of the most intensely studied emerging research areas in science and technology and one of the fastest growing commercial markets in the world today. For the past decade the potential for organic electronic (OE) materials to revolutionize this printed electronics space has been widely promoted. Such conviction in the potential of these carbon-based semiconducting materials arises from their ability to be dissolved in solution, and thus the exciting possibility of simply printing a range of multifunctional devices onto flexible substrates at high speeds for very low cost using standard roll-to-roll printing techniques. However, the transition from promising laboratory innovations to large scale prototypes requires precise control of nanoscale material and device structure across large areas during printing fabrication. Maintaining this nanoscale material control during printing presents a significant new challenge that demands the coupling of OE materials and devices with clever nanoscience fabrication approaches that are adapted to the limited thermodynamic levers available. In this review we present an update on the strategies and capabilities that are required in order to manipulate the nanoscale structure of large area printed organic photovoltaic (OPV), transistor and bioelectronics devices in order to control their device functionality. This discussion covers a range of efforts to manipulate the electroactive ink materials and their nanostructured assembly into devices, and also device processing strategies to tune the nanoscale material properties and assembly routes through printing fabrication. The review finishes by highlighting progress in printed OE devices that provide a feedback loop between laboratory nanoscience innovations and their feasibility in adapting to large scale printing fabrication. The ability to control material properties on the nanoscale whilst simultaneously printing functional devices on the square metre scale is prompting innovative developments in the targeted nanoscience required for OPV, transistor and biofunctional devices.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Reactome and the Gene Ontology: digital convergence of data resources

Abstract Motivation Gene Ontology Causal Activity Models (GO-CAMs) assemble individual associations of gene products with cellular components, molecular functions and biological processes into causally linked activity flow models. Pathway databases such as the Reactome Knowledgebase create detailed molecular process descriptions of reactions and assemble them, based on sharing of entities between individual reactions into pathway descriptions. Results To convert the rich content of Reactome into GO-CAMs, we have developed a software tool, Pathways2GO, to convert the entire set of normal human Reactome pathways into GO-CAMs. This conversion yields standard GO annotations from Reactome content and supports enhanced quality control for both Reactome and GO, yielding a nearly seamless conversion between these two resources for the bioinformatics community. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗

Evaluation of Degradation Mechanisms for Solid Secondary Waste Grout Waste Forms

The overall objective of this work is to provide defensibility for the long-term performance of grouted Hanford SSW streams when disposed in a near surface disposal facility, IDF, on the Hanford Site. Providing defensibly for the long-term performance of the grouted waste forms is consistent with the research and development activities identified in the Performance Assessment Maintenance Plan, (Westcott et al. 2019), that are necessary to address the assumptions made in the PA. Specifically, this work addresses two areas identified for further research and development activities in the plan: (1) “Evaluate ongoing research on transport characteristics of cementitious materials using accelerated tests to approximate the effects of aging/alteration/weathering”; and (2) “Evaluate ongoing research on microbial effects on transport processes in cementitious materials.” The assembled subject matter expert team evaluated a list of degradation mechanisms and supporting processes and provided rankings of areas where further research and development (R&D) are needed. From this assessment, high priority R&D areas include: (1) the effects of carbonation, Ca leaching, and SSW dimensional change in grout waste forms; (2) updated model representations of grouted waste forms; and (3) scaled testing demonstrations. Moderate priority items including a paper study on possible microbial influence, reoxidation rates, radionuclide/contaminant dissolution from SSW in the grout and freeze thaw behavior. Other processes evaluated were either deemed unlikely to occur, to have little impact on the SSW waste forms, or to occur at time frames beyond those considered (>10,000 years). The assessments and proposed R&D approaches are expected to support an update to the WRPS SSW roadmap.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Novel Mechanisms for the Formation of Dislocation Cell Patterns in BCC Metal

In this study, we present the first simulation results of the formation of dislocation cell wall microstructures in tantalum subjected to shock loading. Dislocation patterns and cell wall formation are important to understanding the mechanical properties of the materials in which they spontaneously arise, and yet the processing and self-assembly mechanisms leading to their formation are poorly understood. By employing transmission electron microscopy and discrete dislocation dynamics, we propose a new mechanism involving coplanar dislocations and pseudo-dipole mixed dislocation arrays that is essential to the pattern formation process. Our large-scale 3D DDD simulations demonstrate the self-organization of dislocation networks into cell walls in deformed BCC metal (tantalum) persisting at strain ε = 20%. The simulation analysis captures several crucial aspects of how the dislocation cell pattern affects metal plasticity, as observed in experiments. Although experimental evidence is inconclusive regarding whether cell wall formation takes place at the shock front, after the shock, during release, or when the sample has had enough time to relax post-recovery, our simulations indicate cell wall formation occurs after the shock and before release. The extended Taylor hardening composite model effectively considers the non-uniform dislocation density when cell walls form and accurately describes the corresponding flow stress.

36 MATERIALS SCIENCE↗

Engineering Biomolecular Self–Assembly at Solid–Liquid Interfaces

Biomolecular self–assembly is a key process used by life to build functional materials from the “bottom up.” In the last few decades, bioengineering and bionanotechnology have borrowed this strategy to design and synthesize numerous biomolecular and hybrid materials with diverse architectures and properties. However, engineering biomolecular self–assembly at solid–liquid interfaces into predesigned architectures lags the progress made in bulk solution both in practice and theory. Here, recent achievements in programming self–assembly of peptides, proteins, and peptoids at solid–liquid interfaces are summarized and corresponding applications are described. Recent advances in the physical understandings of self–assembly pathways obtained using in situ atomic force microscopy are also discussed. Furthermore, these advances will lead to novel strategies for designing biomaterials organized at and interfaced with inorganic surfaces.

36 MATERIALS SCIENCE↗

On electrolyte wetting through lithium-ion battery separators

The wettability by electrolyte is a critical characteristic of lithium-ion battery separators since electrolyte absorption is essential for ionic transport. Most importantly, fast absorption of electrolyte facilitates the electrolyte filling and wetting processes during the battery assembly. However, theoretical or experimental investigation of separator wettability has rarely been reported, and thus very little quantitative data can be found in the existing literature. Here, innovative experimental techniques and associated analytical models have been developed to fully characterize the electrolyte wetting behavior through battery separators. Both in-plane and through-plane imbibition processes are investigated. The results show that, electrolyte needs significantly longer time to wet separators than it does for commercial electrodes. The wetting rate depends significantly on the pore size, porosity, and micro-structure of the separators. Electrolyte in-plane wetting is only observed in the separators manufactured by the wet process. Increasing separator porosity and pore size is shown to be substantially increasing through-plane wetting rate. In addition, ceramic coating is shown to increase in-plane wetting but retard through-plane wetting.

25 ENERGY STORAGE↗

MARIE: A Python-Based Framework for Comprehensive Fuel Recycling Modeling

One of the most pressing challenges to the continued deployment of nuclear energy systems is in the ultimate management and disposition of discharged fuel assemblies. While reprocessing and recovery of valuable materials from UNF assemblies has been considered as part of an overall strategy for minimization of the volume of reactor-based wastes to be managed, the deployment of commercial-scale reprocessing facilities presents an enormous economic challenge. The MARIE software package has been developed as a means of confronting this challenge. Representing components of a generic fuel reprocessing operation as individual physical processes, MARIE is designed as a modular framework intended to allow for analysis and cost-optimization for a hypothetical reprocessing facility while realistically accounting for the physical characteristics of the used fuel source term, such as decay heat, activity, and radiation dose (informing corresponding shielding requirements). Capabilities supported by MARIE include head-end operations such as fuel shearing, voloxidation, and dissolution; generic solvent extraction operations informed by available open-literature data; a suite of unit operations intended to represent electrochemical processing of used fuel assemblies (i.e., oxide reduction, electrorefining, and electrowinning); and finally, accounting for both costs and physical features of discharged waste streams, which can be used to inform follow-on analyses such as the feasibility of deep-borehole disposal of HLW. This paper presents an overview of the MARIE software capabilities, including how individual unit operations are implemented to enable a larger-scale optimization of a hypothetical reprocessing operation on aspects such as cost and recovery of valuable materials.

Skutnik, Steve [ORNL] (ORCID:000000016441135X)↗

Sub-100-fs energy transfer in coenzyme NADH is a coherent process assisted by a charge-transfer state

Excitation energy transfer (EET) is a key photoinduced process in biological chromophoric assemblies. Here we investigate the factors which can drive EET into efficient ultrafast sub-ps regimes. We demonstrate how a coherent transport of electronic population could facilitate this in water solvated NADH coenzyme and uncover the role of an intermediate dark charge-transfer state. High temporal resolution ultrafast optical spectroscopy gives a 54 ± 11 fs time constant for the EET process. Nonadiabatic quantum dynamical simulations computed through the time-evolution of multidimensional wavepackets suggest that the population transfer is mediated by photoexcited molecular vibrations due to strong coupling between the electronic states. The polar aqueous solvent environment leads to the active participation of a dark charge transfer state, accelerating the vibronically coherent EET process in favorably stacked conformers and solvent cavities. Our work demonstrates how the interplay of structural and environmental factors leads to diverse pathways for the EET process in flexible heterodimers and provides general insights relevant for coherent EET processes in stacked multichromophoric aggregates like DNA strands.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Standalone Block Copolymer Nanoballoons: Decoupling Self-Assembly from Implementation in Nanomanufacturing

Here we report a facile method to produce isolatable hollow-core elastomeric vesicles, “nanoballoons”, prepared via block copolymer self-assembly in a polymer blend. Poly(isoprene-block-dimethylsiloxane) (PI-PDMS) diblock copolymers are blended with PDMS homopolymers (h-PDMS) as a “solvent” phase to template the self-assembly of PDMS-tethered vesicles with PI walls. The walls are subsequently crosslinked to yield mechanically stabilized elastomeric vesicles. The h-PDMS inner-core and matrix are separated from the vesicles by dialysis to yield the matrix-free nanoballoons. These objects, 0.3 – 1 μm in diameter, can be further reincorporated into a crosslinkable PDMS. Throughout the self-assembly, recovery, and reincorporation processes we apply several techniques including solvent dispersion/dynamic light scattering (DLS) measurements, transmission electron microscopy (TEM)/energy-dispersive X-ray spectroscopy (EDS), and small-angle X-ray scattering (SAXS) to provide a consilient body of evidence that the nanoballoon morphology is retained. Furthermore, this work presents advanced nanomanufacturing schema that illustrate the decoupling of the thermodynamic and dynamic factors that govern macromolecular self-assembly from the environment in which the self-assembled objects are deployed.

36 MATERIALS SCIENCE↗

Coordinated Self-Assembly of Networked Microgrids Using Irving’s Algorithm

Abstract— Microgrid installations have regained significant interest, driven by the increasing adoption of distributed energy resources, decentralized controls, and ongoing technological advancements. While the number of microgrids increases, there are opportunities to coordinate networks of microgrids. In this study, Irving’s algorithm is applied to a framework for the coordinated self-assembly of networked microgrids. Compared with the authors’ previous work, this new study relaxes the constraint on participated microgrids to have a single global objective. Thus, each microgrid can rank others according to its local preference. This reduces the amount of shared information, improves the privacy, and enhances the flexibility. The adaptability to that proposed framework is also maintained. Examples are presented to illustrate the networking processes and self-assembly operations.

Xie, Jing↗

Controlled Pyrolysis: A Robust Scalable Composite Recycling Technology

The reinforced composites industry is facing significant challenges in handling the scrap composite material from automobile manufacturing, the wind turbine industry, and others. The fibers in the material, whether they be carbon, glass, or other materials have commercial value if they can be recovered successfully. Successfully means the fibers are clean with no sizing or other binders and have adequate strength and physical properties that would allow them to be economically reprocessed into valuable product. The composites recycling project was an industry-collaborative effort to develop a composite recycling technology using controlled pyrolysis. Through the recycling of scrap and end-of-life (EOL) cured composite materials, this pilot study was intended to create a business case by realizing a cost-effective means for recycling EOL and production scrap composite materials, ultimately reducing the volume of composite materials destined for landfill. The project was led by the Institute for Advanced Composites Manufacturing Innovation (IACMI), the American Composites Manufacturers Association (ACMA), Oak Ridge National Laboratory (ORNL), Continental Structural Plastics (CSP) a Teijin Group Company, CHZ Technologies, and A. Schulman with support from Owens Corning, John Deere, General Electric (GE), Ashland LLC, and Plastics Europe (CEFIC). The team studied and tested CHZ Technologies’ controlled pyrolysis system, known as the Thermolyzer TM , which operates on a scalable basis to convert organic polymer materials into a clean synthesis gas and char containing the recoverable carbon and glass fiber reinforcement. The recoverable energy contained in the input polymers creates the synthesis gas that can be used to provide heat to the Thermolyzer TM primary reactor in a sustainable manner. That is, once the Thermolyzer TM is started with a small amount of external natural gas, the synthesis gas that is created from the polymers will continue to operate the burners so long as feedstock is supplied. The reinforcing fiber materials remaining in the solid phase char were separated and cleaned for re-use in other polymer systems based on the retained properties of the fibers. The study created reports (attached in the appendix) on the Mass and Energy Balances, syngas analytics, VOC assessment, yield analysis and other analytics necessary for a Techno-Economic Analysis (TEA) to quantify the economic impact of the recovery and sustainable re-use of the carbon and glass fibers. The process consisted of 4 steps: Selection of 4 samples of cured composite waste materials from project partners interested in materials recycling and recovering the reinforcing fibers for best case re-use. The materials included glass fiber (GF) polyester/vinyl ester automotive SMC from CSP, GF epoxy balsa/PVC foam wind blades from GE, carbon fiber (CF) epoxy wind blade laminated spar caps from GE, and GF/CF epoxy hybrid assembly from John Deere. Processing the waste composite samples into 1-2” shreds. Packaging the shredded composites into bulk sacks on international shipping pallets for shipment to KUG in Forst (Lausitz), Germany. Pyrolysis of the shredded composites under controlled conditions designed for each polymer system. Collecting samples of the gas and char for analysis. Shipping the char containing the CF/GF back to the US for the next steps of testing the fibers and developing protocols for sustainable re-use of the fibers in composite applications.

36 MATERIALS SCIENCE↗

Linking the Salmonella enterica 1,2-Propanediol Utilization Bacterial Microcompartment Shell to the Enzymatic Core via the Shell Protein PduB

Bacterial microcompartments (MCPs) are protein-based organelles that house the enzymatic machinery for metabolism of niche carbon sources, allowing enteric pathogens to outcompete native microbiota during host colonization. While much progress has been made toward understanding MCP biogenesis, questions still remain regarding the mechanism by which core MCP enzymes are enveloped within the MCP protein shell. Here, we explore the hypothesis that the shell protein PduB is responsible for linking the shell of the 1,2-propanediol utilization (Pdu) MCP from Salmonella enterica serovar Typhimurium LT2 to its enzymatic core. Using fluorescent reporters, we demonstrate that all members of the Pdu enzymatic core are encapsulated in Pdu MCPs. We also demonstrate that PduB is critical for linking the entire Pdu enzyme core to the MCP shell. Using MCP purifications, transmission electron microscopy, and fluorescence microscopy, we find that shell assembly can be decoupled from the enzymatic core, as apparently empty MCPs are formed in Salmonella strains lacking PduB. Mutagenesis studies reveal that PduB is incorporated into the Pdu MCP shell via a conserved, lysine-mediated hydrogen bonding mechanism. Finally, growth assays and system-level pathway modeling reveal that unencapsulated pathway performance is strongly impacted by enzyme concentration, highlighting the importance of minimizing polar effects when conducting these functional assays. Together, these results provide insight into the mechanism of enzyme encapsulation within Pdu MCPs and demonstrate that the process of enzyme encapsulation and shell assembly are separate processes in this system, a finding that will aid future efforts to understand MCP biogenesis.

1, 2-propanediol utilization↗

Unveiling the nanoscale architectures and dynamics of protein assembly with in situ atomic force microscopy

Proteins play a vital role in different biological processes by forming complexes through precise folding with exclusive inter- and intra-molecular interactions. Understanding the structural and regulatory mechanisms underlying protein complex formation provides insights into biophysical processes. Furthermore, the principle of protein assembly gives guidelines for new biomimetic materials with potential applications in medicine, energy, and nanotechnology. Atomic force microscopy (AFM) is a powerful tool for investigating protein assembly and interactions across spatial scales (single molecules to cells) and temporal scales (milliseconds to days). It has significantly contributed to understanding nanoscale architectures, inter- and intra-molecular interactions, and regulatory elements that determine protein structures, assemblies, and functions. This review describes recent advancements in elucidating protein assemblies with in situ AFM. We discuss the structures, diffusions, interactions, and assembly dynamics of proteins captured by conventional and high-speed AFM in near-native environments and recent AFM developments in the multimodal high-resolution imaging, bimodal imaging, live cell imaging, and machine-learning-enhanced data analysis. These approaches show the significance of broadening the horizons of AFM and enable unprecedented explorations of protein assembly for biomaterial design and biomedical research.

36 MATERIALS SCIENCE↗