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At least 1,063 records · Page 59

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DOE OSTI2015

Fine structure of the vaccinia virion determined by controlled degradation and immunolocalization

The vaccinia virion is a membraned, slightly flattened, barrel-shaped particle, with a complex internal structure featuring a biconcave core flanked by lateral bodies. Although the architecture of the purified mature virion has been intensely characterized by electron microscopy, the distribution of the proteins within the virion has been examined primarily using biochemical procedures. Thus, it has been shown that non-ionic and ionic detergents combined or not with a sulfhydryl reagent can be used to disrupt virions and, to a limited degree, separate the constituent proteins in different fractions. Applying a controlled degradation technique to virions adsorbed on EM grids, we were able to immuno-localize viral proteins within the virion particle. Our results show after NP40 and DTT treatment, membrane proteins are removed from the virion surface revealing proteins that are associated with the lateral bodies and the outer layer of the core wall. Combined treatment using high salt and high DTT removed lateral body proteins and exposed proteins of the internal core wall. Cores treated with proteases could be disrupted and the internal components were exposed. Cts8, a mutant in the A3 protein, produces aberrant virus that, when treated with NP-40 and DTT, releases to the exterior the virus DNA associated with other internal core proteins. With these results, we are able to propose a model for the structure the vaccinia virion.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2020

Dynamic Atom Clusters on AuCu Nanoparticle Surface During CO Oxidation

Supported alloy nanoparticles are prevailing alternative low-cost catalysts for both heterogeneous and electrochemical catalytic processes. Selective interaction of an alloy component with a specific reactant induces a dynamic structural change of alloy nanoparticles under reaction conditions and largely controls their catalytic properties. However, such a multi-component dynamic-interaction-controlled evolution, both structural and chemical, remains far from clear. Herein, by using state-of-the-art environmental TEM, we directly visualize, in-situ at the atomic scale, the evolution of an AuCu alloy nanoparticle supported on CeO2 during CO oxidation. We find that gas molecules can “free” metal atoms on the {001} surface and form highly mobile atom clusters. Remarkably, we discover that CO exposure induces Au segregation and activation on nanoparticle surface, while O2 exposure leads to the segregation and oxidation of Cu on the particle surface. The as-formed Cu2O/AuCu interface may facilitate CO-O interaction corroborated by DFT calculations. These findings provide insights into the atomistic mechanisms on alloy nanoparticles during catalytic CO oxidation reaction, and to a broad scope of rational design of alloy nanoparticle catalysts.

Luo, Langli↗

DOE OSTI2025

Generative AI for design of nanoporous materials: review and future prospects

Generative artificial intelligence (AI) is emerging as a powerful tool for advancing the design of nanoporous materials such as metal–organic frameworks, covalent–organic frameworks, and zeolites. These materials have potential application in important areas such as carbon capture, catalysis, gas storage, chemical separation, and drug delivery due to their modular, tunable structures, and their performance in these areas depends on precise control over their structure, chemical functionalities, and properties. Herein, we provide a review of generative AI algorithms that are emerging as powerful tools for the design of nanoporous materials, namely generative adversarial networks, variational autoencoders, diffusion models, genetic algorithms, reinforcement learning, and large language models. Some models are particularly good at generating diverse and high-quality designs, while others excel at exploring large design spaces or optimizing materials with desired properties. Certain algorithms also allow for efficient transitions between different designs, and some offer versatility in generating materials based on textual input. We discuss the advantages, limitations, and applications of these algorithms in porous material design and emphasize the future potential of integrating AI with experimental workflows to accelerate the development and validation of AI-generated materials.

36 MATERIALS SCIENCE↗

DOE OSTI2015

Design of band pass filter in a modulated magnetic graphene superlattice

Electronic transport of graphene through a modulated magnetic superlattice where the barrier heights present Gaussian profile is studied. It is found that the incident electron could be completely transmitted in the miniband regions and be completely reflected in the bandgap regions. The results suggest an application of the structure as an effectively band pass filter, which can be controlled by the structural parameters. It is concluded that the positions of miniband and bandgap are robust to the Gaussian variation of barrier heights. The effect of this modulated magnetic superlattice is also available for the conventional electrons described by Schrödinger equation.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2015

Structural analysis of DNA binding by C.Csp231I, a member of a novel class of R-M controller proteins regulating gene expression

The structure of the new class of controller proteins (exemplified by C.Csp231I) in complex with its 21 bp DNA-recognition sequence is presented, and the molecular basis of sequence recognition in this class of proteins is discussed. An unusual extended spacer between the dimer binding sites suggests a novel interaction between the two C-protein dimers. In a wide variety of bacterial restriction–modification systems, a regulatory ‘controller’ protein (or C-protein) is required for effective transcription of its own gene and for transcription of the endonuclease gene found on the same operon. We have recently turned our attention to a new class of controller proteins (exemplified by C.Csp231I) that have quite novel features, including a much larger DNA-binding site with an 18 bp (∼60 Å) spacer between the two palindromic DNA-binding sequences and a very different recognition sequence from the canonical GACT/AGTC. Using X-ray crystallography, the structure of the protein in complex with its 21 bp DNA-recognition sequence was solved to 1.8 Å resolution, and the molecular basis of sequence recognition in this class of proteins was elucidated. An unusual aspect of the promoter sequence is the extended spacer between the dimer binding sites, suggesting a novel interaction between the two C-protein dimers when bound to both recognition sites correctly spaced on the DNA. A U-bend model is proposed for this tetrameric complex, based on the results of gel-mobility assays, hydrodynamic analysis and the observation of key contacts at the interface between dimers in the crystal.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2022

Influence on Structural Loading of a Wave Energy Converter by Controlling Variable-Geometry Components and the Power Take-Off

Oceans are harsh environments and can impose significant loads on deployed structures. The deployment of wave energy converters (WECs) faces a design challenge with apparently contradictory goals. A WEC should be designed to maximize the energy absorbed while ensuring the operating wave condition does not exceed the failure limits of the device itself. Therefore, the loads endured by the support structure are a design constraint for the system. Adaptability to different sea states is, therefore, highly desirable. This work uses a WEC-Sim model of a variable-geometry oscillating wave energy converter (VGOSWEC) mounted on a support structure simulated under different wave scenarios. A VGOSWEC resembles a paddle pitching about a fixed hinge perpendicular to the incoming wave fronts. Therefore, the hinge experiences loads perpendicular to its axis as it maintains its position. The geometry of the VGOSWEC is varied by opening a series of controllable flaps on the pitching paddle when the structure experiences threshold loads. Because opening the flaps lets the waves transmit through the paddle, it is hypothesized that opening the flaps should result in load shedding at the base of the support structure. The load shedding is achieved by reducing the moments about the hinge axis. This work compares the hydrodynamic coefficients, natural periods, and response amplitude operators from completely closed to completely open configurations of the controllable flaps. The comparisons quantify the effects of letting the waves transmit through the VGOSWEC. This work shows that the completely open configuration can reduce the pitch and surge loads on the base of the support structure by as much as 80%. It was observed that at the paddle's resonance frequency, the loads on the structure increased substantially. This increase in loads can be mitigated by a rotational power take-off damping about the hinge axis. Changing the rotational power take-off damping was identified as an additional design parameter that can be used to control the loads experienced by the WEC's support structure.

fixed and floating structures↗

DOE OSTI2014

Modulation of Active Site Electronic Structure by the Protein Matrix to Control [NiFe] Hydrogenase Reactivity

Control of the reactivity of the nickel center of the [NiFe] hydrogenase and other metalloproteins commonly involves outer coordination sphere ligands that act to modify the geometry and physical properties of the active site metal centers. We carried out a combined set of classical molecular dynamics and quantum/classical mechanics calculations to provide quantitative estimates of how dynamic fluctuations of the active site within the protein matrix modulate the electronic structure at the catalytic center. Specifically we focused on the dynamics of the inner and outer coordination spheres of the cysteinate-bound Ni–Fe cluster in the catalytically active Ni-C state. There are correlated movements of the cysteinate ligands and the surrounding hydrogen-bonding network, which modulate the electron affinity at the active site and the proton affinity of a terminal cysteinate. On the basis of these findings, we hypothesize a coupling between protein dynamics and electron and proton transfer reactions critical to dihydrogen production.

[NiFe] hydrogenase↗

DOE OSTI2020

The Structural Basis of T4 Phage Lysis Control: DNA as the Signal for Lysis Inhibition

Optimal phage propagation depends on the regulation of the lysis of the infected host cell. In T4 phage infection, lysis occurs when the holin protein (T) forms lesions in the host membrane. However, the lethal function of T can be blocked by an antiholin (RI) during lysis inhibition (LIN). LIN sets if the infected cell undergoes superinfection, then the lysis is delayed until host/phage ratio becomes more favorable for the release of progeny. It has been thought that a signal derived from the superinfection is required to activate RI. Here we report structures that suggest a radically different model in which RI binds to T irrespective of superinfection, causing it to accumulate in a membrane as heterotetrameric 2RI–2T complex. Moreover, we show the complex binds non-specifically to DNA, suggesting that the gDNA from the superinfecting phage serves as the LIN signal and that stabilization of the complex by DNA binding is what defines LIN. Finally, we show that soluble domain of free RI crystallizes in a domain-swapped homotetramer, which likely works as a sink for RI molecules released from the RI–T complex to ensure efficient lysis. These results constitute the first structural basis and a new model not only for the historic LIN phenomenon but also for the temporal regulation of phage lysis in general.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2013

A carbon foam with a bimodal micro–mesoporous structure prepared from larch sawdust for the gas-phase toluene adsorption

Highlights: ► Network carbon foam containing a bimodal pore distribution was prepared from Larch. ► Liquefaction route was used for the preparation of morphology controllable carbon. ► Pore structure of carbon foam was controlled through KOH activation. - Abstract: A carbon foam with a bimodal micro–mesopore distribution, was prepared by submitting larch sawdust to liquefaction, resinification, foaming, carbonization and KOH activation. The morphology, pore texture and crystal microstructure was characterized by scanning and transmission electron microscopy, nitrogen adsorption analysis and X-ray powder diffraction. A honeycomb structure with adjacent cells was observed for the precursor of carbon foam. After KOH activation, the cell wall of precursor shrunk and broke. This lead to the formation of a well-connected 3D network and developed ligament pore structure (surface area of 554–1918 m{sup 2}/g) containing bimodal pores, 2.1 and 3.9 nm in diameter. The porous carbon foam prepared at 700 °C exhibited a much higher gas-phase toluene removal than commercial activated carbon fiber owing to the 3D network and bimodal pore structure.

36 MATERIALS SCIENCE↗

DOE OSTI2014

The filamentary structure of mixing fronts and its control on reaction kinetics in porous media flows

We investigate the effective kinetics of a reaction front for mixing limited bimolecular reaction $A+B\rightarrow C$ in a porous medium. While Fickian diffusion predicts a scaling of the cumulative mass produced as $M_C \propto t^{1/2}$, we observe two time regimes in which the total product mass evolves faster then $t^{1/2}$. At early times the invading solute is organized in fingers of high velocity. Reactions take place only at the fingers boundaries whose surface grows linearly in time. We show that this configuration leads to a mass scaling $M_C \propto t^2$. When diffusion mixes reactants and destroy these finger structures, the effective reaction rate slows down and we relate it to the longitudinal advective spreading providing $M_C \propto \sigma_x$. The transition time between these two regimes is characterized by the diffusion time over the transverse fingers cross section.

reactive transport, multiscale methods, smoothed p↗

DOE OSTI2026

Controlled Placement of Trivalent Heteroatoms in MFI Zeolite Frameworks Using Structure-Directing Agents

MFI zeolites contain distinct confining pore environments, either smaller (∼0.55 nm) channels or larger (∼0.70 nm) intersections. The substitution of trivalent heteroatoms generates Brønsted acid sites of varying acid strength, which, together with their location within different pore environments, dictates the stability of transition states via electrostatic (ion-pair) and van der Waals interactions. Here, we report that structure-directing agents (SDAs) that control Al 3+ substitutional patterns during MFI crystallization analogously position other trivalent heteroatoms (Ga 3+ , Fe 3+ , B 3+ ), altering the distribution of acid sites between channels and intersections, as probed by low-temperature (403 K) toluene methylation kinetics. Heteroatom-substituted MFI crystallized with tetrapropylammonium result in low selectivity toward p-xylene (<30%), while those crystallized using (co-)SDAs containing peripheral hydrogen-bonding groups (e.g., ethylenediamine) show high p-xylene selectivity (∼80%). These selectivities are consistent with DFT-calculated Gibbs free energy barriers for intersection-dominant and channel-dominant active site distributions, respectively. Transition states to form each xylene isomer are similar in size and charge; thus, their rate constants decrease with acid strength similarly, causing isomer selectivity to depend strongly on confinement but not on acid strength. These generalizable synthetic strategies enable independently controlling acid site strength and location in MFI zeolites and, in turn, catalytic rates and selectivities.

36 MATERIALS SCIENCE↗

DOE OSTI2014

A Visual Analytics Approach to Structured Data Analysis to Enhance Nonproliferation and Arms Control Verification Activities

Analysis activities for Nonproliferation and Arms Control verification require the use of many types of data. Tabular structured data, such as Excel spreadsheets and relational databases, have traditionally been used for data mining activities, where specific queries are issued against data to look for matching results. The application of visual analytics tools to structured data enables further exploration of datasets to promote discovery of previously unknown results. This paper discusses the application of a specific visual analytics tool to datasets related to the field of Arms Control and Nonproliferation to promote the use of visual analytics more broadly in this domain. Visual analytics focuses on analytical reasoning facilitated by interactive visual interfaces (Wong and Thomas 2004). It promotes exploratory analysis of data, and complements data mining technologies where known patterns can be mined for. Also with a human in the loop, they can bring in domain knowledge and subject matter expertise. Visual analytics has not widely been applied to this domain. In this paper, we will focus on one type of data: structured data, and show the results of applying a specific visual analytics tool to answer questions in the Arms Control and Nonproliferation domain. We chose to use the T.Rex tool, a visual analytics tool developed at PNNL, which uses a variety of visual exploration patterns to discover relationships in structured datasets, including a facet view, graph view, matrix view, and timeline view. The facet view enables discovery of relationships between categorical information, such as countries and locations. The graph tool visualizes node-link relationship patterns, such as the flow of materials being shipped between parties. The matrix visualization shows highly correlated categories of information. The timeline view shows temporal patterns in data. In this paper, we will use T.Rex with two different datasets to demonstrate how interactive exploration of the data can aid an analyst with arms control and nonproliferation verification activities. Using a dataset from PIERS (PIERS 2014), we will show how container shipment imports and exports can aid an analyst in understanding the shipping patterns between two countries. We will also use T.Rex to examine a collection of research publications from the IAEA International Nuclear Information System (IAEA 2014) to discover collaborations of concern. We hope this paper will encourage the use of visual analytics structured data analytics in the field of nonproliferation and arms control verification. Our paper outlines some of the challenges that exist before broad adoption of these kinds of tools can occur and offers next steps to overcome these challenges.

arms control↗

DOE OSTI2014

Decoupling the Geometric Parameters of Shape-Controlled Pd Nanocatalysts

The structural features of metal nanoparticles such as crystallite size and shape are important to catalytic activity and selectivity. Thus, correlating the performance of metal nanocatalysts to these structural features is important to understanding and designing better catalysts. The size and shape effects of Pd nanocrystals are examined as they are applied as semihydrogenation catalysts. Seed-mediated growth methods were used to achieve samples composed of different-sized {100}-terminated Pd nanocubes and {111}-terminated Pd nanoctahedra, which served as model systems to evaluate the role of surface structure to activity and selectivity. The size of the nanocrystals was easily tuned by controlling the amount of metal deposited per seed. The selection of capping agent provided a means of manipulating the final shape of the nanocrystals. Finally, the catalysis results from this study will facilitate the decoupling of the size and shape contributions to the geometric parameters of Pd nanocatalysts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Design, modeling and experimental validation of a micro cantilever beam with an electro-controllable twisting ability

The structure design of micro cantilever beams (MCBs), which has a significant effect on MCBs' controllable actuation range, is usually restricted by the establishment of the inner electric circuit. This paper proposes the design of a micro electro-controllable twisting cantilever beam (METCB). The architecture and the fabrication diagram of the proposed METCB are presented before its features are theoretically and experimentally validated. In detail, the analytical validation includes a sequence of two models: electro-thermal and thermo-mechanical. Through these two models, the thermal distribution along the METCB and the deformation brought by the thermal distribution are investigated, respectively. On the basis of the design and equations, the METCB samples have been manufactured using a planar deposition technique with an e-beam evaporator. Two in-site experiments are then conducted to sequentially figure out the upper voltage limit of the inner electric circuit and the maximum temperature limit of the METCB. Finally, another experiment is carried out to explore the relation between the applied voltage and the relative twisting angle of the METCB sample. Here, the theoretical prediction and the observed experiment result both prove the feasibility of the proposed METCB and its electro-controllable twisting ability.

36 MATERIALS SCIENCE↗

DOE OSTI2015

Chemical Frustration: A Design Principle for the Discovery of New Complex Alloy and Intermetallic Phases (Final Report)

A limiting factor in the design of new metallic materials for energy applications is the inability to predict or control the crystal structures of intermetallic phases. These compounds exhibit an immense structural diversity, which continues to expand with progress in synthetic exploration. In this project, a concept has been developed through experimental and theoretical endeavors to explain and predict how complex structures can arise in these systems: chemical frustration. Competing interactions were induced synthetically through the selection of ternary combinations of elements, in which incompatibilities are anticipated to arise between the preferred bonding or packing modes of the binary subsystems. These experiments led to a variety of new compounds which were structurally characterized and interpreted in terms of the chemical frustration concept. Theoretical models based on Density Functional Theory (DFT) and semiempircal tightbinding calculations were also developed to account for new compounds encountered during these experimental investigations, as well as relevant intermetallic structures in the literature. Examples include the μ3-acidity model and the reversed approximation Molecular Orbital approach. This research has contributed to the field by proposing an approach to navigating the structural diversity of intermetallics, which has long been difficult to explain or control, and demonstrating its usefulness in the discovery of new compounds. At the same time, it has provided new tools for explaining structural phenomena in metals and forged deeper connections between the fields of materials and molecular chemistry. In terms of technical effectiveness and economic feasibility, the chemical frustration approach is promising. Several of the compounds discovered illustrate the structural features expected for frustration, and can be prepared simply from the elemental metals as thermodynamically stable phases. The future effectiveness of this approach will require criteria for reliably determining which systems will yield chemically-frustrated phases, and which will result in simple phase segregation. One outcome of the project is the refined guidelines for identifying such systems, which will be tested in future research. In addition to the scientific impacts of this research, there are also long-term benefits to the public: this project has opened routes to compounds based on intergrowths of simple intermetallics. When applied to the intergrowth of intermetallic phases with useful properties, this approach could yield new functional composites whose nanostructuring is extremely resilient as it is dictated by thermodynamics.

36 MATERIALS SCIENCE↗

DOE OSTI2017

Robust Structural Analysis and Design of Distributed Control Systems to Prevent Zero Dynamics Attacks

We consider the design and analysis of robust distributed control systems (DCSs) to ensure the detection of integrity attacks. DCSs are often managed by independent agents and are implemented using a diverse set of sensors and controllers. However, the heterogeneous nature of DCSs along with their scale leave such systems vulnerable to adversarial behavior. To mitigate this reality, we provide tools that allow operators to prevent zero dynamics attacks when as many as p agents and sensors are corrupted. Such a design ensures attack detectability in deterministic systems while removing the threat of a class of stealthy attacks in stochastic systems. To achieve this goal, we use graph theory to obtain necessary and sufficient conditions for the presence of zero dynamics attacks in terms of the structural interactions between agents and sensors. We then formulate and solve optimization problems which minimize communication networks while also ensuring a resource limited adversary cannot perform a zero dynamics attacks. Polynomial time algorithms for design and analysis are provided.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2012

Quantitative investigation of the tensile plastic deformation characteristic and microstructure for friction stir welded 2024 aluminum alloy

The effect of the microstructure heterogeneity on the tensile plastic deformation characteristic of friction stir welded (FSW) 2024 aluminum alloy was investigated for the potential applications on light weight design of vehicles. The microstructure characteristics of the FSW joints, such as the grain structure, dislocation density and the distribution of precipitation, were studied by electron backscattered diffraction (EBSD) and transmission electron microscopy (TEM). The tensile deformation characteristic of the FSW joints was examined using the automatic strain measuring system (ASAME) by mapping the global and local strain distribution, and then was analyzed by mechanics calculation. It is found that the tensile deformation of the FSW joints is highly heterogeneous leading to a significant decrease in global ductility. The FSW joints mainly contain two typical deformation zones, which show great effect on the regional inhomogeneous deformation. One is the nugget zone (NZ) with a region of 8 mm in width, and the other is part of the BM with a region of 10 mm in width. The BM of the joints is the weakest region where the strain localizes early and this localization extends until fracture with a strain over 30%, while the strain in the NZ is only 4%. Differences in regional strain of FSW joints, which are essentially controlled by grain structure, the distribution of precipitation and dislocation density, result in decrease on the overall mechanical properties. - Highlights: Black-Right-Pointing-Pointer Microstructure heterogeneity of welds on tensile deformation behavior is studied. Black-Right-Pointing-Pointer The welds contain two typical deformation zones, affecting the global ductility. Black-Right-Pointing-Pointer Regional strain of welds is controlled by grain structure and dislocation density. Black-Right-Pointing-Pointer Theoretical calculation is in good agreement with experimental result.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Characterization of MoS 2 films via simultaneous grazing incidence X-ray diffraction and grazing incidence X-ray fluorescence (GIXRD/GIXRF)

Physical vapor deposited (PVD) molybdenum disulfide (nominal composition MoS 2 ) is employed as a thin film solid lubricant for extreme environments where liquid lubricants are not viable. The tribological properties of MoS 2 are highly dependent on morphological attributes such as film thickness, orientation, crystallinity, film density, and stoichiometry. These structural characteristics are controlled by tuning the PVD process parameters, yet undesirable alterations in the structure often occur due to process variations between deposition runs. Nondestructive film diagnostics can enable improved yield and serve as a means of tuning a deposition process, thus enabling quality control and materials exploration. Grazing incidence X-ray diffraction (GIXRD) for MoS 2 film characterization provides valuable information about film density and grain orientation (texture). However, the determination of film stoichiometry can only be indirectly inferred via GIXRD. The combination of density and microstructure via GIXRD with chemical composition via grazing incidence X-ray fluorescence (GIXRF) enables the isolation and decoupling of film density, composition, and microstructure and their ultimate impact on film layer thickness, thereby improving coating thickness predictions via X-ray fluorescence. We have augmented an existing GIXRD instrument with an additional X-ray detector for the simultaneous measurement of energy-dispersive X-ray fluorescence spectra during the GIXRD analysis. This combined GIXRD/GIXRF analysis has proven synergetic for correlating chemical composition to the structural aspects of MoS 2 films provided by GIXRD. We present the usefulness of the combined diagnostic technique via exemplar MoS 2 film samples and provide a discussion regarding data extraction techniques of grazing angle series measurements.

MoS2↗