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DOE OSTI2015

An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system

Molecular interactions between proteins and DNA molecules underlie many cellular processes, including transcriptional regulation, chromosome replication, and nucleosome positioning. Computational analyses of protein-DNA interactions rely on experimental data characterizing known protein-DNA interactions structurally and biochemically. While many databases exist that contain either structural or biochemical data, few integrate these two data sources in a unified fashion. Such integration is becoming increasingly critical with the rapid growth of structural and biochemical data, and the emergence of algorithms that rely on the synthesis of multiple data types to derive computational models of molecular interactions. We have developed an integrated affinity-structure database in which the experimental and quantitative DNA binding affinities of helix-turn-helix proteins are mapped onto the crystal structures of the corresponding protein-DNA complexes. This database provides access to: (i) protein-DNA structures, (ii) quantitative summaries of protein-DNA binding affinities using position weight matrices, and (iii) raw experimental data of protein-DNA binding instances. Critically, this database establishes a correspondence between experimental structural data and quantitative binding affinity data at the single basepair level. Furthermore, we present a novel alignment algorithm that structurally aligns the protein-DNA complexes in the database and creates a unified residue-level coordinate system for comparing the physico-chemical environments at the interface between complexes. Using this unified coordinate system, we compute the statistics of atomic interactions at the protein-DNA interface of helix-turn-helix proteins. We provide an interactive website for visualization, querying, and analyzing this database, and a downloadable version to facilitate programmatic analysis. Lastly, this database will facilitate the analysis of protein-DNA interactions and the development of programmatic computational methods that capitalize on integration of structural and biochemical datasets. The database can be accessed at http://ProteinDNA.hms.harvard.edu.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2018

Influence of Chemistry and Misfit Dislocation Structure on Dopant Segregation at Complex Oxide Heterointerfaces

Complex oxide heterostructures and thin films have emerged as promising candidates for diverse applications. Lattice mismatch between the two oxides lead to the formation of misfit dislocations, which influence vital material features. Trivalent dopant segregation to misfit dislocations at semi-coherent oxide heterointerfaces, while not well understood, is anticipated to impact interface-governed properties. Atomistic simulations elucidating the influence of misfit dislocations on dopant segregation at SrTiO 3 /MgO heterointerfaces are reported. SrO- and TiO 2 -terminated interfaces that have differing misfit dislocation structure were considered for trivalent dopants segregation. At SrO-terminated interface, dopants tend to segregate toward but not precisely to the heterointerface, whereas at TiO 2 -terminated interface, dopants exhibit a thermodynamic preference to accumulate at the heterointerface. Most favorable segregation sites at SrO-terminated interface are located within the coherent terrace, whereas those at TiO 2 -terminated interface are at misfit dislocation intersections. Atomic layer chemistry and the resulting misfit dislocation structure at the heterointerface, along with concomitant strain at the heterointerface due to mismatched dopants, play a critical role in influencing the observed trends for dopant segregation. Overall, the present results offer a fundamental atomic scale perspective of dopant behavior at semi-coherent complex oxide heterointerfaces and the interplay between dopant chemistry, interface chemistry, and misfit dislocation structure.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2016

Thin sensing layer based on semi-conducting β-cyclodextrin rotaxane for toxic metals detection

Highlights: • Microwave-assisted synthesis of rotaxane based on anthracene and β-cyclodextrin. • Morphological and optical characterization of thin solid film. • Elaboration of impedimetric gold/rotaxane sensor. • Investigation of the membrane sensitivity towards Hg{sup 2+}, Cu{sup 2+} and Pb{sup 2+} cations. - Abstract: An impedimetric sensor based on a new semi-conducting rotaxane has been described for detection of toxic cations. The rotaxane, consists on a π-conjugated material encapsulated into β-cyclodextrin (β-CD); it has been synthesized via the Williamson reaction under microwaves irradiation. The supramolecular structure of the compound was confirmed by NMR and FT-IR spectroscopies. A thin solid film of the rotaxane was deposited by spin-coating to develop a new electrochemical sensor. The morphological properties of the organic membrane were evaluated using contact angle measurements and atomic force microscopy. The gold/rotaxane/solution interfaces were investigated by electrochemical impedance spectroscopy and the obtained data were fitted using an equivalent electrical circuit. The response of the gold/rotaxane membrane towards Hg{sup 2+}, Cu{sup 2+} and Pb{sup 2+} cations was studied and the results showed a good sensitivity to the mercury cations.

36 MATERIALS SCIENCE↗

DOE OSTI2016

Microstructure evolution of a dissimilar junction interface between an Al sheet and a Ni-coated Cu sheet joined by magnetic pulse welding

An Al sheet and a Ni-coated Cu sheet were lap joined by using magnetic pulse welding (MPW). Tensile tests were performed on the joined sheets, and a good lap joint was achieved at a discharge energy of > 0.9 kJ. The weld interface exhibited a wavy morphology and an intermediate layer along the weld interface. Microstructure observations of the intermediate layer revealed that the Ni coating region consisted of a Ni–Al binary amorphous alloy and that the Al sheet region contained very fine Al nanograins. Ni fragments indicative of unmelted residual Ni from the coating were also observed in parts of the intermediate layer. Formation of these features can be attributed to localize melting and a subsequent high rate cooling of molten Al and Ni confined to the interface during the MPW process. In the absence of an oxide film, atomic-scale bonding was also achieved between the intermediate layer and the sheet surfaces after the collision. MPW utilises impact energy, which affects the sheet surfaces. From the obtained results, good lap joint is attributed to an increased contact area, the anchor effect, work hardening, the absence of an oxide film, and suppressed formation of intermetallic compounds at the interface. - Highlights: •Good lap joint of an Al sheet and a Ni-coated Cu sheet was achieved by using magnetic pulse welding. •A Ni–Al binary amorphous alloy was formed as an intermediate layer at weld interface. •Atomic-scale bonding was achieved between the intermediate layer and the sheet surfaces.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Probing electronic and dielectric properties of ultrathin Ga 2 O 3 /Al 2 O 3 atomic layer stacks made with in vacuo atomic layer deposition

Ultrathin (1–4 nm) films of wide-bandgap semiconductors are important to many applications in microelectronics, and the film properties can be sensitively affected by defects especially at the substrate/film interface. Motivated by this, an in vacuo atomic layer deposition (ALD) was developed for the synthesis of ultrathin films of Ga 2 O 3 /Al 2 O 3 atomic layer stacks (ALSs) on Al electrodes. It is found that the Ga 2 O 3 /Al 2 O 3 ALS can form an interface with the Al electrode with negligible interfacial defects under the optimal ALD condition whether the starting atomic layer is Ga 2 O 3 or Al 2 O 3 . Such an interface is the key to achieving an optimal and tunable electronic structure and dielectric properties in Ga 2 O 3 /Al 2 O 3 ALS ultrathin films. In situ scanning tunneling spectroscopy confirms that the electronic structure of Ga 2 O 3 /Al 2 O 3 ALS can have tunable bandgaps (E g ) between ~2.0 eV for 100% Ga 2 O 3 and ~3.4 eV for 100% Al 2 O 3 . With variable ratios of Ga:Al, the measured E g exhibits significant non-linearity, agreeing with the density functional theory simulation, and tunable carrier concentration. Furthermore, the dielectric constant of ultrathin Ga 2 O 3 /Al 2 O 3 ALS capacitors is tunable through the variation in the ratio of the constituent Ga 2 O 3 and Al 2 O 3 atomic layer numbers from 9.83 for 100% Ga 2 O 3 to 8.28 for 100% Al 2 O 3 . The high ε leads to excellent effective oxide thickness ~1.7–2.1 nm for the ultrathin Ga 2 O 3 /Al 2 O 3 ALS, which is comparable to that of high-K dielectric materials.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Bottlebrush Block Copolymer Thin Films

The self-assembly of block copolymers (BCPs) in thin films is governed by interfacial interactions (enthalpy) between the blocks and interfaces (at both the substrate and the surface). Advantage can also be taken of entropy to control the polymer orientation. Here, we synthesized a series of bottlebrush block copolymers (BBCPs), with deuterated polystyrene (DPS) as the core block and poly(solketal acrylate) (PSA) as the corona block, where the backbone length (N BB) and grafting densities (GDs) were varied. The hydrophobic PSA block was converted to a hydrophilic poly(glyceryl acrylate) (PGA) block by solid-state hydrolysis, bringing the BBCP from a disordered state into an ordered state with a lamellar microdomain morphology. The orientation of the morphology as a function of distance from the interfaces was systematically investigated by atomic force microscopy (AFM), interference microscopy, grazing-incidence small-angle X-ray scattering (GISAXS), and grazing-incidence small angle neutron scattering (GISANS). For N BB = 1 (diblock BCP), a mixed lamellar orientation was found. For N BB = 5 (star-like BBCP), a vertical orientation of the lamellar microdomains was found dominantly at the interfaces that propagated into the bulk of the film due to the entropic penalty associated with constraints on the junction points. Increasing the N BB to 50 (rod-like BBCP) and 100 (worm-like BBCP) yielded a random orientation, as the side chains became overcrowded when aligned in the same direction. By reducing the grafting density (GD) of a N BB = 50 BBCP from 100% to 75% and 50% by the incorporation of spacers into the backbone, the steric hindrance of side chains is reduced markedly, facilitating a vertical orientation of the lamellar microdomains. However, the vertical orientation becomes more random within the bulk of the thin film for different BBCP architectures. By modifying the substrate with a layer of PS, the preferential interactions between the core block of the BBCP and the interfaces induce a reconfiguration of the BBCP, drawing the core block out to contact substrate directly driven by enthalpy. Under these conditions, N BB = 5 showed a predominantly parallel orientation of the lamellar microdomains with the corona block minimizing contact with the substrate. Higher N BB values of 50 and 100 showed a more random orientation of the lamellar microdomains at different depths on the PS-modified substrate. Overall, thin-film morphology was regulated by tuning the configuration of the BBCP, varying the entropic contribution to the microdomain orientation.

Chen, Zhan↗

DOE OSTI2022

Measuring and directing charge transfer in heterogenous catalysts

Abstract Precise control of charge transfer between catalyst nanoparticles and supports presents a unique opportunity to enhance the stability, activity, and selectivity of heterogeneous catalysts. While charge transfer is tunable using the atomic structure and chemistry of the catalyst-support interface, direct experimental evidence is missing for three-dimensional catalyst nanoparticles, primarily due to the lack of a high-resolution method that can probe and correlate both the charge distribution and atomic structure of catalyst/support interfaces in these structures. We demonstrate a robust scanning transmission electron microscopy (STEM) method that simultaneously visualizes the atomic-scale structure and sub-nanometer-scale charge distribution in heterogeneous catalysts using a model Au-catalyst/SrTiO 3 -support system. Using this method, we further reveal the atomic-scale mechanisms responsible for the highly active perimeter sites and demonstrate that the charge transfer behavior can be readily controlled using post-synthesis treatments. This methodology provides a blueprint for better understanding the role of charge transfer in catalyst stability and performance and facilitates the future development of highly active advanced catalysts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2016

Structural and Electronic Properties of Interfaces in Graphene and Hexagonal Boron Nitride Lateral Heterostructures

The in-plane heterostructures composed of graphene and hexagonal boron nitride (G/BN), as the first kind of two-dimensional metal/semiconductor heterostructures of one-atom thickness, are attractive for both fundamental low-dimensional physics and nanoscale devices because of the tailorable electronic properties. The atomic structures and electronic properties of interfaces in lateral G/BN heterostructures are investigated by first-principles calculations. The symmetric armchair interfaces have a similar formation energy but a larger band gap compared with the nonsymmetric interfaces. G/BN heterostructures with zigzag-type interfaces constructed under the guide of Clar’s rule are found to possess a lower formation energy than those with abrupt interfaces and open a finite band gap. In addition to the zigzag and armchair interfaces, other misorientated interfaces with pentagon and heptagon rings are also stable with low formation energies of 4.4–6.8 eV/nm. These theoretical results are important to clarify the correlation between atomic structures and electronic properties of in-plane G/BN heterostructures and establish a fundamental picture for further theoretical studies and device design.

36 MATERIALS SCIENCE↗

NASA NTRS1979

Effect of interfacial species on shear strength of metal-sapphire contacts

The interfacial shear strength of the metal-insulator system has been studied by means of the coefficient of static friction of copper, nickel, or gold contacts on sapphire in ultrahigh vacuum. The effect on contact strength of adsorbed oxygen, nitrogen, chlorine, and carbon monoxide on the metal surfaces is reported. It was found that exposures as low as 1 L of O2 on Ni produced observable increases in contact strength, whereas exposures of 3 L of Cl2 lead to a decrease in contact strength. These results imply that submonolayer concentrations of these species at the interface of a thin Ni film on Al2O3 should affect film adhesion similarly. The atomic mechanism by which these surface or interface phases affect interfacial strength is not yet understood.

Pepper, S. V.↗

NASA NTRSDate not supplied

Influence of Microstructural Features on Austenite-Martensite Interfaces in NiTi Shape Memory Alloys

Shape memory alloys (SMAs) exhibit several unique thermomechanical properties due to a reversible martensitic phase transformation. A key aspect of this transformation is the austenite-martensite interface. Here we present a molecular dynamics (MD) simulation methodology to study the atomic-scale features of austenite-martensite interface migration under near-equilibrium conditions. In single crystals, the interfaces migrate rapidly with only a small thermodynamic driving force. In polycrystals, however, interface migration is significantly impeded due to the change in orientation relationship at grain boundaries and the stored elastic energy resulting from microstructural constraints. This behavior can be linked to several mechanisms associated with transformation width and hysteresis in SMAs, properties of great importance for applications involving actuation. Additionally, we will present preliminary MD simulation results on the influence of precipitates on the formation and migration of austenite-martensite interfaces.

Gabriel Plummer↗

NASA NTRSDate not supplied

Influence of Microstructural Features on Austenite-Martensite Interfaces in NiTi Shape Memory Alloys

Gabriel Plummer↗

DOE OSTI2015

The contact area dependent interfacial thermal conductance

The effects of the contact area on the interfacial thermal conductance σ are investigated using the atomic Green’s function method. Different from the prediction of the heat diffusion transport model, we obtain an interesting result that the interfacial thermal conductance per unit area Λ is positively dependent on the contact area as the area varies from a few atoms to several square nanometers. Through calculating the phonon transmission function, it is uncovered that the phonon transmission per unit area increases with the increased contact area. This is attributed to that each atom has more neighboring atoms in the counterpart of the interface with the increased contact area, which provides more channels for phonon transport.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2018

Probing the localization of magnetic dichroism by atomic-size astigmatic and vortex electron beams

We report localization of a magnetic dichroic signal on atomic columns in electron magnetic circular dichroism (EMCD), probed by beam distorted by four-fold astigmatism and electron vortex beam. With astigmatic probe, magnetic signal to noise ratio can be enhanced by blocking the intensity from the central part of probe. However, the simulations show that for atomic resolution magnetic measurements, vortex beam is a more effective probe, with much higher magnetic signal to noise ratio. For all considered beam shapes, the optimal SNR constrains the signal detection at low collection angles of approximately 6–8 mrad. Irrespective of the material thickness, the magnetic signal remains strongly localized within the probed atomic column with vortex beam, whereas for astigmatic probes, the magnetic signal originates mostly from the nearest neighbor atomic columns. Due to excellent signal localization at probing individual atomic columns, vortex beams are predicted to be a strong candidate for studying the crystal site specific magnetic properties, magnetic properties at interfaces, or magnetism arising from individual atomic impurities.

36 MATERIALS SCIENCE↗

DOE OSTI2016

Anomalously deep polarization in SrTiO3 (001) interfaced with an epitaxial ultrathin manganite film

Using atomically-resolved imaging and spectroscopy, we reveal a remarkably deep polarization in non-ferroelectric SrTiO 3 near its interface with an ultrathin nonmetallic film of La 2/3 Sr 1/3 MnO 3 . Electron holography shows an electric field near the interface in SrTiO 3 , yielding a surprising spontaneous polarization density of ~ 21 μC/cm 2 . Combining the experimental results with first principles calculations, we propose that the observed deep polarization is induced by the electric field originating from oxygen vacancies that extend beyond a dozen unit-cells from the interface, thus providing important evidence of the role of defects in the emergent interface properties of transition metal oxides.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2024

Direct Visualization of Defect‐Controlled Diffusion in van der Waals Gaps

Abstract Diffusion processes govern fundamental phenomena such as phase transformations, doping, and intercalation in van der Waals (vdW) bonded materials. Here, the diffusion dynamics of W atoms by visualizing the motion of individual atoms at three different vdW interfaces: hexagonal boron nitride (BN)/vacuum, BN/BN, and BN/WSe 2 , by recording scanning transmission electron microscopy movies is quantified. Supported by density functional theory (DFT) calculations, it is inferred that in all cases diffusion is governed by intermittent trapping at electron beam‐generated defect sites. This leads to diffusion properties that depend strongly on the number of defects. These results suggest that diffusion and intercalation processes in vdW materials are highly tunable and sensitive to crystal quality. The demonstration of imaging, with high spatial and temporal resolution, of layers and individual atoms inside vdW heterostructures offers possibilities for direct visualization of diffusion and atomic interactions, as well as for experiments exploring atomic structures, their in situ modification, and electrical property measurements of active devices combined with atomic resolution imaging.

Chemistry↗

DOE OSTI2020

Picoscale structural insight into superconductivity of monolayer FeSe/SrTiO 3

Remarkable enhancement of the superconducting transition temperature ( c ) has been observed for monolayer (ML) FeSe films grown on SrTiO 3 substrates. The atomic-scale structure of the FeSe/SrTiO 3 interface is an important determinant of both the magnetic and interfacial electron-phonon interactions and is a key ingredient to understanding its high- T c superconductivity. We resolve the atomic-scale structure of the FeSe/SrTiO 3 interface through a complementary analysis of scanning transmission electron microscopy and in situ surface x-ray diffraction. We find that the interface is more strongly bonded for a particular registration, which leads to a coherently strained ML. We also determine structural parameters, such as the distance between ML FeSe and the oxide, Se-Fe-Se bond angles, layer-resolved distances between Fe-Se, and registry of the FeSe lattice relative to the oxide. This picoscale structure determination provides an explicit structural framework and constraint for theoretical approaches addressing the high- T c mechanism in FeSe/SrTiO 3 .

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2025

Investigation of kinetic inductance and microwave loss in thin-film TaC x N 1−x superconducting resonators

The promise of tantalum for realizing superconducting quantum devices has generated interest in its compound films, particularly nitrides. Among these, cubic-phase tantalum carbonitride (TaC x N 1−x ) offers reduced susceptibility to oxidation and a high critical temperature, yet its microwave properties remain largely unexplored. Here, in this study, we investigate plasma-enhanced atomic layer deposition of cubic-phase TaC x N 1−x thin films for superconducting microwave circuits. Structural and transport measurements reveal nanocrystalline morphology with sub-10 nm grains and superconductivity in the dirty limit. Coplanar waveguide resonators exhibit moderately high kinetic inductance (16.8 pH/sq for 30 nm films) with potential for enhancement through dimensional scaling. The films also support high internal quality factors exceeding 10 5 at 50 mK in the single-photon regime, comparable to granular aluminum. Loss analysis identifies the two-level systems as the dominant limiting mechanism, with potential for further reduction through interface engineering. These results establish atomic layer deposited TaC x N 1−x as a promising material for scalable, low-loss, high-inductance superconducting circuits.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2016

Surface and interface analysis of nanomaterials at microfocus beamline (BL-16) of Indus-2

Analysis of chemical nature and electronic structure at the interface of a thin film medium is important in many technological applications as well as to understand overall efficiency of a thin film device. Synchrotron radiation based x-ray spectroscopy is a promising technique to study interface nature of the nanomaterials with atomic resolutions. A combined x-ray reflectivity and grazing incidence x-ray fluorescence measurement facility has been recently constructed at the BL-16 microfocus beamline of Indus-2 synchrotron facility to accomplish surface-interface microstructural characterization of thin layered materials. It is also possible to analyze contaminates or adsorbed ad-atoms on the surface of the thin nanostructure materials. The BL-16 beamline also provides an attractive platform to perform a variety of analytical research activities especially in the field of micro x-ray fluorescence and ultra-trace elements analysis using Synchrotron radiation. We describe various salient features of the BL-16 reflectometer experimental station and the detailed description of its capabilities through the measured results, obtained for various thin layered nanomaterials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗