Effects of Single α-to-β Residue Replacements on Structure and Stability in a Small Protein: Insights from Quasiracemic Crystallization
Abstract not provided
Kreitler, Dale F.↗
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Structure-Guided Identification of a Small Molecule That Inhibits Anaerobic Choline Metabolism by Human Gut Bacteria
Abstract not provided
Orman, Marina↗
Spatio–Temporal Coarse–Graining Decomposition of the Global Ocean Geostrophic Kinetic Energy
We expand on a recent determination of the first global energy spectrum of the ocean’s surface geostrophic circulation using a coarse-graining (CG) method. We compare spectra from CG to those from spherical harmonics by treating land in a manner consistent with the boundary conditions. While the two methods yield qualitatively consistent domain-averaged results, spherical harmonics spectra are too noisy at gyre-scales (> 1000 km). More importantly, spherical harmonics are inherently global and cannot provide local information connecting scales with currents geographically. CG shows that the extra-tropics mesoscales (100–500 km) have a root-mean-square (rms) velocity of ~15 cm/s, which increases to ~30–40 cm/s locally in the Gulf Stream and Kuroshio and to ~16–28 cm/s in the ACC. There is notable hemispheric asymmetry in mesoscale energy-per-area, which is higher in the north due to continental boundaries. We estimate that ≈25–50% of total geostrophic energy is at scales smaller than 100 km, and is un(der)-resolved by pre-SWOT satellite products. Spectra of the time-mean circulation show that most of its energy (up to 70%) resides in stationary eddies with characteristic scales smaller than (< 500 km). This highlights the preponderance of ‘standing’ small-scale structures in the global ocean due to the temporally coherent forcing by boundaries. By coarse-graining in space and time, we compute the first spatio-temporal global spectrum of geostrophic circulation from AVISO and NEMO. These spectra show that every length-scale evolves over a wide range of time-scales with a consistent peak at ≈200 km and ≈2–3 weeks.
54 ENVIRONMENTAL SCIENCES↗
Structural Analysis of Inhibitor Binding to CAMKK1 Identifies Features Necessary for Design of Specific Inhibitors
The calcium/calmodulin-dependent protein kinases (CAMKKs) are upstream activators of CAMK1 and CAMK4 signalling and have important functions in neural development, maintenance and signalling, as well as in other aspects of biology such as Ca 2+ signalling in the cardiovascular system. To support the development of specific inhibitors of CAMKKs we have determined the crystal structure of CAMKK1 with two ATP-competitive inhibitors. The structures reveal small but exploitable differences between CAMKK1 and CAMKK2, despite the high sequence identity, which could be used in the generation of specific inhibitors. Screening of a kinase inhibitor library revealed molecules that bind potently to CAMKK1. Isothermal titration calorimetry revealed that the most potent inhibitors had binding energies largely dependent on favourable enthalpy. Together, the data provide a foundation for future inhibitor development activities.
59 BASIC BIOLOGICAL SCIENCES↗
The structural fate of lipid nanoparticles in the extracellular matrix
Drug-loaded liposomes are the most successful nanomedicine to date, with multiple FDA-approved systems for a myriad of diseases. While liposome circulation time in blood and retention in tissues have been studied in detail, the structural fate of liposomes—and nanoparticles in general—in the body has not been extensively investigated. In this work, we explore the interactions of liposomes with synthetic and natural hydrogel materials to understand how the natural extracellular matrix influences liposome structural characteristics. Small angle X-ray scattering, confocal microscopy, and cryogenic transmission electron microscopy data demonstrate that poly(ethylene glycol) (PEG), gelatin, alginate, and Matrigel ® hydrogels cause 200 nm liposomes of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) to transform into micrometer-sized aggregates. These aggregates are composed of multilamellar vesicles around 100 nm in diameter with a mean interlamellar separation of 5.5 nm. Protecting the liposomes with a corona of PEG damps this restructuring effect, making the multilamellar vesicles less stable. We attribute this unilamellar to multilamellar transition to an osmotic driving force from the hydrogel environment. This lipid restructuring has broad ramifications in the design and use of nanomedicines, and in understanding the fate and function of natural lipid-based materials within the tissue microenvironment.
36 MATERIALS SCIENCE↗
Structural properties of ultra-small thorium and uranium dioxide nanoparticles embedded in a covalent organic framework
ThO 2 and UO 2 nanoparticles synthesized using a COF-5 template exhibit unpassivated surfaces and provide insight into nanoscale properties of actinides.
38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
Carbon nanospike coated nanoelectrodes for measurements of neurotransmitters
Here, carbon nanoelectrodes enable the detection of neurotransmitters at the level of single cells, vesicles, synapses and small brain structures. Previously, the etching of carbon fibers and 3D printing based on direct laser writing have been used to fabricate carbon nanoelectrodes, but these methods lack the ability of mass manufacturing. In this paper, we mass fabricate carbon nanoelectrodes by growing carbon nanospikes (CNSs) on metal wires. CNSs have a short, dense and defect-rich surface that produces remarkable electrochemical properties, and they can be mass fabricated on almost any substrate without using catalysts. Tungsten wires and niobium wires were electrochemically etched in batch to form sub micrometer sized tips, and a layer of CNSs was grown on the metal wires using plasma-enhanced chemical vapor deposition (PE-CVD). The thickness of the CNS layer was controlled by the deposition time, and a thin layer of CNSs can effectively cover the entire metal surface while maintaining the tip size within the sub micrometer scale. The etched tungsten wires produced tapered conical nanotips, while the etched niobium wires were long and thin. Both showed excellent sensitivity for the detection of outer sphere ruthenium hexamine and the inner sphere test compound ferricyanide. The CNS nanosensors were used for the measurement of dopamine, serotonin, ascorbic acid and DOPAC with fast-scan cyclic voltammetry. The CNS nanoelectrodes had a large surface area and numerous defect sites, which improved the sensitivity, electron transfer kinetics and adsorption. Finally, the CNS nanoelectrodes were compared with other nanoelectrode fabrication methods, including flame etching, 3D printing, and nanopipettes, which are slower to make and more difficult for mass fabrication. Thus, CNS nanoelectrodes are a promising strategy for the mass fabrication of nanoelectrode sensors for neurotransmitters.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Porous bipolar polymers as organic cathodes for sustainable sodium/potassium-ion batteries
Redox-active porous polymers are becoming promising organic electrode materials for alkali-ion batteries because of their tunable pore size, flexible chemical structure, and high thermal stability. This work presents various porous bipolar polymers as cathodes in Na-ion batteries (NIBs) and K-ion batteries (KIBs). Two structural units containing carbonyl and amine active centers, respectively, were introduced into the repeating units of the polymers by the polycondensation of N,N,N',N'-tetrakis(4-aminophenyl)-1,4-phenylenediamine (TAP) and various dianhydrides. Here, the resulting bipolar polymers undergo multi-electron redox reactions involving both cations and anions during battery charge and discharge. The impacts of extended conjugation structures and porosity on the electrochemical performances were investigated by tuning the conjugation structures in the dianhydride monomers. The bipolar polymers with extended conjugation structures and small pore size exhibit superior electrochemical performance in NIBs and KIBs in terms of high redox potentials, long cycle life, and fast-charging capability, demonstrating great promise as organic cathode materials for alkali-ion batteries.
25 ENERGY STORAGE↗
Planck 2013 results. XXXI. Consistency of the Planck data
The Planck design and scanning strategy displays many levels of redundancy that can be exploited to provide tests of internal consistency. One of the most important is the comparison of the 70 GHz (amplifier) and 100 GHz (bolometer) channels. Based on different instrument technologies, with feeds located differently in the focal plane, analysed independently by different teams using different software, and near the minimum of diffuse foreground emission, these channels are in effect two different experiments. The 143 GHz channel has the lowest noise level on Planck , and is near the minimum of unresolved foreground emission. In this paper, we analyse the level of consistency achieved in the 2013 Planck data. We concentrate on comparisons between the 70, 100, and 143 GHz channel maps and power spectra, particularly over the angular scales of the first and second acoustic peaks, on maps masked for diffuse Galactic emission and for strong unresolved sources. Difference maps covering angular scales from 8° to 15' are consistent with noise, and show no evidence of cosmic microwave background structure. Including small but important corrections for unresolved-source residuals, we demonstrate agreement (measured by deviation of the ratio from unity) between 70 and 100 GHz power spectra averaged over 70 ≤ ℓ ≤390 at the 0.8% level, and agreement between 143 and 100 GHz power spectra of 0.4% over the same ℓ range. These values are within and consistent with the overall uncertainties in calibration given in the Planck 2013 results. We also present results based on the 2013 likelihood analysis showing consistency at the 0.35% between the 100, 143, and 217 GHz power spectra. We analyse calibration procedures and beams to determine what fraction of these differences can be accounted for by known approximations or systematic errors that could be controlled even better in the future, reducing uncertainties still further. Several possible small improvements are described. Subsequent analysis of the beams quantifies the importance of asymmetry in the near sidelobes, which was not fully accounted for initially, affecting the 70/100 ratio. Correcting for this, the 70, 100, and 143 GHz power spectra agree to 0.4% over the first two acoustic peaks. The likelihood analysis that produced the 2013 cosmological parameters incorporated uncertainties larger than this. We show explicitly that correction of the missing near sidelobe power in the HFI channels would conclude in shifts in the posterior distributions of parameters of less than 0.3σ except for A s , the amplitude of the primordial curvature perturbations at 0.05 Mpc -1 , which changes by about 1σ. We extend these comparisons to include the sky maps from the complete nine-year mission of the Wilkinson Microwave Anisotropy Probe (WMAP), and find a roughly 2% difference between the Planck and WMAP power spectra in the region of the first acoustic peak.
79 ASTRONOMY AND ASTROPHYSICS↗
Quantum ring solitons and nonlocal effects in plasma wake field excitations
A theoretical investigation of the quantum transverse beam motion for a cold relativistic charged particle beam travelling in a cold, collisionless, strongly magnetized plasma is carried out. This is done by taking into account both the individual quantum nature of the beam particles (single-particle uncertainty relations and spin) and the self consistent interaction generated by the plasma wake field excitation. By adopting a fluid model of a strongly magnetized plasma, the analysis is carried out in the overdense regime (dilute beams) and in the long beam limit. It is shown that the quantum description of the collective transverse beam dynamics is provided by a pair of coupled nonlinear governing equations. It comprises a Poisson-like equation for the plasma wake potential (driven by the beam density) and a 2D spinorial Schroedinger equation for the wave function, whose squared modulus is proportional to the beam density, that is obtained in the Hartree's mean field approximation, after disregarding the exchange interactions. The analysis of this pair of equations, which in general exhibits a strong nonlocal character, is carried out analytically as well as numerically in both the linear and the nonlinear regimes, showing the existence of the quantum beam vortices in the form of Laguerre-Gauss modes and ring envelope solitons, respectively. In particular, when the relation between the plasma wake field response and the beam probability density is strictly local, the pair of the governing equations is reduced to the 2D Gross-Pitaevskii equation that allows one to establish the conditions for the self focusing and collapse. These conditions include the quantum nature of the beam particles. Finally, when the relation between the plasma wake field response and the beam probability density is moderately nonlocal, the above pair of equations permits to follow the spatio-temporal evolution of a quantum ring envelope soliton. Such a structure exhibits small or violent breathing, but it remains very stable for long time.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Pinhole mediated electrical transport across LaTiO{sub 3}/SrTiO{sub 3} and LaAlO{sub 3}/SrTiO{sub 3} oxide hetero-structures
Metal-insulator-metal configuration of LaTiO{sub 3}/SrTiO{sub 3} and LaAlO{sub 3}/SrTiO{sub 3} hetero-structures between two dimensional electron gas formed at the interface and different area top electrodes is employed for Conductive Atomic force microscopy (CAFM) imaging, Current–Voltage (I-V), and Capacitance-Voltage (C-V) spectroscopy. Electrode area dependent I-V characteristics are observed for these oxide hetero-structures. With small area electrodes, rectifying I-V characteristics are observed, compared to, both tunneling and leakage current characteristics for large area electrodes. CAFM mapping confirmed the presence of pinholes on both surfaces. Resultant I-V characteristics have a contribution from both tunneling and leakage due to pinholes.
36 MATERIALS SCIENCE↗
Experimental investigation on structures and velocity of liquid jets in a supersonic crossflow
Particle image velocimetry was applied in the study focusing on the structure and velocity of water jets injected into a Ma = 2.1 crossflow. The instantaneous structures of the jet, including surface waves in the near-injector region and vortices in the far-field, were visualized clearly. Spray velocity increases rapidly to 66% of the mainstream velocity in the region of x/d < 15, owing to the strong gas-liquid interaction near the orifice. By contrast, the velocity grows slowly in the far-field region, where the liquid inside the spray is accelerated mainly by the continuous driven force provided by the mainstream with the gas-liquid shear. The injection and atomization of liquid jet in a supersonic crossflow serves as a foundation of scramjet combustion process, by affecting the combustion efficiency and some other performances. With various forces acting on the liquid jet (Mashayek et al. [AIAA J. 46, 2674–2686 (2008)] and Wang et al. [AIAA J. 50, 1360–1366 (2012)]), the atomization process involves very complex flow physics. These physical processes include strong vortical structures, small-scale wave formation, stripping of small droplets from the jet surface, formations of ligaments, and droplets with a wide range of sizes.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Amorphorized tantalum-nickel binary films for metal gate applications
Amorphous metal gates have the potential to eliminate the work function variation due to grain orientation for poly-crystalline metal gate materials, which is a leading contributor to threshold voltage variation for small transistors. Structural and electrical properties of TaNi alloys using co-sputtering with different compositions and multilayer structures with different thicknesses are investigated in this work. It is found that TaNi films are amorphous for a wide range of compositions as deposited, and the films stay amorphous after annealing at 400 °C in RTA for 1 min and up to at least 700 °C depending on the composition. The amorphous films eventually crystallize into Ni, Ta, and TaNi{sub 3} phases at high enough temperature. For multilayer Ta/Ni structures, samples with individual layer thickness of 0.12 nm and 1.2 nm are amorphous as deposited due to intermixing during deposition, and stay amorphous until annealed at 500 °C. The resistivity of the films as-deposited are around 200 μΩ·cm. The work function of the alloy is fixed at close to the Ta work function of 4.6 eV for a wide range of compositions. This is attributed to the segregation of Ta at the metal-oxide interface, which is confirmed by XPS depth profile. Overall, the excellent thermal stability and low resistivity makes this alloy system a promising candidate for eliminating work function variation for gate last applications, as compared to crystalline Ta or TiN gates.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Orbital control of Rashba spin orbit coupling in noble metal surfaces
Rashba spin orbit coupling (SOC) in noble metal surfaces is of great importance for the application of metal films in spintronic devices. By combining the density-functional theory calculations with our recently developed orbital selective external potential method, we investigate the Rashba SOC in the Shockley surface states of Au(111) and Ag(111). We find that the large Rashba SOC in the sp-character surface states of Au(111) is mainly contributed by the minor d-orbitals in the surface states. While for the sd-character surface states, although they are dominated by the d-orbitals, Rashba splitting is found to be rather small. Band structure analysis reveals that this is mainly because the sd-character surface states are well below the Fermi level and can be less influenced by the asymmetric surface potential. We demonstrate that the Rashba SOC in noble metal surfaces can be effectively manipulated by shifting the d-orbitals in the surface states, which can be physically implemented through surface decoration. Our investigation provides a deep understanding on Rashba SOC in noble metal surfaces and could be helpful to their applications in spintronic devices.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Evidence of a rolling motion of a microparticle on a silicon wafer in a liquid environment
The interaction of micro- and nanometer-sized particles with surfaces plays a crucial role when small-scale structures are built in a bottom-up approach or structured surfaces are cleaned in the semiconductor industry. For a reliable quantification of the interaction between individual particles and a specific surface, however, the motion type of the particle must be known. We developed an approach to unambiguously distinguish between sliding and rolling particles. To this end, fluorescent particles were partially bleached in a confocal laser scanning microscope to tailor an optical inhomogeneity, which allowed for the identification of the characteristic motion pattern. For the manipulation, the water flow generated by a fast moving cantilever-tip of an atomic force microscope enabled the contactless pushing of the particle. We thus experimentally evidenced a rolling motion of a micrometer-sized particle directly with a fluorescence microscope. A similar approach could help to discriminate between rolling and sliding particles in liquid flows of microfluidic systems.
42 ENGINEERING↗
Characterization of laser-produced carbon plasmas relevant to laboratory astrophysics
Experiments, analytic modeling, and numerical simulations are presented here to characterize carbon plasmas produced by high-intensity (10 9 -10 13 W cm -2 ) lasers relevant to experimental laboratory astrophysics. In the large-scale limit, the results agree well with a self-similar isentropic, adiabatic fluid model. Laser-target simulations, however, show small-scale structure in the velocity distribution of different ion species, which is also seen in experiments. These distributions indicate that most of the plasma energy resides in moderate charge states (C +3 –C +4 ), most of the mass resides in the lowest charge states, and the highest charge states move fastest.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Formation of collisionless shocks in magnetized plasma interaction with kinetic-scale obstacles
We investigate the formation of collisionless magnetized shocks triggered by the interaction between magnetized plasma flows and miniature-sized (order of plasma kinetic-scales) magnetic obstacles resorting to massively parallel, full particle-in-cell simulations, including the electron kinetics. The critical obstacle size to generate a compressed plasma region ahead of these objects is determined by independently varying the magnitude of the dipolar magnetic moment and the plasma magnetization. Here we find that the effective size of the obstacle depends on the relative orientation between the dipolar and plasma internal magnetic fields, and we show that this may be critical to form a shock in small-scale structures. We also study the microphysics of the magnetopause in different magnetic field configurations in 2D and compare the results with full 3D simulations. Finally, we evaluate the parameter range where such miniature magnetized shocks can be explored in laboratory experiments.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Pt 8 cluster on alumina under a pressure of hydrogen: Support-dependent reconstruction from first-principles global optimization
Alumina supported Pt nano clusters under hydrogen environment play a crucial role for many heterogeneous catalysis applications. As such, we conducted grand canonical genetic algorithm (GCGA) simulations for supported Pt 8 clusters in hydrogen gas environment to study the intra-cluster, cluster-support, and cluster-adsorbate interactions. Two alumina surfaces, α-Al 2 O 3 (0001) and $γ$-Al 2 O 3 (100), and two conditions T=600°C, p H2 = 0.1bar and T=25°C, p H2 = 1.0 bar were considered corresponding to low and high hydrogen chemical potential $μ$ H , respectively. The low free energy ensemble of Pt 8 is decorated by a medium (2–12 H), resp. high (20–30 H), number of hydrogen atoms under equilibrium at low $μ$ H , respectively, high $μ$ H , and undergoes different morphology transformations on the two surfaces. On α-Al2O3(0001), Pt8 is mostly 3D but very fluxional in structure at low μH and converts to open one-layer 2D structures with minimal fluxionality at high μH, whereas on $γ$-Al 2 O 3 (100), the exact opposite occurs, and Pt 8 clusters present one-layer 2D shapes at low $μ$ H and switch into compact 3D shapes under high $μ$ H , during which the Pt 8 cluster preserves moderate fluxionality. Further analysis reveals similar Pt–Pt bond length increase when switching from low $μ$ H to high $μ$ H on both surfaces, though morphology transformations are different. Electronic structure analysis shows the existence of bonding interactions between Pt and Lewis acidic Al 3+ sites along with the Pt – O interaction, which implies the necessity to include Al neighbors to discuss the electronic structure of small Pt clusters.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗