bluuebunny/crossref_metadata_2025 huggingface dataset:
Ligand coverage dependence of structural stability and interparticle spacing of gold supracrystals
Authors: Liu Xuepeng , Lu Pin , Zhai Hua
Published: January 2018

Atomistic molecular dynamics simulations are performed to study the structural stability and interparticle spacing of alkylthiol-capped gold supracrystals with varying ligand coverage on gold nanocrystals. The results show that the gold supracrystal with dense ligand coverage is structurally stable, while a supracrystal with sparse ligand coverage is unstable due to the fusion of gold nanocrystals in the supracrystals. The ligand coverage dependence of the structural stability is attributed to the morphology of surface ligands on gold nanocrystals, which transforms from homogeneous to heterogeneous with decreasing ligand coverage. We show that the heterogeneous ligand distribution contributes to the fusion of gold nanocrystals and induces the structural instability of supracrystals. In addition, the interparticle spacing is found to increase linearly with increasing ligand coverage. The results may deepen our understanding of the origins of structural instability of gold supracrystals.
Advanced platform for the in-plane ZT measurement of thin films
Authors: Linseis V. , Völklein F. , Reith H. , Nielsch K. , Woias P.
Published: January 2018

The characterization of nanostructured samples with at least one restricted dimension like thin films or nanowires is challenging, but important to understand their structure and transport mechanism, and to improve current industrial products and production processes. We report on the 2nd generation of a measurement chip, which allows for a simplified sample preparation process, and the measurement of samples deposited from the liquid phase using techniques like spin coating and drop casting. The new design enables us to apply much higher temperature gradients for the Seebeck coefficient measurement in a shorter time, without influencing the sample holder’s temperature distribution. Furthermore, a two membrane correction method for the 3ω thermal conductivity measurement will be presented, which takes the heat loss due to radiation into account and increases the accuracy of the measurement results significantly. Errors caused by different sample compositions, varying sample geometries, and different heat profiles are avoided with the presented measurement method. As a showcase study displaying the validity and accuracy of our platform, we present temperature-dependent measurements of the thermoelectric properties of an 84 nm Bi87Sb13 thin film and a 15 μm PEDOT:PSS thin film.
MnNi-based spin valve sensors combining high thermal stability, small footprint and pTesla detectivities
Authors: Silva Marília , Leitao Diana C. , Cardoso Susana , Freitas Paulo
Published: January 2018

Magnetoresistive sensors with high thermal robustness, low noise and high spatial resolution are the answer to a number of challenging applications. Spin valve sensors including MnNi as antiferromagnet layer provide higher exchange bias field and improved thermal stability. In this work, the influence of the buffer layer type (Ta, NiFeCr) and thickness on key sensor parameters (e.g. offset field, Hf) is investigated. A Ta buffer layer promotes a strong (111) texture which leads to a higher value of MR. In contrast, Hf is lower for NiFeCr buffer. Micrometric sensors display thermal noise levels of 1 nT/Hz1/2 and 571 pT/Hz1/2 for a sensor height (h) of 2 and 4 μm, respectively. The temperature dependence of MR and sensitivity is also addressed and compared with MnIr based spin valves. In this case, MR abruptly decreases after heating at 160°C (without magnetic field), contrary to MnNi-based spin valves, where only a 10% MR decrease (relative to the initial value) is seen at 275°C. Finally, to further decrease the noise levels and improve detectivity, MnNi spin-valves are deposited vertically, and connected in parallel and series (in-plane) to create a device with low resistance and high sensitivity. A field detection at thermal level of 346 pT/Hz1/2 is achieved for a device with a total of 300 SVs (4 vertical, 15 in series, 5 in parallel).
Upside/Downside statistical mechanics of nonequilibrium Brownian motion. I. Distributions, moments, and correlation functions of a free particle
Authors: Craven Galen T. , Nitzan Abraham
Published: January 2018

Statistical properties of Brownian motion that arise by analyzing, separately, trajectories over which the system energy increases (upside) or decreases (downside) with respect to a threshold energy level are derived. This selective analysis is applied to examine transport properties of a nonequilibrium Brownian process that is coupled to multiple thermal sources characterized by different temperatures. Distributions, moments, and correlation functions of a free particle that occur during upside and downside events are investigated for energy activation and energy relaxation processes and also for positive and negative energy fluctuations from the average energy. The presented results are sufficiently general and can be applied without modification to the standard Brownian motion. This article focuses on the mathematical basis of this selective analysis. In subsequent articles in this series, we apply this general formalism to processes in which heat transfer between thermal reservoirs is mediated by activated rate processes that take place in a system bridging them.
Vacuum-sealed microcavity formed from suspended graphene by using a low-pressure dry-transfer technique
Authors: Takahashi K. , Ishida H. , Sawada K.
Published: January 2018

We report the development of a microcavity drum sealed by suspended graphene. The drum is fabricated by using a low-pressure dry-transfer technique, which involves vacuum de-aeration between a graphene sheet and a substrate and raising the temperature to above the glass transition of the supporting poly(methyl methacrylate) film, which serves to increase the real contact area. The result is a suspended graphene sheet with a maximum diameter of 48.6 μm. The Raman spectrum of the suspended graphene has a 2D/G ratio of 1.79 and a few D peaks, which suggests that the material is high-quality single-layer graphene. The dry-transfer technique yields a vacuum-sealed microcavity drum 1.1 μm deep up to 4.5 μm in diameter. The Raman shift indicates that the suspended graphene is subjected to a tensile strain of 0.05%, which is attributed to the pressure difference between the evacuated cavity and the exterior gas.
Influence of thermal effects on stability of nanoscale films and filaments on thermally conductive substrates
Authors: Seric Ivana , Afkhami Shahriar , Kondic Lou
Published: January 2018

We consider fluid films and filaments of nanoscale thickness on thermally conductive substrates exposed to external heating and discuss the influence of the variation of material parameters with temperature on film stability. Particular focus is on metal films exposed to laser irradiation. Due to the short length scales involved, the absorption of heat in the metal is directly coupled to the film evolution, since the absorption length and the film thickness are comparable. Such a setup requires self-consistent consideration of fluid mechanical and thermal effects. We approach the problem via volume-of-fluid-based simulations that include destabilizing liquid metal–solid substrate interaction potentials. These simulations couple fluid dynamics directly with the spatio-temporal evolution of the temperature field both in the fluid and in the substrate. We focus on the influence of the temperature variation of material parameters, in particular of surface tension and viscosity. Regarding variation of surface tension with temperature, the main finding is that while the Marangoni effect may not play a significant role in the considered setting, the temporal variation of surface tension (modifying normal stress balance) is significant and could lead to complex evolution including oscillatory evolution of the liquid metal-air interface. Temperature variation of film viscosity is also found to be relevant. Therefore, the variations of surface tensions and viscosity could both influence the emerging wavelengths in experiments. By contrast, the filament geometry is found to be much less sensitive to a variation of material parameters with temperature.
Interplay between bulk and edge-bound topological defects in a square micromagnet
Authors: Sloetjes Sam D. , Digernes Einar , Olsen Fredrik K. , Chopdekar Rajesh V. , Retterer Scott T. , Folven Erik , Grepstad Jostein K.
Published: January 2018

A field-driven transformation of a domain pattern in a square micromagnet, defined in a thin film of La0.7Sr0.3MnO3, is discussed in terms of creation and annihilation of bulk vortices and edge-bound topological defects with half-integer winding numbers. The evolution of the domain pattern was mapped with soft x-ray photoemission electron microscopy and magnetic force microscopy. Micromagnetic modeling, permitting detailed analysis of the spin texture, accurately reproduces the measured domain state transformation. The simulations also helped stipulate the energy barriers associated with the creation and annihilation of the topological charges and thus to assess the stability of the domain states in this magnetic microstructure.
Effects of the injected plasma on the breakdown process of the trigatron gas switch under low working coefficient
Authors: Chen Li , Yang Lanjun , Qiu Aici , Huang Dong , Liu Shuai
Published: January 2018

Based on the surface flashover discharge, the injected plasma was generated, and the effects on the breakdown process of the trigatron gas switch were studied in this paper. The breakdown model caused by the injected plasma under the low working coefficient (<0.7) was established. The captured framing images showed that the injected plasma distorted the electrical field of the gap between the frontier of the injected plasma and the opposite electrode, making it easier to achieve the breakdown critical criterion. The calculation results indicated that the breakdown delay time was mainly decided by the development of the injected plasma, as without considering the effects of the photo-ionization and the invisible expansion process, the breakdown delay time of the calculation results was 20% higher than the experimental results. The morphology of the injected plasma generated by polyethylene surface flashover was more stable and regular than ceramic, leading to a 30% lower breakdown delay time when the working coefficient is larger than 0.2, and the difference increased sharply when the working coefficient is lower than 0.2. This was significant for improving the trigger performance of the trigatron gas switch under low working coefficient.
The I-Raum: A new shaped hohlraum for improved inner beam propagation in indirectly-driven ICF implosions on the National Ignition Facility
Authors: Robey H. F. , Berzak Hopkins L. , Milovich J. L. , Meezan N. B.
Published: January 2018

Recent work in indirectly-driven inertial confinement fusion implosions on the National Ignition Facility has indicated that late-time propagation of the inner cones of laser beams (23° and 30°) is impeded by the growth of a “bubble” of hohlraum wall material (Au or depleted uranium), which is initiated by and is located at the location where the higher-intensity outer beams (44° and 50°) hit the hohlraum wall. The absorption of the inner cone beams by this “bubble” reduces the laser energy reaching the hohlraum equator at late time driving an oblate or pancaked implosion, which limits implosion performance. In this article, we present the design of a new shaped hohlraum designed specifically to reduce the impact of this bubble by adding a recessed pocket at the location where the outer cones hit the hohlraum wall. This recessed pocket displaces the bubble radially outward, reducing the inward penetration of the bubble at all times throughout the implosion and increasing the time for inner beam propagation by approximately 1 ns. This increased laser propagation time allows one to drive a larger capsule, which absorbs more energy and is predicted to improve implosion performance. The new design is based on a recent National Ignition Facility shot, N170601, which produced a record neutron yield. The expansion rate and absorption of laser energy by the bubble is quantified for both cylindrical and shaped hohlraums, and the predicted performance is compared.
One-dimensional dielectric bi-periodic photonic structures based on ternary photonic crystals
Authors: Dadoenkova Nataliya N. , Dadoenkova Yuliya S. , Panyaev Ivan S. , Sannikov Dmitry G. , Lyubchanskii Igor L.
Published: January 2018

We investigate the transmittivity spectra, fields, and energy distribution of the electromagnetic eigenwaves propagating in a one-dimensional (1D) dielectric photonic crystal [(TiO2/SiO2)NAl2O3]M with two periods formed by unit cells TiO2/SiO2 and (TiO2/SiO2)NAl2O3. Spectra of TE- and TM-modes depend on the geometric parameters of the structure and undergo modifications with the change in the period numbers, layer thicknesses, and incidence angle. Special attention is paid to the applicability of the hybrid effective medium approximation comprising the long-wave approximation and two-dimensional (2 × 2) transfer matrix method. We demonstrate spectral peculiarities of the bi-periodic structure and also show the differences between the band gap spectra of the bi-periodic and ternary 1D dielectric photonic crystals. The presented photonic crystal structure can find its applications in optoelectronics and nanophotonics areas as omnidirectional reflectors, optical ultra-narrow bandpass filters, and antireflection coatings.
Effects of temperature and mass conservation on the typical chemical sequences of hydrogen oxidation
Authors: Nicholson Schuyler B. , Alaghemandi Mohammad , Green Jason R.
Published: January 2018

Macroscopic properties of reacting mixtures are necessary to design synthetic strategies, determine yield, and improve the energy and atom efficiency of many chemical processes. The set of time-ordered sequences of chemical species are one representation of the evolution from reactants to products. However, only a fraction of the possible sequences is typical, having the majority of the joint probability and characterizing the succession of chemical nonequilibrium states. Here, we extend a variational measure of typicality and apply it to atomistic simulations of a model for hydrogen oxidation over a range of temperatures. We demonstrate an information-theoretic methodology to identify typical sequences under the constraints of mass conservation. Including these constraints leads to an improved ability to learn the chemical sequence mechanism from experimentally accessible data. From these typical sequences, we show that two quantities defining the variational typical set of sequences—the joint entropy rate and the topological entropy rate—increase linearly with temperature. These results suggest that, away from explosion limits, data over a narrow range of thermodynamic parameters could be sufficient to extrapolate these typical features of combustion chemistry to other conditions.
A velocity map imaging mass spectrometer for photofragments of fast ion beams
Authors: Johnston M. David , Pearson Wright L. , Wang Greg , Metz Ricardo B.
Published: January 2018

We present the details of a fast ion velocity map imaging mass spectrometer that is capable of imaging the photofragments of trap-cooled (≥7 K) ions produced in a versatile ion source. The new instrument has been used to study the predissociation of N2O+ produced by electric discharge and the direct dissociation of Al2+ formed by laser ablation. The instrument’s resolution is currently limited by the diameter of the collimating iris to a value of Δv/v = 7.6%. Photofragment images of N2O+ show that when the predissociative state is changed from 2Σ+(200) to 2Σ+(300) the dominant product channel shifts from a spin-forbidden ground state, N (4S) + NO+(v = 5), to a spin-allowed pathway, N*(2D) + NO+. The first photofragment images of Al2+ confirm the existence of a directly dissociative parallel transition (2Σ+u ← 2Σ+g) that yields products with a large amount of kinetic energy. D0 of ground state Al2+ (2Σ+g) measured from these images is 138 ± 5 kJ/mol, which is consistent with the published literature.
Magnetic reconnection in Earth's magnetotail: Energy conversion and its earthward–tailward asymmetry
Authors: Lu San , Pritchett P. L. , Angelopoulos V. , Artemyev A. V.
Published: January 2018

Magnetic reconnection, a fundamental plasma process, releases magnetic energy and converts it to particle energy, by accelerating and heating ions and electrons. This energy conversion plays an important role in the Earth's magnetotail. A two-dimensional particle-in-cell simulation is performed to study such a conversion in a magnetotail topology, one with a nonzero Bz, and the energy conversion is found to be more efficient in the earthward outflow than in the tailward outflow. Such earthward–tailward asymmetry is manifested not only in j·E but also in Poynting flux, Hall electromagnetic fields, bulk kinetic energy flux, enthalpy flux, heat flux, bulk acceleration, heating, and suprathermal particle energization, all of which are more prevalent on the earthward side. Such asymmetries are consistent with spacecraft observations reported in the literature. Our study shows that in the magnetotail, most of the energy converted by reconnection flows predominantly toward the Earth and has the potential of being geoeffective, rather than being expelled to the solar wind by the tailward flow. The energy conversion asymmetry arises from the presence of the non-zero normal magnetic field, the stronger lobe magnetic field, and the stronger cross-tail current earthward of the reconnection site in the pre-reconnecting thin current sheet.
Dielectric fluid directional spreading under the action of corona discharge
Authors: Zhou Shangru , Liu Jie , Hu Qun , Jiang Teng , Yang Jinchu , Liu Sheng , Zheng Huai
Published: January 2018

Liquid spreading is a very common nature phenomenon and of significant importance for a broad range of applications. In this study, a dielectric fluid directional spreading phenomenon is presented. Under the action of corona discharge, a dielectric fluid, here a typical silicone directionally spreads along conductive patterns on conductive/nonconductive substrates. Directional spreading behaviors of silicone were experimentally observed on different conductive patterns in detail. Spreading speeds were analyzed at different driving voltages, which induced the corona discharge. The presented phenomenon may be useful to inspire several techniques of manipulating liquid transportation and fabricating micropatterns.
Impact of vacancies on electronic properties of black phosphorus probed by STM
Authors: Riffle J. V. , Flynn C. , St. Laurent B. , Ayotte C. A. , Caputo C. A. , Hollen S. M.
Published: January 2018

Black phosphorus (BP) is receiving significant attention because of its direct 0.4–1.5 eV layer-dependent bandgap and high mobility. Because BP devices rely on exfoliation from bulk crystals, there is a need to understand the native impurities and defects in the source material. In particular, samples are typically p-doped, but the source of the doping is not well understood. Here, we use scanning tunneling microscopy and spectroscopy to compare the atomic defects of BP samples from two commercial sources. Even though the sources produced crystals with an order of magnitude difference in impurity atoms, we observed a similar defect density and level of p-doping. We attribute these defects to phosphorus vacancies and provide evidence that they are the source of p-doping. We also compare these native defects to those induced by air exposure and show that they are distinct and likely more important for the control of electronic structure. These results indicate that impurities in BP play a minor role compared to vacancies, which are prevalent in commercially available materials, and call for better control of vacancy defects.
Plasma studies of a linear magnetron operating in the range from DC to HiPIMS
Authors: Anders André , Yang Yuchen
Published: January 2018

Plasma properties of magnetrons have been extensively studied in the past with the focus on small, research-style magnetrons with planar disk targets. In this contribution, we report on plasma diagnostics of a linear magnetron because the linear geometry is widely used in industry and, more importantly here, it provides the unique opportunity to align a linear racetrack section with a streak camera's entrance slit. This allows us to follow the evolution of plasma instabilities, i.e., localized ionization zones or spokes, as they travel along the racetrack. This report greatly extends our more limited and focused study on the structure and velocity of spokes [Anders and Yang, Appl. Phys. Lett. 111, 064103 (2017)]. Following recent plasma potential measurements [Panjan and Anders, J. Appl. Phys. 121, 063302 (2017)], we interpret optical emission information with localized electron heating. We confirm that for low direct current operation, spokes move in the −E×B direction, and in the opposite direction in the high current mode. Streak images indicate slower spoke velocities near corners compared to spoke velocities in the straight sections of the racetrack. Spoke splitting and merging are observed supporting the interpretation that spoke motion represents a phase velocity of the region of greatest ionization and is not a motion of plasma. Fast camera investigations are supplemented by measurements of the energy distribution functions of ions emitted from the straight and curved regions of the racetrack, showing notable and reproducible differences.
Energetics of charged metal clusters containing vacancies
Authors: Pogosov Valentin V. , Reva Vitalii I.
Published: January 2018

We study theoretically large metal clusters containing vacancies. We propose an approach, which combines the Kohn-Sham results for monovacancy in a bulk of metal and analytical expansions in small parameters cv (relative concentration of vacancies) and RN,v−1, RN,v being cluster radii. We obtain expressions of the ionization potential and electron affinity in the form of corrections to electron work function, which require only the characteristics of 3D defect-free metal. The Kohn-Sham method is used to calculate the electron profiles, ionization potential, electron affinity, electrical capacitance; dissociation, cohesion, and monovacancy-formation energies of the small perfect clusters NaN, MgN, AlN (N ≤ 270) and the clusters containing a monovacancy (N ≥ 12) in the stabilized-jellium model. The quantum-sized dependences for monovacancy-formation energies are calculated for the Schottky scenario and the “bubble blowing” scenario, and their asymptotic behavior is also determined. It is shown that the asymptotical behaviors of size dependences for these two mechanisms differ from each other and weakly depend on the number of atoms in the cluster. The contribution of monovacancy to energetics of charged clusters and the size dependences of their characteristics and asymptotics are discussed. It is shown that the difference between the characteristics for the neutral and charged clusters is entirely determined by size dependences of ionization potential and electron affinity. Obtained analytical dependences may be useful for the analysis of the results of photoionization experiments and for the estimation of the size dependences of the vacancy concentration including the vicinity of the melting point.
Impact of crystal orientation on the modulation bandwidth of InGaN/GaN light-emitting diodes
Authors: Monavarian M. , Rashidi A. , Aragon A. A. , Oh S. H. , Rishinaramangalam A. K. , DenBaars S. P. , Feezell D.
Published: January 2018

High-speed InGaN/GaN blue light-emitting diodes (LEDs) are needed for future gigabit-per-second visible-light communication systems. Large LED modulation bandwidths are typically achieved at high current densities, with reports close to 1 GHz bandwidth at current densities ranging from 5 to 10 kA/cm2. However, the internal quantum efficiency (IQE) of InGaN/GaN LEDs is quite low at high current densities due to the well-known efficiency droop phenomenon. Here, we show experimentally that nonpolar and semipolar orientations of GaN enable higher modulation bandwidths at low current densities where the IQE is expected to be higher and power dissipation is lower. We experimentally compare the modulation bandwidth vs. current density for LEDs on nonpolar (101¯0), semipolar (202¯1¯), and polar 0001 orientations. In agreement with wavefunction overlap considerations, the experimental results indicate a higher modulation bandwidth for the nonpolar and semipolar LEDs, especially at relatively low current densities. At 500 A/cm2, the nonpolar LED has a 3 dB bandwidth of ∼1 GHz, while the semipolar and polar LEDs exhibit bandwidths of 260 MHz and 75 MHz, respectively. A lower carrier density for a given current density is extracted from the RF measurements for the nonpolar and semipolar LEDs, consistent with the higher wavefunction overlaps in these orientations. At large current densities, the bandwidth of the polar LED approaches that of the nonpolar and semipolar LEDs due to coulomb screening of the polarization field. The results support using nonpolar and semipolar orientations to achieve high-speed LEDs at low current densities.
Studies on the transmission of sub-THz waves in magnetized inhomogeneous plasma sheath
Authors: Yuan Kai , Shen Linfang , Yao Ming , Deng Xiaohua , Chen Zhou , Hong Lujun
Published: January 2018

There have been many studies on the sub-terahertz (sub-THz) wave transmission in reentry plasma sheaths. However, only some of them have paid attention to the transmission of sub-THz waves in magnetized plasma sheaths. In this paper, the transmission of sub-THz waves in both unmagnetized and magnetized reentry plasma sheaths was investigated. The impacts of temporal evolution of the plasma sheath on the wave transmission were studied. The transmission of “atmospheric window” frequencies in a magnetized plasma sheath was discussed in detail. According to the study, the power transmission rates (Tp) for the left hand circular (LHC) and the right hand circular modes in the magnetized plasma sheath are obviously higher and lower than those in the unmagnetized plasma sheath, respectively. The Tp of LHC mode increases with both wave frequency and external magnetic field strength. Also, the Tp of LHC mode in both magnetized and unmagnetized plasma sheaths varies with time due to the temporal evolution of the plasma sheath. Moreover, the performance of sub-THz waves in magnetized plasma sheath hints at a new approach to the “blackout” problem. The new approach, which is in the capability of modern technology, is to utilize the communication system operating at 140 GHz with an onboard magnet installed near the antenna.
Surface tension and viscosity play significant roles in metal nanofilm heat destabilization
Authors: Liebendorfer Adam
Published: January 2018

Self-consistent simulations have started to unravel the mysteries of how heat affects the evolution of nanoscale metal films and filaments.
Kinetics of mercury accumulation by freshwater biofilms
Authors: Dranguet Perrine , Slaveykova Vera I. , Le Faucheur Séverine
Published: January 2018

Environmental contextMercury (Hg) is a major environmental contaminant due to its toxicity, accumulation and biomagnification along the food chain. We demonstrate that Hg accumulation by biofilms, one possible entry point for Hg into food webs, is rapid and depends on biofilm structure and composition. These findings have important implications for the understanding of Hg bioavailability and effects towards aquatic microorganisms. AbstractMercury contamination is of high concern due to its bioaccumulation, toxicity and biomagnification along the food chain. Biofilms can accumulate Hg and contribute to its incorporation in freshwater food webs. Nevertheless, the accumulation kinetics of Hg by biofilms is not well described and understood. The aim of the present study was thus to gain mechanistic understanding of Hg accumulation by biofilms. Kinetics of Hg uptake by biofilms of different ages (e.g. different compositions) was characterised by determining Hg contents in biofilms with and without a cysteine-washing step. Hg accumulation was rapid in both biofilms, with the uptake rate constant of the younger biofilm 10 times higher than that of the older biofilm. Moreover, accumulated Hg reached a plateau at 24h exposure in the younger biofilm, whereas it increased linearly in the older biofilm. The observed difference in Hg uptake by the studied biofilms is likely a result of the difference in biofilm thickness (and thus Hg diffusion inside the biofilm matrix) and microbial composition. These findings have important implications for the understanding of Hg bioavailability and effects towards aquatic microorganisms.
Soil organic carbon retention more affected by altitude than texture in a forested mountain range in Brazil
Authors: Zinn Y. L. , Andrade A. B. , Araujo M. A. , Lal R.
Published: January 2018

Little is known about how soil organic carbon (SOC) under tropical forests is affected by altitude. We investigated the effects of soil texture and altitude on SOC retention under native forests in Brazil, by sampling two pairs of soils of coarser and finer texture, developed respectively from quartzite and mica-schist. One soil pair was sited at altitude 1060 m, and the other at 1230 m, along a mountain range. For 1060 m, the soil with ~36% clay contained 227 Mg SOC ha–1 (0–1 m depth), the double of the soil with ~16% clay. Such effect of texture was negligible at 1230 m, where SOC stocks were 205 Mg ha–1 for the soil with ~12% clay, and 217 Mg ha–1 for the soil with ~21% clay. Furthermore, there were positive correlations between SOC concentrations with clay + silt contents and specific surface area for 1060 m but not 1230 m altitude, suggesting that SOC retention was affected by texture only for altitudes near 1000 m or lower. At 1230 m, lower temperatures were predominant in SOC stabilisation through slower decomposition. In addition, 65–80% of total SOC was associated with clays, indicating a high degree of organic alteration. Interestingly, at 1235 m, SOC concentration in clay fractions reached 17%, much higher than at 1060 m, strongly suggesting SOC saturation. Thus, at 1235 m the interaction of SOC with soil minerals was probably weaker than at 1060 m or lower, and so SOC stocks are more susceptible to decay.
Transit-time and age distributions for nonlinear time-dependent compartmental systems
Authors: Metzler Holger , Müller Markus , Sierra Carlos A.
Published: January 2018

Many processes in nature are modeled using compartmental systems (reservoir/pool/box systems). Usually, they are expressed as a set of first-order differential equations describing the transfer of matter across a network of compartments. The concepts of age of matter in compartments and the time required for particles to transit the system are important diagnostics of these models with applications to a wide range of scientific questions. Until now, explicit formulas for transit-time and age distributions of nonlinear time-dependent compartmental systems were not available. We compute densities for these types of systems under the assumption of well-mixed compartments. Assuming that a solution of the nonlinear system is available at least numerically, we show how to construct a linear time-dependent system with the same solution trajectory. We demonstrate how to exploit this solution to compute transit-time and age distributions in dependence on given start values and initial age distributions. Furthermore, we derive equations for the time evolution of quantiles and moments of the age distributions. Our results generalize available density formulas for the linear time-independent case and mean-age formulas for the linear time-dependent case. As an example, we apply our formulas to a nonlinear and a linear version of a simple global carbon cycle model driven by a time-dependent input signal which represents fossil fuel additions. We derive time-dependent age distributions for all compartments and calculate the time it takes to remove fossil carbon in a business-as-usual scenario.
Antibody detection by agglutination–PCR (ADAP) enables early diagnosis of HIV infection by oral fluid analysis
Authors: Tsai Cheng-ting , Robinson Peter V. , Cortez Felipe de Jesus , Elma Maria L. B. , Seftel David , Pourmandi Narges , Pandori Mark W. , Bertozzi Carolyn R.
Published: January 2018

Significance

There is a substantial public health interest in identifying HIV-infected individuals through population-based screening. Oral fluid (OF) is easier to collect than blood and therefore ideal for such screening efforts. Unfortunately, OF has a very low concentration of anti-HIV antibodies (markers of HIV infection), which current assays cannot detect during the early stage of this disease. Here we report an assay for anti-HIV antibodies in OF that is up to 10,000 times more sensitive than current alternatives. This assay, called Antibody Detection by Agglutination–PCR (ADAP), could be broadly deployed to screen at-risk populations using OF in many settings, including those where cold chain shipping is not available (low-resource settings) and where needles are inconvenient (pediatrics) or unsafe (prisons).
Frequency modulation of neural oscillations according to visual task demands
Authors: Wutz Andreas , Melcher David , Samaha Jason
Published: January 2018

Significance

Neural oscillations are hypothesized to play an important role in modulating perceptual processing in accordance with top-down goals. For instance, the amplitude, phase, and spatial distribution of alpha-band oscillations change with attention. Given recent links between the peak frequency of alpha oscillations and the temporal resolution of perception, we investigated whether frequency modulation occurs when task demands emphasize integration or segregation of visual input over time. We found that alpha frequency in occipital–temporal cortex decreased during, and in anticipation of, stimulus processing when task demands required temporal integration compared with segregation. These results demonstrate a unique top-down mechanism by which the brain controls the temporal resolution of visual processing in accordance with current task demands.
Intracellular Ca
2+
stores control in vivo neuronal hyperactivity in a mouse model of Alzheimer’s disease
Authors: Lerdkrai Chommanad , Asavapanumas Nithi , Brawek Bianca , Kovalchuk Yury , Mojtahedi Nima , Olmedillas del Moral Maria , Garaschuk Olga
Published: January 2018

Significance

Although both patients with Alzheimer’s disease (AD) and mouse models of the disease suffer from a profound neuronal hyperactivity mediating an impairment of memory and cognition, the underlying mechanisms remain elusive. Here, we show that neuronal hyperactivity is a hallmark of healthy aging but is further aggravated by AD-related mutations in presenilin 1 protein. AD-mediated enhancement of neuronal hyperactivity occurred even in the absence of amyloid plaques and neuroinflammation, mainly due to a presenilin-mediated dysfunction of intracellular Ca
2+
stores in presynaptic boutons, likely causing more frequent activation of synaptic NMDA receptors. Emptying the stores normalized neuronal network activity in mutant mice, thus identifying presynaptic Ca
2+
stores as a key element controlling AD-related neuronal hyperactivity and as a target for disease-modifying treatments.
Structure and function of the archaeal response regulator CheY
Authors: Quax Tessa E. F. , Altegoer Florian , Rossi Fernando , Li Zhengqun , Rodriguez-Franco Marta , Kraus Florian , Bange Gert , Albers Sonja-Verena
Published: January 2018

Motility is a central feature of many microorganisms and provides an efficient strategy to respond to environmental changes. Bacteria and archaea have developed fundamentally different rotary motors enabling their motility, termed flagellum and archaellum, respectively. Bacterial motility along chemical gradients, called chemotaxis, critically relies on the response regulator CheY, which, when phosphorylated, inverses the rotational direction of the flagellum via a switch complex at the base of the motor. The structural difference between archaellum and flagellum and the presence of functional CheY in archaea raises the question of how the CheY protein changed to allow communication with the archaeal motility machinery. Here we show that archaeal CheY shares the overall structure and mechanism of magnesium-dependent phosphorylation with its bacterial counterpart. However, bacterial and archaeal CheY differ in the electrostatic potential of the helix α4. The helix α4 is important in bacteria for interaction with the flagellar switch complex, a structure that is absent in archaea. We demonstrated that phosphorylation-dependent activation, and conserved residues in the archaeal CheY helix α4, are important for interaction with the archaeal-specific adaptor protein CheF. This forms a bridge between the chemotaxis system and the archaeal motility machinery. Conclusively, archaeal CheY proteins conserved the central mechanistic features between bacteria and archaea, but differ in the helix α4 to allow binding to an archaellum-specific interaction partner.
Evolutionary history of carbon monoxide dehydrogenase/acetyl-CoA synthase, one of the oldest enzymatic complexes
Authors: Adam Panagiotis S. , Borrel Guillaume , Gribaldo Simonetta
Published: January 2018

Significance

Before the emergence of oxygenic photosynthesis and the accumulation of oxygen on Earth, life was essentially composed of anaerobic microorganisms. However, very little is known about which metabolisms were present at the time. Anaerobic carbon fixation through the Wood–Ljungdahl pathway is believed to be among the most ancient, and still plays a pivotal role in modern ecosystems. However, its origin and evolutionary history has been disputed. We analysed the distribution and phylogeny of carbon monoxide dehydrogenase/acetyl-CoA synthase, the main enzymatic complex of the pathway in thousands of bacterial and archaeal genomes. We show that this complex was already at work in the last universal common ancestor and has been remarkably conserved in microorganisms over more than 3.5 billion years.
Potential for western US seasonal snowpack prediction
Authors: Kapnick Sarah B. , Yang Xiaosong , Vecchi Gabriel A. , Delworth Thomas L. , Gudgel Rich , Malyshev Sergey , Milly P. C. D. , Shevliakova Elena , Underwood Seth , Margulis Steven A.
Published: January 2018

Western US snowpack—snow that accumulates on the ground in the mountains—plays a critical role in regional hydroclimate and water supply, with 80% of snowmelt runoff being used for agriculture. While climate projections provide estimates of snowpack loss by the end of the century and weather forecasts provide predictions of weather conditions out to 2 weeks, less progress has been made for snow predictions at seasonal timescales (months to 2 years), crucial for regional agricultural decisions (e.g., plant choice and quantity). Seasonal predictions with climate models first took the form of El Niño predictions 3 decades ago, with hydroclimate predictions emerging more recently. While the field has been focused on single-season predictions (3 months or less), we are now poised to advance our predictions beyond this timeframe. Utilizing observations, climate indices, and a suite of global climate models, we demonstrate the feasibility of seasonal snowpack predictions and quantify the limits of predictive skill 8 months in advance. This physically based dynamic system outperforms observation-based statistical predictions made on July 1 for March snowpack everywhere except the southern Sierra Nevada, a region where prediction skill is nonexistent for every predictor presently tested. Additionally, in the absence of externally forced negative trends in snowpack, narrow maritime mountain ranges with high hydroclimate variability pose a challenge for seasonal prediction in our present system; natural snowpack variability may inherently be unpredictable at this timescale. This work highlights present prediction system successes and gives cause for optimism for developing seasonal predictions for societal needs.
Humidity determines snowpack ablation under a warming climate
Authors: Harpold Adrian A. , Brooks Paul D.
Published: January 2018

Significance

Changes in the amount and timing of snowmelt have large effects on water for society and ecosystems. Using long-term records from across the western United States, we demonstrate that atmospheric humidity is a major control on how seasonal snow responds to warming temperatures. Specifically, we observe an increase in the frequency and magnitude of episodic winter melt events under higher humidity that may alter the timing of water availability. In lower-humidity regions, however, warming is associated with increased sublimation and/or evaporation from the snowpack further reducing the amount of available water in these dry regions. Management approaches to address these changes in snowmelt water resources from continued warming will require improved estimation of variable and changing atmospheric humidity.
Motile cilia of human airway epithelia contain hedgehog signaling components that mediate noncanonical hedgehog signaling
Authors: Mao Suifang , Shah Alok S. , Moninger Thomas O. , Ostedgaard Lynda S. , Lu Lin , Tang Xiao Xiao , Thornell Ian M. , Reznikov Leah R. , Ernst Sarah E. , Karp Philip H. , Tan Ping , Keshavjee Shaf , Abou Alaiwa Mahmoud H. , Welsh Michael J.
Published: January 2018

Significance

Previous studies localized the hedgehog (HH) signaling system to primary cilia. We discovered that motile cilia on airway epithelia also contain HH signaling proteins, indicating that like primary cilia, these motile cilia have an important sensory function. However, in contrast to the function of HH signaling in most primary cilia, sonic hedgehog (SHH) elicits noncanonical signaling, reducing cellular levels of cAMP. These findings suggest that airway SHH may quiet airway defenses. Involvement of SHH in lung disease and positioning of motile cilia where they sample SHH and other ligands in the airway lumen suggest that noncanonical HH signaling might modulate airway responses to the environment in health and disease.
Efficient ultrafiltration‐based protocol to deplete extracellular vesicles from fetal bovine serum
Authors: Kornilov Roman , Puhka Maija , Mannerström Bettina , Hiidenmaa Hanna , Peltoniemi Hilkka , Siljander Pia , Seppänen‐Kaijansinkko Riitta , Kaur Sippy
Published: January 2018

Fetal bovine serum (FBS) is the most commonly used supplement in studies involving cell‐culture experiments. However, FBS contains large numbers of bovine extracellular vesicles (EVs), which hamper the analyses of secreted EVs from the cell type of preference and, thus, also the downstream analyses. Therefore, a prior elimination of EVs from FBS is crucial. However, the current methods of EV depletion by ultracentrifugation are cumbersome and the commercial alternatives expensive. In this study, our aim was to develop a protocol to completely deplete EVs from FBS, which may have wide applicability in cell‐culture applications. We investigated different EV‐depleted FBS prepared by our novel ultrafiltration‐based protocol, by conventionally used overnight ultracentrifugation, or commercially available depleted FBS, and compared them with regular FBS. All sera were characterized by nanoparticle tracking analysis, electron microscopy, Western blotting and RNA quantification. Next, adipose‐tissue mesenchymal stem cells (AT‐MSCs) and cancer cells were grown in the media supplemented with the three different EV‐depleted FBS and compared with cells grown in regular FBS media to assess the effects on cell proliferation, stress, differentiation and EV production. The novel ultrafiltration‐based protocol depleted EVs from FBS clearly more efficiently than ultracentrifugation and commercial methods. Cell proliferation, stress, differentiation and EV production of AT‐MSCs and cancer cell lines were similarly maintained in all three EV‐depleted FBS media up to 96 h. In summary, our ultrafiltration protocol efficiently depletes EVs, is easy to use and maintains cell growth and metabolism. Since the method is also cost‐effective and easy to standardize, it could be used in a wide range of cell‐culture applications helping to increase comparability of EV research results between laboratories.
The adherens junction–associated LIM domain protein Smallish regulates epithelial morphogenesis
Authors: Beati Hamze , Peek Irina , Hordowska Paulina , Honemann-Capito Mona , Glashauser Jade , Renschler Fabian A. , Kakanj Parisa , Ramrath Andreas , Leptin Maria , Luschnig Stefan , Wiesner Silke , Wodarz Andreas
Published: January 2018

In epithelia, cells adhere to each other in a dynamic fashion, allowing the cells to change their shape and move along each other during morphogenesis. The regulation of adhesion occurs at the belt-shaped adherens junction, the zonula adherens (ZA). Formation of the ZA depends on components of the Par–atypical PKC (Par-aPKC) complex of polarity regulators. We have identified the Lin11, Isl-1, Mec-3 (LIM) protein Smallish (Smash), the orthologue of vertebrate LMO7, as a binding partner of Bazooka/Par-3 (Baz), a core component of the Par-aPKC complex. Smash also binds to Canoe/Afadin and the tyrosine kinase Src42A and localizes to the ZA in a planar polarized fashion. Animals lacking Smash show loss of planar cell polarity (PCP) in the embryonic epidermis and reduced cell bond tension, leading to severe defects during embryonic morphogenesis of epithelial tissues and organs. Overexpression of Smash causes apical constriction of epithelial cells. We propose that Smash is a key regulator of morphogenesis coordinating PCP and actomyosin contractility at the ZA.
Finsler Geometry Modeling of an Orientation-Asymmetric Surface Model for Membranes
Authors: Proutorov Evgenii , Koibuchi Hiroshi
Published: January 2018

In this paper, a triangulated surface model is studied in the context of Finsler geometry (FG) modeling. This FG model is an extended version of a recently reported model for two-component membranes, and it is asymmetric under surface inversion. We show that the definition of the model is independent of how the Finsler length of a bond is defined. This leads us to understand that the canonical (or Euclidean) surface model is obtained from the FG model such that it is uniquely determined as a trivial model from the viewpoint of well definedness.