bluuebunny/crossref_metadata_2025 huggingface dataset:
Mechanism of the fcc-to-hcp phase transformation in solid Ar
Authors: Li Bingxi , Qian Guangrui , Oganov Artem R. , Boulfelfel Salah Eddine , Faller Roland
Published: June 2017

We present an atomistic description of the fcc-to-hcp transformation mechanism in solid argon (Ar) obtained from transition path sampling molecular dynamics simulation. The phase transition pathways collected during the sampling for an 8000-particle system reveal three transition types according to the lattice deformation and relaxation details. In all three transition types, we see a critical accumulation of defects and uniform growth of a less ordered transition state, followed by a homogeneous growth of an ordered phase. Stacking disorder is discussed to describe the transition process and the cooperative motions of atoms in {111} planes. We investigate nucleation with a larger system: in a system of 18 000 particles, the collective movements of atoms required for this transition are facilitated by the formation and growth of stacking faults. However, the enthalpy barrier is still far beyond the thermal fluctuation. The high barrier explains previous experimental observations of the inaccessibility of the bulk transition at low pressure and its sluggishness even at extremely high pressure. The transition mechanism in bulk Ar is different from Ar nanoclusters as the orthorhombic intermediate structure proposed for the latter is not observed in any of our simulations.
On the sighting of unicorns: A variational approach to computing invariant sets in dynamical systems
Authors: Junge Oliver , Kevrekidis Ioannis G.
Published: June 2017

We propose to compute approximations to invariant sets in dynamical systems by minimizing an appropriate distance between a suitably selected finite set of points and its image under the dynamics. We demonstrate, through computational experiments, that this approach can successfully converge to approximations of (maximal) invariant sets of arbitrary topology, dimension, and stability, such as, e.g., saddle type invariant sets with complicated dynamics. We further propose to extend this approach by adding a Lennard-Jones type potential term to the objective function, which yields more evenly distributed approximating finite point sets, and illustrate the procedure through corresponding numerical experiments.
Uniform coating of Ta2O5 on vertically aligned substrate: A prelude to forced flow atomic layer deposition
Authors: Mishra Mrinalini , Kei Chi-Chung , Yu Yu-Hsuan , Liu Wei-Szu , Perng Tsong-Pyng
Published: June 2017

Uniform tantalum oxide thin films, with a growth rate of 0.6 Å/cycle, were fabricated on vertically aligned, 10 cm-long, silicon substrates using an innovative atomic layer deposition (ALD) design. The ALD system, with a reaction chamber depth of 13.3 cm and 18 vertical enclosed channels (inner diameter 1.3 cm), was coupled with a shower-head type precursor conduit plate bearing 6 radial channels. This design enabled deposition on 6 silicon substrates at a time. The degrees of non-uniformity of deposits along the length of the silicon wafer and across different positions in the ALD chamber were found to be 1.77%-6.21% and 3.27%-5.45%, respectively. A further advantage of the design is that the conduit plate may be modified and the number of channels increased to process 18 substrates simultaneously, thus moving toward efficient and expedited ALD systems.
Test-area surface tension calculation of the graphene-methane interface: Fluctuations and commensurability
Authors: d’Oliveira H. D. , Davoy X. , Arche E. , Malfreyt P. , Ghoufi A.
Published: June 2017

The surface tension (γ) of methane on a graphene monolayer is calculated by using the test-area approach. By using a united atom model to describe methane molecules, strong fluctuations of surface tension as a function of the surface area of the graphene are evidenced. In contrast with the liquid-vapor interfaces, the use of a larger cutoff does not fully erase the fluctuations in the surface tension. Counterintuitively, the description of methane and graphene from the Optimized Potentials for Liquid Simulations all-atom model and a flexible model, respectively, led to a lessening in the surface tension fluctuations. This result suggests that the origin of fluctuations in γ is due to a model-effect rather than size-effects. We show that the molecular origin of these fluctuations is the result of a commensurable organization between both graphene and methane. This commensurable structure can be avoided by describing methane and graphene from a flexible force field. Although differences in γ with respect to the model have been often reported, it is the first time that the model drastically affects the physics of a system.
What is special about how roaming chemical reactions traverse their potential surfaces? Differences in geodesic paths between roaming and non-roaming events
Authors: Cofer-Shabica D. Vale , Stratt Richard M.
Published: June 2017

With the notable exception of some illustrative two-degree-of-freedom models whose surprising classical dynamics has been worked out in detail, theories of roaming have largely bypassed the issue of when and why the counterintuitive phenomenon of roaming occurs. We propose that a useful way to begin to address these issues is to look for the geodesic (most efficient) pathways through the potential surfaces of candidate systems. Although roaming manifests itself in an unusual behavior at asymptotic geometries, we found in the case of formaldehyde dissociation that it was the pathways traversing the parts of the potential surface corresponding to highly vibrationally excited reactants that were the most revealing. An examination of the geodesics for roaming pathways in this region finds that they are much less tightly defined than the geodesics in that same region that lead directly to dissociation (whether into closed-shell products or into radical products). Thus, the broader set of options available to the roaming channel gives it an entropic advantage over more conventional reaction channels. These observations suggest that what leads to roaming in other systems may be less the presence of a localized “roaming transition state,” than the existence of an entire region of the potential surface conducive to multiple equivalent pathways.
Reduced-order description of transient instabilities and computation of finite-time Lyapunov exponents
Authors: Babaee Hessam , Farazmand Mohamad , Haller George , Sapsis Themistoklis P.
Published: June 2017

High-dimensional chaotic dynamical systems can exhibit strongly transient features. These are often associated with instabilities that have a finite-time duration. Because of the finite-time character of these transient events, their detection through infinite-time methods, e.g., long term averages, Lyapunov exponents or information about the statistical steady-state, is not possible. Here, we utilize a recently developed framework, the Optimally Time-Dependent (OTD) modes, to extract a time-dependent subspace that spans the modes associated with transient features associated with finite-time instabilities. As the main result, we prove that the OTD modes, under appropriate conditions, converge exponentially fast to the eigendirections of the Cauchy–Green tensor associated with the most intense finite-time instabilities. Based on this observation, we develop a reduced-order method for the computation of finite-time Lyapunov exponents (FTLE) and vectors. In high-dimensional systems, the computational cost of the reduced-order method is orders of magnitude lower than the full FTLE computation. We demonstrate the validity of the theoretical findings on two numerical examples.
Electron emission yield for low energy electrons: Monte Carlo simulation and experimental comparison for Al, Ag, and Si
Authors: Pierron J. , Inguimbert C. , Belhaj M. , Gineste T. , Puech J , Raine M.
Published: June 2017

The electron emission under electron impact between 10 eV and 2 keV is investigated with a Monte Carlo (MC) code in aluminum, silver, and silicon. The code is based on the complex dielectric function theory to describe the inelastic scattering and uses the Mott's model of partial waves to describe the elastic scattering. It takes into account both volume and surface plasmon excitations. The simulation results are compared with the experimental measurements of electron emission yields (EEY) and energy spectra of low energy electrons performed in ultrahigh vacuum on Ar-etched bulk samples. Our MC simulations at low energy are found to be in fairly good agreement with our experimental measurements. The peaks corresponding to the surface plasmon, the volume plasmon and its multiples and to the Auger transitions appear clearly on the energy loss spectra of aluminum, silver, and silicon. The simulated EEY are also in fairly good agreement with our measurements and with data from the literature. The EEY at normal incidence is studied for secondary and backscattered electrons. A focus is made for the EEY below 50 eV where a fairly good agreement is found with Bronstein and Fraiman's measurements on vacuum evaporated samples. Below 2 keV, for silver and aluminum, the total EEY is given for different angles of incidence θ. Some discrepancies are observed between our experimental measurements and our MC simulations for high angles of incidence. These discrepancies can be attributed to the modeling of surface plasmon excitations, surface oxidation, or roughness that occur during the Ar-etching process.
An alternative laser driven photodissociation mechanism of pyrrole via πσ*1∕S conical intersection
Authors: Nandipati K. R. , Lan Z. , Singh H. , Mahapatra S.
Published: June 2017

A first principles quantum dynamics study of N–H photodissociation of pyrrole on the S0−1πσ*(A21) coupled electronic states is carried out with the aid of an optimally designed UV-laser pulse. A new photodissociation path, as compared to the conventional barrier crossing on the πσ*1 state, opens up upon electronic transitions under the influence of pump-dump laser pulses, which efficiently populate both the dissociation channels. The interplay of electronic transitions due both to vibronic coupling and the laser pulse is observed in the control mechanism and discussed in detail. The proposed control mechanism seems to be robust, and not discussed in the literature so far, and is expected to trigger future experiments on the πσ*1 photochemistry of molecules of chemical and biological importance. The design of the optimal pulses and their application to enhance the overall dissociation probability is carried out within the framework of optimal control theory. The quantum dynamics of the system in the presence of pulse is treated by solving the time-dependent Schrödinger equation in the semi-classical dipole approximation.
Complex behavior in chains of nonlinear oscillators
Authors: Alonso Leandro M.
Published: June 2017

This article outlines sufficient conditions under which a one-dimensional chain of identical nonlinear oscillators can display complex spatio-temporal behavior. The units are described by phase equations and consist of excitable oscillators. The interactions are local and the network is poised to a critical state by balancing excitation and inhibition locally. The results presented here suggest that in networks composed of many oscillatory units with local interactions, excitability together with balanced interactions is sufficient to give rise to complex emergent features. For values of the parameters where complex behavior occurs, the system also displays a high-dimensional bifurcation where an exponentially large number of equilibria are borne in pairs out of multiple saddle-node bifurcations.
Broadband millimeter-wave anti-reflection coatings on silicon using pyramidal sub-wavelength structures
Authors: Young Karl , Wen Qi , Hanany Shaul , Imada Hiroaki , Koch Jürgen , Matsumura Tomotake , Suttmann Oliver , Schütz Viktor
Published: June 2017

We used two novel approaches to produce sub-wavelength structure anti-reflection coatings on silicon for millimeter and sub-millimeter wave bands: picosecond laser ablation and dicing with beveled saws. We produced pyramidal structures with both techniques. The diced sample, machined on only one side, had a pitch and a height of 350 μm and 972 μm, respectively. The two laser ablated samples had a pitch of 180 μm and heights of 720 μm and 580 μm; only one of these samples was ablated on both sides. We present measurements of shape and optical performances and comparisons to the optical performance predicted using finite element analysis and rigorous coupled wave analysis. By extending the measured performance of the one-sided diced sample to the two-sided case, we demonstrate a 25% band averaged reflectance of less than 5% over a bandwidth of 97% centered on 170 GHz. Using the two-sided laser ablation sample, we demonstrate a reflectance of less than 5% over a bandwidth of 83% centered on 346 GHz.
Lab-on-chip microfluidic impedance measurement for laminar flow ratio sensing and differential conductivity difference detection
Authors: Kong Tian Fook , Shen Xinhui , Marcos  , Yang Chun
Published: June 2017

We present a microfluidic impedance device for achieving both the flow ratio sensing and the conductivity difference detection between sample stream and reference buffer. By using a flow focusing configuration, with the core flow having a higher conductivity sample than the sheath flow streams, the conductance of the device varies linearly with the flow ratio, with R2 > 0.999. On the other hand, by using deionized (DI)-water sheath flow as a reference, we can detect the difference in conductivity between the buffer of core flow and sheath DI-water with a high detection sensitivity of up to 1 nM of sodium chloride solution. Our study provides a promising approach for on-chip flow mixing characterization and bacteria detection.
On the correlations between the excitonic luminescence efficiency and the QW numbers in multiple InGaN/GaN QW structure
Authors: Hospodková A. , Oswald J. , Zíková M. , Pangrác J. , Kuldová K. , Blažek K. , Ledoux G. , Dujardin C. , Nikl M.
Published: June 2017

In this work, we compare the luminescence results obtained on InGaN/GaN multiple quantum well (QW) structures with different numbers of QWs. Structures are designed for scintillating applications, where large QW number covering particle penetration depth is necessary, and fast luminescence response is required. Special attention is devoted to increase the intensity of fast excitonic QW emission and to decrease the luminescence of the QW defect band, which has slower luminescence response and is undesired for fast scintillator applications. We found that increasing the In content in QWs suppresses the defect band luminescence and decreasing the QW growth rate increases the photoluminescence (PL) intensity of excitonic luminescence. We also show that increasing the number of InGaN further improves the PL properties of InGaN QWs. The photoluminescence and cathodoluminescence characteristics are compared and discussed.
Particle dynamics in wall-bounded thermal counterflow of superfluid helium
Authors: La Mantia M.
Published: June 2017

The motions of relatively small particles in wall-bounded thermal counterflow of superfluid helium are experimentally investigated, above 1 K, by using the particle tracking velocimetry technique. The effect of a solid boundary on this quantum flow has received little attention to date, and the focus here is on the corresponding flow-induced particle dynamics. The velocity and velocity difference statistical distributions of the particles are computed at length scales straddling two orders of magnitude across the mean distance between quantized vortices, the quantum length scale of the flow. The imposed counterflow velocity ranges between about 2 and 7 mm/s, resulting in suitably defined Reynolds numbers up to 20 000. The distributions are found to be wider in the bulk than close to the solid boundary, at small enough scales, and this suggests that the mean distance between the vortices increases with the distance from the wall. The outcome reinforces the view, supported to date solely by numerical simulations, that in thermal counterflow quantized vortices are not homogenously distributed in the channel and that they preferentially concentrate close to its walls. Boundary layers might therefore also exist in quantum flows, although some of their features appear to be significantly different from those attributed to wall-bounded flows of viscous fluids, due to the presence of quantized vortices.
Polarization dependence of tip-enhanced Raman and plasmon-resonance Rayleigh scattering spectra
Authors: Kitahama Yasutaka , Uemura Shohei , Katayama Ryota , Suzuki Toshiaki , Itoh Tamitake , Ozaki Yukihiro
Published: June 2017

Tip-enhanced Raman scattering (TERS) spectroscopy has high sensitivity and high spatial resolution, although it shows low reproducibility due to the variable optical properties of the tips. In the present study, polarized scattering spectra of localized surface plasmon resonance (LSPR) at the apex of the tip induced by conventional dark field illumination were compared with the corresponding TERS spectra, generated by excitation using polarization not only parallel and perpendicular to the tip, but also vertical to the sample plane (z-polarization). The polarization-dependence of LSPR was consistent with that of the TERS. Thus, the optical properties of the tip can be easily optimized before TERS measurement by excitation polarization that induces the largest LSPR signal.
A new class of enhanced kinetic sampling methods for building Markov state models
Authors: Bhoutekar Arti , Ghosh Susmita , Bhattacharya Swati , Chatterjee Abhijit
Published: June 2017

Markov state models (MSMs) and other related kinetic network models are frequently used to study the long-timescale dynamical behavior of biomolecular and materials systems. MSMs are often constructed bottom-up using brute-force molecular dynamics (MD) simulations when the model contains a large number of states and kinetic pathways that are not known a priori. However, the resulting network generally encompasses only parts of the configurational space, and regardless of any additional MD performed, several states and pathways will still remain missing. This implies that the duration for which the MSM can faithfully capture the true dynamics, which we term as the validity time for the MSM, is always finite and unfortunately much shorter than the MD time invested to construct the model. A general framework that relates the kinetic uncertainty in the model to the validity time, missing states and pathways, network topology, and statistical sampling is presented. Performing additional calculations for frequently-sampled states/pathways may not alter the MSM validity time. A new class of enhanced kinetic sampling techniques is introduced that aims at targeting rare states/pathways that contribute most to the uncertainty so that the validity time is boosted in an effective manner. Examples including straightforward 1D energy landscapes, lattice models, and biomolecular systems are provided to illustrate the application of the method. Developments presented here will be of interest to the kinetic Monte Carlo community as well.
High resolution X-ray diffraction studies of epitaxial ZnO nanorods grown by reactive sputtering
Authors: Nandi R. , Appani Shravan K. , Major S. S.
Published: June 2017

Vertically aligned and highly c-axis oriented ZnO nanorods were epitaxially grown on c-sapphire by dc reactive sputtering of zinc target in argon-oxygen atmosphere. Scanning electron microscopy shows that substrate temperature critically controls the morphology of sputtered ZnO films, eventually causing the formation of laterally oriented ZnO nanorods at higher temperatures (700 °C–750 °C), as confirmed by ϕ-scan measurements. High resolution X-ray diffraction was used to obtain the micro-structural parameters of ZnO columnar films/nanorods from Williamson-Hall plots of ω and ω-2θ scans, and rocking curves of asymmetric reflections. These results show that epitaxially grown ZnO nanorods exhibit substantially superior micro-structural parameters, namely, tilt (0.4°), twist (0.5°), and micro-strain (4 × 10−4), compared to columnar ZnO films grown at 500 °C–600 °C. The reciprocal space maps of (0002), (0004), 101¯1, 101¯4, and (112¯0) planes of ZnO nanorods were carried out to obtain the lattice parameters of epitaxial ZnO nanorods and calculate lattice strain (9 × 10−4, for both “a” and “c”), which indicates the absence of biaxial strain. Room temperature photoluminescence of epitaxial ZnO nanorods shows a strong near-band-edge emission along with negligible defect emission, owing to their high crystalline quality and micro-structural parameters.
The phosphorus and boron co-doping behaviors at nanoscale in Si nanocrystals/SiO2 multilayers
Authors: Li Dongke , Jiang Yicheng , Zhang Pei , Shan Dan , Xu Jun , Li Wei , Chen Kunji
Published: June 2017

Phosphorus (P) and Boron (B) co-doping effects at the nanoscale in Si nanocrystals/SiO2 multilayers have been studied in the present work. Several interesting experimental results are achieved which are in contrast to the case in bulk-Si and the previous observations on the doped Si nanocrystals. It is found that all the co-doping samples are n-type regardless of B doping ratios. The P doping efficiency in Si NCs is higher than B dopants, and it can be improved via B co-doping with suitable levels. Raman and ESR spectra indicate that the different occupation preferences of P and B in Si NCs are responsible for the interesting co-doping behaviors. It looks like that the electronic structures and the physical properties of Si NCs can be modulated via the impurities co-doping approach.
Berry phase shift from 2π to π in bilayer graphene by Li-intercalation and sequential desorption
Authors: Akiyama Ryota , Takano Yuma , Endo Yukihiro , Ichinokura Satoru , Nakanishi Ryosuke , Nomura Kentaro , Hasegawa Shuji
Published: June 2017

We have found that the Berry phase of bilayer graphene becomes π from 2π estimated by Shubnikov-de Haas oscillations when the A-B stacked pristine bilayer graphene experiences the Li-intercalation and sequential Li-desorption process in ultrahigh vacuum. Furthermore, the mobility of such processed bilayer graphene increases around four times larger, 8000 cm2/V·s, than that of the pristine bilayer graphene. This is mainly due to increment of the scattering time and decrement of the cyclotron mass, which can be interpreted as a result of the change of the stacking structure of bilayer graphene from A-B to A-A, corresponding to a change from the parabolic to the linear band dispersion.
Influence of exciton-phonons coupling on the exciton binding energy in monolayer transition metal dichalcogenides
Authors: Wang Zi-Wu , Li Wei-Ping , Xiao Yao , Li Run-Ze , Li Zhi-Qing
Published: June 2017

We theoretically investigate the correction of exciton binding energy arising from the exciton-optical phonon coupling in monolayer transition metal dichalcogenides (TMDs) using the linear operator and Lee-Low-Pines unitary transformation methods. We take into account not only the exciton coupling with intrinsic longitudinal optical phonon modes but also the surface optical phonon modes induced by polar substrates supporting monolayer TMDs. We find that the exciton binding energies are corrected on a large scale due to these exciton-optical phonon couplings. We discuss the dependences of exciton binding energy on the cut-off wave vector of optical phonon modes, the polarization strength of substrate materials, and the distance between polar substrates and TMDs. These results provide potential explanations for the divergence of the exciton binding energy between the experiment and theory in TMDs.
Roles of magnetized background ions in determining dynamics of 2D magnetized complex plasmas
Authors: Yang Fang , Kong Wei , Liu Songfen , Shi Feng , Wang Yupei
Published: June 2017

Dynamics of 2D magnetized complex plasmas is investigated based on the driven-dissipative dynamics simulation. Besides the usual Yukawa potential, a modified Yukawa potential which includes the effects of external magnetic field B on the shielding distance of the charged dust particles is used to account for the electrostatic interaction of the charged dust particles. It is found that shielding distance of the charged dust particles is greatly increased due to the magnetization of background ions, and the resulting equilibrium diffusion of the system differs from that of usual Yukawa system. Collective oscillation of the system is discussed in terms of Fourier analysis of velocity-auto-correlation function.
Intrinsic oxygen vacancies mediated multi-mechano-responsive piezoluminescence in undoped zinc calcium oxysulfide
Authors: Pan Cong , Zhang Jun-Cheng , Zhang Min , Yan Xu , Long Yun-Ze , Wang Xusheng
Published: June 2017

Piezoluminescence has achieved enormous advancement in the field of stress sensors, and mechano-driven lightings and displays; however the existing piezoluminescent materials universally need the external dopants of lanthanide or transition metal ions to create efficient luminescence. Herein, we report a bright piezoluminescence in undoped piezoelectric semiconductor CaZnOS, which is multi-mechano-sensitive to ultrasonic vibration, friction, impact and compression. Our experimental and density functional theory computational investigations indicate that the intrinsic oxygen vacancies of VO2+, VO+ and VO0 act as luminescent centers and trap states in multi-colored components of luminescence. In addition to saving resources and protecting environment, our research is expected to open a door for design and development of self-piezoluminescent materials, thereby largely expanding our understanding of piezoluminescent mechanism and promoting further utilization of piezoluminescence.
Modeling nonequilibrium dynamics of phase transitions at the nanoscale: Application to spin-crossover
Authors: Park Sang Tae , van der Veen Renske M.
Published: June 2017

In this article, we present a continuum mechanics based approach for modeling thermally induced single-nanoparticle phase transitions studied in ultrafast electron microscopy. By using coupled differential equations describing heat transfer and the kinetics of the phase transition, we determine the major factors governing the time scales and efficiencies of thermal switching in individual spin-crossover nanoparticles, such as the thermal properties of the (graphite) substrate, the particle thickness, and the interfacial thermal contact conductance between the substrate and the nanoparticle. By comparing the simulated dynamics with the experimental single-particle diffraction time profiles, we demonstrate that the proposed non-equilibrium phase transition model can fully account for the observed switching dynamics.
Analysis of the transfer function for layered piezoelectric ultrasonic sensors
Authors: Gutiérrrez-Reyes E. , García-Segundo C. , García-Valenzuela A. , Reyes-Ramírez B. , Gutiérrez-Juárez G. , Guadarrama-Santana A.
Published: June 2017

We model theoretically the voltage response to an acoustic pulse of a multilayer system forming a low noise capacitive sensor including a Polyvinylidene Fluoride piezoelectric film. First we model a generic piezoelectric detector consisting of a piezoelectric film between two metallic electrodes that are the responsible to convert the acoustic signal into a voltage signal. Then we calculate the pressure-to-voltage transfer function for a N-layer piezo-electric capacitor detector, allowing to study the effects of the electrode and protective layers thickness in typical layered piezoelectric sensors. The derived transfer function, when multiplied by the Fourier transform of the incident acoustic pulse, gives the voltage electric response in the frequency domain. An important concern regarding the transfer function is that it may have zeros at specific frequencies, and thus inverting the voltage Fourier transform of the pulse to recover the pressure signal in the time domain is not always, in principle, possible. Our formulas can be used to predict the existence and locations of such zeroes. We illustrate the use of the transfer function by predicting the electric signal generated at a multilayer piezoelectric sensor to an ultrasonic pulse generated photoacoustically by a laser pulse at a three media system with impedance mismatch. This theoretical calculations are compared with our own experimental measurements.
Xylem vessel length and distribution: does analysis method matter? A study using Acacia
Authors: Williamson Virginia G. , Milburn John A.
Published: June 2017

Knowledge of xylem vessel length is important for several reasons, including the accurate calculation and comparison of hydraulic conductivity studies in excised stems. Vessel length data and distributions are also relevant in some anatomical, ecological, evolutionary, pathological and compatible hydraulic studies. However, determining vessel length is tedious, so is often either avoided or undertaken arbitrarily in hydraulic conductivity studies. We examined four injection media (paints and inks) under transmission electron microscopy to ascertain which was most suitable for determining vessel length. Hunt’s Speedball India ink, with evenly distributed, uniform spherical carbon particles of 33 nm, would avoid premature vessel blockage and, therefore, coupled with the fact that it is non-toxic, is the preferred medium to determine vessel length in Acacia amoena Wendl. terminal stems. The longest vessel was 10 cm, which accounted for 0.4% of vessels. Vessel length distributions were then determined and compared using the same dataset and four established methods. All four methods produced distributions which indicated that the most common vessel length class was short (0–2 cm), and no method was significantly different from the other; however, for ease of calculation, the Christman et al. (2009) method is recommended. Whether vessel length or distribution is necessary for hydraulic-conductivity studies will depend on whether or not merely indicative rates of flow are required, but to provide comparative information for global datasets, then they are needed.
Rice straw mulch for post-fire erosion control: assessing non-target effects on vegetation communities
Authors: Shive Kristen L. , Estes Becky L. , White Angela M. , Safford Hugh D. , O'Hara Kevin L. , Stephens Scott L.
Published: June 2017

Straw mulch is commonly used for post-fire erosion control in severely burned areas but this practice can introduce non-native species, even when certified weed-free straw is used. Rice straw has recently been promoted as an alternative to wheat under the hypothesis that non-native species that are able to grow in a rice field are unlikely to establish in dry forested habitats. We investigated this hypothesis in the severely burned areas of the 2013 Rim Fire in the Sierra Nevada that were treated with rice straw post-fire. In 2014, we installed 134 plots in mulched and control areas with >95% tree mortality and re-measured a subsample in 2015. Mulched areas had significantly higher non-native forb cover, non-native graminoid cover and non-native species richness. In addition, 25 non-native species occurred exclusively in mulched areas; collectively, these responses contributed to more homogenous plant communities in mulched areas than in unmulched areas in 2015. In contrast, mulch had no effect on total plant cover, and conifer regeneration densities were generally unaffected with the exception of a slight positive effect on Douglas-fir. We recommend more stringent testing for weed-free certification and that funding for non-native species eradication be included with post-fire rehabilitation plans.
Adaptive self-organization of Bali’s ancient rice terraces
Authors: Lansing J. Stephen , Thurner Stefan , Chung Ning Ning , Coudurier-Curveur Aurélie , Karakaş Çağil , Fesenmyer Kurt A. , Chew Lock Yue
Published: June 2017

Significance

In Bali, the cooperative management of rice terraces extends beyond villages to whole watersheds. To understand why, we created a model that explores how cooperation can propagate from pairs of individuals to extended groups, creating a resilient system of bottom-up management that both increases and equalizes harvests. Spatial patterns of collective crop management—observable in Google Earth—closely match the predictions of the model. The spatial patterning that emerges is nonuniform and scale-free. Although the model parameters here are tuned to Bali, similar mechanisms of emergent global control should be detectible in other anthropogenic landscapes using multispectral imagery. Recognizing this signature of emergent system-wide cooperation may help planners to avoid unproductive changes to successful bottom-up systems of environmental management.
Paleogenomics of echinoids reveals an ancient origin for the double-negative specification of micromeres in sea urchins
Authors: Thompson Jeffrey R. , Erkenbrack Eric M. , Hinman Veronica F. , McCauley Brenna S. , Petsios Elizabeth , Bottjer David J.
Published: June 2017

Establishing a timeline for the evolution of novelties is a common, unifying goal at the intersection of evolutionary and developmental biology. Analyses of gene regulatory networks (GRNs) provide the ability to understand the underlying genetic and developmental mechanisms responsible for the origin of morphological structures both in the development of an individual and across entire evolutionary lineages. Accurately dating GRN novelties, thereby establishing a timeline for GRN evolution, is necessary to answer questions about the rate at which GRNs and their subcircuits evolve, and to tie their evolution to paleoenvironmental and paleoecological changes. Paleogenomics unites the fossil record and all aspects of deep time, with modern genomics and developmental biology to understand the evolution of genomes in evolutionary time. Recent work on the regulatory genomic basis of development in cidaroid echinoids, sand dollars, heart urchins, and other nonmodel echinoderms provides an ideal dataset with which to explore GRN evolution in a comparative framework. Using divergence time estimation and ancestral state reconstructions, we have determined the age of the double-negative gate (DNG), the subcircuit which specifies micromeres and skeletogenic cells in
Strongylocentrotus purpuratus
. We have determined that the DNG has likely been used for euechinoid echinoid micromere specification since at least the Late Triassic. The innovation of the DNG thus predates the burst of post-Paleozoic echinoid morphological diversification that began in the Early Jurassic. Paleogenomics has wide applicability for the integration of deep time and molecular developmental data, and has wide utility in rigorously establishing timelines for GRN evolution.
Gene regulatory networks and cell lineages that underlie the formation of skeletal muscle
Authors: Buckingham Margaret
Published: June 2017

Skeletal muscle in vertebrates is formed by two major routes, as illustrated by the mouse embryo. Somites give rise to myogenic progenitors that form all of the muscles of the trunk and limbs. The behavior of these cells and their entry into the myogenic program is controlled by gene regulatory networks, where paired box gene 3 (
Pax3
) plays a predominant role. Head and some neck muscles do not derive from somites, but mainly form from mesoderm in the pharyngeal region. Entry into the myogenic program also depends on the myogenic determination factor (
MyoD
) family of genes, but
Pax3
is not expressed in these myogenic progenitors, where different gene regulatory networks function, with T-box factor 1 (
Tbx1
) and paired-like homeodomain factor 2 (
Pitx2
) as key upstream genes. The regulatory genes that underlie the formation of these muscles are also important players in cardiogenesis, expressed in the second heart field, which is a major source of myocardium and of the pharyngeal arch mesoderm that gives rise to skeletal muscles. The demonstration that both types of striated muscle derive from common progenitors comes from clonal analyses that have established a lineage tree for parts of the myocardium and different head and neck muscles. Evolutionary conservation of the two routes to skeletal muscle in vertebrates extends to chordates, to trunk muscles in the cephlochordate
Amphioxus
and to muscles derived from cardiopharyngeal mesoderm in the urochordate
Ciona
, where a related gene regulatory network determines cardiac or skeletal muscle cell fates. In conclusion, Eric Davidson’s visionary contribution to our understanding of gene regulatory networks and their evolution is acknowledged.
Drosophila
Pax6 promotes development of the entire eye-antennal disc, thereby ensuring proper adult head formation
Authors: Zhu Jinjin , Palliyil Sneha , Ran Chen , Kumar Justin P.
Published: June 2017

Paired box 6 (Pax6) is considered to be the master control gene for eye development in all seeing animals studied so far. In vertebrates, it is required not only for lens/retina formation but also for the development of the CNS, olfactory system, and pancreas. Although Pax6 plays important roles in cell differentiation, proliferation, and patterning during the development of these systems, the underlying mechanism remains poorly understood. In the fruit fly,
Drosophila melanogaster
, Pax6 also functions in a range of tissues, including the eye and brain. In this report, we describe the function of Pax6 in
Drosophila
eye-antennal disc development. Previous studies have suggested that the two fly Pax6 genes,
eyeless
(
ey
) and
twin of eyeless
(
toy
), initiate eye specification, whereas
eyegone
(
eyg
) and the
Notch
(
N
) pathway independently regulate cell proliferation. Here, we show that Pax6 controls eye progenitor cell survival and proliferation through the activation of
teashirt
(
tsh
) and
eyg
, thereby indicating that Pax6 initiates both eye specification and proliferation. Although simultaneous loss of
ey
and
toy
during early eye-antennal disc development disrupts the development of all head structures derived from the eye-antennal disc, overexpression of
N
or
tsh
in the absence of Pax6 rescues only antennal and head epidermis development. Furthermore, overexpression of
tsh
induces a homeotic transformation of the fly head into thoracic structures. Taking these data together, we demonstrate that Pax6 promotes development of the entire eye-antennal disc and that the retinal determination network works to repress alternative tissue fates, which ensures proper development of adult head structures.
Dissecting BMP signaling input into the gene regulatory networks driving specification of the blood stem cell lineage
Authors: Kirmizitas Arif , Meiklejohn Stuart , Ciau-Uitz Aldo , Stephenson Rachel , Patient Roger
Published: June 2017

Hematopoietic stem cells (HSCs) that sustain lifelong blood production are created during embryogenesis. They emerge from a specialized endothelial population, termed hemogenic endothelium (HE), located in the ventral wall of the dorsal aorta (DA). InXenopus, we have been studying the gene regulatory networks (GRNs) required for the formation of HSCs, and critically found that the hemogenic potential is defined at an earlier time point when precursors to the DA express hematopoietic as well as endothelial genes, in the definitive hemangioblasts (DHs). The GRN for DH programming has been constructed and, here, we show that bone morphogenetic protein (BMP) signaling is essential for the initiation of this GRN. BMP2, -4, and -7 are the principal ligands expressed in the lineage forming the HE. To investigate the requirement and timing of all BMP signaling in HSC ontogeny, we have used a transgenic line, which inducibly expresses an inhibitor of BMP signaling, Noggin, as well as a chemical inhibitor of BMP receptors, DMH1, and described the inputs from BMP signaling into the DH GRN and the HE, as well as into primitive hematopoiesis. BMP signaling is required in at least three points in DH programming: first to initiate the DH GRN throughgata2expression, then forkdrexpression to enable the DH to respond to vascular endothelial growth factor A (VEGFA) ligand from the somites, and finally forgata2expression in the DA, but is dispensable for HE specification after hemangioblasts have been formed.
Bcl11b and combinatorial resolution of cell fate in the T-cell gene regulatory network
Authors: Longabaugh William J. R. , Zeng Weihua , Zhang Jingli A. , Hosokawa Hiroyuki , Jansen Camden S. , Li Long , Romero-Wolf Maile , Liu Pentao , Kueh Hao Yuan , Mortazavi Ali , Rothenberg Ellen V.
Published: June 2017

T-cell development from hematopoietic progenitors depends on multiple transcription factors, mobilized and modulated by intrathymic Notch signaling. Key aspects of T-cell specification network architecture have been illuminated through recent reports defining roles of transcription factors PU.1, GATA-3, and E2A, their interactions with Notch signaling, and roles of Runx1, TCF-1, and Hes1, providing bases for a comprehensively updated model of the T-cell specification gene regulatory network presented herein. However, the role of lineage commitment factor Bcl11b has been unclear. We use self-organizing maps on 63 RNA-seq datasets from normal and perturbed T-cell development to identify functional targets of Bcl11b during commitment and relate them to other regulomes. We show that both activation and repression target genes can be bound by Bcl11b in vivo, and that Bcl11b effects overlap with E2A-dependent effects. The newly clarified role of Bcl11b distinguishes discrete components of commitment, resolving how innate lymphoid, myeloid, and dendritic, and B-cell fate alternatives are excluded by different mechanisms.
Gene regulation during
Drosophila
eggshell patterning
Authors: Pyrowolakis George , Veikkolainen Ville , Yakoby Nir , Shvartsman Stanislav Y.
Published: June 2017

A common path to the formation of complex 3D structures starts with an epithelial sheet that is patterned by inductive cues that control the spatiotemporal activities of transcription factors. These activities are then interpreted by the
cis-
regulatory regions of the genes involved in cell differentiation and tissue morphogenesis. Although this general strategy has been documented in multiple developmental contexts, the range of experimental models in which each of the steps can be examined in detail and evaluated in its effect on the final structure remains very limited. Studies of the
Drosophila
eggshell patterning provide unique insights into the multiscale mechanisms that connect gene regulation and 3D epithelial morphogenesis. Here we review the current understanding of this system, emphasizing how the recent identification of
cis
-regulatory regions of genes within the eggshell patterning network enables mechanistic analysis of its spatiotemporal dynamics and evolutionary diversification. It appears that
cis
-regulatory changes can account for only some aspects of the morphological diversity of
Drosophila
eggshells, such as the prominent differences in the number of the respiratory dorsal appendages. Other changes, such as the appearance of the respiratory eggshell ridges, are caused by changes in the spatial distribution of inductive signals. Both types of mechanisms are at play in this rapidly evolving system, which provides an excellent model of developmental patterning and morphogenesis.
Mitochondrial dysfunction induced by a SH2 domain-targeting STAT3 inhibitor leads to metabolic synthetic lethality in cancer cells
Authors: Genini Davide , Brambilla Lara , Laurini Erik , Merulla Jessica , Civenni Gianluca , Pandit Shusil , D'Antuono Rocco , Perez Laurent , Levy David E. , Pricl Sabrina , Carbone Giuseppina M. , Catapano Carlo V.
Published: June 2017

Significance

The transcription factor STAT3 is involved in multiple oncogenic signaling pathways and is an attractive therapeutic target. This study shows that a potent inhibitor of STAT3 interferes with mitochondrial activity and protein homeostasis, leading to a synthetic lethality effect in glucose-depleted cancer cells. These findings provide a rationale for novel strategies based on the use of STAT3 inhibitors for cancer treatment.
Stratospheric ozone over the United States in summer linked to observations of convection and temperature via chlorine and bromine catalysis
Authors: Anderson James G. , Weisenstein Debra K. , Bowman Kenneth P. , Homeyer Cameron R. , Smith Jessica B. , Wilmouth David M. , Sayres David S. , Klobas J. Eric , Leroy Stephen S. , Dykema John A. , Wofsy Steven C.
Published: June 2017

Significance

Stratospheric ozone is one of the most delicate aspects of habitability on the planet. Removal of stratospheric ozone over the polar regions in winter/spring has established the vulnerability of ozone to halogen catalytic cycles. Elevated ClO concentrations engendered, in part, by heterogeneous catalytic conversion of inorganic chlorine to free radical form on ubiquitous sulfate−water aerosols, govern the rate of ozone removal. We report here observations of the frequency and depth of penetration of convectively injected water vapor into the stratosphere, triggered by severe storms that are specific to the central United States in summer, and model their effect on lower stratospheric ozone. This effect implies, with observed temperatures, increased risk of ozone loss over the Great Plains in summer.
Entropy in molecular recognition by proteins
Authors: Caro José A. , Harpole Kyle W. , Kasinath Vignesh , Lim Jackwee , Granja Jeffrey , Valentine Kathleen G. , Sharp Kim A. , Wand A. Joshua
Published: June 2017

Significance

Molecular recognition by proteins is a key element of biology. Appreciation of the underlying thermodynamics has been incomplete because of uncertainty in several contributions to the entropy. Here, we demonstrate a way to measure changes in protein conformational entropy using a dynamical proxy provided by NMR relaxation methods. We find that conformational entropy can contribute significantly and variably to the thermodynamics of binding. In addition, we determine the contribution of rotational-translational entropy loss upon forming a high-affinity complex involving a protein. The contribution of solvent entropy is also recalibrated. Thus, a more complete view of entropy in binding has been established and shows that inclusion of conformational entropy is necessary to understanding the origins of high-affinity interactions involving proteins.
Treatment with diphenyl–pyrazole compound anle138b/c reveals that α-synuclein protects melanoma cells from autophagic cell death
Authors: Turriani Elisa , Lázaro Diana F. , Ryazanov Sergey , Leonov Andrei , Giese Armin , Schön Margarete , Schön Michael P. , Griesinger Christian , Outeiro Tiago F. , Arndt-Jovin Donna J. , Becker Dorothea
Published: June 2017

Significance

People with Parkinson’s disease, the second most common neurodegenerative disorder, have a lower risk and decreased incidence of cancer with the one exception being melanoma. The fact that, compared with other malignancies, melanoma occurs more frequently in patients with Parkinson’s disease and vice versa and that there is an association between a history of melanoma and an increased prevalence of prodromal markers of Parkinson’s disease prompted us to explore the possibility of an inverse biological link between these two diseases. The findings of our study suggest that α-synuclein, one of the key regulators in Parkinson’s disease, although toxic to dopaminergic neurons, is protective for advanced melanoma cells.