bluuebunny/crossref_metadata_2025 huggingface dataset:
The classical two-sublattice Landau–Lifshitz–Bloch equation for all temperatures
Authors: Nieves P. , Atxitia U. , Chantrell R. W. , Chubykalo–Fesenko O.
Published: October 2015

Micromagnetic modeling has proved itself as a widely used tool, complimentary in many respects to experimental measurements. The Landau–Lifshitz equation provides a basis for this modeling, especially where the dynamical behaviour is concerned. However, this approach is strictly valid only for zero temperature and for high temperatures must be replaced by a more thermodynamically consistent approach such as the Landau–Lifshitz–Bloch (LLB) equation. Here we review the recently derived LLB equation for two-sublattice systems and extend its derivation for temperatures above the Curie temperature. We present comparison with many-body atomistic simulations and show that this equation can describe the ultra-fast switching in ferrimagnets, observed experimentally.
Probing protein orientation near charged nanosurfaces for simulation-assisted biosensor design
Authors: Cooper Christopher D. , Clementi Natalia C. , Barba Lorena A.
Published: October 2015

Protein-surface interactions are ubiquitous in biological processes and bioengineering, yet are not fully understood. In biosensors, a key factor determining the sensitivity and thus the performance of the device is the orientation of the ligand molecules on the bioactive device surface. Adsorption studies thus seek to determine how orientation can be influenced by surface preparation, varying surface charge, and ambient salt concentration. In this work, protein orientation near charged nanosurfaces is obtained under electrostatic effects using the Poisson-Boltzmann equation, in an implicit-solvent model. Sampling the free energy for protein G B1 D4′ at a range of tilt and rotation angles with respect to the charged surface, we calculated the probability of the protein orientations and observed a dipolar behavior. This result is consistent with published experimental studies and combined Monte Carlo and molecular dynamics simulations using this small protein, validating our method. More relevant to biosensor technology, antibodies such as immunoglobulin G are still a formidable challenge to molecular simulation, due to their large size. With the Poisson-Boltzmann model, we obtained the probability distribution of orientations for the iso-type IgG2a at varying surface charge and salt concentration. This iso-type was not found to have a preferred orientation in previous studies, unlike the iso-type IgG1 whose larger dipole moment was assumed to make it easier to control. Our results show that the preferred orientation of IgG2a can be favorable for biosensing with positive charge on the surface of 0.05 C/m2 or higher and 37 mM salt concentration. The results also show that local interactions dominate over dipole moment for this protein. Improving immunoassay sensitivity may thus be assisted by numerical studies using our method (and open-source code), guiding changes to fabrication protocols or protein engineering of ligand molecules to obtain more favorable orientations.
Lattice equations arising from discrete Painlevé systems. I. (A2 + A1)(1) and (A1+A1′)(1) cases
Authors: Joshi Nalini , Nakazono Nobutaka , Shi Yang
Published: October 2015

We introduce the concept of ω-lattice, constructed from τ functions of Painlevé systems, on which quad-equations of ABS (Adler-Bobenko-Suris) type appear. In particular, we consider the A5(1)- and A6(1)-surface q-Painlevé systems corresponding affine Weyl group symmetries are of (A2 + A1)(1)- and (A1 + A1)(1)-types, respectively.
A novel compact three-dimensional laser-sintered collimator for neutron scattering
Authors: Ridley Christopher J. , Manuel Pascal , Khalyavin Dmitry , Kirichek Oleg , Kamenev Konstantin V.
Published: October 2015

Improvements in the available flux at neutron sources are making it increasingly feasible to obtain refineable neutron diffraction data from samples smaller than 1 mm3. The signal is typically too weak to introduce any further sample environment in the 30–50 mm diameter surrounding the sample (such as the walls of a pressure cell) due to the high ratio of background to sample signal, such that even longer count times fail to reveal reflections from the sample. Many neutron instruments incorporate collimators to reduce parasitic scattering from the instrument and from any surrounding material and larger pieces of sample environment, such as cryostats. However, conventional collimation is limited in the volume it can focus on due to difficulties in producing tightly spaced neutron-absorbing foils close to the sample and in integrating this into neutron instruments. Here we present the design of a novel compact 3D rapid-prototyped (or “printed”) collimator which reduces these limitations and is shown to improve the ratio of signal to background, opening up the feasibility of using additional sample environment for neutron diffraction from small sample volumes. The compactness and ease of customisation of the design allows this concept to be integrated with existing sample environment and with designs that can be tailored to individual detector geometries without the need to alter the setup of the instrument. Results from online testing of a prototype collimator are presented. The proof of concept shows that there are many additional collimator designs which may be manufactured relatively inexpensively, with a broad range of customisation, and geometries otherwise impossible to manufacture by conventional techniques.
Molecular ion sources for low energy semiconductor ion implantation (invited)
Authors: Hershcovitch A. , Gushenets V. I. , Seleznev D. N. , Bugaev A. S. , Dugin S. , Oks E. M. , Kulevoy T. V. , Alexeyenko O. , Kozlov A. , Kropachev G. N. , Kuibeda R. P. , Minaev S. , Vizir A. , Yushkov G. Yu.
Published: October 2015

Smaller semiconductors require shallow, low energy ion implantation, resulting space charge effects, which reduced beam currents and production rates. To increase production rates, molecular ions are used. Boron and phosphorous (or arsenic) implantation is needed for P-type and N-type semiconductors, respectively. Carborane, which is the most stable molecular boron ion leaves unacceptable carbon residue on extraction grids. A self-cleaning carborane acid compound (C4H12B10O4) was synthesized and utilized in the ITEP Bernas ion source resulting in large carborane ion output, without carbon residue. Pure gaseous processes are desired to enable rapid switch among ion species. Molecular phosphorous was generated by introducing phosphine in dissociators via 4PH3 = P4 + 6H2; generated molecular phosphorous in a pure gaseous process was then injected into the HCEI Calutron-Bernas ion source, from which P4+ ion beams were extracted. Results from devices and some additional concepts are described.
Correlations between density distributions, optical spectra, and ion species in a hydrogen plasma (invited)
Authors: Cortázar O. D. , Megía-Macías A. , Tarvainen O. , Kalvas T. , Koivisto H.
Published: October 2015

An experimental study of plasma distributions in a 2.45 GHz hydrogen discharge operated at 100 Hz repetition rate is presented. Ultrafast photography, time integrated visible light emission spectra, time resolved Balmer-alpha emission, time resolved Fulcher Band emission, ion species mass spectra, and time resolved ion species fraction measurements have been implemented as diagnostic tools in a broad range of plasma conditions. Results of plasma distributions and optical emissions correlated with H+, H2+, and H3+ ion currents by using a Wien filter system with optical observation capability are reported. The magnetic field distribution and strength is found as the most critical factor for transitions between different plasma patterns and ion populations.
Analytic energy gradient of excited electronic state within TDDFT/MMpol framework: Benchmark tests and parallel implementation
Authors: Zeng Qiao , Liang WanZhen
Published: October 2015

The time-dependent density functional theory (TDDFT) has become the most popular method to calculate the electronic excitation energies, describe the excited-state properties, and perform the excited-state geometric optimization of medium and large-size molecules due to the implementation of analytic excited-state energy gradient and Hessian in many electronic structure software packages. To describe the molecules in condensed phase, one usually adopts the computationally efficient hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) models. Here, we extend our previous work on the energy gradient of TDDFT/MM excited state to account for the mutual polarization effects between QM and MM regions, which is believed to hold a crucial position in the potential energy surface of molecular systems when the photoexcitation-induced charge rearrangement in the QM region is drastic. The implementation of a simple polarizable TDDFT/MM (TDDFT/MMpol) model in Q-Chem/CHARMM interface with both the linear response and the state-specific features has been realized. Several benchmark tests and preliminary applications are exhibited to confirm our implementation and assess the effects of different treatment of environmental polarization on the excited-state properties, and the efficiency of parallel implementation is demonstrated as well.
Boron ion beam generation utilizing lanthanum hexaboride cathodes: Comparison of vacuum arc and planar magnetron glow
Authors: Nikolaev A. G. , Oks E. M. , Vizir A. V. , Yushkov G. Yu. , Frolova V. P.
Published: October 2015

Boron ion beams are widely used for semiconductor ion implantation and for surface modification for improving the operating parameters and increasing the lifetime of machine parts and tools. For the latter application, the purity requirements of boron ion beams are not as stringent as for semiconductor technology, and a composite cathode of lanthanum hexaboride may be suitable for the production of boron ions. We have explored the use of two different approaches to boron plasma production: vacuum arc and planar high power impulse magnetron in self-sputtering mode. For the arc discharge, the boron plasma is generated at cathode spots, whereas for the magnetron discharge, the main process is sputtering of cathode material. We present here the results of comparative test experiments for both kinds of discharge, aimed at determining the optimal discharge parameters for maximum yield of boron ions. For both discharges, the extracted ion beam current reaches hundreds of milliamps and the fraction of boron ions in the total extracted ion beam is as high as 80%.
Discrimination of time-dependent inflow properties with a cooperative dynamical system
Authors: Ueno Hiroshi , Tsuruyama Tatsuaki , Nowakowski Bogdan , Górecki Jerzy , Yoshikawa Kenichi
Published: October 2015

Many physical, chemical, and biological systems exhibit a cooperative or sigmoidal response with respect to the input. In biochemistry, such behavior is called an allosteric effect. Here, we demonstrate that a system with such properties can be used to discriminate the amplitude or frequency of an external periodic perturbation. Numerical simulations performed for a model sigmoidal kinetics illustrate that there exists a narrow range of frequencies and amplitudes within which the system evolves toward significantly different states. Therefore, observation of system evolution should provide information about the characteristics of the perturbation. The discrimination properties for periodic perturbation are generic. They can be observed in various dynamical systems and for different types of periodic perturbation.
Defect calculations in semiconductors through a dielectric-dependent hybrid DFT functional: The case of oxygen vacancies in metal oxides
Authors: Gerosa Matteo , Bottani Carlo Enrico , Caramella Lucia , Onida Giovanni , Di Valentin Cristiana , Pacchioni Gianfranco
Published: October 2015

We investigate the behavior of oxygen vacancies in three different metal-oxide semiconductors (rutile and anatase TiO2, monoclinic WO3, and tetragonal ZrO2) using a recently proposed hybrid density-functional method in which the fraction of exact exchange is material-dependent but obtained ab initio in a self-consistent scheme. In particular, we calculate charge-transition levels relative to the oxygen-vacancy defect and compare computed optical and thermal excitation/emission energies with the available experimental results, shedding light on the underlying excitation mechanisms and related materials properties. We find that this novel approach is able to reproduce not only ground-state properties and band structures of perfect bulk oxide materials but also provides results consistent with the optical and electrical behavior observed in the corresponding substoichiometric defective systems.
Relaxation mode analysis and Markov state relaxation mode analysis for chignolin in aqueous solution near a transition temperature
Authors: Mitsutake Ayori , Takano Hiroshi
Published: October 2015

It is important to extract reaction coordinates or order parameters from protein simulations in order to investigate the local minimum-energy states and the transitions between them. The most popular method to obtain such data is principal component analysis, which extracts modes of large conformational fluctuations around an average structure. We recently applied relaxation mode analysis for protein systems, which approximately estimates the slow relaxation modes and times from a simulation and enables investigations of the dynamic properties underlying the structural fluctuations of proteins. In this study, we apply this relaxation mode analysis to extract reaction coordinates for a system in which there are large conformational changes such as those commonly observed in protein folding/unfolding. We performed a 750-ns simulation of chignolin protein near its folding transition temperature and observed many transitions between the most stable, misfolded, intermediate, and unfolded states. We then applied principal component analysis and relaxation mode analysis to the system. In the relaxation mode analysis, we could automatically extract good reaction coordinates. The free-energy surfaces provide a clearer understanding of the transitions not only between local minimum-energy states but also between the folded and unfolded states, even though the simulation involved large conformational changes. Moreover, we propose a new analysis method called Markov state relaxation mode analysis. We applied the new method to states with slow relaxation, which are defined by the free-energy surface obtained in the relaxation mode analysis. Finally, the relaxation times of the states obtained with a simple Markov state model and the proposed Markov state relaxation mode analysis are compared and discussed.
On the physics of thermal-stability changes upon mutations of a protein
Authors: Murakami Shota , Oshima Hiraku , Hayashi Tomohiko , Kinoshita Masahiro
Published: October 2015

It is of great interest from both scientific and practical viewpoints to theoretically predict the thermal-stability changes upon mutations of a protein. However, such a prediction is an intricate task. Up to now, significantly many approaches for the prediction have been reported in the literature. They always include parameters which are adjusted so that the prediction results can be best fitted to the experimental data for a sufficiently large set of proteins and mutations. The inclusion is necessitated to achieve satisfactorily high prediction performance. A problem is that the resulting values of the parameters are often physically meaningless, and the physicochemical factors governing the thermal-stability changes upon mutations are rather ambiguous. Here, we develop a new measure of the thermal stability. Protein folding is accompanied by a large gain of water entropy (the entropic excluded-volume (EV) effect), loss of protein conformational entropy, and increase in enthalpy. The enthalpy increase originates primarily from the following: The energy increase due to the break of protein-water hydrogen bonds (HBs) upon folding cannot completely be cancelled out by the energy decrease brought by the formation of protein intramolecular HBs. We develop the measure on the basis of only these three factors and apply it to the prediction of the thermal-stability changes upon mutations. As a consequence, an approach toward the prediction is obtained. It is distinguished from the previously reported approaches in the following respects: The parameters adjusted in the manner mentioned above are not employed at all, and the entropic EV effect, which is ascribed to the translational displacement of water molecules coexisting with the protein in the system, is fully taken into account using a molecular model for water. Our approach is compared with one of the most popular approaches, FOLD-X, in terms of the prediction performance not only for single mutations but also for double, triple, and higher-fold (up to sevenfold) mutations. It is shown that on the whole our approach and FOLD-X exhibit almost the same performance despite that the latter uses the adjusting parameters. For multiple mutations, however, our approach is far superior to FOLD-X. Five multiple mutations for staphylococcal nuclease lead to highly enhanced stabilities, but we find that this high enhancement arises from the entropic EV effect. The neglect of this effect in FOLD-X is a principal reason for its ill success. A conclusion is that the three factors mentioned above play essential roles in elucidating the thermal-stability changes upon mutations.
Investigation of abrupt degradation of drain current caused by under-gate crack in AlGaN/GaN high electron mobility transistors during high temperature operation stress
Authors: Zeng Chang , Liao XueYang , Li RuGuan , Wang YuanSheng , Chen Yiqiang , Su Wei , Liu Yuan , Wang Li Wei , Lai Ping , Huang Yun , En YunFei
Published: October 2015

In this paper, we investigate the degradation mode and mechanism of AlGaN/GaN based high electron mobility transistors (HEMTs) during high temperature operation (HTO) stress. It demonstrates that there was abrupt degradation mode of drain current during HTO stress. The abrupt degradation is ascribed to the formation of crack under the gate which was the result of the brittle fracture of epilayer based on failure analysis. The origin of the mechanical damage under the gate is further investigated and discussed based on top-down scanning electron microscope, cross section transmission electron microscope and energy dispersive x-ray spectroscopy analysis, and stress simulation. Based on the coupled analysis of the failure physical feature and stress simulation considering the coefficient of thermal expansion (CTE) mismatch in different materials in gate metals/semiconductor system, the mechanical damage under the gate is related to mechanical stress induced by CTE mismatch in Au/Ti/Mo/GaN system and stress concentration caused by the localized structural damage at the drain side of the gate edge. These results indicate that mechanical stress induced by CTE mismatch of materials inside the device plays great important role on the reliability of AlGaN/GaN HEMTs during HTO stress.
Network representation of conformational transitions between hidden intermediates of Rd-apocytochrome b562
Authors: Duan Mojie , Liu Hanzhong , Li Minghai , Huo Shuanghong
Published: October 2015

The folding kinetics of Rd-apocytochrome b562 is two-state, but native-state hydrogen exchange experiments show that there are discrete partially unfolded (PUF) structures in equilibrium with the native state. These PUF structures are called hidden intermediates because they are not detected in kinetic experiments and they exist after the rate-limiting step. Structures of the mimics of hidden intermediates of Rd-apocytochrome b562 are resolved by NMR. Based upon their relative stability and structural features, the folding mechanism was proposed to follow a specific pathway (unfolded → rate-limiting transition state → PUF1 → PUF2 → native). Investigating the roles of equilibrium PUF structures in folding kinetics and their interrelationship not only deepens our understanding of the details of folding mechanism but also provides guides in protein design and prevention of misfolding. We performed molecular dynamics simulations starting from a hidden intermediate and the native state of Rd-apocytochrome b562 in explicit solvent, for a total of 37.18 μs mainly with Anton. We validated our simulations by detailed comparison with experimental data and other computations. We have verified that we sampled the post rate-limiting transition state region only. Markov state model was used to analyze the simulation results. We replace the specific pathway model with a network model. Transition-path theory was employed to calculate the net effective flux from the most unfolded state towards the most folded state in the network. The proposed sequential folding pathway via PUF1 then more stable, more native-like PUF2 is one of the routes in our network, but it is not dominant. The dominant path visits PUF2 without going through PUF1. There is also a route from PUF1 directly to the most folded state in the network without visiting PUF2. Our results indicate that the PUF states are not necessarily sequential in the folding. The major routes predicted in our network are testable by future experiments such as single molecule experiment.
Microfluidic size separation of cells and particles using a swinging bucket centrifuge
Authors: Yeo Joo Chuan , Wang Zhiping , Lim Chwee Teck
Published: October 2015

Biomolecular separation is crucial for downstream analysis. Separation technique mainly relies on centrifugal sedimentation. However, minuscule sample volume separation and extraction is difficult with conventional centrifuge. Furthermore, conventional centrifuge requires density gradient centrifugation which is laborious and time-consuming. To overcome this challenge, we present a novel size-selective bioparticles separation microfluidic chip on a swinging bucket minifuge. Size separation is achieved using passive pressure driven centrifugal fluid flows coupled with centrifugal force acting on the particles within the microfluidic chip. By adopting centrifugal microfluidics on a swinging bucket rotor, we achieved over 95% efficiency in separating mixed 20 μm and 2 μm colloidal dispersions from its liquid medium. Furthermore, by manipulating the hydrodynamic resistance, we performed size separation of mixed microbeads, achieving size efficiency of up to 90%. To further validate our device utility, we loaded spiked whole blood with MCF-7 cells into our microfluidic device and subjected it to centrifugal force for a mere duration of 10 s, thereby achieving a separation efficiency of over 75%. Overall, our centrifugal microfluidic device enables extremely rapid and label-free enrichment of different sized cells and particles with high efficiency.
Ionic liquid induced dehydration and domain closure in lysozyme: FCS and MD simulation
Authors: Ghosh Shirsendu , Parui Sridip , Jana Biman , Bhattacharyya Kankan
Published: October 2015

Effect of a room temperature ionic liquid (RTIL, [pmim][Br]) on the structure and dynamics of the protein, lysozyme, is investigated by fluorescence correlation spectroscopy (FCS) and molecular dynamic (MD) simulation. The FCS data indicate that addition of the RTIL ([pmim][Br]) leads to reduction in size and faster conformational dynamics of the protein. The hydrodynamic radius (rH) of lysozyme decreases from 18 Å in 0 M [pmim][Br] to 11 Å in 1.5 M [pmim][Br] while the conformational relaxation time decreases from 65 μs to 5 μs. Molecular origin of the collapse (size reduction) of lysozyme in aqueous RTIL is analyzed by MD simulation. The radial distribution function of water, RTIL cation, and RTIL anion from protein clearly indicates that addition of RTIL causes replacement of interfacial water by RTIL cation ([pmim]+) from the first solvation layer of the protein providing a comparatively dehydrated environment. This preferential solvation of the protein by the RTIL cation extends up to ∼30 Å from the protein surface giving rise to a nanoscopic cage of overall radius 42 Å. In the nanoscopic cage of the RTIL (42 Å), volume fraction of the protein (radius 12 Å) is only about 2%. RTIL anion does not show any preferential solvation near protein surface. Comparison of effective radius obtained from simulation and from FCS data suggests that the “dry” protein (radius 12 Å) alone diffuses in a nanoscopic cage of RTIL (radius 42 Å). MD simulation further reveals a decrease in distance (“domain closure”) between the two domains (alpha and beta) of the protein leading to a more compact structure compared to that in the native state.
Unraveling the luminescence signatures of chemical defects in polyethylene
Authors: Chen Lihua , Tran Huan Doan , Wang Chenchen , Ramprasad Rampi
Published: October 2015

Chemical defects in polyethylene (PE) can deleteriously downgrade its electrical properties and performance. Although these defects usually leave spectroscopic signatures in terms of characteristic luminescence peaks, it is nontrivial to make unambiguous assignments of the peaks to specific defect types. In this work, we go beyond traditional density functional theory calculations to determine intra-defect state transition and charge recombination process derived emission and absorption energies in PE. By calculating the total energy differences of the neutral defect at excited and ground states, the emission energies from intra-defect state transition are obtained, reasonably explaining the photoluminescence peaks in PE. In order to study the luminescence emitted in charge recombination processes, we characterize PE defect levels in terms of thermodynamic and optical charge transition levels that involve total energy calculations of neutral and charged defects. Calculations are performed at several levels of theory including those involving (semi)local and hybrid electron exchange-correlation functionals, and many-body perturbation theory. With these critical elements, the emission energies are computed and further used to clarify and confirm the origins of the observed electroluminescence and thermoluminescence peaks.
Mixed random walks with a trap in scale-free networks including nearest-neighbor and next-nearest-neighbor jumps
Authors: Zhang Zhongzhi , Dong Yuze , Sheng Yibin
Published: October 2015

Random walks including non-nearest-neighbor jumps appear in many real situations such as the diffusion of adatoms and have found numerous applications including PageRank search algorithm; however, related theoretical results are much less for this dynamical process. In this paper, we present a study of mixed random walks in a family of fractal scale-free networks, where both nearest-neighbor and next-nearest-neighbor jumps are included. We focus on trapping problem in the network family, which is a particular case of random walks with a perfect trap fixed at the central high-degree node. We derive analytical expressions for the average trapping time (ATT), a quantitative indicator measuring the efficiency of the trapping process, by using two different methods, the results of which are consistent with each other. Furthermore, we analytically determine all the eigenvalues and their multiplicities for the fundamental matrix characterizing the dynamical process. Our results show that although next-nearest-neighbor jumps have no effect on the leading scaling of the trapping efficiency, they can strongly affect the prefactor of ATT, providing insight into better understanding of random-walk process in complex systems.
Study on hexagonal super-lattice pattern with surface discharges in dielectric barrier discharge
Authors: Liu Ying , Dong Lifang , Niu Xuejiao , Gao Yenan , Zhang Chao
Published: October 2015

The hexagonal super-lattice pattern with surface discharges (SDs) in dielectric barrier discharge is investigated by intensified charge-coupled device. The pattern is composed of the bright spot and the dim spot which is located at the centroid of surrounding other three bright spots. The phase diagram of the pattern as a function of the gas pressure and the argon concentration is given. The instantaneous images indicate that the bright spot emerging at the front of the current pulse is formed by the volume discharge (VD), and dim spot occurring at the tail of the current pulse is formed by the SD. The above result shows that the SD is induced by the VD. The simulation of the electric fields of wall charges accumulated by VDs confirms that the dim spot is formed by the confluences of the SDs of surrounding other three bright spots. By using optical emission spectrum method, both the molecule vibration temperature and electron density of the SD are larger than that of the VD.
Power efficiency improvements with the radio frequency H− ion source
Authors: Kalvas T. , Tarvainen O. , Komppula J. , Koivisto H. , Tuunanen J. , Potkins D. , Stewart T. , Dehnel M.
Published: October 2015

CW 13.56 MHz radio frequency-driven H− ion source is under development at the University of Jyväskylä for replacing an existing filament-driven ion source at the MCC30/15 cyclotron. Previously, production of 1 mA H− beam, which is the target intensity of the ion source, has been reported at 3 kW of RF power. The original ion source front plate with an adjustable electromagnet based filter field has been replaced with a new front plate with permanent magnet filter field. The new structure is more open and enables a higher flux of ro-vibrationally excited molecules towards the plasma electrode and provides a better control of the potential near the extraction due to a stronger separation of the main plasma from the plasma electrode. While the original system provided better control over the e−/H− ratio, the new configuration has led to a higher production efficiency of 1 mA H− at 1.75 kW RF power. The latest results and upgrade plans are presented.
Giant negative thermal expansion covering room temperature in nanocrystalline GaNxMn3
Authors: Lin J. C. , Tong P. , Zhou X. J. , Lin H. , Ding Y. W. , Bai Y. X. , Chen L. , Guo X. G. , Yang C. , Song B. , Wu Y. , Lin S. , Song W. H. , Sun Y. P.
Published: October 2015

Nanocrystalline antiperovskite GaNxMn3 powders were prepared by mechanically milling. The micrograin GaNxMn3 exhibits an abrupt volume contraction at the antiferromagnetic (AFM) to paramagnetic (PM) (AFM-PM) transition. The temperature window of volume contraction (ΔT) is broadened to 50 K as the average grain size (⟨D⟩) is reduced to ∼30 nm. The corresponding coefficient of linear thermal expansion (α) reaches ∼ −70 ppm/K, which are comparable to those of giant NTE materials. Further reducing ⟨D⟩ to ∼10 nm, ΔT exceeds 100 K and α remains as large as −30 ppm/K (−21 ppm/K) for x = 1.0 (x = 0.9). Excess atomic displacements together with the reduced structural coherence, revealed by high-energy X-ray pair distribution functions, are suggested to delay the AFM-PM transition. By controlling ⟨D⟩, giant NTE may also be achievable in other materials with large lattice contraction due to electronic or magnetic phase transitions.
Self-assembly of an NbO2 interlayer and configurable resistive switching in Pt/Nb/HfO2/Pt structures
Authors: Nandi Sanjoy Kumar , Liu Xinjun , Venkatachalam Dinesh Kumar , Elliman Robert Glen
Published: October 2015

A configurable resistive switching response is reported for Pt/Nb/HfO2/Pt devices subjected to different set compliance currents. When operated at a low compliance-current (∼100 μA), devices show uniform bipolar resistive switching behavior. As the compliance current is increased (∼500 μA), the switching mode changes to integrated threshold-resistive (1S1M) switching, and at still higher currents (∼1 mA), it changes to symmetric threshold switching (1S) characteristic of threshold switching in NbO2−δ. These switching transitions are shown to be consistent with the development of an NbO2−δ interlayer at the Nb/HfO2 interface that is limited by the set compliance current due to its effect on oxygen transport and local Joule heating. The proposed mechanism is supported by finite element modeling of the 1S1M response assuming the presence of such an interlayer. These findings help to understand role of interface reactions in controlling device performance and provide a means for the self-assembly of integrated 1S1M resistive random access memory structures.
Frequency-tunable continuous-wave terahertz sources based on GaAs plasmonic photomixers
Authors: Yang Shang-Hua , Jarrahi Mona
Published: October 2015

We present frequency-tunable, continuous-wave terahertz sources based on GaAs plasmonic photomixers, which offer high terahertz radiation power levels at 50% radiation duty cycle. The use of plasmonic contact electrodes enhances photomixer quantum efficiency while maintaining its ultrafast operation by concentrating a large number of photocarriers in close proximity to the device contact electrodes. Additionally, the relatively high thermal conductivity and high resistivity of GaAs allow operation under high optical pump power levels and long duty cycles without reaching the thermal breakdown limit of the photomixer. We experimentally demonstrate continuous-wave terahertz radiation with a radiation frequency tuning range of more than 2 THz and a record-high radiation power of 17 μW at 1 THz through plasmonic photomixers fabricated on a low temperature grown GaAs substrate at 50% radiation duty cycle.
Carbon nanotube forests as top electrode in electroacoustic resonators
Authors: Esconjauregui Santiago , Makaryan Taron , Mirea Teona , DeMiguel-Ramos Mario , Olivares Jimena , Guo Yuzheng , Sugime Hisashi , D'Arsié Lorenzo , Yang Junwei , Bhardwaj Sunil , Cepek Cinzia , Robertson John , Iborra Enrique
Published: October 2015

We grow carbon nanotube forests on piezoelectric AlN films and fabricate and characterize nanotube-based solidly mounted bulk acoustic wave resonators employing the forests as the top electrode material. The devices show values for quality factor at anti-resonance of ∼430, and at resonance of ∼100. The effective coupling coefficient is of ∼6%, and the resonant frequencies are up to ∼800 MHz above those observed with metallic top electrodes. AlN promotes a strong catalyst-support interaction, which reduces Fe catalyst mobility, and thus enforces the growth of forests by the base growth mechanism.
Note: Ion-induced secondary electron emission from oxidized metal surfaces measured in a particle beam reactor
Authors: Marcak Adrian , Corbella Carles , de los Arcos Teresa , von Keudell Achim
Published: October 2015

The secondary electron emission of metals induced by slow ions is characterized in a beam chamber by means of two coaxial semi-cylindrical electrodes with different apertures. The voltages of the outer electrode (screening), inner electrode (collector), and sample holder (target) were set independently in order to measure the effective yield of potential and kinetic electron emissions during ion bombardment. Aluminum samples were exposed to quantified beams of argon ions up to 2000 eV and to oxygen atoms and molecules in order to mimic the plasma-surface interactions on metallic targets during reactive sputtering. The variation of electron emission yield was correlated to the ion energy and to the oxidation state of Al surfaces. This system provides reliable measurements of the electron yields in real time and is of great utility to explore the fundamental surface processes during target poisoning occurring in reactive magnetron sputtering applications.
Elliptically polarized terahertz radiation from a chiral oxide
Authors: Takeda R. , Kida N. , Sotome M. , Okamoto H.
Published: October 2015

Polarization control of terahertz wave is a challenging subject in terahertz science and technology. Here, we report a simple method to control polarization state of the terahertz wave in terahertz generation process. At room temperature, terahertz radiation from a noncentrosymmetric and chiral oxide, sillenite Bi12GeO20, is observed by the irradiation of linearly polarized femtosecond laser pulses at 800 nm. The polarization state of the emitted terahertz wave is found to be elliptic with an ellipticity of ∼0.37 ± 0.10. Furthermore, the ellipticity was altered to a nearly zero (∼0.01 ± 0.01) by changing the polarization of the incident linearly polarized femtosecond laser pulses. Such a terahertz radiation characteristic is attributable to variation of the polarization state of the emitted terahertz waves, which is induced by retardation due to the velocity mismatch between the incident femtosecond laser pulse and generated terahertz wave and by the polarization tilting due to the optical activity at 800 nm.
Isotope program expands activities
Authors: Feder Toni
Published: October 2015

To meet the growing demand for isotopes and lessen dependence on foreign sources, the Department of Energy has been realigning its capabilities and connecting with universities.
New MIT design revives interest in high-field approach to fusion
Authors: Kramer David
Published: October 2015

Tokamaks made with high-temperature superconductors may offer a less expensive, more compact route to fusion power, if their coils can withstand the tremendous forces.
Could an outlier beat the establishment to fusion power?
Authors: Kramer David
Published: October 2015

Buoyed by recent experimental results, a stealthy company is already making plans to commercialize its aneutronic approach to producing electricity.
Lack of soil seedbank change with time since fire: relevance to seed supply after prescribed burns
Authors: Chick Matthew P. , Cohn Janet S. , Nitschke Craig R. , York Alan
Published: October 2015

Soil seedbanks play a key role in the post-fire recruitment of many plant species. Seedbank diversity can be influenced by spatial variability (e.g. geographic location), environmental variability (e.g. soils) and temporal disturbance heterogeneity (e.g. time since fire, TSF) across the landscape. Unlike for aboveground vegetation, relationships between these factors and soil seedbank diversity remain largely unknown. Partitioning the influence of spatial and environmental variability from that of TSF, and explaining how these factors interact with seedbank diversity, will assist conservation managers in their application of prescribed burning. We germinated soil seedbank samples from sites ranging from 1 to 75 years since fire in a heathy-woodland ecosystem across the Otway Ranges in Victoria, Australia. We also measured spatial and environmental variability across sites to partition the influence of these variables and TSF on propagules available for recruitment. We found weak positive relationships between seedbank richness and TSF; however, these relationships varied across the landscape. We found composition did not change considerably over time, suggesting, in this ecosystem, pre-fire age is not strongly influencing propagules available for recruitment post-fire. Our results suggest that spatial and environmental variability influence seedbank composition more than TSF.
Drosophila
E-cadherin is required for the maintenance of ring canals anchoring to mechanically withstand tissue growth
Authors: Loyer Nicolas , Kolotuev Irina , Pinot Mathieu , Le Borgne Roland
Published: October 2015

Significance

This work addresses the interplay among membrane trafficking, cell adhesion, and tissue integrity maintenance in the
Drosophila
female germline. The clathrin adaptor protein 1 (AP-1) complex is shown to regulate the trafficking of E-cadherin to ring canals (RCs), a structure resulting from incomplete cytokinesis and allowing intercellular communication. E-cadherin assembles adhesive clusters that, as revealed by EM analyses, organize a dense microvilli meshwork wrapping around RCs. Although dispensable for RC biogenesis and maturation, AP-1 and E-cadherin are required to maintain RCs’ anchoring to the plasma membrane at the onset of vitellogenesis, when cells experience exponential growth and increased mechanical stress. Our study unravels a previously unidentified function for E-cadherin in maintaining RC anchoring to the plasma membrane.
ACHT4-driven oxidation of APS1 attenuates starch synthesis under low light intensity in
Arabidopsis
plants
Authors: Eliyahu Erez , Rog Ido , Inbal Dangoor , Danon Avihai
Published: October 2015

Significance

Regulation of protein activity by redox state changes of a disulfide bond between two intrinsic cysteine residues requires both reductive and oxidative signals, yet very little is known of the oxidative pathway. Deciphering the oxidative pathway is further complicated by an increased level of reactive oxygen species when plants are stressed. Here, we show that the chloroplastic atypical thioredoxin (ACHT4) participates under homeostasis conditions in an oxidative signal that diminishes AGPase activity, the first committed enzyme of starch synthesis, during the transition from day to night and attenuates AGPase activity in a dynamic response to small fluctuations in light intensity during the day.
Reporting practices in multimodal viewpoint research
Authors: Stec Kashmiri
Published: October 2015

This study assesses methodological reporting practices in multimodal viewpoint research using the 51 primary studies previously synthesized by Stec (2012). These studies were coded for the designs and reporting practices associated with the collection and analysis of multimodal data in order to facilitate a discussion on current reporting practices. Results point to several systematic strengths, as well as to several systematic weaknesses. I discuss these trends in light of methodological reviews in other fields (e.g., Plonsky, 2013) and make a number of suggestions for reforming reporting practices with an aim to increase transparency and replicability.
Microbiome engineering could select for more virulent pathogens
Authors: McNally Luke , Vale Pedro F. , Brown Sam P.
Published: October 2015

Recent insights into the human microbiome offer the hope of manipulating its composition to help fight infectious diseases1–7. While this strategy has shown huge potential, its consequences for pathogen evolution have not been explored. Here we show that manipulating the microbiome to increase the competition that pathogens face could lead to the evolution of increased production of virulence factors that pathogens use to combat commensals, an evolutionary response that can increase total disease induced mortality in the long-term. However, if treatment with microbiome engineering is sufficiently aggressive this evolutionary response can be avoided and the pathogen eradicated. Furthermore, we show that using damage limitation therapies8(e.g. antivirulence and anti-inflammatory drugs) in combination with microbiome manipulation increases the potential for pathogen eradication. While manipulating our microbiota offers a promising alternative to antibiotics, our results show that these treatments must be designed with careful consideration of the potential evolutionary responses of target pathogens.
Parlez-vous VUS?
Authors: Cooper Gregory M.
Published: October 2015

Human genome sequencing is routine and will soon be a staple in research and clinical genetics. However, the promise of sequencing is often just that, with genome data routinely failing to reveal useful insights about disease in general or a person's health in particular. Nowhere is this chasm between promise and progress more evident than in the designation, “variant of uncertain significance” (VUS). Although it serves an important role, careful consideration of VUS reveals it to be a nebulous description of genomic information and its relationship to disease, symptomatic of our inability to make even crude quantitative assertions about the disease risks conferred by many genetic variants. In this perspective, I discuss the challenge of “variant interpretation” and the value of comparative and functional genomic information in meeting that challenge. Although already essential, genomic annotations will become even more important as our analytical focus widens beyond coding exons. Combined with more genotype and phenotype data, they will help facilitate more quantitative and insightful assessments of the contributions of genetic variants to disease.
Epigenomics and the structure of the living genome
Authors: Friedman Nir , Rando Oliver J.
Published: October 2015

Eukaryotic genomes are packaged into an extensively folded state known as chromatin. Analysis of the structure of eukaryotic chromosomes has been revolutionized by development of a suite of genome-wide measurement technologies, collectively termed “epigenomics.” We review major advances in epigenomic analysis of eukaryotic genomes, covering aspects of genome folding at scales ranging from whole chromosome folding down to nucleotide-resolution assays that provide structural insights into protein-DNA interactions. We then briefly outline several challenges remaining and highlight new developments such as single-cell epigenomic assays that will help provide us with a high-resolution structural understanding of eukaryotic genomes.
Defining cell types and states with single-cell genomics
Authors: Trapnell Cole
Published: October 2015

A revolution in cellular measurement technology is under way: For the first time, we have the ability to monitor global gene regulation in thousands of individual cells in a single experiment. Such experiments will allow us to discover new cell types and states and trace their developmental origins. They overcome fundamental limitations inherent in measurements of bulk cell population that have frustrated efforts to resolve cellular states. Single-cell genomics and proteomics enable not only precise characterization of cell state, but also provide a stunningly high-resolution view of transitions between states. These measurements may finally make explicit the metaphor that C.H. Waddington posed nearly 60 years ago to explain cellular plasticity: Cells are residents of a vast “landscape” of possible states, over which they travel during development and in disease. Single-cell technology helps not only locate cells on this landscape, but illuminates the molecular mechanisms that shape the landscape itself. However, single-cell genomics is a field in its infancy, with many experimental and computational advances needed to fully realize its full potential.
Functional genomics bridges the gap between quantitative genetics and molecular biology
Authors: Lappalainen Tuuli
Published: October 2015

Deep characterization of molecular function of genetic variants in the human genome is becoming increasingly important for understanding genetic associations to disease and for learning to read the regulatory code of the genome. In this paper, I discuss how recent advances in both quantitative genetics and molecular biology have contributed to understanding functional effects of genetic variants, lessons learned from eQTL studies, and future challenges in this field.
The path to routine use of genomic biomarkers in the cancer clinic
Authors: Boutros Paul C.
Published: October 2015

It has been almost 15 years since the first microarray-based studies creating multigene biomarkers to subtype and predict survival of cancer patients. This Perspective looks at why only a handful of genomic biomarkers have reached clinical application and what advances are needed over the next 15 years to grow this number. I discuss challenges in creating biomarkers and reproducing them at the genomic and computational levels, including the problem of spatio-genomic heterogeneity in an individual cancer. I then outline the challenges in translating newly discovered genome-wide or regional events, like trinucleotide mutation signatures, kataegis, and chromothripsis, into biomarkers, as well as the importance of incorporating prior biological knowledge. Lastly, I outline the practical problems of pharmaco-economics and adoption: Are new biomarkers viewed as economically rational by potential funders? And if they are, how can their results be communicated effectively to patients and their clinicians? Genomic-based diagnostics have immense potential for transforming the management of cancer. The next 15 years will see a surge of research into the topics here that, when combined with a stream of new targeted therapies being developed, will personalize the cancer clinic.