bluuebunny/crossref_metadata_2025 huggingface dataset:
Development of polaron-transformed explicitly correlated full configuration interaction method for investigation of quantum-confined Stark effect in GaAs quantum dots
Authors: Blanton Christopher J. , Brenon Christopher , Chakraborty Arindam
Published: February 2013

The effect of external electric field on electron-hole (eh) correlation in gallium arsenide quantum dots is investigated. The electron-hole Schrodinger equation in the presence of an external electric field is solved using explicitly correlated full configuration interaction method and accurate exciton binding energy and electron-hole recombination probability are obtained. The effect of the electric field was included in the 1-particle single component basis functions by performing variational polaron transformation. The quality of the wavefunction at small inter-particle distances was improved by using Gaussian-type geminal function that depended explicitly on the electron-hole separation distance. The parameters of the explicitly correlated function were determined variationally at each field strength. The scaling of total exciton energy, exciton binding energy, and electron-hole recombination probability with respect to the strength of the electric field was investigated. It was found that a 500 kV/cm change in field strength reduces the binding energy and recombination probability by a factor of 2.6 and 166, respectively. The results show that the eh-recombination probability is affected much more strongly by the electric field than the exciton binding energy. Analysis using the polaron-transformed basis indicates that the exciton binding should asymptotically vanish in the limit of large field strength.
Shear behavior of a confined thin film: Influence of the molecular dynamics scheme employed
Authors: Hoang Hai , Galliero Guillaume
Published: February 2013

In this work, we have considered and compared two molecular dynamics schemes widely used when studying a thin fluid film confined between solid surfaces and undergoing boundary shear. In the first approach, the non-equilibrium simulations are performed on a confined fluid explicitly connected to bulk reservoirs. In the second one, non-equilibrium simulations are carried out on the confined fluid only, in which the average density is deduced from a prior simulation in the grand canonical ensemble. We have found that the apparent properties (average density and effective viscosity) of a strongly confined Lennard-Jones liquid are significantly different using one scheme or the other when the solid surfaces induce a strong structure in the whole fluid, i.e., for small separations between the solid surfaces. Furthermore, the shear velocity dependence of the friction force has been found to be as well very sensitive to the approach chosen and can be well understood in terms of the fluid structure, which can even lead to a visco-plastic behavior of the fluid in some cases. Finally, it is shown that the first scheme is the only one usable to explore the history-dependence of the friction force as observed in experiments.
Effect of presence of salt on the dynamics of water in uncharged nanochannels
Authors: Bakli Chirodeep , Chakraborty Suman
Published: February 2013

Energy conversion and generation mechanisms at nano-scales often include tapping power from pressure-driven flow of water containing dissolved salts in nanofluidic channels. The deviation of such flows from continuum behaviour can often be advantageously utilized to enhance the energy conversion efficiency. Here, by executing molecular dynamics simulations, we pinpoint alterations in effective stick-slip at the solid-liquid interface as a function of variation in the nature of the salt as well as salt solution concentration for different substrate wettabilities, which could possibly act as a control towards modulating energy conversion efficiencies of nanofluidic devices. Our results reveal that the presence of salt has distinctive effects in wettable and non-wettable channels. Finally, we address the observed slip length deviation quantitatively based on hydration energy of the individual ionic species.
Frequency domain analysis of spreading-constriction thermal impedance
Authors: Casalegno Francesco , De Marchi Andrea , Giaretto Valter
Published: February 2013

Spreading-constriction effects are analyzed in the frequency domain. The existence of a half-pole altering the steady state solution at high frequencies is pointed out. Application to the case of thermoelectric devices allows direct comparison with experimental data because thermal quantities can be measured as electrical signals at the very spot where spreading takes place. Good agreement with theory is shown here for a thermoelectric device in which the particular constriction geometry enhances its effect, making easily observable the difference between frequency domain and the steady state approaches.
High speed synchrotron x-ray phase contrast imaging of dynamic material response to split Hopkinson bar loading
Authors: Hudspeth M. , Claus B. , Dubelman S. , Black J. , Mondal A. , Parab N. , Funnell C. , Hai F. , Qi M. L. , Fezzaa K. , Luo S. N. , Chen W.
Published: February 2013

The successful process of amalgamating both the time-resolved imaging capabilities present at the Advanced Photon Source beamline 32ID-B and the proficiency of high-rate loading offered by the split Hopkinson or Kolsky compression/tension bar apparatus is discussed and verification of system effectiveness is expressed via dynamic experiments on various material systems. Single particle sand interaction along with glass cracking during dynamic compression, and fiber-epoxy interfacial failure, ligament-bone debonding, and single-crystal silicon fragmentation due to dynamic tension, were imaged with 0.5 μs temporal resolution and μm-level spatial resolution. Synchrotron x-ray phase contrast imaging of said material systems being loaded with the Kolsky bar apparatus demonstratively depicts the effectiveness of the novel union between these two powerful techniques, thereby allowing for in situ analysis of the interior of the material system during high-rate loading for a variety of applications.
Conceptual design and scaled experimental validation of an actively damped carbon tie rods support system for the stabilization of future particle collider superstructures
Authors: Collette C. , Tshilumba D. , Fueyo-Rosa L. , Romanescu I.
Published: February 2013

This paper presents a simple solution to increase the stability of the large superstructures supporting the final electromagnets of future linear particle collider. It consists of active carbon fiber tie rods, fixed at one end on the structure and at the other end to the detector through active tendons. In the first part of the paper, the solution has been tested on a finite element model of one half of the CLIC_ILD final focus structure. With a reasonable design, it is shown numerically that the compliance can be decreased by at least a factor 4, i.e., that the structure is 4 times more robust to technical noise at low frequency. Two additional features of the active rods are that they can also actively damp the structural resonances and realign the superstructures. The second part of the paper presents a successful experimental validation of the concept, applied to a scaled test bench, especially designed to contain the same modal characteristics as the full scale superstructure.
On numerical turbulence generation for test-particle simulations
Authors: Tautz R. C. , Dosch A.
Published: February 2013

A modified method is presented to generate artificial magnetic turbulence that is used for test-particle simulations. Such turbulent fields are obtained from the superposition of a set of wave modes with random polarizations and random directions of propagation. First, it is shown that the new method simultaneously fulfils requirements of isotropy, equal mean amplitude and variance for all field components, and vanishing divergence. Second, the number of wave modes required for a stochastic particle behavior is investigated by using a Lyapunov approach. For the special case of slab turbulence, it is shown that already for 16 wave modes the particle behavior agrees with that shown for considerably larger numbers of wave modes.
Two-dimensional quasi-double-layers in two-electron-temperature, current-free plasmas
Authors: Merino Mario , Ahedo Eduardo
Published: February 2013

The expansion of a plasma with two disparate electron populations into vacuum and channeled by a divergent magnetic nozzle is analyzed with an axisymmetric model. The purpose is to study the formation and two-dimensional shape of a current-free double-layer in the case when the electric potential steepening can still be treated within the quasineutral approximation. The properties of this quasi-double-layer are investigated in terms of the relative fraction of the high-energy electron population, its radial distribution when injected into the nozzle, and the geometry and intensity of the applied magnetic field. The two-dimensional double layer presents a curved shape, which is dependent on the natural curvature of the equipotential lines in a magnetically expanded plasma and the particular radial distribution of high-energy electrons at injection. The double layer curvature increases the higher the nozzle divergence is, the lower the magnetic strength is, and the more peripherally hot electrons are injected. A central application of the study is the operation of a helicon plasma thruster in space. To this respect, it is shown that the curvature of the double layer does not increment the thrust, it does not modify appreciably the downstream divergence of the plasma beam, but it increases the magnetic-to-pressure thrust ratio. The present study does not attempt to cover current-free double layers involving plasmas with multiple populations of positive ions.
Two-dimensional space-resolved emission spectroscopy of laser ablation plasma in water
Authors: Matsumoto Ayumu , Tamura Ayaka , Fukami Kazuhiro , Ogata Yukio H. , Sakka Tetsuo
Published: February 2013

We developed a method for two-dimensional space-resolved emission spectroscopy of laser-induced plasma in water to investigate the spatial distribution of atomic species involved in the plasma. Using this method, the laser ablation plasma produced on a Cu target in 5 mM NaCl aqueous solution was examined. The emission spectrum varied considerably depending on the detecting position. The temperature and the atomic density ratio NNa/NCu at various detecting positions were evaluated by fitting emission spectra to a theoretical model based on the Boltzmann distribution. We are successful in observing even a small difference between the distributions of the plasma parameters along the directions vertical and horizontal to the surface. The present approach gives direct information for sound understanding of the behavior of laser ablation plasma produced on a solid surface in water.
Thermal conductivity of 4H-SiC single crystals
Authors: Wei Rusheng , Song Sheng , Yang Kun , Cui Yingxin , Peng Yan , Chen Xiufang , Hu Xiaobo , Xu Xiangang
Published: February 2013

Thermal diffusivity and specific heat of 4H-SiC crystals as a function of temperature are measured, respectively, from room temperature to 600 °C. The thermal conductivity normal to c-axis was calculated from the measured data for both N-type and V-doped semi-insulating (SI) 4H-SiC single crystals. The thermal conductivity of N-type sample normal to c axis is proportional to T−1.26. It is approximately 280 W/mK at the room temperature. For V-doped SI sample, the thermal conductivity is proportional to T−1.256 and it is about 347 W/mK at room temperature, bigger than that of N-type sample. For semiconductor materials, total thermal conductivity is the sum of the contributions of lattice and carrier thermal conductivities. Temperature dependent Raman spectrum showed that the life time of phonons for N-type sample is shorter than that for SI sample. Accordingly thermal conductivity contributions from both lattice and carrier components are relatively small for N-type sample.
Mechanical self-confinement to enhance energy storage density of antiferroelectric capacitors
Authors: Young S. E. , Zhang J. Y. , Hong W. , Tan X.
Published: February 2013

The energy storage density of electrical capacitors utilizing antiferroelectric compositions Pb0.99Nb0.02[(Zr0.57Sn0.43)1−yTiy]0.98O3 as dielectrics is measured at a series of temperatures in a series of dielectric compositions with and without self-confinement. Under the applied electric field of 70 kV/cm, a maximum energy density of 1.3 J/cm3 is achieved. The mechanical self-confinement was introduced by partially electroding the central portion of the dielectric ceramic disk. A phase-field model was developed and it confirms the presence of compressive stresses ∼30 MPa in the electroded portion of the dielectric disk and the contribution to the increased energy density from the mechanical confinement.
Elastocaloric and magnetocaloric effects in Ni-Mn-Sn(Cu) shape-memory alloy
Authors: Castillo-Villa Pedro O. , Mañosa Lluís , Planes Antoni , Soto-Parra Daniel E. , Sánchez-Llamazares J. L. , Flores-Zúñiga H. , Frontera Carlos
Published: February 2013

We have studied magnetocaloric and elastocaloric properties of a Ni-Mn-Sn(Cu) metamagnetic shape-memory alloy undergoing a magneto-structural transition (martensitic type) close to room temperature. Changes of entropy have been induced by isothermally applying both mechanical (uniaxial stress) and magnetic fields. These entropy changes have been, respectively, estimated from dilatometric measurements giving the length of the sample as a function of temperature at selected applied forces and magnetic fields and from magnetization measurements as a function of temperature at selected applied magnetic fields. Our results indicate that the elastocaloric effect is conventional and occurs in two steps which reflect the interplay between the martensitic and the incipient magnetic transitions. By contrast, the magnetocaloric effect is inverse and occurs in a single step that encompasses the effect arising from both transitions.
Near-field radiative heat transfer between doped silicon nanowire arrays
Authors: Basu Soumyadipta , Wang Liping
Published: February 2013

In this letter, we investigate the near-field radiative heat transfer between two doped silicon nanowire arrays separated by a vacuum gap. Using effective medium theory and fluctuational electrodynamics, the radiative heat transfer is calculated for the silicon nanowire arrays with different filling fractions at different vacuum gaps. The energy transfer increases as the nanowire array becomes less dense due to enhancement in channels available for heat transfer. To further understand the impact of filling fraction to the total heat transfer, the dispersion relation of coupled surface plasmon polaritons is calculated inside the vacuum gap by considering temperature-dependent dielectric functions for the doped silicon nanowires. When the filling fraction is 0.5, the radiative heat transfer at a vacuum gap of 20 nm between the nanowire arrays is almost three times of that between two doped silicon plates. Results from this study will facilitate the application of doped silicon nanowires for energy harvesting and thermal management.
Mechanic and electromechanic effects in biaxially stretched liquid crystal elastomers
Authors: Diaz-Calleja Ricardo , Llovera-Segovia Pedro , Riande Evaristo , Quijano López Alfredo
Published: February 2013

The effect of combined electromechanic force fields in nematic side chain liquid crystal elastomers will be analyzed. A biaxially stretched plate in the x- and y-directions under an electric field applied in the perpendicular direction to the plate will be considered. A neo-Hookean model is chosen, which implies Gaussian behaviour. Results are obtained for both a soft and semisoft case showing the effect of the electric field on the rotation of the director and the free energy density function.
Versatile scanning tunneling microscopy with 120 ps time resolution
Authors: Saunus Christian , Raphael Bindel Jan , Pratzer Marco , Morgenstern Markus
Published: February 2013

We describe a fully ultra-high vacuum compatible scanning tunneling microscope (STM) optimized for radio-frequency signals. It includes in-situ exchangeable tips adapted to high frequency cabling and a standard sample holder, which offer access to the whole range of samples typically investigated by STM. We demonstrate a time resolution of 120 ps using the nonlinear I(V)-characteristic of the surface of highly oriented pyrolithic graphite. We provide atomically resolved images in pulse mode related to a spatially varying nonlinearity of the local density of states of the sample, thus, demonstrating the possible spatial resolution of the instrument in pulse mode. Analysis of the noise reveals that changes in the tunneling junction of 50 pA are dynamically detectable at 120 ps time resolution.
Identification of the native defect doping mechanism in amorphous indium zinc oxide thin films studied using ultra high pressure oxidation
Authors: Lee Sunghwan , Paine David C.
Published: February 2013

The mechanism of native defect doping in amorphous In-Zn-O (a-IZO) has not previously been established but is likely associated with native oxygen defect doping. We have used high pressure oxidation and defect equilibrium analysis to show a −1/6 power dependence of carrier density on oxygen fugacity in a-IZO. This dependency is predicted for oxygen vacancy-like donor defects. Extrapolation of equilibrium constants established at high pressures to atmospheric pressure reveals that the equilibrium carrier density in a-IZO at 200 °C is higher (>1020/cm3) than typical as-deposited channel carrier densities (<1017/cm3). This is consistent with observed increases in channel carrier density and negative threshold voltage shift in annealed a-IZO thin film transistor devices.
Significantly enhanced thermoelectric properties of ultralong double-walled carbon nanotube bundle
Authors: Miao Tingting , Ma Weigang , Zhang Xing , Wei Jinquan , Sun Jialin
Published: February 2013

A T-type method is developed to comprehensively evaluate the thermoelectric properties of materials. The thermoelectric properties, including thermal conductivity, thermopower, and electrical conductivity of an ultralong double-walled carbon nanotube bundle are studied from 240 K to 340 K by applying the T-type method. The determined figure of merit achieves 10−3 which is significantly larger than that reported for carbon nanotubes samples. The bundle consists of thousands of nanotubes aligned along the long axis with low levels of impurities, and the thermal conductivity is significantly reduced compared to that of individual double-walled nanotube, while the electrical conductivity is superior to most of the carbon nanotubes samples.
A high-temperature piezoelectric linear actuator operating in two orthogonal first bending modes
Authors: Chen Jianguo , Chen Zhijiang , Li Xiaotian , Dong Shuxiang
Published: February 2013

Conventionally, piezoelectric ultrasonic linear actuators operate in longitudinal and bending combination (degenerate) modes for producing an elliptic motion which drives a slider moving linearly. With the increasing temperature, the degenerate mode will split into two separated modes again, resulting in piezoelectric actuators working to fail. Here, we report a miniature piezoelectric ultrasonic linear actuator made of Mn modified (1−x)BiScO3–xPbTiO3 piezoelectric ceramics operating in two orthogonal first bending modes (B1-B1). The B1-B1 mode linear actuator showed much better load and speed temperature stability than piezoelectric actuators operating in different combination mode in the investigated temperature range of room temperature to 200 °C.
Magnetic behavior of graphene sheets embedded carbon film originated from graphene nanocrystallite
Authors: Wang Chao , Diao Dongfeng
Published: February 2013

We found paramagnetic behavior at 300 K of graphene sheets embedded carbon (GSEC) film, which is deposited under low energy electron irradiation in electron cyclotron resonance plasma. The origin of the magnetic properties of GSEC film is ascribed to the formation of graphene nanocrystallite. With higher irradiation energy, the size of nanocrystallite barely changed, while the density in GSEC film became higher, leading to a dramatically increase of saturation magnetization and residual magnetism. This finding indicates that GSEC film with higher magnetization can be expected, which has the potential for magnetic and spintronics applications.
Enhanced acousto-optic interaction in two-dimensional phoxonic crystals with a line defect
Authors: Lin Tzy-Rong , Lin Chiang-Hsin , Hsu Jin-Chen
Published: February 2013

This study presents acousto-optic interaction of optical waves in a two-dimensional phoxonic crystal with a line defect. Because of dual photonic and phononic band gaps generated in the phoxonic crystal, optical waves and acoustic modes can be guided and amplified, respectively, along the line defect that serves simultaneously as an optical waveguide and acoustic wave cavity. By means of finite-element analysis, we show that the confinement of the optical waves and acoustic modes in the same region of space (i.e., in the defect) leads to enhanced modulation of the optical waves by an acoustic cavity mode, and obvious shifts in eigenfrequencies and transmission peaks are observed. Stronger acousto-optic interaction is caused by the amplified acoustic fields and by the long-lifetime interaction of photons and phonons in the line defect.
Interaction of surface and interface plasmons in extremely thin Al films on Si(111)
Authors: Qin Huajun , Jiang Ying , Zhang Guanhua , Wu Kehui
Published: February 2013

The collective electronic excitations in Al thin films with thickness down to mono-atomic layer were studied by scanning tunneling microscopy and angle-resolved high resolution electron energy loss spectroscopy. Clear evidences for a coupling of the Al surface plasmon and Al/Si interface plasmon were observed for the film thickness below 3 ML, which induces a splitting of the normal Al surface plasmon mode. The experimental results can be well explained by a classical model for surface plasmon excitations.
Controlling output pulse and prepulse in a resonant microwave pulse compressor
Authors: Shlapakovski A. , Artemenko S. , Chumerin P. , Yushkov Yu.
Published: February 2013

A resonant microwave pulse compressor with a waveguide H-plane-tee-based energy extraction unit was studied in terms of its capability to produce output pulses that comprise a low-power long-duration (prepulse) and a high-power short-duration part. The application of such combined pulses with widely variable prepulse and high-power pulse power and energy ratios is of interest in the research area of electronic hardware vulnerability. The characteristics of output radiation pulses are controlled by the variation of the H-plane tee transition attenuation at the stage of microwave energy storage in the compressor cavity. Results of theoretical estimations of the parameters tuning range and experimental investigations of the prototype S-band compressor (1.5 MW, 12 ns output pulse; ∼13.2 dB gain) are presented. The achievable maximum in the prepulse power is found to be about half the power of the primary microwave source. It has been shown that the energy of the prepulse becomes comparable with that of the short-duration (nanosecond) pulse, while the power of the latter decreases insignificantly. The possible range of variation of the prepulse power and energy can be as wide as 40 dB. In the experiments, the prepulse level control within the range of ∼10 dB was demonstrated.
Electrical switching of quantum tunneling through p-n junction in a quantum spin Hall bar
Authors: Cheng Fang , Lin L. Z. , Zhang L. B. , Zhou Guanghui
Published: February 2013

We demonstrate theoretically electrical switching of the edge state transport via a transverse electric field in a quantum spin Hall bar. By tuning the electric fields, the Fermi energy and the gate voltage, the edge channels in the both topological insulator (TI)/band insulator (BI) and TI/TI p-n junctions can be transited from opaque to transparent. This electrical switching behavior offers us an efficient way to control the topological edge state transport which is robust against the local perturbation.
Structure and multiferroic properties of Bi(1-x)DyxFe0.90Mg0.05Ti0.05O3 solid solution
Authors: Li Nan , Wu Jiangtao , Jiang Yaqi , Xie Zhaoxiong , Zheng Lansun , Ye Zuo-Guang
Published: February 2013

Chemical modification is proven to be an effective way to improve the properties of perovskite BiFeO3 (BFO). In this paper, we studied the effects of the A-site Dy3+ ion substitution on the structure and multiferroic properties of BFO in which the Fe3+ ion on the B-site is partially co-substituted for by Mg2+ and Ti4+ ions. The solid solution compounds of Bi(1-x)DyxFe0.90Mg0.05Ti0.05O3 (x = 0 – 1) were synthesized by a tartaric acid-assisted solution process, followed by thermal treatments at 850 °C. The structural transition and the ferroelectric and magnetic properties as a function of composition were investigated. It is found that the structure transforms from a rhombohedral (R3c) to an orthorhombic phase (Pn21a) when x is increased to ≥ 0.15. The ferroelectric measurements indicate that the sample with x = 0.15 possesses the best ferroelectric property, and the remnant polarization of the samples with orthorhombic symmetry decreases with the increase of Dy3+ concentration. The compounds of Bi(1-x)DyxFe0.90Mg0.05Ti0.05O3 (x = 0.05 – 1.00) exhibit weakly ferromagnetic properties at low temperatures, but antiferromagnetic behavior at high temperatures. The magnetization of the solid solution increases linearly with the increase of the Dy3+ amount.
A giant polarization value of Zn and Mn co-modified bismuth ferrite thin films
Authors: Wu Jiagang , Qiao Sha , Wang John , Xiao Dingquan , Zhu Jianguo
Published: February 2013

A giant remanent polarization of BiFeO3 thin films is obtained by introducing Zn and Mn, and Bi(Fe0.93Mn0.05Zn0.02)O3 (BFMZO) thin films were prepared on SrRuO3-buffered silicon substrates by the radio-frequency sputtering. An (111) orientation is induced in such a film because of the introduction of an SrRuO3 buffer layer. An enhanced ferroelectric behavior of 2Pr ∼ 235 μC/cm2 and 2Ec ∼ 612 kV/cm is observed in BFMZO thin films, together with a fatigue-free behavior. As a result, the introduction of Zn and Mn is a good way to improve the electrical behavior of BiFeO3 thin films.
Carrier transport mechanism of low resistance Ti/Al/Au ohmic contacts to AlInN/GaN heterostructures
Authors: Kim Seongjun , Ryou Jae-Hyun , Dupuis Russell D. , Kim Hyunsoo
Published: February 2013

The carrier transport mechanism of a low resistance Ti/Al/Au Ohmic contact to AlInN/GaN heterostructures was investigated. The Ohmic contact produced upon thermal annealing was due to the generation of TiN contact inclusions with a density of 2.8 × 108 cm−2, i.e., spike mechanism. The sheet resistance of channel layer was found to follow power law, yielding the power index of −1.57. Temperature dependent contact resistance could be understood based on the parallel network model consisting of distributed resistance components of TiN contact inclusion (predominant) and the rest sound region (negligible), giving the barrier height of 0.65 eV and the carrier density of 2.3 × 1019 cm−3 at the TiN/GaN interfaces.
Role of photo-assisted tunneling in time-dependent second-harmonic generation from Si surfaces with ultrathin oxides
Authors: An Yong Q. , Price J. , Lei Ming , Downer M. C.
Published: February 2013

Optical second-harmonic generation (SHG) from Si surfaces covered with nanometer-thin SiO2 varies with the laser exposure time because of photo-injection and charge trapping. We use UV lamp excitation to decompose the effects of photo-injection and charge trapping on the time-dependence of SHG of 1.65 eV photons at the Si/SiO2 interface. We find that the time-dependence of SHG in air arises mainly from the cooperative effect of three-photon photo-injection and charge trapping by surface O2. When the oxide is ultrathin (≤1.5 nm), the time-dependence also includes a significant contribution from one and two-photon photo-assisted tunneling.
Near-field optical microscopy with an infra-red free electron laser applied to cancer diagnosis
Authors: Smith A. D. , Siggel-King M. R. F. , Holder G. M. , Cricenti A. , Luce M. , Harrison P. , Martin D. S. , Surman M. , Craig T. , Barrett S. D. , Wolski A. , Dunning D. J. , Thompson N. R. , Saveliev Y. , Pritchard D. M. , Varro A. , Chattopadhyay S. , Weightman P.
Published: February 2013

We show that the combination of a scanning near field optical microscope and an infra-red free electron laser yields chemical images with sub-cellular spatial resolution that have the potential to provide a diagnostic for oesophageal adenocarcinoma.
Nanoscale structure of protamine/DNA complexes for gene delivery
Authors: Motta Simona , Brocca Paola , Del Favero Elena , Rondelli Valeria , Cantù Laura , Amici Augusto , Pozzi Daniela , Caracciolo Giulio
Published: February 2013

Understanding the internal packing of gene carriers is a key-factor to realize both gene protection during transport and de-complexation at the delivery site. Here, we investigate the structure of complexes formed by DNA fragments and protamine, applied in gene delivery. We found that complexes are charge- and size-tunable aggregates, depending on the protamine/DNA ratio, hundred nanometers in size. Their compactness and fractal structure depend on the length of the DNA fragments. Accordingly, on the local scale, the sites of protamine/DNA complexation assume different morphologies, seemingly displaying clumping ability for the DNA network only for shorter DNA fragments.
Infrared reflectivity spectra of gas-source molecular beam epitaxy grown dilute InNxAs1−x/InP (001)
Authors: Talwar Devki N. , Yang Tzuen-Rong , Hsiung Lin Hao , Chuan Feng Zhe
Published: February 2013

Vibrational spectra of gas-source molecular beam epitaxy grown dilute InNxAs1−x/InP (001) alloys are obtained using a Fourier-transform infrared (IR) spectroscopy. A triply degenerate NAs local vibrational mode of Td-symmetry is observed near 438 cm−1 corresponding to the In-N bond energy. The analysis of composition dependent infrared reflectivity spectra in InNAs has predicted a two-phonon-mode behavior. In In(Ga)-rich GaInNAs alloys the observed splitting of the NAs local mode into a doublet for the NAs–Ga1(In1)In3(Ga3) pair-defect of C3v-symmetry is consistent with our simulated results based on a sophisticated Green's function theory.
Phosphorus doping of 4H SiC by liquid immersion excimer laser irradiation
Authors: Ikeda Akihiro , Nishi Koji , Ikenoue Hiroshi , Asano Tanemasa
Published: February 2013

Phosphorus doping of 4H SiC is performed by KrF excimer laser irradiation of 4H SiC immersed in phosphoric acid. Phosphorus is incorporated to a depth of a few tens of nanometers at a concentration of over 1020/cm3 without generating significant crystal defects. Formation of a pn junction diode with an ideality factor of 1.06 is demonstrated.
High-brightness tapered quantum cascade lasers
Authors: Gökden Burç , Mansuripur Tobias S. , Blanchard Romain , Wang Christine , Goyal Anish , Sanchez-Rubio Antonio , Turner George , Capasso Federico
Published: February 2013

An index-guided tapered quantum cascade laser emitting near 9.5 μm with sloped sidewalls and no anti-reflection coating is presented, and the performance for devices with taper half-angles of 1° and 2° is investigated. The 1° device delivers up to 2.5 W of peak optical power at room temperature with beam quality-factor M2 = 2.08, while the two-degree device outputs 3.8 W with M2 = 2.25 for a maximum brightness of 1.87 MW cm−2 sr−1.
Active microwave absorber with the dual-ability of dividable modulation in absorbing intensity and frequency
Authors: Wu Xiaoyu , Hu Chenggang , Wang Yanqin , Pu Mingbo , Huang Cheng , Wang Changtao , Luo Xiangang
Published: February 2013

We present the design, fabrication and experimental demonstration of an electrically active absorber at microwave frequency. Unlike those proposed before, simulation and experiment data present that its working frequency and absorbing intensity can be both but separately controlled. The electromagnetic coupling analysis reveals that the feature arises from the dividable frequency and amplitude modulation on an active magnetic resonator controlled by varactor and pin diodes. Such separable modulating behaviors are further confirmed by the equivalent LC circuit model. It is believed that this will be an important step towards smart application of active absorber.
Synergistic interaction of an endo-β-1,4-glucanase and a β-glucohydrolase leads to more efficient hydrolysis of cellulose-like polymers in the gecarcinid land crab, Gecarcoidea natalis
Authors: Allardyce Benjamin J. , Linton Stuart M.
Published: February 2013

This study investigated synergism between endo-β-1,4-glucanase and β-glucohydrolase enzymes from Gecarcoidea natalis. Together, these enzymes efficiently hydrolyse the cellulose-like polymer, carboxymethyl cellulose, to glucose. Endo-β-1,4-glucanase and β-glucohydrolase, isolated previously from G. natalis, were incubated in vitro using a ratio of the measured activities that matches that found in their digestive juice (5.4 : 1). Their combined activity, measured as the release of glucose from carboxymethyl cellulose, was greater than the sum of their separate activities. Hence they synergistically released glucose from carboxymethyl cellulose (degree of synergy: 1.27). This may be due to the complementary nature of the products of endo-β-1,4-glucanase activity and the preferred substrates of the β-glucohydrolase. β-glucohydrolase may also enhance cellulose hydrolysis by removing cellobiose, a potential competitive inhibitor of endo-β-1,4-glucanase. The synergistic interaction of these two enzymes further supports the previous suggestion that this species possesses a novel two-enzyme cellulase system that differs from the traditional three-enzyme fungal model.
Players of Matching Pennies automatically imitate opponents’ gestures against strong incentives
Authors: Belot Michèle , Crawford Vincent P. , Heyes Cecilia
Published: February 2013

There is a large body of evidence of apparently spontaneous mimicry in humans. This phenomenon has been described as “automatic imitation” and attributed to a mirror neuron system, but there is little direct evidence that it is involuntary rather than intentional. Cook et al. supplied the first such evidence in a unique strategic game design that gave all subjects a pecuniary incentive to avoid imitation [Cook R, Bird G, Lünser G, Huck S, Heyes C (2012)
Proc Biol Sci
279(1729):780–786]. Subjects played Rock-Paper-Scissors repeatedly in matches between fixed pairs, sometimes with one and sometimes with both subjects blindfolded. The frequency of draws in the blind-blind condition was at chance, but in the blind-sighted condition it was significantly higher, suggesting automatic imitation had occurred. Automatic imitation would raise novel issues concerning how strategic interactions are modeled in game theory and social science; however, inferring automatic imitation requires significant incentives to avoid it, and subjects’ incentives were less than 3 US cents per 60-game match. We replaced Cook et al.’s Rock-Paper-Scissors with a Matching Pennies game, which allows far stronger incentives to avoid imitation for some subjects, with equally strong incentives to imitate for others. Our results are important in providing evidence of automatic imitation against significant incentives. That some of our subjects had incentives to imitate also enables us clearly to distinguish intentional responding from automatic imitation, and we find evidence that both occur. Thus, our results strongly confirm the occurrence of automatic imitation, and illuminate the way that automatic and intentional processes interact in a strategic context.
Genome-wide analysis of thyroid hormone receptors shared and specific functions in neural cells
Authors: Chatonnet Fabrice , Guyot Romain , Benoît Gérard , Flamant Frederic
Published: February 2013

Significance

This article presents a unique genome-wide transcriptome and cistrome analysis for thyroid hormone receptors. It defines 3,3′,5-triiodo-
L
-thyronine (T3) target genes in a neural cell line expressing either TRα1 or TRβ1. A substantial fraction of the T3 target genes display a marked preference for one of the two receptors. However, receptor-selective regulation of T3 target genes does not result from receptor-selective chromatin occupancy of their promoter regions. We conclude that modification of TRα1 and TRβ1 intrinsic properties contributes to the divergent evolution of the receptors’ function.
PLGG1
, a plastidic glycolate glycerate transporter, is required for photorespiration and defines a unique class of metabolite transporters
Authors: Pick Thea R. , Bräutigam Andrea , Schulz Matthias A. , Obata Toshihiro , Fernie Alisdair R. , Weber Andreas P. M.
Published: February 2013

Photorespiratory carbon flux reaches up to a third of photosynthetic flux, thus contributes massively to the global carbon cycle. The pathway recycles glycolate-2-phosphate, the most abundant byproduct of RubisCO reactions. This oxygenation reaction of RubisCO and subsequent photorespiration significantly limit the biomass gains of many crop plants. Although photorespiration is a compartmentalized process with enzymatic reactions in the chloroplast, the peroxisomes, the mitochondria, and the cytosol, no transporter required for the core photorespiratory cycle has been identified at the molecular level to date. Using transcript coexpression analyses, we identified Plastidal glycolate glycerate translocator 1 (PLGG1) as a candidate core photorespiratory transporter. Related genes are encoded in the genomes of archaea, bacteria, fungi, and all Archaeplastida and have previously been associated with a function in programmed cell-death. A mutant deficient in PLGG1 shows WT-like growth only in an elevated carbon dioxide atmosphere. The mutant accumulates glycolate and glycerate, leading to the hypothesis that PLGG1 is a glycolate/glycerate transporter. This hypothesis was tested and supported by in vivo and in vitro transport assays and
18
O
2
-metabolic flux profiling. Our results indicate that PLGG1 is the chloroplastidic glycolate/glycerate transporter, which is required for the function of the photorespiratory cycle. Identification of the PLGG1 transport function will facilitate unraveling the role of similar proteins in bacteria, archaea, and fungi in the future.
Computational modeling and experimental validation of the
Legionella
and
Coxiella
virulence-related type-IVB secretion signal
Authors: Lifshitz Ziv , Burstein David , Peeri Michael , Zusman Tal , Schwartz Kierstyn , Shuman Howard A. , Pupko Tal , Segal Gil
Published: February 2013

Legionella
and
Coxiella
are intracellular pathogens that use the virulence-related Icm/Dot type-IVB secretion system to translocate effector proteins into host cells during infection. These effectors were previously shown to contain a C-terminal secretion signal required for their translocation. In this research, we implemented a hidden semi-Markov model to characterize the amino acid composition of the signal, thus providing a comprehensive computational model for the secretion signal. This model accounts for dependencies among sites and captures spatial variation in amino acid composition along the secretion signal. To validate our model, we predicted and synthetically constructed an optimal secretion signal whose sequence is different from that of any known effector. We show that this signal efficiently translocates into host cells in an Icm/Dot-dependent manner. Additionally, we predicted
in silico
and experimentally examined the effects of mutations in the secretion signal, which provided innovative insights into its characteristics. Some effectors were found to lack a strong secretion signal according to our model. We demonstrated that these effectors were highly dependent on the IcmS-IcmW chaperons for their translocation, unlike effectors that harbor a strong secretion signal. Furthermore, our model is innovative because it enables searching ORFs for secretion signals on a genomic scale, which led to the identification and experimental validation of 20 effectors from
Legionella pneumophila
,
Legionella longbeachae
, and
Coxiella burnetii.
Our combined computational and experimental methodology is general and can be applied to the identification of a wide spectrum of protein features that lack sequence conservation but have similar amino acid characteristics.
Ikaros promotes early-born neuronal fates in the cerebral cortex
Authors: Alsiö Jessica M. , Tarchini Basile , Cayouette Michel , Livesey Frederick J.
Published: February 2013

During cerebral cortex development, a series of projection neuron types is generated in a fixed temporal order. In
Drosophila
neuroblasts, the transcription factor
hunchback
encodes first-born identity within neural lineages. One of its mammalian homologs, Ikaros, was recently reported to play an equivalent role in retinal progenitor cells, raising the question as to whether Ikaros/Hunchback proteins could be general factors regulating the development of early-born fates throughout the nervous system. Ikaros is also expressed in progenitor cells of the mouse cerebral cortex, and this expression is highest during the early stages of neurogenesis and thereafter decreases over time. Transgenic mice with sustained Ikaros expression in cortical progenitor cells and neurons have developmental defects, including displaced progenitor cells within the cortical plate, increased early neural differentiation, and disrupted cortical lamination. Sustained Ikaros expression results in a prolonged period of generation of deep layer neurons into the stages when, normally, only late-born upper layer neurons are generated, as well as a delayed production of late-born neurons. Consequently, more early-born and fewer late-born neurons are present in the cortex of these mice at birth. This phenotype was observed in all parts of the cortex, including those with minimal structural defects, demonstrating that it is not secondary to abnormalities in cortical morphogenesis. These data suggest that Ikaros plays a similar role in regulating early temporal fates in the mammalian cerebral cortex as Ikaros/Hunchback proteins do in the
Drosophila
nerve cord.
H3K4 methyltransferase Set1 is involved in maintenance of ergosterol homeostasis and resistance to Brefeldin A
Authors: South Paul F. , Harmeyer Kayla M. , Serratore Nina D. , Briggs Scott D.
Published: February 2013

Set1 is a conserved histone H3 lysine 4 (H3K4) methyltransferase that exists as a multisubunit complex. Although H3K4 methylation is located on many actively transcribed genes, few studies have established a direct connection showing that loss of Set1 and H3K4 methylation results in a phenotype caused by disruption of gene expression. In this study, we determined that cells lacking Set1 or Set1 complex members that disrupt H3K4 methylation have a growth defect when grown in the presence of the antifungal drug Brefeldin A (BFA), indicating that H3K4 methylation is needed for BFA resistance. To determine the role of Set1 in BFA resistance, we discovered that Set1 is important for the expression of genes in the ergosterol biosynthetic pathway, including the rate-limiting enzyme HMG-CoA reductase. Consequently, deletion of
SET1
leads to a reduction in HMG-CoA reductase protein and total cellular ergosterol. In addition, the lack of Set1 results in an increase in the expression of
DAN1
and
PDR11
, two genes involved in ergosterol uptake. The increase in expression of uptake genes in
set1Δ
cells allows sterols such as cholesterol and ergosterol to be actively taken up under aerobic conditions. Interestingly, when grown in the presence of ergosterol
set1Δ
cells become resistant to BFA, indicating that proper ergosterol levels are needed for antifungal drug resistance. These data show that H3K4 methylation impacts gene expression and output of a biologically and medically relevant pathway and determines why cells lacking H3K4 methylation have antifungal drug sensitivity.
Evolution of a genetic polymorphism with climate change in a Mediterranean landscape
Authors: Thompson John , Charpentier Anne , Bouguet Guillaume , Charmasson Faustine , Roset Stephanie , Buatois Bruno , Vernet Philippe , Gouyon Pierre-Henri
Published: February 2013

Many species show changes in distribution and phenotypic trait variation in response to climatic warming. Evidence of genetically based trait responses to climate change is, however, less common. Here, we detected evolutionary variation in the landscape-scale distribution of a genetically based chemical polymorphism in Mediterranean wild thyme (
Thymus vulgaris
) in association with modified extreme winter freezing events. By comparing current data on morph distribution with that observed in the early 1970s, we detected a significant increase in the proportion of morphs that are sensitive to winter freezing. This increase in frequency was observed in 17 of the 24 populations in which, since the 1970s, annual extreme winter freezing temperatures have risen above the thresholds that cause mortality of freezing-sensitive morphs. Our results provide an original example of rapid ongoing evolutionary change associated with relaxed selection (less extreme freezing events) on a local landscape scale. In species whose distribution and genetic variability are shaped by strong selection gradients, there may be little time lag associated with their ecological and evolutionary response to long-term environmental change.
Transforming mutations of RAC guanosine triphosphatases in human cancers
Authors: Kawazu Masahito , Ueno Toshihide , Kontani Kenji , Ogita Yoshitaka , Ando Mizuo , Fukumura Kazutaka , Yamato Azusa , Soda Manabu , Takeuchi Kengo , Miki Yoshio , Yamaguchi Hiroyuki , Yasuda Takahiko , Naoe Tomoki , Yamashita Yoshihiro , Katada Toshiaki , Choi Young Lim , Mano Hiroyuki
Published: February 2013

Members of the RAS superfamily of small guanosine triphosphatases (GTPases) transition between GDP-bound, inactive and GTP-bound, active states and thereby function as binary switches in the regulation of various cellular activities. Whereas HRAS, NRAS, and KRAS frequently acquire transforming missense mutations in human cancer, little is known of the oncogenic roles of other small GTPases, including Ras-related C3 botulinum toxin substrate (RAC) proteins. We show that the human sarcoma cell line HT1080 harbors both NRAS(Q61K) and RAC1(N92I) mutant proteins. Whereas both of these mutants were able to transform fibroblasts, knockdown experiments indicated that RAC1(N92I) may be the essential growth driver for this cell line. Screening for RAC1, RAC2, or RAC3 mutations in cell lines and public databases identified several missense mutations for RAC1 and RAC2, with some of the mutant proteins, including RAC1(P29S), RAC1(C157Y), RAC2(P29L), and RAC2(P29Q), being found to be activated and transforming. P29S, N92I, and C157Y mutants of RAC1 were shown to exist preferentially in the GTP-bound state as a result of a rapid transition from the GDP-bound state, rather than as a result of a reduced intrinsic GTPase activity. Activating mutations of RAC GTPases were thus found in a wide variety of human cancers at a low frequency; however, given their marked transforming ability, the mutant proteins are potential targets for the development of new therapeutic agents.