bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of phase transition on the optoelectronic properties of Zn1−xMgxS
Authors: Khan Imad , Ahmad Iftikhar , Rahnamaye Aliabad H. A. , Maqbool M.
Published: October 2012

Density functional calculations are performed to investigate the structural, electronic, and optical properties of Zn1−xMgxS (0 ≤ x ≤ 1). In the present DFT calculations, we used modified Becke-Johnson potential in the exchange and correlation energy, which is effective for the treatment of the d-orbitals. A structural phase transition from zinc-blende to rock-salt is observed at 73% magnesium, which is consistent with the experimental results. Furthermore, the alloy has direct band gap nature for the whole range of Mg concentration in the zinc-blende structure, while the band gap nature for the rock-salt phase is indirect. The zinc-blende crystal structure has many established applications in the UV optoelectronic devices, and therefore the maintenance of the compound in zinc-blende crystal structure for the maximum range of Mg-composition is highly desirable which is dependent on the composition rate, external environment, and thickness of the film. Keeping in view the importance of ZnMgS in UV optical devices, its optical properties like dielectric functions, refractive indices, reflectivity, and energy loss function are also investigated.
Direct electrostatic toner marking with poly(3,4-ethylenedioxythiophene)polystyrenesulfonate bilayer devices
Authors: Kanungo Mandakini , Law Kock-Yee , Zhang Yuanjia
Published: October 2012

Poly(3,4-ethylenedioxythiophene)polystyrenesulfonate (PEDOT:PSS) is the one of the most promising and widely used materials for low cost large area flexible displays, owing to its easy solution processing and micro/nano scale patternability. In this work, hole injection between PEDOT:PSS thin film and molecularly doped polymer layers of arylamine has been studied in a bilayer device configuration. The electrical properties of the bilayer devices have been examined by studying their charge-discharge behavior, current-voltage (I-V), and time-of-flight (TOF) characteristics. The work function of the PEDOT:PSS and arylamine has been estimated by electrochemical measurements. Results show that PEDOT:PSS is an efficient hole injector to arylamine owing to its favorable molecular energetics. The efficiency of hole injection depends on the conductivity of the PEDOT:PSS film and the strength of the electric field across the bilayer device. The interfacial electrical contact behavior between PEDOT and arylamine studied by steady state I-V measurements and TOF measurements suggests that for highly conductive PEDOT:PSS, the discharge of the bilayer device is limited by the hole mobility in the charge transport layer whereas it is injection limited for more resistive PEDOT:PSS films. Printing experiments were performed on a modified xerographic DC12 printer as well as a modified DC8000 development housing. The overall results show that the latent image produced by discharging the bilayer device can be developed electrostatically with toner. More importantly, we found that the PEDOT:PSS bilayer device can be charged, discharged, and developed by just loading it against a negatively biased magnetic toner brush. We suggest coupling this direct toner marking process with an active backplane for digital printing application. The proposed digital printer appears to be very simple and compact as printing can be done without using a charger and the laser ROS system and replacing the photoreceptor with the PEDOT bilayer device that is controlled by an active backplane. The operating bias estimated for the Thin Film Transistors (TFTs) in the backplane is about −200 V. We believe that the bias voltage can be further reduced by using a thinner charge transport layer and by optimizing the toner development process. Although the bias voltage is still high, it is within reach for today's high-voltage TFT technology.
Tm3+ doped silicon thin film and waveguides for mid-infrared sources
Authors: Murray Matthew , Toney Fernandez T. , Richards Billy , Jose Gin , Jha Animesh
Published: October 2012

A Tm3+ doped nanoparticulate silicon thin film and subsequent surface waveguides fully fabricated by using femtosecond (fs) pulsed laser are reported. The thin film exhibits strong room temperature fluorescence peaked at 2.04 μm when using an 808 nm diode laser. The fs-pulsed laser deposited film was then processed using fs-laser micromachining for the formation of channel waveguides, which were subsequently coupled with a 1550 nm laser and characterized for their infrared mode propagation.
Influence of electromagnetic radiation on the power balance in a radiofrequency microdischarge with a hollow needle electrode
Authors: Despax B. , Pascal O. , Gherardi N. , Naude N. , Belinger A. , Pitchford L. C.
Published: October 2012

This study is focused on the power deposition in microplasma jet discharges generated by application of radiofrequency (RF) excitation to a hollow needle electrode. The plasma jet is initiated at atmospheric pressure in open air with a flow of helium through the electrode. We show that in this configuration, a significant part of the injected power is dissipated in electromagnetic radiation. Many recent works have demonstrated the potential of either cold plasma jets or of RF radiation for applications in medicine, and therefore a source that produces both a cold plasma jet and RF radiation could be of interest.
Highly promising electrooptic material: Distorted helix ferroelectric liquid crystal with a specific tilt angle
Authors: Abdulhalim I.
Published: October 2012

Short pitch deformable helix ferroelectric liquid crystals are shown to become optically isotropic at certain critical tilt angle with an average dielectric constant (ε1+ε2+ε3)/3. For uniaxial medium, this angle equals θd=cos−1(1/3), and it depends weakly on the local biaxial anisotropy. The degeneracy is removed upon the application of a small electric field and the medium becomes optically biaxial. A high contrast fast electrooptic modulation and display devices can be built using such materials even when aligned in a multi-domain. For tilt angles very near the degeneracy angle, ultrasensitivity of the eigenaxes rotation to the applied field is found.
Highly versatile ultra-low density GaAs quantum dots fabricated by filling of self-assembled nanoholes
Authors: Sonnenberg D. , Graf A. , Paulava V. , Hansen W. , Heyn Ch.
Published: October 2012

GaAs quantum dots (QDs) of ultra-low density (ULD) are fabricated by filling of nanoholes in AlGaAs surfaces. The holes are drilled using self-assembled local droplet etching with Al droplets. By precisely controlling the arsenic flux and the substrate temperature, the QD density is reduced down to the 106 cm−2 range uniformly over the whole wafer. The QD size is precisely adjustable via the hole filling level. By this, the optical emission energy of the QDs can be adjusted over a wide energy range of at least 120 meV. The surface visibility of ULD QDs allows their simple integration into lithographic processing.
Photonic crystal fabrication in lithium niobate via pattern transfer through wet and dry etched chromium mask
Authors: Yavuzcetin Ozgur , Novikov Herman P. , Dally Rebecca L. , Malley Sean T. , Perry Nicholas R. , Ozturk Birol , Sridhar Srinivas
Published: October 2012

The need to fabricate photonic crystals from lithium niobate (LN) with accurate feature sizes is important to the development of optoelectronic devices. This paper reports a fabrication process to dry etch X-cut LN at a submicron scale using electron beam lithography and chromium as a hard mask. The chromium mask was used for both dry-etching and wet-etching in a unique method. Problems and solutions found during fabrication are presented. Arrays consisting of 400 nm diameter holes with a high aspect ratio were etched in LN, creating photonic crystals modeled to transmit light in the infrared spectrum.
Analysis of long-range interaction effects on phase transitions in two-step spin-crossover chains by using Ising-type systems and Monte Carlo entropic sampling technique
Authors: Chiruta D. , Linares J. , Dahoo P. R. , Dimian M.
Published: October 2012

The analysis of two-step spin crossover phenomena in one-dimensional systems is performed in the framework of Ising-type model by using Monte Carlo entropic sampling technique. Both short-range and long-range interactions are considered in the Hamiltonian which also takes into account different degeneracies between the molecular states. The density of states associated to each macrostate is computed by using entropic sampling, via a biased Monte Carlo sampling technique, and the corresponding Ising-type Hamiltonian can thus be solved by using a self-consistent approach. By using this semi-analytical method, the effects of long-range interactions on phase transition driven by temperature variation in spin crossover chains have been investigated. Various types of spin crossover phenomena have been identified from gradual two-step transition to the one accompanied by multiple hysteresis loops, which was also recently observed experimentally. A metastable “plateau” has been observed at a high-spin fraction approximately equal to ½ for intermediate temperature region, but this plateau is not part of the low-to-high spin transition in strong cooperative systems and might be reached only by using special reversal curves or other external factors, such as light or pressure. In addition, a standard Monte-Carlo algorithm with Arrhenius dynamics is applied to this system in order to better understand its molecular behavior during the intermediate phase.
InAsP-based quantum wells as infrared pressure gauges for use in a diamond anvil cell
Authors: Trushkin S. , Kamińska A. , Trzeciakowski W. , Hopkinson M. , Suchocki A.
Published: October 2012

The results of high-pressure, low-temperature luminescence measurements of three InAsP-based multiple quantum well structures are reported for application as pressure sensors for diamond anvil cells working in the near-infrared spectral range. The multiple quantum well structures exhibit a much higher pressure shift of the luminescence lines as compared with ruby, typically used as the pressure sensor for diamond anvil cell. However, the full width at half maximum of the quantum wells is much higher than that for ruby. This reduces the available sensitivity gain exhibited by the InAsP-based quantum wells, but the improvement is still 2–3 times higher than that of ruby. Three InAsP multiple quantum well samples were examined, which exhibited luminescence at various wavelengths. The wavelength shift of these samples could be calibrated using similar parameters.
Structural, elastic, and polarization parameters and band structures of wurtzite ZnO and MgO
Authors: Jang S.-H. , Chichibu S. F.
Published: October 2012

Ab initio calculations were carried out to predict lattice constants, elastic stiffness constants, spontaneous polarization, piezoelectric constants, and band structure of virtually wurtzite (wz)-MgO. The ground-state properties for both wz-ZnO and wz-MgO were computed using the pseudopotential-planewave method in conjunction with the local density approximation adding the Hubbard parameter to density functional theory. From the results of fitting to reliable in-plane and out-of-plane lattice constants for strain-free and perfectly pseudomorphic wz-MgxZn1−xO alloys, the elastic stiffness constant C33 of the alloy system is revealed to deviate from Vegard's law. The validity of other calculated results for virtually wz-MgO is discussed based on the physical meaning and accuracy, making a comparison with the results shown in previous reports.
Polaronic behavior of MnO doped LiI-AgI-B2O3 glass
Authors: Filipič C. , Moguš-Milanković A. , Pavić L. , Srilatha K. , Veeraiah N. , Levstik A.
Published: October 2012

The ac electrical conductivity and dielectric constant of LiI-AgI-B2O3 glass doped with 0.1 mol. % MnO were investigated in the frequency range from 1 Hz to 1 MHz and the temperature range from 5 K to 450 K. At temperatures below 450 K, an ac conductivity and dielectric constant follow the universal dielectric response (UDR), being typical for hopping or tunneling of localized charge carriers. A detailed analysis of the temperature dependence of the UDR parameter s in terms of the theoretical model for tunneling of small polarons revealed that, below 450 K, this mechanism governs the charge transport in this glass. The comparison of the values of characteristic coefficients W∞ and Eac determined by two different methods confirms the polaronic behavior of this system.
FePtCu alloy thin films: Morphology, L1 chemical ordering, and perpendicular magnetic anisotropy
Authors: Brombacher C. , Schletter H. , Daniel M. , Matthes P. , Jöhrmann N. , Maret M. , Makarov D. , Hietschold M. , Albrecht M.
Published: October 2012

Rapid thermal annealing was applied to transform sputter-deposited Fe51Pt49/Cu bilayers into L10 chemically ordered ternary (Fe51Pt49)100−xCux alloys with (001) texture on amorphous SiO2/Si substrates. It was found that for thin film samples, which were processed at 600 °C for 30 s, the addition of Cu strongly favors the L10 ordering and (001) texture formation. Furthermore, it could be revealed by transmission electron microscopy and electron backscatter diffraction that the observed reduction of the ordering temperature with Cu content is accompanied by an increased amount of nucleation sites forming L10 ordered grains. The change of the structural properties with Cu content and annealing temperature is closely related to the magnetic properties. While an annealing temperature of 800 °C induces strong perpendicular magnetic anisotropy (PMA) in binary Fe51Pt49 films, the addition of Cu systematically reduces the PMA. However, due to the enhancement of both the A1-L10 phase transformation and the development of the (001) texture with increasing Cu content, lowering of the annealing temperature leads to a shift of the maximum perpendicular magnetic anisotropy towards alloys with higher Cu content. Thus, for an annealing temperature of 600 °C, the highest perpendicular magnetic anisotropy energy is found for the (Fe51Pt49)91Cu9 alloy. The smooth surface morphology, adjustable PMA, and high degree of intergranular exchange coupling make these films suitable for post-processing required for specific applications such as for sensorics or magnetic data storage.
Electron transporting water-gated thin film transistors
Authors: Al Naim Abdullah , Grell Martin
Published: October 2012

We demonstrate an electron-transporting water-gated thin film transistor, using thermally converted precursor-route zinc-oxide (ZnO) intrinsic semiconductors with hexamethyldisilazene (HMDS) hydrophobic surface modification. Water gated HMDS-ZnO thin film transistors (TFT) display low threshold and high electron mobility. ZnO films constitute an attractive alternative to organic semiconductors for TFT transducers in sensor applications for waterborne analytes. Despite the use of an electrolyte as gate medium, the gate geometry (shape of gate electrode and distance between gate electrode and TFT channel) is relevant for optimum performance of water-gated TFTs.
Design of lumpy metallic nanoparticles for broadband and wide-angle light scattering
Authors: Stokes Nicholas , Jia Baohua , Gu Min
Published: October 2012

Broadband and wide-angle light scattering media are highly desirable in photonic applications. In this paper, we theoretically investigate the light scattering properties of lumpy nanoparticles of silver, aluminum, and copper compared to those of smooth nanospheres with the same volume. The lumpy nanoparticles are found to provide broadband scattering enhancement over the smooth nanoparticles in a variety of dielectric environments. A maximum 18% enhancement in angular scattering for Al lumpy particles was found. More importantly, near-field scattering intensity mapping confirms that the enhanced scattering is achieved in all directions, making them more attractive in diverse photonic applications.
Ion-acoustic cnoidal wave and associated non-linear ion flux in dusty plasma
Authors: Jain S. L. , Tiwari R. S. , Mishra M. K.
Published: October 2012

Using reductive perturbation method with appropriate boundary conditions, coupled evolution equations for first and second order potentials are derived for ion-acoustic waves in a collisionless, un-magnetized plasma consisting of hot isothermal electrons, cold ions, and massive mobile charged dust grains. The boundary conditions give rise to renormalization term, which enable us to eliminate secular contribution in higher order terms. Determining the non secular solution of these coupled equations, expressions for wave phase velocity and averaged non-linear ion flux associated with ion-acoustic cnoidal wave are obtained. Variation of the wave phase velocity and averaged non-linear ion flux as a function of modulus (k2) dependent wave amplitude are numerically examined for different values of dust concentration, charge on dust grains, and mass ratio of dust grains with plasma ions. It is found that for a given amplitude, the presence of positively (negatively) charged dust grains in plasma decreases (increases) the wave phase velocity. This behavior is more pronounced with increase in dust concentrations or increase in charge on dust grains or decrease in mass ratio of dust grains. The averaged non-linear ion flux associated with wave is positive (negative) for negatively (positively) charged dust grains in the plasma and increases (decreases) with modulus (k2) dependent wave amplitude. For given amplitude, it increases (decreases) as dust concentration or charge of negatively (positively) charged dust grains increases in the plasma.
Note: Development of a microfabricated sensor to measure thermal conductivity of picoliter scale liquid samples
Authors: Park Byoung Kyoo , Yi Namwoo , Park Jaesung , Kim Dongsik
Published: October 2012

This paper presents a thermal analysis device, which can measure thermal conductivity of picoliter scale liquid sample. We employ the three omega method with a microfabricated AC thermal sensor with nanometer width heater. The liquid sample is confined by a micro-well structure fabricated on the sensor surface. The performance of the instrument was verified by measuring the thermal conductivity of 27-picoliter samples of de-ionized (DI) water, ethanol, methanol, and DI water-ethanol mixtures with accuracies better than 3%. Furthermore, another analytical scheme allows real-time thermal conductivity measurement with 5% accuracy. To the best of our knowledge, this technique requires the smallest volume of sample to measure thermal property ever.
First-principles study of charging effect on magnetism of Pd (100) ultrathin films
Authors: Aihara Shogo , Kageshima Hiroyuki , Sakai Tomohiro , Sato Tetsuya
Published: October 2012

Calculations of electronic structure of free-standing Pd (100) ultrathin films of 2–6 monolayers (MLs), using first-principles calculation with pseudopotential method, show stable ferromagnetism in 4 ML and induced magnetic phase transition in 3 and 4 MLs by charging. The ferromagnetism, appearing due to large density of states attributed to 4dxz,yz flat bands at Fermi energy εF, can be manipulated by charging through the change in the contribution of the 4d flat bands to εF, where the surface carrier density of >1013 cm−2 is necessary for the magnetic phase transition. This can be experimentally realized using techniques such as electric double layer transistors.
Investigation of vertically trapped charge locations in Cr-doped-SrTiO3-based charge trapping memory devices
Authors: Seo Yujeong , Yeong Song Min , An Ho-Myoung , Soo Kim Yeon , Ho Park Bae , Geun Kim Tae
Published: October 2012

In this paper, vertically trapped charge location is investigated to understand the carrier-transport dynamics in chromium-doped strontium titanate (Cr-SrTiO3 (STO))-based charge trapping memory devices using a transient analysis method. The vertical location of trapped charges is found to move from the Cr-SrTiO3/Si3N4 interface to the bulk region of Si3N4 with an increasing of the electric field, and, particularly, available trap sites are limited at the Cr-SrTiO3/Si3N4 interface by hole injection from the Si substrate into the Si3N4 layer at a high electric field (EOX > 7 MV/cm). In addition, some of these charges passing across the SiO2 (OX) layer generate many Si-SiO2 interface traps (Dit: 1.58 × 1012 cm−2 eV−1) that may degrade the device. However, the trapping efficiency can be improved by using sufficiently thick ( > 10 nm) bottom layers and by preventing direct hole tunneling and thereby, reducing the interface trap density.
Enhanced photocurrent and open-circuit voltage in a 3-layer cascade organic solar cell
Authors: Cnops Kjell , Rand Barry P. , Cheyns David , Heremans Paul
Published: October 2012

We demonstrate a cascade architecture for organic solar cells with two planar donor/acceptor (DA) heterojunctions operating in series. In a 3-layered structure, subphthalocyanine (SubPc) acts as an ambipolar interlayer between a tetracene (Tc) donor and a C60 acceptor. The Tc/SubPc and SubPc/C60 interfaces are both able to contribute to the photocurrent, which results in a short-circuit current in the 3-layer cascade cell larger than in any of the constituent bi-layer DA combinations. Furthermore, the open-circuit voltage is increased due to reduced recombination losses at the DA interface.
Depth profile of the tetragonal distortion in thick GaMnAs layers grown on GaAs by Rutherford backscattering/channeling
Authors: Zhou Shengqiang , Chen Lin , Shalimov Artem , Zhao Jianhua , Helm Manfred
Published: October 2012

We provide a direct measurement of the tetragonal distortion in thick GaMnAs as a function of depth by Rutherford backscattering combining with channeling. The thick GaMnAs film is tetragonally strained and the tetragonal distortion is found to be depth independent. Our finding excludes strain relaxation as the origin of the uniaxial in-plane magnetic anisotropy observed in GaMnAs.
The limitations on applying classical thin plate theory to thin annular plates clamped on the inner boundary
Authors: Zietlow Daniel W. , Griffin Donald C. , Moore Thomas R.
Published: October 2012

The experimentally measured resonance frequencies of a thin annular plate with a small ratio of inner to outer radii and clamped on the inner boundary are compared to the predictions of classical thin-plate (CTP) theory and a finite-element (FE) model. The results indicate that, contrary to the conclusions presented in a number of publications, CTP theory does not accurately predict the frequencies of a relatively small number of resonant modes at lower frequencies. It is shown that these inaccuracies are attributable to shear deformations, which are thought to be negligible in thin plates and are neglected in CTP theory. Of particular interest is the failure of CTP theory to accurately predict the resonance frequency of the lowest vibrational mode, which was shifted approximately 30% by shear motion at the inner boundary.
Deterministic separation of cancer cells from blood at 10 mL/min
Authors: Loutherback Kevin , D'Silva Joseph , Liu Liyu , Wu Amy , Austin Robert H. , Sturm James C.
Published: October 2012

Circulating tumor cells (CTCs) and circulating clusters of cancer and stromal cells have been identified in the blood of patients with malignant cancer and can be used as a diagnostic for disease severity, assess the efficacy of different treatment strategies and possibly determine the eventual location of metastatic invasions for possible treatment. There is thus a critical need to isolate, propagate and characterize viable CTCs and clusters of cancer cells with their associated stroma cells. Here, we present a microfluidic device for mL/min flow rate, continuous-flow capture of viable CTCs from blood using deterministic lateral displacement (DLD) arrays. We show here that a DLD array device can isolate CTCs from blood with capture efficiency greater than 85% CTCs at volumetric flow rates of up to 10 mL/min with no effect on cell viability.
Responses to rhetorical questions in English and German Internet public news groups
Authors: Kleinke Sonja
Published: October 2012

This study investigates an area of interpersonal pragmatic meaning in which the specific framing conditions of public Internet message boards seem to be particularly relevant: patterns of responses to rhetorical questions as one aspect of the negotiation of the rhetorical force of such questions among the participants in a discussion. Rhetorical questions are complex linguistic structures which are described in terms of a set of characteristic pragmatic features, including their answerhood (Ilie 1994, 1999). An analysis of approximately 900 postings to 22 English and 22 German Internet discussion threads on a range of comparable topics showed that rhetorical questions are often subject to negotiation by the participants in an interaction. The responses to such rhetorical questions play a crucial role in this process. This work examines all textual responses to questions that were interpreted as rhetorical and describes their structural patterns and frequency of use as well as different types and functions in the English- and the German-speaking groups. It also discusses the different patterns of use against the background of more general observations on communicative styles and practices across the two language communities.
Examining Bargaining Power in the Northeast Multispecies Days-at-Sea Market
Authors: Lee Min-Yang
Published: October 2012

The Northeast U.S. groundfish fishery is economically large and culturally important. Between 2004 and 2009, the primary management control used in this fishery was a tradable input allowance system known as Days at Sea (DAS); however, many regulatory institutions limited trading. These barriers included a set of “conservation equivalency” restrictions based on length and horsepower that were explicitly designed to restrain increases in the fishing power of the fleet. Despite these limitations, trade in the DAS market was fairly robust; by 2008, over 40% of all used DAS were traded. This research uses ordinary least squares and quantile regression to examine the effects of these institutional limitations on the bargaining power of traders in this market. The conservation equivalency restrictions adversely impacted the bargaining power of both small sellers and large buyers of DAS. Despite these bargaining power effects, prices were responsive to changes in aggregate supply and productivity in economically reasonable ways. Finally, the downward intrayear trend in price is consistent with decay in the time value component of financial options.

Received June 21, 2011; accepted June 21, 2012
Comparison of impact characteristics of four different ice hockey arena dasher boards
Authors: Poutiainen Piritta , Peltonen Jussi , Isolehto Juha , Avela Janne
Published: October 2012

During recent years the incidence of ice hockey related concussions has increased. Therefore, the main aim of this study was to determine how dasher board materials and structures affect impact characteristics and thereby concussion risk. The measurements were divided into two parts; 1. physiological characteristics of body checks were determined in real game measurements, and 2. simulation of body checks in the laboratory. Peak forces and stopping distances were determined from the high‐speed camera data, and stiffness values were subsequently calculated. Dasher board materials and structures had a clear effect on impact characteristics. Flexible protective shielding material resulted in 17% and 16% lower peak forces, 110% and 136% greater stopping distances and 62% and 56% lower stiffness values in the straight and the corner parts of the dasher board, respectively, compared to the reference dasher board. However, the dasher board with flexible protective shielding material including metal shielding support posts between each shielding panel yielded inconsistent results. The shielding support posts were much stiffer compared to the protective shielding. The single‐framed dasher board was found to be 29% and 11% more flexible than its dual‐framed counterpart, and heavier protective shielding resulted in 33% and 19% higher element stiffness in the straight and the corner parts of the dasher board, respectively. In light of the results and the epidemiology of concussions, it seems that the most safe dasher board would be single‐framed with light and flexible protective shielding material, and would not include shielding support posts.
From behavioural analyses to models of collective motion in fish schools
Authors: Lopez Ugo , Gautrais Jacques , Couzin Iain D. , Theraulaz Guy
Published: October 2012

Fish schooling is a phenomenon of long-lasting interest in ethology and ecology, widely spread across taxa and ecological contexts, and has attracted much interest from statistical physics and theoretical biology as a case of self-organized behaviour. One topic of intense interest is the search of specific behavioural mechanisms at stake at the individual level and from which the school properties emerges. This is fundamental for understanding how selective pressure acting at the individual level promotes adaptive properties of schools and in trying to disambiguate functional properties from non-adaptive epiphenomena. Decades of studies on collective motion by means of individual-based modelling have allowed a qualitative understanding of the self-organization processes leading to collective properties at school level, and provided an insight into the behavioural mechanisms that result in coordinated motion. Here, we emphasize a set of paradigmatic modelling assumptions whose validity remains unclear, both from a behavioural point of view and in terms of quantitative agreement between model outcome and empirical data. We advocate for a specific and biologically oriented re-examination of these assumptions through experimental-based behavioural analysis and modelling.
Pattern-formation mechanisms in motility mutants of
Myxococcus xanthus
Authors: Starruß Jörn , Peruani Fernando , Jakovljevic Vladimir , Søgaard-Andersen Lotte , Deutsch Andreas , Bär Markus
Published: October 2012

Formation of spatial patterns of cells is a recurring theme in biology and often depends on regulated cell motility. Motility of the rod-shaped cells of the bacterium
Myxococcus xanthus
depends on two motility machineries, type IV pili (giving rise to S-motility) and the gliding motility apparatus (giving rise to A-motility). Cell motility is regulated by occasional reversals. Moving
M. xanthus
cells can organize into spreading colonies or spore-filled fruiting bodies, depending on their nutritional status. To ultimately understand these two pattern-formation processes and the contributions by the two motility machineries, as well as the cell reversal machinery, we analyse spatial self-organization in three
M. xanthus
strains: (i) a mutant that moves unidirectionally without reversing by the A-motility system only, (ii) a unidirectional mutant that is also equipped with the S-motility system, and (iii) the wild-type that, in addition to the two motility systems, occasionally reverses its direction of movement. The mutant moving by means of the A-engine illustrates that collective motion in the form of large moving clusters can arise in gliding bacteria owing to steric interactions of the rod-shaped cells, without the need of invoking any biochemical signal regulation. The two-engine strain mutant reveals that the same phenomenon emerges when both motility systems are present, and as long as cells exhibit unidirectional motion only. From the study of these two strains, we conclude that unidirectional cell motion induces the formation of large moving clusters at low and intermediate densities, while it results in vortex formation at very high densities. These findings are consistent with what is known from self-propelled rod models, which strongly suggests that the combined effect of self-propulsion and volume exclusion interactions is the pattern-formation mechanism leading to the observed phenomena. On the other hand, we learn that when cells occasionally reverse their moving direction, as observed in the wild-type, cells form small but strongly elongated clusters and self-organize into a mesh-like structure at high enough densities. These results have been obtained from a careful analysis of the cluster statistics of ensembles of cells, and analysed in the light of a coagulation Smoluchowski equation with fragmentation.
Three-dimensional tracking and behaviour monitoring of multiple fruit flies
Authors: Ardekani Reza , Biyani Anurag , Dalton Justin E. , Saltz Julia B. , Arbeitman Michelle N. , Tower John , Nuzhdin Sergey , Tavaré Simon
Published: October 2012

The increasing interest in the investigation of social behaviours of a group of animals has heightened the need for developing tools that provide robust quantitative data.Drosophila melanogasterhas emerged as an attractive model for behavioural analysis; however, there are still limited ways to monitor fly behaviour in a quantitative manner. To study social behaviour of a group of flies, acquiring the position of each individual over time is crucial. There are several studies that have tried to solve this problem and make this data acquisition automated. However, none of these studies has addressed the problem of keeping track of flies for a long period of time in three-dimensional space. Recently, we have developed an approach that enables us to detect and keep track of multiple flies in a three-dimensional arena for a long period of time, using multiple synchronized and calibrated cameras. After detecting flies in each view, correspondence between views is established using a novel approach we call the ‘sequential Hungarian algorithm’. Subsequently, the three-dimensional positions of flies in space are reconstructed. We use the Hungarian algorithm and Kalman filter together for data association and tracking. We evaluated rigorously the system's performance for tracking and behaviour detection in multiple experiments, using from one to seven flies. Overall, this system presents a powerful new method for studying complex social interactions in a three-dimensional environment.
Autonomous Boolean modelling of developmental gene regulatory networks
Authors: Cheng Xianrui , Sun Mengyang , Socolar Joshua E. S.
Published: October 2012

During early embryonic development, a network of regulatory interactions among genes dynamically determines a pattern of differentiated tissues. We show that important timing information associated with the interactions can be faithfully represented in autonomous Boolean models in which binary variables representing expression levels are updated in continuous time, and that such models can provide a direct insight into features that are difficult to extract from ordinary differential equation (ODE) models. As an application, we model the experimentally well-studied network controlling fly body segmentation. The Boolean model successfully generates the patterns formed in normal and genetically perturbed fly embryos, permits the derivation of constraints on the time delay parameters, clarifies the logic associated with different ODE parameter sets and provides a platform for studying connectivity and robustness in parameter space. By elucidating the role of regulatory time delays in pattern formation, the results suggest new types of experimental measurements in early embryonic development.
Insect wet steps: loss of fluid from insect feet adhering to a substrate
Authors: Kovalev Alexander E. , Filippov Alexander E. , Gorb Stanislav N.
Published: October 2012

Reliable attachment ability of insect adhesive pads is proposed to be due to pad secretion. It has been shown that surface roughness strongly reduces adhesion forces of insect pads. This effect has been explained by decreased contact area and rapid fluid absorption from the pad surface by rough surfaces. However, it remains unclear how the fluid flows on rough substrates having different roughness parameters and surface energy. In this paper, we numerically studied the fluid flow on rough substrates during contact formation. The results demonstrate that an increase in the density of the substrate structures leads to an increase in fluid loss from the pad: substrates with a fine roughness absorb pad fluid faster. Decreased affinity of the solid substrate to the fluid has a more remarkable effect on the fluid loss and leads to a decrease in the fluid loss. With an increase in the aspect ratio of the substrate irregularities (porosity), the fluid loss is decreased. The numerical results obtained agree well with previous observations on insects and experimental results on nanoporous substrata. The significance of the obtained results for understanding biological wet adhesives is discussed.
Modelling mechanical characteristics of microbial biofilms by network theory
Authors: Ehret Alexander E. , Böl Markus
Published: October 2012

In this contribution, we present a constitutive model to describe the mechanical behaviour of microbial biofilms based on classical approaches in the continuum theory of polymer networks. Although the model is particularly developed for the well-studied biofilms formed by mucoid
Pseudomonas aeruginosa
strains, it could easily be adapted to other biofilms. The basic assumption behind the model is that the network of extracellular polymeric substances can be described as a superposition of worm-like chain networks, each connected by transient junctions of a certain lifetime. Several models that were applied to biofilms previously are included in the presented approach as special cases, and for small shear strains, the governing equations are those of four parallel Maxwell elements. Rheological data given in the literature are very adequately captured by the proposed model, and the simulated response for a series of compression tests at large strains is in good qualitative agreement with reported experimental behaviour.
Einstein's special relativity beyond the speed of light
Authors: Hill James M. , Cox Barry J.
Published: October 2012

We propose here two new transformations between inertial frames that apply for relative velocities greater than the speed of light, and that are complementary to the Lorentz transformation, giving rise to the Einstein special theory of relativity that applies to relative velocities less than the speed of light. The new transformations arise from the same mathematical framework as the Lorentz transformation, displaying singular behaviour when the relative velocity approaches the speed of light and generating the same addition law for velocities, but, most importantly, do not involve the need to introduce imaginary masses or complicated physics to provide well-defined expressions. Making use of the dependence on relative velocity of the Lorentz transformation, the paper provides an elementary derivation of the new transformations between inertial frames for relative velocities
v
in excess of the speed of light
c
, and further we suggest two possible criteria from which one might infer one set of transformations as physically more likely than the other. If the energy–momentum equations are to be invariant under the new transformations, then the mass and energy are given, respectively, by the formulae

and

where

denotes the limiting momentum for infinite relative velocity. If, however, the requirement of invariance is removed, then we may propose new mass and energy equations, and an example having finite non-zero mass in the limit of infinite relative velocity is given. In this highly controversial topic, our particular purpose is not to enter into the merits of existing theories, but rather to present a succinct and carefully reasoned account of a new aspect of Einstein's theory of special relativity, which properly allows for faster than light motion.
Transversely isotropic cyclic stress-softening model for the Mullins effect
Authors: Rickaby Stephen R. , Scott Nigel H.
Published: October 2012

This paper models stress softening during cyclic loading and unloading of an elastomer. The paper begins by remodelling the primary loading curve to include a softening function and goes on to derive nonlinear transversely isotropic constitutive equations for the elastic response, stress relaxation, residual strain and creep of residual strain. These ideas are combined with a transversely isotropic version of the Arruda–Boyce eight-chain model to develop a constitutive relation that is capable of accurately representing the Mullins effect during cyclic stress softening for a transversely isotropic, hyperelastic material, in particular, a carbon-filled rubber vulcanizate.
Diverse pollinator communities enhance plant reproductive success
Authors: Albrecht Matthias , Schmid Bernhard , Hautier Yann , Müller Christine B.
Published: October 2012

Understanding the functional consequences of biodiversity loss is a major goal of ecology. Animal-mediated pollination is an essential ecosystem function and service provided to mankind. However, little is known how pollinator diversity could affect pollination services. Using a substitutive design, we experimentally manipulated functional group (FG) and species richness of pollinator communities to investigate their consequences on the reproductive success of an obligate out-crossing model plant species,
Raphanus sativus
. Both fruit and seed set increased with pollinator FG richness. Furthermore, seed set increased with species richness in pollinator communities composed of a single FG. However, in multiple-FG communities, highest species richness resulted in slightly reduced pollination services compared with intermediate species richness. Our analysis indicates that the presence of social bees, which showed roughly four times higher visitation rates than solitary bees or hoverflies, was an important factor contributing to the positive pollinator diversity–pollination service relationship, in particular, for fruit set. Visitation rate at different daytimes, and less so among flower heights, varied among social bees, solitary bees and hoverflies, indicating a niche complementarity among these pollinator groups. Our study demonstrates enhanced pollination services of diverse pollinator communities at the plant population level and suggests that both the niche complementarity and the presence of specific taxa in a pollinator community drive this positive relationship.
Evidence for determinism in species diversification and contingency in phenotypic evolution during adaptive radiation
Authors: Burbrink Frank T. , Chen Xin , Myers Edward A. , Brandley Matthew C. , Pyron R. Alexander
Published: October 2012

Adaptive radiation (AR) theory predicts that groups sharing the same source of ecological opportunity (EO) will experience deterministic species diversification and morphological evolution. Thus, deterministic ecological and morphological evolution should be correlated with deterministic patterns in the tempo and mode of speciation for groups in similar habitats and time periods. We test this hypothesis using well-sampled phylogenies of four squamate groups that colonized the New World (NW) in the Late Oligocene. We use both standard and coalescent models to assess species diversification, as well as likelihood models to examine morphological evolution. All squamate groups show similar early pulses of speciation, as well as diversity-dependent ecological limits on clade size at a continental scale. In contrast, processes of morphological evolution are not easily predictable and do not show similar pulses of early and rapid change. Patterns of morphological and species diversification thus appear uncoupled across these groups. This indicates that the processes that drive diversification and disparification are not mechanistically linked, even among similar groups of taxa experiencing the same sources of EO. It also suggests that processes of phenotypic diversification cannot be predicted solely from the existence of an AR or knowledge of the process of diversification.
Quorum-sensing and cheating in bacterial biofilms
Authors: Popat Roman , Crusz Shanika A. , Messina Marco , Williams Paul , West Stuart A. , Diggle Stephen P.
Published: October 2012

The idea from human societies that self-interest can lead to a breakdown of cooperation at the group level is sometimes termed the public goods dilemma. We tested this idea in the opportunistic bacterial pathogen,Pseudomonas aeruginosa, by examining the influence of putative cheats that do not cooperate via cell-to-cell signalling (quorum-sensing, QS). We found that: (i) QS cheating occurs in biofilm populations owing to exploitation of QS-regulated public goods; (ii) the thickness and density of biofilms was reduced by the presence of non-cooperative cheats; (iii) population growth was reduced by the presence of cheats, and this reduction was greater in biofilms than in planktonic populations; (iv) the susceptibility of biofilms to antibiotics was increased by the presence of cheats; and (v) coercing cooperator cells to increase their level of cooperation decreases the extent to which the presence of cheats reduces population productivity. Our results provide clear support that conflict over public goods reduces population fitness in bacterial biofilms, and that this effect is greater than in planktonic populations. Finally, we discuss the clinical implications that arise from altering the susceptibility to antibiotics.
Constraints on the coevolution of contemporary human males and females
Authors: Stearns Stephen C. , Govindaraju Diddahally R. , Ewbank Douglas , Byars Sean G.
Published: October 2012

Because autosomal genes in sexually reproducing organisms spend on average half their time in each sex, and because the traits that they influence encounter different selection pressures in males and females, the evolutionary responses of one sex are constrained by processes occurring in the other sex. Although intralocus sexual conflict can restrict sexes from reaching their phenotypic optima, no direct evidence currently supports its operation in humans. Here, we show that the pattern of multivariate selection acting on human height, weight, blood pressure and glucose, total cholesterol, and age at first birth differs significantly between males and females, and that the angles between male and female linear (77.8 ± 20.5°) and nonlinear (99.1 ± 25.9°) selection gradients were closer to orthogonal than zero, confirming the presence of sexually antagonistic selection. We also found evidence for intralocus sexual conflict demonstrated by significant changes in the predicted male and female responses to selection of individual traits when cross-sex genetic covariances were included and a significant reduction in the angle between male- and female-predicted responses when cross-sex covariances were included (16.9 ± 15.7°), compared with when they were excluded (87.9 ± 31.6°). We conclude that intralocus sexual conflict constrains the joint evolutionary responses of the two sexes in a contemporary human population.