Rheotaxis and migration of cells in a flow field have been investigated intensively owing to their importance in biology, physiology and engineering. In this study, first, we report our experiments showing that the microalgae Chlamydomonas can orient against the channel flow and migrate to the channel centre. Second, by performing boundary element simulations, we demonstrate that the mechanism of the observed rheotaxis and migration has a physical origin. Last, using a simple analytical model, we reveal the novel physical mechanisms of rheotaxis and migration, specifically the interplay between cyclic body deformation and cyclic swimming velocity in the channel flow. The discovered mechanism can be as important as phototaxis and gravitaxis, and likely plays a role in the movement of other natural microswimmers and artificial microrobots with non-reciprocal body deformation.

A concentrated, vertical monolayer of identical spherical squirmers, which may be bottom heavy, and which are subjected to a linear shear flow, is modelled computationally by two different methods: Stokesian dynamics, and a lubrication-theory-based method. Inertia is negligible. The aim is to compute the effective shear viscosity and, where possible, the normal stress differences as functions of the areal fraction of spheres $\phi$, the squirming parameter $\beta$ (proportional to the ratio of a squirmer's active stresslet to its swimming speed), the ratio $Sq$ of swimming speed to a typical speed of the shear flow, the bottom-heaviness parameter $G_{bh}$, the angle $\alpha$ that the shear flow makes with the horizontal and two parameters that define the repulsive force that is required computationally to prevent the squirmers from overlapping when their distance apart is less than a critical value. The Stokesian dynamics method allows the rheological quantities to be computed for values of $\phi$ up to $0.75$; the lubrication-theory method can be used for $\phi > 0.5$. For non-bottom-heavy squirmers, which are unaffected by gravity, the effective shear viscosity is found to increase more rapidly with $\phi$ than for inert spheres, whether the squirmers are pullers ($\beta > 0$) or pushers ($\beta < 0$); it also varies with $\beta$, although not by very much. However, for bottom-heavy squirmers the behaviour for pullers and pushers as $G_{bh}$ and $\alpha$ are varied is very different, since the viscosity can fall even below that of the suspending fluid for pushers at high $G_{bh}$. The normal stress differences, which are small for inert spheres, can become very large for bottom-heavy squirmers, increasing with $\beta$, and varying dramatically as the orientation $\alpha$ of the flow is varied from 0 to ${\rm \pi} /2$. A major finding is that, despite very different assumptions, the two methods of computation give overlapping results for viscosity as a function of $\phi$ in the range $0.5 < \phi < 0.75$. This suggests that lubrication theory, based on near-field interactions alone, contains most of the relevant physics, and that taking account of interactions with more distant particles than the nearest is not essential to describe the dominant physics.

The Global Yield Gap Atlas (GYGA) is an international project that addresses global food production capacity in the form of yield gaps (Yg). The GYGA project is unique in employing its original Climate Zonation Scheme (CZS) composed of three indexed factors, i.e. Growing Degree Days (GDD) related to temperature, Aridity Index (AI) related to available water and Temperature Seasonality (TS) related to annual temperature range, creating 300 Climate Zones (CZs) theoretically across the globe. In the present study, the GYGA CZs were identified for Japan on a municipality basis and analysis of variance (ANOVA) was performed on irrigated rice yield data sets, equating to actual yields (Ya) in the GYGA context, from long-term government statistics. The ANOVA was conducted for the data sets over two decades between 1994 and 2016 by assigning the GDD score of 6 levels and the TS score of 2 levels as fixed factors. Significant interactions with respect to Ya were observed between GDD score and TS score for 13 years out of 21 years implying the existence of favourable combinations of the GDD score and the TS score for rice cultivation. The implication was also supported by the observation with Yg. The lower values of coefficient of variance obtained from the CZs characterized by medium GDD scores indicated the stability over time of rice yields in these areas. These findings suggest a possibility that the GYGA-CZS can be recognized as a tool suitable to identify favourable CZs for growing crops.

Biflagellate algal cells of the genus Volvox form spherical colonies that propel themselves, vertically upwards in still fluid, by the coordinated beating of thousands of flagella, that also cause the colonies to rotate about their vertical axes. When they are swimming in a chamber of finite depth, pairs (or more) of Volvox carteri colonies were observed by Drescher et al. (Phys. Rev. Lett., vol. 102, 2009, 168101) to exhibit hydrodynamic bound states when they are close to a rigid horizontal boundary. When the boundary is above, the colonies are attracted to each other and orbit around each other in a ‘waltz’; when the boundary is below they perform more complex ‘minuet’ motions. These dances are simulated in the present paper, using a novel ‘spherical squirmer’ model of a colony in which, instead of a time-independent but $\theta$-dependent tangential velocity being imposed on the spherical surface (radius $a$; $\theta$ is the polar angle), a time-independent and uniform tangential shear stress is applied to the fluid on a sphere of radius $(1+\epsilon )a, \epsilon \ll 1$, where $\epsilon a$ represents the length of the flagella. The fluid must satisfy the no-slip condition on the sphere at radius $a$. In addition to the shear stress, the motions depend on two dimensionless parameters that describe the effect of gravity on a colony: $F_g$, proportional to the ratio of the sedimentation speed of a non-swimming colony to its swimming speed, and $G_{bh}$, that represents the fact that colonies are bottom heavy; $G_{bh}$ is the ratio of the time scale to swim a distance equal to the radius, to the time scale for gravitational reorientation of the colony's axis to the vertical when it is disturbed. In addition to reproducing both of the dancing modes, the simulations are able to determine values of $F_g$ and $G_{bh}$ for which they are stable (or not); there is reasonable agreement with the experiments. A far-field model for the minuet motions is also shown to have qualitative agreement, but does not describe some features that are reproduced in the full simulations.

We report the investigation on the properties of a novel Te precursor (i-C3H7)2Te and its effectiveness in fabricating MoTe2. The vapor pressure of the precursor was obtained by measuring the pressure as a function of its temperature in a sealed chamber. As a result it showed a high vapor pressure of 552.1 Pa at room temperature. The decomposition of the precursor was also investigated using DFT calculation. It was shown that the most likely reaction during the course of the decomposition of (i-C3H7)2Te is (i-C3H7)2Te → H2Te + 2 C3H7. The effectiveness of the precursor on the fabrication of MoTe2 was also investigated. Sputter-deposited MoO3 was tellurized in a quartz-tube furnace at the temperature up to 440°C. The resulting film showed that the 80% of the original MoO3 was tellurized to form MoTe2. It was also shown that further optimization of tellurization is required in order to prevent formation of metal Mo and elemental Te.

We report the synthesis of MoS2(1-x)Te2x by co-sputtering deposition and effect of mixture on its bandgap. The deposition was carried out at room temperature, and the sputtering power on individual MoS2 and MoTe2 targets were varied to obtain films with different compositions. Investigation with X-ray photoelectron spectroscopy confirmed the formation of Mo-Te and Mo-S bonds after post-deposition annealing (PDA), and one of the samples exhibited composition ratio of Mo:S:Te = 1:1.2:0.8 and 1:1.9:0.1 achieving 1:2 ratio of metal to chalcogen. Bandgap of MoS1.2Te0.8 and MoS1.9Te0.1 was evaluated with Tauc plot analysis from the extinction coefficient obtained by spectroscopic ellipsometry measurements. The obtained bandgaps were 1.0 eV and 1.3 eV. The resulting bandgap was lower than that of bulk MoS2 and higher than that of bulk MoTe2 suggesting mixture of both materials was achieved by co-sputtering.

Molybdenum disulfide (MoS2) thin films were fabricated by two-step chemical vapor deposition (CVD) using (t-C4H9)2S2 and the effects of temperature, gas flow rate, and atmosphere on the formation were investigated in order to achieve high-speed low-temperature MoS2 film formation. From the results of X-ray photoelectron spectroscopy (XPS) and transmission electron microscopy (TEM) investigations, it was confirmed that c-axis orientation of the pre-deposited Mo film has a significant involvement in the crystal orientation after the reaction low temperature sulfurization annealing and we successfully obtained 3 nm c-axis oriented MoS2 thin film. From the S/Mo ratios in the films, it was revealed that the sulfurization reaction proceeds faster with increase in the sulfurization temperature and the gas flow rate. Moreover, the sulfurization under the H2 atmosphere promotes decomposition reaction of (t-C4H9)2S2, which were confirmed by XPS and density functional theory (DFT) simulation.

The reorientation phenomenon of a single red blood cell during sedimentation is simulated using the boundary element method. The cell settles downwards due to a density difference between the internal and external fluids, and it changes orientation toward a vertical orientation regardless of Bond number or viscosity ratio. The reorientation phenomenon is explained by a shape asymmetry caused by the gravitational driving force, and the shape asymmetry increases almost linearly with the Bond number. When velocities are normalised by the driving force, settling/drifting velocities are weak functions of the Bond number and the viscosity ratio, while the angular velocity of the reorientation drastically changes with these parameters: the angular velocity is smaller for lower Bond number or higher viscosity ratio. As a consequence, trajectories of the sedimentation are also affected by the angular velocity, and blood cells with slower reorientation travel longer distances in the drifting direction. We also explain the mechanism of the reorientation using an asymmetric dumbbell. From the analysis, we show that the magnitude of the angular velocity is explained by two main factors: the shape asymmetry and the instantaneous orientation angle.

We present a numerical analysis of the rheology of a dense suspension of spherical capsules in simple shear flow in the Stokes flow regime. The behaviour of neo-Hookean capsules is simulated for a volume fraction up to ${\it\phi}=0.4$ by graphics processing unit computing based on the boundary element method with a multipole expansion. To describe the specific viscosity using a polynomial equation of the volume fraction, the coefficients of the equation are calculated by least-squares fitting. The results suggest that the effect of higher-order terms is much smaller for capsule suspensions than rigid sphere suspensions; for example, $O({\it\phi}^{3})$ terms account for only 8 % of the specific viscosity even at ${\it\phi}=0.4$ for capillary numbers $Ca\geqslant 0.1$ . We also investigate the relationship between the deformation and orientation of the capsules and the suspension rheology. When the volume fraction increases, the deformation of the capsules increases while the orientation angle of the capsules with respect to the flow direction decreases. Therefore, both the specific viscosity and the normal stress difference increase with volume fraction due to the increased deformation, whereas the decreased orientation angle suppresses the specific viscosity, but amplifies the normal stress difference.

Molybdenum disulfide (MoS2), one of the transition-metal dichalcogenides, is a 2-dimensional semiconducting material that has a layered structure. Owing to excellent optical and electronic properties, the ultra-thin MoS2 film is expected to be used for various devices, such as transistors and flexible displays. In this study, we investigated the physical and chemical properties of sputtered-MoS2 film in the sub-10-nm region by Raman spectroscopy and X-ray photoelectron spectroscopy (XPS). As the results of Raman spectroscopy investigations, we observed two Raman modes, E1 2g and A1g, in the 2-dimensional MoS2 films. As the thickness of the MoS2 film decreased, the peak frequency difference between E1 2g and A1g modes increased. From the XPS investigations, we confirmed sulfur reductions from the 2-dimensional MoS2 films. Therefore, we considered that the sulfur vacancies in the MoS2 film affected the Raman peak positions. Moreover, we performed the additional sulfurization of sputtered-MoS2 films. From the XPS and Raman investigations, the quality of the sputtered-MoS2 films was improved by the additional sulfurization.

A fully coherent free electron laser (FEL) seeded with a higher-order harmonic (HH) pulse from high-order harmonic generation (HHG) is successfully operated for a sufficiently prolonged time in pilot user experiments by using a timing drift feedback. For HHG-seeded FELs, the seeding laser pulses have to be synchronized with electron bunches. Despite seeded FELs being non-chaotic light sources in principle, external laser-seeded FELs are often unstable in practice because of a timing jitter and a drift between the seeding laser pulses and the accelerated electron bunches. Accordingly, we constructed a relative arrival-timing monitor based on non-invasive electro-optic sampling (EOS). The EOS monitor made uninterrupted shot-to-shot monitoring possible even during the seeded FEL operation. The EOS system was then used for arrival-timing feedback with an adjustability of 100 fs for continual operation of the HHG-seeded FEL. Using the EOS-based beam drift controlling system, the HHG-seeded FEL was operated over half a day with an effective hit rate of 20%–30%. The output pulse energy was $20~{\rm\mu}\text{J}$ at the 61.2 nm wavelength. Towards seeded FELs in the water window region, we investigated our upgrade plan to seed high-power FELs with HH photon energy of 30–100 eV and lase at shorter wavelengths of up to 2 nm through high-gain harmonic generation (HGHG) at the energy-upgraded SPring-8 Compact SASE Source (SCSS) accelerator. We studied a benefit as well as the feasibility of the next HHG-seeded FEL machine with single-stage HGHG with tunability of a lasing wavelength.

The deformation of a spherical capsule in oscillating shear flow is presented. The boundary element method is used to simulate the capsule motion under Stokes flow. We show that a capsule at high frequencies follows the deformation given by a leading-order prediction, which is derived from an assumption of small deformation limit. At low frequencies, on the other hand, a capsule shows an overshoot phenomenon where the maximum deformation is larger than that in steady shear flow. A larger overshoot is observed for larger capillary number or viscosity ratio. Using the maximum deformation in start-up shear flow, we evaluate the upper limit of deformation in oscillating shear flow. We also show that the overshoot phenomenon may appear when the quasi-steady orientation angle under steady shear flow is less than $9.0^{\circ }$ . We propose an equation to estimate the threshold frequency between the low-frequency range, where the capsule may have an overshoot, and the high-frequency range, where the deformation is given by the leading-order prediction. The equation only includes the viscosity ratio and the Taylor parameter under simple shear flow, so it can be extended to other deformable particles, such as bubbles and drops.

Polysilsesquioxane passivation layers were used to passivate bottom gate a-InGaZnO (a-IGZO) thin film transistors (TFT). The a-IGZO TFTs passivated with polysilsesquioxane showed highly stable behavior during positive bias stress, negative bias stress, and negative bias illumination stress. A voltage threshold shift of up to 0.1 V, less than -0.1 V and -2.3 V for positive bias stress, negative bias stress, and negative bias illumination stress, respectively. We also report the effect of reactive ion etching (RIE) on the electrical characteristics of a-InGaZnO (a-IGZO) thin-film transistors (TFT) passivated with the polysilsesquioxane-based passivation layers. We show how post-annealing treatment using two different atmosphere conditions: under O2 ambient and combination of N2 and O2 ambient (20% O2), can be performed to recover the initial characteristics. Furthermore, we present a highly stable novel polysilsesquioxane photosensitive passivation material that can be used to completely circumvent the reactive ion etching effects.

Extended abstract of a paper presented at Microscopy and Microanalysis 2013 in Indianapolis, Indiana, USA, August 4 – August 8, 2013.

Extended abstract of a paper presented at Microscopy and Microanalysis 2013 in Indianapolis, Indiana, USA, August 4 – August 8, 2013.