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The dynamic structure factor

Plant genomes remain highly fragmented and are often characterized by hundreds to thousands of assembly gaps. Here, we report chromosome-level reference and phased genome assembly of Ophiorrhiza pumila, a camptothecin-producing medicinal plant, through an ordered multi-scaffolding and experimental validation approach. With 21 assembly gaps and a contig N50 of 18.49 Mb, Ophiorrhiza genome is one of the most complete plant genomes assembled to date. We also report 273 nitrogen-containing metabolites, including diverse monoterpene indole alkaloids (MIAs). A comparative genomics approach identifies strictosidine biogenesis as the origin of MIA evolution. The emergence of strictosidine biosynthesis-catalyzing enzymes precede downstream enzymes’ evolution post γ whole-genome triplication, which occurred approximately 110 Mya in O. pumila, and before the whole-genome duplication in Camptotheca acuminata identified here. Combining comparative genome analysis, multi-omics analysis, and metabolic gene-cluster analysis, we propose a working model for MIA evolution, and a pangenome for MIA biosynthesis, which will help in establishing a sustainable supply of camptothecin., Ophiorrhiza pumila is a medicinal plant that can produce the anti-cancer monoterpene indole alkaloid (MIA) camptothecin. Here, the authors report its genome assembly and propose a working model for MIA evolution and biosynthesis through comparative genomics, synteny, and metabolic gene cluster analyses.

Elastic stiffness constants, C ijs, of single crystal of NaCl B1 phase have been determined at pressure up to 20 GPa using inelastic x-ray scattering to measure elastic wave velocities and x-ray di...

The longitudinal sound velocity (VP) and the density (ρ) of wüstite, FeO, were measured at pressures of up to 112.3 GPa and temperatures of up to 1700 K using both inelastic X-ray scattering and X-ray diffraction combined with a laser-heated diamond-anvil cell. The linear relationship between VP and ρ, Birch’s law, for wüstite can be expressed as VP = 1.55 (1) × ρ [g/cm3] − 2.03 (8) [km/s] at 300 K and VP = 1.61 (1) × ρ [kg/m3] − 2.82 (10) [km/s] at 1700 K. The sound velocity of wüstite is significantly lower than that of bridgmanite and ferropericlase under lower mantle conditions. In other words, the existence of wüstite in the lower mantle can efficiently decrease the seismic velocity. Considering its slow velocity and several mechanisms for the formation of FeO-rich regions at the core–mantle boundary, we confirm earlier suggestions indicating that wüstite enrichment at the bottom of the Earth’s mantle may contribute to the formation of denser ultra-low velocity zones.

The dynamic structure factor S ( Q , E ) , where Q and E are momentum and energy transfer, respectively, has been measured for liquid Eu8Ga16Ge30 (EGG), using inelastic x-ray scattering. The excitation energy of the longitudinal acoustic mode in the liquid was scaled to that in liquid Ba8Ga16Sn30 (BGS) with the effective mass. This result means that the local structure in both liquids are similar. The longitudinal acoustic excitation energy of type-I clathrate compound EGG disperses faster than that in the liquid, suggesting that the interatomic force is weakened on melting. The lower energy excitation was observed in both liquid EGG and liquid BGS. In comparison with the longitudinal phonon dispersion in crystalline clathrate compound EGG obtained by density functional theory-based calculations, the lower energy in the liquid was found to be near the optical mode energy. The result indicates that the lower energy mode arises from the relative motion between Eu and (Ga, Ge) atoms.

The dynamic structure factor $S(Q,E)$ of liquid ${\mathrm{Ge}}_{2}{\mathrm{Sb}}_{2}{\mathrm{Te}}_{5}$ has been obtained by inelastic x-ray scattering, where $Q$ and $E$ are momentum and energy transfer, respectively. The dispersion curve of the longitudinal acoustic excitation energy exhibits flat-topped $Q$ dependence similarly to that in liquid GeTe and liquid Bi, where the local structure is modulated by Peierls distortion. The flat-topped energy in liquid ${\mathrm{Ge}}_{2}{\mathrm{Sb}}_{2}{\mathrm{Te}}_{5}$ is split into low and high energy parts arising from Sb-Te and Ge-Te correlations, respectively. Furthermore, the high energy part depends on $Q$ like an optical mode with decreasing $Q$ to zero, and it approaches the vibrational energy of fourfold coordinated Ge atoms with octahedral configurations. The result indicates that a majority of Ge in the liquid stays in octahedral order as predicted by first-principles molecular dynamics simulations.

The sound velocity of Fe3C was measured at pressures from 33 to 86 GPa and at ambient and high temperatures up to 2300 K using inelastic X-ray scattering (IXS) from laser-heated samples in diamond anvil cells (DACs). The compressional velocity (VP) and density of Fe3C at room temperature were observed to follow a linear relationship (Birch's law). The temperature dependency of Birch's law was not clearly observed and can be ignored. Birch's law for Fe3C is expressed by: V P = 1.09 ± 0.14 × ρ − 1.79 ± 1.26 . The result indicates that VP and VS (shear velocity) of the preliminary reference Earth model (PREM) inner core at the Inner Core Boundary (ICB) were by 12% and 48% smaller than those of Fe3C, which could be accounted for by the premelting effect by analogy from pure Fe or by partial melting of the Fe–Fe3C mixture in the inner core.

We report on the behavior of an acoustic phonon spectral linewidth of bulk single-crystalline Si1− xGe x alloy with the x of 0.16, 0.32, and 0.45 in the phonon dispersion relation along the Γ–X ([00 q]) direction. Broadening of both transverse acoustic (TA) and longitudinal acoustic (LA) modes of the bulk Si1− xGe x alloy was directly observed using inelastic x-ray scattering (IXS) with increasing momentum (from Γ to X points in the Brillouin zone), which cannot be observed in pure Si or pure Ge. The IXS spectral linewidth of the TA mode indicated Ge dependence, which suggests the overlapping of a low-energy local vibration mode (LVM) caused by Ge clusters surrounded by Si atoms around the X point. Although the behavior of the IXS spectral linewidth of the LA mode showed almost no dependence on Ge fraction, the IXS spectra of the LA mode indicated broadening after crossing with a low-energy LVM with increasing momentum. The results obtained by molecular dynamics showed almost the same behavior of the acoustic phonon spectral linewidth. These results suggest that a change in the acoustic phonon spectral linewidth between the Γ and X points indicates a reduction in the acoustic phonon lifetime caused by the appearance of a localized mode originated from a random atom position in the alloy structure, leading to suppression of the thermal transport in the SiGe alloy.

We measured single crystal elasticity of Ta under high pressures up to 54 GPa at room temperature using inelastic x-ray scattering at room temperature. Simultaneously, we measured the density of Ta using x-ray diffraction. Combining the bulk modulus and density, we obtain an equation of state of Ta as a primary scale. The Vinet equation was fitted to the pressure–volume data and we found consistency with previous work including experimental static and shock compressions and theoretical calculation. We proposed a parameter set for the Vinet equation [ K0 = 191.1(3) GPa, K′0 = 4.006(2)] which is consistent with the pressure based on extrapolated velocities within 2% up to ∼80 GPa. Furthermore, we found the present scale to be consistent with a recent ruby scale (Ruby2020) up to ∼50 GPa.

Interactions between nematic fluctuations, magnetic order and superconductivity are central to the physics of iron-based superconductors. Here we report on in-plane transverse acoustic phonons in hole-doped ${\mathrm{Sr}}_{1\ensuremath{-}x}{\mathrm{Na}}_{x}{\mathrm{Fe}}_{2}{\mathrm{As}}_{2}$ measured via inelastic x-ray scattering, and extract both the nematic susceptibility and the nematic correlation length. By a self-contained method of analysis, for the underdoped ($x=0.36$) sample, which harbors a magnetically ordered tetragonal phase, we find it hosts a short nematic correlation length $\ensuremath{\xi}\ensuremath{\sim}10\text{ }\text{ }\AA{}$ and a large nematic susceptibility ${\ensuremath{\chi}}_{\mathrm{nem}}$. The optimal-doped ($x=0.55$) sample exhibits weaker phonon softening effects, indicative of both reduced $\ensuremath{\xi}$ and ${\ensuremath{\chi}}_{\mathrm{nem}}$. Our results suggest short-range nematic fluctuations may favor superconductivity, placing emphasis on the nematic correlation length for understanding the iron-based superconductors.

The dynamic structure factor $S(Q,E)$, where $Q$ and $E$ are momentum and energy transfer, respectively, has been measured for liquid Sb, using inelastic x-ray scattering. A modified damped harmonic oscillator model function was applied to analyse $S(Q,E)$ of liquid Sb and also to that of liquid Bi [M. Inui et al. {\it Phys. Rev.} B {\bf 92}, 054206]. The obtained excitation energy was in fairly good agreement with that predicted by ab initio molecular dynamics simulations on these liquid semi-metals. The excitation energy of the longitudinal acoustic mode in liquid Sb and liquid Bi exhibits flat-topped $Q$ dependence whereas the lower excitation energy below the longitudinal acoustic excitation shows $Q$-gap behaviour. From the viscosity estimated from the $Q$-gap experimentally obtained, it is inferred that the lower energy excitation arises from the transverse acoustic excitation in the liquids.

Interactions between nematic fluctuations, magnetic order and superconductivity are central to the physics of iron-based superconductors. Here we report on in-plane transverse acoustic phonons in hole-doped Sr_{1-x}Na_{x}Fe_{2}As_{2} measured via inelastic x-ray scattering, and extract both the nematic susceptibility and the nematic correlation length. By a self-contained method of analysis, for the underdoped (x=0.36) sample, which harbors a magnetically ordered tetragonal phase, we find it hosts a short nematic correlation length ξ∼10 Å and a large nematic susceptibility χ_{nem}. The optimal-doped (x=0.55) sample exhibits weaker phonon softening effects, indicative of both reduced ξ and χ_{nem}. Our results suggest short-range nematic fluctuations may favor superconductivity, placing emphasis on the nematic correlation length for understanding the iron-based superconductors.

We measure the dispersion of the Cu-O bond-stretching phonon mode in the high-temperature superconducting parent compound ${\mathrm{Ca}}_{2}{\mathrm{CuO}}_{2}{\mathrm{Cl}}_{2}$. Our density functional theory calculations predict a cosine-shaped bending of the dispersion along both the $(\ensuremath{\xi}00$) and $(\ensuremath{\xi}\ensuremath{\xi}0$) directions, while comparison with previous results on ${\mathrm{Ca}}_{1.84}{\mathrm{CuO}}_{2}{\mathrm{Cl}}_{2}$ show it only along $(\ensuremath{\xi}00$), suggesting an anisotropic effect which is not reproduced in calculation. Comparison with isostructural ${\text{La}}_{2\ensuremath{-}x}{\text{Sr}}_{x}{\text{CuO}}_{4}$ and literature suggests that these calculations reproduce well the dispersion in the overdoped regime.

Significance Although it is believed that the raft formation in a cell membrane is governed by a selective interaction of different lipids and proteins, mechanisms driving and regulating the lateral membrane heterogeneity remain poorly understood. Here, using multicomponent lipid mixtures and inelastic X-ray scattering, we provide a spatial–temporal window to study lipid–lipid interactions. We show experimental evidence for the formation of dynamic lipid pairs, which are subnanometer in size and have a subnanosecond lifetime. These pairs form transient nanoscopic substructures in the liquid-ordered phase. The presented approach to study membrane heterogeneity is universal and can be applied to more realistic lipid mixtures, offering the possibility to discern differences between the structures of ordered and disordered phases in a cell membrane., Biological membranes exhibit a great deal of compositional and phase heterogeneity due to hundreds of chemically distinct components. As a result, phase separation processes in cell membranes are extremely difficult to study, especially at the molecular level. It is currently believed that the lateral membrane heterogeneity and the formation of domains, or rafts, are driven by lipid–lipid and lipid–protein interactions. Nevertheless, the underlying mechanisms regulating membrane heterogeneity remain poorly understood. In the present work, we combine inelastic X-ray scattering with molecular dynamics simulations to provide direct evidence for the existence of strongly coupled transient lipid pairs. These lipid pairs manifest themselves experimentally through optical vibrational (a.k.a. phononic) modes observed in binary (1,2-dipalmitoyl-sn-glycero-3-phosphocholine [DPPC]–cholesterol) and ternary (DPPC–1,2-dioleoyl-sn-glycero-3-phosphocholine/1-palmitoyl-2-oleoyl-glycero-3-phosphocholine [DOPC/POPC]–cholesterol) systems. The existence of a phononic gap in these vibrational modes is a direct result of the finite size of patches formed by these lipid pairs. The observation of lipid pairs provides a spatial (subnanometer) and temporal (subnanosecond) window into the lipid–lipid interactions in complex mixtures of saturated/unsaturated lipids and cholesterol. Our findings represent a step toward understanding the lateral organization and dynamics of membrane domains using a well-validated probe with a high spatial and temporal resolution.

Background Myanmar is one of the hotspots of biodiversity and is a rapidly developing country. Performing floristic research in Myanmar is an urgent issue, and ethnobotanical studies of wild edible plants (WEPs) will provide new information on natural plant resources. Method Ethnobotanical data were collected in three villages with different historical backgrounds in Southern Shan State, Myanmar. A total of 19 key informants were interviewed, and specimens were collected in the fields with the participation of key informants in June–July 2015. Group discussions were organized during 2016 and 2017 to reinforce the information on use of WEPs. DNA barcoding was used to facilitate species identification. Results A total of 83 species from 44 families of angiosperms were recorded as WEPs. Most of the species were used as wild vegetables (47 species), followed by fruits and nuts (31 species). Eighteen WEPs were consumed as medicinal foods. Differences in use of WEPs between the communities of the villages were observed. The age class of 30–39 years was more familiar with the environments where they could collect WEPs and had more knowledge of WEPs than did the older groups. The use of Elaeocarpus floribundus as an edible oil is a very interesting tradition. Conclusion WEPs play an important role in the livelihood of local communities. The indigenous society has maintained traditional knowledge of the WEPs. Historical background, land use system and surrounding vegetation could have effects on the variation in the traditional uses of WEPs. Increasing awareness of the importance of WEPs will encourage the conservation of traditional knowledge of indigenous populations.

Inelastic X-ray scattering (IXS) experiments were carried out at room temperature at BL35XU of the SPring-8 on a single crystal Mg85Zn6Y9 alloy with a synchronized long-period stacking ordered (LPSO) phase of purely 18R type. The IXS measurements were carried out in both the longitudinal and transverse directions along the Γ -K and Γ -M (momentum vector q ⊥ lattice axis c ), and Γ -A ( q ∥ c ) directions for the energy transfers ω below 40 meV. Peaks arising from longitudinal and transverse acoustic (LA and TA) modes were clearly observed in the IXS spectra. The dispersion relations of the LA and TA modes in the Mg85Zn6Y9 LPSO alloy are mostly similar to those of previous INS data on single crystal pure Mg. New impurity-derived dispersion-less excitation modes are observed along all of the crystal directions at about 5, 10, and 17 meV. Partial vibrational density of states (vDOS) was obtained using an a b i n i t i o molecular dynamics simulation, and it was found that the ∼ 10 meV peak mainly originates from the phonon excitations inside the L12-type Zn6Y8 clusters and the ∼ 17 meV peak from those between the cluster and the host Mg atoms, and a small shoulder at 5 meV consists of motions of all the elements. These findings clarify that the dispersion-less modes mainly correspond to localized stretching and twisting modes around the impurity clusters in the LPSO alloys.

The inelastic X-ray scattering for the nanofluid composed of silicon dioxide (SiO2) nanoparticles (various sizes exceeding 100 nm) and ethylene glycol aqueous solution has revealed one of the mechanisms for the thermal conductivity enhancement of nanofluids, which the addition of a small amount of nanoparticles can improve the thermal conductivity of nanofluids beyond the theoretical value. The high-frequency sound velocity derived from the inelastic X-ray scattering spectra of nanofluids may be generally correlated with the structural relaxation of solvent molecules and corresponding thermal conductivity. It can also clarify the effect of nanoparticles on the thermal transport in nanofluids and the molecular dynamics of the solvent around nanoparticles. The size of the SiO2 particles in the nanofluid, which are 100, 300, 500, and 1000 nm, is approximately 10 times larger than the typical size of nanoparticles considered in research. Nevertheless, the experimental results indicate that SiO2 particles may increase the high-frequency sound velocity in the ethylene glycol aqueous solution because of the highly restricted movement of the solvent molecules around these nanoparticles. The high-frequency sound velocity in the SiO2 nanofluid is proportional to the thermal conductivity and that containing particles 300 nm in size is higher than those of other nanofluids containing particles 100, 500, and 1000 nm in size.

Inelastic x-ray scattering is conducted to investigate the reason why the thermal conductivity of nanofluids increases beyond a theoretical value by the addition of a small amount of nanoparticles (NPs). High-frequency sound velocity is obtained by analyzing inelastic x-ray scattering data of nanofluids. Since the high-frequency sound velocity reflects thermal conductivity and structural relaxation of solvent molecules, the effect of nanoparticles on heat transport and molecular dynamics of the medium of nanofluids could be clarified. Cu nanoparticles (Cu NPs) are found to be extremely effective to largely increase the high-frequency sound velocity of medium ethylene glycol, while the effect of alumina NPs on water is limited. The increase in high-frequency sound velocity agrees well with that in thermal conductivity. It is concluded that solvent molecules are highly restrained by Cu NPs in nanofluid, leading to high thermal conductivity.

The dynamic structure factor, S ( Q , ω ), of liquid benzene was measured by meV-resolved inelastic X-ray scattering (IXS) and analyzed using a generalized Langevin model with a memory function including fast, μ-relaxation and slow, structural, α-relaxation. The model well reproduced the experimental S ( Q , ω ) of liquid benzene. The dispersion relation of the collective excitation energy yields the high-frequency sound velocity for liquid benzene as related to the α-relaxation. The ratio of the high-frequency to the adiabatic sound velocity is approximately 1.5, larger to that of carbon tetrachloride and smaller than those of methanol and water, reflecting the nature of intermolecular interactions.

Phonon velocities and densities for Pt were measured based on inelastic X-ray scattering from ambient pressure to 20 GPa in order to independently determine its equation of state (EOS). Phonon velocities were determined with sine dispersion relations. Cij values were obtained by fitting phonon velocities and densities to the Christoffel equation. We found that the obtained Cijs were in good agreement with previously reported Cijs at ambient condition. Based on the Cij values in various conditions, experimental pressures were calculated. The EOS of Pt as a primary pressure scale was determined based on the experimental pressures. We report K’ = 5.17 with fixed KT = 274.1 GPa and V0 = 60.360 A3 for Vinet EOS. Our scale is in good agreement with several previously published scales based on shock experiments and XRD.

The impact of Sn on Si1-xGex through its thermal conductivity and phonon properties was investigated to develop an attractive material for thermoelectric devices. The Si-rich polycrystalline Si1-x-yGexSny alloy was synthesized by ball-milling technique. The as-synthesized alloy had substitutional Sn content of 1.60%, which it maintained as high as 0.54% after sintering at 1000 °C. The thermal conductivity was found to be reduced by the introduction of this tiny amount of Sn. Inelastic X-ray scattering measurements were carried out and we observed the longitudinal acoustic phonon mode superimposed along all crystallographic directions. In addition, the signal that originated from a local vibration at the Ge-related local structure was also successfully detected. It was found that the introduction of Sn affects the local vibration mode in the alloy. It is proposed that the incorporation of Sn atom into the local structure to make Ge–Sn pairs be considered to reduce the material’s thermal conductivity in addition to the mass difference effect.

To clarify microscopic elastic properties of a Pd40Ni40P20 bulk metallic glass, inelastic X-ray scattering (IXS) experiments were carried out using high-resolution IXS spectrometer installed at BL35XU/SPring-8. Clear longitudinal acoustic (LA) excitation modes are observed in the whole momentum transfer Q range up to ~22 nm-1. The microscopic sound velocity of the LA modes obtained from the Q → 0 limit of the dispersion relation is about 12% faster than the macroscopic value, suggesting the microscopic heterogeneity in the elastic properties of this BMG. In addition, transverse acoustic (TA) modes can be deduced from a detailed analysis of the IXS spectra. The microscopic Poisson’s ratio obtained from the ratio of the excitation energies of the TA and LA modes is 0.47 ± 0.04, larger than the macroscopic value of 0.40. Thus, the fragile nature of this BMG already found in the macroscopic sense is much enhanced in the microscopic view.

Chinese liquorice/licorice (Glycyrrhiza uralensis) is a leguminous plant species whose roots and rhizomes have been widely used as a herbal medicine and natural sweetener. Whole-genome sequencing is essential for gene discovery studies and molecular breeding in liquorice. Here, we report a draft assembly of the approximately 379-Mb whole-genome sequence of strain 308-19 of G. uralensis; this assembly contains 34 445 predicted protein-coding genes. Comparative analyses suggested well-conserved genomic components and collinearity of gene loci (synteny) between the genome of liquorice and those of other legumes such as Medicago and chickpea. We observed that three genes involved in isoflavonoid biosynthesis, namely, 2-hydroxyisoflavanone synthase (CYP93C), 2,7,4'-trihydroxyisoflavanone 4'-O-methyltransferase/isoflavone 4'-O-methyltransferase (HI4OMT) and isoflavone-7-O-methyltransferase (7-IOMT) formed a cluster on the scaffold of the liquorice genome and showed conserved microsynteny with Medicago and chickpea. Based on the liquorice genome annotation, we predicted genes in the P450 and UDP-dependent glycosyltransferase (UGT) superfamilies, some of which are involved in triterpenoid saponin biosynthesis, and characterised their gene expression with the reference genome sequence. The genome sequencing and its annotations provide an essential resource for liquorice improvement through molecular breeding and the discovery of useful genes for engineering bioactive components through synthetic biology approaches.

1. Introduction Silicon germanium (SiGe) is one of the promising candidates as a next-generation material for thermoelectric devices as an ambient energy harvesting technique because it has low thermal conductivity. For a SiGe thermoelectric device, it is important to reveal the phonon scattering mechanism for the alloy material and the thermal transport in miniaturization to the nanoscale. However, the origin of the low thermal conductivity of the SiGe alloy has not been investigated in a sufficiently rigorous manner yet. In addition, the correlation among the thermal conductivity, the phonon dispersion curve, and the lifetime remains mostly unclear. From the above, we focused on direct phonon properties evaluation by inelastic X-ray scattering (IXS) with synchrotron radiation. IXS is a powerful technique that reveals the phonon dispersion curves in contrast to Raman spectroscopy, which can only give optical phonon modes at the Brillouin zone center (the Γ point). In this study, we evaluated the phonon dispersion curve of bulk SiGe by IXS. 2. Experimental method The single-crystalline SiGe samples for IXS were prepared by two different growth methods: the Czochralski (Cz) [1] and traveling liquidus zone (TLZ) methods [2]. The sample information is summarized in Table 1. Prior to the IXS measurements, the crystal orientation and Ge fraction were confirmed by X-ray diffraction (XRD) and electron backscattering pattern (EBSP) measurements, respectively. The IXS measurements were performed at the BL35XU beamline of the SPring-8 synchrotron facility. The measurements were conducted at room temperature using a reflection geometry. The incident X-ray energy was set to 17.795 keV, which corresponds to Si (9 9 9) reflection, and the overall energy resolution was around 3 meV. The incident X-ray beam size was approximately 60 x 75 μm2. The measurements were conducted along the Γ-X ([00q]) direction. 3. Results and Discussion As an example of phonon dispersion of bulk Si1-x Ge x , we show the IXS results of x = 0.45 in Fig. 1 obtained by peak positions of IXS spectra. As a result, all optical and acoustic phonon modes for bulk SiGe were observed as shown in Fig. 1. In addition, the energy of the optical phonon modes (Si-Si, Si-Ge, and Ge-Ge modes) obtained by IXS at the zone center (Γ point) was good agreement with results of Raman spectroscopy (λ = 532 nm). Both Raman and IXS indicate that, at around Γ point, the phonon energies of Si-Si and Ge-Ge modes tend to be lower than that of pure Si and Ge, respectively. These behaviors can be considered to be caused by random distribution of Si and Ge atoms in the alloy. On the other hand, it was revealed that the acoustic phonon (LA and TA modes) energies are located between those of pure Si [3] and Ge [4]. Based on the above, the origin of the dramatic thermal conductivity reduction of the SiGe alloy, which has been reported in previous study [5], may not be derived from the reduction of group velocity, but the low phonon lifetime reduction. Acknowledgements The IXS measurements were performed at SPring-8 with the approval of JASRI (Proposal Nos. 2016A1496, 2017B1630, 2019A1678, and 2019B1750). The authors thank Dr. Koji Usuda (KIOXIA Corp.) for his great support with analyzing the IXS results throughout the work. References [1] I. Yonenaga, J. Cryst. Growth 275, 91 (2005). [2] K. Kinoshita et al., Jpn. J. Appl. Phys. 54, 04DH03 (2015). [3] A. Valentin et al., Phys.: Condens. Matter 20, 145213 (2008). [4] M. Mohr et al., Phys. Rev. B 73, 035217 (2006). [5] M. Tomita et al., Jpn. J. Appl. Phys. 57, 04FB04 (2018). Figure 1

Epitaxial metal/semiconductor superlattice heterostructures with lattice-matched abrupt interfaces and suitable Schottky barrier heights are attractive for thermionic energy conversion, hot electron-based solar energy conversion, and optical hyperbolic metamaterials. HfN/ScN is one of the earliest demonstrations of epitaxial single-crystalline metal/semiconductor heterostructures and has attracted significant interest in recent years to harness its excellent properties in device applications. Although the understanding of the mechanism of thermal transport in HfN/ScN superlattices is extremely important for their practical applications, not much attention has been devoted to measuring their phonon dispersion and related properties. In this Letter, we employ non-resonant meV-resolution inelastic x-ray scattering to determine the momentum-dependent phonon modes in epitaxial metallic HfN and lattice-matched HfN/ScN metal/semiconductor superlattices. HfN exhibits a large phononic bandgap (∼40 meV) and Kohn anomaly in the longitudinal and transverse acoustic phonon modes at q ∼ 0.73 along the [100] and [110] directions of the Brillouin zone due to the nesting of the Fermi surface by the wave vector ( q). The in-plane [100] acoustic phonon dispersion of the HfN/ScN superlattices is found to be dominated by the HfN phonons, while the optical phonons exhibit both ScN and HfN characteristics. First-principles density functional perturbation theory modeling is performed to explain the experimental phonon spectra, and temperature-dependent thermal conductivity is measured using a pump-probe spectroscopic technique. These results will help understand the phonons in HfN and HfN/ScN metal/semiconductor superlattices for thermionic energy conversion.

We report on an anomalous mode distinct from both optical and acoustic modes in phonon dispersion curves of bulk Si1−xGex alloy with x taking the values of 0.16, 0.32, 0.45, and 0.72. The anomalous mode at approximately 13 meV was observed directly using inelastic x-ray scattering along the Γ–X ([00q]) direction. The phonon dispersion relations of the anomalous mode indicate that there was no momentum dependence, similar to those of the longitudinal and transverse optical modes (Ge–Ge, Si–Ge, and Si–Si modes). In contrast to the acoustic and optical phonon modes, the energy of the anomalous mode shows no Ge fraction dependence. The molecular dynamics simulation corroborates that the Ge–Ge pairs or Ge atom clusters, which are surrounded by Si atoms, provide the anomalous mode, which is unique to the alloy structure. It has been suggested that such a localized vibration mode with no propagation significantly affects the acoustic modes, leading to low thermal conductivity in the SiGe alloy.

Inelastic x-ray scattering (IXS) measurements were carried out on liquid Se50Te50 at temperatures up to 1323 K to investigate how the atomic dynamics changes with temperature through the semiconductor-metal transition. The acoustic mode was clearly observed in the dynamic structure factor and its energy was determined using a damped harmonic oscillator model. The dynamical sound speed obtained by IXS for [Formula: see text] nm-1 was found to behave similarly to the temperature dependence of ultrasonic sound velocity with a minimum near the semiconductor metal transition. The results can be explained by taking liquid Se50Te50 to be an inhomogeneous liquid consisting of metallic and semiconducting domains whose size is approximately 3 nm. The relaxation time obtained from frequency dependence of the dynamical sound speed was on a picosecond time scale.

Transition metal dichalcogenides like MoS$_2$, MoSe$_2$, WS$_2$, and WSe$_2$ have attracted enormous interest during recent years. They are van-der-Waals crystals with highly anisotropic properties, which allows exfoliation of individual layers. Their remarkable physical properties make them promising for applications in optoelectronic, spintronic, and valleytronic devices. Phonons are fundamental to many of the underlying physical processes, like carrier and spin relaxation or exciton dynamics. However, experimental data of the complete phonon dispersion relations in these materials is missing. Here we present the phonon dispersion of bulk MoS$_2$ in the high-symmetry directions of the Brillouin zone, determined by inelastic X-ray scattering. Our results underline the two-dimensional nature of MoS$_2$. Supported by first-principles calculations, we determine the phonon displacement patterns, symmetry properties, and scattering intensities. The results will be the basis for future experimental and theoretical work regarding electron-phonon interactions, intervalley scattering, as well as phonons in related 2D materials.

Temperature-gradient spherical analyzers allow us to improve the resolution of meV-scale inelastic X-ray scattering., The use of temperature-gradient analyzers for non-resonant high-resolution inelastic X-ray scattering is investigated. The gradient compensates for geometrical broadening of the energy resolution by adjusting the lattice spacing of the analyzer crystal. Applying a ∼12 mK temperature gradient across a 9.5 cm analyzer, resolutions of 0.75 (2) meV FWHM at 25.7 keV for Si(13 13 13) and 1.25 (2) meV at 21.7 keV for Si(11 11 11) were measured, while retaining large (250 mm) clearance between the sample position and detector, and reasonable (9.3 mrad × 8.8 mrad) analyzer acceptance. The temperature control and stability are discussed.

Ailanthus altissima is a woody plant that has become invasively naturalized in many countries. Using nuclear SSR markers, we studied specimens of this species collected throughout Japan and found an individual (labeled Aa-1) that was not diploid. We examined pollen morphology and ploidy level of Aa-1 by optical microscopy and flow cytometry (FCM), respectively. Some pollen grains were morphologically abnormal and much larger than normal. FCM analysis demonstrated that Aa-1 was triploid. Formation of abnormal pollen indicates that Aa-1 may well have reduced fertility compared to normal diploids. If this were the case, vegetative progeny Aa-1 could be used as ornamentals without attendant risks of future naturalization.

Inelastic and elastic X-ray scattering are used to investigate the structural phase transition which occurs in EuTiO3 at ~287 K. The dispersion of the soft phonon mode associated with the transition was measured about the R-point at 300 K, slightly above the transition, and is compared against a shell model. Below the structural transition temperature, a single R-point Bragg peak was observed, without any indication of more complex streaking reported from differently prepared samples.

The K computer, released on September 29, 2012, is a large-scale parallel supercomputer system consisting of 82,944 compute nodes. We have been able to resolve a significant number of operation issues since its release. Some system software components have been fixed and improved to obtain higher stability and utilization. We achieved 94% service availability because of a low hardware failure rate and approximately 80% node utilization by careful adjustment of operation parameters. We found that the K computer is an extremely stable and high utilization system.

Several genes of model and crop species that function in plant adaptation to acid soils have recently been characterized, but little is known about the molecular basis of the stress tolerance of woody plants. In the present study, using cell suspension cultures of Acacia mangium, a leguminous tree habituated to tropical acid soils, genes up-regulated in response to lowering the medium pH and addition of AlCl3 were screened by successive differential display and semiquantitative RT-PCRs, followed by full-length determination by RACE (rapid amplification of cDNA ends)-PCR. A total of 57 genes were shown to be induced by low-pH and/or aluminum stresses, and 44 full-length sequences were identified and cloned. They included genes of a multidrug and toxic compound extrusion transporter that secretes citrate ions to chelate aluminum, ATP-binding cassette transporters, a plasma membrane H+-ATPase, and a CYP94A, known in other plants to be responsive to low-pH and/or aluminum stresses. Genes that have not been recognized to be stress-responsive were also up-regulated by low-pH/aluminum treatments. Many of these genes were induced in the stressed A. mangium seedling roots. The cloned genes should provide the resources for the identification of the factors that play roles in the adaptation of A. mangium to acid soils.

Structure and dynamical properties of hydrated actin filament (F-actin) are revealed by X-ray diffraction and inelastic X-ray scattering (IXS) in a temperature range of 180–298 K, respectively. We assigned the peaks in the radial distribution functions of the hydrated F-actin by molecular dynamics (MD) simulation for F-actin in water. Although the hydration water of F-actin does not freeze in the temperature range measured, the hydrogen-bonded network where hydration water molecules mediate the hydrophilic groups of F-action becomes enhanced with decreasing temperature, as previously seen for many hydrated proteins. By applying a damped harmonic oscillator model to the dynamical structure factor obtained from the IXS spectra of hydrated F-actin, we investigated the intensity and energy of the phonon excitation as a function of temperature. The phonon excitation energy decreased and the phonon population which is proportional to the intensity of the phonon excitation increased with increasing temperature as previously reported for hydrated lysozyme and could be related to the conformational flexibility of the protein regarding the intraprotein short-time collective vibrational motions. In contrast to hydrated lysozyme, these phenomena for hydrated F-actin were observed at ~11 nm−1 of momentum transfer, Q, indicating that they arise from water dimer mediating the hydrophilic parts of F-actin.