First-principles lattice dynamics is applied to symmetric tilt grain boundaries (GBs) in Al, Si and MgO, with the goal of revealing critical factors in determining excess vibrational entropies at the ...atomic level. Excess vibrational entropies at GBs are found to vary depending on the substances. Al GBs tend to show larger excess entropies and hence larger temperature dependence of the GB free energies than those in Si and MgO. Most of the Si GBs show small excess entropies. For Al and MgO, atom-projected vibrational entropies are well correlated with bond-length changes at GB cores, and have large positive values as bond lengths increase for GB atoms. This demonstrates that a similar mechanism likely dominates excess vibrational entropies of GBs for both substances, despite their dissimilar bonding nature. For Si GBs, atoms with threefold coordination do not simply follow such a correlation, implying the importance of other factors that are different from bond-length changes. These systematic comparisons will be a foothold for understanding a physical origin of excess entropies at GBs even in more complex substances.
Excess vibrational entropies are examined by performing first-principle lattice dynamics for grain boundaries in MgO, Al and Si. Bond-length changes are critical for excess entropy, although their bonding nature is originally very different.
A simulated annealing (SA) method based on molecular dynamics is employed to reveal atomic structures of asymmetric tilt grain boundaries (ATGBs) in MgO. Σ5 and Σ13 ATGBs with the 001 tilt axis are ...systematically investigated. The ATGBs after SA simulations dissociate into saw-toothed nanofacets composed of multiple structural units. These nanofacets are lower in GB energy than those obtained from a γ-surface method with structural optimization, demonstrating the importance of SA-based methods for obtaining low-energy structures of ATGBs. For most of the Σ5 ATGBs, the nanofacets consist of only structural units of Σ5 symmetric tilt GBs (STGBs). For the Σ13 ATGBs studied, their nanofacets do not consist of only Σ13 STGBs but always contain non-Σ13 structural units, which probably results from a large difference between the excess volume of Σ13(510) and Σ13(320) STGBs. It is also found that ATGBs have a larger number of metastable structures whose GB energies are close to the lowest energy structure than STGBs, due to the fact that ATGB nanofacets are more tolerant of variation in facet junction, structural units and their arrangement. Consequently, the lowest energy structures have low probabilities of being formed than metastable structures.
Surface charge states of biomaterials are often important for the adsorption of cells, proteins, and foreign ions on their surfaces, which should be clarified at the atomic and electronic levels. ...First-principles calculations were performed to reveal thermodynamically stable surface atomic structures and their charge states in hydroxyapatite (HAp). Effects of aqueous environments on the surface stability were considered using an implicit solvation model. It was found that in an air atmosphere, stoichiometric {0001} and P-rich {101&cmb.macr;0} surfaces are energetically favorable, whereas in an aqueous solution, a Ca-rich {101&cmb.macr;0} surface is the most stable. This difference suggests that preferential surface structures strongly depend on chemical environments with and without aqueous solutions. Their surface potentials at zero charge were calculated to obtain the isoelectric points (pH
PZC
). pH
PZC
values for the {0001} surface and the Ca-rich {101&cmb.macr;0} surface were obtained to be 4.8 and 8.7, respectively. This indicates that in an aqueous solution at neutral pH, the {0001} and Ca-rich {101&cmb.macr;0} surfaces are negatively and positively charged, respectively. This trend agrees with experimental data from chromatography and zeta potential measurements. Our methodology based on first-principles calculations enables determining macroscopic charge states of HAp surfaces from atomic and electronic levels.
Macroscopic charge states for hydroxyapatite surfaces have been quantitatively determined using an implicit solvation model based on first-principles calculations.
The evolution of complex rooting systems during the Devonian had significant impacts on global terrestrial ecosystems and the evolution of plant body plans. However, detailed understanding of the ...pathways of root evolution and the architecture of early rooting systems is currently lacking. We describe the architecture and resolve the structural homology of the rooting system of an Early Devonian basal lycophyte. Insights gained from these fossils are used to address lycophyte root evolution and homology.
Plant fossils are preserved as carbonaceous compressions at Cottonwood Canyon (Wyoming), in the Lochkovian-Pragian (∼411 Ma; Early Devonian) Beartooth Butte Formation. We analysed 177 rock specimens and documented morphology, cuticular anatomy and structural relationships, as well as stratigraphic position and taphonomic conditions.
The rooting system of the Cottonwood Canyon lycophyte is composed of modified stems that bear fine, dichotomously branching lateral roots. These modified stems, referred to as root-bearing axes, are produced at branching points of the above-ground shoot system. Root-bearing axes preserved in growth position exhibit evidence of positive gravitropism, whereas the lateral roots extend horizontally. Consistent recurrence of these features in successive populations of the plant preserved in situ demonstrates that they represent constitutive structural traits and not opportunistic responses of a flexible developmental programme.
This is the oldest direct evidence for a rooting system preserved in growth position. These rooting systems, which can be traced to a parent plant, include some of the earliest roots known to date and demonstrate that substantial plant-substrate interactions were under way by Early Devonian time. The morphological relationships between stems, root-bearing axes and roots corroborate evidence that positive gravitropism and root identity were evolutionarily uncoupled in lycophytes, and challenge the hypothesis that roots evolved from branches of the above-ground axial system, suggesting instead that lycophyte roots arose as a novel organ.
Impurity doping often alters or improves the properties of materials. In alumina, grain boundaries play a key role in deformation mechanisms, particularly in the phenomenon of grain boundary sliding ...during creep at high temperatures. We elucidated the atomic-scale structure in alumina grain boundaries and its relationship to the suppression of creep upon doping with yttrium by using atomic resolution microscopy and high-precision calculations. We find that the yttrium segregates to very localized regions along the grain boundary and alters the local bonding environment, thereby strengthening the boundary against mechanical creep.
Pine wilt disease (PWD) affects forests globally and is caused by the pinewood nematode (PWN)
Bursaphelenchus xylophilus
. It has been proposed that PWD development has a strong association with air ...temperature. Because symptom development is related to the number of PWNs and they are poikilothermic animals whose development and multiplication are affected by temperature; it appears that temperature conditions affect the PWN multiplication rate, which leads to difference in disease progression. However, limited information is available about the temperatures inside pine trees, and the understanding of how temperature affects PWN multiplication and PWD progression remains incomplete. Therefore, in the present study, we evaluated the temperature, number of PWNs, and external symptoms of PWD in
Pinus thunbergii
seedlings infected with PWNs at air temperatures of 20 °C, 25 °C, and 30 °C over time. We found that the seedling temperatures were slightly higher than the air temperature under each temperature condition and that the effective accumulated temperature calculated using a base temperature of 10 °C was related to the number of PWNs and symptom development in all temperature test groups. However, at 20 °C, there were very few PWNs in some seedlings and none of the seedlings showed partial or full wilting. These findings suggest that PWD progression is greatly affected by ambient temperature and facilitated by increase in PWN populations with effective accumulated temperature especially in the range of 25 °C–30 °C.
First-principles calculations are made for five Ga2O3 polymorphs. The structure of epsilon-Ga2O3 with the space group Pna 21 (No. 33, orthorhombic), which is sometimes called kappa-Ga2O3 in the ...literature, is consistent with experimental reports. The structure of gamma-Ga2O3 is optimized within 14 inequivalent configurations of defective spinel structures. Phonon dispersion curves of four polymorphs are obtained. The volume expansivity, bulk modulus, and specific heat at constant volume are computed as a function of temperature within the quasi-harmonic approximation. The Helmholtz free energies of the polymorphs are thus compared. The expansivity shows a relationship of beta < epsilon < alpha < delta, while beta < epsilon < delta < alpha for the bulk modulus. The formation free energies have the tendency beta < epsilon < alpha < delta < gamma at low temperatures. With the increase of temperature, the difference in free energy between the beta-phase and the epsilon-phase becomes smaller. Eventually the epsilon phase becomes more stable at above 1600 K.
Stevens-Johnson syndrome and toxic epidermal necrolysis (SJS/TEN) are severe, cutaneous adverse drug reactions that are rare but life threatening. Genetic biomarkers for allopurinol-related SJS/TEN ...in Japanese were examined in a genome-wide association study in which Japanese patients (n=14) were compared with ethnically matched healthy controls (n=991). Associations between 890 321 single nucleotide polymorphisms and allopurinol-related SJS/TEN were analyzed by the Fisher's exact test (dominant genotype mode). A total of 21 polymorphisms on chromosome 6 were significantly associated with allopurinol-related SJS/TEN. The strongest association was found at rs2734583 in BAT1, rs3094011 in HCP5 and GA005234 in MICC (P=2.44 × 10(-8); odds ratio=66.8; 95% confidence interval, 19.8-225.0). rs9263726 in PSORS1C1, also significantly associated with allopurinol-related SJS/TEN, is in absolute linkage disequilibrium with human leukocyte antigen-B*5801, which is in strong association with allopurinol-induced SJS/TEN. The ease of typing rs9263726 makes it a useful biomarker for allopurinol-related SJS/TEN in Japanese.
Fossil plants are found as fragmentary remains and understanding them as natural species requires assembly of whole-organism concepts that integrate different plant parts. Such concepts are essential ...for incorporating fossils in hypotheses of plant evolution and phylogeny. Plants of the Early Devonian are crucial to reconstructing the initial radiation of tracheophytes, yet few are understood as whole organisms.
This study assembles a whole-plant concept for the Early Devonian lycophyte Sengelia radicans gen. et sp. nov., based on morphometric data and taphonomic observations from >1000 specimens collected in the Beartooth Butte Formation (Wyoming, USA).
Sengelia radicans occupies a key position between stem-group and derived lycophyte lineages. Sengelia had a rooting system of downward-growing root-bearing stems, formed dense monotypic mats of prostrate shoots in areas that experienced periodic flooding, and was characterized by a life-history strategy adapted for survival after floods, dominated by clonality, and featuring infrequent sexual reproduction.
Sengelia radicans is the oldest among the very few early tracheophytes for which a detailed, rigorous whole-plant concept integrates morphology, growth habit, life history and growth environment. This plant adds to the diversity of body plans documented among lycophytes and may help elucidate patterns of morphological evolution in the clade.
PDF
