Berry's Phase for Standing Wave Near Graphene Edge

Standing waves near the zigzag and armchair edges, and their Berry's phases are investigated. It is suggested that the Berry's phase for the standing wave near the zigzag edge is trivial, while that near the armchair edge is non-trivial. A non-trivial Berry's phase implies the presence of a singularity in parameter space. We have confirmed that the Dirac singularity is absent (present) in the parameter space for the standing wave near the zigzag (armchair) edge. The absence of the Dirac singularity has a direct consequence in the local density of states near the zigzag edge. The transport properties of graphene nanoribbons observed by recent numerical simulations and experiments are discussed from the point of view of the Berry's phases for the standing waves.Comment: 6 pages, 4 figure

Hamiltonian decomposition for bulk and surface states

We demonstrate that a tight-binding Hamiltonian with nearest- and next-nearest-neighbor hopping integrals can be decomposed into bulk and boundary parts in a general lattice system. The Hamiltonian decomposition reveals that next nearest-neighbor hopping causes sizable changes in the energy spectrum of surface states even if the correction to the energy spectrum of bulk states is negligible. By applying the Hamiltonian decomposition to edge states in graphene systems, we show that the next nearest-neighbor hopping stabilizes the edge states.Comment: 5 pages, 4 figure

Modulation of Chlamydomonas reinhardtii flagellar motility by redox poise

Redox-based regulatory systems are essential for many cellular activities. Chlamydomonas reinhardtii exhibits alterations in motile behavior in response to different light conditions (photokinesis). We hypothesized that photokinesis is signaled by variations in cytoplasmic redox poise resulting from changes in chloroplast activity. We found that this effect requires photosystem I, which generates reduced NADPH. We also observed that photokinetic changes in beat frequency and duration of the photophobic response could be obtained by altering oxidative/reductive stress. Analysis of reactivated cell models revealed that this redox poise effect is mediated through the outer dynein arms (ODAs). Although the global redox state of the thioredoxin-related ODA light chains LC3 and LC5 and the redox-sensitive Ca2+-binding subunit of the docking complex DC3 did not change upon light/dark transitions, we did observe significant alterations in their interactions with other flagellar components via mixed disulfides. These data indicate that redox poise directly affects ODAs and suggest that it may act in the control of flagellar motility

Soliton Trap in Strained Graphene Nanoribbons

The wavefunction of a massless fermion consists of two chiralities, left-handed and right-handed, which are eigenstates of the chiral operator. The theory of weak interactions of elementally particle physics is not symmetric about the two chiralities, and such a symmetry breaking theory is referred to as a chiral gauge theory. The chiral gauge theory can be applied to the massless Dirac particles of graphene. In this paper we show within the framework of the chiral gauge theory for graphene that a topological soliton exists near the boundary of a graphene nanoribbon in the presence of a strain. This soliton is a zero-energy state connecting two chiralities and is an elementally excitation transporting a pseudospin. The soliton should be observable by means of a scanning tunneling microscopy experiment.Comment: 7 pages, 4 figure

Protein–protein interactions between intermediate chains and the docking complex of Chlamydomonas flagellar outer arm dynein

AbstractOuter arm dynein (OAD) is bound to specific loci on outer-doublet-microtubules by interactions at two sites: via intermediate chain 1 (IC1) and the outer dynein arm docking complex (ODA-DC). Studies using Chlamydomonas mutants have suggested that the individual sites have rather weak affinities for microtubules, and therefore strong OAD attachment to microtubules is achieved by their cooperation. To test this idea, we examined interactions between IC1, IC2 (another intermediate chain) and ODA-DC using recombinant proteins. Recombinant IC1 and IC2 were found to form a 1:1 complex, and this complex associated with ODA-DC in vitro. Binding of IC1 to mutant axonemes revealed that there are specific binding sites for IC1. From these data, we propose a novel model of OAD-outer doublet association

Identification of the agg1 mutation responsible for negative phototaxis in a “wild-type” strain of Chlamydomonas reinhardtii

AbstractThe unicellular green alga Chlamydomonas reinhardtii is a model organism for various studies in biology. CC-124 is a laboratory strain widely used as a wild type. However, this strain is known to carry agg1 mutation, which causes cells to swim away from the light source (negative phototaxis), in contrast to the cells of other wild-type strains, which swim toward the light source (positive phototaxis). Here we identified the causative gene of agg1 (AGG1) using AFLP-based gene mapping and whole genome next-generation sequencing. This gene encodes a 36-kDa protein containing a Fibronectin type III domain and a CHORD-Sgt1 (CS) domain. The gene product is localized to the cell body and not to flagella or basal body

Enlargement of accessory spleen subsequent to splenectomy associated with gastrectomy can mimic a solitary tumor : report of a case

We report a case of a 65-year-old woman with an incidental about 20-mm solitary mass between the lateralsegment of the left lobe of the liver and left kidney 5 years after splenectomy associated with total gastrectomy. The mass wassurgically resected, and histological examination revealed it to be an accessory spleen. Small accessory spleens mostly locatednear the splenic hilus, but large accessory spleens are unusual after total gastrectomy with regional lymph nodes resection. Theremaining accessory splenic tissue would undergo compensatory hypertrophy. Hence, the possibility of accessory spleens mustbe considered when an intra-abdominal mass is identified in a patient with splenectomy associated with gastrectomy

Cooperative binding of the outer arm-docking complex underlies the regular arrangement of outer arm dynein in the axoneme

Outer arm dynein (OAD) in cilia and flagella is bound to the outer doublet microtubules every 24 nm. Periodic binding of OADs at specific sites is important for efficient cilia/flagella beating; however, the molecular mechanism that specifies OAD arrangement remains elusive. Studies using the green alga Chlamydomonas reinhardtii have shown that the OAD-docking complex (ODA-DC), a heterotrimeric complex present at the OAD base, functions as the OAD docking site on the doublet. We find that the ODA-DC has an ellipsoidal shape approximately 24 nm in length. In mutant axonemes that lack OAD but retain the ODA-DC, ODA-DC molecules are aligned in an end-to-end manner along the outer doublets. When flagella of a mutant lacking ODA-DCs are supplied with ODA-DCs upon gamete fusion, ODA-DC molecules first bind to the mutant axonemes in the proximal region, and the occupied region gradually extends toward the tip, followed by binding of OADs. This and other results indicate that a cooperative association of the ODA-DC underlies its function as the OAD-docking site and is the determinant of the 24-nm periodicity

X-ray and Neutron Study on the Structure of Hydrous SiO2 Glass up to 10 GPa

The structure of hydrous amorphous SiO2 is fundamental in order to investigate the effects of water on the physicochemical properties of oxide glasses and magma. The hydrous SiO2 glass with 13 wt.% D2O was synthesized under high-pressure and high-temperature conditions and its structure was investigated by small angle X-ray scattering, X-ray diffraction, and neutron diffraction experiments at pressures of up to 10 GPa and room temperature. This hydrous glass is separated into two phases: a major phase rich in SiO2 and a minor phase rich in D2O molecules distributed as small domains with dimensions of less than 100 angstrom. Medium-range order of the hydrous glass shrinks compared to the anhydrous SiO2 glass by disruption of SiO4 linkage due to the formation of Si-OD deuterioxyl, while the response of its structure to pressure is almost the same as that of the anhydrous SiO2 glass. Most of D2O molecules are in the small domains and hardly penetrate into the void space in the ring consisting of SiO4 tetrahedra