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Tsukada M.,Tohoku University | Watanabe N.,Mizuho Information and Research Institute | Harada M.,AdvanceSoft Corporation | Tagami K.,AdvanceSoft Corporation
Journal of Vacuum Science and Technology B:Nanotechnology and Microelectronics | Year: 2010

Methods of theoretical simulations of noncontact atomic force microscopy in liquids have been developed. Though there are several difficult issues for the theoretical simulations in liquids, the authors introduce here the simulation methods for the cantilever oscillation in liquids and the tip-sample interaction force mediated by water molecules. As for the cantilever motion, a very efficient numerical method is proposed which solves the oscillation of the elastic beam cantilever and fluid dynamics simultaneously. The results reproduce fairly well the resonant curve and related properties of the Si beam cantilever. As for the simulation of the tip-sample interaction force in water, classical molecular dynamics (MD) method is adopted in the present work. The case study by MD for the mica surface in water revealed new features that appeared in the three-dimensional force map. © 2010 American Vacuum Society.

Kobayashi T.,Geospatial Information Authority of Japan | Ohminato T.,University of Tokyo | Ida Y.,Advance Soft Corporation | Fujita E.,Japan National Research Institute for Earth Science and Disaster Prevention
Earth and Planetary Science Letters | Year: 2012

Very-long-period (VLP) pulses with widths of 20. s on velocity seismograms were observed during volcanic activity at Miyake-jima Volcano, Japan in 2000. The VLP events occurred repeatedly during a few days prior to caldera formation and essentially vanished following the onset of caldera collapse. Waveform inversions of the pulse-like signals point to a source offset 3.5. km beneath and 1. km south of the summit. A candidate for the source mechanism is the inflation of an elliptical cylinder with axis tilted 20-30° from vertical and major axis of the elliptical cross section oriented northeast-southwest. The inferred mechanism appears consistent with a step-like pressurization of a magma reservoir impacted by a falling rock mass in response to gravitational instability. The repeated occurrences of the rock collapses lead to the caldera formation at Miyake-jima. © 2012 Elsevier B.V.

Fujita E.,Japan National Research Institute for Earth Science and Disaster Prevention | Kozono T.,Japan National Research Institute for Earth Science and Disaster Prevention | Ueda H.,Japan National Research Institute for Earth Science and Disaster Prevention | Kohno Y.,Japan National Research Institute for Earth Science and Disaster Prevention | And 4 more authors.
Bulletin of Volcanology | Year: 2013

Crustal deformation by the Mw 9. 0 megathrust Tohoku earthquake causes the extension over a wide region of the Japanese mainland. In addition, a triggered Mw 5. 9 East Shizuoka earthquake on March 15 occurred beneath the south flank, just above the magma system of Mount Fuji. To access whether these earthquakes might trigger the eruption, we calculated the stress and pressure changes below Mount Fuji. Among the three plausible mechanisms of earthquake-volcano interactions, we calculate the static stress change around volcano using finite element method, based on the seismic fault models of Tohoku and East Shizuoka earthquakes. Both Japanese mainland and Mount Fuji region are modeled by seismic tomography result, and the topographic effect is also included. The differential stress given to Mount Fuji magma reservoir, which is assumed to be located to be in the hypocentral area of deep long period earthquakes at the depth of 15 km, is estimated to be the order of about 0. 001-0. 01 and 0. 1-1 MPa at the boundary region between magma reservoir and surrounding medium. This pressure change is about 0. 2 % of the lithostatic pressure (367. 5 MPa at 15 km depth), but is enough to trigger an eruptions in case the magma is ready to erupt. For Mount Fuji, there is no evidence so far that these earthquakes and crustal deformations did reactivate the volcano, considering the seismicity of deep long period earthquakes. © 2013 Springer-Verlag Berlin Heidelberg.

Ishikita H.,Kyoto University | Ishikita H.,Japan Science and Technology Agency | Hasegawa K.,AdvanceSoft Corporation | Noguchi T.,Nagoya University
Biochemistry | Year: 2011

The redox potential of the primary quinone Q A [E m(Q A)] in photosystem II (PSII) is lowered by replacement of the native plastoquinone (PQ) with bromoxynil (BR) at the secondary quinone Q B binding site. Using the BR-bound PSII structure presented in the previous Fourier transform infrared and docking calculation studies, we calculated E m(Q A) considering both the protein environment in atomic detail and the protonation pattern of the titratable residues. The calculated E m(Q A) shift in response to the replacement of PQ with deprotonated BR at the Q B binding site [ΔE m(Q A) PQ→BR] was -55 mV when the three regions, Q A, the non-heme iron complex, and Q B (Q B = PQ or BR), were treated as a conjugated supramolecule (Q A-Fe-Q B). The negative charge of BR apparently contributes to the downshift in ΔE m(Q A) PQ→BR. This downshift, however, is mostly offset by the influence of the residues near Q B. The charge delocalization over the Q A-Fe-Q B complex and the resulting H-bond strength change between Q A and D2-His214 are crucial factors that yield a ΔE m(Q A) PQ→BR of -55 mV by (i) altering the electrostatic influence of the H-bond donor D2-His214 on E m(Q A) and (ii) suppressing the proton uptake events of the titratable residues that could otherwise upshift ΔE m(Q A) PQ→BR during replacement of PQ with BR at the Q B site. © 2011 American Chemical Society.

Ren S.,Tokyo Institute of Technology | Sato R.,Tokyo Institute of Technology | Hasegawa K.,Advancesoft Corporation | Ohta H.,Tokyo Institute of Technology | And 2 more authors.
Biochemistry | Year: 2013

PixD is a blue light-using flavin (BLUF) photoreceptor that controls phototaxis in the cyanobacterium Synechocystis sp. PCC6803. PixD interacts with the response regulator-like protein PixE in a light-dependent manner, and this interaction is critical for light signal transduction in vivo. However, the structure of the PixD-PixE complex has not been determined. To improve our understanding of how PixD transmits its captured light signal to PixE, we used blue-native polyacrylamide gel electrophoresis to characterize the molecular mass of a recombinant PixD-PixE complex purified from Escherichia coli and found it to be 342 kDa, suggesting that the complex contains 10 PixD and 4 PixE monomers. The stoichiometry of the complex was confirmed by Western blotting. Specifically, three intermediate states, PixD10-PixE1, PixD10-PixE2, and PixD10-PixE3, were detected. The apparent dissociation constant for PixE and PixD is ∼5 μM. A docking simulation was performed using a modeled PixE structure and the PixD10 crystal structure. The docking simulation showed how the molecules in the PixD10-PixE4 structure interact. To verify the accuracy of the docked model, a site-directed mutagenesis study was performed in which Arg80 of PixE, which appears to be capable of interacting electrostatically with Asp135 of PixD in the predicted structure, was shown to be critical for complex formation as mutation of PixE Arg80 to Asp or Ala prevented PixD-PixE complex formation. This study provides a structural basis for future investigations of the light signal transduction mechanism involving PixD and PixE. © 2013 American Chemical Society.

Ren S.,Tokyo Institute of Technology | Sawada M.,Tokyo Institute of Technology | Hasegawa K.,Advancesoft Corporation | Hayakawa Y.,Aichi Institute of Technology | And 3 more authors.
Plant and Cell Physiology | Year: 2012

Blue light-using flavin (BLUF) proteins form a subfamily of blue light photoreceptors, are found in many bacteria and algae, and are further classified according to their structures. For one type of BLUF-containing protein, e.g. PixD, the central axes of its two C-terminal α-helices are perpendicular to the β-sheet of its N-terminal BLUF domain. For another type, e.g. PapB, the central axes of its two C-terminal α-helices are parallel to its BLUF domain β-sheet. However, the functional significance of the different orientations with respect to phototransduction is not clear. For the study reported herein, we constructed a chimeric protein, Pix0522, containing the core of the PixD BLUF domain and the C-terminal region of PapB, including the two α-helices, and characterized its biochemical and spectroscopic properties. Fourier transform infrared spectroscopy detected similar light-induced conformational changes in the C-terminal α-helices of Pix0522 and PapB. Pix0522 interacts with and activates the PapB-interacting enzyme, PapA, demonstrating the functionality of Pix0522. These results provide direct evidence that the BLUF C-terminal α-helices function as an intermediary that accepts the flavin-sensed blue light signal and transmits it downstream during phototransduction. © The Author 2012. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists.

Hasegawa K.,Advancesoft Corporation | Mohri S.,Japanese National Institute of Animal Health | Yokoyama T.,Japanese National Institute of Animal Health
Prion | Year: 2010

The e200K mutation of the human prion protein (PrP) is known to cause familial creutzfeldt-Jakob disease. In order to elucidate the effects of the mutation on the local structural stability of PrP, we performed ab initio fragment molecular orbital calculations for the wild-type human PrP and the e200K variant modeled under neutral and mild acidic conditions. The calculations revealed that this substitution markedly altered the intramolecular interactions in the PrP, suggesting that the local structural instabilities induced by the e200K mutation might cause initial denaturation of the PrP and its subsequent conversion to a pathogenic form. This work presents a new approach for quantitatively elucidating structural instabilities in proteins that cause misfolding diseases.

Ida Y.,Advance Soft Corporation
Journal of Volcanology and Geothermal Research | Year: 2010

Time-dependent magma ascent processes were analyzed using a computer simulation of bubbly and gassy (gas-particle dispersion) magma flows in a vertical conduit connected at its bottom to a magma chamber having finite capacity. Volatile elements in the bubbly flow were assumed to escape from the magma through lateral permeable gas flow driven by the pressure gradient originating from viscous resistance to the ascent velocity-dependent expansion of bubbles. The bubbly flow was assumed to fragment and to transform into a gassy flow when its gas volume fraction exceeded a critical value. Based on the simulation, an eruption is predicted to be explosive or effusive when a dimensionless degassing factor, which is proportional to the permeability and viscosity of the magma, is smaller or greater than a critical value, respectively. The state of gassy flow was calculated from the mass and momentum conservations that are met quasi-statically with continuities of mass flux and pressure at the interface with the underlying bubbly flow. The inertia force and an effective wall friction were considered as resistive forces working on the gassy flow. Some of the results of the simulation are shown to be consistent with observations of some recent eruptions. An effusive or explosive eruption is predicted to have relatively high activity with large exit velocities at its initial stage. The initial high activity is particularly significant for explosive eruptions that involve the rapid growth of a gassy flow zone. Explosive eruptions are shown to involve more efficient magma transport with higher mass flow rates than effusive eruptions, as has been predicted by some previous analyses of stationary magma flow. The efficient magma transport of explosive eruptions is associated with a peculiar pressure distribution consisting of gentler and steeper pressure gradients in the gassy and bubbly flow zones, respectively. At the interface between bubbly and gassy flows, the pressure scaled by that at the conduit bottom was found to be nearly constant through time. This peculiar pressure distribution allows explosive eruptions to be fed with more magma than has been stored in excess of the lithostatic balance. This mechanism can produce such anomalously low pressure in the chamber that significant surface subsidence and caldera formation may result. © 2010 Elsevier B.V.

Takahashi R.,University of Tsukuba | Hasegawa K.,AdvanceSoft Corporation | Takano A.,University of Tsukuba | Noguchi T.,Nagoya University | Noguchi T.,University of Tsukuba
Biochemistry | Year: 2010

Herbicides targeting photosystem II (PSII) block the electron transfer beyond QA by binding to the QB site. Upon binding, the redox potential of QA shifts differently depending on the types of herbicides. In this study, we have investigated the structures, interactions, and locations of phenolic herbicides in the QB site to clarify the molecular mechanism of the QA potential shifts by herbicides. Fourier transform infrared (FTIR) difference spectra upon photoreduction of the preoxidized non-heme iron (Fe2+/Fe3+ difference) were measured with PSII membranes in the presence of bromoxynil or ioxynil. The CN and CO stretching vibrations of these phenolic herbicides were identified at 2215-2200 and 1516-1505 cm-1, respectively, in the Fe 2+/Fe3+ difference spectra. Comparison with the spectra of bromoxynil in ethanol solutions along with density functional theory analysis strongly suggests that the phenolic herbicides take a deprotonated form in the binding pocket. In addition, the CN stretching, NH bending, and NH stretching vibrations of a His side chain, which were found at 1109-1101, 1187-1185, and 3000-2500 cm-1, respectively, in the Fe2+/Fe3+ difference spectra, showed characteristic features in the presence of phenolic herbicides. These signals are probably attributed to D1-His215, one of the ligands to the non-heme iron. Docking calculations for herbicides to the Q B pocket confirmed the binding of deprotonated bromoxynil to D1-His215 at the CO group, whereas the protonated form of bromoxynil and DCMU were found to bind to the opposite side of the pocket without an interaction with D1-His215. From these results, it is proposed that a strong hydrogen bond of the phenolate CO group with D1-His215 induces the change in the hydrogen bond strength of the QA CO group through the QA-His-Fe-His- phenolate bridge causing the downshift of the QA redox potential. © 2010 American Chemical Society.

Hasegawa K.,AdvanceSoft Corporation | Mohri S.,Japanese National Institute of Animal Health | Yokoyama T.,Japanese National Institute of Animal Health
Prion | Year: 2013

Bovine spongiform encephalopathy (BSE ), a member of the prion diseases, is a fatal neurodegenerative disorder suspected to be caused by a malfunction of prion protein (PrP). Although BSE prions have been reported to be transmitted to a wide range of animal species, dogs and hamsters are known to be BSE -resistant animals. Analysis of canine and hamster PrP could elucidate the molecular mechanisms supporting the species barriers to BSE prion transmission. The structural stability of six mammalian PrPs, including human, cattle, mouse, hamster, dog and cat, was analyzed. We then evaluated intramolecular interactions in PrP by fragment molecular orbital (FMO) calculations. Despite similar backbone structures, the PrP side-chain orientations differed among the animal species examined. The pair interaction energies between secondary structural elements in the PrPs varied considerably, indicating that the local structural stabilities of PrP varied among the different animal species. Principal component analysis (PCA) demonstrated that different local structural stability exists in bovine PrP compared with the PrP of other animal species examined. The results of the present study suggest that differences in local structural stabilities between canine and bovine PrP link diversity in susceptibility to BSE prion infection. © 2013 Landes Bioscience.

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