Biomedical subjects

Takahisa Ohno

Publications and source records attributed to Takahisa Ohno.

8 recordsLinked to original sources

PubMed2006

Multiregional hybrid method and its application: formation of an atomic protrusion at an atomic force microscope tip apex.

We present a multiregional hybrid scheme which incorporates first-principles (FP), tight-binding (TB), and molecular mechanical calculations. The key to this hybrid scheme is to find an explicit description of the FP-TB region coupling. We apply it to the atomic structure of a clean silicon atomic force microscope tip, and find the formation of a distinct atomic protrusion at the tip apex. The present study gives the reason why the atomic protrusion exits at the apex despite the fact that the atomic geometry of the very end of the tip is practically uncontrollable in the tip preparation.

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PubMed2006

Real-time propagation time-dependent density functional theory study on the ring-opening transformation of the photoexcited crystalline benzene.

Mechanism of the ring-opening transformation in the photoexcited crystalline benzene is investigated on the femtosecond scale by a computational method based on the real-time propagation (RTP) time-dependent density functional theory (TDDFT). The excited-state dynamics of the benzene molecule is also examined not only for the distinction between the intrinsic properties of molecule and the intermolecular interaction but for the first validation using the vibration frequencies for the RTP-TDDFT approach. It is found that the vibration frequencies of the excited and ground states in the molecule are well reproduced. This demonstrates that the present method of time evolution using the Suzuki-Trotter-type split operator technique starting with the Franck-Condon state approximated by the occupation change of the Kohn-Sham orbitals is adequately accurate. For the crystalline benzene, we carried out the RTP-TDDFT simulations for two typical pressures. At both pressures, large swing of the C-H bonds and subsequent twist of the carbon ring occurs, leading to tetrahedral (sp3-like) C-H bonding. The nu4 and nu16 out-of-plane vibration modes of the benzene molecule are found mostly responsible for these motions, which is different from the mechanism proposed for the thermal ring-opening transformation occurring at higher pressure. Comparing the results between different pressures, we conclude that a certain increase of the intermolecular interaction is necessary to make seeds of the ring opening (e.g., radical site formation and breaking of the molecular character) even with the photoexcitation, while the hydrogen migration to fix them requires more free volume, which is consistent with the experimental observation that the transformation substantially proceeds on the decompression.

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PubMed2005

A practical treatment for the three-body interactions in the transcorrelated variational Monte Carlo method: application to atoms from lithium to neon.

We suggest a practical solution to dealing with the three-body interactions in the transcorrelated variational Monte Carlo method (TC-VMC). In the TC-VMC method, which was suggested in our previous paper [N. Umezawa and S. Tsuneyuki, J. Chem. Phys. 119, 10015 (2003)], the Jastrow-Slater-type wave function is efficiently optimized through a self-consistent procedure by minimizing the variance of the local energy. The three-body terms in the transcorrelated self-consistent-field equation, which have been simply ignored in our previous works, are efficiently calculated by the Monte Carlo numerical integration. We found that our treatment for the three-body interactions is successful for atoms from Li to Ne.

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PubMed2005

A theoretical study for mechanical contact between carbon nanotubes.

We have theoretically investigated motions of single-walled carbon nanotubes (SWNTs) which are mounted on a flat substrate layer of SWNTs by tight-binding molecular dynamics simulations. One of the most interesting motions is the conversion of force and torque, where the force and torque acting initially on the mounted tube finally results in the lateral motion and rolling of the supporting tubes in the substrate. This motion is well understood in terms of the total energy surface of the SWNT/SWNT system. It is suggested that an undulation of the total energy surface plays a role as an atomic-scale gear tooth in the field of nanomechanics, in spite of the atomically smooth surface of SWNT.

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PubMed2004

Migration processes of the 30 degrees partial dislocation in silicon.

The migration processes of the 30 degrees partial dislocation in silicon have been investigated using first-principles total-energy calculations. We have presented for the first time a reliable determination of the formation and migration energies of kinks, which are consistent with experiments. The obtained results indicate that the 30 degrees partial dominates the dislocation dynamics in Si and suggest the dislocation glide picture based on the no-collision model. We suggest that the interpretation of experimental studies on the dislocation dynamics should be reexamined in light of these results.

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PubMed2004

Theoretical investigation on electron transport through an organic molecule: effect of the contact structure.

Knowing how the contact geometry influences the conductance of a molecular wire junction requires both a precise determination of the molecule/metallic-electrode interface structure and an evaluation of the conductance for different contact geometries with a fair accuracy. With a greatly improved method to solve the Lippmann-Schwinger equation, we are able to include at least one atomic layer of each electrode into the extended molecule. The artificial effect of the jellium model used for the electrodes is therefore significantly reduced. Our first-principles calculations on the transport properties of a single benzene dithiolate molecule sandwiched between Au(111) surfaces show that the transmission of the bridge site contact, which is the most stable adsorption configuration in equilibrium, displays different features from those of other configurations, and that the inclusion of the surface layers of Au electrodes into the extended molecule shifts and broadens the transmission peaks due to a stronger and more realistic S-Au bonding. We discuss the geometry dependence of the transport properties by analyzing the density of states of the molecular orbitals.

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PubMed2004

Tail molecule dependence of thiolate adsorption on Au(111) surface: Theoretical study.

The adsorption of thiolates with various tail molecules on the Au(111) surface has been investigated by first-principles calculations. We have considered six typical thiolate molecules, that is, methylthiolate, ethylthiolate, ethylenethiolate, acetylenethiolate, benzenethiolate, and thiophenethiolate. It is found that these thiolates exhibit little difference in their stable adsorption geometries. They are adsorbed at the bridge site with being significantly tilted from the surface normal. The adsorption energy of thiolate on Au, on the other hand, largely varies depending on the type of tail molecule, and is linearly proportional to the binding energy of thiolate with H. We discuss the tail molecule dependence in terms of the bonding environment around the C atom connected to the head S atom.

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PubMed2004

Density functional theory investigation of benzenethiol adsorption on Au(111).

We have studied the adsorption of benzenethiol molecules on the Au(111) surface by using first principles total energy calculations. A single thiolate molecule is adsorbed at the bridge site slightly shifted toward the fcc-hollow site, and is tilted by 61 degrees from the surface normal. As for the self-assembled monolayer (SAM) structures, the (2 square root of 3 x square root of 3)R30 degrees herringbone structure is stabilized against the (square root 3 x square root 3)R30 degrees structure by large steric relaxation. In the most stable (2 square root 3 x square root 3)R30 degrees SAM structure, the molecule is adsorbed at the bridge site with the tilting angle of 21 degrees, which is much smaller compared with the single molecule adsorption. The van der Waals interaction plays an important role in forming the SAM structure. The adsorption of benzenethiolates induces the repulsive interaction between surface Au atoms, which facilitates the formation of surface Au vacancy.

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