Takahiro Saitoh

A Three-Dimensional FRET Analysis to Construct an Atomic Model of the Actin-Tropomyosin-Troponin Core Domain Complex on a Muscle Thin Filament

It is essential to know the detailed structure of the thin filament to understand the regulation mechanism of striated muscle contraction. Fluorescence resonance energy transfer (FRET) was used to construct an atomic model of the actin-tropomyosin (Tm)-troponin (Tn) core domain complex. We generated single-cysteine mutants in the 167-195 region of Tm and in TnC, TnI, and the β-TnT 25-kDa fragment, and each was attached with an energy donor probe. An energy acceptor probe was located at actin Gln41, actin Cys374, or the actin nucleotide-binding site. From these donor-acceptor pairs, FRET efficiencies were determined with and without Ca(2+). Using the atomic coordinates for F-actin, Tm, and the Tn core domain, we searched all possible arrangements for Tm or the Tn core domain on F-actin to calculate the FRET efficiency for each donor-acceptor pair in each arrangement. By minimizing the squared sum of deviations for the calculated FRET efficiencies from the observed FRET efficiencies, we determined the location of Tm segment 167-195 and the Tn core domain on F-actin with and without Ca(2+). The bulk of the Tn core domain is located near actin subdomains 3 and 4. The central helix of TnC is nearly perpendicular to the F-actin axis, directing the N-terminal domain of TnC toward the actin outer domain. The C-terminal region in the I-T arm forms a four-helix-bundle structure with the Tm 175-185 region. After Ca(2+) release, the Tn core domain moves toward the actin outer domain and closer to the center of the F-actin axis.

Parallelized fast multipole BEM based on the convolution quadrature method for 3-D wave propagation problems in time-domain

This paper presents a new time-domain boundary element method (BEM) using a convolution quadrature method (CQM) and a fast multipole method (FMM) in 3-D scalar wave propagation. In general, the use of direct time-domain BEM sometimes causes the numerical instability of time-stepping solutions and needs much computational time and memory. To overcome these difficulties, in this paper, the convolution quadrature method developed by Lubich is applied to establish the stability behavior of the time-stepping scheme. Moreover, the fast multipole method and parallelization techniques are adapted to improve the computational efficiency for large size problems. The formulation and numerical implementation of the new boundary element method, and the basic formulas for the fast multipole method such as the multipole expansion, the local expansion, and the translation relations of them in the fast multipole algorithm are presented. The accuracy, the computational efficiency and the applicability are checked by solving 3-D large scale wave scattering problems.

A Three-Dimensional FRET Analysis to Construct an Atomic Model of the Actin–Tropomyosin Complex on a Reconstituted Thin Filament

Fluorescence resonance energy transfer (FRET) was used to construct an atomic model of the actin-tropomyosin (Tm) complex on a reconstituted thin filament. We generated five single-cysteine mutants in the 146-174 region of rabbit skeletal muscle α-Tm. An energy donor probe was attached to a single-cysteine Tm residue, while an energy acceptor probe was located in actin Gln41, actin Cys374, or the actin nucleotide binding site. From these donor-acceptor pairs, FRET efficiencies were determined with and without Ca(2+). Using the atomic coordinates for F-actin and Tm, we searched all possible arrangements for Tm segment 146-174 on F-actin to calculate the FRET efficiency for each donor-acceptor pair in each arrangement. By minimizing the squared sum of deviations for the calculated FRET efficiencies from the observed FRET efficiencies, we determined the location of the Tm segment on the F-actin filament. Furthermore, we generated a set of five single-cysteine mutants in each of the four Tm regions 41-69, 83-111, 216-244, and 252-279. Using the same procedures, we determined each segments location on the F-actin filament. In the best-fit model, Tm runs along actin residues 217-236, which were reported to compose the Tm binding site. Electrostatic, hydrogen-bonding, and hydrophobic interactions are involved in actin and Tm binding. The C-terminal region of Tm was observed to contact actin more closely than did the N-terminal region. Tm contacts more residues on actin without Ca(2+) than with it. Ca(2+)-induced changes on the actin-Tm contact surface strongly affect the F-actin structure, which is important for muscle regulation.

Application of Fast Multipole Boundary Element Method to Multiple Scattering Analysis of Acoustic and Elastic Waves

A fast multipole boundary element method (FMBEM) is developed for multiple scattering of 2‐D elastic and 3‐D acoustic waves. In the numerical calculation for 2‐D multiple scattering of elastic waves, reflection and transmission coefficients are obtained as a function of the wave number for the periodically distributed inclusions in the direction perpendicular to the incident wave propagation direction. In addition, numerical results for 3‐D multiple scattering of acoustic waves are demonstrated with considering the accuracy and computational efficiency of FMBEM.

3‐D Flaw Imaging by Inverse Scattering Analysis Using Ultrasonic Array Transducer

Ultrasonic matrix array transducers have the advantage of receiving flaw echoes simultaneously at various points on a flat surface of the test material. Here we propose 3‐D imaging techniques to reconstruct flaw shapes with the array transducer. These techniques are based on linearized inverse scattering methods in the frequency domain. The principal operation of these methods is the integration of the wave data in the K‐space. In this study, the 3‐D fast Fourier transform is introduced into the inversion algorithm to evaluate the integral in the K‐space. Performance of the 3‐D imaging technique is demonstrated by using the numerically calculated waveforms by the fast multipole BEM.

ACCELERATION OF THE 3D IMAGE-BASED FIT WITH AN EXPLICIT PARALLELIZATION APPROACH

Three dimensional (3D) image-based FIT has been proposed to predict ultrasonic wave in a target material with complex outer surfaces or various inclusions. In this study, we accelerate the 3D image-based FIT by means of some explicit parallelization techniques. By adopting flat MPI and MPI I/O techniques, our programming code can execute with a high speed and show good scalabilities in large size problems. Here we introduce a new image-based modeling that the target model can be made with a 3D curve measurement apparatus based on the light pattern projection method. The surface irregularities of the corroded part in a steel plate can be precisely modeled and the ultrasonic wave simulation for the corroded steel plate is demonstrated.

A boundary element method for wave scattering in fluid-saturated porous rocks

Wave analysis in rocks is widely used in earthquake engineering and geophysical exploration. Rocks under the ground include pores and cracks which are saturated with pore fluid. Waves which propagate in the rocks are affected by these cracks and pore fluid. Therefore, in the numerical simulation of the rocks, it is necessary to consider the effects of both anisotropy and pore fluid. Biot has been proposed as a mechanical model for describing the behavior of such a rock, and this model forms a foundation for wave analysis of general anisotropic fluid-saturated porous solids. This study aims to develop a boundary element method for wave scattering in general anisotropic fluid-saturated porous solids. Formulation is based on the following two kinds of boundary integral equations: one is those for displacement of the solid skeleton and the other is for fluid pressure. Green’s function for wave analysis in general anisotropic fluid-saturated porous solids is derived by using Radon and Fourier transforms in space. Some numerical examples show the validity of our proposed method.

Numerical Simulation of Nonlinear Ultrasonic Waves Due to Bi-material Interface Contact

Boundary integral equations are formulated to investigate nonlinear waves generated by a debonding interface of bi-material subjected to an incident plane wave. For the numerical simulation, the IRK (Implicit Runge-Kutta method) based CQ-BEM (Convolution Quadrature-Boundary Element Method) is developed. The interface conditions for a debonding area, consisting of three phases of separation, stick, and slip, are developed for the simulation of nonlinear ultrasonic waves. Numerical results are obtained and discussed for normal incidence of a plane longitudinal wave onto the nonlinear interface with a static compressive stress.

Simulation for air-coupled ultrasound testing using time-domain BEM

Air-coupled ultrasound testing is known as one of attractive non-contact ultrasonic NDE methods. However, the sensitivity of the air-coupled method greatly depends on the positioning of transducers, because the difference of acoustic impedance between air and solid is very large. In order to use this method for quantitative detection and evaluation of material flaws, it is necessary to simulate ultrasonic wave propagation and scattering in a solid. For a coupling problem between two media, in which ultrasonic waves travel at greatly different velocities, it is difficult to obtain stable solutions by means of a conventional time-domain boundary element method (BEM). A convolution quadrature time-domain fast multipole BEM (CQ-FMBEM) has been developed for the simulation of ultrasonic wave propagation and scattering in a solid. In the CQ-FMBEM, a convolution quadrature method (CQM) is introduced to make BEM solutions stable by evaluating a convolution integral in a very accurate numerical manner, while a fas...