Atsushi Tokuhisa

Classifying and assembling two-dimensional X-ray laser diffraction patterns of a single particle to reconstruct the three-dimensional diffraction intensity function: resolution limit due to the quantum noise

A new algorithm is developed for reconstructing the high-resolution three-dimensional diffraction intensity function of a globular biological macromolecule from many quantum-noise-limited two-dimensional X-ray laser diffraction patterns, each for an unknown orientation. The structural resolution is expressed as a function of the incident X-ray intensity and quantities characterizing the target molecule.

High‐speed classification of coherent X‐ray diffraction patterns on the K computer for high‐resolution single biomolecule imaging

A code with an algorithm for high-speed classification of X-ray diffraction patterns has been developed. Results obtained for a set of 1 × 106 simulated diffraction patterns are also reported.

Calculation of Molecular-Structure-Based Damage Caused by Short-Pulse High-Intensity X-ray Lasers

We developed a molecular-structure-based simulation to calculate the time dependence of damage caused to a single biomolecule by irradiation through short, high-intensity X-ray pulses. We consider the atomic processes of photoionization, Compton scattering, Auger decay, and electric-field ionization. The latter has yet to be included in simulations based on molecular structure. In the present study we use the small protein lysozyme as a target and calculate the average number of electrons bound to the atoms or ions of the protein molecule. The protein undergoes Coulomb explosion when exposed to a 5 fs pulse with photon energy of 12.4 keV. The atoms or ions of the protein are ionized by electric-field ionization when the incident X-ray-pulse intensity exceeds \(10^{20}\) photons/mm2, and Coulomb explosion of the protein at the peak intensity of the X-ray pulse is caused by strong generation of photoelectrons at incident X-ray intensities near \(10^{21}\) photons/mm2. We found that the upper limit of incide...

Intensity of Diffracted X-rays from Biomolecules with Radiation Damage Caused by Strong X-ray Pulses

In order to realize the coherent X-ray diffractive imaging of single biomolecules, the diffraction intensities, per effective pixel of a single biomolecule with radiation damage, caused by irradiation using a strong coherent X-ray pulse, were examined. A parameter survey was carried out for various experimental conditions, using a developed simulation program that considers the effect of electric field ionization, which was slightly reported on in previous studies. The two simple relationships among the parameters were identified as follows: (i) the diffraction intensity of a biomolecule slightly increases with the incident X-ray energy; and that (ii) the diffraction intensity is approximately proportional to the target radius, when the radius is longer than 400 A, since the upper limit of the incident intensity for damage to the biomolecules marginally changes with respect to the target radius.