Atsushi Tokuhisa

Bio: Atsushi Tokuhisa is an academic researcher from Nara Institute of Science and Technology. The author has contributed to research in topics: Diffraction & Resolution (electron density). The author has an hindex of 6, co-authored 16 publications receiving 1413 citations.

A compact X-ray free-electron laser emitting in the sub-ångström region

Abstract: Researchers report sub-angstrom fundamental-wavelength lasing at the SPring-8 Angstrom Compact Free-Electron Laser in Japan. The output has a maximum power of more than 10 GW, a pulse duration of 10−14 s and a lasing wavelength of 0.634 A.

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.

Abstract: A new two-step algorithm is developed for reconstructing the three-dimensional diffraction intensity of a globular biological macromolecule from many experimentally measured quantum-noise-limited two-dimensional X-ray laser diffraction patterns, each for an unknown orientation. The first step is classification of the two-dimensional patterns into groups according to the similarity of direction of the incident X-rays with respect to the molecule and an averaging within each group to reduce the noise. The second step is detection of common intersecting circles between the signal-enhanced two-dimensional patterns to identify their mutual location in the three-dimensional wavenumber space. The newly developed algorithm enables one to detect a signal for classification in noisy experimental photon-count data with as low as ∼0.1 photons per effective pixel. The wavenumber of such a limiting pixel determines the attainable structural resolution. From this fact, the resolution limit due to the quantum noise attainable by this new method of analysis as well as two important experimental parameters, the number of two-dimensional patterns to be measured (the load for the detector) and the number of pairs of two-dimensional patterns to be analysed (the load for the computer), are derived as a function of the incident X-ray intensity and quantities characterizing the target molecule.

High-Precision Atomic Charge Prediction for Protein Systems Using Fragment Molecular Orbital Calculation and Machine Learning

Abstract: Here, we have constructed neural network-based models that predict atomic partial charges with high accuracy at low computational cost. The models were trained using high-quality data acquired from quantum mechanics calculations using the fragment molecular orbital method. We have succeeded in obtaining highly accurate atomic partial charges for three representative molecular systems of proteins, including one large biomolecule (approx. 2000 atoms). The novelty of our approach is the ability to take into account the electronic polarization in the system, which is a system-dependent phenomenon, being important in the field of drug design. Our high-precision models are useful for the prediction of atomic partial charges and expected to be widely applicable in structure-based drug designs such as structural optimization, high-speed and high-precision docking, and molecular dynamics calculations.

Non-gaussian behavior of elastic incoherent neutron scattering profiles of proteins studied by molecular dynamics simulation

Abstract: Elastic incoherent neutron scattering (EINS) data can be approximated with a Gaussian function of $q$ in a low $q$ region. However, in a higher $q$ region the deviation from a Gaussian function becomes non-negligible. Protein dynamic properties can be derived from the analyses of the non-Gaussian behavior, which has been experimentally investigated. To evaluate the origins of the non-Gaussian behavior of protein dynamics, we conducted a molecular dynamics (MD) simulation of staphylococcal nuclease. Instead of the ordinary cumulant expansion, we decomposed the non-Gaussian terms into three components: (i) the component originating from the heterogeneity of the mean-square fluctuation, (ii) that from the anisotropy, and (iii) that from higher-order terms such as anharmonicity. The MD simulation revealed various dynamics for each atom. The atomic motions are classified into three types: (i) ``harmonic,'' (ii) ``anisotropic,'' and (iii) ``anharmonic.'' However, each atom has a different degree of anisotropy. The contribution of the anisotropy to the total scattering function averages out due to these differences. Anharmonic motion is described as the jump among multiple minima. The jump distance and the probability of the residence at one site vary from atom to atom. Each anharmonic component oscillates between positive and negative values. Thus, the contribution of the anharmonicity to the total scattering is canceled due to the variations in the anharmonicity. Consequently, the non-Gaussian behavior of the total EINS from a protein can be analyzed by the dynamical heterogeneity.

Phase Retrieval with Application to Optical Imaging: A contemporary overview

Abstract: i»?The problem of phase retrieval, i.e., the recovery of a function given the magnitude of its Fourier transform, arises in various fields of science and engineering, including electron microscopy, crystallography, astronomy, and optical imaging. Exploring phase retrieval in optical settings, specifically when the light originates from a laser, is natural since optical detection devices [e.g., charge-coupled device (CCD) cameras, photosensitive films, and the human eye] cannot measure the phase of a light wave. This is because, generally, optical measurement devices that rely on converting photons to electrons (current) do not allow for direct recording of the phase: the electromagnetic field oscillates at rates of ~1015 Hz, which no electronic measurement device can follow. Indeed, optical measurement/detection systems measure the photon flux, which is proportional to the magnitude squared of the field, not the phase. Consequently, measuring the phase of optical waves (electromagnetic fields oscillating at 1015 Hz and higher) involves additional complexity, typically by requiring interference with another known field, in the process of holography.

Highly coherent and stable pulses from the FERMI seeded free-electron laser in the extreme ultraviolet

Abstract: Researchers demonstrate the FERMI free-electron laser operating in the high-gain harmonic generation regime, allowing high stability, transverse and longitudinal coherence and polarization control.

X-Rays and Extreme Ultraviolet Radiation: Principles and Applications

Abstract: This self-contained, comprehensive book describes the fundamental properties of soft x-rays and extreme ultraviolet (EUV) radiation and discusses their applications in a wide variety of fields, including EUV lithography for semiconductor chip manufacture and soft x-ray biomicroscopy. The author begins by presenting the relevant basic principles such as radiation and scattering, wave propagation, diffraction, and coherence. He then goes on to examine a broad range of phenomena and applications. The topics covered include EUV lithography, biomicroscopy, spectromicroscopy, EUV astronomy, synchrotron radiation, and soft x-ray lasers. He also provides a great deal of useful reference material such as electron binding energies, characteristic emission lines and photo-absorption cross-sections. The book will be of great interest to graduate students and researchers in engineering, physics, chemistry, and the life sciences. It will also appeal to practicing engineers involved in semiconductor fabrication and materials science.

DIALS: implementation and evaluation of a new integration package

Abstract: The DIALS project is a collaboration between Diamond Light Source, Lawrence Berkeley National Laboratory and CCP4 to develop a new software suite for the analysis of crystallographic X-ray diffraction data, initially encompassing spot finding, indexing, refinement and integration. The design, core algorithms and structure of the software are introduced, alongside results from the analysis of data from biological and chemical crystallography experiments.

Femtosecond x rays from laser-plasma accelerators

Abstract: Relativistic interaction of short-pulse lasers with underdense plasmas has recently led to the emergence of a novel generation of femtosecond x-ray sources. Based on radiation from electrons accelerated in plasma, these sources have the common properties to be compact and to deliver collimated, incoherent, and femtosecond radiation. In this article, within a unified formalism, the betatron radiation of trapped and accelerated electrons in the so-called bubble regime, the synchrotron radiation of laser-accelerated electrons in usual meter-scale undulators, the nonlinear Thomson scattering from relativistic electrons oscillating in an intense laser field, and the Thomson backscattered radiation of a laser beam by laser-accelerated electrons are reviewed. The underlying physics is presented using ideal models, the relevant parameters are defined, and analytical expressions providing the features of the sources are given. Numerical simulations and a summary of recent experimental results on the different mechanisms are also presented. Each section ends with the foreseen development of each scheme. Finally, one of the most promising applications of laser-plasma accelerators is discussed: the realization of a compact free-electron laser in the x-ray range of the spectrum. In the conclusion, the relevant parameters characterizing each sources are summarized. Considering typical laser-plasma interaction parameters obtained with currently available lasers, examples of the source features are given. The sources are then compared to each other in order to define their field of applications.