Three-dimensional double helical DNA structure directly revealed from its X-ray fiber diffraction pattern by iterative phase retrieval

Coherent diffraction imaging (CDI) allows the retrieval of the structure of an isolated object, such as a macromolecule, from its diffraction pattern. CDI requires the fulfilment of two conditions: the imaging radiation must be coherent and the object must be isolated. We discuss that it is possible to directly retrieve the molecular structure from its diffraction pattern which was acquired neither with coherent radiation nor from an individual molecule, provided the molecule exhibits periodicity in one direction, as in the case of fiber diffraction. We demonstrate that by applying iterative phase retrieval methods to a fiber diffraction pattern, the repeating unit, that is, the molecule structure, can directly be reconstructed without any prior modeling. As an example, we recover the structure of the DNA double helix in three-dimensions from its two-dimensional X-ray fiber diffraction pattern, Photograph 51, acquired in the famous experiment by Raymond Gosling and Rosalind Franklin, at a resolution of 3.4 Angstrom

Practical algorithms for simulation and reconstruction of digital in-line holograms

Here we present practical methods for simulation and reconstruction of in-line digital holograms recorded with plane and spherical waves. The algorithms described here are applicable to holographic imaging of an object exhibiting absorption as well as phase shifting properties. Optimal parameters, related to distances, sampling rate, and other factors for successful simulation and reconstruction of holograms are evaluated and criteria for the achievable resolution are worked out. Moreover, we show that the numerical procedures for the reconstruction of holograms recorded with plane and spherical waves are identical under certain conditions. Experimental examples of holograms and their reconstructions are also discussed.Comment: including MATLAB code

Molecular particle-core model and its application to 13C-13C scattering

On the basis of the two-center shell model a theory is developed for the excitation of loosely bound nucleons in heavy ion collisions. These nucleons move in the two-center shell model potential generated by all the nucleons and are described by molecular wave functions. The model is applied to calculate the cross sections for the elastic and inelastic 13C-13C scattering. The cross sections show intermediate structures caused by the excitation of quasibound resonances in the molecular nucleus-nucleus potential. NUCLEAR REACTIONS 13C(13C,13C) molecular wave functions, dynamical two-center shell model, quasimolecular resonances, radial and Coriolis coupling, coupled channel calculations for σ(θ)

Imaging outside the box: Resolution enhancement in X-ray coherent diffraction imaging by extrapolation of diffraction patterns

Coherent diffraction imaging is a high-resolution imaging technique whose potential can be greatly enhanced by applying the extrapolation method presented here. We demonstrate enhancement in resolution of a non-periodical object reconstructed from an experimental X-ray diffraction record which contains about 10% missing information, including the pixels in the center of the diffraction pattern. A diffraction pattern is extrapolated beyond the detector area and as a result, the object is reconstructed at an enhanced resolution and better agreement with experimental amplitudes is achieved. The optimal parameters for the iterative routine and the limits of the extrapolation procedure are discussed.Comment: 12 pages, 4 figure

Resolution enhancement in in-line holography by numerical compensation of vibrations

Mechanical vibrations of components of the optical system is one of the sources of blurring of interference pattern in coherent imaging systems. The problem is especially important in holography where the resolution of the reconstructed objects depends on the effective size of the hologram, that is on the extent of the interference pattern, and on the contrast of the interference fringes. We discuss the mathematical relation between the vibrations, the hologram contrast and the reconstructed object. We show how vibrations can be post-filtered out from the hologram or from the reconstructed object assuming a Gaussian distribution of the vibrations. We also provide a numerical example of compensation for directional motion blur. We demonstrate our approach for light optical and electron holograms, acquired with both, plane- as well as spherical-waves. As a result of such hologram deblurring, the resolution of the reconstructed objects is enhanced by almost a factor of 2. We believe that our approach opens up a new venue of post-experimental resolution enhancement in in-line holography by adapting the rich database/catalogue of motion deblurring algorithms developed for photography and image restoration applications

Inverted Gabor holography principle for tailoring arbitrary shaped three-dimensional beams

It is well known that by modifying the wavefront in a certain manner, the light intensity can be turned into a certain shape. However, all known light modulation techniques allow for limited light modifications only: focusing within a restricted region in space, shaping into a certain class of parametric curves along the optical axis or bending described by a quadratic-dependent deflection as in the case of Airy beams. We show a general case of classical light wavefront shaping that allows for intensity and phase redistribution into an arbitrary profile including pre-determined switching-off of the intensity. To create an arbitrary three-dimensional path of intensity, we represent the path as a sequence of closely packed individual point-like absorbers and simulate the in-line hologram of the created object set; when such a hologram is contrast inverted, thus giving rise to a diffractor, it creates the pre-determined three-dimensional path of intensity behind the diffractor under illumination. The crucial parameter for a smooth optical path is the sampling of the predetermined curves, which is given by the lateral and axial resolution of the optical system. We provide both, simulated and experimental results to demonstrate the power of this novel method

Reconstruction of purely absorbing, absorbing and phase-shifting, and strong phase-shifting objects from their single-shot in-line holograms

We address the problem of reconstructing phase-shifting objects from their single shot in-line holograms. We show that a phase-shifting object cannot be reliably recovered from its in-line hologram by non-iterative reconstruction routines, and that an iterative reconstruction should be applied. We demonstrate examples of simulated in-line holograms of objects with the following properties: purely absorbing, both absorbing and phase shifting, and strong phase-shifting. We investigate the effects of noise and interference contrast in holograms on the reconstruction results and discuss details of an optimal iterative procedure to quantitatively recover the correct absorbing and phase-shifting properties of the object. We also review previously published reconstructions of experimental holograms and summarize the optimal parameters for retrieval of phase-shifting objects from their in-line holograms