scholarly journals Wavefront Modulation and Beam Shaping into Arbitrary Three-Dimensional Intensity Distributions

Photonics ◽  
2021 ◽  
Vol 8 (6) ◽  
pp. 179
Author(s):  
Tatiana Latychevskaia
Keyword(s):  
Three Dimensional ◽  
Beam Shaping ◽  
Intensity Modulation ◽  
Particle Trapping ◽  
X Ray ◽  
3D Structures ◽  
Spherical Waves

In this study the methods of three-dimensional (3D) wavefront intensity modulation by employing contrast-inverted holography, previously introduced as Gabor inverted holography, are further investigated. The present study provides the recipes for creating 3D wavefront intensity modulations using phase-only and amplitude-only modulators and compares the results. The 3D wavefront modulation using spherical waves is also demonstrated, and the miniaturization of 3D intensity beams is discussed; it is shown that both the resolution and the size of the created 3D structures are ultimately given by the wavelength of the employed radiation. The manuscript also addresses the quality of the formed 3D intensity curves and determines the parameters that provide the best smooth appearance of the 3D curves. The presented methods of 3D intensity wavefront modulation can be realized for all kinds of waves: light, X-ray, electron, etc, provided the modulator can be manufactured for the corresponding wavelength. The methods of 3D intensity wavefront modulation can be applied in various techniques: lithography, micro-robotics, particle trapping, etc.

ASSESSING THE QUALITY OF THE HOMOLOGY-MODELED 3D STRUCTURES FROM ELECTROSTATIC STANDPOINT: TEST ON BACTERIAL NUCLEOSIDE MONOPHOSPHATE KINASE FAMILIES

2007 ◽  
Vol 05 (03) ◽  
pp. 693-715 ◽  
Author(s):  
PETRAS KUNDROTAS ◽  
PAULINA GEORGIEVA ◽  
ALEXANDRA SHOSHEVA ◽  
PETYA CHRISTOVA ◽  
EMIL ALEXOV
Keyword(s):  
3D Structure ◽  
Three Dimensional ◽  
3D Models ◽  
Structural Defects ◽  
Large Protein ◽  
Homologous Proteins ◽  
X Ray ◽  
3D Structures ◽  
Large Sets

In this study, we address the issue of performing meaningful pKa calculations using homology modeled three-dimensional (3D) structures and analyze the possibility of using the calculated pKa values to detect structural defects in the models. For this purpose, the 3D structure of each member of five large protein families of a bacterial nucleoside monophosphate kinases (NMPK) have been modeled by means of homology-based approach. Further, we performed pKa calculations for the each model and for the template X-ray structures. Each bacterial NMPK family used in the study comprised on average 100 members providing a pool of sequences and 3D models large enough for reliable statistical analysis. It was shown that pKa values of titratable groups, which are highly conserved within a family, tend to be conserved among the models too. We demonstrated that homology modeled structures with sequence identity larger than 35% and gap percentile smaller than 10% can be used for meaningful pKa calculations. In addition, it was found that some highly conserved titratable groups either exhibit large pKa fluctuations among the models or have pKa values shifted by several pH units with respect to the pKa calculated for the X-ray structure. We demonstrated that such case usually indicates structural errors associated with the model. Thus, we argue that pKa calculations can be used for assessing the quality of the 3D models by monitoring fluctuations of the pKa values for highly conserved titratable residues within large sets of homologous proteins.

scholarly journals Three-dimensional propagation in near-field tomographic X-ray phase retrieval

2016 ◽  
Vol 72 (2) ◽  
pp. 215-221 ◽  
Author(s):  
Aike Ruhlandt ◽  
Tim Salditt
Keyword(s):  
Phase Retrieval ◽  
Near Field ◽  
Three Dimensional ◽  
Three Dimensions ◽  
Current Phase ◽  
Computationally Efficient ◽  
X Ray ◽  
Reconstruction Quality ◽  
Consistency Constraints

This paper presents an extension of phase retrieval algorithms for near-field X-ray (propagation) imaging to three dimensions, enhancing the quality of the reconstruction by exploiting previously unused three-dimensional consistency constraints. The approach is based on a novel three-dimensional propagator and is derived for the case of optically weak objects. It can be easily implemented in current phase retrieval architectures, is computationally efficient and reduces the need for restrictive prior assumptions, resulting in superior reconstruction quality.

A modified discrete tomography for improving the reconstruction of unknown multi-gray-level material in the `missing wedge' situation

2018 ◽  
Vol 25 (6) ◽  
pp. 1847-1859 ◽  
Author(s):  
Jianhong Liu ◽  
Zhiting Liang ◽  
Yong Guan ◽  
Wenbin Wei ◽  
Haobo Bai ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Iteration Process ◽  
Reconstruction Technique ◽  
Morphological Operations ◽  
Algebraic Reconstruction Technique ◽  
Discrete Tomography ◽  
Boundary Extraction ◽  
X Ray ◽  
Dimensional Reconstruction

Full angular rotational projections cannot always be acquired in tomographic reconstructions because of the limited space in the experimental setup, leading to the `missing wedge' situation. In this paper, a recovering `missing wedge' discrete algebraic reconstruction technique algorithm (rmwDART) has been proposed to solve the `missing wedge' problem and improve the quality of the three-dimensional reconstruction without prior knowledge of the material component's number or the material's values. By using oversegmentation, boundary extraction and mathematical morphological operations, `missing wedge' artifact areas can be located. Then, in the iteration process, by updating the located areas and regions, high-quality reconstructions can be obtained from the simulations, and the reconstructed images based on the rmwDART algorithm can be obtained from soft X-ray nano-computed tomography experiments. The results showed that there is the potential for discrete tomography.

Effect of X-ray CT resolution on the quality of permeability computation for granular soils: definition of a criterion based on morphological properties

Soil Research ◽  
2019 ◽  
Vol 57 (6) ◽  
pp. 589 ◽  
Author(s):  
Miriam Patricia Ortega Ramírez ◽  
Laurent Oxarango ◽  
Alfonso Gastelum Strozzi
Keyword(s):  
Volume Fraction ◽  
Three Dimensional ◽  
Flow Distribution ◽  
Reference Value ◽  
Image Resolution ◽  
Morphological Properties ◽  
Morphological Description ◽  
Granular Soils ◽  
X Ray

In this study, the quality of soil permeability estimation based on computational fluid dynamics is discussed. Two types of three-dimensional geometries were considered: an image of Fontainebleau sand obtained from X-ray computed micro-tomography and a virtual pack of spheres. Numerical methods such as finite difference or lattice Boltzmann can conveniently use the image voxels as computational mesh elements. In this framework, the image resolution is directly associated with quality of the numerical computation. A higher resolution should promote both a better morphological description and discretisation. However, increasing the resolution may prevent the studied volume from being representative. Here, each sample was scaled and analysed at five resolutions. The dependence of soil properties with respect to the image resolution is discussed. As resolution decreased, the permeability and specific surface values tended to diverge from the reference value. This deterioration could be attributed to the shift of the pore size distribution towards badly resolved pores in the voxelised geometry. As long as granular soils are investigated, the volume fraction of pores smaller than six voxels in diameter should not exceed 50% to ensure the validity of permeability computation. In addition, based on an analysis of flow distribution, the volume fraction of pores smaller than four voxels should not exceed 25% in order to limit the flow rate occurring in badly discretised pores under 10%. For the Fontainebleau sand and virtual pack of spheres, the maximum voxel size meeting this criterion corresponded to 1/14 and 1/20 of the mean grain size respectively.

scholarly journals Worldwide Protein Data Bank validation information: usage and trends

2018 ◽  
Vol 74 (3) ◽  
pp. 237-244 ◽  
Author(s):  
Oliver S. Smart ◽  
Vladimír Horský ◽  
Swanand Gore ◽  
Radka Svobodová Vařeková ◽  
Veronika Bendová ◽  
...  
Keyword(s):  
Protein Data Bank ◽  
Three Dimensional ◽  
Data Bank ◽  
Resonance Spectroscopy ◽  
X Ray ◽  
Validation Metrics ◽  
Task Forces ◽  
X Ray Crystallography ◽  
Structure Properties

Realising the importance of assessing the quality of the biomolecular structures deposited in the Protein Data Bank (PDB), the Worldwide Protein Data Bank (wwPDB) partners established Validation Task Forces to obtain advice on the methods and standards to be used to validate structures determined by X-ray crystallography, nuclear magnetic resonance spectroscopy and three-dimensional electron cryo-microscopy. The resulting wwPDB validation pipeline is an integral part of the wwPDB OneDep deposition, biocuration and validation system. The wwPDB Validation Service webserver (https://validate.wwpdb.org) can be used to perform checks prior to deposition. Here, it is shown how validation metrics can be combined to produce an overall score that allows the ranking of macromolecular structures and domains in search results. The ValTrendsDBdatabase provides users with a convenient way to access and analyse validation information and other properties of X-ray crystal structures in the PDB, including investigating trends in and correlations between different structure properties and validation metrics.

scholarly journals Reconstruction of crystal shapes by X-ray nanodiffraction from three-dimensional superlattices

2014 ◽  
Vol 47 (6) ◽  
pp. 2030-2037 ◽  
Author(s):  
Mojmír Meduňa ◽  
Claudiu V. Falub ◽  
Fabio Isa ◽  
Daniel Chrastina ◽  
Thomas Kreiliger ◽  
...  
Keyword(s):  
Structural Model ◽  
Three Dimensional ◽  
Three Dimensions ◽  
Semiconductor Layer ◽  
Dimensional Structure ◽  
Solid State Lasers ◽  
X Ray ◽  
Nondestructive Imaging ◽  
Low Dimensional

Quantitative nondestructive imaging of structural properties of semiconductor layer stacks at the nanoscale is essential for tailoring the device characteristics of many low-dimensional quantum structures, such as ultrafast transistors, solid state lasers and detectors. Here it is shown that scanning nanodiffraction of synchrotron X-ray radiation can unravel the three-dimensional structure of epitaxial crystals containing a periodic superlattice underneath their faceted surface. By mapping reciprocal space in all three dimensions, the superlattice period is determined across the various crystal facets and the very high crystalline quality of the structures is demonstrated. It is shown that the presence of the superlattice allows the reconstruction of the crystal shape without the need of any structural model.

scholarly journals Real-space quantum-based refinement for cryo-EM: Q|R#3

2020 ◽  
Vol 76 (12) ◽  
pp. 1184-1191
Author(s):  
Lum Wang ◽  
Holger Kruse ◽  
Oleg V. Sobolev ◽  
Nigel W. Moriarty ◽  
Mark P. Waller ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Real Space ◽  
Average Quality ◽  
X Ray ◽  
X Ray Crystallography ◽  
Large Structures ◽  
Model Geometry ◽  
Technological Improvements ◽  
Semi Empirical

Electron cryo-microscopy (cryo-EM) is rapidly becoming a major competitor to X-ray crystallography, especially for large structures that are difficult or impossible to crystallize. While recent spectacular technological improvements have led to significantly higher resolution three-dimensional reconstructions, the average quality of cryo-EM maps is still at the low-resolution end of the range compared with crystallography. A long-standing challenge for atomic model refinement has been the production of stereochemically meaningful models for this resolution regime. Here, it is demonstrated that including accurate model geometry restraints derived from ab initio quantum-chemical calculations (HF-D3/6-31G) can improve the refinement of an example structure (chain A of PDB entry 3j63). The robustness of the procedure is tested for additional structures with up to 7000 atoms (PDB entry 3a5x and chain C of PDB entry 5fn5) using the less expensive semi-empirical (GFN1-xTB) model. The necessary algorithms enabling real-space quantum refinement have been implemented in the latest version of qr.refine and are described here.

Single-crystal x-ray diffraction structures of covalent organic frameworks

Science ◽  
2018 ◽  
Vol 361 (6397) ◽  
pp. 48-52 ◽  
Author(s):  
Tianqiong Ma ◽  
Eugene A. Kapustin ◽  
Shawn X. Yin ◽  
Lin Liang ◽  
Zhengyang Zhou ◽  
...  
Keyword(s):  
Single Crystal ◽  
Single Crystals ◽  
Diffraction Data ◽  
General Procedure ◽  
Three Dimensional ◽  
Electron Diffraction Data ◽  
Covalent Organic Frameworks ◽  
X Ray Diffraction ◽  
X Ray

The crystallization problem is an outstanding challenge in the chemistry of porous covalent organic frameworks (COFs). Their structural characterization has been limited to modeling and solutions based on powder x-ray or electron diffraction data. Single crystals of COFs amenable to x-ray diffraction characterization have not been reported. Here, we developed a general procedure to grow large single crystals of three-dimensional imine-based COFs (COF-300, hydrated form of COF-300, COF-303, LZU-79, and LZU-111). The high quality of the crystals allowed collection of single-crystal x-ray diffraction data of up to 0.83-angstrom resolution, leading to unambiguous solution and precise anisotropic refinement. Characteristics such as degree of interpenetration, arrangement of water guests, the reversed imine connectivity, linker disorder, and uncommon topology were deciphered with atomic precision—aspects impossible to determine without single crystals.

A discrete tomography algorithm for improving the quality of three-dimensional X-ray diffraction grain maps

2006 ◽  
Vol 39 (4) ◽  
pp. 582-588 ◽  
Author(s):  
A. Alpers ◽  
H. F. Poulsen ◽  
E. Knudsen ◽  
G. T. Herman
Keyword(s):  
Monte Carlo ◽  
Diffraction Data ◽  
Three Dimensional ◽  
Simulation Studies ◽  
Discrete Structure ◽  
X Ray Diffraction ◽  
Discrete Tomography ◽  
X Ray ◽  
Restoration Method

A discrete tomography algorithm is presented for the reconstruction of grain maps based on X-ray diffraction data. This is the first algorithm for this task, inherently exploiting the discrete structure of grain maps. Gibbs potentials serve to characterize the statistics of the local morphology of the grain boundaries. A Monte Carlo based algorithm is applied as a restoration method for improving the quality of grain maps produced by a classical (non-discrete) tomography algorithm (ART). The quality of the restored maps is demonstrated and quantified by simulation studies. The robustness of the algorithm with respect to the choice of Gibbs potentials is investigated.

Three Dimensional Characterization of Grain Structures by EBSP and 3DXRD

2007 ◽  
Vol 558-559 ◽  
pp. 751-756 ◽  
Author(s):  
Kristofer Hannesson ◽  
Dorte Juul Jensen
Keyword(s):  
Three Dimensional ◽  
Polycrystalline Materials ◽  
Serial Sectioning ◽  
X Ray Diffraction ◽  
X Ray ◽  
3D Structures ◽  
3 Dimensional ◽  
Grain Structures ◽  
Non Destructive

Grain structures in polycrystalline materials are typically three dimensional (3D) structures, but by far the most characterizations of grain structures are done by microscopy and are thus limited to 2D. In the present work 3D grain structures in a well-annealed cylindrical aluminium (AA1050) sample is characterized and analyzed. The characterization is done by 2 methods i) by non-destructive 3-dimensional x-ray diffraction (3DXRD) ii) by serial sectioning and subsequent EBSP mapping of entire circular 2D sample sections; 50 sections are mapped In total 333 grains are reconstructed. It is found that the 3D grain morphologies can be quite complex in particular for the larger grains, the number of neighbours varies significantly and values above 20 are not unusual. When the results from the 2 methods are compared, it is found that the crystallographic agreement is very good and within experimental uncertainties. Slightly more significant differences are found when the reconstructed grain morphologies are compared. Reasons for this are discussed.

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