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Physical Methods for Characterizing Solids
Published in Elaine A. Moore, Lesley E. Smart, Solid State Chemistry, 2020
The electron beam is produced by heating a tungsten filament, a lanthanum hexaboride, LaB6, crystal, or from a field emission gun, FEG, which uses a cathode of either tungsten or zirconium oxide. The beam is focused by magnetic coil magnets in a high vacuum (the vacuum prevents interaction of the beam with any extraneous particles) to a fine spot. Detection can be by scintillation counter, film, CCD, or monolithic active pixel sensors, also called CMOS (complementary metal–oxide–semiconductor) detectors. Through the most recent development of Cryo Electron Microscopy (Cryo EM), for which Dubochet, Frank, and Henderson were awarded the Nobel Prize in Chemistry 2017, resolution down to sub-nanometer levels can be achieved in the best instruments. The 3D structure of molecules (proteins, enzymes) of a molecular weight larger than 50,000 g/mol can be elucidated and thus, Cryo EM has become a true alternative to protein crystallography, mostly because there is no need to crystallise the compound.
Statistical Reconstruction and Heterogeneity Characterization in 3-D Biological Macromolecular Complexes
Published in Jeffrey P. Simmons, Lawrence F. Drummy, Charles A. Bouman, Marc De Graef, Statistical Methods for Materials Science, 2019
Recent success with 3-dimensional reconstructions of biological macromolecular particles employing single-particle cryo electron microscopy (cryo EM) has been remarkable. Subnanometer icosahedral virus structures are virtually routine and protein and nucleo-protein structures, without symmetry, are appearing more frequently at comparable resolution. Structures of icosahedral viruses at near-atomic resolution have been achieved with this technology in recent years [585, 43, 1200]. Cryo EM data captures biological macromolecular particles that are trapped in one of a smooth continuum of conformations at the moment of vitrification in liquid ethane. The amount of conformational change accessible to the particle is presumably space dependent, but there are limited tools available for assessing the global amount of conformational change let alone creating a spatial map of the amount of conformational change occurring. Heterogeneity among a set of particles can be detected by methods such as cross-common lines residuals [340]. In this chapter, maximum likelihood estimation is used not to estimate a single reconstruction or to find a homogeneous subset of particles but rather to estimate the statistics of an entire ensemble of reconstructions where the statistics of the images predicted by the statistics of the ensemble of reconstructions match the statistics of the experimental images.
Introduction and Pipelines
Published in Yongjie Jessica Zhang, Geometric Modeling and Mesh Generation from Scanned Images, 2018
There are many techniques and processes developed to create images, such as CT, MRI, nuclear medicine, ultrasound, and fluorescence for biomedical imaging. CT utilizes X-rays while MRI utilizes radio wave and magnetic field to scan objects. For both CT and MRI, the resulting images provide anatomy structure. Unlike CT and MRI, Nuclear Medicine injects radioactive source into the body, and then measures the radiation emitted from the body. The resulting images provide physiological functions of the object. Ultrasound utilizes high frequency sound waves in real time, generally 3~10 megahertz. Fluoroscopy uses a constant of X-rays, and it is also in real time. Cryo-EM (cryo-electron microscopy) is a popular scanning technique in structural biology to study small-scale objects like viruses at the level of Angstroms. In addition, people also scan metal materials. For example, electron backscatter diffraction (EBSD) is a microstructural-crystallographic technique used to examine the crystallographic orientation and elucidate texture or preferred orientation of polycrystalline materials. Instead of destroying the metal material like EBSD, high-energy X-ray is a nondestructive scanning technique to study polycrystalline materials. These various scanning techniques produce images for different types of objects. In some research areas like computer-aided design (CAD), people also use computational ways like signed distance function to compute volumetric imaging data. For biomolecules or proteins, people use the atomic resolution information to build electron density map and solve partial differential equations to obtain electron static potential distribution on regular grids.
Cluster formation of initiators as a tool to impose conformational stability to unstructured regions of a protein
Published in Molecular Physics, 2021
B. Lakshitha A. Perera, Coray M. Colina
Both previous experimental [19] and simulation [20–22] studies have highlighted the significance of determining the factors that could affect the subsequent polymer growth efficiency of initiators [23], but all these studies were focused on ATRP initiators attached to uniform solid surface supports [19,21,23], with a clear void of such studies performed on protein surfaces. In contrast to uniform solid surfaces, the protein surfaces possess additional complexities introduced by various amino acid compositions, their chemical properties, different secondary and tertiary structure features, and shapes. Therefore, studying the behaviour of initiators conjugated on to different protein surfaces/structures will prove beneficial to assess their ability to subsequently grow into polymers, and predict the possibility of forming different bio-conjugate products. It is known that in areas of high grafting density, not all conjugated initiators would equally facilitate the growth of polymers from them. This is often explained as a result of the steric hindrance imposed by the adjacently grown long polymer chains on the nearby grafting sites, hindering their ability to similarly grow into polymers [19–21,23]. Yet, there is no atomistic level information available to explain why some of the closely grafted initiators would start growing polymers faster than others, causing this issue and resulting in positional isomers and thus increasing dispersity between products. The importance of producing homogeneous bioconjugates has been continuously highlighted, as the heterogeneity of the created bioconjugates not only give rise to utilisation issues, but also hinders the applicability of certain characterisation techniques, such as X-ray crystallography, Cryo-Electron Microscopy, and light scatter techniques which are sensitive to the heterogeneity of the samples.