A5090856594- Enzyme Structure and Function
- Advanced Electron Microscopy Techniques and Applications
- X-ray Diffraction in Crystallography
- Advanced Radiotherapy Techniques
- Advanced X-ray Imaging Techniques
- Optical Coherence Tomography Applications
- Microfluidic and Capillary Electrophoresis Applications
- Biosensors and Analytical Detection
- Electron and X-Ray Spectroscopy Techniques
- Medical Imaging Techniques and Applications
- Protein Structure and Dynamics
- Ion-surface interactions and analysis
- Magnetic and Electromagnetic Effects
- Advanced X-ray and CT Imaging
- Advanced Optical Sensing Technologies
- Optical Systems and Laser Technology
- Freezing and Crystallization Processes
- Machine Learning in Materials Science
- Optical measurement and interference techniques
- Crystallization and Solubility Studies
- Photoacoustic and Ultrasonic Imaging
- Biochemical and Molecular Research
- Advanced Proteomics Techniques and Applications
- Erythrocyte Function and Pathophysiology
- Advanced Fluorescence Microscopy Techniques
Diamond Light Source
2013-2024
Rosalind Franklin Institute
2021-2024
MRC Laboratory of Molecular Biology
2016-2020
Didcot Community Hospital
2019
The Christie NHS Foundation Trust
2009-2013
Rutherford Appleton Laboratory
2013
The DIALS project is a collaboration between Diamond Light Source, Lawrence Berkeley National Laboratory and CCP4 to develop new software suite for the analysis of crystallographic X-ray diffraction data, initially encompassing spot finding, indexing, refinement integration. design, core algorithms structure are introduced, alongside results from data biological chemical crystallography experiments.
The Collaborative Computational Project No. 4 (CCP4) is a UK-led international collective with mission to develop, test, distribute and promote software for macromolecular crystallography. CCP suite multiplatform collection of programs brought together by familiar execution routines, set common libraries graphical interfaces. has experienced several considerable changes since its last reference article, involving new infrastructure, original This which intended as general literature citation...
Rapid data collection and modern computing resources provide the opportunity to revisit task of optimizing model diffraction geometry prior integration. A comprehensive description is given new software that builds upon established methods by performing a single global refinement procedure, utilizing smoothly varying crystal lattice where appropriate. This technique extends multiple sets, providing useful constraints handle problem correlated parameters, particularly for small wedges data....
In processing X-ray diffraction data, the intensities obtained from integration of images must be corrected for experimental effects in order to place all on a common scale both within and between data collections. Scaling corrects such as changes sample illumination, absorption and, some extent, global radiation damage that cause measured symmetry-equivalent observations differ throughout set. This necessarily requires prior evaluation point-group symmetry crystal. paper describes evaluates...
Electron diffraction is a relatively novel alternative to X-ray crystallography for the structure determination of macromolecules from three-dimensional nanometre-sized crystals. The continuous-rotation method data collection has been adapted electron microscope. However, there are important differences in geometry that must be considered successful integration. wavelength electrons TEM typically around 40 times shorter than X-rays, implying nearly flat Ewald sphere, and consequently low...
The DIALS diffraction-modeling software package has been applied to serial crystallography data. Diffraction modeling is an exercise in determining the experimental parameters, such as incident beam wavelength, crystal unit cell and orientation, detector geometry, that are most consistent with observed positions of Bragg spots. These parameters can be refined by nonlinear least-squares fitting. In previous work, it challenging refine both sensors (metrology) on multipanel imaging detectors...
A new indexing method is presented which capable of multiple crystal lattices from narrow wedges diffraction data. The takes advantage a simplification Fourier transform-based methods that applicable when the unit-cell dimensions are known priori. efficacy this demonstrated with both semi-synthetic multi-lattice data and real recorded crystals ∼1 µm in size, where it shown up to six can be successfully indexed subsequently integrated 1° wedge Analysis shows improvements data-quality...
Phase reconstruction is important in transmission electron microscopy for structural studies. We describe Fourier ptychography and its application to phase of both radiation-resistant beam-sensitive materials. demonstrate that the exit wave can be reconstructed at high resolution using a modified iterative retrieval algorithm with data collected an alternative optical geometry. This method achieves spatial 0.63 nm fluence $4.5 \times 10^2 \, e^-/\text{nm}^2$, as validated on Cry11Aa protein...
A method for estimating the background under each reflection during integration that is robust in presence of pixel outliers presented. The uses a generalized linear model approach more appropriate use with Poisson distributed data than traditional approaches to outlier handling programs. algorithm most applicable very low level where assumptions normal distribution are no longer valid as an approximation distribution. It shown methods can result systematic underestimation values. This then...
Data formats for recording X-ray diffraction data continue to evolve rapidly accommodate new detector technologies developed in response more intense light sources. Processing the from single-crystal experiments therefore requires ability read, and correctly interpret, image metadata a variety of instruments employing different experimental representations. Tools that have previously been address this problem limited either by lack extensibility or inconsistent treatment metadata. The dxtbx...
MicroED has recently emerged as a powerful method for the analysis of biological structures at atomic resolution. This technique been largely limited to protein nanocrystals which grow either needles or plates measuring only few hundred nanometers in thickness. Furthermore, traditional microED data processing uses established X-ray crystallography software that is not optimized handling compound effects are unique electron diffraction data. Here, we present an integrated workflow microED,...
Three-dimensional electron diffraction (3DED) from nanocrystals of biological macromolecules requires the use very small crystals. These are typically less than 300 nm-thick in direction beam due to strong interaction between electrons and matter. In recent years, focused-ion-beam (FIB) milling has been used preparation thin samples for 3DED. instruments a gallium liquid metal ion source. Inductively coupled plasma (ICP) sources principle offer faster rates. Little work done quantify damage...
Optical measurements are increasingly used in radiotherapy. In this paper we present, detail, the design and implementation of a multi-channel optical system optimized for fast, high spatial resolution, dynamic body surface measurement guided therapy. We include all algorithmic modifications calibration procedures required to create robust, practical clinical use. Comprehensive static phantom validation radiotherapy treatment room show: conformance with simultaneously measured cone beam CT...
In this paper, AUSPEX , a new software tool for experimental X-ray data analysis, is presented. Exploring the behaviour of diffraction intensities and associated estimated uncertainties facilitates discovery underlying problems can help users to improve their acquisition processing in order obtain better structural models. The program enables inspect distribution observed (or amplitudes) against resolution as well (sigmas). It demonstrated how be used visually automatically detect ice-ring...
An evaluation of the suitability eight existing phase unwrapping algorithms to be used in a real-time optical body surface sensor based on Fourier fringe profilometry is presented. The are assessed both robustness results they give and their speed execution. evaluated using four sets real human data, each containing five-hundred frames, obtained from patients undergoing radiotherapy, where discontinuity significant. We also present modifications an algorithm, noncontinuous quality-guided...
For cryo-electron tomography (cryo-ET) of beam-sensitive biological specimens, a planar sample geometry is typically used. As the tilted, effective thickness along direction electron beam increases and signal-to-noise ratio concomitantly decreases, limiting transfer information at high tilt angles. In addition, range where data can be collected limited by combination various sample-environment constraints, including space in objective lens pole piece possible use fixed conductive braids to...
An algorithm for modelling the background each Bragg reflection in a series of X-ray diffraction images containing Debye–Scherrer from ice sample is presented. The method involves use global model which generated complete data set. Fitting this to pixels then performed independently. uses static that does not vary over course scan. greatest improvement can be expected where rings are present throughout set and local shape at size spot on detector exhibit large time-dependent variation....
Conformational heterogeneity of biological macromolecules is a challenge in single-particle averaging (SPA). Current standard practice to employ classification and filtering methods that may allow discrete number conformational states be reconstructed. However, the conformation space accessible these molecules continuous and, therefore, explored incompletely by small classes. Recently developed heterogeneous reconstruction algorithms (HRAs) analyse rely on machine-learning low-dimensional...
In cryo-electron tomography (cryo-ET) of biological samples, the quality tomographic reconstructions can vary depending on transmission electron microscope (TEM) instrument and data acquisition parameters. this paper, we present Parakeet, a ‘digital twin’ software pipeline for assessment impact various TEM experiment parameters three-dimensional reconstructions. The Parakeet digital twin is model that be used to optimize performance utilization physical enable in silico optimization sample...
Patient motion is an important factor affecting the quality of external beam radiotherapy in breast patients. We analyse a dense set surface points on patients throughout their treatment schedule to assess magnitude and stability motion, particular, with respect volume. use optical sensor measure 13 cancer Patients were divided into two cohorts dependent upon Measurements made during delivery for average 12 fractions per patient (total 158 datasets). The each point parameterized terms its...
Simulations of cryo-electron microscopy (cryo-EM) images biological samples can be used to produce test datasets support the development instrumentation, methods, and software, as well assess data acquisition analysis strategies. To useful, these simulations need based on physically realistic models which include large volumes amorphous ice. The gold standard model for EM image simulation is a physical atom-based ice produced using molecular dynamics simulations. Although practical small...
This study describes a method to estimate the likelihood of success in determining macromolecular structure by X-ray crystallography and experimental single-wavelength anomalous dispersion (SAD) or multiple-wavelength (MAD) phasing based on initial data-processing statistics sample crystal properties. Such predictive tool can rapidly assess usefulness data guide collection an optimal set. The increase rates from modern beamlines, together with demand users for real-time feedback, has led...
In image guided radiotherapy (IGRT) two of the most promising recent developments are four dimensional cone beam CT (4D CBCT) and dynamic optical metrology patient surfaces. 4D CBCT is now becoming commercially available finds use in treatment planning verification, whilst monitoring a young technology, its ability to measure during delivery without dose consequences has led uptake many institutes. this paper, we demonstrate surfaces, simultaneously captured acquisition using an sensor,...