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Angus I. Kirkland

Publications and source records attributed to Angus I. Kirkland.

At least 19 recordsLinked to original sources

Updated all-electron Dirac--Fock densities and an element-adaptive parameterisation of scattering factors and potentials for neutral atoms

Updated reference data and an analytic parameterisation of elastic electron and X-ray scattering are presented for all 118 neutral atoms. The reference electron densities for the multi-electron elements $Z=2$--$118$ are computed with the relativistic B-spline Dirac--Fock code atomx, while hydrogen is constructed from the exact relativistic one-electron Dirac $1s$ solution; the electron scattering factor $f_e(g)$, X-ray scattering factor $f_x(g)$ and radial moments are derived from these densities. The reported parameterisation extends the fixed-size Lobato--Van Dyck hydrogenic expansion while retaining closed-form expressions for $f_x(g)$, $ρ(r)$, the electrostatic potential $V(r)$ and the projected potential $V(R)$. These extensions are an element-adaptive basis size $n_t(Z)$, a simultaneous real- and reciprocal-space fit, an exact $\langle r^4\rangle$ constraint in place of the non-relativistic Kato cusp, and a charge-carrying Dirac--Padé basis term that adds a polynomial-times-exponential shape channel without replacing the hydrogenic basis by a tabulated Dirac radial function or assigning the term to a physical shell. For the same total parameter count, the Dirac--Padé-enriched basis improves on the parameter-matched non-relativistic basis for 111 of the 118 elements, lowering the mean total cost by 39\%. Relative to a controlled fixed five-term refit on the same reference grid and objective, the element-adaptive bases improve the median reciprocal-space deviations by about three to four orders of magnitude and resolve shell structure in $4πr^2ρ(r)$ that the fixed five-term basis cannot. The largest changes occur near the nucleus and in the reciprocal-space tail beyond the legacy 12 inverse angstroms range, which is directly relevant to quantitative high-angle scattering and electron-diffraction measurements.

physics.comp-ph

Detective Quantum Efficiency of the Timepix4 Hybrid Pixel Detector and its Application to Parallel-Beam Diffraction

The detective quantum efficiency (DQE) and normalised noise power spectrum (NNPS) of the Timepix4 hybrid pixel detector in event-driven mode in TEM have been measured at 100 kV and 200 kV. In a raw data readout mode, the zero-frequency DQE exceeds 0.9 at both 100 kV and 200 kV. At the Nyquist frequency, the DQE remains above 0.2 at 100 kV but drops close to zero at 200 kV. Initial parallel-beam diffraction data from a polycrystalline gold nanoparticle sample is reported which shows that at 200 kV Timepix4 can detect weak diffracted information beyond a 75 mrad half-angle.

physics.ins-det

Physics-Informed 3D Atomic Reconstruction and Dynamics of Free-Standing Graphene from Single Low-Dose TEM Images

Resolving the three-dimensional (3D) atomic geometry of free-standing graphene in real time is essential for understanding how intrinsic rippling governs its electronic properties. However, the low electron doses required to mitigate radiation damage impose severe signal-to-noise constraints that limit conventional reconstruction methods. Here, we present a physics-informed computational framework that reconstructs 3D atomic coordinates of single-layer graphene from individual low-dose transmission electron microscopy (TEM) frames (8x10^3 e-/Ang^2, 1 ms temporal resolution). The approach combines simulated annealing optimisation with molecular dynamics regularisation, achieving sub-angstrom out-of-plane accuracy (sigma_z < 0.45 Ang), validated against ground-truth simulations. A Kullback-Leibler divergence-based calibration aligns the forward model with experimental image statistics, reducing systematic bias. Applied to high-speed time-series data, the framework enables simultaneous extraction of real-time ripple dynamics, strain tensors, surface curvature, bond-length distributions, and density functional theory (DFT)-derived electron localisation functions (ELF). We establish quantitative relationships linking local geometry, strain, and bond-length variations to electron localisation, demonstrating that sub-angstrom structural fluctuations drive spatially localised, millisecond-scale electronic modulation. A critical dose threshold is identified below which structural information becomes irrecoverable, providing practical guidance for experimental design. The framework is broadly applicable to beam-sensitive two-dimensional materials.

cond-mat.mtrl-sci

Detective quantum efficiency based comparison of HRTEM and ptychography phase imaging

High-resolution transmission electron microscopy (HRTEM) is an important method for imaging beam sensitive materials often under cryo conditions. Electron ptychography in the scanning transmission electron microscope (STEM) has been shown to reconstruct low-noise phase data at a reduced fluence for such materials. This raises the question of whether ptychography or HRTEM provides a more fluence-efficient imaging technique. Even though the transfer function is a common metric for evaluating the performance of an imaging method, it only describes the signal transfer with respect to spatial frequency, irrespective of the noise transfer. It can also not be well defined for methods, such as ptychography, that use an algorithm to form the final image. Here we apply the concept of detective quantum efficiency (DQE) to electron microscopy as a fluence independent and sample independent measure of technique performance. We find that, for a weak-phase object, ptychography can never reach the efficiency of a perfect Zernike phase imaging microscope but that ptychography is more robust to partial coherence.

cond-mat.mtrl-sci

Electron Fourier ptychography for phase reconstruction

Phase reconstruction is important in transmission electron microscopy for structural studies. We describe electron Fourier ptychography and its application to phase reconstruction of both radiation-resistant and beam-sensitive materials. We demonstrate that the phase of the exit wave can be reconstructed to high resolution using a modified iterative phase retrieval algorithm using data collected in an alternative optical geometry. This method achieves a spatial resolution of 0.63 nm at a fluence of $4.5 \times 10^2 \, e^-/\text{nm}^2$, as validated on Cry11Aa protein crystals under cryogenic conditions. Notably, this method requires no additional hardware modifications, is straightforward to implement, and can be seamlessly integrated with existing data collection software, providing a broadly accessible alternative approach to structural studies.

physics.app-ph

Fast Simulation of Damage Diffusion Distribution in Scanning Transmission Electron Microscopy

Scanning Transmission Electron Microscopy (STEM) is a critical tool for imaging the properties of materials and biological specimens at atomic scale, yet our understanding of relevant electron beam damage mechanisms is incomplete. Recent studies suggest that certain types of damage can be modelled as a diffusion process. However, numerical simulation of such diffusion processes has remained computationally intensive. This work introduces a high-performance C++ framework for simulating damage diffusion process in STEM that combines efficient numerical computation, advanced visualisations, and multithreading to achieve efficient runtime while maintaining accuracy.

eess.SP

On Overlap Ratio in Defocused Electron Ptychography

Four-dimensional Scanning Transmission Electron Microscopy (4D STEM) with data acquired using a defocused electron probe is a promising tool for characterising complex biological specimens and materials through a phase retrieval process known as Electron Ptychography (EP). The efficacy of 4D STEM acquisition and the resulting quality of EP reconstruction depends on the overlap ratio of adjacent illuminated areas. This paper demonstrates how the overlap ratio impacts the data redundancy and the quality of the EP reconstruction. We define two quantities as a function of the overlap ratio that are independent of both the object and the EP algorithm. Subsequently, we evaluate an EP algorithm for varying overlap ratios using simulated 4D STEM datasets. Notably, a 40% or greater overlap ratio yields stable, high-quality reconstructions.

eess.SP

LoRePIE: $\ell_0$ Regularised Extended Ptychographical Iterative Engine for Low-dose and Fast Electron Ptychography

The extended Ptychographical Iterative Engine (ePIE) is a widely used phase retrieval algorithm for Electron Ptychography from 4-dimensional (4-D) Scanning Transmission Electron Microscopy (4-D STEM) measurements acquired with a focused or defocused electron probe. However, ePIE relies on redundancy in the data and hence requires adjacent illuminated areas to overlap. In this paper, we propose a regularised variant of ePIE that is more robust to low overlap ratios. We examine the performance of the proposed algorithm on an experimental 4-D STEM data of double layered Rotavirus particles acquired in a full scan with 85% overlap. By artificial down-sampling of the probe positions, we have created synthetic 4-D STEM datasets with different overlap ratios and use these to show that a high quality reconstruction of Rotavirus particles can be obtained from data with an overlap as low as 56%.

physics.app-ph

Compressive Electron Backscatter Diffraction Imaging

Electron backscatter diffraction (EBSD) has developed over the last few decades into a valuable crystallographic characterisation method for a wide range of sample types. Despite these advances, issues such as the complexity of sample preparation, relatively slow acquisition, and damage in beam-sensitive samples, still limit the quantity and quality of interpretable data that can be obtained. To mitigate these issues, here we propose a method based on the subsampling of probe positions and subsequent reconstruction of an incomplete dataset. The missing probe locations (or pixels in the image) are recovered via an inpainting process using a dictionary-learning based method called beta-process factor analysis (BPFA). To investigate the robustness of both our inpainting method and Hough-based indexing, we simulate subsampled and noisy EBSD datasets from a real fully sampled Ni-superalloy dataset for different subsampling ratios of probe positions using both Gaussian and Poisson noise models. We find that zero solution pixel detection (inpainting un-indexed pixels) enables higher quality reconstructions to be obtained. Numerical tests confirm high quality reconstruction of band contrast and inverse pole figure maps from only 10% of the probe positions, with the potential to reduce this to 5% if only inverse pole figure maps are needed. These results show the potential application of this method in EBSD, allowing for faster analysis and extending the use of this technique to beam sensitive materials.

eess.IV

Diffusion Distribution Model for Damage Mitigation in Scanning Transmission Electron Microscopy

Despite the widespread use of Scanning Transmission Electron Microscopy (STEM) for observing the structure of materials at the atomic scale, a detailed understanding of some relevant electron beam damage mechanisms is limited. Recent reports suggest that certain types of damage can be modeled as a diffusion process and that the accumulation effects of this process must be kept low in order to reduce damage. We therefore develop an explicit mathematical formulation of spatiotemporal diffusion processes in STEM that take into account both instrument and sample parameters. Furthermore, our framework can aid the design of Diffusion Controlled Sampling (DCS) strategies using optimally selected probe positions in STEM, that constrain the cumulative diffusion distribution. Numerical simulations highlight the variability of the cumulative diffusion distribution for different experimental STEM configurations. These analytical and numerical frameworks can subsequently be used for careful design of 2- and 4-dimensional STEM experiments where beam damage is minimised.

cond-mat.mtrl-sci

Calibrating coordinate system alignment in a scanning transmission electron microscope using a digital twin

In four-dimensional scanning transmission electron microscopy (4D STEM) a focused beam is scanned over a specimen and a diffraction pattern is recorded at each position using a pixelated detector. During the experiment, it must be ensured that the scan coordinate system of the beam is correctly calibrated relative to the detector coordinate system. Various simplified and approximate models are used implicitly and explicitly for understanding and analyzing the recorded data, requiring translation between the physical reality of the instrument and the abstractions used in data interpretation. Here, we introduce a calibration method where interactive live data processing in combination with a digital twin is used to match a set of models and their parameters with the action of a real-world instrument.

physics.ins-det

Simultaneous High-Speed and Low-Dose 4-D STEM Using Compressive Sensing Techniques

Here we show that compressive sensing allow 4-dimensional (4-D) STEM data to be obtained and accurately reconstructed with both high-speed and low fluence. The methodology needed to achieve these results compared to conventional 4-D approaches requires only that a random subset of probe locations is acquired from the typical regular scanning grid, which immediately generates both higher speed and the lower fluence experimentally. We also consider downsampling of the detector, showing that oversampling is inherent within convergent beam electron diffraction (CBED) patterns, and that detector downsampling does not reduce precision but allows faster experimental data acquisition. Analysis of an experimental atomic resolution yttrium silicide data-set shows that it is possible to recover over 25dB peak signal-to-noise in the recovered phase using 0.3% of the total data.

cond-mat.mtrl-sci

The Potential of Subsampling and Inpainting for Fast Low-Dose Cryo FIB-SEM Imaging and Tomography

Traditional image acquisition for cryo focused ion-beam scanning electron microscopy tomography often sees thousands of images being captured over a period of many hours, with immense data sets being produced. When imaging beam sensitive materials, these images are often compromised by additional constraints related to beam damage and the devitrification of the material during imaging, which renders data acquisition both costly and unreliable. Subsampling and inpainting are proposed as solutions for both of these aspects, allowing fast and low-dose imaging to take place in the FIB-SEM without an appreciable low in image quality. In this work, experimental data is presented which validates subsampling and inpainting as a useful tool for convenient and reliable data acquisition in a FIB-SEM, with new methods of handling 3-dimensional data being employed in context of dictionary learning and inpainting algorithms using a newly developed microscope control software and data recovery algorithm.

physics.med-ph

Cryo-Electron Ptychography: Applications and Potential in Biological Characterisation

There is a clear need for developments in characterisation techniques that provide detailed information about structure-function relationships in biology. Using electron microscopy to achieve high resolution while maintaining a broad field of view remains a challenge, particularly for radiation sensitive specimens where the signal-to-noise ratio required to maintain structural integrity is limited by low electron fluence. In this review, we explore the potential of cryogenic electron ptychography as an alternative method for characterisation of biological systems under low fluence conditions. Using this method with increased information content from multiple sampled regions of interest, potentially allows 3D reconstruction with far fewer particles than required in conventional cryo-electron microscopy. This is important for achieving higher resolution for systems where distributions of homogeneous single particles are difficult to obtain. We discuss the progress, limitations and potential areas for future development of this approach for both single particle analysis and in applications to heterogeneous large objects.

q-bio.QM

Scan Coil Dynamics Simulation for Subsampled Scanning Transmission Electron Microscopy

Subsampling and fast scanning in the scanning transmission electron microscope is problematic due to scan coil hysteresis - the mismatch between the actual and assumed location of the electron probe beam as a function of the history of the scan. Hysteresis limits the resolution of the microscope and can induce artefacts in our images, particularly during flyback. In this work, we aim to provide insights on the effects of hysteresis during image formation. To accomplish this, a simulation has been developed to model a scanning system as a damped double-harmonic oscillator, with the simulation being capable of managing many microscope dependant parameters to study the effect on the resultant scan trajectories. The model developed shows that the trajectory of the electron beam probe is not obvious and the relationship between scanning pattern and probe trajectory is complex.

physics.comp-ph

In silico Ptychography of Lithium-ion Cathode Materials from Subsampled 4-D STEM Data

High quality scanning transmission electron microscopy (STEM) data acquisition and analysis has become increasingly important due to the commercial demand for investigating the properties of complex materials such as battery cathodes; however, multidimensional techniques (such as 4-D STEM) which can improve resolution and sample information are ultimately limited by the beam-damage properties of the materials or the signal-to-noise ratio of the result. subsampling offers a solution to this problem by retaining high signal, but distributing the dose across the sample such that the damage can be reduced. It is for these reasons that we propose a method of subsampling for 4-D STEM, which can take advantage of the redundancy within said data to recover functionally identical results to the ground truth. We apply these ideas to a simulated 4-D STEM data set of a LiMnO2 sample and we obtained high quality reconstruction of phase images using 12.5% subsampling.

cond-mat.mtrl-sci

A Targeted Sampling Strategy for Compressive Cryo Focused Ion Beam Scanning Electron Microscopy

Cryo Focused Ion-Beam Scanning Electron Microscopy (cryo FIB-SEM) enables three-dimensional and nanoscale imaging of biological specimens via a slice and view mechanism. The FIB-SEM experiments are, however, limited by a slow (typically, several hours) acquisition process and the high electron doses imposed on the beam sensitive specimen can cause damage. In this work, we present a compressive sensing variant of cryo FIB-SEM capable of reducing the operational electron dose and increasing speed. We propose two Targeted Sampling (TS) strategies that leverage the reconstructed image of the previous sample layer as a prior for designing the next subsampling mask. Our image recovery is based on a blind Bayesian dictionary learning approach, i.e., Beta Process Factor Analysis (BPFA). This method is experimentally viable due to our ultra-fast GPU-based implementation of BPFA. Simulations on artificial compressive FIB-SEM measurements validate the success of proposed methods: the operational electron dose can be reduced by up to 20 times. These methods have large implications for the cryo FIB-SEM community, in which the imaging of beam sensitive biological materials without beam damage is crucial.

eess.SP

SIM-STEM Lab: Incorporating Compressed Sensing Theory for Fast STEM Simulation

Recently it has been shown that precise dose control and an increase in the overall acquisition speed of atomic resolution scanning transmission electron microscope (STEM) images can be achieved by acquiring only a small fraction of the pixels in the image experimentally and then reconstructing the full image using an inpainting algorithm. In this paper, we apply the same inpainting approach (a form of compressed sensing) to simulated, sub-sampled atomic resolution STEM images. We find that it is possible to significantly sub-sample the area that is simulated, the number of g-vectors contributing the image, and the number of frozen phonon configurations contributing to the final image while still producing an acceptable fit to a fully sampled simulation. Here we discuss the parameters that we use and how the resulting simulations can be quantifiably compared to the full simulations. As with any Compressed Sensing methodology, care must be taken to ensure that isolated events are not excluded from the process, but the observed increase in simulation speed provides significant opportunities for real time simulations, image classification and analytics to be performed as a supplement to experiments on a microscope to be developed in the future.

cond-mat.mtrl-sci