Lewys Jones

Bio: Lewys Jones is an academic researcher from Trinity College, Dublin. The author has contributed to research in topics: Scanning transmission electron microscopy & Ptychography. The author has an hindex of 22, co-authored 105 publications receiving 1757 citations. Previous affiliations of Lewys Jones include University of Oxford & University of Antwerp.

Smart Align—a new tool for robust non-rigid registration of scanning microscope data

Abstract: Many microscopic investigations of materials may benefit from the recording of multiple successive images. This can include techniques common to several types of microscopy such as frame averaging to improve signal-to-noise ratios (SNR) or time series to study dynamic processes or more specific applications. In the scanning transmission electron microscope, this might include focal series for optical sectioning or aberration measurement, beam damage studies or camera-length series to study the effects of strain; whilst in the scanning tunnelling microscope, this might include bias-voltage series to probe local electronic structure. Whatever the application, such investigations must begin with the careful alignment of these data stacks, an operation that is not always trivial. In addition, the presence of low-frequency scanning distortions can introduce intra-image shifts to the data. Here, we describe an improved automated method of performing non-rigid registration customised for the challenges unique to scanned microscope data specifically addressing the issues of low-SNR data, images containing a large proportion of crystalline material and/or local features of interest such as dislocations or edges. Careful attention has been paid to artefact testing of the non-rigid registration method used, and the importance of this registration for the quantitative interpretation of feature intensities and positions is evaluated.

Simultaneous atomic-resolution electron ptychography and Z-contrast imaging of light and heavy elements in complex nanostructures.

Abstract: The aberration-corrected scanning transmission electron microscope (STEM) has emerged as a key tool for atomic resolution characterization of materials, allowing the use of imaging modes such as Z-contrast and spectroscopic mapping. The STEM has not been regarded as optimal for the phase-contrast imaging necessary for efficient imaging of light materials. Here, recent developments in fast electron detectors and data processing capability is shown to enable electron ptychography, to extend the capability of the STEM by allowing quantitative phase images to be formed simultaneously with incoherent signals. We demonstrate this capability as a practical tool for imaging complex structures containing light and heavy elements, and use it to solve the structure of a beam-sensitive carbon nanostructure. The contrast of the phase image contrast is maximized through the post-acquisition correction of lens aberrations. The compensation of defocus aberrations is also used for the measurement of three-dimensional sample information through post-acquisition optical sectioning. The use of ptychography with electrons has been limited. Here, Yang et al. demonstrate that the combination of Z-contrast and phase imaging reveals the structure of complex nanomaterials. This practical tool can be used to solve the structure of a beam-sensitive carbon nanostructure at atomic-resolution.

Identifying and correcting scan noise and drift in the scanning transmission electron microscope.

Abstract: The aberration-corrected scanning transmission electron microscope has great sensitivity to environmental or instrumental disturbances such as acoustic, mechanical, or electromagnetic interference. This interference can introduce distortions to the images recorded and degrade both signal noise and resolution performance. In addition, sample or stage drift can cause the images to appear warped and leads to unreliable lattice parameters being exhibited. Here a detailed study of the sources, natures, and effects of imaging distortions is presented, and from this analysis a piece of image reconstruction code has been developed that can restore the majority of the effects of these detrimental image distortions for atomic-resolution data. Example data are presented, and the performance of the restored images is compared quantitatively against the as-recorded data. An improvement in apparent resolution of 16% and an improvement in signal-to-noise ratio of 30% were achieved, as well as correction of the drift up to the precision to which it can be measured.

Towards data-driven next-generation transmission electron microscopy.

Abstract: Electron microscopy touches on nearly every aspect of modern life, underpinning materials development for quantum computing, energy and medicine. We discuss the open, highly integrated and data-driven microscopy architecture needed to realize transformative discoveries in the coming decade.

I and i

Abstract: There is, I think, something ethereal about i —the square root of minus one. I remember first hearing about it at school. It seemed an odd beast at that time—an intruder hovering on the edge of reality. Usually familiarity dulls this sense of the bizarre, but in the case of i it was the reverse: over the years the sense of its surreal nature intensified. It seemed that it was impossible to write mathematics that described the real world in …

Fast parallel algorithms for short-range molecular dynamics

Abstract: Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Mathematical Methods Of Statistics

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Microscopy and Microanalysis

Abstract: Vascular stenosis triggers adaptive cellular responses that induce adverse remodeling, which can progress to partial or complete vessel occlusion. Despite its severity, cellular interactions and biophysical cues that regulate pathological progression are poorly understood. We report the design and fabrication of a three-dimensional in vitro system to model vascular stenosis so that specific cellular interactions and responses to hemodynamic stimuli can be investigated. Tubular cellularized constructs (cytotubes) were produced using a collagen casting system to generate a stenotic arterial model. Fabrication methods were developed to create cytotubes containing co-cultured vascular cells, where cell viability, distribution, morphology, and contraction were examined (Figure). Fibroblasts, bone marrow primary cells, smooth muscle cells (SMCs), and endothelial cells (ECs) remained viable during culture and developed locationand time-dependent morphologies. We found cytotube contraction to depend on cellular composition, where SMC-EC co-cultures adopted intermediate contractile phenotypes between SMCand EC-only cytotubes. Our fabrication approach and resulting artery model can serve as an in vitro 3D culture system to investigate vascular pathogenesis.