Self-Supervised Deep Learning for Model Correction in the Computational Crystallography Toolbox.

The Computational Crystallography Toolbox (cctbx) is open-source software that allows for processing of crystallographic data, including from serial femtosecond crystallography (SFX), for macromolecular structure determination. We aim to use the modules in cctbx to determine the oxidation state of individual metal atoms in a macromolecule. Changes in oxidation state are reflected in small shifts of the atom's X-ray absorption edge. These energy shifts can be extracted from the diffraction images recorded in serial femtosecond crystallography, given knowledge of a forward physics model. However, as the diffraction changes only slightly due to the absorption edge shift, inaccuracies in the forward physics model make it extremely challenging to observe the oxidation state. In this work, we describe the potential impact of using self-supervised deep learning to correct the scientific model in cctbx and provide uncertainty quantification. We provide code for forward model simulation and data analysis, built from cctbx modules, at https://github.com/gigantocypris/SPREAD, which can be integrated with machine learning. We describe open questions in algorithm development to help spur advances through dialog between crystallographers and machine learning researchers. New methods could help elucidate charge transfer processes in many reactions, including key events in photosynthesis.

Ultraefficient thermophotovoltaic power conversion by band-edge spectral filtering.

Thermophotovoltaic power conversion utilizes thermal radiation from a local heat source to generate electricity in a photovoltaic cell. It was shown in recent years that the addition of a highly reflective rear mirror to a solar cell maximizes the extraction of luminescence. This, in turn, boosts the voltage, enabling the creation of record-breaking solar efficiency. Now we report that the rear mirror can be used to create thermophotovoltaic systems with unprecedented high thermophotovoltaic efficiency. This mirror reflects low-energy infrared photons back into the heat source, recovering their energy. Therefore, the rear mirror serves a dual function; boosting the voltage and reusing infrared thermal photons. This allows the possibility of a practical >50% efficient thermophotovoltaic system. Based on this reflective rear mirror concept, we report a thermophotovoltaic efficiency of 29.1 ± 0.4% at an emitter temperature of 1,207 °C.

Illumination pattern design with deep learning for single-shot Fourier ptychographic microscopy.

Fourier ptychographic microscopy allows for the collection of images with a high space-bandwidth product at the cost of temporal resolution. In Fourier ptychographic microscopy, the light source of a conventional widefield microscope is replaced with a light-emitting diode (LED) matrix, and multiple images are collected with different LED illumination patterns. From these images, a higher-resolution image can be computationally reconstructed without sacrificing field-of-view. We use deep learning to achieve single-shot imaging without sacrificing the space-bandwidth product, reducing the acquisition time in Fourier ptychographic microscopy by a factor of 69. In our deep learning approach, a training dataset of high-resolution images is used to jointly optimize a single LED illumination pattern with the parameters of a reconstruction algorithm. Our work paves the way for high-throughput imaging in biological studies.

Optimal physical preprocessing for example-based super-resolution.

Fourier ptychographic microscopy is a technique that achieves a high space-bandwidth product, i.e. high resolution and high field-of-view. In Fourier ptychographic microscopy, variable illumination patterns are used to collect multiple low-resolution images. These low-resolution images are then computationally combined to create an image with resolution exceeding that of any single image from the microscope. Due to the necessity of acquiring multiple low-resolution images, Fourier ptychographic microscopy has poor temporal resolution. Our aim is to improve temporal resolution in Fourier ptychographic microscopy, achieving single-shot imaging without sacrificing space-bandwidth product. We use example-based super-resolution to achieve this goal by trading off generality of the imaging approach. In example-based super-resolution, the function relating low-resolution images to their high-resolution counterparts is learned from a given dataset. We take the additional step of modifying the imaging hardware in order to collect more informative low-resolution images to enable better high-resolution image reconstruction. We show that this "physical preprocessing" allows for improved image reconstruction with deep learning in Fourier ptychographic microscopy. In this work, we use deep learning to jointly optimize a single illumination pattern and the parameters of a post-processing reconstruction algorithm for a given sample type. We show that our joint optimization yields improved image reconstruction as compared with sole optimization of the post-processing reconstruction algorithm, establishing the importance of physical preprocessing in example-based super-resolution.

Single spherical mirror optic for extreme ultraviolet lithography enabled by inverse lithography technology.

Traditionally, aberration correction in extreme ultraviolet (EUV) projection optics requires the use of multiple lossy mirrors, which results in prohibitively high source power requirements. We analyze a single spherical mirror projection optical system where aberration correction is built into the mask itself, through Inverse Lithography Technology (ILT). By having fewer mirrors, this would reduce the power requirements for EUV lithography. We model a single spherical mirror system with orders of magnitude more spherical aberration than would ever be tolerated in a traditional multiple mirror system. By using ILT, (implemented by an adjoint-based gradient descent optimization algorithm), we design photomasks that successfully print test patterns, in spite of these enormous aberrations. This mathematical method was tested with a 6 plane wave illumination source. Nonetheless, it would have poor power throughput from a totally incoherent source.