arXiv subjects
Publications and source records attributed to Richard Bean.
We give a tight single-change covering design with $v=26$ and $k=6$. This answers Problem 1 of the Nineteenth British Combinatorial Conference, which asked whether such a design exists with block size greater than $5$. We also describe the satisfiability search that found the design, including negative search results at the smallest admissible order $v=21$.
X-ray free-electron lasers (XFELs) enable diffraction-before-destruction measurements of individual nanosized bioparticles, making it possible to study the structure and dynamics of non-crystalline targets under near-biologically relevant conditions. In this work, we employ rotational invariants for model-guided and ab initio three-dimensional (3D) structure determination of aerosolized bacteriophages PR772 measured with an XFEL. The rotational invariants derived from diffraction patterns collected during multiple independent XFEL experiments facilitate the characterization of similarities and structural variations within the measured ensembles of PR772 particles. Despite modest experimental resolution, we can identify various structural features of the viruses, including the asymmetric nature of capsid distortions from the perfect icosahedral shape, density variations in the encapsulated content, and an extension at one of the capsid vertices. Rotational invariants combine structural sensitivity with applicability to forward-scattering modeling and inverse problem solving, making them powerful tools for probing the structure and temporal evolution of nano- and bioparticles using an XFEL, particularly enhancing the fidelity of structural analysis at limited experimental resolution.
A defining set of a Latin square is a partially filled-in Latin square which completes to no other Latin square of the same order. We introduce the concept of a $k$-strong defining set, in which if less than $k$ entries are deleted, the property of being a defining set is retained. Equivalently, a $k$-strong defining set intersects every Latin trade in the Latin square at least $k$ times. In the addition table for integers modulo $n$, when $n$ is even we determine the minimum size of a $k$-strong defining set for any $k$. For odd $n$ we give a construction for a minimally $2$-strong defining set. We furthermore give computational results for Latin squares of small orders.
Femtosecond laser-induced alloying presents a novel approach to modifying bimetallic systems. Visualizing ultrafast processes during laser-induced alloying is essential to uncover fundamental mechanisms associated with phase transformations, which enables precise control over material composition and structure at the atomic level. In this study, we investigated the ultrafast dynamics of laser-induced alloying of Au/Pd core-shell nanorods using a time-resolved X-ray diffraction technique at an X-ray free-electron laser facility, capturing the structural evolution from picoseconds to microsecond timescales. We found that a laser fluence threshold of ~ 48 mJ/cm2 with 800 nm excitation is sufficient for melting and subsequent alloy formation. Above this threshold, the formation of Au1.51Pd0.49 was observed, and we found that alloying is not a single-step phenomenon; instead, it is a dynamic process involving interdiffusion.
Single-particle small-angle X-ray scattering (SP-SAXS) enables quantitative morphological analysis by recording diffraction snapshots from isolated particles using X-ray free-electron laser (XFEL) pulses. Unlike conventional X-ray techniques, which average over the entire illuminated sample volume, SP-SAXS resolves low-contrast, less abundant, or transient species within heterogeneous particle populations that would otherwise remain hidden. Here, we apply SP-SAXS to investigate the solvothermal formation of CoO nanocrystal assemblies from a Co(acac)$_3$ precursor in benzyl alcohol. The single-particle data reveal amorphous, uniform-density Co(acac)$_2$ spheres as transient intermediates that directly crystallize into cavernous CoO nanocrystal assemblies, which explains why CoO forms as hierarchical aggregates rather than as isolated nanocrystals. These results demonstrate that SP-SAXS provides a powerful framework for disentangling morphological heterogeneity in nanoparticle formation processes.
We demonstrate element-specific incoherent diffractive imaging (IDI) of single copper nanocubes using intensity correlations of K$\alpha$ fluorescence at a hard X-ray free-electron laser. Combining single particle diffraction classification with IDI, we retrieve the form factor of 88 nm cubes with 20 nm resolution, extending IDI to the destructive single-particle regime with a large gain in resolution. IDI visibility drops sharply above a fluence of $10^2$ J/cm$^2$, consistent with the assumption of amplified spontaneous emission. Our results reveal fundamental limits for high-fluence nanoimaging towards future single-particle X-ray imaging.
Materials exposed to intense femtosecond X-ray pulses with energies above their K-shell absorption edge can enter an extremely ionized state, which could give rise to nonlinear phenomena, such as saturable absorption and reverse saturable absorption. In this work, we investigate these effects on single copper nanoparticles irradiated by an X-ray free-electron laser pulse. We study the properties of the K$\alpha$ fluorescence for two different short pulse durations and three X-ray incident energies below and above the K-shell absorption edge, and correlate these with incident fluence estimates based on coherent diffraction. We observe that the incident fluence of the pulse and not its duration, is the main factor that modulates the nonlinear response, which leads to an effective shortening of the fluorescence emission. Our findings have implications for fluorescence-based methods for imaging single particles using transiently coherent fluorescence, or diffractive imaging through transient resonances.
The outstanding opto-electronic properties of lead halide perovskites have been related to the formation of polarons. Nevertheless, the observation of the atomistic deformation brought about by one electron-hole pair in these materials has remained elusive. Here, we measure the diffraction patterns of single CsPbBr$_3$ quantum dots (QDs) with and without resonant excitation in the single exciton limit using serial femtosecond crystallography (SFX). By reconstructing the 3D differential diffraction pattern, we observe small shifts of the Bragg peaks indicative of a crystal-wide deformation field. Building on DFT calculations, we show that these shifts are consistent with the lattice distortion induced by a delocalized electron and a localized hole, forming a mixed large/small exciton polaron. This result creates a clear picture of the polaronic deformation in CsPbBr$_3$ QDs, highlights the exceptional sensitivity of SFX to lattice distortions in few-nanometer crystallites, and establishes an experimental platform for future studies of electron-lattice interactions.
Single-stranded RNA viruses co-assemble their capsid with the genome and variations in capsid structures can have significant functional relevance. In particular, viruses need to respond to a dehydrating environment to prevent genomic degradation and remain active upon rehydration. Theoretical work has predicted low-energy buckling transitions in icosahedral capsids which could protect the virus from further dehydration. However, there has been no direct experimental evidence, nor molecular mechanism, for such behaviour. Here we observe this transition using X-ray single particle imaging of MS2 bacteriophages after aerosolization. Using a combination of machine learning tools, we classify hundreds of thousands of single particle diffraction patterns to learn the structural landscape of the capsid morphology as a function of time spent in the aerosol phase. We found a previously unreported compact conformation as well as intermediate structures which suggest an incoherent buckling transition which does not preserve icosahedral symmetry. Finally, we propose a mechanism of this buckling, where a single 19-residue loop is destabilised, leading to the large observed morphology change. Our results provide experimental evidence for a mechanism by which viral capsids protect themselves from dehydration. In the process, these findings also demonstrate the power of single particle X-ray imaging and machine learning methods in studying biomolecular structural dynamics.
X-ray Multi-Projection Imaging (XMPI) is an emerging technology that allows for the acquisition of millions of 3D images per second in samples opaque to visible light. This breakthrough capability enables volumetric observation of fast stochastic phenomena, which were inaccessible due to the lack of a volumetric X-ray imaging probe with kHz to MHz repetition rate. These include phenomena of industrial and societal relevance such as fractures in solids, propagation of shock waves, laser-based 3D printing, or even fast processes in the biological domain. Indeed, the speed of traditional tomography is limited by the shear forces caused by rotation, to a maximum of 1000 Hz in state-of-the-art tomography. Moreover, the shear forces can disturb the phenomena in observation, in particular with soft samples or sensitive phenomena such as fluid dynamics. XMPI is based on splitting an X-ray beam to generate multiple simultaneous views of the sample, therefore eliminating the need for rotation. The achievable performances depend on the characteristics of the X-ray source, the detection system, and the X-ray optics used to generate the multiple views. The increase in power density of the X-ray sources around the world now enables 3D imaging with sampling speeds in the kilohertz range at synchrotrons and megahertz range at X-ray Free-Electron Lasers (XFELs). Fast detection systems are already available, and 2D MHz imaging was already demonstrated at synchrotron and XFEL. In this work, we explore the properties of X-ray splitter optics and XMPI schemes that are compatible with synchrotron insertion devices and XFEL X-ray beams. We describe two possible schemes designed to permit large samples and complex sample environments. Then, we present experimental proof of the feasibility of MHz-rate XMPI at the European XFEL.
Nanoparticles, exhibiting functionally relevant structural heterogeneity, are at the forefront of cutting-edge research. Now, high-throughput single-particle imaging (SPI) with x-ray free-electron lasers (XFELs) creates unprecedented opportunities for recovering the shape distributions of millions of particles that exhibit functionally relevant structural heterogeneity. To realize this potential, three challenges have to be overcome: (1) simultaneous parametrization of structural variability in real and reciprocal spaces; (2) efficiently inferring the latent parameters of each SPI measurement; (3) scaling up comparisons between $10^5$ structural models and $10^6$ XFEL-SPI measurements. Here, we describe how we overcame these three challenges to resolve the non-equilibrium shape distributions within millions of gold nanoparticles imaged at the European XFEL. These shape distributions allowed us to quantify the degree of asymmetry in these particles, discover a relatively stable `shape envelope' amongst nanoparticles, discern finite-size effects related to shape-controlling surfactants, and extrapolate nanoparticles' shapes to their idealized thermodynamic limit. Ultimately, these demonstrations show that XFEL SPI can help transform nanoparticle shape characterization from anecdotally interesting to statistically meaningful.
X-ray Free Electron Lasers (XFELs) can probe chemical and biological reactions as they unfold with unprecedented spatial and temporal resolution. A principal challenge in this pursuit is the delivery of samples to the X-ray interaction point in a way that produces data of the highest possible quality and efficiency. This is hampered by constraints posed by the light source and operation within a beamline environment. For liquid samples, the solution typically involves a high-speed liquid jet, capable of keeping up with the rate of X-ray pulses. However, conventional jets are not ideal because of radiation-induced explosions of the jet, as well as their cylindrical geometry combined with the X-ray pointing instability of many beamlines causes the interaction volume to differ for every pulse. This complicates data analysis and contributes to measurement errors. An alternative geometry is a liquid sheet jet which, with its constant thickness over large areas, eliminates the X-ray pointing related problems. Since liquid sheets can be made very thin, the radiation-induced explosion is reduced, boosting their stability. They are especially attractive for experiments which benefit from small interaction volumes such as fluctuation X-ray scattering and several types of spectroscopy. Although they have seen increasing use for soft X-ray applications in recent years, there has not yet been wide-scale adoption at XFELs. Here, we demonstrate liquid sheet jet sample injection at the European XFEL. We evaluate several aspects of its performance relative to a conventional liquid jet including thickness profile, stability, and radiation-induced explosion dynamics at high repetition rates. The sheet jet exhibits superior performance across these critical experimental parameters. Its minute thickness also suggests ultrafast single-particle solution scattering is a possibility.
X-ray time-resolved tomography is one of the most popular X-ray techniques to probe dynamics in three dimensions (3D). Recent developments in time-resolved tomography opened the possibility of recording kilohertz-rate 3D movies. However, tomography requires rotating the sample with respect to the X-ray beam, which prevents characterization of faster structural dynamics. Here, we present megahertz (MHz) X-ray multi-projection imaging (MHz-XMPI), a technique capable of recording volumetric information at MHz rates and micrometer resolution without scanning the sample. We achieved this by harnessing the unique megahertz pulse structure and intensity of the European X-ray Free-electron Laser with a combination of novel detection and reconstruction approaches that do not require sample rotations. Our approach enables generating multiple X-ray probes that simultaneously record several angular projections for each pulse in the megahertz pulse burst. We provide a proof-of-concept demonstration of the MHz-XMPI technique's capability to probe 4D (3D+time) information on stochastic phenomena and non-reproducible processes three orders of magnitude faster than state-of-the-art time-resolved X-ray tomography, by generating 3D movies of binary droplet collisions. We anticipate that MHz-XMPI will enable in-situ and operando studies that were impossible before, either due to the lack of temporal resolution or because the systems were opaque (such as for MHz imaging based on optical microscopy).
Ultrasonic liquid phase exfoliation is a promising method for the production of two-dimensional (2D) layered materials. A large number of studies have been made in investigating the underlying ultrasound exfoliation mechanisms. However, due to the experimental challenges for capturing the highly transient and dynamic phenomena in real-time at sub-microsecond time and micrometer length scales simultaneously, most theories reported to date still remain elusive. Here, using the ultra-short X-ray Free Electron Laser pulses (~25ps) with a unique pulse train structure, we applied MHz X-ray Microscopy and machine-learning technique to reveal unambiguously the full cycles of the ultrasound cavitation and graphite layer exfoliation dynamics with sub-microsecond and micrometer resolution. Cyclic fatigue shock wave impacts produced by ultrasound cloud implosion were identified as the dominant mechanism to deflect and exfoliate graphite layers mechanically. For the graphite flakes, exfoliation rate as high as ~5 angstroms per shock wave impact was observed. For the HOPG graphite, the highest exfoliation rate was ~0.15 angstroms per impact. These new findings are scientifically and technologically important for developing industrial upscaling strategies for ultrasonic exfoliation of 2D materials.
At modern X-ray sources, such as synchrotrons and X-ray Free-Electron Lasers (XFELs), it is important to measure the absolute value of the photon energy directly. Here, a method for absolute spectral metrology is presented. A photon energy estimation method based on the spectral measurements and rocking of diffracting crystals is presented. The photon energy of SASE1 channel of the European XFEL was measured, and the benefits and applications of the precise photon energy evaluation are discussed.
Predict+Optimize frameworks integrate forecasting and optimization to address real-world challenges such as renewable energy scheduling, where variability and uncertainty are critical factors. This paper benchmarks solutions from the IEEE-CIS Technical Challenge on Predict+Optimize for Renewable Energy Scheduling, focusing on forecasting renewable production and demand and optimizing energy cost. The competition attracted 49 participants in total. The top-ranked method employed stochastic optimization using LightGBM ensembles, and achieved at least a 2% reduction in energy costs compared to deterministic approaches, demonstrating that the most accurate point forecast does not necessarily guarantee the best performance in downstream optimization. The published data and problem setting establish a benchmark for further research into integrated forecasting-optimization methods for energy systems, highlighting the importance of considering forecast uncertainty in optimization models to achieve cost-effective and reliable energy management. The novelty of this work lies in its comprehensive evaluation of Predict+Optimize methodologies applied to a real-world renewable energy scheduling problem, providing insights into the scalability, generalizability, and effectiveness of the proposed solutions. Potential applications extend beyond energy systems to any domain requiring integrated forecasting and optimization, such as supply chain management, transportation planning, and financial portfolio optimization.
In this paper, we examine the concept of the predict and optimise problem with specific reference to the third Technical Challenge of the IEEE Computational Intelligence Society. In this competition, entrants were asked to forecast building energy use and solar generation at six buildings and six solar installations, and then use their forecast to optimize energy cost while scheduling classes and batteries over a month. We examine the possible effect of underforecasting and overforecasting and asymmetric errors on the optimisation cost. We explore the different nature of loss functions for the prediction and optimisation phase and propose to adjust the final forecasts for a better optimisation cost. We report that while there is a positive correlation between these two, more appropriate loss functions can be used to optimise the costs associated with final decisions.
This report provides a description of the methodology I used in the IEEE-CIS 3rd Technical Challenge. For the forecast, I used a quantile regression forest approach using the solar variables provided by the Bureau of Meterology of Australia (BOM) and many of the weather variables from the European Centre for Medium-Range Weather Forecasting (ECMWF). Groups of buildings and all of the solar instances were trained together as they were observed to be closely correlated over time. Other variables used included Fourier values based on hour of day and day of year, and binary variables for combinations of days of the week. The start dates for the time series were carefully tuned based on phase 1 and cleaning and thresholding was used to reduce the observed error rate for each time series. For the optimization, a four-step approach was used using the forecast developed. First, a mixed-integer program (MIP) was solved for the recurring and recurring plus once-off activities, then each of these was extended using a mixed-integer quadratic program (MIQP). The general strategy was chosen from one of two ("array" from the "array" and "tuples" approaches) while the specific step improvement strategy was chosen from one of five ("no forced discharge").