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Phay J. Ho

Publications and source records attributed to Phay J. Ho.

At least 19 recordsLinked to original sources

Multi-Task Graph Neural Network Predictions of Auger-Electron and X-ray Photoelectron Spectroscopy

Auger-electron spectroscopy has long accompanied x-ray photoelectron spectroscopy as a second modality to resolve chemical states with overlapping core-electron binding energies. However, analyzing the Auger spectrum is challenged by its complexity and the computational expense of its simulation. Here we demonstrate that the physical connection, and thus inter-task relationship, between the generation of a core-hole and its corresponding Auger-Meitner decay enables inductive knowledge transfer through the training of a multi-task graph neural network to predict both observables from a common graph embedding. Both task losses are combined with learned weights via the uncertainty weighting procedure. Overall, the single-task and multi-task models predict calculated and experimental Auger lineshapes with good accuracy in most cases. The performance between the two task regimes is similar, with the single-task models generally having better predictions of the finer peak structures in the spectrum. The present results demonstrate that multi-task training is a promising avenue for future developments of universal x-ray spectroscopy models with learned representations that map the molecular structure to a multitude of techniques.

physics.chem-ph

X-ray diffraction from chiral molecules with twisted beams

Structured x-rays carrying an orbital angular momentum break spatial inversion symmetry and have been proposed as probes of chirality. We theoretically investigate twisted non-resonant x-ray diffraction from chiral molecules and demonstrate that no dichroic signal can arise from randomly oriented molecules, irrespective of the beam spatial profile. However, a dichroic response emerges for oriented molecules. Our results establish the beam and sample conditions for which a measurable dichroic scattering signal survives axial and focal averaging.

physics.optics

Graph Neural Network Predictions of Carbon 1s Binding Energies with Near-Experimental Accuracy

Graph neural networks are promising architectures for fast, accurate and transferable predictions of core-electron binding energies, which depend on the local bond environment. Here we present a graph neural network model for predicting carbon 1s core-electron binding energies in organic molecules. The model is trained with multiconfiguration pair-density functional theory on 8637 carbon atoms in 2116 molecules with 4-16 atoms and evaluated against 570 experimental values in 113 different molecules containing 3-45 atoms. Previous work benchmarked a mean absolute error of 0.27 eV to experiment for the training data level of theory [J. Phys. Chem. A 2025, 129, 36, 8419-8431] and the present model demonstrates an experimental evaluation error of 0.33 eV with good size transferability to larger organic molecules. An equivariant graph neural network is benchmarked against its rotationally invariant analogue and a model comprised of the smooth overlap of atomic positions descriptors and kernel ridge regression for training data efficiency and stability to non-equilibrium geometries absent from the training data. All models show good training data efficiency and the graph based models have improved transferability to non-equilibrium geometries. The use of chemically informed, graph-normalized node features reduces the graph neural network's dependence on message passing depth. A case study on the 45 atom avobenzone tautomers demonstrates the model's ability for instant and precise analysis of complex molecules. The software and data are provided by the open-source AugerNet package at https://doi.org/10.5281/zenodo.19689244.

physics.chem-ph

Generative Modeling Enables Molecular Structure Retrieval from Coulomb Explosion Imaging

Capturing the structural changes that molecules undergo during chemical reactions in real space and time is a long-standing dream and an essential prerequisite for understanding and ultimately controlling femtochemistry. A key approach to tackle this challenging task is Coulomb explosion imaging, which benefited decisively from recently emerging high-repetition-rate X-ray free-electron laser sources. With this technique, information on the molecular structure is inferred from the momentum distributions of the ions produced by the rapid Coulomb explosion of molecules. Retrieving molecular structures from these distributions poses a highly non-linear inverse problem that remains unsolved for molecules consisting of more than a few atoms. Here, we address this challenge using a diffusion-based Transformer neural network. We show that the network reconstructs unknown molecular geometries from ion-momentum distributions with a mean absolute error below one Bohr radius, which is half the length of a typical chemical bond.

physics.chem-ph

Quantum Interference in Two-Atom Resonant X-ray Scattering of an Intense Attosecond Pulse

We theoretically investigate resonant x-ray scattering from two non-interacting Ne+ ions driven by an intense attosecond pulse using a non-relativistic, QED-based time-dependent framework. Our model includes Rabi oscillations, photoionization, Auger decay, and quantum interference among elastic scattering and resonance fluorescence pathways. We analyze how the total scattering signal depends on pulse intensity, atomic configuration, and initial electronic state. We find that the total resonant scattering yield exceeds its non-resonant counterpart; the angular dependence of the signal qualitatively resembles a two-atom structure factor; and the visibility of interference fringes is sensitive to pulse area and the initial electronic state. Only a subset of final states reached via resonance fluorescence exhibits interference, determined by the indistinguishability of photon emission pathways. Fringe visibility is maximized in the linear scattering regime, where ionization is minimal and resonance fluorescence pathways can be largely indistinguishable. These results highlight optimal conditions for applying ultrafast resonant x-ray scattering to single-particle imaging.

physics.atom-ph

Impact of Atomic Substitution on Core-Hole Relaxation Dynamics: A Study of Br$_2$ and IBr

Understanding inner-shell decay processes in heavy-element molecules is essential for unraveling x-ray-induced photodynamics and advancing molecular imaging techniques. In this study, we investigate the influence of atomic substitution on core-hole relaxation dynamics and molecular fragmentation in Br2 and IBr, initiated by x-ray absorption at the Br K-edge. Using a combination of X-ray/ion coincidence measurements and Monte Carlo/molecular dynamics simulations, we track charge distribution and the kinetic energy release (KER) of fragment ions with a total charge from 2+ to 8+. For both molecules, the simulated KER values show good agreement with experiment across different fragmentation channels. Our comparison reveals that substituting Br with the heavier I atom in IBr has minimal impact on the inner-shell electronic decay process, but significantly influences nuclear motion, leading to slower dissociation, thereby a KER close to the Coulomb limit, an effect attributed to the atomic mass. These findings highlight the interplay between electronic and nuclear effects in molecular fragmentation, particularly in heavy-element species, and provide new insights into medical therapies, structural biology, and astrophysics.

physics.atm-clus

Nonlinear reversal of photo-excitation on the attosecond time scale improves ultrafast x-ray diffraction images

The advent of isolated and intense sub-femtosecond X-ray pulses enables tracking of quantummechanical motion of electrons in molecules and solids. The combination of X-ray spectroscopy and diffraction imaging is a powerful approach to visualize non-equilibrium dynamics in systems beyond few atoms. However, extreme x-ray intensities introduce significant electronic damage, limiting material contrast and spatial resolution. Here we show that newly available intense subfemtosecond (sub-fs) x-ray FEL pulses can outrun most ionization cascades and partially reverse x-ray damage through stimulated x-ray emission in the vicinity of a resonance. In our experiment, we compared thousands of coherent x-ray diffraction patterns and simultaneously recorded ion spectra from individual Ne nanoparticles injected into the FEL focus. Our experimental results and theoretical modeling reveal that x-ray diffraction increases and the average charge state decreases in particles exposed to sub-fs pulses compared to those illuminated with 15-femtosecond pulses. Sub-fs exposures outrun most Auger decays and impact ionization processes, and enhance nonlinear effects such as stimulated emission, which cycle bound electrons between different states. These findings demonstrate that intense sub-fs x-ray FEL pulses are transformative for advancing high-resolution imaging and spectroscopy in chemical and material sciences, and open the possibilities of coherent control of the interaction between x-rays and complex specimen beyond few atoms.

physics.optics

Computation of Auger Electron Spectra in Organic Molecules with Multiconfiguration Pair-Density Functional Theory

Efficiently and accurately computing molecular Auger electron spectra for larger systems is limited by the increasing complexity of the scaling in the number of doubly ionized final states with respect to the system size. In this work, we benchmark the application of multiconfiguration pair-density functional theory with a restricted active space (RAS) reference wave function, for computing the carbon K-edge decay spectra of 21 organic molecules, with decay rates computed within the one-center approximation. The performance of different basis sets and on-top functionals is evaluated and the results show that multiconfiguration pair-density functional theory is comparable in accuracy to RAS followed by second-order perturbation theory, but at a significantly reduced cost and both methods demonstrate good agreement with experiment.

physics.chem-ph

Theory of resonant x-ray scattering with ultrafast intense pulses

We present a time-dependent Schrödinger equation (TDSE) approach within a non-relativistic quantum electrodynamics (QED) framework to investigate resonant x-ray scattering under intense x-ray pulses. This method enables us to explore how coherent x-ray electron dynamics affect scattering signals from Ne$^+$. We account for both resonant fluorescence and elastic scattering channels, while also considering competing photoionization and inner-shell decay processes. By computing the angular distribution and energy spectrum of scattered photons, we uncover the interference effects between elastic scattering and resonant fluorescence pathways. Notably, our results reveal a small asymmetry in the energy spectrum as a result of this interference. We discuss the experimental potential for detecting signatures of interference. Our findings demonstrate that the x-ray Rabi dynamics can be used to control scattering responses and offer new insights into interference mechanisms and scattering efficiency in high-intensity x-ray regimes.

physics.atom-ph

Effect of Rabi dynamics in resonant x-ray scattering of intense attosecond pulses

We theoretically study the effects of Rabi oscillations on resonant x-ray scattering in Ne$^+$ using intense attosecond and few-femtosecond pulses. The total photon yield strongly depends on the pulse area and has an upper bound at high intensities. Resonant scattering yields with attosecond pulses can be an order of magnitude higher than those far from resonances. Interference between resonant fluorescence and elastic scattering channels depends on the pulse area and initial state. Our results suggest that resonant x-ray scattering can be exploited for high-resolution, site-specific imaging.

physics.atom-ph

Quantum Molecular Charge-Transfer Model for Multi-step Auger-Meitner Decay Cascade Dynamics

The fragmentation of molecular cations following inner-shell decay processes in molecules containing heavy elements underpins the x-ray damage effects observed in x-ray scattering measurements of biological and chemical materials, as well as in medical applications involving Auger-electron emitting radionuclides. Traditionally, these processes are modeled using simulations that describe the electronic structure at an atomic level, thereby omitting molecular bonding effects. This work addresses the gap by introducing a novel approach that couples a decay spawning dynamics algorithm with ab initio molecular dynamics simulations to characterize ultrafast dynamics on the potential energy surfaces. We apply our method to a model decay cascade following K-shell ionization of IBr and subsequent K\b{eta} fluorescence decay. We examine two competing channels that undergo two decay steps, resulting in ion pairs with a total +3 charge state. This approach provides a continuous description of the electron transfer dynamics occurring during the multi-step decay cascade and molecular fragmentation, revealing the combined inner-shell decay and charge transfer timescale to be approximately 75 fs. Our computed kinetic energies of ion fragments show good agreement with experimental data.

physics.chem-ph

X-ray induced electron and ion fragmentation dynamics in IBr

Characterization of the inner-shell decay processes in molecules containing heavy elements is key to understanding x-ray damage of molecules and materials and for medical applications with Auger-electron-emitting radionuclides. The 1s hole states of heavy atoms can be produced by absorption of tunable x-rays and the resulting vacancy decays characterized by recording emitted photons, electrons, and ions. The 1s hole states in heavy elements have large x-ray fluorescence yields that transfer the hole to intermediate electron shells that then decay by sequential Auger-electron transitions that increase the ion's charge state until the final state is reached. In molecules the charge is spread across the atomic sites, resulting in dissociation to energetic atomic ions. We have used x-ray/ion coincidence spectroscopy to measure charge states and energies of I$^{q+}$ and Br$^{q'+}$ atomic ions following 1s ionization at the I and Br \textit{K}-edges of IBr. We present the charge states and kinetic energies of the two correlated fragment ions associated with core-excited states produced during the various steps of the cascades. To understand the dynamics leading to the ion data, we develop a computational model that combines Monte-Carlo/Molecular Dynamics simulations with a classical over-the-barrier model to track inner-shell cascades and redistribution of electrons in valence orbitals and nuclear motion of fragments.

physics.atom-ph

Resonant Double-Core Excitations with Ultrafast, Intense Pulses

Intense few-to-sub-femtosecond soft x-ray pulses can produce neutral, two-site excited double-core-hole states by promoting two core electrons to the same unoccupied molecular orbital. We theoretically investigate double nitrogen K-edge excitations of nitrous oxide (N2O) with multiconfigurational electronic structure calculations. We show that the second core-excitation energy is reduced with respect to its ground state value. A site-selective double core-excitation mechanism using intense few-femtosecond x-rays is investigated using time-dependent Schrodinger equation (TDSE) simulations. The subsequent two-step Auger-Meitner and two-electrons-one-electron decay spectra of the double core-excited states are analyzed using a Mulliken population analysis of the multiconfirational wavefunctions. The change in the electron emission lineshape between the absorption of 1 or 2 photons in the resonant core-excitation is predicted by combining this approach with the TDSE simulations. We examine the possibility of resolving the double core-excited states with x-ray pump-probe techniques by calculating the chemical shifts of the core-electron binding energy of the core-excited states and decay products.

physics.chem-ph

Enhanced ultrafast X-ray diffraction by transient resonances

Diffraction-before-destruction imaging with single ultrashort X-ray pulses has the potential to visualise non-equilibrium processes, such as chemical reactions, at the nanoscale with sub-femtosecond resolution in the native environment without the need of crystallization. Here, a nanospecimen partially diffracts a single X-ray flash before sample damage occurs. The structural information of the sample can be reconstructed from the coherent X-ray interference image. State-of-art spatial resolution of such snapshots from individual heavy element nanoparticles is limited to a few nanometers. Further improvement of spatial resolution requires higher image brightness which is ultimately limited by bleaching effects of the sample. We compared snapshots from individual 100 nm Xe nanoparticles as a function of the X-ray pulse duration and incoming X-ray intensity in the vicinity of the Xe M-shell resonance. Surprisingly, images recorded with few femtosecond and sub-femtosecond pulses are up to 10 times brighter than the static linear model predicts. Our Monte-Carlo simulation and statistical analysis of the entire data set confirms these findings and attributes the effect to transient resonances. Our simulation suggests that ultrafast form factor changes during the exposure can increase the brightness of X-ray images by several orders of magnitude. Our study guides the way towards imaging with unprecedented combination of spatial and temporal resolution at the nanoscale.

physics.optics

Fluorescence intensity correlation imaging with high resolution and elemental contrast using intense x-ray pulses

We theoretically investigate the fluorescence intensity correlation (FIC) of Ar clusters and Mo-doped iron oxide nanoparticles subjected to intense, femtosecond and sub-femtosecond XFEL pulses for high-resolution and elemental contrast imaging. We present the FIC of {\Ka} and {\Kah} emission in Ar clusters and discuss the impact of sample damage on retrieving high-resolution structural information and compare the obtained structural information with those from the coherent difractive imaging (CDI) approach. We found that, while sub-femtosecond pulses will substantially benefit the CDI approach, few-femtosecond pulses may be sufficient for achieving high-resolution information with FIC. Furthermore, we show that the fluorescence intensity correlation computed from the fluorescence of Mo atoms in Mo-doped iron oxide nanoparticles can be used to image dopant distributions.

physics.atm-clus

Ultraintense, ultrashort pulse x-ray scattering in small molecules

We examine x-ray scattering from an isolated organic molecule from the linear to nonlinear absorptiveregime. In the nonlinear regime, we explore the importance of both the elastic and inelastic channelsand observe the onset of nonlinear behavior as a function of pulse duration and energy. In the linearregime, we test the sensitivity of the scattering signal to molecular bonding and electronic correlationvia calculations using the independent atom model (IAM), Hartree-Fock (HF) and density functionaltheory (DFT). Finally, we describe how coherent x-ray scattering can be used to directly visualizefemtosecond charge transfer and dissociation within a single molecule undergoing x-ray multiphotonabsorption.

physics.chem-ph

Resonant propagation of x-rays from the linear to the nonlinear regime

We present a theoretical study of temporal, spectral, and spatial reshaping of intense, ultrafast x-ray pulses propagating through a resonant medium. Our calculations are based on the solution of a 3D time-dependent Schrödinger-Maxwell equation, with the incident x-ray photon energy on resonance with the core-level 1s-3p transition in neon. We study the evolution of the combined incident and medium-generated field, including the effects of stimulated emission, absorption, ionization and Auger decay, as a function of the input pulse energy and duration. We find that stimulated Raman scattering between core-excited states $1s^{-1}3p$ and $2p^{-1}3p$ occurs at high x-ray intensity, and that the emission around this frequency is strongly enhanced when also including the similar $1s^{-1}-2p^{-1}$ response of the ion. We also explore the dependence of x-ray self-induced transparency (SIT) and self-focusing on the pulse intensity and duration, and we find that the stimulated Raman scattering plays an important role in both effects. Finally, we discuss how these nonlinear effects may potentially be exploited as control parameters for pulse properties of x-ray free-electron laser sources.

physics.atom-ph

Optically-dressed resonant Auger processes induced by high-intensity x rays

We have unveiled coherent multiphoton interferences originating from different quantum paths taken by the Auger electron induced by a high-intensity x-ray/XUV pulse under the presence of a strong optical field. These interferences give rise to a clear signature in the angle-resolved Auger electron spectrum: an asymmetry with respect to the energy of the Auger decay channel. In order to illustrate this effect we have considered the resonant Auger decay of the transition $2p^{5} \!\leftrightarrow\! 1s^{-1}2p^{6}$ in Ne$^{+}$. The simulations show that these interferences are very sensitive to the parameters of the x-ray and optical fields.

quant-ph