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Creators/Authors contains: "John, M"

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  1. Free, publicly-accessible full text available November 19, 2026
  2. Modeling L-edge spectra at X-ray wavelengths requires consideration of spin–orbit splitting of the 2p orbitals. We introduce a low-cost tool to compute core-level spectra that combines a spin–orbit mean-field description of the Breit–Pauli Hamiltonian with nonrelativistic excited states computed using the semi-empirical density-functional theory configuration-interaction singles (DFT/CIS) method, within the state-interaction approach. Our version of DFT/CIS was introduced recently for K-edge spectra and includes a semi-empirical correction to the core orbital energies, significantly reducing ad hoc shifts that are typically required when time-dependent (TD-)DFT is applied to core-level excitations. In combination with the core/valence separation approximation and spin–orbit couplings, the DFT/CIS method affords semiquantitative L-edge spectra at CIS cost. Spin–orbit coupling has a qualitative effect on the spectra, as demonstrated for a variety of 3d transition metal systems and main-group compounds. The use of different active orbital spaces helps to facilitate spectral assignments. We find that spin–orbit splitting has a negligible effect on M-edge spectra for 3d transition metal species. 
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    Free, publicly-accessible full text available July 11, 2026
  3. High-harmonic generation (HHG) has been established as a powerful tool for studying structure and dynamics of quantum systems in gas and solid phases. To date, only a few studies have extended HHG spectroscopy to liquids, and much remains unresolved concerning the information that can be extracted from HHG spectra about the local liquid environment and the potential of HHG as a nonlinear probe of solvation dynamics. In this work, we investigate HHG in liquid binary solutions consisting of mixtures of aromatic benzene derivatives solvated in methanol. We observe evidence of a localized solvation structure that is imprinted on the harmonic spectra in the form of a strongly suppressed harmonic order, and an overall reduction of the total harmonic yield. We characterize this behavior as a function of laser parameters, concentration, and other halogenated benzene derivatives in methanol solution. Guided by theory, we interpret the results in terms of a localized solvation shell that is formed in specific solutions and acts like a local scattering barrier in the HHG process. This work demonstrates the potential of high-harmonic spectroscopy in liquids to extract detailed information about the structure and dynamics of solvation while expanding our understanding of the fundamental mechanism of HHG in systems with short-range order. 
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    Free, publicly-accessible full text available November 25, 2026
  4. Voronoi diagrams are widely used to model disperse systems such as foams, powders, polycrystals and atoms in the classical limit. Voronoi tessellations partition the continuous phase into compartments, or cells, that encompass all space closer to the assigning dispersed object than any other in the system. To account for heterogeneity in object size, weights are applied to avoid unphysical partitioning across non-contacting objects. Power and additive weighting are the most common weighting schemes, wherein power is more computationally tractable but additive weighting correlates more directly with size. In general, the two schemes produce distinct spatial decompositions for any non-monodisperse system. To calibrate the divergent volumetric metrics from the two schemes, and to gain physical insight into their divergence, we compared power and additively weighted Voronoi diagrams of polydisperse ensembles representing physically relevant ranges of polydispersity, density, and overlap. When tested against experimental distributions of gas foams, the results related their divergent power and additively weighted decompositions to the polydispersity of their particle size distributions. Geometric analysis of the Voronoi cells implicated the subpopulation of small objects as the primary contributors to the divergence through their preferential assignment of larger, aspherical power cells relative to their additively weighted counterparts. 
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    Free, publicly-accessible full text available July 30, 2026
  5. Abstract Observational studies of Hiiregion–molecular cloud interactions constrain models of feedback and quantify its impact on the surrounding environment. A recent hypothesis proposes that a characteristic spectral signature in ground state hyperfine lines of hydroxyl (OH)—the OH flip—may trace gas that is dynamically interacting with an expanding Hiiregion, offering a new means of probing such interactions. We explore this hypothesis using dedicated Jansky Very Large Array observations of three Galactic Hiiregions, G049.205−0.343, G034.256+0.145, and G024.471+0.492, in 1–2 GHz continuum emission, all four 18 cm ground-state OH lines, and multiple hydrogen radio recombination lines. A Gaussian decomposition of the molecular gas data reveals complex OH emission and absorption across our targets. We detect the OH flip toward two of our sources, G049.205−0.343 and G034.256+0.145, finding agreement between key predictions of the flip hypothesis and the observed multiwavelength spectra, kinematics, and morphology. Specifically, we demonstrate a strong spatial and kinematic association between the OH flip and the ionized gas of the Hiiregions—the first time this has been demonstrated for resolved sources—and evidence from13CO(1–0) data that the expected OH component originates from the nondisturbed gas of the parent cloud. While we detect no flip in G024.471+0.492, we do find evidence of interacting molecular gas traced by OH, providing further support for OH’s ability to trace Hiiregion–molecular cloud interactions. 
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    Free, publicly-accessible full text available December 22, 2026
  6. Free, publicly-accessible full text available August 1, 2026
  7. Exact probabilistic inference is a requirement for many applications of probabilistic programming languages (PPLs) such as in high-consequence settings or verification. However, designing and implementing a PPL with scalable high-performance exact inference is difficult: exact inference engines, much like SAT solvers, are intricate low-level programs that are hard to implement. Due to this implementation challenge, PPLs that support scalable exact inference are restrictive and lack many features of general-purpose languages. This paper presents Roulette, the first discrete probabilistic programming language that combines high-performance exact inference with general-purpose language features. Roulette supports a significant subset of Racket, including data structures, first-class functions, surely-terminating recursion, mutable state, modules, and macros, along with probabilistic features such as finitely supported discrete random variables, conditioning, and top-level inference. The key insight is that there is a close connection between exact probabilistic inference and the symbolic evaluation strategy of Rosette. Building on this connection, Roulette generalizes and extends the Rosette solver-aided programming system to reason about probabilistic rather than symbolic quantities. We prove Roulette sound by generalizing a proof of correctness for Rosette to handle probabilities, and demonstrate its scalability and expressivity on a number of examples. 
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    Free, publicly-accessible full text available June 10, 2026
  8. Free, publicly-accessible full text available May 1, 2026
  9. Bonin, Aurélie (Ed.)
    ABSTRACT Molecular tools are increasingly being used to survey the presence of biodiversity and their interactions within ecosystems. Indirect methods, like environmental DNA (eDNA) and invertebrate‐derived DNA (iDNA), are dependent on sequence databases with accurate and sufficient taxonomic representation. These methods are increasingly being used in regions and habitats where direct detection or observations can be difficult for a variety of reasons. Madagascar is a biodiversity hotspot with a high proportion of endemic species, many of which are threatened or endangered. Here we describe a new resource, VoronaGasyCodes, a curated database of newly published genetic sequences from Malagasy birds. Our database is currently populated with six mitochondrial genes or DNA barcodes for 142 species including 70% of the birds endemic to the island and will be periodically updated as new data become available. We demonstrate the utility of our database with an iDNA study of leech blood meals where we successfully identified 77% of the hosts to species. These types of resources for characterising biodiversity are critical for insights into species distribution, discovery of new taxa, novel ecological connections and advancing conservation and restoration measures. 
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    Free, publicly-accessible full text available August 7, 2026
  10. Free, publicly-accessible full text available July 16, 2026