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Jonathan Tennyson

Publications and source records attributed to Jonathan Tennyson.

At least 19 recordsLinked to original sources
arXiv2026

PyExoCross 2.0: A Python Framework for LTE and non-LTE Spectra, Cross Sections, and Spectroscopic Post-processing of Atomic and Molecular Line Lists

PyExoCross is a Python-based spectroscopic post-processing framework for converting large atomic and molecular line lists into scientifically useful quantities, including partition function, specific heats, cooling functions, lifetimes, oscillator strengths, line intensities, stick spectra, and absorption and emission cross sections. It is intended for applications in astrophysics, planetary atmospheres, laboratory spectroscopy, and other high-temperature environments where large modern databases require efficient and reproducible computational treatment. The new release provides both a configuration-file-driven command-line interface (CLI) and a Python application programming interface (API) within a unified computational framework. The original input file workflow is retained, while the Python API enables direct use in scripts, notebooks, and automated pipelines. The version PyExoCross 2.0 also adds explicit support for non-local thermodynamic equilibrium (non-LTE) calculations, including two-temperature models and user-defined density and population treatments for both absorption and emission spectra. In addition, database compatibility has been expanded beyond ExoMol, HITRAN, and HITEMP line lists to include high-resolution molecular database ExoMolHR and atomic database ExoAtom. GPU acceleration is also introduced for computationally intensive intensity and cross-section calculations and is available for all currently supported database formats. These developments improve workflow flexibility, reproducibility, and integration with modern data-analysis environments, while extending the physical modelling capabilities of the code. PyExoCross therefore provides a more general and extensible platform for large-scale spectroscopic simulations based on modern atomic and molecular databases.

astro-ph.IM↗
arXiv2026

Automated AFGL quantum number assignment for CO$_2$ isotopologues using a graph neural network

Accurate quantum number assignment for calculated molecular energy levels is a critical bottleneck in generating line broadening parameters for comprehensive line lists for radiative transfer applications. We present an automated pipeline for assigning Air Force Geophysics Laboratory (AFGL) quantum numbers to CO2 calculated rovibrational states lying below 15,000cm$^{-1}$ across all 12 stable isotopologues. A GraphSAGE graph neural network is trained transductively on empirical (MARVEL) energy levels, exploiting inter-isotopologue perturbation chains and intra-isotopologue rotational ladder edges to propagate assignment information to unlabelled calculated states. Physical uniqueness is enforced locally by a Hungarian algorithm solver operating within groups of states sharing the same polyad, rotational quantum number, and parity. A five-generation bootstrap loop iteratively promotes high-confidence predictions into the training set, expanding coverage without additional labelling effort. The pipeline assigns 224,650 previously unlabelled states over 12 isotopologues, accounting for 10.7$\%$ of all available states (including MARVEL-derived levels), with coverage now increased to 97.4$\%$ below 5000cm$^{-1}$. The pipeline includes a novel decision tree method for converting AFGL to Herzberg notation in asymmetric isotopologues, while the architecture and Hungarian uniqueness enforcement are applicable beyond CO2, any molecular system with a conserved polyad-like quantum number and a large body of unlabelled computed states is a natural target for this approach, suggesting a pathway toward automated quantum number annotation for the next generation of large-scale computed line lists.

physics.chem-ph↗
arXiv2026

Symmetry-adapted qubit encoding with complete active space and Bravyi--Kitaev mapping for quantum chemistry on a quantum computer

We present a symmetry-adapted qubit encoding with complete active space (SAE-CAS) for quantum chemistry on fault-tolerant and near-term quantum processors. Building on exact-symmetry encodings, we extend symmetry-adapted mappings to approximate $Z$-symmetries corresponding to frozen-core and virtual orbitals, thereby reducing qubit requirements without significant loss of accuracy. We derive the mapping from the second-quantised Hamiltonian to active-space qubit Hamiltonians, prove its equivalence to the canonical CAS Hamiltonian with frozen-core and virtual-orbital projection, and integrate it with point-group and spin-parity symmetry encodings via affine Clifford transformations to maximise qubit reduction while preserving the target symmetry sector. The same framework also accommodates the Bravyi--Kitaev mapping, yielding an SAE-CAS-BK variant that is unitarily equivalent to SAE-CAS. Numerical benchmarking on nine small molecules using UCCSD and a hardware-efficient shifted-circular-alternating (HE-SCA) ansatz shows that SAE-CAS reduces qubit counts and Pauli-operator weight, yields shallower circuits with fewer parameters, and often accelerates VQE convergence; with HE-SCA it consistently reaches CAS reference energies in cases where JW-CAS does not converge within the tested budgets. We provide an open-source implementation in the Python package QuantumSymmetry. SAE-CAS offers a route to resource-efficient molecular simulations on fault-tolerant and near-term quantum processors.

quant-ph↗
arXiv2026

Electron-molecule scattering via R-matrix variational algorithms on a quantum computer

Electron-molecule collisions play a central role in both natural processes and modern technological applications, particularly in plasma processing. Conventional computational strategies such as the R-matrix method have been widely adopted yet encounter significant scaling challenges in treating more complex systems. In this work we present a quantum computational approach that utilises the variational quantum eigensolver (VQE) and variations thereof to overcome these limitations. We explore a number of methods, including the use of number projection operators and simultaneous optimisation. We demonstrate the feasibility of our method on a model problem of electron scattering from the hydrogen molecule, with numerical results obtained using a noiseless classical simulator. We recover the full spectrum of the Hamiltonian within a chosen symmetry sector. Moreover, the optimal circuit parameters directly encode the R-matrix boundary amplitudes needed for subsequent scattering computations. To our knowledge, this is the first application of quantum algorithms to electron--molecule scattering, and specifically the first formulation of the R-matrix inner-region problem on a quantum computer.

quant-ph↗
arXiv2026

A new look into the atmospheric composition of WASP-39 b

Being one of the first exoplanets observed by the James Webb Space Telescope, WASP-39 b has become an iconic target and many transit spectra recorded with different instruments (NIRISS, NIRCAM, NIRSpec G395H, NIRSpec PRISM and MIRI) are currently available, allowing in-depth studies of its atmosphere. We present here a novel approach to interpret WASP-39 b's transit spectroscopic data, consisting of a multi-step process where ab initio equilibrium chemistry models and blind retrievals are used iteratively to find physically robust, optimal solutions. Following this approach, we have identified a new scenario to explain WASP-39 b's atmospheric composition, in which silicon-based chemistry plays a major role. In this scenario, SiO may explain the spectral absorption at 4.1 $μ$m, currently interpreted as being due to SO$_2$. SiO and the other gas species identified by the retrieval models, i.e. H$_2$O, CO$_2$, Na and K, are consistent with an atmosphere in chemical equilibrium with a temperature-pressure profile constrained by H$_2$O and CO$_2$ absorption bands. In addition, silicate clouds and hazes can produce the spectral features observed by MIRI in the spectral window 5-12 $μ$m. While we advocate the need for more data, possibly at higher spectral resolution, to confirm our results for WASP-39 b's atmospheric composition, we highlight a refined atmospheric retrieval strategy with pre-selection and post-reconstruction to guide the next generation of transit spectroscopy.

astro-ph.EP↗
arXiv2026

Machine learning isotope shifts in molecular energy levels

Recent advances in the use of High-Resolution Cross-Correlation Spectroscopy (HRCCS) to detect molecular species in exoplanet atmospheres, presents a new challenge for the accuracy of reference spectroscopic line lists. While parent isotopologues of key atmospheric tracers are often well-characterized, minor isotopologues, crucial for diagnosing planetary formation histories and evolution, suffer from a scarcity of experimental data, often leading to reliance on less accurate theoretical predictions. In this work, a comprehensive machine learning framework is designed to mitigate these inaccuracies by modelling the residual errors of the isotopologue extrapolation (IE) method used within the ExoMol project. A fully connected neural network architecture for carbon dioxide (CO$_2$) is shown to predict energy corrections with high fidelity, reducing the mean absolute error (MAE) relative to the original IE approach for more than 87\% of the levels when benchmarked against empirical (\Marvel) energies. Furthermore, development of a novel hybrid, molecule-aware transfer learning architecture is presented that successfully propagates correction patterns from the data-rich CO$_2$ system to the data-poor carbon monoxide (CO) system. This transfer learning approach yields MAE improvements in over 93\% of CO samples, demonstrating that physical correction factors related to isotopic substitution can be generalized across chemically related molecular systems. Updated and improved line lists are presented for 11 CO$_2$ isotopologues and energy levels for excited states of CO isotopologues are predicted. The methodology establishes a scalable, data-driven paradigm for refining molecular line lists, helping to bridge the gap between theoretical calculations and experimental precision.

astro-ph.EP↗
arXiv2026

Atmospheric Characterisation with the Twinkle Space Telescope Following Advances from JWST Observations

The Twinkle Space Telescope is a satellite designed for spectroscopic observations of a wide range of extrasolar and solar system objects. Equipped with a 0.45 m diameter telescope and a spectrometer covering from 0.5 to 4.5 μm simultaneously, Twinkle will be launched in a sun-synchronous, low-Earth orbit, and it is expected to operate for seven years. Twinkle is developed, managed and operated by Blue Skies Space (BSSL), a space science data company whose vision is to accelerate and expand the availability of new, high-quality datasets to researchers worldwide, complementing the space-observatories delivered by government space agencies. Over its life-time, Twinkle will conduct large-scale survey programs. The scientific objectives and observational strategy of these surveys are defined by researchers who join the Science Team. Leveraging advances made possible by recent observations with the James Webb Space Telescope, we present here updated simulations evaluating Twinkle's observational capabilities in the context of exoplanet atmospheres. Through retrieval analyses of HD 209458 b, WASP-107 b, GJ 3470 b, and 55 Cnc e, we demonstrate how increasing observational investment enhances the retrieval of atmospheric parameters and molecular abundances. Our sensitivity study highlights Twinkle's capability to detect less abundant/detectable molecules depending on the observing strategies adopted. This work provides practical guidance for developing targeted observational strategies to maximize Twinkle's scientific return.

astro-ph.IM↗
arXiv2026

The Preliminary Mauve Science Programme: Science themes identified for the first year of operations

Mauve is a low-cost small satellite developed and operated by Blue Skies Space Ltd. The payload features a 13 cm telescope connected with a fibre that feeds into a UV-Vis spectrometer. The detector covers the 200-700 nm range in a single shot, obtaining low resolution spectra at R~20-65. Mauve has launched on 28th November 2025, reaching a 510 km Low-Earth Sun-synchronous orbit. The satellite will enable UV and visible observations of a variety of stellar objects in our Galaxy, filling the gaps in the ultraviolet space-based data. The researchers that have already joined the mission have defined the science themes, observational strategy and targets that Mauve will observe in the first year of operations. To date 10 science themes have been developed by the Mauve science collaboration for year 1, with observational strategies that include both long duration monitoring and short cadence snapshots. Here, we describe these themes and the science that Mauve will undertake in its first year of operations.

astro-ph.SR↗
arXiv2026

MARVEL Analysis of the Measured High-resolution Spectra of CO Isotopologues

Carbon monoxide is thought to be the second most abundant molecule in the Universe. This makes observation of both its parent isotopologue ($^{12}$C$^{16}$O) and its stable isotopologues, $^{13}$C$^{16}$O, $^{12}$C$^{18}$O, $^{12}$C$^{17}$O, $^{13}$C$^{18}$O and $^{13}$C$^{17}$O, important in variety of objects. Here the MARVEL (Measured Active Rotational-Vibrational Energy Levels) algorithm is used to determine precise rotational vibrational energy levels for the five minor isotopologues of carbon monoxide in their electronic ground state. A review of 27 literature sources yields 3716, 1454, 89, 728 and 57 validated transitions for $^{13}$C$^{16}$O, $^{12}$C$^{18}$O, $^{12}$C$^{17}$O, $^{13}$C$^{18}$O and $^{13}$C$^{17}$O, respectively, giving 863, 499, 33, 345 and 45 empirically determined, rotation vibration energy levels, respectively.

astro-ph.GA↗
arXiv2026

ExoMol line lists -- LXIII: ExoMol line lists for 12 isotopologues of CO$_2$

Extensive rovibrational line lists are constructed for 12 isotopologues of carbon dioxide: $^{12}$C$^{16}$O$_2$, $^{13}$C$^{16}$O$_2$, $^{12}$C$^{17}$O$_2$, $^{13}$C$^{17}$O$_2$, $^{12}$C$^{18}$O$_2$, $^{13}$C$^{18}$O$_2$, $^{16}$O$^{12}$C$^{17}$O, $^{16}$O$^{12}$C$^{18}$O, $^{16}$O$^{13}$C$^{17}$O, $^{16}$O$^{13}$C$^{18}$O, $^{17}$O$^{12}$C$^{18}$O, and $^{17}$O$^{13}$C$^{18}$O. The variational program TROVE was employed together with an exact kinetic energy operator, accurate empirical potential energy surface (Ames-2) and the ab initio dipole moment surface Ames-2021-40K. Empirical energy levels from the most recent MARVEL analyses, as well as from the HITRAN and CDSD databases, are used to replace calculated values where available. The line lists are further supplemented by assigning AFGL quantum numbers using machine-learning based estimators. The resulting data were employed to generate opacities with four radiative transfer codes, TauREx, ARCiS, NEMESIS, and petitRADTRANS, both for individual isotopologues and for CO$_2$ at terrestrial isotopic natural abundance. All line lists and associated data are available at www.exomol.com.

astro-ph.EP↗
arXiv2025

ExoAtom: A Database of Atomic Spectra in ExoMol Format

We present the ExoAtom database, www.exomol.com/exoatom, an extension of the ExoMol database to provide atomic line lists in the ExoMol format. ExoAtom is designed for detailed astrophysical, planetary, and laboratory applications. ExoAtom currently includes atomic data for 80 neutral atoms and 74 singly charged ions. These data are extracted from both the NIST and Kurucz databases, with 79/71 atoms/ions sourced from NIST and 38/37 atoms/ions sourced from Kurucz. ExoAtom uses the file types .all, .def, .states, .trans and .pf as fundamental components for structuring atomic data in a consistent hierarchy. The .states file contains quantum numbers, uncertainties, lifetimes, etc. The .trans file specifies Einstein A coefficients and their associated wavenumbers. The .pf file provides partition functions over a wide grid of temperatures. Post-processing of the ExoAtom data is provided by the program PyExoCross. Future development of ExoAtom will include additional ionization stages.

physics.atom-ph↗
arXiv2025

Data availability and requirements relevant for the Ariel space mission and other exoplanet atmosphere applications

The goal of this white paper is to provide a snapshot of the data availability and data needs primarily for the Ariel space mission, but also for related atmospheric studies of exoplanets and brown dwarfs. It covers the following data-related topics: molecular and atomic line lists, line profiles, computed cross-sections and opacities, collision-induced absorption and other continuum data, optical properties of aerosols and surfaces, atmospheric chemistry, UV photodissociation and photoabsorption cross-sections, and standards in the description and format of such data. These data aspects are discussed by addressing the following questions for each topic, based on the experience of the "data-provider" and "data-user" communities: (1) what are the types and sources of currently available data, (2) what work is currently in progress, and (3) what are the current and anticipated data needs. We present a GitHub platform for Ariel-related data, with the goal to provide a go-to place for both data-users and data-providers, for the users to make requests for their data needs and for the data-providers to link to their available data. Our aim throughout the paper is to provide practical information on existing sources of data whether in databases, theoretical, or literature sources.

astro-ph.IM↗
arXiv2025

Effective Core Potentials for calculations of continuum spectra of molecules using the molecular R-matrix method

Implementation of Effective Core Potentials (ECPs) into the molecular scattering suite UKRmol+ is presented together with a set of calculations for a range of targets relevant for plasma modeling. Continuum description in scattering and photoionization calculations for large targets or high-energy electrons often requires the use of numerical continuum functions and the associated molecular integrals. We derive expressions for ECP integrals over B-spline type orbitals using their momentum-space representation and describe their implementation. Sample calculations are presented for electron collision from bromine molecule (Br$_2$), silicon tetrabromide (SiBr$_4$) and tungsten hydride (WH) as well as photoionisation of methyl iodide (CH$_3$I).

physics.chem-ph↗
arXiv2025

VVV-WIT-13: an eruptive young star with cool molecular features

Here we investigate an infrared eruptive source, identified from the decade-long VISTA Variables in the Via Lactea survey (VVV). We named this target after a group of variable sources discovered by VVV, as VVV-WIT-13, with WIT standing for "What Is This?", due to its unique photometric variation behaviour and the mysterious origin of the outburst. This target exhibited an outburst with a 5.7 mag amplitude in the Ks-band, remained on its brightness plateau for 3.5 years, and then rapidly faded to its pre-eruptive brightness afterwards. We aim to reveal the variable nature and outburst origin of VVV-WIT-13 by presenting our follow-up photometric and spectroscopic observations along with theoretical models. We gathered photometric time series in both near- and mid-infrared wavelengths. We obtained near-infrared spectra during the outburst and decaying stages on XSHOOTER/VLT and FIRE/Magellan, and then fitted the detected molecular absorption features using models from ExoMol. We applied 2D numerical simulations to re-create the observables of the eruptive phenomenon. We observe deep AlO absorption bands in the infrared spectra of VVV-WIT-13, during the outburst stage, along with other more common absorption bands (e.g. CO). Our best-fit model suggests a 600 K temperature of the AlO absorption band. In the decaying stage, the AlO bands disappeared, whilst broad blue-shifted H2 lines arose, a common indicator of stellar wind and outflow. The observational evidence suggests that the CO and TiO features originate from an outflow or a wind environment. We find that VVV-WIT-13 is an eruptive young star with instability occurring in the accretion disk. One favoured theoretical explanation of this event is a disrupted gas clump at a distance of 3 au from the source. If confirmed, this would be the first such event observed in real time.

astro-ph.SR↗
arXiv2025

Dissociative recombination of NeH+ with low-energy electrons: Multichannel quantum defect theory including non-adiabatic couplings

Theoretical investigation of the dissociative recombination (DR) of NeH+ with low-energy electrons in the regime where the process occurs without direct potential energy curve crossings is presented. The calculations are performed using multichannel quantum defect theory, incorporating non-adiabatic couplings between electronic states. Unlike the previous treatment of the DR of HeH+, where only first-order radial couplings A(R) were considered, our formulation also incorporates the second-order terms B(R), together with a radial density of states \b{eta}ν (R) to describe the transition into the ionization continuum. This development uses a large number of potential energy curves and non-adiabatic couplings of NeH characterized by us previously, enabling a consistent modeling of the DR process. The resulting cross sections show good agreement with the available experimental data and fill a gap in theoretical data below 4.5 eV, where no detailed quantum calculations are currently available.

physics.atm-clus↗
arXiv2025

TIRAMISU: Non-LTE radiative transfer for molecules in exoplanet atmospheres

The TIRAMISU code, a new program for computing on-the-fly non-LTE molecular spectra and opacities for solving self-consistent radiative transfer problems in exoplanet atmospheres, is presented. The ultra-hot Jupiter KELT-20 b is used as a case study to identify the wavelength regions at which non-LTE effects may be detectable. It is shown that upper atmospheric OH in vibrational non-LTE should be observable primarily via hot bands in the mid-infrared and enhanced photodissociation in the visible. Varying the abundance of OH in non-LTE demonstrates a non-linear relationship between the abundance and the strength of non-LTE effects. Using recent calculations of the photodissociation probabilities of OH it is shown that non-LTE effects can increase the total photodissociation rate by two orders of magnitude in the upper atmosphere, which is likely to have a significant impact on atmospheric and chemical modelling. Increases and reductions in the molecular opacities under non-LTE conditions may lead to the mischaracterisation of molecular abundances in retrievals that only consider opacities computed under LTE. Collisional data requirements to support future non-LTE modelling for a variety of exoplanet atmospheres and across a wide range of wavelengths are discussed.

astro-ph.EP↗
arXiv2025

ExoPhoto: A Database of Temperature-Dependent Photodissociation Cross Sections

We present the ExoPhoto database (https://exomol.com/exophoto/), an extension of the ExoMol database, specifically developed to address the growing need for high-accuracy, temperature-dependent photodissociation cross section data towards short-UV wavelengths. ExoPhoto combines theoretical models from three major computational databases (ExoMol, UGAMOP and PhoMol) and experimental datasets from two experimental groups, providing extensive wavelength and temperature coverage. ExoPhoto currently includes photodissociation data for 20 molecules: AlH, HCl, HF, MgH, OH, NaO, MgO, O2, AlCl, AlF, CS, HeH+, CO, CO2, H2O, SO2, C2H2, C2H4, H2CO, and NH3, derived from theoretical models and supported by experimental data from 5 databases. ExoPhoto also includes detailed data on branching ratios and quantum yields for selected datasets. The data structure of ExoPhoto follows the ExoMol framework, with a consistent naming convention and hierarchical JSON-based organization. Photodissociation cross sections are stored in a set of .photo files which provide data as a function of wavelength with one file for each target molecule temperature. Future developments aim to include more photodissociation cross section data and to provide data for molecules in non-local thermodynamic equilibrium (non-LTE). These will expand the utility of ExoPhoto for advanced astrophysical, planetary modeling and industrial applications.

astro-ph.EP↗
arXiv2025

ExoMolHR: A Relational Database of Empirical High-Resolution Molecular Spectra

ExoMolHR is an empirical, high-resolution molecular spectrum calculator for the high-temperature molecular line lists available from the ExoMol molecular database. Uncertainties, where available, in recommended ExoMol datasets are used to select highly accurate spectral lines. These lines largely rely on empirical energy levels generated through the MARVEL (measured active rotation vibration energy levels) procedure, which is being systematically used to improve the energy and transition data provided by the ExoMol database. The freely accessible ExoMolHR database provides line positions with calculated intensities for a user-specified wavenumber/wavelength range and temperature. Spectra can be plotted on the ExoMolHR website (https://www.exomol.com/exomolhr/) or downloaded as a CSV file. Cross sections can be calculated using the Python program PyExoCross. The ExoMolHR database currently provides 24307135 spectral lines for 33 molecules and 58 isotopologues; these numbers will increase as the ExoMol database is updated.

astro-ph.EP↗