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We present the Python-based Molecule Builder for ESPResSo (pyMBE), an open source software to design custom Coarse-Grained (CG) models, as well as pre-defined models of polyelectrolytes, peptides and globular proteins in the Extensible…

Transiting exoplanet parameter estimation from time-series photometry and Doppler spectroscopy is fundamental to study planets' internal structures and compositions. Here we present the code pyaneti, a powerful and user-friendly software…

Earth and Planetary Astrophysics · Physics 2018-09-19 O. Barragán , D. Gandolfi , G. Antoniciello

The new generation of observatories and instruments (VLT/ERIS, JWST, ELT) motivate the development of robust methods to detect and characterise faint and close-in exoplanets. Molecular mapping and cross-correlation for spectroscopy use…

A computed line list for formaldehyde, H$_2{}^{12}$C$^{16}$O, applicable to temperatures up to $T=1500$~K is presented. An empirical potential energy and {\it ab initio} dipole moment surfaces are used as the input to nuclear motion program…

Astrophysics of Galaxies · Physics 2015-06-02 Ahmed F. Al-Refaie , Andrey Yachmenev , Jonathan Tennyson , Sergei N. Yurchenko

PyECLOUD is a newly developed code for the simulation of the electron cloud (EC) build-up in particle accelerators. Almost entirely written in Python, it is mostly based on the physical models already used in the ECLOUD code but, thanks to…

Accelerator Physics · Physics 2013-09-27 G. Iadarola , G. Rumolo

Background: The study of genome-scale metabolic models and their underlying networks is one of the most important fields in systems biology. The complexity of these models and their description makes the use of computational tools an…

Molecular Networks · Quantitative Biology 2012-12-03 D. Gamermann , A. Montagud , R. A. Jaime Infante , J. Triana , P. F. de Córdoba , J. F. Urchueguía

The objective of Information Extraction (IE) is to derive structured representations from unstructured or semi-structured documents. However, developing IE models is complex due to the need of integrating several subtasks. Additionally,…

Information Retrieval · Computer Science 2024-06-04 Arne Binder , Leonhard Hennig , Christoph Alt

The GYT line list covering rotational, rovibrational and rovibronic transitions of the mercapto radical SH is presented. This work extends and replaces the SNaSH line list [Yurchenko et al., 2018, MNRAS, 478, 270] which covers the ground…

Earth and Planetary Astrophysics · Physics 2019-10-25 Maire N. Gorman , Sergei N. Yurchenko , Jonathan Tennyson

Two FORTRAN programs are presented which plot the Hertzsprung-Russell diagram and the temporal evolution of such stellar quantities as: central and photospheric isotopic abundances, central densities and temperatures, luminosities,effective…

Astrophysics · Physics 2007-05-23 Theodore Liolios

Hyperspectral pansharpening consists of fusing a high-resolution panchromatic band and a low-resolution hyperspectral image to obtain a new image with high resolution in both the spatial and spectral domains. These remote sensing products…

Computer Vision and Pattern Recognition · Computer Science 2024-12-30 Matteo Ciotola , Giuseppe Guarino , Gemine Vivone , Giovanni Poggi , Jocelyn Chanussot , Antonio Plaza , Giuseppe Scarpa

We describe PyRaTE, a new, non-local thermodynamic equilibrium (non-LTE) line radiative transfer code developed specifically for post-processing astrochemical simulations. Population densities are estimated using the escape probability…

Astrophysics of Galaxies · Physics 2018-05-30 Aris Tritsis , Harold W. Yorke , Konstantinos Tassis

We present the pyerrors python package for statistical error analysis of Monte Carlo data. Linear error propagation using automatic differentiation in an object oriented framework is combined with the $\Gamma$-method for a reliable…

High Energy Physics - Lattice · Physics 2023-05-03 Fabian Joswig , Simon Kuberski , Justus T. Kuhlmann , Jan Neuendorf

Single molecule F\"orster resonance energy transfer (smFRET) is a powerful experimental technique for studying the properties of individual biological molecules in solution. However, as adoption of smFRET techniques becomes more widespread,…

Computational Engineering, Finance, and Science · Computer Science 2014-12-22 Rebecca R. Murphy , Sophie E. Jackson , David Klenerman

Comprehensive vibration-rotation line lists for eight isotopologues of carbon monosulphide (CS) ($^{12}$C$^{32}$S, $^{12}$C$^{33}$S, $^{12}$C$^{34}$S, $^{12}$C$^{36}$S, $^{13}$C$^{32}$S, $^{13}$C$^{33}$S, $^{13}$C$^{34}$S, $^{13}$C$^{36}$S)…

Astrophysics of Galaxies · Physics 2015-10-21 Geethu Paulose , Emma J. Barton , Sergei N. Yurchenko , Jonathan Tennyson

Silicon dioxide (SiO$_2$) is expected to occur in the atmospheres of hot rocky super-Earth exoplanets but a lack of spectroscopic data is hampering its possible detection. Here, we present the first, comprehensive molecular line list for…

Earth and Planetary Astrophysics · Physics 2020-05-29 A. Owens , E. K. Conway , J. Tennyson , S. N. Yurchenko

SiH has long been observed in the spectrum of our Sun and other cool stars. Computed line lists for the main isotopologues of silicon monohydride, $^{28}$SiH, $^{29}$SiH, $^{30}$SiH and $^{28}$SiD are presented. These line lists consider…

Solar and Stellar Astrophysics · Physics 2017-12-13 Sergei N. Yurchenko , Frances Sinden , Lorenzo Lodi , Christian Hill , Maire N. Gorman , Jonathan Tennyson

A new line list for ethylene, $^{12}$C$_2$$^1$H$_4$ is presented. The line list is based on high level ab initio potential energy and dipole moment surfaces. The potential energy surface is refined by fitting to experimental energies. The…

Earth and Planetary Astrophysics · Physics 2018-08-21 Barry P. Mant , Andrey Yachmenev , Jonathan Tennyson , Sergei N. Yurchenko

H$_3^+$ is a ubiquitous and important astronomical species whose spectrum has been observed in the interstellar medium, planets and tentatively in the remnants of supernova SN1897a. Its role as a cooler is important for gas giant planets…

$clustertools$ is a Python package for analyzing star cluster simulations. The package is built around the $StarCluster$ class, which stores all data read in from the snapshot of a given model star cluster. The package contains functions…

Astrophysics of Galaxies · Physics 2023-05-22 Jeremy J. Webb

We introduce pyGSL, a Python library that provides efficient implementations of state-of-the-art graph structure learning models along with diverse datasets to evaluate them on. The implementations are written in GPU-friendly ways, allowing…

Machine Learning · Computer Science 2022-11-08 Max Wasserman , Gonzalo Mateos