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We present a numerical tool Shiva designed to simulate the dust destruction in warm neutral, warm ionized, and hot ionized media under the influence of photo-processing, sputtering, and shattering. The tool is designed primarily to study…

Astrophysics of Galaxies · Physics 2019-06-28 M. S. Murga , D. S. Wiebe , E. E. Sivkova , V. V. Akimkin

Protein dynamics play a crucial role in protein biological functions and properties, and their traditional study typically relies on time-consuming molecular dynamics (MD) simulations conducted in silico. Recent advances in generative…

Biomolecules · Quantitative Biology 2025-06-02 Jiarui Lu , Xiaoyin Chen , Stephen Zhewen Lu , Aurélie Lozano , Vijil Chenthamarakshan , Payel Das , Jian Tang

X-ray astronomy is an important tool in the astrophysicist's toolkit to investigate high-energy astrophysical phenomena. Theoretical numerical simulations of astrophysical sources are fully three-dimensional representations of physical…

Instrumentation and Methods for Astrophysics · Physics 2015-02-18 John A. ZuHone , Veronica Biffi , Eric J. Hallman , Scott W. Randall , Adam R. Foster , Christian Schmid

The spatial and temporal relationships between stellar age, kinematics, and chemistry are a fundamental tool for uncovering the physics driving galaxy formation and evolution. Observationally, these trends are derived using carefully…

Astrophysics of Galaxies · Physics 2022-10-26 M. S. Miranda , B. A. Macfarlane , B. K. Gibson

We present the python package DiPolMol-Py, which can be used to calculate the rotational and hyperfine structure of $^2\Sigma$ molecules. The calculations can be performed in the presence of dc magnetic fields, dc electric fields and far…

Atomic Physics · Physics 2025-09-01 Bethan Humphreys , Alex J. Matthies , Hannah J. Williams

We consider basket trials in which a biomarker-targeting drug may be efficacious for patients across different disease indications. Patients are enrolled if their cells exhibit some levels of biomarker expression. The threshold level is…

Applications · Statistics 2025-05-20 Shijie Yuan , Jiaxin Liu , Zhihua Gong , Xia Qin , Crystal Qin , Yuan Ji , Peter Müller

The dynamic mode decomposition (DMD) is a simple and powerful data-driven modeling technique that is capable of revealing coherent spatiotemporal patterns from data. The method's linear algebra-based formulation additionally allows for a…

PyLlama is a handy Python toolkit to compute the electromagnetic reflection and transmission properties of arbitrary multilayered linear media, including the case of anisotropy. Relying on a $4 \times 4$-matrix formalism, PyLlama implements…

Optics · Physics 2021-12-24 Mélanie M. Bay , Silvia Vignolini , Kevin Vynck

Logical models offer a simple but powerful means to understand the complex dynamics of biochemical regulation, without the need to estimate kinetic parameters. However, even simple automata components can lead to collective dynamics that…

Other Computer Science · Computer Science 2018-08-30 Rion Brattig Correia , Alexander J. Gates , Xuan Wang , Luis M. Rocha

Physicochemical models can be powerful tools to trace the chemical evolution of a protostellar system and allow to constrain its physical conditions at formation. The aim of this work is to assess whether source-tailored modelling is needed…

Solar and Stellar Astrophysics · Physics 2020-08-19 Beatrice M. Kulterer , Maria N. Drozdovskaya , Audrey Coutens , Sébastien Manigand , Gwendoline Stéphan

We use a simple one-zone galactic chemical evolution model to quantify the uncertainties generated by the input parameters in numerical predictions, for a galaxy with properties similar to those of the Milky Way. We compiled several studies…

Astrophysics of Galaxies · Physics 2016-06-22 Benoit Côté , Christian Ritter , Brian W. O'Shea , Falk Herwig , Marco Pignatari , Samuel Jones , Chris Fryer

Major advancements in fields as diverse as biology and quantum computing have relied on a multitude of microscopic techniques. All optical, electron and scanning probe microscopy advanced with new detector technologies and integration of…

Instrumentation and Detectors · Physics 2023-03-01 Rama Vasudevan , Mani Valleti , Maxim Ziatdinov , Gerd Duscher , Suhas Somnath

The oxidation of human sebum, a lipid mixture covering our skin, generates a range of volatile and semi-volatile carbonyl compounds that contribute largely to indoor air pollution in crowded environments. Kinetic models have been developed…

Soft Condensed Matter · Physics 2025-02-20 Rinto Thomas , Praveen Ranganath Prabhakar , Douglas J. Tobias , Michael von Domaros

Scanning tunneling and atomic force microscopies (STM/nc-AFM) are rapidly progressing to offer unprecedented spatial resolution of a diverse array of chemical species. In particular, they are employed to characterize on-surface chemical…

Mesoscale and Nanoscale Physics · Physics 2022-05-12 Jack Hellerstedt , Aleš Cahlík , Martin Švec , Oleksandr Stetsovych , Tyler Hennen

We present a Python package together with a practical guide for the implementation of a lightweight diversity-enhanced genetic algorithm (GA) approach for the exploration of multi-dimensional parameter spaces. Searching a parameter space…

Neural and Evolutionary Computing · Computer Science 2024-12-24 Jonas Wessén , Eliel Camargo-Molina

We present ELSA, a new modular software package, written in C, to analyze and manage spectroscopic data from emission-line objects. In addition to calculating plasma diagnostics and abundances from nebular emission lines, the software…

Astrophysics · Physics 2009-11-11 M. D. Johnson , J. S. Levitt , R. B. C. Henry , K. B. Kwitter

The phase-field method has become a useful tool for the simulation of classical metallurgical phase transformations as well as other phenomena related to materials science. The thermodynamic consistency that forms the basis of these…

We have extended our chemical and cosmological galaxy evolution model to calculate the abundance evolution for altogether 16 different elements in spiral galaxies in a chemically consistent way which is a considerable step towards a more…

Astrophysics · Physics 2007-05-23 Ulrich Lindner , Uta Fritze -- von Alvensleben , Klaus J. Fricke

Point cloud completion is a fundamental task in 3D vision. A persistent challenge in this field is simultaneously preserving fine-grained details present in the input while ensuring the global structural integrity of the completed shape.…

Computer Vision and Pattern Recognition · Computer Science 2025-11-21 Lirui Zhang , Zhengkai Zhao , Zhi Zuo , Pan Gao , Jie Qin

The increasing availability of high-quality optical and near-infrared spectroscopic data, as well as advances in modelling techniques, have greatly expanded the scientific potential of spectroscopic studies. However, the software tools…

Instrumentation and Methods for Astrophysics · Physics 2025-12-23 Daniele Gasparri , Lorenzo Morelli , Umberto Battino , Jairo Méndez Abreu , Adriana de Lorenzo-Cáceres