AuRaCh is a tool for simulation of radiolysis of liquids under exposure to ionizing radiation. Albeit it has been primarily written for liquid-phase transmission electron microscopy, it can be used for other ionizing sources than electrons, such as x-rays, as well. Its main advantage is the automation of the creation of coupled differential equation sets. Consequently, AuRaCh can be employed for non-irradiated chemical reaction kinetic engineering, as well, simply by setting the dose rate to 0.
Its working principle is described in:
B. Fritsch, T.S. Zech, M.P. Bruns, A. Körner, S. Khadivianazar, M. Wu, N. Zargar Talebi, S. Virtanen, T. Unruh, M.P.M. Jank, E. Spiecker, A. Hutzler, Radiolysis‐Driven Evolution of Gold Nanostructures – Model Verification by Scale Bridging in situ Liquid‐Phase Transmission Electron Microscopy and X‐Ray Diffraction, Advanced Science 2022, 9 (25), 2202803. DOI:10.1002/advs.202202803.
If you are new to running python scripts, I propose to use Anaconda: https://www.anaconda.com/products/distribution. I used Notepad++ to set up the reaction text file, so the spacing is adjusted to display properly using this software. https://notepad-plus-plus.org/
Naturally, this code is still under ongoing development. I invite you to contribute :)
The folder "working example" provides code to perform a simulation of the HAuCl4 reaction set taken off the original AuRaCh publication as exemplary usecase scenario. To run the code, please acknowledge the required dependencies. Its default environment should be able to run all files uploaded here.
"AuRaCh reaction networks - Radiolytic Acidity" contains the reaction networks and initial concentrations/g-values file for the simulations performed in
B. Fritsch, A. Körner, T. Couasnon, R. Blukis, M. Taherkhani, L.G. Benning, M.P.M. Jank, E. Spiecker, A. Hutzler, Tailoring the Acidity of Liquid Media with Ionizing Radiation: Rethinking the Acid-Base Correlation Beyond pH, The Journal of Physical Chemistry Letters 2023, 14 (20), 4644–4651. DOI:10.1021/acs.jpclett.3c00593.
A reaction file for simulating an aqueous solution containing Fe(II)/Fe(III) can be found in "AuRaCh reaction network - Fe". It is introduced in
T. Couasnon, B. Fritsch, M.P.M. Jank, R. Blukis, A. Hutzler, L. Benning, Goethite Mineral Dissolution to Probe the Chemistry of Radiolytic Water in Liquid-Phase Transmission Electron Microscopy, Advanced Science 2023, 10 (25), 2301904. DOI:10.1002/advs.202301904.
To create subsets of reaction networks (sparse reaction sets), the script in the folder "Sparse Reaction Files" can be used. Alongside, you'll find three examples. Those, as well as the concept, are explained in
B. Fritsch, P. Malgareti, J. Harting, Karl J.J. Mayrhofer, A. Hutzler, Precision of Radiation Chemistry Networks: Playing Jenga with Kinetic Models for Liquid-Phase Electron Microscopy, Precision Chemistry 2023, 1 (10), 592-601. DOI:10.1021/prechem.3c00078.
Reaction files for simulating aqueous AgNO3 solutions with and without tert-butanol are found in "AuRach reaction networks AgNO3". When using them, please cite
J. Sun, B. Fritsch, A. Körner, M. Taherkhani, C. Park, M. Wang, A. Hutzler and T. Woehl, Discovery of molecular intermediates and non-classical nanoparticle formation mechanisms by liquid phase electron microscopy and reaction throughput analysis, ChemRxiv 2024, Preprint. DOI:10.26434/chemrxiv-2024-r636h
Please use the AuRaCh code file or the GUI to run the simulations or contact me in case of further questions.