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SViMULATE: a computer program facilitating interactive, multi-mode simulation of analytical ultracentrifugation data

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Abstract

The ability to simulate sedimentation velocity (SV) analytical ultracentrifugation (AUC) experiments has proved to be a valuable tool for research planning, hypothesis testing, and pedagogy. Several options for SV data simulation exist, but they often lack interactivity and require up-front calculations on the part of the user. This work introduces SViMULATE, a program designed to make AUC experimental simulation quick, straightforward, and interactive. SViMULATE takes user-provided parameters and outputs simulated AUC data in a format suitable for subsequent analyses, if desired. The user is not burdened by the necessity to calculate hydrodynamic parameters for simulated macromolecules, as the program can compute these properties on the fly. It also frees the user of decisions regarding simulation stop time. SViMULATE features a graphical view of the species that are under simulation, and there is no limit on their number. Additionally, the program emulates data from different experimental modalities and data-acquisition systems, including the realistic simulation of noise for the absorbance optical system. The executable is available for immediate download.

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Data availability

A compiled version of the software is freely available at https://www.utsouthwestern.edu/research/core-facilities/mbr/software.

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Acknowledgements

The author wishes to thank Dr. Peter Schuck for helpful discussions, Dr. Walter Stafford for providing exemplary code, and Drs. Lake Paul and Alexander Yarawsky for beta-testing SViMULATE and offering helpful suggestions.

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No funding was received for this work.

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  1. Departments of Biophysics and Microbiology, UT Southwestern Medical Center, Dallas, TX, 75390, USA

    Chad A. Brautigam

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  1. Chad A. Brautigam
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Correspondence to Chad A. Brautigam.

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Special Issue: Analytical Ultracentrifugation 2022.

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Brautigam, C.A. SViMULATE: a computer program facilitating interactive, multi-mode simulation of analytical ultracentrifugation data. Eur Biophys J 52, 293–302 (2023). https://doi.org/10.1007/s00249-023-01637-0

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  • DOI: https://doi.org/10.1007/s00249-023-01637-0

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