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<p>The simulation of analytical ultracentrifugation data in the sedimentation velocity (SV) mode is extremely useful for experimental planning and hypothesis testing. However, undertaking such simulations can be daunting, especially if one is unpracticed in SV analytic software and the underlying hydrodynamic precepts of the method. Recently, to address this need, the software SViMULATE was introduced. This software featured a simple user interface and facile, on-the-fly conversions of familiar macromolecular properties (e.g., molar mass, shape) to the quantities needed for a successful SV simulation (the sedimentation coefficient, <i>s</i>, and the translational diffusion coefficient, <i>D</i><sub>T</sub>). The software offered an easy route to simulate an unlimited number of species, and two experimental modes, normal and difference SV, were enabled. In the current work, features added to SViMULATE since its initial release are detailed. These include new experimental modes: two interacting systems, nonideal sedimentation, flotation, and band (or “analytical zone”) SV. Further, the modeling of polydisperse species as a series of related individual species has been enabled, and more sophisticated radial and time discretizations enhance the numerical stability of the simulation engine. These features significantly expand the scope and utility of the software, and the advances described herein are immediately available in version 1.4.0 of SViMULATE.</p>

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Facilitating the simulation of sedimentation velocity data: new features of SViMULATE

  • 期刊论文

  • 发表日期：

    2025年5月5日

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  • Chad A. Brautigam

摘要

The simulation of analytical ultracentrifugation data in the sedimentation velocity (SV) mode is extremely useful for experimental planning and hypothesis testing. However, undertaking such simulations can be daunting, especially if one is unpracticed in SV analytic software and the underlying hydrodynamic precepts of the method. Recently, to address this need, the software SViMULATE was introduced. This software featured a simple user interface and facile, on-the-fly conversions of familiar macromolecular properties (e.g., molar mass, shape) to the quantities needed for a successful SV simulation (the sedimentation coefficient, s, and the translational diffusion coefficient, DT). The software offered an easy route to simulate an unlimited number of species, and two experimental modes, normal and difference SV, were enabled. In the current work, features added to SViMULATE since its initial release are detailed. These include new experimental modes: two interacting systems, nonideal sedimentation, flotation, and band (or “analytical zone”) SV. Further, the modeling of polydisperse species as a series of related individual species has been enabled, and more sophisticated radial and time discretizations enhance the numerical stability of the simulation engine. These features significantly expand the scope and utility of the software, and the advances described herein are immediately available in version 1.4.0 of SViMULATE.