Suppr超能文献

促进沉降速度数据的模拟:SViMULATE的新特性

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

作者信息

Brautigam Chad A

机构信息

Departments of Biophysics and Microbiology, UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, 75390-8816, USA.

出版信息

Eur Biophys J. 2025 May 5. doi: 10.1007/s00249-025-01753-z.

Abstract

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, D). 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.

摘要

沉降速度(SV)模式下分析超速离心数据的模拟对于实验规划和假设检验极为有用。然而,进行此类模拟可能颇具挑战性,尤其是对于那些不熟悉SV分析软件及该方法背后流体动力学原理的人而言。最近,为满足这一需求,推出了软件SViMULATE。该软件具有简单的用户界面,能轻松地将常见的大分子性质(如摩尔质量、形状)即时转换为成功进行SV模拟所需的量(沉降系数s和平动扩散系数D)。该软件提供了一种简便的途径来模拟无限数量的物种,并启用了两种实验模式,即常规SV模式和差异SV模式。在当前工作中,详细介绍了自SViMULATE首次发布以来新增的功能。这些功能包括新的实验模式:两种相互作用体系、非理想沉降、浮选以及带(或“分析区”)SV模式。此外,已实现将多分散物种建模为一系列相关的单个物种,并且更复杂的径向和时间离散化提高了模拟引擎的数值稳定性。这些功能显著扩展了该软件的范围和实用性,本文所述的改进在SViMULATE 1.4.0版本中即可立即使用。

文献AI研究员

20分钟写一篇综述,助力文献阅读效率提升50倍。

立即体验

用中文搜PubMed

大模型驱动的PubMed中文搜索引擎

马上搜索

文档翻译

学术文献翻译模型,支持多种主流文档格式。

立即体验