Modeling analytical ultracentrifugation experiments with an adaptive space-time finite element solution for multicomponent reacting systems
Modeling analytical ultracentrifugation experiments with an adaptive space-time finite element solution for multicomponent reacting systems
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DOI：
10.1529/biophysj.107.123950
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发表时间：
2008-07-01
影响因子：
3.4
通讯作者：
Demeler, Borries
中科院分区：
文献类型：
--
作者：
Cao, Weiming;Demeler, Borries
我们描述了用于求解Lamm方程的自适应时空有限元方法（ASTFEM）到多组分反应体系情况的扩展。我们使用一个算子分裂技术解耦的反应过程的沉积扩散过程。前者采用基于Petrov-Galerkin方法和自适应移动网格的ASTFEM方法求解，后者采用隐式中点欧拉方法求解。我们的解决方案可以有效地消除沉降误差的每一个组成部分或物种参与的反应，它是免费的振荡附近的细胞底部。它提供了二阶精度，并保证质量守恒，无需任何额外的后处理，它允许多组分，平衡系统的反应速率可以在瞬时反应和非相互作用的混合物之间进行动力学控制建模。与经典方法相比，所提出的ASTFEM解决方案提供了更高的效率和准确性，特别是当中型和大型分子建模时。
We describe an extension of the adaptive space-time finite element method (ASTFEM) used in the solution of the Lamm equation to the case of multicomponent reacting systems. We use an operator splitting technique to decouple the sedimentation-diffusion process from the reaction process. The former is solved with an ASTFEM approach based on the Petrov-Galerkin method and on adaptive moving grids, and the latter is solved with the implicit midpoint Euler's method. Our solution can effectively eliminate the sedimentation errors for each component or species involved in the reaction, and it is free from oscillation near the cell bottom. It offers second-order accuracy, and guarantees conservation of mass without any additional postprocessing, and it permits modeling of multicomponent, equilibrating systems where the reaction rate can be kinetically controlled between an instantaneous reaction and a noninteracting mixture. The proposed ASTFEM solution provides improved efficiency and accuracy compared to classical approaches, especially when medium-sized and large molecules are modeled.