Cheng Bin, Riedel Marc
Electrical and Computer Engineering University of Minnesota, 200 Union Street S.E., Minneapolis, MN 55455, USA.
Pac Symp Biocomput. 2009:4-14.
In order to better characterize the behavior of biochemical systems, it is sometimes helpful and necessary to introduce time-dependent input signals. If the state of a biochemical system with such signals is assumed to evolve deterministically and continuously, then it can be readily analyzed by solving ordinary differential equations. However, if it assumed to evolve discretely and stochastically, then existing simulation methods cannot be applied. In this paper, we incorporate conditions for transient analysis into stochastic simulation and we develop the corresponding simulation algorithm. Applying our method to examples, we demonstrate that it can yield new insights into the dynamics of biochemical systems; specifically, it can be used to verify the design of biochemical logic gates.
为了更好地表征生化系统的行为，引入随时间变化的输入信号有时是有益且必要的。如果假设具有此类信号的生化系统的状态确定性且连续地演化，那么通过求解常微分方程就可以轻松对其进行分析。然而，如果假设其离散且随机地演化，那么现有的模拟方法就无法应用。在本文中，我们将瞬态分析的条件纳入随机模拟，并开发了相应的模拟算法。将我们的方法应用于实例，我们证明它可以为生化系统的动力学带来新的见解；具体而言，它可用于验证生化逻辑门的设计。
