An efficient stochastic diffusion algorithm for modeling second messengers in dendrites and spines
An efficient stochastic diffusion algorithm for modeling second messengers in dendrites and spines
复制标题
DOI：
10.1016/j.jneumeth.2006.04.003
复制
发表时间：
2006-10-15
影响因子：
3
通讯作者：
Blackwell, Kim T.
中科院分区：
文献类型：
--
作者：
Blackwell, Kim T.
细胞内信号传导途径，其中包括生化反应和第二信使扩散，相互作用的非线性与神经元膜的性质，在其作为突触可塑性和神经调节的重要中介的作用。计算建模是研究这些现象的有效方法;然而，目前大多数神经元建模策略都不包括信号通路。为了克服这一缺陷，提出了一种新的算法来模拟随机扩散在一个高效的方式。通过考虑分子的集合而不是跟踪单个分子的运动来获得速度的增益。分子离开空间离散隔室的概率用于创建存储k的概率的查找表。离开隔室的分子作为隔室中分子总数的函数。在模拟过程中，使用均匀随机数作为查找表的索引来确定离开隔室的分子数量。仿真结果表明，该算法的准确性，通过比较它与确定性扩散的理论解。另外的模拟显示了树枝状分支上的刺是如何区分可扩散分子的。该算法的效率足以允许在整个神经元上的多个棘中模拟第二信使通路。(c)2006 Elsevier B. V.保留所有权利。
Intracellular signaling pathways, which encompass both biochemical reactions and second messenger diffusion, interact non-linearly with neuronal membrane properties in their role as essential intermediaries for synaptic plasticity and neuromodulation. Computational modeling is a productive approach for investigating these phenomena; however, most current strategies for modeling neurons exclude signaling pathways. To overcome this deficiency, a new algorithm is presented to simulate stochastic diffusion in a highly efficient manner. The gain in speed is obtained by considering collections of molecules, instead of tracking the movement of individual molecules. The probability of a molecule leaving a spatially discrete compartment is used to create a lookup table that stores the probability of k. molecules leaving the compartment as a function of the total number of molecules in the compartment. During the simulation, the number of molecules leaving the compartment is determined using a uniform random number as an index into the lookup table. Simulations illustrate the accuracy of this algorithm by comparing it with the theoretical solution for deterministic diffusion. Additional simulations show how spines on a dendritic branch compartmentalize diffusible molecules. The efficiency of the algorithm is sufficient to allow simulation of second messenger pathways in a multitude of spines on an entire neuron. (c) 2006 Elsevier B.V. All rights reserved.