Multiscale Modeling of Diffusion in a Crowded Environment.
Multiscale Modeling of Diffusion in a Crowded Environment.
复制标题
拥挤环境中扩散的多尺度建模。
DOI：
10.1007/s11538-017-0346-6
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发表时间：
2017
影响因子：
3.5
通讯作者：
Meinecke,Lina
中科院分区：
文献类型：
--
作者：
Meinecke,Lina
我们提出了一个多尺度的方法来模拟在拥挤的环境中的扩散及其对反应速率的影响。生物系统中的扩散通常通过离散空间跳跃过程来建模，以捕获生物系统的固有噪声，这在低拷贝数区域中变得重要。为了有效地模拟拥挤的细胞环境中的扩散，我们从局部第一次退出时间计算在这个介观模型中的跳跃率，这占拥挤分子的微观位置，而扩散分子在一个粗糙的笛卡尔网格上跳跃。然后，我们提取一个宏观的描述所产生的跳跃率，排除体积效应是由扩散方程与空间相关的扩散系数。拥挤的分子可以是任意形状和大小，和数值实验表明，这些因素与扩散分子的大小起着至关重要的作用，在扩散运动的减少的幅度。当校正反应速率的改变扩散，我们可以表明，分子拥挤增强或抑制化学反应，这取决于局部波动的障碍密度。
We present a multiscale approach to model diffusion in a crowded environment and its effect on the reaction rates. Diffusion in biological systems is often modeled by a discrete space jump process in order to capture the inherent noise of biological systems, which becomes important in the low copy number regime. To model diffusion in the crowded cell environment efficiently, we compute the jump rates in this mesoscopic model from local first exit times, which account for the microscopic positions of the crowding molecules, while the diffusing molecules jump on a coarser Cartesian grid. We then extract a macroscopic description from the resulting jump rates, where the excluded volume effect is modeled by a diffusion equation with space-dependent diffusion coefficient. The crowding molecules can be of arbitrary shape and size, and numerical experiments demonstrate that those factors together with the size of the diffusing molecule play a crucial role on the magnitude of the decrease in diffusive motion. When correcting the reaction rates for the altered diffusion we can show that molecular crowding either enhances or inhibits chemical reactions depending on local fluctuations of the obstacle density.