Biophysically realistic filament bending dynamics in agent-based biological simulation.
Biophysically realistic filament bending dynamics in agent-based biological simulation.
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DOI：
10.1371/journal.pone.0004748
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发表时间：
2009
期刊：
影响因子：
3.7
通讯作者：
Alberts JB
中科院分区：
文献类型：
--
作者：
Alberts JB
对于研究简单分子相互作用网络中可能出现的复杂生物行为，一个有吸引力的工具是基于代理的计算模拟，它明确地跟踪小规模的局部相互作用--跟踪数千到数百万个状态。对于许多关键的细胞过程(如细胞动态沟、核集中、胞质分裂)，细胞骨架细丝的柔韧性可能是至关重要的。因此，任何希望解释这些过程中复杂的紧急行为的计算机模型都需要以一种现实的方式编码细丝的灵活性。在这里，我提出了一种在数值上方便和生物物理上逼真的方法来模拟硅胶中细胞骨架纤维的柔韧性。每个细胞骨架细丝由一系列端到端串联的刚性段表示，该刚性段具有用于平移弹性元件的可变附着点。这种连接方案允许对大范围的片段大小、粘度和时间步长进行经验调整，从而使任何细丝物种具有实验观察到的(或理论上预期的)静力偏转、松弛时间常数和热扭转运动。此外，我还采用了一对独特的弹性元件--一个表示轴向刚度，另一个表示弯曲刚度--以单时间步约束解析的形式表示恢复力。这种方法是高度局部性的--灯丝的刚性段仅通过约束力相互作用，因此非常适合于可能存在任意附加力(例如，代表灯丝与其他物体的相互作用或灯丝之间的交叉链接/纠缠的那些力)的模拟。用代码实现很简单；Java源代码可以在www.cell Dynamics.org上找到。
An appealing tool for study of the complex biological behaviors that can emerge from networks of simple molecular interactions is an agent-based, computational simulation that explicitly tracks small-scale local interactions – following thousands to millions of states through time. For many critical cell processes (e.g. cytokinetic furrow specification, nuclear centration, cytokinesis), the flexible nature of cytoskeletal filaments is likely to be critical. Any computer model that hopes to explain the complex emergent behaviors in these processes therefore needs to encode filament flexibility in a realistic manner. Here I present a numerically convenient and biophysically realistic method for modeling cytoskeletal filament flexibility in silico. Each cytoskeletal filament is represented by a series of rigid segments linked end-to-end in series with a variable attachment point for the translational elastic element. This connection scheme allows an empirically tuning, for a wide range of segment sizes, viscosities, and time-steps, that endows any filament species with the experimentally observed (or theoretically expected) static force deflection, relaxation time-constant, and thermal writhing motions. I additionally employ a unique pair of elastic elements – one representing the axial and the other the bending rigidity– that formulate the restoring force in terms of single time-step constraint resolution. This method is highly local –adjacent rigid segments of a filament only interact with one another through constraint forces—and is thus well-suited to simulations in which arbitrary additional forces (e.g. those representing interactions of a filament with other bodies or cross-links / entanglements between filaments) may be present. Implementation in code is straightforward; Java source code is available at www.celldynamics.org.
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