Quantifying dissipation in actomyosin networks
Quantifying dissipation in actomyosin networks
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DOI：
10.1098/rsfs.2018.0078
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发表时间：
2019-06-06
期刊：
影响因子：
4.4
通讯作者：
Jarzynski, Christopher
中科院分区：
文献类型：
--
作者：
Floyd, Carlos;Papoian, Garegin A.;Jarzynski, Christopher
量化各种活跃物质相的熵产生将为探索这些远离平衡系统的自组织原理开辟新途径。据推测，活性物质系统的自由能耗散可能会得到优化，导致系统轨迹具有大量耗散的历史，并伴随出现有序动态状态。这个有趣的想法尚未得到广泛测试。特别是，目前尚不清楚肌动球蛋白网络的涌现状态（代表生物活性物质的一个突出例子）是否遵循耗散优化原理进行自组织。为了开始使用详细的计算模型来解决这个问题，我们依靠 MEDYAN 模拟平台，该平台允许从基本分子原理模拟活性物质网络。我们扩展了 MEDYAN 的功能，可以量化模拟轨迹期间化学反应和机械应力松弛产生的耗散率。这是通过使用新颖的公式计算伴随化学反应的吉布斯自由能的精确变化以及通过系统机械能的瞬时值的详细计算来完成的。我们用平均场模型验证了我们的方法，该模型估计了长丝跑步机的耗散率。将这种方法应用于小型无序肌动球蛋白网络的自组织，我们发现紧凑且高度交联的网络往往允许更有效地将化学自由能转化为机械能。在这些简单的系统中，我们观察到自发的网络重组往往会导致总耗散率降低至较低的稳态值。未来的研究可能会仔细测试耗散驱动的适应假设是否适用于这种情况以及更复杂的细胞骨架几何形状。
Quantifying entropy production in various active matter phases will open new avenues for probing self-organization principles in these far-from-equilibrium systems. It has been hypothesized that the dissipation of free energy by active matter systems may be optimized, leading to system trajectories with histories of large dissipation and an accompanying emergence of ordered dynamical states. This interesting idea has not been widely tested. In particular, it is not clear whether emergent states of actomyosin networks, which represent a salient example of biological active matter, self-organize following the principle of dissipation optimization. In order to start addressing this question using detailed computational modelling, we rely on the MEDYAN simulation platform, which allows simulating active matter networks from fundamental molecular principles. We have extended the capabilities of MEDYAN to allow quantification of the rates of dissipation resulting from chemical reactions and relaxation of mechanical stresses during simulation trajectories. This is done by computing precise changes in Gibbs free energy accompanying chemical reactions using a novel formula and through detailed calculations of instantaneous values of the system's mechanical energy. We validate our approach with a mean-field model that estimates the rates of dissipation from filament treadmilling. Applying this methodology to the self-organization of small disordered actomyosin networks, we find that compact and highly cross-linked networks tend to allow more efficient transduction of chemical free energy into mechanical energy. In these simple systems, we observe that spontaneous network reorganizations tend to result in a decrease in the total dissipation rate to a low steady-state value. Future studies might carefully test whether the dissipation-driven adaptation hypothesis applies in this instance, as well as in more complex cytoskeletal geometries.