Experiments with synthetic genetic logic circuits can be time-consuming and expensive. Accordingly, advances in the field of computer-aided design and simulation of genetic circuits have reduced the cost and time required for experimentation. D-VASim is the first genetic circuit simulation tool that allows users to interact with the model during run-time. In contrast to electronic circuits, genetic circuits have different threshold values for different circuits, which need to be estimated prior to simulation. D-VASim allows the user to perform threshold concentration and propagation delay analysis before simulating the circuit. The algorithm currently used in D-VASim has considerable scope for improvements. Thus, we propose a parallel implementation of the algorithm, significantly faster by up to 16 times. In adddition, we improve the algorithm for consistent runtimes across multiple simulation runs under the same parameter settings, reducing the worst-case standard deviation in runtime from 6.637 to 1.841. Our algorithm also estimates the threshold value more accurately, as evident from experimentation for long runtimes. With these modifications, the utility of D-VASim as a virtual laboratory environment has been significantly enhanced.

中文翻译：

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遗传逻辑电路模型的阈值和传播延迟分析的并行方法

使用合成遗传逻辑电路进行的实验可能既耗时又昂贵。因此，计算机辅助设计和遗传电路仿真领域的进步降低了实验所需的成本和时间。D-VASim是第一个遗传电路仿真工具，允许用户在运行时与模型进行交互。与电子电路相反，遗传电路对于不同的电路具有不同的阈值，需要在仿真之前对其进行估算。D-VASim允许用户在模拟电路之前执行阈值集中和传播延迟分析。D-VASim中当前使用的算法有很大的改进空间。因此，我们提出了该算法的并行实现，速度明显提高了多达16倍。另外，我们改进了算法，以在相同参数设置下跨多个模拟运行实现一致的运行时，从而将运行时的最坏情况标准差从6.637降低到1.841。我们的算法还可以更准确地估算阈值，从长时间运行的实验中可以明显看出。通过这些修改，大大增强了D-VASim作为虚拟实验室环境的实用性。