论文标题
Eggtart：一种可视化生物物理传输过程动态的计算工具，在不均匀的$ \ ell $ -tasep下
EGGTART: A computational tool to visualize the dynamics of biophysical transport processes under the inhomogeneous $\ell$-TASEP
论文作者
论文摘要
在过去的几十年中，已经积极研究了完全不对称的简单排除过程（TASEP），该过程描述了晶格上相互作用颗粒的随机动力学，并应用于建模重要的生物传输过程。在这里，我们提出了一个称为EGGTART的软件包（广泛的GUI实时给出了Tasep-sealization），该软件包可以量化和可视化与tasep的广义版本相关的动力学，并具有扩展的粒径和异质的跳跃速率。该计算工具基于通过得出和解决该过程的流体动力学极限获得的分析公式。它允许立即量化粒子密度，通量和相图，这是与系统相关的一些关键参数的函数，这将很难通过常规的随机模拟实现。因此，我们的软件应该对研究一般运输过程的生物物理学家感兴趣，并且可以在基因表达的背景下使用以建模和量化不同编码序列的mRNA翻译。
The totally asymmetric simple exclusion process (TASEP), which describes the stochastic dynamics of interacting particles on a lattice, has been actively studied over the past several decades and applied to model important biological transport processes. Here we present a software package, called EGGTART (Extensive GUI gives TASEP-realization in real time), which quantifies and visualizes the dynamics associated with a generalized version of the TASEP with an extended particle size and heterogeneous jump rates. This computational tool is based on analytic formulas obtained from deriving and solving the hydrodynamic limit of the process. It allows an immediate quantification of the particle density, flux, and phase diagram, as a function of a few key parameters associated with the system, which would be difficult to achieve via conventional stochastic simulations. Our software should therefore be of interest to biophysicists studying general transport processes, and can in particular be used in the context of gene expression to model and quantify mRNA translation of different coding sequences.
