PHYSICAL INFRASTRUCT: ALGORITHMS FOR STOCHASTIC SIMULASTIONS

这个子项目是许多研究子项目中利用 资源由NIH/NCRR资助的中心拨款提供。子项目和 调查员(PI)可能从NIH的另一个来源获得了主要资金， 并因此可以在其他清晰的条目中表示。列出的机构是 该中心不一定是调查人员的机构。 当参与分子的拷贝数相对较少，并且由于内部或外部噪声引起的波动变得显著时，对随机过程进行建模至关重要。一个例子是细胞内颗粒运输。在虚拟细胞项目的早期阶段，虚拟细胞C++库通过模拟空间布朗动力学的能力得到了增强，在空间布朗动力学中，系统的状态通过“粒子”的位置和状态来描述，“粒子”是一个点状物体。虚拟细胞粒子可以在1维、2维或3维随机游动，同时与连续分布的物种随机相互作用，这些随机相互作用由偏微分方程式确定地描述。后来，我们进一步开发了我们的“随机”代码来解释颗粒与微管的结合和运动驱动的定向运动。为此，一个新的类-轮廓，或有向曲线-被引入到虚拟细胞C++库中，它将代表微管和细丝。该项目的目标是为当前的工作提供必要的算法，使虚拟细胞随机能力可以通过用户界面访问。这个想法是让用户可以选择随机或确定性地对待生物模型。我们设想了几种类型的蒙特卡罗类型的建模：(I)跟踪粒子(布朗动力学，主要用于空间模型)，(Ii)“添加噪声”，和(Iii)精确的吉莱斯皮类型的算法。

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Modeling stochastic processes is crucially important when numbers of copies of participating molecules is relatively small and fluctuations due to intrinsic or external noise become significant. One example is intracellular granule trafficking. At the early stages of the Virtual Cell project the Virtual Cell C++ library was enhanced by a capability to simulate spatial Brownian dynamics, where the state of a system is described by location and a state of "particles", a point-like objects. The Virtual Cell particles can undergo random walks in 1-, 2-, or 3 dimensions and simultaneously interact stochastically with continuously distributed species, which are described deterministically by partial differential equations. Later, we further developed our "stochastic" code to account for granule binding to microtubules and motor-driven directed motion. To this end, a new class - contours, or directed curves - was introduced into the Virtual Cell C++ library, which would represent microtubules and filaments. The goal of this project is to provide algorithms necessary for the current effort to make the Virtual Cell stochastic capabilities accessible through the user interface. The idea is to give a user a choice to treat a bio-model either stochastically or deterministically. We envision several types of Monte-Carlo-type modeling: (i) tracking particles (Brownian dynamics, predominantly for spatial models), (ii) "adding noise", and (iii) exact Gillespie-type algorithms.