PHYSICAL INFRASTRUCT: ALGORITHMS FOR STOCHASTIC SIMULASTIONS

物理基础设施：随机模拟算法

• 批准号: 7722717
• 负责人: BORIS SLEPCHENKO
• 金额: $ 1.38万
• 依托单位: UNIVERSITY OF CONNECTICUT SCH OF MED/DNT
• 依托单位国家: 美国
• 财政年份: 2008
• 资助国家: 美国
• 起止时间: 2008-08-01 至 2009-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7722717
• 关键词: Accounting; Algorithms; Binding; Cells; Class; Code; Computer Retrieval of Information on Scientific Projects Database; Cytoplasmic Granules; Dimensions; Equation; Filament; Funding; Goals; Grant; Institution; Libraries; Location; Microtubules; Modeling; Motion; Motor; Noise; Numbers; Research; Research Personnel; Resources; Simulate; Source; Staging; Stochastic Processes; Structure of thyroid parafollicular cell; System; United States National Institutes of Health; Walking; particle; trafficking; virtual

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.

这个子项目是许多研究子项目中的一个 由NIH/NCRR资助的中心赠款提供的资源。子项目和 研究者（PI）可能从另一个NIH来源获得了主要资金， 因此可以在其他CRISP条目中表示。所列机构为 研究中心，而研究中心不一定是研究者所在的机构。 当参与分子的拷贝数相对较小时，由于内在或外部噪声引起的波动变得很大时，建模随机过程至关重要。一个例子是细胞内颗粒运输。在Virtual Cell项目的早期阶段，Virtual Cell C++库通过模拟空间布朗动力学的能力得到了增强，其中系统的状态由“粒子”（点状物体）的位置和状态描述。虚拟细胞粒子可以在1维、2维或3维中进行随机行走，同时与连续分布的物种随机相互作用，这些物种由偏微分方程确定性地描述。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电机驱动的定向运动。为此，在Virtual Cell C++库中引入了一个新的类-轮廓或有向曲线，它将表示微管和细丝。这个项目的目标是提供必要的算法，目前的努力，使虚拟小区的随机能力，通过用户界面访问。这个想法是给用户一个选择来对待生物模型随机或确定性。我们设想了几种类型的蒙特-卡罗型建模：（i）跟踪粒子（布朗动力学，主要用于空间模型），（ii）“添加噪声”，（iii）精确Gillespie型算法。