The Brownian dynamics simulator PyRID for reacting and interacting particles written in Python.

IF 4.5 Q1 BIOCHEMICAL RESEARCH METHODS
Moritz Becker, Nahid Safari, Christian Tetzlaff
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引用次数: 0

Abstract

Recent advances in molecular biology have led to large-scale datasets providing new insights into the molecular organization of cells. To fully exploit their potential, computer simulations are essential to gain in-depth understanding of molecular principles. We developed the Python reaction interaction diffusion simulator (PyRID), a Python-based reaction-diffusion simulator designed for the efficient simulation of molecular biological systems. PyRID incorporates unimolecular and bimolecular reactions as well as pair interactions and simulation of individual interacting proteins to polydisperse molecular assemblies. It supports mesh-based compartments and surface diffusion of particles, enabling analyses of interactions between (trans)membrane proteins with intra- and extracellular proteins. Distinctively, PyRID uses hierarchical grids for polydisperse systems, supports rigid bead models, and calculates diffusion tensors internally. Validation against theoretical results and established models confirms PyRID's accuracy in reproducing key physical properties. PyRID is written entirely in Python, making it accessible to the broader scientific community, facilitating customization and integration into diverse research workflows.

用Python编写的用于反应和相互作用粒子的布朗动力学模拟器PyRID。
分子生物学的最新进展带来了大规模的数据集,为细胞的分子组织提供了新的见解。为了充分利用它们的潜力,计算机模拟对于深入了解分子原理至关重要。我们开发了Python反应相互作用扩散模拟器(PyRID),这是一个基于Python的反应扩散模拟器,旨在有效地模拟分子生物系统。PyRID结合了单分子和双分子反应,以及对相互作用和模拟单个相互作用的蛋白质到多分散分子组装。它支持基于网格的隔室和颗粒的表面扩散,能够分析(反)膜蛋白与细胞内和细胞外蛋白之间的相互作用。独特的是,PyRID对多分散系统使用分层网格,支持刚性头模型,并在内部计算扩散张量。对理论结果和已建立模型的验证证实了PyRID在再现关键物理性质方面的准确性。PyRID完全是用Python编写的,这使得更广泛的科学社区可以访问它,促进定制和集成到各种研究工作流程中。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
Cell Reports Methods
Cell Reports Methods Chemistry (General), Biochemistry, Genetics and Molecular Biology (General), Immunology and Microbiology (General)
CiteScore
3.80
自引率
0.00%
发文量
0
审稿时长
111 days
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