标题： 如何模拟DNA折纸 显示英文标题

标题： How we simulate DNA origami

摘要： DNA折纸由一条长的支架链和几条短的 Staple 链组成，这些链自组装成目标的二维或三维形状。 它是一种广泛使用的核酸纳米技术构建体，提供了一种经济有效的方法来设计和创建各种纳米级形状。 由于其在纳米制造、诊断和治疗等领域的潜在应用，DNA折纸已成为生物纳米技术领域的重要工具。 对这些结构的模拟可以提供有关其形状和功能的见解，从而加快并简化设计过程。 然而，由于这些结构通常由数千个碱基对组成，因此对其进行模拟带来了挑战。 OxDNA 是一种专门设计用于DNA纳米技术的粗粒度模型，提供了强大的模拟能力。 其相关的可视化和分析工具生态系统可以通过计算机模拟表征补充实验工作。 本教程提供了一种使用OxDNA生态系统模拟DNA折纸结构的一般方法，旨在帮助希望将其计算分析整合到设计流程中的实验学家。 显示英文摘要

摘要： DNA origami consists of a long scaffold strand and short staple strands that self-assemble into a target 2D or 3D shape. It is a widely used construct in nucleic acid nanotechnology, offering a cost-effective way to design and create diverse nanoscale shapes. With promising applications in areas such as nanofabrication, diagnostics, and therapeutics, DNA origami has become a key tool in the bionanotechnology field. Simulations of these structures can offer insight into their shape and function, thus speeding up and simplifying the design process. However, simulating these structures, often comprising thousands of base pairs, poses challenges due to their large size. OxDNA, a coarse-grained model specifically designed for DNA nanotechnology, offers powerful simulation capabilities. Its associated ecosystem of visualization and analysis tools can complement experimental work with in silico characterization. This tutorial provides a general approach to simulating DNA origami structures using the oxDNA ecosystem, tailored for experimentalists looking to integrate computational analysis into their design workflow.