DMREF: Computational Design Principles for Functional DNA-Based Materials

设计材料革命和工程我们的未来（DMREF）赠款为开发计算工具提供资金，以确定基于DNA的材料合成的最佳设计参数。开发的工具将确定最佳的DNA序列和环境组装条件，包括溶剂和温度，以实现基于二维和三维DNA的纳米级结构和材料的预定设计标准。基于物理的计算模型将用于将机械，静电和杂交自由能纳入目标DNA为基础的组件的整体结构热力学模型。该模型将与数值优化和高度并行计算一起使用，以优化设计和合成过程。详细的实验将用于测试和验证计算工具，包括目标结构特性和组装动力学的二维和三维表征，这项研究的结果将导致一个广泛使用的自动化设计工具，用于生产定制的基于DNA的纳米结构和材料。最佳序列设计和组装条件的目标DNA为基础的材料性能将使用该工具，使其广泛使用在不同的纳米技术应用。目标特性可以包括复杂的二维和三维纳米级结构特征、机械响应以及操作温度和溶剂条件。通过计算确定序列设计参数以实现这些目标特性将减少制造基于DNA的材料所需的财务成本和时间，以及优化最终产品的质量和均匀性。该计算工具还将使用互补的计算建模方法来模拟和设计定制的基于DNA的纳米材料的各种功能方面。

This Designing Materials to Revolutionize and Engineer our Future (DMREF) grant provides funding for the development of a computational tool to determine optimal design parameters for the synthesis of DNA-based materials. The developed tool will determine the optimal DNA sequences and environmental assembly conditions, including solvent and temperature, to realize pre-specified design criteria for two-dimensional and three-dimensional DNA-based nanoscale structures and materials. Physics-based computational models will be used to incorporate mechanical, electrostatic, and hybridization free energies into an overall structural-thermodynamic model of the target DNA-based assembly. This model will be used together with numerical optimization and highly parallel computation to optimize the design and synthesis process. Detailed experimentation will be used to test and validate the computational tool, including two-dimensional and three-dimensional characterization of target structural properties and assembly kinetics.The results of this research will lead to a broadly accessible, automated design tool for the production of custom DNA-based nanostructures and materials. Optimal sequence design and assembly conditions for target DNA-based material properties will be generated using this tool, enabling its broad use in diverse nanotechnology applications. Target properties may include complex two- and three-dimensional nanoscale structural features, mechanical response, and operating temperature and solvent conditions. Determining computationally the sequence design parameters to achieve these target properties will reduce the financial cost and time required to manufacture DNA-based materials, as well as optimize the quality and uniformity of the final product. This computational tool will also enable the simulation and design of diverse functional aspects of custom DNA-based nanomaterials using complementary computational modeling approaches.