IONIC DISTRIBUTIONS IN POLYNUCLEOTIDE SOLUTIONS

高电荷态多核苷酸与核糖核酸的强相互作用 形成它们环境的离子溶液是无处不在的 这一现象对核酸的影响广为人知 生物化学。然而，由于缺乏这方面的详细结构图 环境和无法适当地解释其对 大分子行为仍然是快速发展的主要障碍。 先进的高分子模型化技术。建议进行的研究 结合并行的理论努力，旨在第一，发展 对棒状离子环境的定量描述 多核苷酸结构(包括详细的基础 对这些离子的实验结构探针的解释 发行版)，第二，开发和实现 能够提供必要的环境反馈的技术 对生物聚合物的作用力。这些研究将主要集中在详细的 显式考虑分子水溶液的多核苷酸模型 影响，因为已经研究的更简化的模型不够充分 详细说明以提供所需信息。将使用的方法 包括通过蒙特卡罗和随机动力学进行计算机模拟 算法，以及新积分和标准积分的组合 方程式技术已被证明提供了可行的途径 感兴趣的信息，包括水中的离子间相互作用。 这些平行研究的合并将提供关于 多核苷酸环境，并提供了可行性和非经验性 将环境与大分子结构和 动力学。

The strong mutual interaction between highly charged polynucleotides and the ionic solution that forms their environment is an ubiquitous phenomenon, with a widely appreciated influence on nucleic acid biochemistry. However, the lack of a detailed structural picture of this environment and an inability to properly account for its influence on macromolecular behavior continues to be a major barrier to the rapidly advancing technology of macromolecular modeling. The proposed studies incorporate parallel theoretical efforts aimed at, first, the development of a quantitative description of the ionic environment of rod-like polynucleotide structures (including a detailed basis for the interpretation of experimental structural probes of these ionic distributions) and, second, the development and implementation of techniques capable of providing the necessary feedback of environmental forces on the biopolymer. The studies will focus primarily on detailed polynucleotide models with explicit account of molecular aqueous solvent effects, as more simplified models already studied are insufficiently detailed to provide the required information. The methods to be used include computer simulation via both Monte Carlo and stochastic dynamics algorithms, as well as a combination of both new and standard integral equation techniques that have been shown to provide viable routes to the information of interest, including interionic interactions in water. The merging of these parallel studies will provide a detailed account of the polynucleotide environment and provide feasible and nonempirical methods for coupling the environment with macromolecular structure and dynamics.