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Theory of wavelet-based coarse-graining hierarchies for molecular dynamics

机译：基于小波的分子动力学的小波粗粗磨床理论

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摘要

We present a multiresolution approach to compressing the degrees of freedom and potentials associated with molecular dynamics, such as the bond potentials. The approach suggests a systematic way to accelerate large-scale molecular simulations with more than two levels of coarse graining, particularly applications of polymeric materials. In particular, we derive explicit models for (arbitrarily large) linear (homo)polymers and iterative methods to compute large-scale wavelet decompositions from fragment solutions. This approach does not require explicit preparation of atomistic-to-coarse-grained mappings, but instead uses the theory of diffusion wavelets for graph Laplacians to develop system-specific mappings. Our methodology leads to a hierarchy of system-specific coarse-grained degrees of freedom that provides a conceptually clear andmathematically rigorous framework for modeling chemical systems at relevant model scales. The approach is capable of automatically generating as many coarse-grained model scales as necessary, that is, to go beyond the two scales in conventional coarse-grained strategies; furthermore, the wavelet-based coarse-grained models explicitly link time and length scales. Furthermore, a straightforward method for the reintroduction of omitted degrees of freedom is presented, which plays a major role in maintaining model fidelity in long-time simulations and in capturing emergent behaviors.
机译：我们提出了一种压缩与分子动力学相关的自由度和电位等多种求解方法，例如债券电位。该方法表明，通过两种以上粗糙的粗粒，特别是聚合物材料的粗糙粗磨，特别是在聚合物材料中加速大规模分子模拟的系统方法。特别是，我们推导出（任意大）线性（HOMO）聚合物和迭代方法的显式模型，以从片段溶液计算大规模小波分解。这种方法不需要明确准备原子对粗粒映射的映射，而是利用图形拉普拉斯人的扩散小波理论来开发特定于系统的映射。我们的方法导致系统特定的粗粒度自由度的层次结构，提供了在相关模型尺度上建模化学系统的概念性明确的和多种式严格的框架。根据需要，该方法能够自动地产生许多粗粒模型尺度，即超越传统粗粒策略的两种尺度;此外，基于小波的粗粒模型明确地链接时间和长度尺度。此外，提出了一种用于重新引入省略自由度的直接方法，其在维持长时间模拟中和捕获新的行为中的模型保真度方面发挥着重要作用。

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