使用各向异性粗粒度位点对序列特异性聚合物进行建模，
Modeling sequence-specific polymers using anisotropic coarse-grained sites allows quantitative comparison with experiment
摘要：
某些序列的类肽聚合物（肽的合成类似物）通过在空气-水界面处的吸附、压缩和塌陷的非平衡组装途径组装成双层纳米片。与生物学和材料科学中的其他大规模动态过程一样，了解这种超分子组装过程的细节需要一种建模方法，该方法可以在广泛的长度和时间尺度上捕获行为，从单个侧链波动的行为到聚合物组装进化的行为。在这里，我们证明了一种新的粗粒度建模方法是准确的，计算效率足以做到这一点。我们的方法只使用了最少数量的粗粒度的网站，但保留独立波动的取向自由度为每个网站。这些取向的自由度使我们能够准确地参数化键合和非键合的相互作用，并生成具有足够精度的全原子配置，以执行原子散射计算，并与全原子模拟接口。我们已经使用这种方法来重现所有可用的实验X射线散射光谱（堆叠的纳米片，以及吸附在空气-水界面和溶液中的类肽），以解决负责这些傅立叶空间特征的微观真实空间结构。通过与全原子模拟接口，我们还为未来跨尺度双向通信的序列特异性聚合物的多尺度模拟奠定了基础。
英文摘要：
Certain sequences of peptoid polymers (synthetic analogs of peptides) assemble into bilayer nanosheets via a nonequilibrium assembly pathway of adsorption, compression, and collapse at an air-water interface. As with other large-scale dynamic processes in biology and materials science, understanding the details of this supramolecular assembly process requires a modeling approach that captures behavior on a wide range of length and time scales, from those on which individual sidechains fluctuate to those on which assemblies of polymers evolve. Here we demonstrate that a new coarse-grained modeling approach is accurate and computationally efficient enough to do so. Our approach uses only a minimal number of coarse-grained sites, but retains independently fluctuating orientational degrees of freedom for each site. These orientational degrees of freedom allow us to accurately parameterize both bonded and nonbonded interactions, and to generate all-atom configurations with sufficient accuracy to perform atomic scattering calculations and to interface with all-atom simulations. We have used this approach to reproduce all available experimental X-ray scattering spectra (for stacked nanosheets, and for peptoids adsorbed at air-water interfaces and in solution), in order to resolve the microscopic, real-space structures responsible for these Fourier-space features. By interfacing with all-atom simulations, we have also laid the foundations for future multiscale simulations of sequence-specific polymers that communicate in both directions across scales.
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