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首页> 外文期刊>Proceedings of the National Academy of Sciences of the United States of America >Simplifying the representation of complex free-energy landscapes using sketch-map
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Simplifying the representation of complex free-energy landscapes using sketch-map

机译：使用素描图简化复杂自由能景观的表示

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摘要

A new scheme, sketch-map, for obtaining a low-dimensional representation of the region of phase space explored during an enhanced dynamics simulation is proposed. We show evidence, from an examination of the distribution of pairwise distances between frames, that some features of the free-energy surface are inherently high-dimensional. This makes dimensionality reduction problematic because the data does not satisfy the assumptions made in conventional manifold learning algorithms We therefore propose that when dimensionality reduction is performed on trajectory data one should think of the resultant embedding as a quickly sketched set of directions rather than a road map. In other words, the embedding tells one about the connectivity between states but does not provide the vectors that correspond to the slow degrees of freedom. This realization informs the development of sketch-map, which endeavors to reproduce the proximity information from the high-dimensionality description in a space of lower dimensionality even when a faithful embedding is not possible.
机译：提出了一种新的草图草图方案，用于获得在增强动力学仿真过程中探索的相空间区域的低维表示。通过检查框架之间成对距离的分布，我们显示出证据，表明自由能表面的某些特征本质上是高维的。这使降维成为问题，因为数据不满足常规流形学习算法中的假设。因此，我们建议，当对轨迹数据执行降维时，应将生成的嵌入视为快速绘制的一组方向，而不是路线图。换句话说，嵌入告诉人们状态之间的连通性，但是不提供与慢自由度相对应的向量。该实现通知了草图的发展，即使在不可能进行忠实嵌入的情况下，该图也试图在较低维度的空间中从高维度描述中再现出邻近信息。

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  • 作者

    Michele Ceriotti; Gareth A. Tribello; Michele Parrinello;

  • 作者单位

    Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford 0X1 3QZ, United Kingdom;

    Computational Science,Department of Chemistry and Applied Biosciences, Eidgendssiche Technische Hochschule Zurich, Universita della Svizzera Italiana Campus,Via Giuseppe Buffi 13 C-6900 Lugano, Switzerland;

    Computational Science,Department of Chemistry and Applied Biosciences, Eidgendssiche Technische Hochschule Zurich, Universita della Svizzera Italiana Campus,Via Giuseppe Buffi 13 C-6900 Lugano, Switzerland;

  • 收录信息 美国《科学引文索引》(SCI);美国《生物学医学文摘》(MEDLINE);美国《化学文摘》(CA);
  • 原文格式 PDF
  • 正文语种 eng
  • 中图分类
  • 关键词

    nonlinear dimensionality reduction; proteins; molecular dynamics;

    机译：非线性降维;蛋白质;分子动力学;

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