Research Institute for Electronic Science, Hokkaido University, Kita 20 Nishi 10, Kita-ku, Sapporo 001-0020, Japan.
Phys Chem Chem Phys. 2011 Jan 28;13(4):1395-406. doi: 10.1039/c0cp00694g. Epub 2010 Dec 7.
We present a new self-consistent procedure to construct a multidimensional effective free energy landscape from a scalar single molecule time series, when single molecules experience the landscape within a given timescale of "observation." The theory is based on a framework we recently developed to extract a set of local equilibrium states (LESs) and their network from a scalar time series, such as distance between dye molecules tagged in a biomolecule. We scrutinize the appropriateness of the assumptions of local equilibration and local detailed balance among LESs at the single molecule level within the given timescale, rather than postulating them a priori. The self-consistent procedure in this article incorporates the effect of local correlation of the system dynamics inside potential basins, and the effect of finiteness of the sampled data points in assigning the boundary between different LESs. We propose a new simple scheme to assign the dimensionality of the energy landscape from a single molecule time series. We also address the question of what the molecules actually "feel" from the underlying landscape at the single molecule level.
我们提出了一种新的自洽方法，从标量单分子时间序列构建多维有效自由能景观，此时单分子在给定的“观测”时间尺度内经历景观。该理论基于我们最近开发的一个框架，用于从标量时间序列（例如标记在生物分子中的染料分子之间的距离）中提取一组局部平衡态（LES）及其网络。我们在给定的时间尺度内仔细检查了单分子水平上 LES 之间局部平衡和局部详细平衡假设的适当性，而不是先验地假设它们。本文中的自洽方法包括在势能盆地内系统动力学局部相关的影响，以及在分配不同 LES 之间边界时采样数据点有限性的影响。我们提出了一种新的简单方案，从单分子时间序列分配能量景观的维度。我们还在单分子水平上解决了分子实际上从潜在景观中“感受到”什么的问题。
