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探索映射空间之旅：表征大分子简化表示的统计和度量性质

A journey through mapping space: characterising the statistical and metric properties of reduced representations of macromolecules.

作者信息

Menichetti Roberto, Giulini Marco, Potestio Raffaello

机构信息

Physics Department, University of Trento, via Sommarive, 14, 38123 Trento, Italy.

INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, via Sommarive, 14, 38123 Trento, Italy.

出版信息

Eur Phys J B. 2021;94(10):204. doi: 10.1140/epjb/s10051-021-00205-9. Epub 2021 Oct 12.

DOI:10.1140/epjb/s10051-021-00205-9
PMID:34720709
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC8550479/
Abstract

ABSTRACT

A mapping of a macromolecule is a prescription to construct a simplified representation of the system in which only a subset of its constituent atoms is retained. As the specific choice of the mapping affects the analysis of all-atom simulations as well as the construction of coarse-grained models, the characterisation of the has recently attracted increasing attention. We here introduce a notion of scalar product and distance between reduced representations, which allows the study of the metric and topological properties of their space in a quantitative manner. Making use of a Wang-Landau enhanced sampling algorithm, we exhaustively explore such space, and examine the qualitative features of mappings in terms of their squared norm. A one-to-one correspondence with an interacting lattice gas on a finite volume leads to the emergence of discontinuous phase transitions in mapping space, which mark the boundaries between qualitatively different reduced representations of the same molecule.

摘要

摘要

大分子的映射是一种构建系统简化表示的方法，其中仅保留其组成原子的一个子集。由于映射的具体选择会影响全原子模拟的分析以及粗粒度模型的构建，因此对映射的表征最近受到了越来越多的关注。我们在此引入简化表示之间的标量积和距离的概念，这使得能够以定量方式研究其空间的度量和拓扑性质。利用王-朗道增强采样算法，我们详尽地探索了这样的空间，并根据其平方范数研究映射的定性特征。与有限体积上的相互作用晶格气体的一一对应导致映射空间中出现不连续相变，这些相变标志着同一分子的定性不同简化表示之间的边界。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7c63/8550479/09e0d06f18ed/10051_2021_205_Fig14_HTML.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7c63/8550479/0157dbc83f3e/10051_2021_205_Fig1_HTML.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7c63/8550479/25476b5e56ea/10051_2021_205_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7c63/8550479/0b947ca51fd2/10051_2021_205_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7c63/8550479/378481b110dc/10051_2021_205_Fig8_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7c63/8550479/26a8920cd2fc/10051_2021_205_Fig9_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7c63/8550479/6f8391b1a967/10051_2021_205_Fig10_HTML.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7c63/8550479/535634961232/10051_2021_205_Fig13_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7c63/8550479/09e0d06f18ed/10051_2021_205_Fig14_HTML.jpg

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