分类: 信息科学与系统科学 >> 信息科学与系统科学基础学科 分类: 生物学 >> 生物进化论 分类: 生物学 >> 生物数学 分类: 物理学 >> 交叉学科物理及相关领域的科学与技术 分类: 生物学 >> 遗传学 提交时间: 2023-10-15
摘要: Background: In bioinformatics, tools like multiple sequence alignment and entropy methods probe sequence information and evolutionary relationships between species. Although powerful, they might miss crucial hierarchical relationships formed by the reuse of repetitive subsequences like duplicons and transposable elements. Such relationships are governed by evolutionary tinkering'', as described by Fran c{c}ois Jacob. The newly developed Ladderpath theory provides a quantitative framework to describe these hierarchical relationships.Results: Based on this theory, we introduce two indicators: order-rate $ eta$, characterizing sequence pattern repetitions and regularities, and ladderpath-complexity $ kappa$, characterizing hierarchical richness within sequences, considering sequence length. Statistical analyses on real amino acid sequences showed: (1) Among the typical species analyzed, humans possess relatively more sequences with large $ kappa$ values. (2) Proteins with a significant proportion of intrinsically disordered regions exhibit increased $ eta$ values. (3) There are almost no super long sequences with low $ eta$. We hypothesize that this arises from varied duplication and mutation frequencies across different evolutionary stages, which in turn suggests a zigzag pattern for the evolution of protein complexity. This is supported by our simulations and examples from protein families such as Ubiquitin and NBPF.Conclusions: Our method emphasizes how objects are generated'', capturing the essence of evolutionary tinkering and reuse. The findings hint at a connection between sequence orderliness and structural uncertainty, and suggest that different species or those in varied environments might adopt distinct protein elongation strategies. These insights highlight our method's value for further in-depth evolutionary biology applications.
分类: 信息科学与系统科学 >> 信息科学与系统科学基础学科 分类: 物理学 >> 交叉学科物理及相关领域的科学与技术 提交时间: 2022-08-15
摘要: The notion of information and complexity are important concepts in many scientific fields such as molecular biology, evolutionary theory and exobiology. Many measures of these quantities are either difficult to compute, rely on the statistical notion of information, or can only be applied to strings. Based on assembly theory, we propose the notion of a ladderpath, which describes how an object can be decomposed into hierarchical structures using repetitive elements. From the ladderpath two measures naturally emerge: the ladderpath-index and the order-index, which represent two axes of complexity. We show how the ladderpath approach can be applied to both strings and spatial patterns and argue that all systems that undergo evolution can be described as ladderpaths. Further, we discuss possible applications to human language and the origin of life. The ladderpath approach provides an alternative characterization of the information that is contained in a single object (or a system) and could aid in our understanding of evolving systems and the origin of life in particular.
分类: 数学 >> 应用数学 分类: 计算机科学 >> 计算机软件 分类: 信息科学与系统科学 >> 信息与系统科学其他学科 提交时间: 2021-10-11
摘要: The shortest path problem (SPP) is a classic problem and appears in a wide range of applications. Although a variety of algorithms already exist, new advances are still being made, mainly tuned for particular scenarios to have better performances. As a result, they become more and more technically complex and sophisticated. Here we developed a novel nature-inspired algorithm to compute all possible shortest paths between two nodes in a graph: Resonance Algorithm (RA), which is surprisingly simple and intuitive. Besides its simplicity, RA turns out to be much more time-efficient for large-scale graphs than the extended Dijkstra's algorithm (such that it gives all possible shortest paths). Moreover, RA can handle any undirected, directed, or mixed graphs, irrespective of loops, unweighted or positively-weighted edges, and can be implemented in a fully decentralized manner. These good properties ensure RA a wide range of applications.
分类: 地球科学 >> 空间物理学 提交时间: 2016-05-12
摘要: We present high-resolution observations of a quiescent solar prominence that consists of a vertical and a horizontal foot encircled by an overlying spine and has ubiquitous counter-streaming mass flows. While the horizontal foot and the spine were connected to the solar surface, the vertical foot was suspended above the solar surface and was supported by a semicircular bubble structure. The bubble first collapsed, then reformed at a similar height, and finally started to oscillate for a long time. We find that the collapse and oscillation of the bubble boundary were tightly associated with a flare-like feature located at the bottom of the bubble. Based on the observational results, we propose that the prominence should be composed of an overlying horizontal spine encircling a low-lying horizontal and vertical foot, in which the horizontal foot consists of shorter field lines running partially along the spine and has ends connected to the solar surface, while the vertical foot consists of piling-up dips due to the sagging of the spine fields and is supported by a bipolar magnetic system formed by parasitic polarities (i.e., the bubble). The upflows in the vertical foot were possibly caused by the magnetic reconnection at the separator between the bubble and the overlying dips, which intruded into the persistent downflow field and formed the picture of counter-streaming mass flows. In addition, the counter-streaming flows in the horizontal foot were possibly caused by the imbalanced pressure at the both ends.