Piangerelli Marco, Maestri Stefano, Merelli Emanuela
Computer Science, School of Science and Technologies, University of Camerino, Via Madonna delle Carceri 7, Camerino, 62032, Italy.
Computer Science, School of Science and Technologies, University of Camerino, Via Madonna delle Carceri 7, Camerino, 62032, Italy; CPT - Centre de Physique Théorique, Aix-Marseille University, 163 Avenue de Luminy, 13288, Marseille Cedex 9, France.
J Mol Graph Model. 2020 Jun;97:107576. doi: 10.1016/j.jmgm.2020.107576. Epub 2020 Mar 5.
Understanding in silico the dynamics of metabolic reactions made by a large number of molecules has led to the development of different tools for visualising molecular interactions. However, most of them are mainly focused on quantitative aspects. We investigate the potentiality of the topological interpretation of the interaction-as-perception at the basis of a multiagent system, to tackle the complexity of visualising the emerging behaviour of a complex system. We model and simulate the glycolysis process as a multiagent system, and we perform topological data analysis of the molecular perceptions graphs, gained during the formation of the enzymatic complexes, to visualise the set of emerging patterns. Identifying expected patterns in terms of simplicial structures allows us to characterise metabolic reactions from a qualitative point of view and conceivably reveal the simulation reactivity trend.
通过计算机模拟理解大量分子所进行的代谢反应动力学，已促使人们开发出不同的工具来可视化分子间的相互作用。然而，其中大多数工具主要关注定量方面。我们基于多智能体系统，研究将相互作用视为感知的拓扑解释在应对复杂系统涌现行为可视化复杂性方面的潜力。我们将糖酵解过程建模并模拟为一个多智能体系统，并对在酶复合物形成过程中获得的分子感知图进行拓扑数据分析，以可视化涌现模式集。根据单纯形结构识别预期模式，使我们能够从定性角度表征代谢反应，并有望揭示模拟反应性趋势。
