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Human society and natural environment form a complex giant ecosystem, where human activities not only lead to the change of environmental states, but also react to them. By using collective-risk social dilemma game, some studies have…
Natural selection acts on traits at different scales, often with opposing consequences. This article identifies the particular forces that act at each scale and how those forces combine to determine the overall evolutionary outcome. A…
Advancements in neural machinery have led to a wide range of algorithmic solutions for molecular property prediction. Two classes of models in particular have yielded promising results: neural networks applied to computed molecular…
Cooperation and competition coexist and coevolve in natural and social systems. Cooperation generates resources, which in turn, drive non-cooperative competition to secure individual shares. How this complex interplay between cooperation…
Open-ended evolution requires unbounded possibilities that evolving entities can explore. The cardinality of a set of those possibilities thus has a significant implication for the open-endedness of evolution. We propose that facilitating…
The emergence of collective cooperation in competitive environments is a well-known phenomenon in biology, economics, and social systems. While most evolutionary game models focus on the evolution of strategies for a fixed game, how…
The evolution of cooperation often depends upon population structure, yet nearly all models of cooperation implicitly assume that this structure remains static. This is a simplifying assumption, because most organisms possess genetic traits…
To analyze the evolutionary emergence of structural complexity in physical processes we introduce a general, but tractable, model of objects that interact to produce new objects. Since the objects--\emph{$epsilon$-machines}--have well…
Recently supervised machine learning has been ascending in providing new predictive approaches for chemical, biological and materials sciences applications. In this Perspective we focus on the interplay of machine learning algorithm with…
This study presents the approach to analyzing the evolution of an arbitrary complex system whose behavior is characterized by a set of different time-dependent factors. The key requirement for these factors is only that they must contain an…
The properties and fundamental limits of chemical computers have recently attracted significant interest as a model of computation, an unifying principle of cellular organisation and in the context of bio-engineering. As of yet, research in…
For prebiotic chemistry to succeed in producing a starting metastable, autocatalytic and reproducing system subject to evolutionary selection it must satisfy at least two apparently contradictory requirements: Because such systems are rare,…
Reduction of information entropy along with ever-increasing complexity are among the key signatures of living matter. Understanding the onset of such behavior in early prebiotic world is essential for solving the problem of origins of life.…
Protocells are supposed to have played a key role in the self-organizing processes leading to the emergence of life. Existing models either (i) describe protocell architecture and dynamics, given the existence of sets of collectively…
Kin selection and direct reciprocity are two most basic mechanisms for promoting cooperation in human society. Generalizing the standard models of the multi-player Prisoner's Dilemma and the Public Goods games for heterogeneous populations,…
This paper is a continuation of a previous work about the study of the survival probability modelizing the molecular predissociation in the Born-Oppenheimer framework. Here we consider the critical case where the reference energy…
Life occurs in concentrated `Ringer Solutions' derived from seawater that Lesser Blum studied for most of his life. As we worked together, Lesser and I realized that the questions asked of those solutions were quite different in biology…
Protein evolution underpins life, and understanding its behavior as a system is of great importance. However, our current models of protein evolution are arguably too simplistic to allow quantitative interpretation and prediction of…
How do mammalian cells that share the same genome exist in notably distinct phenotypes, exhibiting differences in morphology, gene expression patterns, and epigenetic chromatin statuses? Furthermore how do cells of different phenotypes…
In many indigenous societies, people are categorised into several cultural groups, or clans, within which they believe to share ancestors. Clan attributions provide certain rules for marriage and descent. Such rules between clans constitute…