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One of the properties that make ecological systems so unique is the range of complex behavioural patterns that can be exhibited by even the simplest communities with only a few species. Much of this complexity is commonly attributed to…
We present a spatially-extended system of chemical reactions exhibiting adaptation to time-dependent influxes of reactants. Here adaptation is defined as improved reproductive success, namely the ability of one of the many locally stable…
A review of the mechanisms of speciation is performed. The mechanisms of the evolution of species, taking into account the feedback of the state of the environment and mechanisms of the emergence of complexity, are considered. It is shown…
Molecular phenotypes link genomic information with organismic functions, fitness, and evolution. Quantitative traits are complex phenotypes that depend on multiple genomic loci. In this paper, we study the adaptive evolution of a…
We show that macro-molecular self-assembly can recognize and classify high-dimensional patterns in the concentrations of $N$ distinct molecular species. Similar to associative neural networks, the recognition here leverages dynamical…
Molecular circuits capable of autonomous learning could unlock novel applications in fields such as bioengineering and synthetic biology. To this end, existing chemical implementations of neural computing have mainly relied on emulating…
Retrieval-Augmented Large Language Models (LLMs), which incorporate the non-parametric knowledge from external knowledge bases into LLMs, have emerged as a promising approach to enhancing response accuracy in several tasks, such as…
The capacity of cells and organisms to respond to challenging conditions in a repeatable manner is limited by a finite repertoire of pre-evolved adaptive responses. Beyond this capacity, cells can use exploratory dynamics to cope with a…
Tokenization is a promising path to multi-modal models capable of jointly understanding protein sequences, structure, and function. Existing protein structure tokenizers create tokens by pooling information from local neighborhoods, an…
T cells are central to the adaptive immune response, capable of detecting pathogenic antigens while ignoring healthy tissues with remarkable specificity and sensitivity. Quantitatively understanding how T cell receptors (TCRs) discriminate…
Evolution produces complex and structured networks of interacting components in chemical, biological, and social systems. We describe a simple mathematical model for the evolution of an idealized chemical system to study how a network of…
Competition between independently arising beneficial mutations is enhanced in spatial populations due to the linear rather than exponential growth of clones. Recent theoretical studies have pointed out that the resulting fitness dynamics is…
The evolution of complexity has been a central theme for Biology [2] and Artificial Life research [1]. It is generally agreed that complexity has increased in our universe, giving way to life, multi-cellularity, societies, and systems of…
Animals often demonstrate a remarkable ability to adapt to their environments during their lifetime. They do so partly due to the evolution of morphological and neural structures. These structures capture features of environments shared…
There has been a long debate on how new levels of organization have evolved. It might seem unlikely, as cooperation must prevail over competition. One well-studied example is the emergence of autocatalytic sets, which seem to be a…
Enzyme is the major workhorse to carry out the diverse cellular functions. It catalyzes the biological reactions with a high specificity, with its topology playing a crucial role. For ecologically safe production of numerous bioproducts…
We show that neural networks trained by evolutionary reinforcement learning can enact efficient molecular self-assembly protocols. Presented with molecular simulation trajectories, networks learn to change temperature and chemical potential…
Evolutionary dynamics is often viewed as a subtle process of change accumulation that causes a divergence among organisms and their genomes. However, this interpretation is an inheritance of a gradualistic view that has been challenged at…
Feature interaction selection is a fundamental problem in commercial recommender systems. Most approaches equally enumerate all features and interactions by the same pre-defined operation under expert guidance. Their recommendation is…
Cells generally change their internal state to adapt to an environmental change, and accordingly evolve in response to the new conditions. This process involves phenotypic changes that occur over several different time scales, ranging from…