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We consider a generic proto-cell model consisting of any conservative chemical reaction network embedded within a membrane. The membrane results from the self-assembly of one of the chemical species (membrane precursor) and is…
Motile microorganisms, like bacteria and algae, unify abilities like self-propulsion, autonomous navigation, and decision-making on the micron scale. While recent breakthroughs have led to the creation of synthetic microswimmers and…
Microbiological systems evolve to fulfill their tasks with maximal efficiency. The immune system is a remarkable example, where self-non self distinction is accomplished by means of molecular interaction between self proteins and antigens,…
Emergence and maintenance of polymers with complex sequences is a major question in the study of origins of life. To answer this, we studied a model polymerization reaction, where polymers are synthesized by stepwise ligation from two types…
Background: Autocatalytic sets are often considered a necessary (but not sufficient) condition for the origin and early evolution of life. Although the idea of autocatalytic sets was already conceived of many years ago, only recently have…
Research investigating the origins of life usually focuses on exploring possible life-bearing chemistries in the pre-biotic Earth, or else on synthetic approaches. Little work has been done exploring fundamental issues concerning the…
A model of $s$ interacting species is considered with two types of dynamical variables. The fast variables are the populations of the species and slow variables the links of a directed graph that defines the catalytic interactions among…
Many models for the origin of life have focused on understanding how evolution can drive the refinement of a preexisting enzyme, such as the evolution of efficient replicase activity. Here we present a model for what was, arguably, an even…
How could primordial life, before the evolution of genetic systems, adapt to fluctuating environments and achieve homeostasis? This study proposes a minimal, chemically plausible model where homeostasis emerges from a simple chemical…
Understanding the rules underlying organismal development is a major unsolved problem in biology. Each cell in a developing organism responds to signals in its local environment by dividing, excreting, consuming, or reorganizing, yet how…
In this work we introduce some preliminary analyses on the role of a semi-permeable membrane in the dynamics of a stochastic model of catalytic reaction sets (CRSs) of molecules. The results of the simulations performed on ensembles of…
Engineering simple, artificial models of living cells allows synthetic biologists to study cellular functions under well-controlled conditions. Reconstituting multicellular behaviors with synthetic cell-mimics is still a challenge because…
Our knowledge of how individual cells self-organize to form complex multicellular systems is being revolutionized by a data outburst, coming from high-throughput experimental breakthroughs such as single-cell RNA sequencing and spatially…
Dynamics maintaining diversity of cell types in a multi-cellular system are studied in relationship with the plasticity of cellular states. By adopting a simple theoretical framework for intra-cellular chemical reaction dynamics with…
In this study, we provide a relatively simple simulation framework for constructing artificial life (ALife) with both autonomous and evolutionary aspects by extending chemoton model. While the original chemoton incorporates metabolism,…
One of the great challenges in science is determining when, where, why, and how life first arose as well as the form taken by this life. In the present study, life was assumed to be (1) bounded, (2) replicating, (3) able to inherit…
A dynamic model for cell differentiation is studied, where cells with internal chemical reaction dynamics interact with each other and replicate. It leads to spontaneous differentiation of cells and determination, as is discussed in the…
The emergence of autocatalytic sets of molecules seems to have played an important role in the origin of life context. Although the possibility to reproduce this emergence in laboratory has received considerable attention, this is still far…
Proliferation and motility are ubiquitous drivers of activity in biological systems. Here, we study a dense binary mixture of motile and proliferating particles with exclusively repulsive interactions, where homeostasis in the proliferating…
Cells operate in part by compartmentalizing chemical reactions. For example, recent work has shown that chromatin, the material that contains the cell's genome, can auto-regulate its structure by utilizing reaction products (proteins, RNA)…