Related papers: A stochastic model of catalytic reaction networks …
Biological cells with all of their surface structure and complex interior stripped away are essentially vesicles - membranes composed of lipid bilayers which form closed sacs. Vesicles are thought to be relevant as models of primitive…
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…
Cellular life requires the presence of a set of biochemical mechanisms in order to maintain a predictable process of growth and division. Several attempts have been made towards the building of minimal protocells from a top-down approach,…
We present a simple mathematical model that captures the evolutionary capabilities of a prebiotic compartment or protocell. In the model the protocell contains an autocatalytic set whose chemical dynamics is coupled to the growth-division…
Stochasticity is a key characteristic of intracellular processes such as gene regulation and chemical signalling. Therefore, characterising stochastic effects in biochemical systems is essential to understand the complex dynamics of living…
We construct a simple model of a proto-cell that simulates a stochastic dynamics of abstract chemicals on a two-dimensional lattice. We assume that chemicals catalyze their reproduction through interaction with each other, and that between…
For understanding the origin of life, it is essential to explain the development of a compartmentalized structure, which undergoes growth and division, from a set of chemical reactions. In this study, a hypercycle with two chemicals that…
A great variety of molecular components is encapsulated in cells. Each of these components is replicated for cell reproduction. To address an essential role of the huge diversity of cellular components, we study a model of protocells that…
It has been pointed out that if an autocatalytic cycle produces primitive membrane chemicals, it can compose a self-maintaining proto cell. Moreover, it is known that a proto cell can divide itself spontaneously as it grows. An unsolved…
Over the last years, analyses performed on a stochastic model of catalytic reaction networks have provided some indications about the reasons why wet-lab experiments hardly ever comply with the phase transition typically predicted by…
All cells derive nutrition by absorbing some chemical and energy resources from the environment; these resources are used by the cells to reproduce the chemicals within them, which in turn leads to an increase in their volume. In this…
Explaining the origin of life requires us to explain how self-replication arises. To be specific, how can a self-replicating entity develop spontaneously from a chemical reaction system in which no reaction is self-replicating? Previously…
Cells of the human body have nearly identical genome but exhibit very different phenotypes that allow them to carry out specific functions and react to changes in their surrounding environment. This division of labour is achieved by…
The building of minimal self-reproducing systems with a physical embodiment (generically called protocells) is a great challenge, with implications for both theory and applied sciences. Although the classical view of a living protocell…
Compartmentalization of biochemical processes underlies all biological systems, from the organelle to the tissue scale. Theoretical models to study the interplay between noisy reaction dynamics and compartmentalization are sparse, and…
In this thesis we present a mathematical model describing the population dynamics of molecules in an artificial chemistry where large molecules can be produced by successive ligation of pairs of smaller molecules. The chemistry contains a…
Stochastic reaction network models are widely utilized in biology and chemistry to describe the probabilistic dynamics of biochemical systems in general, and gene interaction networks in particular. Most often, statistical analysis and…
Many cellular behaviors are regulated by gene regulation networks, kinetics of which is one of the main subjects in the study of systems biology. Because of the low number molecules in these reacting systems, stochastic effects are…
A high activity of reactions can be confined in a model cell with a semipermeable membrane in the Schl\"ogl model. It is interpreted as a model of primitive metabolism in a cell. We study two generalized models to understand the creation of…
To unveil the logic of cell from a level of chemical reaction dynamics, we need to clarify how ensemble of chemicals can autonomously produce the set of chemical, without assuming a specific external control echanism. A cell consists of a…