Related papers: Autocatalytic Sets and Biological Specificity
Over the past decade, extensive research into single-atom catalysts (SACs) has revealed that the catalytic behavior of metal adatoms is highly dependent on how they interact with their support. A strong dependence on the local coordination…
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…
The self-consistent rate theory for surface growth in the submonolayer regime is generalized from mono- to multi-component systems, which are formed by codeposition of different types of atoms or molecules. As a new feature, the theory…
Collective motion in actively propelled particle systems is triggered on the very local scale by nucleation of coherently moving units consisting of just a handful of particles. These units grow and merge over time, ending up in a…
Recent research in both the experimental and mathematical communities has focused on biochemical interaction systems that satisfy an "absolute concentration robustness" (ACR) property. The ACR property was first discovered experimentally…
The goal of the paper is to automatize the selection of mechanisms which are able to describe a set of measurements. In order to do so first we construct a set of possible mechanism fulfilling chemically reasonable requirements with a given…
Longitudinal studies with binary or ordinal responses are widely encountered in various disciplines, where the primary focus is on the temporal evolution of the probability of each response category. Traditional approaches build from the…
We propose an exactly solvable simplified statistical mechanical model for the thermodynamics of beta-amyloid aggregation, generalizing a well-studied model for protein folding. The monomer concentration is explicitly taken into account as…
We study a simple solvable model describing the genesis of monomer sequences for hetero-polymers (such as proteins), as the result of the equilibration of a slow stochastic genetic selection process which is assumed to be driven by the…
Mathematical models are increasingly being used to understand complex biochemical systems, to analyze experimental data and make predictions about unobserved quantities. However, we rarely know how robust our conclusions are with respect to…
Although pathway-specific kinetic theories are fundamentally important to describe and understand reversible polymerisation kinetics, they come in principle at a cost of having a large number of system-specific parameters. Here, we…
The notion of (auto) catalytic networks has become a cornerstone in understanding the possibility of a sudden dramatic increase of diversity in biological evolution as well as in the evolution of social and economical systems. Here we study…
The statistical thermodynamics of binary mixtures of polyatomic species was developed on a generalization in the spirit of the lattice-gas model and the quasi-chemical approximation (QCA). The new theoretical framework is obtained by…
An autocatalytic reacting system with particles interacting at a finite distance is studied. We investigate the effects of the discrete-particle character of the model on properties like reaction rate, quenching phenomenon and front…
This paper develops some basic principles to study autocatalytic networks and exploit their structural properties in order to characterize their inherent fundamental limits and tradeoffs. In a dynamical system with autocatalytic structure,…
Self-organized emergent patterns can be widely seen in particle interactions producing complex structures such as chemical elements and molecules. Inspired by these interactions, this work presents a novel stochastic approach that allows a…
We study kinetics of diffusion-limited catalytically-activated $A + B \to B$ reactions taking place in three dimensional systems, in which an annihilation of diffusive $A$ particles by diffusive traps $B$ may happen only if the encounter of…
We analyzed the stochastic behavior of systems controlled by autocatalytic reaction A+X -> X+X. Assuming the distribution of reacting particles in the system volume to be uniform, we introduced the notion of the point model of reaction…
We consider the population dynamics of a set of species whose network of catalytic interactions is described by a directed graph. The relationship between the attractors of this dynamics and the underlying graph theoretic structures like…
Chemotaxis is a directed cell movement in response to external chemical stimuli. In this paper, we propose a simple model for the origin of chemotaxis - namely how a directed movement in response to an external chemical signal may occur…