Related papers: Autocatalytic Sets and Biological Specificity
This document presents a combinatorial framework for analyzing assembly systems using generating functions. We explore the theory through concrete examples, such as linear polymers, and develop recursive equations to characterize valid…
Network models are widely used as structural summaries of biochemical systems. Statistical estimation of networks is usually based on linear or discrete models. However, the dynamics of these systems are generally nonlinear, suggesting that…
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…
In this paper we develop further the formalism of fibrations of configuration spaces as a tool for modelling motion of autonomous systems in variable environments. We analyse the situations when the external conditions may change during the…
The main motivation of this work is to assess the validity of a LWR traffic flow model to model measurements obtained from trajectory data, and propose extensions of this model to improve it. A formulation for a discrete dynamical system is…
At higher altitudes, for high temperature gases, for instance near space shuttles moving at hypersonic speed, not only mechanical collisions are affecting the gas flow, but also chemical reactions have an impact on such hypersonic flows. In…
Analyzing kinetic experiments on protein aggregation using integrated rate laws has led to numerous advances in our understanding of the fundamental chemical mechanisms behind amyloidogenic disorders such as Alzheimer's and Parkinson's…
The kinetic folding of RNA sequences into secondary structures is modeled as a complex adaptive system, the components of which are possible RNA structural rearrangements (SRs) and their associated bases and base pairs. RNA bases and base…
A mystery about the origins of life is which molecular structures $-$ and what spontaneous processes $-$ drove the autocatalytic transition from simple chemistry to biology? Using the HP lattice model of polymer sequence spaces leads to the…
In this paper, we propose a new method to identify biochemical reaction networks (i.e. both reactions and kinetic parameters) from heterogeneous datasets. Such datasets can contain (a) data from several replicates of an experiment performed…
We develop a simple, chemostat-based model illustrating how a process analogous to associative learning can occur in a biochemical network. Associative learning is a form of learning whereby a system "learns" to associate two stimuli with…
The origin of life must have been preceded by Darwin-like evolutionary dynamics that could propagate it. How did that adaptive dynamics arise? And from what prebiotic molecules? Using evolutionary invasion analysis, we develop a universal…
A system of replicators with Hebbian random couplings is studied using dynamical methods. The self-reproducing species are here characterized by a set of binary traits and interact based on complementarity. In the case of an extensive…
We consider restricted Boltzmann machines with a binary visible layer and a Gaussian hidden layer trained by an unlabelled dataset composed of noisy realizations of a single ground pattern. We develop a statistical mechanics framework to…
Information processing relying on biochemical interactions in the cellular environment is essential for biological organisms. The implementation of molecular computational systems holds significant interest and potential in the fields of…
How do complex adaptive systems, such as life, emerge from simple constituent parts? In the 1990s Walter Fontana and Leo Buss proposed a novel modeling approach to this question, based on a formal model of computation known as $\lambda$…
We review the properties of biological motor proteins which move along linear filaments that are polar and periodic. The physics of the operation of such motors can be described by simple stochastic models which are coupled to a chemical…
We present a universal approach to the investigation of the dynamics in generalized models. In these models the processes that are taken into account are not restricted to specific functional forms. Therefore a single generalized models can…
The macroscopic behavior of the solution of a coupled system of partial differential equations arising in the modeling of reaction-diffusion processes in periodic porous media is analyzed. Our mathematical model can be used for studying…
Species or population that proliferate faster than others become dominant in numbers. Catalysis allows catalytic sets within a molecular reaction network to dominate the non catalytic parts of the network by processing most of the available…