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The present view of biological phenomena is based on a biochemical paradigm that development of living organisms is defined by information stored in a molecular form as some genetic code. However, new discoveries indicate that biological…

A multiscale mathematical model describing the genesis and ecology of algal-bacterial photogranules and the metals biosorption on their solid matrix within a sequencing batch reactor (SBR) is presented. The granular biofilm is modelled as a…

Delay is an important and ubiquitous aspect of many biochemical processes. For example, delay plays a central role in the dynamics of genetic regulatory networks as it stems from the sequential assembly of first mRNA and then protein.…

Motivation: Modeling biological signaling networks using ordinary differential equations (ODEs) has proven to be a powerful technique for generating insight into cellular dynamics, but it typically requires estimating rate parameters based…

High-throughput data acquisition in synthetic biology leads to an abundance of data that need to be processed and aggregated into useful biological models. Building dynamical models based on this wealth of data is of paramount importance to…

We study a system of self-propelled disks that perform run-and-tumble motion, where particles can adopt more than one internal state. One of those internal states can be transmitted to another particle if the particle carrying this state…

The recently introduced method of excess collisions (MEC) is modified to estimate diffusion-controlled reaction times inside systems of arbitrary size. The resulting MEC-E equations contain a set of empirical parameters, which have to be…

As a cornerstone in the Evolutionary Computation (EC) domain, Differential Evolution (DE) is known for its simplicity and effectiveness in handling challenging black-box optimization problems. While the advantages of DE are well-recognized,…

Biochemical molecules interact through modification and binding reactions, giving raise to a combinatorial number of possible biochemical species. The time-dependent evolution of concentrations of the species is commonly described by a…

A combustion chemistry acceleration scheme is developed based on deep operator networks (DeepONets). The scheme is based on the identification of combustion reaction dynamics through a modified DeepOnet architecture such that the solutions…

The concept of (auto)catalytic systems has become a cornerstone in understanding evolutionary processes in various fields. The common ground is the observation that for the production of new species/goods/ideas/elements etc. the…

The functioning of machines typically requires a concerted action of their parts. This requirement also holds for molecular motors that drive vital cellular processes and imposes constraints on their conformational changes as well as the…

A new delay equation is introduced to describe the punctuated evolution of complex nonlinear systems. A detailed analytical and numerical investigation provides the classification of all possible types of solutions for the dynamics of a…

Time delays are ubiquitous in industry and nature, and they significantly affect both transient dynamics and stability properties. Consequently, it is often necessary to identify and account for the delays when, e.g., designing a…

The analysis of the dynamics of delays propagation is one of the major topics inside Air Transport Management research. Delays are generated by the elements of the system, but their propagation is a global process fostered by relationships…

Autocatalysis is an important feature of metabolic networks, contributing crucially to the self-maintenance of organisms. Autocatalytic subsystems of chemical reaction networks (CRNs) are characterized in terms of algebraic conditions on…

This paper concerns a general class of PDE-ODE reaction-diffusion systems, which features a singular fast-reaction limit towards a reaction-diffusion equation coupled to a scalar hysteresis operator. As prototypical application, we present…

In closed hydroponic systems, periodic readjustment of nutrient solution is necessary to continuously provide stable environment to plant roots because the interaction between plant and nutrient solution changes the rate of ions in it. The…

Thermodynamic constraints on reactions directions are inherent in the structure of a given biochemical network. However, concrete procedures for determining feasible reaction directions for large-scale metabolic networks are not well…

Body size or mass is one of the main factors underlying food webs structure. A large number of evolutionary models have shown that indeed, the adaptive evolution of body size (or mass) can give rise to hierarchically organised trophic…