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In-vivo, real-time study of the local and collective cellular biomechanical responses requires the fine and selective manipulation of the cellular environment. One innovative pathway is the use of photoactive bio-substrates such as…
Cellular automata are a class of computational models based on simple rules and algorithms that can simulate a wide range of complex phenomena. However, when using conventional computers, these 'simple' rules are only encapsulated at the…
The role of dynamics in spin observables for pseudoscalar meson photoproduction is investigated using a density matrix approach in a multipole truncated framework. Extraction of novel rules for $\gamma p \rightarrow \pi^+ n,~ K^+ \Lambda$…
In this paper homogenization of a mathematical model for plant tissue biomechanics is presented. The microscopic model constitutes a strongly coupled system of reaction-diffusion-convection equations for chemical processes in plant cells,…
The process of photosynthesis, the main source of energy in the animate world, converts sunlight into chemical energy. The surprisingly high efficiency of this process is believed to be enabled by an intricate interplay between the quantum…
The new experimental data of kaon photoproduction on the nucleon, gamma p -> K+ Lambda, have been analyzed by means of a multipoles model. Different from the previous models, in this analysis the resonance decay widths are constrained to…
Recent work of M.D. Johnston et al. has produced sufficient conditions on the structure of a chemical reaction network which guarantee that the corresponding discrete state space system exhibits an extinction event. The conditions consist…
In this paper, we aim at modelling and analyzing the regulation processes in multi-cellular biological systems, in particular tissues. The modelling framework is based on interconnected logical regulatory networks a la Rene Thomas equipped…
Regulation of cell proliferation is a crucial aspect of tissue development and homeostasis and plays a major role in morphogenesis, wound healing, and tumor invasion. A phenomenon of such regulation is contact inhibition, which describes…
A popular numerical method to model the dynamics of a 'full spectrum' of cosmic rays (CRs), also applicable to radiation/neutrino hydrodynamics (RHD), is to discretize the spectrum at each location/cell as a piecewise power law in 'bins' of…
The aim of this paper is to further develop mathematical models for bleb formation in cells, including cell-membrane interactions with linker proteins. This leads to nonlinear reaction-diffusion equations on a surface coupled to fluid…
We propose a universal approach for modeling complex integrated photonic resonators based on the scattering matrix method. By dividing devices into basic elements including directional cou-plers and connecting waveguides, our approach can…
The kinetics of the photochromic reaction of oxygen-containing rare-earth hydrides is commonly described by an exponential function assuming a single-step process. In this paper, we elaborate on the origin of the photochromic effect in…
Photon subtraction is useful to produce nonclassical states of light addressed to applications in photonic quantum technologies. After a very accelerated development, this technique makes possible obtaining either single photons or optical…
The theory of biochemical processes needs simple but realistic models of phenomena underlying microscopic dynamics of proteins. Many experiments performed in the 1980s have demonstrated that within the protein native state, apart from usual…
The thermodynamical properties of the photon-plasma system had been studied using statistical physics approach. Photons develop an effective mass in the medium thus -- as a result of the finite chemical potential -- a photon Bose-Einstein…
We present a detailed physiological model of the retina that includes the biochemistry and electrophysiology of phototransduction, neuronal electrical coupling, and the spherical geometry of the eye. The model is a parabolic-elliptic system…
We study the thermodynamics and kinetics of folding for a small peptide. Our data rely on Monte Carlo simulations where the interactions among all atoms are taken into account. Monte Carlo kinetics is used to study folding of the peptide at…
The modelling and analysis of biological systems has deep roots in Mathematics, specifically in the field of Ordinary Differential Equations. Alternative approaches based on formal calculi, often derived from process algebras or term…
Traditional stochastic modeling of reactive systems limits the domain of applicability of the associated path thermodynamics to systems involving a single elementary reaction at the origin of each observed change in composition. An…