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The large-scale properties of chemical reaction systems, such as the metabolism, can be studied with graph-based methods. To do this, one needs to reduce the information -- lists of chemical reactions -- available in databases. Even for the…
Numerical computations have become a pillar of all modern quantitative sciences. Any computation involves modeling--even if often this step is not made explicit--and any model has to neglect details while still being physically accurate.…
Biological networks are one of the most studied object in computational biology. Several methods have been developed for studying qualitative properties of biological networks. Last decade had seen the improvement of molecular techniques…
Empirical studies of graphs have contributed enormously to our understanding of complex systems. Known today as network science, what was originally a theoretical study of graphs has grown into a more scientific exploration of communities…
Homogeneous Boltzmann-type equations are an established tool for modelling interacting multi-agent systems in sociophysics by means of the principles of statistical mechanics and kinetic theory. A customary implicit assumption is that…
Recent progress in experimental techniques has enabled us to quantitatively study stochastic and flexible behavior of biological systems. For example, gene regulatory networks perform stochastic information processing and their…
We introduce an algorithmic model of heat conduction, the thermodynamic graph. The thermodynamic graph is analogous to meshes in the finite difference method in the sense that the calculation of temperature is carried out at the vertices of…
Investigations of molecular bonds between single molecules and molecular complexes by the dynamic force spectroscopy are subject to large fluctuations at nanoscale and possible other aspecific binding, which mask the experimental output.…
Recent advances in single cell sequencing and multi-omics techniques have significantly improved our understanding of biological phenomena and our capacity to model them. Despite combined capture of data modalities showing similar progress,…
In the theoretical modelling of a physical system a crucial step consists in the identification of those degrees of freedom that enable a synthetic, yet informative representation of it. While in some cases this selection can be carried out…
In this paper homogenization of a mathematical model for biomechanics of a plant tissue with randomly distributed cells is considered. Mechanical properties of a plant tissue are modelled by a strongly coupled system of…
In recent times whole-genome gene expression analysis has turned out to be a highly important tool to study the coordinated function of a very large number of genes within their corresponding cellular environment, especially in relation to…
The growing complexity of the power grid, driven by increasing share of distributed energy resources and by massive deployment of intelligent internet-connected devices, requires new modelling tools for planning and operation. Physics-based…
In this paper, we propose a novel approach that employs kinetic equations to describe the collective dynamics emerging from graph-mediated pairwise interactions in multi-agent systems. We formally show that for large graphs and specific…
The process of protein folding from an unfolded state to a biologically active, folded conformation is governed by many parameters e.g the sequence of amino acids, intermolecular interactions, the solvent, temperature and chaperon…
The increasing complexity of energy systems due to sector coupling and decarbonization calls for unified modeling frameworks that capture the physical and structural interactions between electricity, gas, and heat networks. This paper…
Virtually every organism gathers information about its noisy environment and builds models from that data, mostly using neural networks. Here, we use stochastic thermodynamics to analyse the learning of a classification rule by a neural…
Choice models for populations of agents on graphs are studied in terms of statistical thermodynamics. Equations of state are derived and discussed for different connectivity schemes, utility approximations, and temperature and volume…
We develop a model of molecular binding based on the Bohr-Sommerfeld description of atoms together with a constraint taken from conventional quantum mechanics. The model can describe the binding energy curves of H2, H3 and other molecules…
One approach to studying the system-wide organization of biochemistry is to use statistical graph theory. Even in such a heavily simplified method, which disregards most of the dynamic aspects of biochemistry, one is faced with fundamental…