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Modeling the spontaneous evolution of morphology in natural systems and its preservation by proportionate growth remains a major scientific challenge. Yet, it is conceivable that if the basic mechanisms of growth and the coupled kinetic…
The work analyzes a one-dimensional viscoelastic model of blood vessel growth under nonlinear friction with surroundings, and provides numerical simulations for various growing cases. For the nonlinear differential equations, two sufficient…
A continuum model of epithelial tissue mechanics was formulated using cellular-level mechanical ingredients and cell morphogenetic processes, including cellular shape changes and cellular rearrangements. This model can include finite…
This thesis focuses on the applications of mathematical tools and concepts brought from nonequilibrium statistical physics to the modeling of ecological problems. The first part provides a short introduction where the theoretical concepts…
Protein synthesis is one of the most fundamental biological processes, which consumes a significant amount of cellular resources. Despite existence of multiple mathematical models of translation, varying in the level of mechanistical…
Sperm traverse their microenvironment through viscous fluid by propagating flagellar waves; the waveform emerges as a consequence of elastic structure, internal active moments, and low Reynolds number fluid dynamics. Engineered…
We study the transport of bacteria in a porous media modeled by a square channel containing one cylindrical obstacle via molecular dynamics simulations coupled to a lattice Boltzmann fluid. Our bacteria model is a rod-shaped rigid body…
Biomolecular condensates are formed via liquid-liquid phase separation of proteins, often together with nucleic acids, typically driven by interactions between low-affinity binding sites. The computational study of such condensates that…
The motility mechanism of certain rod-shaped bacteria has long been a mystery, since no external appendages are involved in their motion which is known as gliding. However, the physical principles behind gliding motility still remain poorly…
Flagellar-driven locomotion plays a critical role in bacterial attachment and colonization of surfaces, contributing to the risks of contamination and infection. Tremendous attempts to uncover the underlying principles governing bacterial…
For the first time the phenomenon of cellular structure coarsening are consistently analysed from the positions of kinetic, hydrodynamic and stochastodynamic theories of nonequilibrium statistical systems. Thereby micro-, meso- and…
Liquid-liquid phase separation is emerging as a crucial phenomenon in several fundamental cell processes. A range of eukaryotic systems exhibit liquid condensates. However, their function in bacteria, which in general lack membrane-bound…
Recent experiments have revealed that the diffusivity of exothermic and fast enzymes is enhanced when they are catalytically active, and different physical mechanisms have been explored and quantified to account for this observation. We…
The growth of plants is a hydromechanical phenomenon in which cells enlarge by absorbing water, while their walls expand and remodel under turgor-induced tension. In multicellular tissues, where cells are mechanically interconnected,…
The dynamics of a membrane is a coupled system comprising a moving elastic surface and an incompressible membrane fluid. We will consider a reduced elastic surface model, which involves the evolution equations of the moving surface, the…
Chemotaxis of enzymes in response to gradients in the concentration of their substrate has been widely reported in recent experiments, but a basic understanding of the process is still lacking. Here, we develop a microscopic theory for…
This paper concerns a model for tumor cell migration through the surrounding extracellular matrix by considering mass balance phenomena involving the chemical interactions produced on the cell surface. The well-posedness of this model is…
We present a continuum model of the coupling between cells and substrate that accounts for some of the observed substrate-stiffness dependence of cell properties. The cell is modeled as an elastic active gel, adapting recently developed…
We present a general formalism able to derive the kinetic equations of polymer dynamics. It is based on the application of nonequilibrium thermodynamics to analyze the irreversible processes taking place in the conformational space of the…
A multiscale mathematical model is presented to describe the de novo granulation and the evolution of multispecies granular biofilms within a continuous reactor. The granule is modelled as a spherical free boundary domain with radial…