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In multicellular organisms, several cell states coexist. For determining each cell type, cell-cell interactions are often essential, in addition to intracellular gene expression dynamics. Based on dynamical systems theory, we propose a…

We investigate a model of a stochastic engine operating cyclically at constant bath temperature, which consists of an overdamped Brownian harmonic oscillator that plays the role of working substance and is elastically coupled to an active…

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…

While it is commonly observed that the shape dynamics of mammalian cells can undergo large random fluctuations, theoretical models aiming at capturing cell mechanics often focus on the deterministic part of the motion. In this paper, we…

Many biological processes involve the action of molecular motors that interact with the cell cytoskeleton. Some processes, such as the transport of cargoes is achieved mainly by the action of individual motors. Other, such as cell motility…

The spatiotemporal coordination and regulation of cell proliferation is fundamental in many aspects of development and tissue maintenance. Cells have the ability to adapt their division rates in response to mechanical constraints, yet we do…

Most computer simulations of molecular dynamics take place under equilibrium conditions--in a closed, isolated system, or perhaps one held at constant temperature or pressure. Sometimes, extra tensions, shears, or temperature gradients are…

The ability of cells to sense and respond to the mechanical properties of their environments is fundamental to a range of cellular behaviours, with substrate stiffness increasingly being found to be a key signalling factor. Although active…

Motor-driven intracellular transport of organelles, vesicles, and other molecular cargo is a highly collective process. An individual cargo is often pulled by a team of transport motors, with numbers ranging from only a few to several…

This paper focuses on studying a model for molecular motors responsible for the bending of the axoneme in the flagella of microorganisms. The model is a coupled system of partial differential equations inspired by J\"ulicher et al. or…

Mutation rate is a key determinant of the pace as well as outcome of evolution, and variability in this rate has been shown in different scenarios to play a key role in evolutionary adaptation and resistance evolution under stress caused by…

The performance of a molecular motor, characterized by its power output and energy efficiency, is investigated in the motor design space spanned by the stepping rate function and the motor-track interaction potential. Analytic results and…

It has long been hypothesized that futile cycles in cellular metabolism are involved in the regulation of biochemical pathways. Following the work of Newsholme and Crabtree, we develop a quantitative theory for this idea based on…

Energy transfer plays a vital role in many natural and technological processes. In this work, we study the effects of mechanical motion on the excitation transfer through a chain of interacting molecules with application to biological…

The magnetoquasistatic simulation of large power converters, in particular transformers, requires efficient models for their foils windings by means of homogenization techniques. In this article, the classical foil conductor model is…

GB migration plays a central role in microstructural evolution. Many experiments and simulations have been conducted to clarify the relationships between GB velocity and various parameters to tailor GB networks. However, the complexity of…

Adherent cells have long been known to display two modes during migration: a faster mode that is persistent in direction and a slower one where they turn. Compared to the persistent mode, the turns are less studied. Here we develop a simple…

Bacterial populations in natural conditions are expected to experience stochastic environmental fluctuations, and in addition, environments are affected by bacterial activities since they consume substrates and excrete various chemicals. We…

The intricate wobbling motion of flagellated bacteria, characterized by the periodic precession of the cell body, is a determinant factor in their motility and navigation within complex fluid environments. While well-studied in quiescent…

Brownian particles interacting sequentially with distinct temperatures and driving forces at each stroke have been tackled as a reliable alternative for the construction of engine setups. However they can behave very inefficiently depending…