Related papers: Adaptation dynamics in densely clustered chemorece…
Chemically active colloids or enzymes cluster into dense droplets driven by their phoretic response to collectively generated chemical gradients. Employing Brownian dynamics simulation techniques, our study of the dynamics of such a…
We examine the stochastic dynamics of two enzymes that are mechanically coupled to each other, e.g., through an elastic substrate or a fluid medium. The enzymes undergo conformational changes during their catalytic cycle, which itself is…
Transmembrane receptor clustering is a ubiquitous phenomenon in pro- and eukaryotic cells to physically sense receptor/ligand interactions and subsequently translate an exogenous signal into a cellular response. Despite that receptor…
Chemotaxis plays a crucial role in a variety of processes in biology and ecology. Quite often it acts to improve efficiency of biological reactions; one example is the immune system signalling, where infected tissues release chemokines…
When exposed to a time-periodic chemical signal, an \textit{E.~coli} cell responds by modulating its receptor activity in a similar time-periodic manner. However, there exists a phase lag between the applied signal and the activity…
Signaling networks are designed to sense an environmental stimulus and adapt to it. We propose and study a minimal model of signaling network that can sense and respond to external stimuli of varying strength in an adaptive manner. The…
Living organisms rely on endogenous feedback mechanisms to maintain homeostasis in the presence of uncertainty and environmental fluctuations. An emerging challenge at the interface of control systems engineering and synthetic biology is…
Biological evolution of a population is governed by the fitness landscape, which is a map from genotype to fitness. However, a fitness landscape depends on the organisms environment, and evolution in changing environments is still poorly…
How can a microorganism adapt to a variety of environmental conditions despite there exists a limited number of signal transduction machineries? We show that for any growing cells whose gene expression is under stochastic fluctuations,…
Cells adapt their metabolic fluxes in response to changes in the environment. We present a framework for the systematic construction of flux-based graphs derived from organism-wide metabolic networks. Our graphs encode the directionality of…
Enzymes have been recently proposed to have mechanical activity associated with their chemical activity. In a number of recent studies, it has been reported that enzymes undergo enhanced diffusion in the presence of their corresponding…
Cells are constantly exposed to diverse stimuli-chemical, mechanical, or electrical-that guide their movement. In physiological conditions, these signals often overlap, as seen during infections, where neutrophils and dendritic cells…
Understanding protein dynamics are essential for deciphering protein functional mechanisms and developing molecular therapies. However, the complex high-dimensional dynamics and interatomic interactions of biological processes pose…
We propose a minimal mathematical model to explain long-range coordination of dynamics of multiple cells in epithelial spreading, which may be induced, under different conditions, by a chemical signal, or mechanical stress, or both. The…
Coherent oscillatory activity can arise spontaneously as a result of increased coupling in a system of excitable and passive cells, each being quiescent in isolation. This can potentially explain the appearance of spontaneous rhythmic…
Many biological systems can sense periodical variations in a stimulus input and produce well-timed, anticipatory responses after the input is removed. Such systems show memory effects for retaining timing information in the stimulus and…
Cellular signaling networks have evolved to cope with intrinsic fluctuations, coming from the small numbers of constituents, and the environmental noise. Stochastic chemical kinetics equations govern the way biochemical networks process…
Cells generally convert nutrient resources to useful products via energy transduction. Accordingly, the thermodynamic efficiency of this conversion process is one of the most essential characteristics of living organisms. However, although…
Cells often have tens of thousands of receptors, even though only a few activated receptors can trigger full cellular responses. Reasons for the overabundance of receptors remain unclear. We suggest that, in certain conditions, the large…
Colonies of bacteria grown on thin agar plate exhibit fractal patterns as a result of adaptation to their environments. The bacterial colony pattern formation is regulated crucially by chemotaxis, the movement of cells along a chemical…