Related papers: Relationship between cellular response and behavio…
Biochemical reaction networks in living cells usually involve reversible covalent modification of signaling molecules, such as protein phosphorylation. Under conditions of small molecule numbers, as is frequently the case in living cells,…
When a single cell senses a chemical gradient and chemotaxes, stochastic receptor-ligand binding can be a fundamental limit to the cell's accuracy. For clusters of cells responding to gradients, however, there is a critical difference: even…
Single eukaryotic cells commonly sense and follow chemical gradients, performing chemotaxis. Recent experiments and theories, however, show that even when single cells do not chemotax, clusters of cells may, if their interactions are…
Chemotaxis is the physical phenomenon that bacteria adjust their motions according to chemical stimulus. A classical model for this phenomenon is a kinetic equation that describes the velocity jump process whose tumbling/transition kernel…
The metabolic network plays a crucial role in regulating bacterial metabolism and growth, but it is subject to inherent molecular stochasticity. Previous studies have utilized flux balance analysis and the maximum entropy method to predict…
We study methylation dynamics of the chemoreceptors as an {\sl E.coli} cell moves around in a spatially varying chemo-attractant environment. We consider attractant concentration with strong and weak spatial gradient. During the uphill and…
The migratory dynamics of cells in physiological processes, ranging from wound healing to cancer metastasis, rely on contact-mediated cell-cell interactions. These interactions play a key role in shaping the stochastic trajectories of…
Collective motion of chemotactic bacteria as E. Coli relies, at the individual level, on a continuous reorientation by runs and tumbles. It has been established that the length of run is decided by a stiff response to a temporal sensingof…
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…
Evolution has provided many organisms with sophisticated sensory systems that enable them to respond to signals in their environment. The response frequently involves alteration in the pattern of movement, such as the chemokinesis of the…
Bacterial chemotaxis is controlled by the signalling of a cluster of receptors. A cooperative model is presented, in which coupling between neighbouring receptor dimers enhances the sensitivity with which stimuli can be detected, without…
We study single cell E.coli chemotaxis in a spatio-temporally varying attractant environment. Modeling the attractant concentration in the form of a traveling sine wave, we measure in our simulations, the chemotactic drift velocity of the…
In nature, microorganisms must often cope with hostile environmental conditions. To do so they have developed sophisticated cooperative behavior and intricate communication capabilities, such as: direct cell-cell physical interactions via…
Understanding the organization of reaction fluxes in cellular metabolism from the stoichiometry and the topology of the underlying biochemical network is a central issue in systems biology. In this task, it is important to devise reasonable…
Cell-to-cell variability is inherent to numerous biological processes, including cell migration. Quantifying and characterizing the variability of migrating cells is challenging, as it requires monitoring many cells for long time windows…
The chemotaxis pathway of the bacterium Rhodobacter sphaeroides has many similarities to the well-studied pathway in Escherichia coli. It exhibits robust adaptation and has several homologues of the latter's chemotaxis proteins. Recent…
Many processes in biology involve both reactions and chemotaxis. However, to the best of our knowledge, the question of interaction between chemotaxis and reactions has not yet been addressed either analytically or numerically. We consider…
Unlike macroscopic engines, the molecular machinery of living cells is strongly affected by fluctuations. Stochastic Thermodynamics uses Markovian jump processes to model the random transitions between the chemical and configurational…
Recent work on synthetic rescues has shown that the targeted deletion of specific metabolic genes can often be used to rescue otherwise non-viable mutants. This raises a fundamental biophysical question: to what extent can the whole-cell…
Collective migration -- the directed, coordinated motion of many self-propelled agents -- is a fascinating emergent behavior exhibited by active matter that has key functional implications for biological systems. Extensive studies have…