Related papers: Protein connectivity in chemotaxis receptor comple…
Cytoskeletal motors known as motor proteins are molecules that drive cellular transport along several parallel cytoskeletal filaments and support many biological processes. Experimental evidences suggest that they interact with the nearest…
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…
Many membrane channels and receptors exhibit adaptive, or desensitized, response to a strong sustained input stimulus, often supported by protein activity-dependent inactivation. Adaptive response is thought to be related to various…
Predicting compound-protein affinity is critical for accelerating drug discovery. Recent progress made by machine learning focuses on accuracy but leaves much to be desired for interpretability. Through molecular contacts underlying…
{\sl Escherichia coli} ({\sl E. coli}) bacteria govern their trajectories by switching between running and tumbling modes as a function of the nutrient concentration they experienced in the past. At short time one observes a drift of the…
The analysis of correlations of amino acid occurrences in globular proteins has led to the development of statistical tools that can identify native contacts -- portions of the chains that come to close distance in folded structural…
Chemotaxis is the response of a particle to a gradient in the chemical composition of the environment. While it was originally observed for biological organisms, it is of great interest in the context of synthetic active particles such as…
The adhesion of cell membranes is mediated by the binding of membrane-anchored receptor and ligand proteins. In this article, we review recent results from simulations and theory that lead to novel insights on how the binding equilibrium…
The adhesion of cells is mediated by receptors and ligands anchored in apposing membranes. A central question is how to characterize the binding affinity of these membrane-anchored molecules. For soluble molecules, the binding affinity is…
Hybrid models of chemotaxis combine agent-based models of cells with partial differential equation models of extracellular chemical signals. In this paper, travelling wave properties of hybrid models of bacterial chemotaxis are…
In the chemotactic motion of Escherichia coli, the switching of transmembrane chemoreceptors between active and inactive states is one of the most important steps of the signaling pathway. We study the effect of this switching time-scale on…
The chemotactic pathway allows bacteria to respond and adapt to environmental changes, by tuning the tumbling and running motions that are due to clockwise and counterclockwise rotations of their flagella. The pathway is tightly regulated…
Most of our understanding of bacterial chemotaxis comes from studies of Escherichia coli. However, recent evidence suggests significant departures from the E. coli paradigm in other bacterial species. This variation may stem from different…
Clustering of molecules on biological membranes is a widely observed phenomenon. In some cases, such as the clustering of Ras proteins on the membranes of mammalian cells, proper cell signaling is critically dependent on the maintenance of…
Bacterial motility, and in particular repulsion or attraction towards specific chemicals, has been a subject of investigation for over 100 years, resulting in detailed understanding of bacterial chemotaxis and the corresponding sensory…
Micro-organisms aggregate through chemotaxis against a concentration gradient of signals secreted by themselves. We have numerically studied a model consisting of elements with intracellular dynamics, random walks with a state-dependent…
Mechanical coupling between a cell and substrate relies on focal adhesions, clusters of adhesion proteins linking stress fibers (bundles of actin proteins) inside the cell with surrounding tissue. Focal adhesions have been demonstrated to…
To survive in ever-changing environments, living organisms need to continuously combine the ongoing external inputs they receive, representing present conditions, with their dynamical internal state, which includes influences of past…
The structural properties of suspensions and other multiphase systems are vital to overall processability, functionality and acceptance among consumers. Therefore, it is crucial to understand the intrinsic connection between the…
Extending the classic works of Berg and Purcell on the biophysics of bacterial chemotaxis, we find the optimal chemotactic strategy for the peritrichous bacterium E. Coli in the high and low signal to noise ratio limits. The optimal…