Related papers: Maximum likelihood and the single receptor
In genetic networks, information of relevance to the organism is represented by the concentrations of transcription factor molecules. In order to extract this information the cell must effectively "measure"' these concentrations, but there…
Information of relevance to the organism often is represented by the concentrations of particular molecules inside a cell. As outside observers we can now measure these concentrations precisely, but the cell's own mechanisms must be…
Eukaryotic cells perform chemotaxis by determining the direction of chemical gradients based on stochastic sensing of concentrations at the cell surface. To examine the efficiency of this process, previous studies have investigated the…
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…
Autologous chemotaxis, in which cells secrete and detect molecules to determine the direction of fluid flow, is thwarted at high cell density because molecules from other cells interfere with a given cell's signal. Using a minimal model of…
A key challenge in molecular biology is to decipher the mapping of protein sequence to function. To perform this mapping requires the identification of sequence features most informative about function. Here, we quantify the amount of…
Experimental evidence lends support to the conjecture that the ability of chains of cells to sense the gradient of an external chemical concentration could rely on cell-to-cell communication. This is the basis for the gradient sensing…
The mammalian brain is a metabolically expensive device, and evolutionary pressures have presumably driven it to make productive use of its resources. For sensory areas, this concept has been expressed more formally as an optimality…
In this paper, a diffusion-based molecular communication channel is modeled in presence of a probabilistic absorber. The probabilistic absorber is an absorber which absorbs molecules upon collision with probability q. With random walk…
The phenomenon of molecular binding, where two molecules, referred to as a receptor and a ligand, bind together to form a ligand-receptor complex, is ubiquitous in biology and essential for the accurate functioning of all life-sustaining…
How can cells embedded into a gradient concentration triangulate the position of the source and migrate toward their final destination? The source triangulation requires to recover the three dimensional coordinates of the source from the…
Experiments show that cellular uptake of nanoparticles, via receptor-mediated endocytosis, strongly depends on nanoparticle size. There is an optimal size, approximately 50 nm in diameter, at which cellular uptake is the highest. In…
Bacterial chemotactic sensing converts noisy chemical signals into running and tumbling. We analyze the static sensing limits of mixed Tar/Tsr chemoreceptor clusters in individual Escherichia coli cells using a heterogeneous…
Multivalency is prevalent in various biological systems and applications due to the superselectivity that arises from the cooperativity of multivalent binding. Traditionally, it was thought that weaker individual binding would improve the…
Experimenters report an upper limit if the signal they are trying to detect is non-existent or below their experiment's sensitivity. Such experiments may be contaminated with a background too poorly understood to subtract. If the background…
Eukaryotic cells generally sense chemical gradients using the binding of chemical ligands to membrane receptors. In order to perform chemotaxis effectively in different environments, cells need to adapt to different concentrations. We…
After application of a step stimulus, in the form of a sudden change in attractant environment, the receptor activity and tumbling bias of an {\sl E. coli} cell change sharply to reach their extremal values before they gradually relax to…
This work introduces the particle-intensity channel (PIC) as a model for molecular communication systems and characterizes the properties of the optimal input distribution and the capacity limits for this system. In the PIC, the transmitter…
Clinical biosensors with low detection limit hold significant promise in the early diagnosis of debilitating diseases. Recent progress in sensor development has led to the demonstration of detection capable of detecting target molecules…
Many chemotactic bacteria inhabit environments in which chemicals appear as localized pulses and evolve by processes such as diffusion and mixing. We show that, in such environments, physical limits on the accuracy of temporal gradient…