Related papers: Optimal control of protein copy number
The interactions between diffusing molecules and membrane-bound receptors drive numerous cellular processes. In this work, we develop a spatial model of molecular interactions with membrane receptors by homogenizing the cell membrane and…
We typically think of cells as responding to external signals independently by regulating their gene expression levels, yet they often locally exchange information and coordinate. Can such spatial coupling be of benefit for conveying…
In order to survive, reproduce and (in multicellular organisms) differentiate, cells must control the concentrations of the myriad different proteins that are encoded in the genome. The precision of this control is limited by the inevitable…
We devise a method for predicting certain receptor-ligand binding behaviors, based on stochastic dynamical modelling. We consider the dynamics of a receptor binding to a ligand on the cell membrane, where the receptor and ligand perform…
Living cells use readout molecules to record the state of receptor proteins, similar to measurements or copies in typical computational devices. But is this analogy rigorous? Can cells be optimally efficient, and if not, why? We show that,…
Biological information processing as implemented by regulatory and signaling networks in living cells requires sufficient specificity of molecular interaction to distinguish signals from one another, but much of regulation and signaling…
Translation is a key step in the synthesis of proteins. Accordingly, cells have evolved an intricate array of control mechanisms to regulate this process. By constructing a multi-component mathematical framework for translation we uncover…
We quantify the influence of the topology of a transcriptional regulatory network on its ability to process environmental signals. By posing the problem in terms of information theory, we may do this without specifying the function…
How do single cell fate decisions induced by activation of key signaling proteins above threshold concentrations within a time interval are affected by stochastic fluctuations in biochemical reactions? We address this question using minimal…
Peripheral membrane proteins can reversibly and specifically bind to biological membranes to carry out functions such as cell signalling, enzymatic activity, or membrane remodelling. Structures of these proteins and of their lipid-binding…
Biological cells are able to accurately sense chemicals with receptors at their surfaces, allowing cells to move towards sources of attractant and away from sources of repellent. The accuracy of sensing chemical concentration is ultimately…
Cellular reprogramming, the conversion of one cell type to another, has fundamentally transformed our conception of cell types. Cellular reprogramming induces global changes in gene expression involving hundreds of transcription factors and…
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…
We present a new modeling approach for G protein coupled receptors signaling systems, that take into account the compartmentalization of receptors and their effectors, both at plasma membrane and in dynamic intra-cellular vesicles called…
Cells can utilize chemical communication to exchange information and coordinate their behavior in the presence of noise. Communication can reduce noise to shape a collective response, or amplify noise to generate distinct phenotypic…
This paper considers the capacity of a diffusion-based molecular communication link assuming the receiver uses chemical reactions. The key contribution is we show that enzymatic reaction cycles, which is a class of chemical reactions…
Cells measure concentrations of external ligands by capturing ligand molecules with cell surface receptors. The numbers of molecules captured by different receptors co-vary because they depend on the same extrinsic ligand fluctuations.…
Cells use temporal dynamical patterns to transmit information via signaling pathways. As optimality with respect to the environment plays a fundamental role in biological systems, organisms have evolved optimal ways to transmit information.…
Translation of proteins is a fundamental part of gene expression that is mediated by ribosomes. As ribosomes significantly contribute to both cellular mass and energy consumption, achieving efficient management of the ribosome population is…
In this paper, a simple memory limited transmitter for molecular communication is proposed, in which information is encoded in the diffusion rate of the molecules. Taking advantage of memory, the proposed transmitter reduces the ISI problem…