Related papers: Optimal control of protein copy number
Living cells presumably employ optimized information transfer methods, enabling efficient communication even in noisy environments. As expected, the efficiency of chemical communications between cells depends on the properties of the…
Living cells can enhance their fitness by anticipating environmental change. We study how accurately linear signaling networks in cells can predict future signals. We find that maximal predictive power results from a combination of…
Cells process external and internal signals through chemical interactions. Cells that constitute the immune system (e.g., antigen presenting cell, T-cell, B-cell, mast cell) can have different functions (e.g., adaptive memory, inflammatory…
Engineering biology requires precise control of biomolecular circuits, and Cybergenetics is the field dedicated to achieving this goal. A significant challenge in developing controllers for cellular functions is designing systems that can…
In biological cells and novel diagnostic devices biochemical receptors need to be sensitive to extremely small concentration changes of signaling molecules. The accuracy of such molecular signaling is ultimately limited by the counting…
Development in multi-cellular organisms is marked by a high degree of spatial organization of the cells attaining distinct fates in the embryo. We show that receptor-ligand interaction between cells in close physical proximity adaptively…
In this paper, we propose adding enzymes to the propagation environment of a diffusive molecular communication system as a strategy for mitigating intersymbol interference. The enzymes form reaction intermediates with information molecules…
This paper studies the mitigation of intersymbol interference in a diffusive molecular communication system using enzymes that freely diffuse in the propagation environment. The enzymes form reaction intermediates with information molecules…
Specific binding of proteins to DNA is one of the most common ways in which gene expression is controlled. Although general rules for the DNA-protein recognition can be derived, the ambiguous and complex nature of this mechanism precludes a…
Central to the functioning of a living cell is its ability to control the readout or expression of information encoded in the genome. In many cases, a single transcription factor protein activates or represses the expression of many genes.…
Cells receive signaling molecules by receptors and relay information via sensory networks so that they can respond properly depending on the type of signal. Recent studies have shown that cells can extract multi-dimensional information from…
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,…
Living cells often need to measure chemical concentrations that vary in time. To this end, they deploy many resources, e.g. receptors, downstream signaling molecules, time and energy. Here, we present a theory for the optimal design of a…
Many cellular networks rely on the regulated transport of their components to transduce extracellular information into precise intracellular signals. The dynamics of these networks is typically described in terms of compartmentalized…
Cells use biochemical networks to translate environmental information into intracellular responses. These responses can be highly dynamic, but how the information is encoded in these dynamics remains poorly understood. Here we investigate…
Cells constantly need to monitor the state of the environment to detect changes and timely respond. The detection of concentration changes of a ligand by a set of receptors can be cast as a problem of hypothesis testing, and the cell viewed…
Central to understanding membrane bound cell signaling is to quantify how the membrane ultra-structure consisting of transient spatial domains modulates signaling and how the signaling influences this ultra-structure. Yet, measuring the…
Given the stochastic nature of gene expression, genetically identical cells exposed to the same environmental inputs will produce different outputs. This heterogeneity has been hypothesized to have consequences for how cells are able to…
Cell signaling networks are complex and often incompletely characterized, making it difficult to obtain a comprehensive picture of the mechanisms they encode. Mathematical modeling of these networks provides important clues, but the models…
The spatio-temporal organization of proteins and the associated morphological changes in membranes are of importance in cell signaling. Several mechanisms that promote the aggregation of proteins at low cell surface concentrations have been…