Related papers: Information Transmission and Processing in G-Prote…
Signaling in enzymatic networks is typically triggered by environmental fluctuations, resulting in a series of stochastic chemical reactions, leading to corruption of the signal by noise. For example, information flow is initiated by…
In this paper, for linear time-invariant plants, where a collection of possible inputs and outputs are known a priori, we address the problem of determining the communication between outputs and inputs, i.e., information patterns, such that…
Water molecules inside G-protein coupled receptor have recently been spotlighted in a series of crystal structures. To decipher the dynamics and functional roles of internal waters in GPCR activity, we studied A$_{\text{2A}}$ adenosine…
Many biological regulatory systems process signals out of steady state and respond with a physiological delay. A simple model of regulation which respects these features shows how the ability of a delayed output to transmit information is…
This paper presents novel stabilizability conditions for switched linear systems with arbitrary and uncontrollable underlying switching signals. We distinguish and study two particular settings: i) the \emph{robust} case, in which the…
Phosphorelays are a class of signaling mechanisms used by cells to respond to changes in their environment. Phosphorelays (of which two-component systems constitute a special case) are particularly abundant in prokaryotes and have been…
Dynamics of reaction coordinates during barrier-crossing are key to understand activated processes in complex systems such as proteins. The default assumption from Kramers physical intuition is that of a diffusion process. However, the…
Biological molecular machines are proteins that operate under isothermal conditions hence are referred to as free energy transducers. They can be formally considered as enzymes that simultaneously catalyze two chemical reactions: the free…
Chemical reaction networks (CRN) comprise an important class of models to understand biological functions such as cellular information processing, the robustness and control of metabolic pathways, circadian rhythms, and many more. However,…
A master equation describing the evolution of averaged molecular state occupancies in molecular systems where alternation of molecular energy levels is caused by discrete dichotomous and trichotomous stochastic fields, is derived. This…
A variety of oscillations are observed in pancreatic islets.We establish a model, incorporating two oscillatory systems of different time scales: One is the well-known bursting model in pancreatic beta-cells and the other is the…
Eukaryotic gene regulation is based on stochastic yet controlled promoter switching, during which genes transition between transcriptionally active and inactive states. Despite the molecular complexity of this process, recent studies reveal…
Time resolved intensity cross-correlation measurements of radiative cascades are used for studying non-radiative relaxation processes of excited carriers confined in semiconductor quantum dots. We spectrally identify indirect radiative…
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.…
A model of sensory information processing is presented. The model assumes that learning of internal (hidden) generative models, which can predict the future and evaluate the precision of that prediction, is of central importance for…
Signal transduction in biological cells is effected by signaling pathways that typically include multiple feedback loops. Here we analyze information transfer through a prototypical signaling module with biochemical feedback. The module…
Transport of ions and small molecules across the cell membrane against electrochemical gradients is catalyzed by integral membrane proteins that use a source of free energy to drive the energetically uphill flux of the transported…
The theory of receptor-ligand binding equilibria has long been well-established in biochemistry, and was primarily constructed to describe dilute aqueous solutions. Accordingly, few computational approaches have been developed for making…
Heat transfer in semiconductor devices is dominated by chip and substrate assemblies, where heat generated within a finite chip layer dissipates into a semi-infinite substrate with much higher thermophysical properties. This mismatch…
While information processing in complex systems can be described in abstract, general terms, there are cases in which the relation between these computations and the physical substrate of the underlying system is itself of interest.…