Related papers: Dynamic sampling and information encoding in bioch…
Equation learning methods present a promising tool to aid scientists in the modeling process for biological data. Previous equation learning studies have demonstrated that these methods can infer models from rich datasets, however, the…
Biopolymer Networks play an important role in coordinating and regulating collective cellular dynamics via a number of signaling pathways. Here, we investigate the mechanical response of a model biopolymer network due to the active…
Understanding the rules underlying organismal development is a major unsolved problem in biology. Each cell in a developing organism responds to signals in its local environment by dividing, excreting, consuming, or reorganizing, yet how…
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…
In biochemical signaling, information is often encoded in oscillatory signals. However, the advantages of such a coding strategy over an amplitude encoding scheme of constant signals remain unclear. Here we study the dynamics of a simple…
The propagation of signalling molecules within cellular networks is affected by network topology, but also by the spatial arrangement of cells in the networks. Understanding the collective reaction--diffusion behaviour in space of signals…
In view of ever-changing conditions both in the external world and in intrinsic brain states, maintaining the robustness of computations poses a challenge, adequate solutions to which we are only beginning to understand. At the level of…
Cells generally convert nutrient resources to useful products via energy transduction. Accordingly, the thermodynamic efficiency of this conversion process is one of the most essential characteristics of living organisms. However, although…
In recent years it is increasingly being recognized that biochemical signals are not necessarily constant in time and that the temporal dynamics of a signal can be the information carrier. Moreover, it is now well established that…
Information storage is a key element of autonomous, out-of-equilibrium dynamics, especially for biological and synthetic active matter. In synthetic active matter however, the implementation of internal memory in self-propelled systems is…
Many engineering, social, and biological complex systems consist of dynamical elements connected via a large-scale network. Monitoring the network's dynamics is essential for a variety of maintenance and scientific purposes. Whilst we…
We explore the dynamics of information systems. We show that the driving force for information dynamics is determined by both the information landscape and information flux which determines the equilibrium time reversible and the…
Despite substantial research into the biological basis of memory, the precise mechanisms by which experiences are encoded, stored, and retrieved in the brain remain incompletely understood. A growing body of evidence supports the engram…
Much of our mechanistic understanding of the functions of biological macromolecules is based on static structural experiments, which can be modelled either as single structures or conformational ensembles. While these provide us with…
Signal duration (e.g. the time scales over which an active signaling intermediate persists) is a key regulator of biological decisions in myriad contexts such as cell growth, proliferation, and developmental lineage commitments.…
Quantum many-body dynamics generically results in increasing entanglement that eventually leads to thermalization of local observables. This makes the exact description of the dynamics complex despite the apparent simplicity of…
The internal dynamics of macro-molecular systems is characterized by widely separated time scales, ranging from fraction of ps to ns. In ordinary molecular dynamics simulations, the elementary time step dt used to integrate the equation of…
Living cells can leverage correlations in environmental fluctuations to predict the future environment and mount a response ahead of time. To this end, cells need to encode the past signal into the output of the intracellular network from…
It is important to understand the coordinated performance of cells in tissue. One possible mechanism in this coordination involves intracellular calcium signaling. The topology of intercellular connections in tissue should also play an…
In this letter we present the results of a simple model for intercellular communication via calcium oscillations, motivated in part by a recent experimental study. The model describes two cells (a "donor" and "sensor") whose intracellular…