Related papers: Information propagation in time through allosteric…
To maintain homeostasis, living cells process information with networks of interacting molecules. Traditional models for cellular information processing have focused on networks of chemical reactions between molecules. Here, we describe how…
The spread of disease through a physical-contact network and the spread of information about the disease on a communication network are two intimately related dynamical processes. We investigate the asymmetrical interplay between the two…
Biological information processing manifests a huge variety in its complexity and capability among different organisms, which presumably stems from the evolutionary optimization under limited computational resources. Starting from the…
When analysing gene expression time series data an often overlooked but crucial aspect of the model is that the regulatory network structure may change over time. Whilst some approaches have addressed this problem previously in the…
Gene expression is a noisy process and several mechanisms, both transcriptional and posttranscriptional, can stabilize protein levels in cells. Much work has focused on the role of miRNAs, showing in particular that miRNA-mediated…
Network inference approaches are widely used to shed light on regulatory interplay between molecular players such as genes and proteins. Biochemical processes underlying networks of interest (e.g. gene regulatory or protein signalling…
The formation of condensates is now considered as a major organization principle of eukaryotic cells. Several studies have recently shown that the properties of these condensates are affected by enzymatic reactions. We propose here a simple…
The survival and proliferation of cells and organisms require a highly coordinated allocation of cellular resources to ensure the efficient synthesis of cellular components. In particular, the total enzymatic capacity for cellular…
Modern applied optimization problems become more and more complex every day. Due to this fact, distributed algorithms that can speed up the process of solving an optimization problem through parallelization are of great importance. The main…
Exploiting the information provided by the molecular noise of a biological process has proven to be valuable in extracting knowledge about the underlying kinetic parameters and sources of variability from single cell measurements. However,…
Allosteric interactions occur when binding at one part of a complex affects the interactions at another part. Allostery offers a high degree of control in multi-species processes, and these interactions play a crucial role in many…
Recent whole genome polymerase binding assays have shown that a large proportion of unexpressed genes have pre-assembled RNA pol II transcription initiation complex stably bound to their promoters. Some such promoter proximally paused genes…
Multistationarity in biological systems is a mechanism of cellular decision making. In particular, signaling pathways regulated by protein phosphorylation display features that facilitate a variety of responses to different biological…
The learning rate is an information-theoretical quantity for bipartite Markov chains describing two coupled subsystems. It is defined as the rate at which transitions in the downstream subsystem tend to increase the mutual information…
Elastomers that can sustain large reversible strain are essential components for stretchable electronics. The stretchability and mechanical robustness of unfilled elastomers can be enhanced by introducing easier-to-break cross-links, e.g.…
Synthetic data becomes crucial for large language model training, but its effectiveness is highly inconsistent. We provide an information-theoretic account of this inconsistency: synthetic data improves a model only when the…
A key goal of systems biology is the predictive mathematical description of gene regulatory circuits. Different approaches are used such as deterministic and stochastic models, models that describe cell growth and division explicitly or…
In this work, we present a paradigm bridging electromagnetic (EM) and molecular communication through a stimuli-responsive intra-body model. It has been established that protein molecules, which play a key role in governing cell behavior,…
Neuronal avalanches, measured in vitro and in vivo, exhibit a robust critical behaviour. Their temporal organization hides the presence of correlations. Here we present experimental measurements of the waiting time distribution between…
We revisit the dynamics of a gene repressed by its own protein in the case where the transcription rate does not adapt instantaneously to protein concentration but is a dynamical variable. We derive analytical criteria for the appearance of…