Related papers: Irreversibility in Bacterial Regulatory Networks
We consider a free fermion chain with uniform nearest-neighbor hopping and let it evolve from an arbitrary initial state with a fixed macroscopic number of particles. We then prove that, at a sufficiently large and typical time, the…
Bacteria live in environments that are continuously fluctuating and changing. Exploiting any predictability of such fluctuations can lead to an increased fitness. On longer timescales bacteria can "learn" the structure of these fluctuations…
We investigate the predictive power of recurrent neural networks for oscillatory systems not only on the attractor, but in its vicinity as well. For this we consider systems perturbed by an external force. This allows us to not merely…
Cell fate determination, the process through which cells commit to differentiated states is commonly mediated by gene regulatory motifs with mutually exclusive expression states. The classical deterministic picture for cell fate…
Behavioral changes in animals and humans, as a consequence of an error or a verbal instruction, can be extremely rapid. Improvement in behavioral performances are usually associated in machine learning and reinforcement learning to synaptic…
Gene regulatory networks are powerful abstractions of biological systems. Since the advent of high-throughput measurement technologies in biology in the late 90s, reconstructing the structure of such networks has been a central…
We investigate the evolution of Boolean networks subject to a selective pressure which favors robustness against noise, as a model of evolved genetic regulatory systems. By mapping the evolutionary process into a statistical ensemble and…
We study the effects of nonreciprocity and network structure on percolation. To this end, we investigate nonreciprocal random networks - directed networks for which the probability of a link occurring from node i to node j differs from the…
Turing instability in activator-inhibitor systems provides a paradigm of nonequilibrium pattern formation; it has been extensively investigated for biological and chemical processes. Turing pattern formation should furthermore be possible…
Microbial ecosystems exhibit a surprising amount of functionally relevant diversity at all levels of taxonomic resolution, presenting a significant challenge for most modeling frameworks. A long-standing hope of theoretical ecology is that…
Microbiome studies increasingly indicate that disease-associated shifts cannot be understood from compositional changes alone. The functional architecture of microbial communities encoded in patterns of association among microbial gene…
A complex network processing information or physical flows is usually characterized by a number of macroscopic quantities such as the diameter and the betweenness centrality. An issue of significant theoretical and practical interest is how…
The state of many physical, biological and socio-technical systems evolves by combining smooth local transitions and abrupt resetting events to a set of reference values. The inclusion of the resetting mechanism not only provides the…
Biological information processing is often carried out by complex networks of interconnected dynamical units. A basic question about such networks is that of reliability: if the same signal is presented many times with the network in…
Genetic regulatory networks (GRNs) have been widely studied, yet there is a lack of understanding with regards to the final size and properties of these networks, mainly due to no network currently being complete. In this study, we analyzed…
In the postgenome era many efforts have been dedicated to systematically elucidate the complex web of interacting genes and proteins. These efforts include experimental and computational methods. Microarray technology offers an opportunity…
Homeostasis of protein concentrations in cells is crucial for their proper functioning, and this requires concentrations (at their steady-state levels) to be stable to fluctuations. Since gene expression is regulated by proteins such as…
Fluctuations of observables as functions of time, or "fluctuation patterns", are studied in a chaotic microscopically reversible system that has irreversibly reached a nonequilibrium stationary state. Supposing that during a certain, long…
The Turing patterning mechanism is believed to underly the formation of repetitive structures in development, such as zebrafish stripes and mammalian digits, but it has proved difficult to isolate the specific biochemical species…
The functioning of many biochemical networks is often robust -- remarkably stable under changes in external conditions and internal reaction parameters. Much recent work on robustness and evolvability has focused on the structure of neutral…