Related papers: Threshold Response to Stochasticity in Morphogenes…
We study the impact of stochastic perturbations to deterministic dynamical systems using the formalism of the Ruelle response theory and explore how stochastic noise can be used to explore the properties of the underlying deterministic…
Stochastic dynamics of several systems can be modeled via piecewise deterministic time evolution of the state, interspersed by random discrete events. Within this general class of systems, we consider time-triggered stochastic hybrid…
Adversarial examples are often cited by neuroscientists and machine learning researchers as an example of how computational models diverge from biological sensory systems. Recent work has proposed adding biologically-inspired components to…
Stochastic resonance is a phenomenon in which noise enhances the response of a system to an input signal. The brain is an example of a system that has to detect and transmit signals in a noisy environment, suggesting that it is a good…
Search for possible relationships between phylogeny and ontogeny is one of the most important issues in the field of evolutionary developmental biology. By representing developmental dynamics of spatially located cells with gene expression…
We construct a stochastic dynamical systems theory in which sustainability is a structural boundary property of a fully coupled Earth--Human--Production system. Each subsystem is modelled as a vector-valued process governed by stochastic…
Gene regulatory network of lambda phage is one the best studied model systems in molecular biology. More 50 years of experimental study has provided a tremendous amount of data at all levels: physics, chemistry, DNA, protein, and function.…
Establishing sharp and correctly positioned boundaries in spatial gene expression patterns is a central task, both in developmental and synthetic biology. We consider situations where a global morphogen gradient provides positional…
We investigate Turing pattern formation in a stochastic and spatially discretized version of a reaction diffusion advection (RDA) equation, which was previously introduced to model synaptogenesis in \textit{C. elegans}. The model describes…
Turgor is the driving force of plant growth, making possible for roots to overcome soil resistance or for stems to counteract gravity. Maintaining a constant growth rate while avoiding the cell content dilution, which would progressively…
In this paper we present a general framework in which one can rigorously study the effect of spatio-temporal noise on traveling waves, stationary patterns and oscillations that are invariant under the action of a finite-dimensional set of…
Gene expression in cells is stochastic, yet differentiation is robust. We propose a mechanism in which frustrated genes with weakly stable intermediate expression undergo noise-driven switching between basins of attraction, followed by…
Robust machine learning for regulatory genomics is studied under biologically and technically induced distribution shifts. Deep convolutional and attention based models achieve strong in distribution performance on DNA regulatory sequence…
A model to describe the arising of new structures in an initial homogeneous biological system is proposed. The essay is motivated by the intention to work on a non-equilibrium situation grouping together several mechanisms and processes as:…
We study the self-assembly of colloidal microgel particles at a quasi-two-dimensional air-water interface of a drying droplet. Using bright-field microscopy, we demonstrate that increasing particle elasticity drives interfacial organization…
We consider a generalization of the classical logistic growth model introducing more than one inflection point. The growth, called multi-sigmoidal, is firstly analyzed from a deterministic point of view in order to obtain the main…
In multi-cellular organisms, cells differentiate into multiple types as they divide. States of these cell types, as well as their numbers, are known to be robust to external perturbations; as conceptualized by Waddington's epigenetic…
Bistable biological regulatory systems need to cope with stochastic noise to fine-tune their function close to bifurcation points. Here, we study stability properties of this regime in generic systems to demonstrate that cooperative…
Conventional wisdom suggests that environmental noise drives populations toward extinction. In contrast, we report a paradoxical phenomenon in which stochasticity reverses a deterministic tipping point, thereby preventing collapse. Using a…
Cells and tissues exhibit oscillatory deformations during remodelling, migration or embryogenesis. Although it has been shown that these oscillations correlate with cell biochemical signalling, it is yet unclear the role of these…