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The presence of one or more species at some spatial locations but not others is a central matter in ecology. This phenomenon is related to ecological pattern formation. Nonlocal interactions can be considered as one of the mechanisms…
This paper proposes a control theoretic framework to model and analyze the self-organized pattern formation of molecular concentrations in biomolecular communication networks, emerging applications in synthetic biology. In biomolecular…
Understanding how the structure of community interactions is modified by coevolution is vital for understanding system responses to change at all scales. However, in absence of a group selection process, collective community behaviours…
Unlike many physical nonequilibrium systems, in biological systems, the coupling to external energy sources is not a fixed parameter but adaptively controlled by the system itself. We do not have theoretical frameworks that allow for such…
Elucidating the neurophysiological mechanisms underlying neural pattern formation remains an outstanding challenge in Computational Neuroscience. In this paper, we address the issue of understanding the emergence of neural patterns by…
Understanding the dynamics of complex molecular processes is often linked to the study of infrequent transitions between long-lived stable states. The standard approach to the sampling of such rare events is to generate an ensemble of…
Recent progress in diverse intelligence has shown simple learning capacities below the organism level - single cells and even molecular networks. However, there are still many knowledge gaps around learning capacity above the organism…
A biochemical oscillator model, describing developmental stage of myxobacteria, is analyzed mathematically. Observations from numerical simulations show that in a certain range of parameters, the corresponding system of ordinary…
We propose conditions for the emergence of Turing patterns in a domain that changes in size by homogeneous growth/shrinkage. These conditions to determine the bifurcation are based on considering the geometric change of a potential function…
This study investigates transient wave dynamics in Turing pattern formation, focusing on waves emerging from localised disturbances. While the traditional focus of diffusion-driven instability has primarily centred on stationary solutions,…
Systems Biology has emerged in the last years as a new holistic approach based on the global understanding of cells instead of only being focused on their individual parts (genes or proteins), to better understand the complexity of human…
Ecologists are interested in understanding and predicting how ecological communities change through time. While it might seem natural to measure this through changes in species' abundances, computational limitations mean transitions between…
Topological phases of matter$\unicode{x2013}$comprising both insulators and semimetals$\unicode{x2013}$offer great potential for quantum applications, but identifying new candidates remains challenging due to expensive first-principles…
Biological sequences do not come at random. Instead, they appear with particular frequencies that reflect properties of the associated system or phenomenon. Knowing how biological sequences are distributed in sequence space is thus a…
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…
Random heteropolymers are a minimal description of biopolymers and can provide a theoretical framework to the investigate the formation of loops in biophysical experiments. A two--state model provides a consistent and robust way to study…
Modeling biological rhythms helps understand the complex principles behind the physical and psychological abnormalities of human bodies, to plan life schedules, and avoid persisting fatigue and mood and sleep alterations due to the…
We set up a rigorous thermodynamic description of reaction-diffusion systems driven out of equilibrium by time-dependent space-distributed chemostats. Building on the assumption of local equilibrium, nonequilibrium thermodynamic potentials…
Automated verification of living organism models allows us to gain previously unknown knowledge about underlying biological processes. In this paper, we show the benefits to use parametric time Petri nets in order to analyze precisely the…
In this work, we present and analyze a general framework for vegetation dynamics in arid and semi-arid ecosystems in which non-local interactions are purely competitive. The generality of the formulation enables a systematic search for…