Related papers: A population-based microbial oscillator
In this work we use multiple scattering in conjunction with a genetic algorithm to reliably determine the optimized photonic-crystal-based structure able to perform a specific optical task. The genetic algorithm operates on a population of…
We investigate the ability of a genetic algorithm to design cellular automata that perform computations. The computational strategies of the resulting cellular automata can be understood using a framework in which ``particles'' embedded in…
We study a triangular network of three populations of coupled phase oscillators with identical frequencies. The populations interact nonlocally, in the sense that all oscillators are coupled to one another, but more weakly to those in…
Intrinsic or demographic noise has been shown to play an important role in the dynamics of a variety of systems including predator-prey populations, intracellular biochemical reactions, and oscillatory chemical reaction systems, and is…
A big challenge in current biology is to understand the exact self-organization mechanism underlying complex multi-physics coupling developmental processes. With multiscale computations of from subcellular gene expressions to cell…
Rhythmic and sequential segmentation of the embryonic body plan is a vital developmental patterning process in all vertebrate species. However, a theoretical framework capturing the emergence of dynamic patterns of gene expression from the…
Multicellular systems play a key role in bioprocess and biomedical engineering. Cell ensembles encountered in these setups show phenotypic variability like size and biochemical composition. As this variability may result in undesired…
Oscillations are omnipresent in neural population signals, like multi-unit recordings, EEG/MEG, and the local field potential. They have been linked to the population firing rate of neurons, with individual neurons firing in a…
Synthetic biology is a recent area of biological engineering, whose aim is to provide cells with novel functionalities. A number of important results regarding the development of control circuits in synthetic biology have been achieved…
Coarse graining techniques offer a promising alternative to large-scale simulations of complex dynamical systems, as long as the coarse-grained system is truly representative of the initial one. Here, we investigate how the dynamical…
This chapter gives a synopsis of recent approaches to model and analyse the evolution of microbial populations under selection. The first part reviews two population genetic models of Lenski's long-term evolution experiment with Escherichia…
A large variety of rhythms are observed in nature. Rhythms such as electroencephalogram signals in the brain can often be regarded as interacting. In this study, we investigate the dynamical properties of rhythmic systems in two populations…
The human microbiome is a complex ecological system, and describing its structure and function under different environmental conditions is important from both basic scientific and medical perspectives. Viewed through a biostatistical lens,…
Segregation of populations is a key question in evolution theory. One important aspect is the relation between spatial organization and the population's composition. Here we study a specific example -- sectors in expanding bacterial…
Many combinatorial optimization problems can be mapped to finding the ground states of the corresponding Ising Hamiltonians. The physical systems that can solve optimization problems in this way, namely Ising machines, have been attracting…
We present a family of one-dimensional cellular automata modeling the diffusion of an innovation in a population. Starting from simple deterministic rules, we construct models parameterized by the interaction range and exhibiting a…
Sustained rhythmic oscillations, pulsing dynamics, emerge spontaneously when the local connection scheme is randomised in 3-value cellular automata that feature"glider" dynamics. Time-plots of pulsing measures maintain a distinct waveform…
We propose a model for bacterial Quorum Sensing based on an auxiliary electrostatic-like interac-tion originating from a fictitious electrical charge that represents bacteria activity. A cooperative mechanism for charge/activity exchange is…
We analyze the interplay of synchronization and structure evolution in an evolving network of phase oscillators. An initially random network is adaptively rewired according to the dynamical coherence of the oscillators, in order to enhance…
Artificial biological pacemakers were developed and tested in canine ventricles. Next steps will require obtaining oscillations sensitive to external regulations, and robust with respect to long term drifts of expression levels of pacemaker…