Related papers: A population-based microbial oscillator
Synthetic biologists have made great progress over the past decade in developing methods for modular assembly of genetic sequences and in engineering biological systems with a wide variety of functions in various contexts and organisms.…
Ring topologies of repressing genes have qualitatively different long-term dynamics if the number of genes is odd (they oscillate) or even (they exhibit bistability). However, these attractors may not fully explain the observed behavior in…
Temporal evolution of a clonal bacterial population is modelled taking into account reversible mutation and selection mechanisms. For the mutation model, an efficient algorithm is proposed to verify whether experimental data can be…
Computationally expensive simulators, implementing mathematical models in computer codes, are commonly approximated using statistical emulators. We develop and assess novel emulation methods for systems best modelled via a chain, series or…
We investigate a coherent nonlinear feedback circuit constructed from pre-existing superconducting microwave devices. The network exhibits emergent bistable and astable states, and we demonstrate its operation as a latch and the frequency…
We demonstrate the utility of machine learning algorithms for the design of Oscillatory Neural Networks (ONNs). After constructing a circuit model of the oscillators in a machine-learning-enabled simulator and performing Backpropagation…
Microbes constantly interact with their environment by depleting and transforming food sources. Theoretical studies have mainly focused on Lotka-Volterra models, which do not account for food source dynamics. In contrast, consumer-resource…
We study the noise characteristics of stochastic oscillations in protein number dynamics of simple genetic oscillatory systems. Using the three-component negative feedback transcription regulatory system called the repressilator as a…
Here we introduce a new design framework for synthetic biology that exploits the advantages of Bayesian model selection. We will argue that the difference between inference and design is that in the former we try to reconstruct the system…
The smart integrated systems of tomorrow would demand a combination of micromechanical components and traditional electronics. On-chip solutions will be the ultimate goal. One way of making such systems is to implement the mechanical parts…
Engineering genetic networks to be both predictable and robust is a key challenge in synthetic biology. Synthetic circuits must reliably function in dynamic, stochastic and heterogeneous environments, and simple circuits can be studied to…
Long and stable timescales are often observed in complex biochemical networks, such as in emergent oscillations. How these robust dynamics persist remains unclear, given the many stochastic reactions and shorter time scales demonstrated by…
While measurement advances now allow extensive surveys of gene activity (large numbers of genes across many samples), interpretation of these data is often confounded by noise -- expression counts can differ strongly across samples due to…
The activity of growing living bacteria was investigated using real-time and in situ rheology -- in stationary and oscillatory shear. Two different strains of the human pathogen Staphylococcus aureus -- strain COL and its isogenic cell wall…
We propose a probabilistic framework for developing computational models of biological neural systems. In this framework, physiological recordings are viewed as discrete-time partial observations of an underlying continuous-time stochastic…
We present a flexible branching process model for cell population dynamics in synchrony/time-series experiments used to study important cellular processes. Its formulation is constructive, based on an accounting of the unique cohorts in the…
Among the different computational approaches modelling the dynamics of isogenic cell populations, discrete stochastic models can describe with sufficient accuracy the evolution of small size populations. However, for a systematic and…
A system architecture is suggested for a System on Chip that will combine several different memristor-based, bio-inspired computation arrays with inter- and intra-chip communication. It will serve as a benchmark system for future…
Living systems, from single cells to higher vertebrates, receive a continuous stream of non-stationary inputs that they sense, e.g., via cell surface receptors or sensory organs. Integrating these time-varying, multi-sensory, and often…
We analyze the collective behavior of a lattice model of pulse-coupled oscillators. By means of computer simulations we find the relation between the intrinsic dynamics of each member of the population and their mutual interaction that…