Related papers: What Makes a Bacterial Model a Good Reservoir Comp…
Cell growth is determined by substrate availability and the cell's metabolic capacity to assimilate substrates into building blocks. Metabolic genes that determine growth rate may interact synergistically or antagonistically, and can…
The ability to absorb mutations while retaining structure and function, or mutational robustness, is a remarkable property of natural proteins. In this Letter, we use a computational model of organismic evolution [Zeldovich et al, PLOS Comp…
In this talk I discuss the general question of the portability of Molecular Dynamics codes for diffusive systems on parallel computers of the APE family. The intrinsic single precision arithmetics of the today available APE platforms does…
Recurrent neural networks are used to forecast time series in finance, climate, language, and from many other domains. Reservoir computers are a particularly easily trainable form of recurrent neural network. Recently, a "next-generation"…
The field of active matter explores the behaviors of self propelled agents out of equilibrium, with active suspensions, such as swimming bacteria in solutions, serving as impactful models. These systems exhibit spatio-temporal patterns akin…
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…
A new machine learning scheme, termed versatile reservoir computing, is proposed for sustaining the dynamics of heterogeneous complex networks. We show that a single, small-scale reservoir computer trained on time series from a subset of…
Reservoir computing is a computational framework suited for temporal/sequential data processing. It is derived from several recurrent neural network models, including echo state networks and liquid state machines. A reservoir computing…
Navigation of microorganisms is controlled by internal processes ultimately sensitive to mechanical or chemical signaling encountered along the path. In many natural environments, such as porous soils or physiological ducts, motile species…
An evolving yeast colony is simulated by means of a cellular automaton that takes care of many important features of the system under study. A complete survey of the properties of the colony is done and a set of scaling relations is found,…
Experimentalists have observed phenotypic variability in isogenic bacteria populations. We explore the hypothesis that in fluctuating environments this variability is tuned to maximize a bacterium's expected log growth rate, potentially…
Mathematical models are increasingly used in both academia and the pharmaceutical industry to understand how phenotypes emerge from systems of molecular interactions. However, their current construction as monolithic sets of equations…
The topology of a network associated with a reservoir computer is often taken so that the connectivity and the weights are chosen randomly. Optimization is hardly considered as the parameter space is typically too large. Here we investigate…
Nutrient gradients and limitations play a pivotal role in the life of all microbes, both in their natural habitat as well as in artificial, microfluidic systems. Spatial concentration gradients of nutrients in densely packed cell…
Models of bacterial growth tend to be `irreversible', allowing for the number of bacteria in a colony to increase but not to decrease. By contrast, models of molecular self-assembly are usually `reversible', allowing for addition and…
Nonlinear photonic sources including semiconductor lasers have recently been utilized as ideal computation elements for information processing. They supply energy-efficient way and rich dynamics for classification and recognition tasks. In…
Reservoir computing (RC) offers efficient temporal data processing with a low training cost by separating recurrent neural networks into a fixed network with recurrent connections and a trainable linear network. The quality of the fixed…
Biological cells replicate their genomes in a well-planned manner. The DNA replication program of an organism determines the timing at which different genomic regions are replicated, with fundamental consequences for cell homeostasis and…
Transient compartments have been recently shown to be able to maintain functional replicators in the context of prebiotic studies. Motivated by this experiment, we show that a broad class of selection dynamics is able to achieve this goal.…
Heterologous gene expression draws resources from host cells. These resources include vital components to sustain growth and replication, and the resulting cellular burden is a widely recognised bottleneck in the design of robust circuits.…