Integrated culturing, modeling and transcriptomics uncovers complex interactions and emergent behavior in a three-species synthetic gut community.

The composition of the human gut microbiome is well resolved, but predictive understanding of its dynamics is still lacking. Here, we followed a bottom-up strategy to explore human gut community dynamics: we established a synthetic community composed of three representative human gut isolates ( L1-82, A2-165 and S5a33) and explored their interactions under well-controlled conditions in vitro. Systematic mono- and pair-wise fermentation experiments confirmed competition for fructose and cross-feeding of formate.

Monostable multivibrators as novel artificial neurons.

Retriggerable and non-retriggerable monostable multivibrators are simple timers with a single characteristic, their period. Motivated by the fact that monostable multivibrators are implementable in large quantities as counters in digital programmable hardware, we set out to investigate their applicability as building blocks of artificial neural networks. We derive the nonlinear input-output firing rate relations for single multivibrator neurons as well as the equilibrium firing rate of large recurrent networks.

Bistability in a system of two species interacting through mutualism as well as competition: Chemostat vs. Lotka-Volterra equations.

We theoretically study the dynamics of two interacting microbial species in the chemostat. These species are competitors for a common resource, as well as mutualists due to cross-feeding. In line with previous studies (Assaneo, et al.

Do Optomechanical Metasurfaces Run Out of Time?

Artificially structured metasurfaces make use of specific configurations of subwavelength resonators to efficiently manipulate electromagnetic waves. Additionally, optomechanical metasurfaces have the desired property that their actual configuration may be tuned by adjusting the power of a pump beam, as resonators move to balance pump-induced electromagnetic forces with forces due to elastic filaments or substrates. Although the reconfiguration time of optomechanical metasurfaces crucially determines their performance, the transient dynamics of unit cells from one equilibrium state to another is not understood.

Slow passage through thresholds in quantum dot lasers.

A turn on of a quantum dot (QD) semiconductor laser simultaneously operating at the ground state (GS) and excited state (ES) is investigated both experimentally and theoretically. We find experimentally that the slow passage through the two successive laser thresholds may lead to significant delays in the GS and ES turn ons. The difference between the turn-on times is measured as a function of the pump rate of change ɛ and reveals no clear power law.

Reducing the phase sensitivity of laser-based optical reservoir computing systems.

Optical implementations of reservoir computing systems are very promising because of their high processing speeds and the possibility to process several tasks in parallel. These systems can be implemented using semiconductor lasers subject to optical delayed feedback and optical injection. While the amount of the feedback/injection can be easily controlled, it is much more difficult to control the optical feedback/injection phase.

Computational Methods to Model Persistence.

Bacterial persister cells are dormant cells, tolerant to multiple antibiotics, that are involved in several chronic infections. Toxin-antitoxin modules play a significant role in the generation of such persister cells. Toxin-antitoxin modules are small genetic elements, omnipresent in the genomes of bacteria, which code for an intracellular toxin and its neutralizing antitoxin.

Simultaneous Computation of Two Independent Tasks Using Reservoir Computing Based on a Single Photonic Nonlinear Node With Optical Feedback.

In this brief, we numerically demonstrate a photonic delay-based reservoir computing system, which processes, in parallel, two independent computational tasks even when the two tasks have unrelated input streams. Our approach is based on a single-longitudinal mode semiconductor ring laser (SRL) with optical feedback. The SRL emits in two directional optical modes.

Delay-based reservoir computing: noise effects in a combined analog and digital implementation.

Reservoir computing is a paradigm in machine learning whose processing capabilities rely on the dynamical behavior of recurrent neural networks. We present a mixed analog and digital implementation of this concept with a nonlinear analog electronic circuit as a main computational unit. In our approach, the reservoir network can be replaced by a single nonlinear element with delay via time-multiplexing.

All-optical controlled switching between time-periodic square waves in diode lasers with delayed feedback.

We investigate the square-wave (SW) self-modulation output of an edge-emitting diode laser subject to polarization rotated optical feedback in detail, both experimentally and theoretically. Our experimental results show that the 2τ-periodic SW, where τ is the delay of the feedback, coexists with other SW oscillations of shorter periods. We have found that these new SWs are specific harmonics of the fundamental one and their periods are P(n)≃2τ/(1+2n), where n is an integer.

Controlling Cherenkov radiation with transformation-optical metamaterials.

In high energy physics, unknown particles are identified by determining their mass from the Cherenkov radiation cone that is emitted as they pass through the detector apparatus. However, at higher particle momentum, the angle of the Cherenkov cone saturates to a value independent of the mass of the generating particle, making it difficult to effectively distinguish between different particles. Here, we show how the geometric formalism of transformation optics can be applied to describe the Cherenkov cone in an arbitrary anisotropic medium.

Fast phase response and chaos bandwidth enhancement in semiconductor lasers subject to optical feedback and injection.

We numerically show the quantitative relation between the chaos bandwidth enhancement and fast phase dynamics in semiconductor lasers with optical feedback and optical injection. The injection increases the coupling between the intensity and the phase leading to a competition between the relaxation oscillation (RO) frequency and the intrinsic response frequency of the phase. For large feedback strengths, it is found that the chaos bandwidth is determined by the intrinsic phase response frequency.

Fast photonic information processing using semiconductor lasers with delayed optical feedback: role of phase dynamics.

Semiconductor lasers subject to delayed optical feedback have recently shown great potential in solving computationally hard tasks. By optically implementing a neuro-inspired computational scheme, called reservoir computing, based on the transient response to optical data injection, high processing speeds have been demonstrated. While previous efforts have focused on signal bandwidths limited by the semiconductor laser's relaxation oscillation frequency, we demonstrate numerically that the much faster phase response makes significantly higher processing speeds attainable.

Relaxation and square-wave oscillations in a semiconductor laser with polarization rotated optical feedback.

The rate equations for a laser with a polarization rotated optical feedback are investigated both numerically and analytically. The frequency detuning between the polarization modes is now taken into account and we review all earlier studies in order to motivate the range of values of the fixed parameters. We find that two basic Hopf bifurcations leading to either stable sustained relaxation or square-wave oscillations appear in the detuning versus feedback rate diagram.

Analytical and experimental study of two delay-coupled excitable units.

We investigate the onset of time-periodic oscillations for a system of two identical delay-coupled excitable (nonoscillatory) units. We first analyze these solutions by using asymptotic methods. The oscillations are described as relaxation oscillations exhibiting successive slow and fast changes.

Constructing optimized binary masks for reservoir computing with delay systems.

Reservoir computing is a novel bio-inspired computing method, capable of solving complex tasks in a computationally efficient way. It has recently been successfully implemented using delayed feedback systems, allowing to reduce the hardware complexity of brain-inspired computers drastically. In this approach, the pre-processing procedure relies on the definition of a temporal mask which serves as a scaled time-mutiplexing of the input.

A general model for toxin-antitoxin module dynamics can explain persister cell formation in E. coli.

Toxin-Antitoxin modules are small operons involved in stress response and persister cell formation that encode a "toxin" and its corresponding neutralizing "antitoxin". Regulation of these modules involves a complex mechanism known as conditional cooperativity, which is supposed to prevent unwanted toxin activation. Here we develop mathematical models for their regulation, based on published molecular and structural data, and parameterized using experimental data for F-plasmid ccdAB, bacteriophage P1 phd/doc and E.

Slow-fast dynamics of a time-delayed electro-optic oscillator.

Square-wave oscillations exhibiting different plateau lengths have been observed experimentally by investigating an electro-optic oscillator. In a previous study, we analysed the model delay differential equations and determined an asymptotic approximation of the two plateaus. In this paper, we concentrate on the fast transition layers between plateaus and show how they contribute to the total period.

Controlled multiwavelength emission using semiconductor ring lasers with on-chip filtered optical feedback.

We report on an integrated approach to obtain multiwavelength emission from semiconductor ring lasers with filtered optical feedback. The filtered feedback is realized on-chip employing two arrayed-waveguide gratings to split/recombine light into different wavelength channels. Through experimental observations and numerical simulations, we find that the effective gain of the different modes is the key parameter which has to be balanced in order to achieve multiwavelength emission.

Fast random bits generation based on a single chaotic semiconductor ring laser.

The use of the postprocessing method consisting of bitwise Exclusive-OR and least significant bits extraction to generate random bit sequences typically requires two distinct chaotic outputs. While the two signals are, in general, generated using two separated devices, e.g.

Strongly asymmetric square waves in a time-delayed system.

Time-delayed systems are known to exhibit symmetric square waves oscillating with a period close to twice the delay. Here, we show that strongly asymmetric square waves of a period close to one delay are possible. The plateau lengths can be tuned by changing a control parameter.

Square-wave oscillations in semiconductor ring lasers with delayed optical feedback.

We analyze experimentally and theoretically the effects of delayed optical cross-feedback in semiconductor ring lasers. We show that under appropriate conditions, feeding of only one directional mode back into the counter-propagating mode leads to square-wave oscillations. In this regime, the laser switches regularly between the two counter-propagating modes with a period close to twice the roundtrip time in the external feedback loop.

Spectral and correlation properties of rings of delay-coupled elements: comparing linear and nonlinear systems.

The dynamical properties of delay-coupled systems are currently of great interest. So far the analysis has concentrated primarily on identical synchronization properties. Here we study the dynamics of rings of delay-coupled nodes, a topology that cannot show identical synchronization, and compare its properties to those of linear stochastic maps.

Characterization of a low-speckle laser line generator.

The goal of our investigation is to design a low-speckle laser line generator based on partial spatially coherent laser light. Low speckle is achieved by exploiting a regime of strongly reduced spatial coherence of a broad-area vertical-cavity surface-emitting laser, which is used as the line generator's light source. A comparative experimental study of different optical configurations is conducted, leading to the design of an optimal optical system.