A phase-space approach to directional switching in semiconductor ring lasers

We show that a topological investigation of the phase space of a Semiconductor Ring Laser can be used to devise switching schemes which are alternative to optical pulse injection of counter-propagating light. To provide physical insight in these switching mechanisms, a full bifurcation analysis and an investigation of the topology is performed on a two-dimensional asymptotic model. Numerical simulations confirm the topological predictions.Comment: 9 pages, 7 figure

Excitability in semiconductor microring lasers: Experimental and theoretical pulse characterization

We characterize the operation of semiconductor microring lasers in an excitable regime. Our experiments reveal a statistical distribution of the characteristics of noise-triggered optical pulses that is not observed in other excitable systems. In particular, an inverse correlation exists between the pulse amplitude and duration. Numerical simulations and an interpretation in an asymptotic phase space confirm and explain these experimentally observed pulse characteristics.Comment: 9 pages, 10 figure

Exploring multi-stability in semiconductor ring lasers: theory and experiment

We report the first experimental observation of multi-stable states in a single-longitudinal mode semiconductor ring laser. We show how the operation of the device can be steered to either monostable, bistable or multi-stable dynamical regimes in a controlled way. We observe that the dynamical regimes are organized in well reproducible sequences that match the bifurcation diagrams of a two-dimensional model. By analyzing the phase space in this model, we predict how the stochastic transitions between multi-stable states take place and confirm it experimentally.Comment: 4 pages, 5 figure

Sulphur-bearing molecules in AGB stars I: The occurrence of hydrogen sulfide

Through a survey of (sub-)millimetre emission lines of various sulphur-bearing molecules, we aim to determine which molecules are the primary carriers of sulphur in different types of AGB stars. In this paper, the first in a series, we investigate the occurrence of H$_2$S in AGB circumstellar envelopes and determine its abundance, where possible. We have surveyed 20 AGB stars with a range of mass-loss rates and of different chemical types using the APEX telescope to search for rotational transition lines of five key sulphur-bearing molecules: CS, SiS, SO, SO$_2$ and H$_2$S. Here we present our results for H$_2$S, including detections, non-detections and detailed radiative transfer modelling of the detected lines. We compare results based on different descriptions of the molecular excitation of H$_2$S and different abundance distributions, including those derived from chemical modelling results. We detected H$_2$S towards five AGB stars, all of which have high mass-loss rates of $\dot{M}\geq 5\times 10^{-6}M_\odot$ yr$^{-1}$ and are oxygen-rich. H$_2$S was not detected towards the carbon or S-type stars that fall in a similar mass-loss range. For the stars in our sample with detections, we find peak o-H$_2$S abundances relative to H$_2$ between $4\times 10^{-7}$ and $2.5\times 10^{-5}$. Overall, we conclude that H$_2$S can play a significant role in oxygen-rich AGB stars with higher mass-loss rates, but is unlikely to play a key role in stars of other chemical types or the lower mass-loss rate oxygen-rich stars. For two sources, V1300 Aql and GX Mon, H$_2$S is most likely the dominant sulphur-bearing molecule in the circumstellar envelope.Comment: 14 pages, 7 figures, accepted in A&

Disentangling physics and chemistry in AGB outflows: revealing degeneracies when adding complexity

Observations of the outflows of asymptotic giant branch (AGB) stars continue to reveal their chemical and dynamical complexity. Spherical asymmetries, such as spirals and disks, are prevalent and thought to be caused by binary interaction with a (sub)stellar companion. Furthermore, high density outflows show evidence of dust-gas interactions. The classical chemical model of these outflows - a gas-phase only, spherically symmetric chemical kinetics model - is hence not appropriate for a majority of observed outflows. We have included several physical and chemical advancements step-by-step: a porous density distribution, dust-gas chemistry, and internal UV photons originating from a close-by stellar companion. Now, we combine these layers of complexity into the most chemically and physically advanced chemical kinetics model of AGB outflows to date. By varying over all model parameters, we obtain a holistic view of the outflow's composition and how it (inter)depends on the different complexities. A stellar companion has the largest influence, especially when combined with a porous outflow. We compile sets of gas-phase molecules that trace the importance of dust-gas chemistry and allow us to infer the presence of a companion and porosity of the outflow. This shows that our new chemical model can be used to infer physical and chemical properties of specific outflows, as long as a suitable range of molecules is observed.Comment: Faraday Discussions 2023, accepted manuscript. 15 pages, 7 figures, 4 tables. Supplementary information can be found at https://pubs.rsc.org/en/content/articlelanding/2023/fd/d3fd00039

Impact of nonlocal interactions in dissipative systems: towards minimal-sized localized structures

In order to investigate the size limit on spatial localized structures in a nonlinear system, we explore the impact of linear nonlocality on their domains of existence and stability. Our system of choice is an optical microresonator containing an additional metamaterial layer in the cavity, allowing the nonlocal response of the material to become the dominating spatial process. In that case, our bifurcation analysis shows that this nonlocality imposes a new limit on the width of localized structures going beyond the traditional diffraction limit.Comment: 4 pages, 4 figure

genomepy: genes and genomes at your fingertips

Analyzing a functional genomics experiment, such as ATAC-, ChIP- or RNA-sequencing, requires reference data including a genome assembly and gene annotation. These resources can generally be retrieved from different organizations and in different versions. Most bioinformatic workflows require the user to supply this genomic data manually, which can be a tedious and error-prone process. Here we present genomepy, which can search, download, and preprocess the right genomic data for your analysis. Genomepy can search genomic data on NCBI, Ensembl, UCSC and GENCODE, and compare available gene annotations to enable an informed decision. The selected genome and gene annotation can be downloaded and preprocessed with sensible, yet controllable, defaults. Additional supporting data can be automatically generated or downloaded, such as aligner indexes, genome metadata and blacklists. Genomepy is freely available at https://github.com/vanheeringen-lab/genomepy under the MIT license and can be installed through pip or bioconda

Dawn of the red and dead : stellar kinematics of massive quiescent galaxies out to z = 2

The first massive elliptical galaxies were already in place when the Universe was only 3 billions years old. Surprisingly, they are more compact in comparison to their present-day counterparts. In this thesis these recent findings are assessed by measuring the stellar kinematics of massive z=2 galaxies from spectra obtained with X-Shooter on the Very Large Telescope. This thesis work shows that high-redshift galaxies are truly very massive and structurally very different from present-day galaxies, yet they follow the same scaling relations.Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO) en het Leids Kerkhoven Bosscha fonds (LKBF).UBL - phd migration 201

Hydrophobic drug/toxin binding sites in voltage-dependent K+ and Na+ channels

In the Na(v)channel family the lipophilic drugs/toxins binding sites and the presence of fenestrations in the channel pore wall are well defined and categorized. No such classification exists in the much larger K(v)channel family, although certain lipophilic compounds seem to deviate from binding to well-known hydrophilic binding sites. By mapping different compound binding sites onto 3D structures of Kv channels, there appear to be three distinct lipid-exposed binding sites preserved in K(v)channels: the front and back side of the pore domain, and S2-S3/S3-S4 clefts. One or a combination of these sites is most likely the orthologous equivalent of neurotoxin site 5 in Na(v)channels. This review describes the different lipophilic binding sites and location of pore wall fenestrations within the K(v)channel family and compares it to the knowledge of Na(v)channels

Topological insight into the non-Arrhenius mode hopping of semiconductor ring lasers

We investigate both theoretically and experimentally the stochastic switching between two counter-propagating lasing modes of a semiconductor ring laser. Experimentally, the residence time distribution cannot be described by a simple one parameter Arrhenius exponential law and reveals the presence of two different mode-hop scenarios with distinct time scales. In order to elucidate the origin of these two time scales, we propose a topological approach based on a two-dimensional dynamical system.Comment: 4 pages, 3 figure