Tuning a synthetic in vitro oscillator using control-theoretic tools

This paper demonstrates the effectiveness of simple control-theoretic tools in generating simulation-guided experiments on a synthetic in vitro oscillator. A theoretical analysis of the behavior of such system is motivated by high cost, time consuming experiments, together with the excessive number of tuning parameters. A simplified model of the synthetic oscillator is chosen to capture only its essential features. The model is analyzed using the small gain theorem and the theory of describing functions. Such analysis reveals what are the parameters that primarily determine when the system can admit stable oscillations. Experimental verification of the theoretical and numerical findings is carried out and confirms the predicted results regarding the role of production and degradation rates

The effect of heterogeneity on invasion in spatial epidemics: from theory to experimental evidence in a model system

Heterogeneity in host populations is an important factor affecting the ability of a pathogen to invade, yet the quantitative investigation of its effects on epidemic spread is still an open problem. In this paper, we test recent theoretical results, which extend the established “percolation paradigm” to the spread of a pathogen in discrete heterogeneous host populations. In particular, we test the hypothesis that the probability of epidemic invasion decreases when host heterogeneity is increased. We use replicated experimental microcosms, in which the ubiquitous pathogenic fungus Rhizoctonia solani grows through a population of discrete nutrient sites on a lattice, with nutrient sites representing hosts. The degree of host heterogeneity within different populations is adjusted by changing the proportion and the nutrient concentration of nutrient sites. The experimental data are analysed via Bayesian inference methods, estimating pathogen transmission parameters for each individual population. We find a significant, negative correlation between heterogeneity and the probability of pathogen invasion, thereby validating the theory. The value of the correlation is also in remarkably good agreement with the theoretical predictions. We briefly discuss how our results can be exploited in the design and implementation of disease control strategies

Supersymmetry Breaking from a Calabi-Yau Singularity

We conjecture a geometric criterion for determining whether supersymmetry is spontaneously broken in certain string backgrounds. These backgrounds contain wrapped branes at Calabi-Yau singularites with obstructions to deformation of the complex structure. We motivate our conjecture with a particular example: the $Y^{2,1}$ quiver gauge theory corresponding to a cone over the first del Pezzo surface, $dP_1$. This setup can be analyzed using ordinary supersymmetric field theory methods, where we find that gaugino condensation drives a deformation of the chiral ring which has no solutions. We expect this breaking to be a general feature of any theory of branes at a singularity with a smaller number of possible deformations than independent anomaly-free fractional branes.Comment: 32 pages, 6 figures, latex, v2: minor changes, refs adde

Generation of ultrabright tunable polarization entanglement without spatial, spectral, or temporal constraints

The need for spatial and spectral filtering in the generation of polarization entanglement is eliminated by combining two coherently-driven type-II spontaneous parametric downconverters. The resulting ultrabright source emits photon pairs that are polarization entangled over the entire spatial cone and spectrum of emission. We detect a flux of $\sim$12 000 polarization-entangled pairs/s per mW of pump power at 90% quantum-interference visibility, and the source can be temperature tuned for 5 nm around frequency degeneracy. The output state is actively controlled by precisely adjusting the relative phase of the two coherent pumps.Comment: 10 pages, 5 figure

Complexity and anisotropy in host morphology make populations safer against epidemic outbreaks

One of the challenges in epidemiology is to account for the complex morphological structure of hosts such as plant roots, crop fields, farms, cells, animal habitats and social networks, when the transmission of infection occurs between contiguous hosts. Morphological complexity brings an inherent heterogeneity in populations and affects the dynamics of pathogen spread in such systems. We have analysed the influence of realistically complex host morphology on the threshold for invasion and epidemic outbreak in an SIR (susceptible-infected-recovered) epidemiological model. We show that disorder expressed in the host morphology and anisotropy reduces the probability of epidemic outbreak and thus makes the system more resistant to epidemic outbreaks. We obtain general analytical estimates for minimally safe bounds for an invasion threshold and then illustrate their validity by considering an example of host data for branching hosts (salamander retinal ganglion cells). Several spatial arrangements of hosts with different degrees of heterogeneity have been considered in order to analyse separately the role of shape complexity and anisotropy in the host population. The estimates for invasion threshold are linked to morphological characteristics of the hosts that can be used for determining the threshold for invasion in practical applications.Comment: 21 pages, 8 figure

Tuning a synthetic in vitro oscillator using control-theoretic tools

This paper demonstrates the effectiveness of simple control-theoretic tools in generating simulation-guided experiments on a synthetic in vitro oscillator. A theoretical analysis of the behavior of such system is motivated by high cost, time consuming experiments, together with the excessive number of tuning parameters. A simplified model of the synthetic oscillator is chosen to capture only its essential features. The model is analyzed using the small gain theorem and the theory of describing functions. Such analysis reveals what are the parameters that primarily determine when the system can admit stable oscillations. Experimental verification of the theoretical and numerical findings is carried out and confirms the predicted results regarding the role of production and degradation rates

Metropolitan quantum key distribution with silicon photonics

Photonic integrated circuits (PICs) provide a compact and stable platform for quantum photonics. Here we demonstrate a silicon photonics quantum key distribution (QKD) transmitter in the first high-speed polarization-based QKD field tests. The systems reach composable secret key rates of 950 kbps in a local test (on a 103.6-m fiber with a total emulated loss of 9.2 dB) and 106 kbps in an intercity metropolitan test (on a 43-km fiber with 16.4 dB loss). Our results represent the highest secret key generation rate for polarization-based QKD experiments at a standard telecom wavelength and demonstrate PICs as a promising, scalable resource for future formation of metropolitan quantum-secure communications networks

Exceptional Collections and del Pezzo Gauge Theories

Stacks of D3-branes placed at the tip of a cone over a del Pezzo surface provide a way of geometrically engineering a small but rich class of gauge/gravity dualities. We develop tools for understanding the resulting quiver gauge theories using exceptional collections. We prove two important results for a general quiver gauge theory: 1) we show the ordering of the nodes can be determined up to cyclic permutation and 2) we derive a simple formula for the ranks of the gauge groups (at the conformal point) in terms of the numbers of bifundamentals. We also provide a detailed analysis of four node quivers, examining when precisely mutations of the exceptional collection are related to Seiberg duality.Comment: 26 pages, 1 figure; v2 footnote 2 amended; v3 ref adde

Brane Tilings and Exceptional Collections

Both brane tilings and exceptional collections are useful tools for describing the low energy gauge theory on a stack of D3-branes probing a Calabi-Yau singularity. We provide a dictionary that translates between these two heretofore unconnected languages. Given a brane tiling, we compute an exceptional collection of line bundles associated to the base of the non-compact Calabi-Yau threefold. Given an exceptional collection, we derive the periodic quiver of the gauge theory which is the graph theoretic dual of the brane tiling. Our results give new insight to the construction of quiver theories and their relation to geometry.Comment: 46 pages, 37 figures, JHEP3; v2: reference added, figure 13 correcte