Ising model for distribution networks

An elementary Ising spin model is proposed for demonstrating cascading failures (break-downs, blackouts, collapses, avalanches, ...) that can occur in realistic networks for distribution and delivery by suppliers to consumers. A ferromagnetic Hamiltonian with quenched random fields results from policies that maximize the gap between demand and delivery. Such policies can arise in a competitive market where firms artificially create new demand, or in a solidary environment where too high a demand cannot reasonably be met. Network failure in the context of a policy of solidarity is possible when an initially active state becomes metastable and decays to a stable inactive state. We explore the characteristics of the demand and delivery, as well as the topological properties, which make the distribution network susceptible of failure. An effective temperature is defined, which governs the strength of the activity fluctuations which can induce a collapse. Numerical results, obtained by Monte Carlo simulations of the model on (mainly) scale-free networks, are supplemented with analytic mean-field approximations to the geometrical random field fluctuations and the thermal spin fluctuations. The role of hubs versus poorly connected nodes in initiating the breakdown of network activity is illustrated and related to model parameters

Trading interactions for topology in scale-free networks

Scale-free networks with topology-dependent interactions are studied. It is shown that the universality classes of critical behavior, which conventionally depend only on topology, can also be explored by tuning the interactions. A mapping, $\gamma' = (\gamma - \mu)/(1-\mu)$, describes how a shift of the standard exponent $\gamma$ of the degree distribution $P(q)$ can absorb the effect of degree-dependent pair interactions $J_{ij} \propto (q_iq_j)^{-\mu}$. Replica technique, cavity method and Monte Carlo simulation support the physical picture suggested by Landau theory for the critical exponents and by the Bethe-Peierls approximation for the critical temperature. The equivalence of topology and interaction holds for equilibrium and non-equilibrium systems, and is illustrated with interdisciplinary applications.Comment: 4 pages, 5 figure

Dynamic calcium-mediated stress response and recovery signatures in the fungal pathogen, Candida albicans

Acknowledgements AB conceived the project and wrote the manuscript. CVG conceived the experimental design. SW designed the GCaMP reporter. AM, KL, LV-M, SC and TB constructed strains and optimised imaging. MF developed the image analysis software. CVG and CP carried out the microfluidics experiments and imaging analysis. NG assisted with preparation of the manuscript. PS, SN and DMR developed and undertook the theoretical data analysis and contributed to the interpretation of the results. Funding AB, CG and TB were funded by the Wellcome Trust [Grant number 206412/A/17/Z]. AB and DR were supported by a Wellcome Trust Institutional Strategic Support Award (WT204909/Z/16/Z). CP was funded by a University of Exeter studentship (113516). This work was also supported by a Royal Society URF (UF080611), an MRC NIRG (G0900211/90671) and the MRC-Centre for Medical Mycology at the University of Exeter (MR/N006364/2). DR was funded by the Medical Research Council (MR/P022405/1). SN was supported by the Medical Research Council via the GW4 BioMed2 DTP (MR/W006308/1). MCA was supported by a European Commission ITN ‘FungiBrain’ studentship (607963). LL and SC were funded by a Wellcome Trust Institutional Strategic Support Award to the University of Aberdeen. NG acknowledges support of Wellcome Trust Investigator, Collaborative, Equipment, Strategic and Biomedical Resource awards (101873, 200208, 215599, 224323). NG and AB thank the MRC (MR/M026663/2) for support. This study/research is funded by the National Institute for Health and Care Research (NIHR) Exeter Biomedical Research Centre (BRC). The views expressed are those of the author(s) and not necessarily those of the NIHR or the Department of Health and Social Care. For the purpose of open access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission.Peer reviewedPublisher PD

Evidence for nonmonotonic magnetic field penetration in a type-I superconductor

Polarized neutron reflectometry (PNR) provides evidence that nonlocal electrodynamics governs the magnetic field penetration in an extreme low-k superconductor. The sample is an indium film with a large elastic mean free path (11 mkm) deposited on a silicon oxide wafer. It is shown that PNR can resolve the difference between the reflected neutron spin asymmetries predicted by the local and nonlocal theories of superconductivity. The experimental data support the nonlocal theory, which predicts a nonmonotonic decay of the magnetic field.Comment: 5 pages, 4 figures, LaTex, corrected typos and figure

Gateway vectors for efficient artificial gene assembly in vitro and expression in yeast Saccharomyces cerevisiae

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Dynamic calcium-mediated stress response and recovery signatures in the fungal pathogen, Candida albicans

This is the final version. Available on open access from the American Society for Microbiology via the DOI in this recordIntracellular calcium signaling plays an important role in the resistance and adaptation to stresses encountered by fungal pathogens within the host. This study reports the optimization of the GCaMP fluorescent calcium reporter for live-cell imaging of dynamic calcium responses in single cells of the pathogen, Candida albicans, for the first time. Exposure to membrane, osmotic or oxidative stress generated both specific changes in single cell intracellular calcium spiking and longer calcium transients across the population. Repeated treatments showed that calcium dynamics become unaffected by some stresses but not others, consistent with known cell adaptation mechanisms. By expressing GCaMP in mutant strains and tracking the viability of individual cells over time, the relative contributions of key signaling pathways to calcium flux, stress adaptation, and cell death were demonstrated. This reporter, therefore, permits the study of calcium dynamics, homeostasis, and signaling in C. albicans at a previously unattainable level of detail.Wellcome TrustUniversity of ExeterRoyal SocietyMedical Research Council (MRC)European CommissionNational Institute for Health and Care Research (NIHR

Criticality on networks with topology-dependent interactions

Weighted scale-free networks with topology-dependent interactions are studied. It is shown that the possible universality classes of critical behavior, which are known to depend on topology, can also be explored by tuning the form of the interactions at fixed topology. For a model of opinion formation, simple mean field and scaling arguments show that a mapping gamma(')=(gamma-mu)/(1-mu) describes how a shift of the standard exponent gamma of the degree distribution can absorb the effect of degree-dependent pair interactions J(ij)proportional to(k(i)k(j))(-mu), where k(i) stands for the degree of vertex i. This prediction is verified by extensive numerical investigations using the cavity method and Monte Carlo simulations. The critical temperature of the model is obtained through the Bethe-Peierls approximation and with the replica technique. The mapping can be extended to nonequilibrium models such as those describing the spreading of a disease on a network

Dynamic calcium-mediated stress response and recovery signatures in the fungal pathogen, Candida albicans

ABSTRACT Calcium (Ca2+) is an important second messenger for activating stress response signaling and cell adaptation in eukaryotic cells yet intracellular Ca2+-dynamics in fungi are poorly understood due to lack of effective real-time Ca2+ reporters. We engineered the GCaMP6f construct for use in the fungal pathogen, Candida albicans, and used live-cell imaging to observe both dynamic Ca2+ spiking and slower changes in non-spiking Ca2+-GCaMP signals elicited by stress or gene deletion. Short-term exposure to membrane, osmotic or oxidative stress generated immediate stress-specific responses and repeated exposure revealed differential recovery signatures. Osmotic stress caused yeast cell shrinkage and no adaptation response, where Ca2+-GCaMP spiking was inhibited by 1 M NaCl but not by 0.666 M CaCl2. Treatment with sodium dodecylsulfate (SDS) caused a spike-burst, raised the non-spiking Ca2+-GCaMP signals, and caused significant cell death, but surviving cells adapted over subsequent exposures. Treatment with 5 mM H2O2 abolished spiking and caused transient non-GCaMP-related autofluorescence, but cells adapted such that spiking returned and autofluorescence diminished on repeated exposure. Adaptation to H2O2 was dependent on Cap1, extracellular Ca2+, and calcineurin but not on its downstream target, Crz1. Ca2+-dynamics were not affected by H2O2 in the hog1Δ or yvc1Δ mutants, suggesting a pre-adapted, resistant state, possibly due to changes in membrane permeability. Live-cell imaging of Ca2+-GCaMP responses in individual cells has, therefore, revealed the dynamics of Ca2+-influx, signaling and homeostasis, and their role in the temporal stress response signatures of C. albicans. IMPORTANCE Intracellular calcium signaling plays an important role in the resistance and adaptation to stresses encountered by fungal pathogens within the host. This study reports the optimization of the GCaMP fluorescent calcium reporter for live-cell imaging of dynamic calcium responses in single cells of the pathogen, Candida albicans, for the first time. Exposure to membrane, osmotic or oxidative stress generated both specific changes in single cell intracellular calcium spiking and longer calcium transients across the population. Repeated treatments showed that calcium dynamics become unaffected by some stresses but not others, consistent with known cell adaptation mechanisms. By expressing GCaMP in mutant strains and tracking the viability of individual cells over time, the relative contributions of key signaling pathways to calcium flux, stress adaptation, and cell death were demonstrated. This reporter, therefore, permits the study of calcium dynamics, homeostasis, and signaling in C. albicans at a previously unattainable level of detail