144,462 research outputs found

    Transcriptional delay stabilizes bistable gene networks

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    Transcriptional delay can significantly impact the dynamics of gene networks. Here we examine how such delay affects bistable systems. We investigate several stochastic models of bistable gene networks and find that increasing delay dramatically increases the mean residence times near stable states. To explain this, we introduce a non-Markovian, analytically tractable reduced model. The model shows that stabilization is the consequence of an increased number of failed transitions between stable states. Each of the bistable systems that we simulate behaves in this manner

    An integrated neuro-mechanical model of C. elegans forward locomotion

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    One of the most tractable organisms for the study of nervous systems is the nematode Caenorhabditis elegans, whose locomotion in particular has been the subject of a number of models. In this paper we present a first integrated neuro-mechanical model of forward locomotion. We find that a previous neural model is robust to the addition of a body with mechanical properties, and that the integrated model produces oscillations with a more realistic frequency and waveform than the neural model alone. We conclude that the body and environment are likely to be important components of the worm’s locomotion subsystem

    Evolution of the Internet AS-Level Ecosystem

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    We present an analytically tractable model of Internet evolution at the level of Autonomous Systems (ASs). We call our model the multiclass preferential attachment (MPA) model. As its name suggests, it is based on preferential attachment. All of its parameters are measurable from available Internet topology data. Given the estimated values of these parameters, our analytic results predict a definitive set of statistics characterizing the AS topology structure. These statistics are not part of the model formulation. The MPA model thus closes the "measure-model-validate-predict" loop, and provides further evidence that preferential attachment is a driving force behind Internet evolution

    Dividing the Ontology Alignment Task with Semantic Embeddings and Logic-based Modules

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    Large ontologies still pose serious challenges to state-of-the-art ontology alignment systems. In this paper we present an approach that combines a neural embedding model and logic-based modules to accurately divide an input ontology matching task into smaller and more tractable matching (sub)tasks. We have conducted a comprehensive evaluation using the datasets of the Ontology Alignment Evaluation Initiative. The results are encouraging and suggest that the proposed method is adequate in practice and can be integrated within the workflow of systems unable to cope with very large ontologies

    An integrated neuro-mechanical model of C. elegans forward locomotion

    Get PDF
    One of the most tractable organisms for the study of nervous systems is the nematode Caenorhabditis elegans, whose locomotion in particular has been the subject of a number of models. In this paper we present a first integrated neuro-mechanical model of forward locomotion. We find that a previous neural model is robust to the addition of a body with mechanical properties, and that the integrated model produces oscillations with a more realistic frequency and waveform than the neural model alone. We conclude that the body and environment are likely to be important components of the worm’s locomotion subsystem

    Quantum Rabi model for N-state atoms

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    A tractable N-state Rabi Hamiltonian is introduced by extending the parity symmetry of the two-state model. The single-mode case provides a few-parameter description of a novel class of periodic systems, predicting that the ground state of certain four-state atom-cavity systems will undergo parity change at strong coupling. A group-theoretical treatment provides physical insight into dynamics and a modified rotating wave approximation obtains accurate analytical energies. The dissipative case can be applied to study excitation energy transfer in molecular rings or chains.Comment: 5 pages, 3 figures + supplement (2 pages); to appear in Phys. Rev. Let
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