Split digraphs

We generalize the class of split graphs to the directed case and show that these split digraphs can be identified from their degree sequences. The first degree sequence characterization is an extension of the concept of splittance to directed graphs, while the second characterization says a digraph is split if and only if its degree sequence satisfies one of the Fulkerson inequalities (which determine when an integer-pair sequence is digraphic) with equality.Comment: 14 pages, 2 figures; Accepted author manuscript (AAM) versio

Effect of Node-Degree Correlation on Synchronization of Identical Pulse-Coupled Oscillators

We explore the effect of correlations between the in and out degrees of random directed networks on the synchronization of identical pulse-coupled oscillators. Numerical experiments demonstrate that the proportion of initial conditions resulting in a globally synchronous state (prior to a large but finite time) is an increasing function of node-degree correlation. For those networks observed to globally synchronize, both the mean and standard deviation of time to synchronization are decreasing functions of node-degree correlation. Pulse-coupled oscillator networks with negatively correlated node degree often exhibit multiple coherent attracting states, with trajectories performing fast transitions between them. These effects of node-degree correlation on dynamics of pulse-coupled oscillators are consistent with aspects of network topology (e.g., the effect of node-degree correlation on the eigenvalues of the Laplacian matrix) that have been shown to affect synchronization in other contexts

Algorithm and Complexity for a Network Assortativity Measure

We show that finding a graph realization with the minimum Randi\'c index for a given degree sequence is solvable in polynomial time by formulating the problem as a minimum weight perfect b-matching problem. However, the realization found via this reduction is not guaranteed to be connected. Approximating the minimum weight b-matching problem subject to a connectivity constraint is shown to be NP-Hard. For instances in which the optimal solution to the minimum Randi\'c index problem is not connected, we describe a heuristic to connect the graph using pairwise edge exchanges that preserves the degree sequence. In our computational experiments, the heuristic performs well and the Randi\'c index of the realization after our heuristic is within 3% of the unconstrained optimal value on average. Although we focus on minimizing the Randi\'c index, our results extend to maximizing the Randi\'c index as well. Applications of the Randi\'c index to synchronization of neuronal networks controlling respiration in mammals and to normalizing cortical thickness networks in diagnosing individuals with dementia are provided.Comment: Added additional section on application

Modeling Vocal Fold Motion with a New Hydrodynamic Semi-Continuum Model

Vocal fold (VF) motion is a fundamental process in voice production, and is also a challenging problem for direct numerical computation because the VF dynamics depend on nonlinear coupling of air flow with the response of elastic channels (VF), which undergo opening and closing, and induce internal flow separation. A traditional modeling approach makes use of steady flow approximation or Bernoulli's law which is known to be invalid during VF opening. We present a new hydrodynamic semi-continuum system for VF motion. The airflow is modeled by a quasi-one dimensional continuum aerodynamic system, and the VF by a classical lumped two mass system. The reduced flow system contains the Bernoulli's law as a special case, and is derivable from the two dimensional compressible Navier-Stokes equations. Since we do not make steady flow approximation, we are able to capture transients and rapid changes of solutions, e.g. the double pressure peaks at opening and closing stages of VF motion consistent with experimental data. We demonstrate numerically that our system is robust, and models in-vivo VF oscillation more physically. It is also much simpler than a full two-dimensional Navier-Stokes system.Comment: 27 pages,6 figure

21st century reform efforts in undergraduate quantitative biology education: Conversations, initiatives, and curriculum change in the United States of America

In the United States, there are multiple reports from both mathematics and biology communities that address the quantitative preparation of undergraduate life science students. Many of these reports make broad recommendations for the revision of life science curriculum to incorporate more quantitative techniques. Here, we review initiatives and progress in the United States on the state of quantitative biology education in the context of the mathematics education, biology research frontiers, and the funding system and other sources of support for systemic change to meet new demands

Threshold Digraphs

A digraph whose degree sequence has a unique vertex labeled realization is called threshold. In this paper we present several characterizations of threshold digraphs and their degree sequences, and show these characterizations to be equivalent. Using this result, we obtain a new, short proof of the Fulkerson-Chen theorem on degree sequences of general digraphs

Mechanisms Leading to Rhythm Cessation in the Respiratory PreBotzinger Complex Due to Piecewise Cumulative Neuronal Deletions

The brainstem pre-Botzinger complex (preBotC) generates the rhythm underlying inspiratory breathing movements and its core interneurons are derived from Dbx-1 expressing precursors. Recurrent synaptic excitation is required to initiate inspiratory bursts, but whether excitatory synaptic mechanisms also contribute to inspiratory–expiratory phase transition is unknown. Here, we examined the role of short-term synaptic depression using a rhythmically active neonatal mouse brainstem slice preparation. We show that different axonal projections to Dbx-1 PreBotC neurons undergo activity-dependent depression and we identify a refractory period (approx. 2 s) after endogenous inspiratory bursts that precludes light-evoked bursts in channelrhodopsin-expressing Dbx1 Pre-BotC neurons. We demonstrate that the duration of the refractory period---but neither the cycle period nor the magnitude of endogenous inspiratory burst---is sensitive to changes in extracellular Ca^2+. Further, we show that postsynaptic factors are unlikely to explain the refractory period or its modulation by Ca^2+. Our findings are consistent with the hypothesis that short-term synaptic depression in Dbx-1 Pre-BotC neurons influences the inspiratory-expiratory phase transition during respiratory rhythmogenesis