Macrophage phenotype transitions in a stochastic gene-regulatory network model.

Polarization is the process by which a macrophage cell commits to a phenotype based on external signal stimulation. To know how this process is affected by random fluctuations and events within a cell is of utmost importance to better understand the underlying dynamics and predict possible phenotype transitions. For this purpose, we develop a stochastic modeling approach for the macrophage polarization process.

Patterns of synchronization in 2D networks of inhibitory neurons.

Neural firing in many inhibitory networks displays synchronous assembly or clustered firing, in which subsets of neurons fire synchronously, and these subsets may vary with different inputs to, or states of, the network. Most prior analytical and computational modeling of such networks has focused on 1D networks or 2D networks with symmetry (often circular symmetry). Here, we consider a 2D discrete network model on a general torus, where neurons are coupled to two or more nearest neighbors in three directions (horizontal, vertical, and diagonal), and allow different coupling strengths in all directions.

Spatially localized cluster solutions in inhibitory neural networks.

Neurons in the inhibitory network of the striatum display cell assembly firing patterns which recent results suggest may consist of spatially compact neural clusters. Previous computational modeling of striatal neural networks has indicated that non-monotonic, distance-dependent coupling may promote spatially localized cluster firing. Here, we identify conditions for the existence and stability of cluster firing solutions in which clusters consist of spatially adjacent neurons in inhibitory neural networks.

Stability, bifurcation and phase-locking of time-delayed excitatory-inhibitory neural networks.

We study a model for a network of synaptically coupled, excitable neurons to identify the role of coupling delays in generating different network behaviors. The network consists of two distinct populations, each of which contains one excitatory-inhibitory neuron pair. The two pairs are coupled via delayed synaptic coupling between the excitatory neurons, while each inhibitory neuron is connected only to the corresponding excitatory neuron in the same population.

Bifurcation and sensitivity analysis reveal key drivers of multistability in a model of macrophage polarization.

In this paper, we present and analyze a mathematical model for polarization of a single macrophage which, despite its simplicity, exhibits complex dynamics in terms of multistability. In particular, we demonstrate that an asymmetry in the regulatory mechanisms and parameter values is important for observing multiple phenotypes. Bifurcation and sensitivity analyses show that external signaling cues are necessary for macrophage commitment and emergence to a phenotype, but that the intrinsic macrophage pathways are equally important.

Geometric analysis of synchronization in neuronal networks with global inhibition and coupling delays.

We study synaptically coupled neuronal networks to identify the role of coupling delays in network synchronized behaviour. We consider a network of excitable, relaxation oscillator neurons where two distinct populations, one excitatory and one inhibitory, are coupled with time-delayed synapses. The excitatory population is uncoupled, while the inhibitory population is tightly coupled without time delay.

Tubular fluid flow and distal NaCl delivery mediated by tubuloglomerular feedback in the rat kidney.

The glomerular filtration rate in the kidney is controlled, in part, by the tubuloglomerular feedback (TGF) system, which is a negative feedback loop that mediates oscillations in tubular fluid flow and in fluid NaCl concentration of the loop of Henle. In this study, we developed a mathematical model of the TGF system that represents NaCl transport along a short loop of Henle with compliant walls. The proximal tubule and the outer-stripe segment of the descending limb are assumed to be highly water permeable; the thick ascending limb (TAL) is assumed to be water impermeable and have active NaCl transport.

Signal transduction in a compliant short loop of Henle.

To study the transformation of fluctuations in filtration rate into tubular fluid chloride concentration oscillations alongside the macula densa, we have developed a mathematical model for tubuloglomerular feedback (TGF) signal transduction along the pars recta, the descending limb, and the thick ascending limb (TAL) of a short-looped nephron. The model tubules are assumed to have compliant walls and, thus, a tubular radius that depends on the transmural pressure difference. Previously, it has been predicted that TGF transduction by the TAL is a generator of nonlinearities: if a sinusoidal oscillation is added to a constant TAL flow rate, then the time required for a fluid element to traverse the TAL is oscillatory in time but nonsinusoidal.

Effect of tubular inhomogeneities on feedback-mediated dynamics of a model of a thick ascending limb.

One of the key mechanisms that mediate renal autoregulation is the tubuloglomerular feedback (TGF) system, which is a negative feedback loop in the kidney that balances glomerular filtration with tubular reabsorptive capacity. Tubular fluid flow, NaCl concentration and other related variables are known to exhibit TGF-mediated oscillations. In this study, we used a mathematical model of the thick ascending limb (TAL) of a short loop of Henle of the rat kidney to study the effects of (i) spatially inhomogeneous TAL NaCl active transport rate, (ii) spatially inhomogeneous tubular radius and (iii) compliance of the tubular walls on TGF-mediated dynamics.