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1.  Synaptic and Intrinsic Determinants of the Phase Resetting Curve for Weak Coupling 
A phase resetting curve (PRC) keeps track of the extent to which a perturbation at a given phase advances or delays the next spike, and can be used to predict phase locking in networks of oscillators. The PRC can be estimated by convolving the waveform of the perturbation with the infinitesimal PRC (iPRC) under the assumption of weak coupling. The iPRC is often defined with respect to an infinitesimal current as zi(ϕ), where ϕ is phase, but can also be defined with respect to an infinitesimal conductance change as zg(ϕ). In this paper, we first show that the two approaches are equivalent. Coupling waveforms corresponding to synapses with different time courses sample zg(ϕ) in predictably different ways. We show that for oscillators with Type I excitability, an anomalous region in zg(ϕ) with opposite sign to that seen otherwise is often observed during an action potential. If the duration of the synaptic perturbation is such that it effectively samples this region, PRCs with both advances and delays can be observed despite Type I excitability. We also show that changing the duration of a perturbation so that it preferentially samples regions of stable or unstable slopes in zg(ϕ) can stabilize or destabilize synchrony in a network with the corresponding dynamics.
doi:10.1007/s10827-010-0264-1
PMCID: PMC3059351  PMID: 20700637
2.  Stability of Two Cluster Solutions in Pulse Coupled Networks of Neural Oscillators 
Phase response curves (PRCs) have been widely used to study synchronization in neural circuits comprised of pacemaking neurons. They describe how the timing of the next spike in a given spontaneously firing neuron is affected by the phase at which an input from another neuron is received. Here we study two reciprocally coupled clusters of pulse coupled oscillatory neurons. The neurons within each cluster are presumed to be identical and identically pulse coupled, but not necessarily identical to those in the other cluster. We investigate a two cluster solution in which all oscillators are synchronized within each cluster, but in which the two clusters are phase locked at nonzero phase with each other. Intuitively, one might expect this solution to be stable only when synchrony within each isolated cluster is stable, but this is not the case. We prove rigorously the stability of the two cluster solution and show how reciprocal coupling can stabilize synchrony within clusters that cannot synchronize in isolation. These stability results for the two cluster solution suggest a mechanism by which reciprocal coupling between brain regions can induce local synchronization via the network feedback loop.
doi:10.1007/s10827-010-0268-x
PMCID: PMC3059341  PMID: 20725773
neuronal networks; synchronization; clustering; phase response curves; pulse coupled oscillators
3.  A modified Stokes-Einstein equation for Aβ aggregation 
BMC Bioinformatics  2011;12(Suppl 10):S13.
Background
In all amyloid diseases, protein aggregates have been implicated fully or partly, in the etiology of the disease. Due to their significance in human pathologies, there have been unprecedented efforts towards physiochemical understanding of aggregation and amyloid formation over the last two decades. An important relation from which hydrodynamic radii of the aggregate is routinely measured is the classic Stokes-Einstein equation. Here, we report a modification in the classical Stokes-Einstein equation using a mixture theory approach, in order to accommodate the changes in viscosity of the solvent due to the changes in solute size and shape, to implement a more realistic model for Aβ aggregation involved in Alzheimer’s disease. Specifically, we have focused on validating this model in protofibrill lateral association reactions along the aggregation pathway, which has been experimentally well characterized.
Results
The modified Stokes-Einstein equation incorporates an effective viscosity for the mixture consisting of the macromolecules and solvent where the lateral association reaction occurs. This effective viscosity is modeled as a function of the volume fractions of the different species of molecules. The novelty of our model is that in addition to the volume fractions, it incorporates previously published reports on the dimensions of the protofibrils and their aggregates to formulate a more appropriate shape rather than mere spheres. The net result is that the diffusion coefficient which is inversely proportional to the viscosity of the system is now dependent on the concentration of the different molecules as well as their proper shapes. Comparison with experiments for variations in diffusion coefficients over time reveals very similar trends.
Conclusions
We argue that the standard Stokes-Einstein’s equation is insufficient to understand the temporal variations in diffusion when trying to understand the aggregation behavior of Aβ42 proteins. Our modifications also involve inclusion of improved shape factors of molecules and more appropriate viscosities. The modification we are reporting is not only useful in Aβ aggregation but also will be important for accurate measurements in all protein aggregation systems.
doi:10.1186/1471-2105-12-S10-S13
PMCID: PMC3236835  PMID: 22166081
4.  Pulse Coupled Oscillators and the Phase Resetting Curve 
Mathematical biosciences  2010;226(2):77-96.
Limit cycle oscillators that are coupled in a pulsatile manner are referred to as pulse coupled oscillators. In these oscillators, the interactions take the form of brief pulses such that the effect of one input dies out before the next is received. A phase resetting curve (PRC) keeps track of how much an input advances or delays the next spike in an oscillatory neuron depending upon where in the cycle the input is applied. PRCs can be used to predict phase locking in networks of pulse coupled oscillators. In some studies of pulse coupled oscillators, a specific form is assumed for the interactions between oscillators, but a more general approach is to formulate the problem assuming a PRC that is generated using a perturbation that approximates the input received in the real biological network. In general, this approach requires that circuit architecture and a specific firing pattern be assumed. This allows the construction of discrete maps from one event to the next. The fixed points of these maps correspond to periodic firing modes and are easier to locate and analyze for stability compared to locating and analyzing periodic modes in the original network directly. Alternatively, maps based on the PRC have been constructed that do not presuppose a firing order. Specific circuits that have been analyzed under the assumption of pulsatile coupling include one to one lockings in a periodically forced oscillator or an oscillator forced at a fixed delay after a threshold event, two bidirectionally coupled oscillators with and without delays, a unidirectional N-ring of oscillators, and N all-to-all networks.
doi:10.1016/j.mbs.2010.05.001
PMCID: PMC3022482  PMID: 20460132
Pulse coupled oscillators; Phase resetting; Phase locking; Synchronization; Splay; Clustering
7.  Phase Resetting Curves Determine Synchronization, Phase-locking, and Clustering in Networks of Neural Oscillators 
Networks of model neurons were constructed and their activity was predicted using an iterated map based solely on the phase resetting curves (PRCs). The predictions were quite accurate provided that the resetting to simultaneous inputs was calculated using the sum of the simultaneously active conductances, obviating the need for weak coupling assumptions. Fully synchronous activity was observed only when the slope of the PRC at a phase of zero, corresponding to spike initiation, was positive. A novel stability criterion was developed and tested for all to all networks of identical, identically connected neurons. When the PRC generated using N-1 simultaneously active inputs becomes too steep, the fully synchronous mode loses stability in a network of N model neurons. Therefore, the stability of synchrony can be lost by increasing the slope of this PRC either by increasing the network size or the strength of the individual synapses. Existence and stability criteria were also developed and tested for the splay mode in which neurons fire sequentially. Finally, N/M synchronous sub-clusters of M neurons were predicted using the intersection of parameters that supported both between cluster splay and within cluster synchrony. Surprisingly, the splay mode between clusters could enforce synchrony on sub-clusters that were incapable of synchronizing themselves. These results can be used to gain insights into the activity of networks of biological neurons whose PRCs can be measured.
doi:10.1523/JNEUROSCI.0426-09.2009
PMCID: PMC2765798  PMID: 19386918
Network; Synchronization; Oscillator; Rhythm; Phase shift; Synchrony

Results 1-7 (7)