| | Models | Description |
| 1. |
Brain networks simulators - a comparative study (Tikidji-Hamburyan et al 2017)
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" ... In this article, we select the three most popular simulators, as determined by the number of models in the ModelDB database, such as NEURON, GENESIS, and BRIAN, and perform an independent evaluation of these simulators. In addition, we study NEST, one of the lead simulators of the Human Brain Project. First, we study them based on one of the most important characteristics, the range of supported models. Our investigation reveals that brain network simulators may be biased toward supporting a specific set of models. ... we carry out an evaluation using two case studies: a large network with simplified neural and synaptic models and a small network with detailed models. These two case studies allow us to avoid any bias toward a particular software package ..." |
| 2. |
Cycle skipping in ING Type 1 / Type 2 networks (Tikidji-Hamburyan & Canavier 2020)
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"All-to-all homogeneous networks of inhibitory neurons synchronize completely under the right conditions; however, many modeling studies have shown that biological levels of heterogeneity disrupt synchrony. Our fundamental scientific question is “how can neurons maintain partial synchrony in the presence of heterogeneity and noise?” A particular subset of strongly interconnected interneurons, the PV+ fast spiking basket neurons, are strongly implicated in gamma oscillations and in phase locking of nested gamma oscillations to theta. Their excitability type apparently varies between brain regions: in CA1 and the dentate gyrus they have type 1 excitability, meaning that they can fire arbitrarily slowly, whereas in the striatum and cortex they have type 2 excitability, meaning that there is a frequency threshold below which they cannot sustain repetitive firing. We constrained the models to study the effect of excitability type (more precisely bifurcation type) in isolation from all other factors. We use sparsely connected, heterogeneous, noisy networks with synaptic delays to show that synchronization properties, namely the resistance to suppression and the strength of theta phase to gamma amplitude coupling, are strongly dependent on the pairing of excitability type with the type of inhibition. ..." |
| 3. |
Decorrelation in the developing visual thalamus (Tikidji-Hamburyan et al, accepted)
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The developing visual thalamus and cortex extract positional information encoded in
the correlated activity of retinal ganglion cells by synaptic plasticity, allowing for the refinement of
connectivity. Here, we use a biophysical model of the visual thalamus during the initial visual circuit
refinement period to explore the role of synaptic and circuit properties in the regulation of such
neural correlations. We find that the NMDA receptor dominance, combined with weak recurrent
excitation and inhibition characteristic of this age, prevents the emergence of spike-correlations
between thalamocortical neurons on the millisecond timescale. Such precise correlations, which
would emerge due to the broad, unrefined connections from the retina to the thalamus, reduce the
spatial information contained by thalamic spikes, and therefore we term them "parasitic" correlations.
Our results suggest that developing synapses and circuits evolved mechanisms to compensate for
such detrimental parasitic correlations arising from the unrefined and immature circuit. |
| 4. |
Interaural time difference detection by slowly integrating neurons (Vasilkov Tikidji-Hamburyan 2012)
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For localization of a sound source, animals and humans process the microsecond interaural time differences of arriving sound waves. How nervous systems, consisting of elements with time constants of about and more than 1 ms, can reach such high precision is still an open question. This model shows that population of 10000 slowly integrating Hodgkin-Huxley neurons with inhibitory and excitatory inputs (EI neurons) can detect minute temporal disparities in input signals which are significantly less than any time constant in the system. |
| 5. |
Models of visual topographic map alignment in the Superior Colliculus (Tikidji-Hamburyan et al 2016)
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We develop two novel computational models of
visual map alignment in the SC that incorporate distinct activity-dependent
components. First, a Correlational Model assumes that V1 inputs achieve alignment
with established retinal inputs through simple correlative firing mechanisms. A second
Integrational Model assumes that V1 inputs contribute to the firing of SC neurons
during alignment. Both models accurately replicate in vivo findings in wild type,
transgenic and combination mutant mouse models, suggesting either activity-dependent
mechanism is plausible. |
| 6. |
Phase response theory in sparsely + strongly connected inhibitory NNs (Tikidji-Hamburyan et al 2019)
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| 7. |
PIR gamma oscillations in network of resonators (Tikidji-Hamburyan et al. 2015)
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" ... The coupled oscillator model implemented with Wang–Buzsaki model neurons is not
sufficiently robust to heterogeneity in excitatory drive, and therefore intrinsic frequency, to account for in vitro models of ING. Similarly, in a
tightly synchronized regime, the stochastic population oscillator model is often characterized by sparse firing, whereas interneurons both in vivo
and in vitro do not fire sparsely during gamma,but rather on average every other cycle. We substituted so-called resonator neural models, which
exhibit class 2 excitability and postinhibitory rebound (PIR), for the integrators that are typically used. This results in much greater robustness
to heterogeneity that actually increases as the average participation in spikes per cycle approximates physiological levels. Moreover, dynamic
clamp experiments that show autapse-induced firing in entorhinal cortical interneurons support the idea that PIR can serve as a network gamma
mechanism. ..." |
| 8. |
PLS-framework (Tikidji-Hamburyan and Colonnese 2021)
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"Numerical simulations become incredibly challenging when an extensive network with a detailed representation of each neuron needs to be modeled over a long time interval to study slow evolving processes, e.g. development of the thalamocortical circuits. Here we suggest a simple, powerful and flexible approach in which we approximate the right-hand sides of differential equations by combinations of functions from three families: Polynomial, piecewise-Linear, Step (PLS). To obtain a single coherent framework, we provide four core principles in which PLS functions should be combined. We show the rationale behind each of the core principles. Two examples illustrate how to build a conductance-based or phenomenological model using the PLS-framework. We use the first example as a benchmark on three different computational platforms: CPU, GPU, and mobile system-on-chip devices." |
