Key Publications

The Fruits of My Labor

Here you will find information about the research publications I’ve been involved with. Throughout my research, I’ve had the opportunity to work on many interesting projects that have enriched my understanding and paved the path towards my successful Scientist career. I’m proud to showcase my hard work with the list of publications below.


A Thalamo-cortical

Spiking neural network model of

deep brain stimulation 

AmirAli Farokhniaee* and Madeleine M. Lowery

"Cortical Network Effects of Subthalamic Deep Brain Stimulation in a Thalamo-Cortical Microcircuit Model", Journal of Neural Engineering. in press

This is my major work in the lab of Prof. Lowery. We designed a multi-layer thalamo-cortical network of Izhikevich neurons, based on the most recent neurophysiological and computational studies that is capable of replicating experimental recordings of parkinsonian rats. This model is beneficial to study network effects of DBS and testing different hypotheses of DBS mechanisms of action. We have done both temporal and spectral analyse of the thalamo-cortical neural network and currently are wrapping up the coherence and synchronization analysis leading to understanding the causal effects of multiple layers of motor cortex on the network.


Synaptic suppression

and its contribution to 

deep brain stimulation

mechanisms of action

AmirAli Farokhniaee and Cameron C. McIntyre* "Theoretical Principles of Deep Brain Stimulation Induced Synaptic Suppression", Brain Stimulation, (2019)
DOI: 10.1016/j.brs.2019.07.005.
This paper reports my major achievements during my first postdoc in the lab of Prof. McIntyre that covers an overall understanding of glutamatergic synapses in the cortex and their contribution in the cortical neuron firing patterns during DBS. We were able to model the firing pattern of M1 cortical neurons recorded during 1 minute of DBS on a monkey (recorded in another lab), by computational modelling of LIF neurons. Based on these results we proposed a novel DBS pattern with less stimulation time periods that enhances the battery life of the implanted device for DBS and probably less side effects for the PD patients.


Arnold tongues
izhikevich neurons

AmirAli Farokhniaee* and Edward W. Large "Mode-locking behavior of Izhikevich neurons under periodic external forcing", Physical Review E, 95, 062414 (2017) DOI: 10.1103/Phys-RevE.95.062414
This paper reports my major computational achievements during my PhD studies. It explains the single neuron responses to periodical stimuli and how their response gets temporally locked (phase-locked) to the stimulus, depending on the amplitude and frequency. This is a very basic phenomenon that manifests in many parts of the brain.


A Canonical Model of Wilson-Cowan type mean field models

AmirAli Farokhniaee*, Felix V. Almonte, Susanne Yelin and Edward W. Large "Entrainment of Weakly Coupled Canonical Oscillators with Applications in Gradient Frequency Neural Networks Using Approximating Analytical Methods", Mathematics, (2020) 8,1312; DOI: 10.3390/math8081312
This paper contains my major achievements in the theoretical aspects of my Ph.D. studies. This work reports implementation of normal form theory on Wilson-Cowan type neuronal populations to obtain a canonical model, which eases the synchronization analysis of WC type models.


Initiation and Propagation of
action potentials via cortical pyramidal neurons

Ross W. Anderson, AmirAli Farokhniaee, Kabilar Gunalan, Bryan Howell, Cameron C. McIntyre* "Action potential initiation, propagation, and cortical invasion in the hyperdirect pathway during subthalamic deep brain stimulation", Brain Stimulation, (2018) DOI: 10.1016/j.brs.2018.05.008
I was involved in this project during my postdoc research in the lab of Prof. McIntyre by evaluating the synaptic depletions induced by DBS to synaptic terminals of a pyramidal model neuron in layer 5 of the cortex, investigating the hypothesis that synaptic suppression has a major contribution to the network effects of DBS.