Dr. AmirAli Farokhniaee (Project Lead)

Key Capabilities

• Theoretical & Computational Neuroscience

  Mathematical and computational brain modeling, spiking neural networks, neural mass models, dynamical systems, network neuroscience and simulation of thalamo-cortical and basal ganglia microcircuits.

• Deep Brain Stimulation & Neuromodulation

  Modeling and analysis of DBS mechanisms, design of novel closed-loop and adaptive stimulation strategies, and inventor of a US-patented DBS pulsing pattern based on synaptic suppression.

• Neural Data Analysis & Signal Processing

  EEG and local field potential analysis, network oscillations, phase-amplitude coupling, causality and information-theoretic methods using Brainstorm, CHRONUX, BSMART, MVGC and JIDT.

• Neurotechnology & Applied R&D

  EEG device development and validation protocols, MR/VR/XR experiment design, and management of clinical recordings and data-harmonization pipelines for Parkinson's disease studies.

• Research Leadership

  Principal investigator and scientific coordinator roles, project management, grant capture (SFI Industrial Fellowship, four EU Seal of Excellence awards) and technical communication across disciplines.

Work Experience

• Researcher — METRE Lab, McMaster University

  Department of Psychology, Neuroscience & Behavior, Hamilton, Canada · Sep 2025 – present

  Investigating the role of dopamine in rhythm perception and production through spiking neural network models of the basal ganglia validated with intracranial LFP and dopaminergic data.

• R&D Specialist, Project Manager & Scientific Coordinator — Thimus

  Italy · Aug 2025 – Jan 2026

  Evaluated the effects of GLP-1 medication on food and beverage preferences; heavily involved in EEG device development and data validation protocols.

• Postdoctoral Researcher in Neuromodulation — SoundMind Project, University College Cork

  Ireland · Dec 2023 – Feb 2025

  Neuromodulation analysis of EEG data in healthy subjects and patients with Alzheimer's disease and mild cognitive impairment, studying entrainment of neural oscillations to sound stimuli.

• Senior Research Fellow & Consultant — Grigioni Foundation for Parkinson's Disease

  Milan, Italy · Jun 2021 – Dec 2022

  Gait analysis research in collaboration with University Hospital Würzburg.

• Principal Investigator & Research Scientist — Newronika S.p.A. & University College Dublin

  Milan, Italy / Dublin, Ireland · Jun 2020 – Nov 2021

  Science Foundation Ireland Industrial Fellow, developing new adaptive strategies for closed-loop deep brain stimulators.

• Postdoctoral Research Fellow — University College Dublin

  Neuromuscular Systems Lab · 2018 – 2020

  Multiscale modeling of deep brain stimulation, connecting brain dynamics and muscular activity for novel Parkinson's disease therapeutics.

• Postdoctoral Research Fellow — Case Western Reserve University

  Department of Biomedical Engineering, Cleveland, Ohio · 2016 – 2018

  Discovered that synaptic depletion at high-frequency DBS is a robust phenomenon in cortical microcircuits, informing novel neuromodulation techniques; work led to a US patent.

• Lecturer & Instructor — University of Connecticut

  Department of Physics · 2014 – 2016

  Taught Elements of Physics, Environmental Physics, General Physics II (Electromagnetism, Optics, Modern Physics).

Selected Projects

• US Patent US11654286B2 (2023): Optimizing deep brain stimulation pulsing based on synaptic suppression, co-invented with Prof. Cameron McIntyre.

• Computational platform identifying effective stimulation paradigms and thalamo-cortical targets for less-invasive Parkinson's disease stimulation (2021), co-invented with Prof. Madeleine Lowery at University College Dublin.

• Improved thalamo-cortical spiking network model of deep brain stimulation, published in Frontiers in Computational Neuroscience (2025), with GPU and multithread computing support.

• Gait-related beta-gamma phase-amplitude coupling in the subthalamic nucleus of parkinsonian patients, published in Scientific Reports (2024).

• Discovery of synaptic suppression principles in DBS, published in Brain Stimulation (2019), proposing stimulation patterns that extend implanted-device battery life.

• Science Foundation Ireland Industrial Fellowship (€82,437) for adaptive closed-loop deep brain stimulators; four Horizon MSCA Seal of Excellence awards (2018–2024).

Education

• Ph.D. in Physics — University of Connecticut, 2016 · Thesis: Simulation and Analysis of Gradient Frequency Neural Networks

• M.Sc. in Physics — Florida Atlantic University, 2013

• B.Sc. in Atomic-Molecular Physics — University of Tehran, 2009

• Awards: Outstanding Dissertation Fellowship, Marshall J. Walker Outstanding Teaching Award, Ann and Win Smith Outstanding Physics Graduate Student Award (University of Connecticut).

Multi-component Systems Design

Design and integration of closed-loop neuromodulation systems spanning neural hardware, signal acquisition, real-time analysis and adaptive stimulation control, alongside MR/VR/XR experiment platforms combining neurophysiological monitoring with advanced analytics.

Advanced Programming

• Scientific Computing

  MATLAB and Python development for large-scale neuronal simulations, including Dynasim, PyNN, NEURON and Simulink, with GPU-accelerated and multithread computing.

• Software Development

  MATLAB App Designer applications, statistical analysis with linear mixed effects models, STATA and SPSS, and algorithms for clinical data harmonization and categorization.