1.  PyRho: A virtual optogenetics lab

PyRho logo Multiscale computational tools for Optogenetics, include a GUI and installations of NEURON and Brian. PyRhO project page.  

2.  Photocycles of Channelrhodopsin-2 

    A systematic investigation of the possible models of the ChR2 photocycle. The final model consists of two closed and two open states. Simulation results suggest that they might represent the dark-adapted and light-adapted branc4-state modelhes. It reveals an adaptation mechanism of the ChR2 molecule. Hence very simple organisms (such as green algae) expressing ChR2 can use this form of light adaptation. The model is widely used for functional modelling of the ChR2 photocycles. It is an essential tool for computational neuroscience simulations of neurons expressing ChR2.   

    K. Nikolic et.al, PHOTOCHEMISTRY and PHOTOBIOLOGY 85: 400-411 (2009)


    3.   Multi-site optical excitation using ChR2 and micro-LED array

    This paper represents a multidisciplinary effort of several groups from King‚Äôs College London (biologists), University of Strathclyde (LED arrays) and Imperial College (IBE, Physics, Bioengineering) in creating a new tool for generating light stimulus patterns. This paper also introduces a novel technique for high-resolution, multi-site stimulation of subcellular stimindividual neurons or sections of dendritic tree. My role was in designing this device on the basis of insights gained from my models, and also analysing the experimental results and writing the paper.  

    N. Grossman, et al. Journal of NEURAL ENGINEERING 7 (1): 0164004 (13pp), 2010

    4.  Optobionic vision - A new genetically enhanced light on retinal prosthesis

    An illustration of our optogenetic retinal prosthesis concept. Despite more than 25 years of efforts to create a viable retinal implant that goal still seems to be elusive. There are several clinical trials of electrical retinal implants with up to hundred electrodes which stimulate retinal ganglion cells, but all that blind patients are able to "see" are flashes of white noisy dots (phosphenes). However, the optogenetic route holds a new promise and it has been investigated by several groups. Retinal Prosthesis

    P. Degenaar, M.A. Memon, N. Grossman, J. Burrone, M. Dawson, E. Drakakis, M. Neil, E, K. Nikolic, Journal of NEURAL ENGINEERING 6 (3): 035007 (10pp), 2009.