Publications
129 results found
Grossman N, Nikolic K, Grubb M, et al., 2011, High-frequency limit of neural stimulation with ChR2, Conf Proc IEEE Eng Med Biol Soc, Pages: 4167-4170, ISSN: 1557-170X
Optogenetic technology based on light activation of genetically targeted single component opsins such as Channelrhodopsin-2 (ChR2) has been changing the way neuroscience research is conducted. This technology is becoming increasingly important for neural engineering as well. The efficiency of neural stimulation with ChR2 drops at high frequencies, often before the natural limit of the neuron is reached. This study aims to investigate the underlying mechanisms that limit the efficiency of the stimulation at high frequencies. The study analyzes the dynamics of the spikes induced by ChR2 in comparison to control stimulations using patch clamp current injection. It shows that the stimulation dynamics is limited by two mechanisms: 1) a frequency independent reduction in the conductance-to-irradiance yield due to the ChR2 light adaptation process and 2) a frequency dependent reduction in the conductance-to-current yield due to a decrease in membrane re-polarization level between spikes that weakens the ionic driving force. The effect of the first mechanism can be minimized by using ChR2 mutants with lower irradiance threshold. In contrast the effect of the second mechanism is fundamentally limited by the rate the native ion channels re-polarize the membrane potential.
Nikolic K, San Segundo Bello D, Delbruck T, et al., 2011, High-sensitivity silicon retina for robotics and prosthetics, SPIE Newsroom
Grossman N, Nikolic K, Toumazou C, et al., 2011, Modeling Study of the Light Stimulation of a Neuron Cell With Channelrhodopsin-2 Mutants, IEEE TRANSACTIONS ON BIOMEDICAL ENGINEERING, Vol: 58, Pages: 1742-1751, ISSN: 0018-9294
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Serb A, Nikolic K, Constandinou TG, 2011, A CMOS-based light modulator for contactless data transfer: theory and concept, Silicon Photonics VI, Publisher: SPIE, Pages: 794317-794325
A new technique pertaining to the optical contactless chip-to-board communication using a commercially available CMOS technology is under development. The main concept is to use mid-IR light from a small LED which will enter an IC from the underside, impinge upon one or more pn-junctions and be reflected by a metallic sheet so that it falls on an external, discrete photodetector. After propagation through the doped semiconductor, the light undergoes attenuation due to free carrier absorption. By varying the reverse bias across the pn-junction(s), the depletion region widths are changed and therefore modulation of light intensity can be achieved. Through this scheme, data readout can be realized optically, thus alleviating the need for galvanic contacts (most notably wirebonds).
Grossman N, Degenaar P, Nikolic K, 2011, Spike engineering with Channelrhodopsin-2, Neuroscience Letters
Serb A, Nikolic K, Constandinou TG, 2011, Feasibility of an Electro-Optic Link for Bondpad-less CMOS Lab-on-Chips, IEEE Biomedical Circuits and Systems (BioCAS) conference, Publisher: IEEE, Pages: 353-356
This paper explores the feasibility of developing CMOS-based lab-on-chips to analyse the properties of a fluid, without the need for bond wires. Both inductive and electro-optical schemes are suggested as possible solutions. Specifically, this paper details a novel approach in achieving electro-optical modulation in unmodified, commercially-available CMOS technology. By exploiting the plasma dispersion effect, it is shown how mid-infrared light can be modulated using parasitic structures designed in a CMOS integrated circuit. Both the fundamental theory and practical realisation are supported with measured data from an experimental setup.
Nikolic K, Loizu J, 2010, Drosophila Phototransduction Simulator
This code contains detailed modelling of the single photon response, the quantum bump, of fly photoreceptors. All known components participating in the primary phototransduction process are taken into account, and estimates are given for the both the physical and the chemical parameters. The same model can be used for multiphoton response, i.e. in the case of higher light intensity stimuli. The model successfully reproduces the experimental results for the statistical features of quantum bumps (average shape, peak current average value and variance, the latency distribution, etc), arrestin mutant behaviour, low extracellular Ca cases, etc. The TRP channel activity is modelled using the Monod-Wyman-Changeux (MWC) theory for allosteric interaction. The model can combine deterministic and stochastic approaches and allows for a detailed noise analysis. The computational model was coded in Matlab using the Parallel Computing Toolbox, which allows computations on multicore computers and computer clusters. An appropriate graphic user interface was developed which gives very convenient and instructive presentation of the parameters used in the modelling and could easily be expanded to other G-protein coupled cascade processes.Code covered by the BSD License (Matlab Central, File exchange), please see BSD_License.txt file or visit: http://www.mathworks.com/matlabcentral/fileexchange/view_license?file_info_id=22942 If you use this code please cite the papers [1] and [2].The main file "Drosophila_Phototransduction.m" opens the GUI. The GUI contains the preloaded values for parameters and should be mostly self-explanatory in combination with the paper [1]. It is possible to run stochastic and deterministic models for single and multiple runs. The output consists of a table for some average values and three graphs (for the average quantum bump, latency times distribution and peak current distribution). It is possible to produce some other plots currently commented out
Nikolic K, Toumazou C, 2010, A bio-inspired ultrasensitive imaging chip — Phase one: Design paradigm, Proceedings of the IEEE International Symposium on Circuits and Systems (ISCAS), 2010, Pages: 345-348
Grossman N, Poher V, Grubb MS, et al., 2010, Multisite optical excitation using ChR2 and micro-LED array, Journal of Neural Engineering, Vol: 7, ISSN: 1741-2560
Nikolic K, Loizu J, Degenaar P, et al., 2010, A stochastic model of the single photon response in Drosophila photoreceptors, Integrative Biology, Vol: 2, Pages: 354-370
We present a quantitative model for the phototransduction cascade in Drosophila photoreceptors. The process consists of four stages: (1) light absorption by Rhodopsin, (2) signal amplification phase mediated by a G-protein coupled cascade, (3) close/open state kinetics of the transient receptor potential (TRP) ion channels which regulate the ionic current in/out of the cell and (4) Ca regulated positive and negative feedbacks.The model successfully reproduces the experimental results for: single photon absorption "quantum bump" (QB), statistical features for QB (average shape, peak current average value and variance, the latency distribution, etc), arrestin mutant behaviour, low extracellular Ca2+ cases, etc. The TRP channel activity is modeled by a Monod-Wyman-Changeux (MWC) model for allosteric interaction, instead of using the usual ad hoc Hill equation. This approach allows for a plausible physical explanation how Ca/calmodulin regulate the protein activity. The cooperative nature of the TRP channel activation leads to "dark current" suppression at the output allowing for reliable detection of a single photon. Stochastic simulations were produced by using the standard rate equations combined with the Poisson distribution for generating random events from the forward and the reverse reaction rates. Noise is inherent to the system but appears to be crucial for producing such reliable responses in this complex, highly nonlinear system. The approach presented here may serve as a useful example how to treat complex cellular mechanisms underlying sensory processes.
Nikolic K, Loizou J, Degenaar P, 2010, Computational Modelling of the Drosophila Phototransduction Cascade, Biophysical Journal 98
Degenaar P, Grossman N, Berlinguer-Palmini R, et al., 2010, Optoelectronic microarrays for retinal prosthesis, IEEE Biomedical Circuits and Systems Conference, BioCAS 2009, Pages: 183-186
Nikolic K, Grossman N, Grubb M, et al., 2009, Photocycles of Channelrhodopsin-2, Photochemistry and Photobiology, Vol: 85, Pages: 400-411
Degenaar P, Grossman N, Memon MA, et al., 2009, Optobionic vision-a new genetically enhanced light on retinal prosthesis, Journal of Neural Engineering, Vol: 6, ISSN: 1741-2560
Degenaar P, Grossman N, McGovern B, et al., 2009, Seeing the light: a photonic visual prosthesis for the blind, Conference on Photons and Neurons, Publisher: Society of Photo-optical Instrumentation Engineers, ISSN: 0277-786X
Grossman N, Nikolic K, Poher V, et al., 2009, Photostimulator for Optogenetic Retinal Prosthesis, IEEE EMBS Conference on Neural Engineering, Publisher: IEEE, Pages: 68-71
Nikolic K, Loizu J, Degenaar P, et al., 2008, Noise reduction in analogue computation of Drosophila photoreceptors, Journal of Computational Electronics, Vol: 7, Pages: 458-461, ISSN: 1569-8025
Degenaar P, Nikolic K, Banks D, et al., 2008, Organic and Inorganic Semiconductor Photoreceptors Mimicking the Human Rods and Cones, Next Generation Artificial Vision Systems: Reverse Engineering the Human Visual System, Editors: Bharath, Petrou, Publisher: Artech House Publishers, Pages: 251-288, ISBN: 978-1596932241
Grossman N, Nikolic K, Huang Y, et al., 2008, Non-invasive approach to the Bionic Eye, Encyclopedia of Healthcare Information Systems, Editors: Wickramasinghe, Geisler, USA, Publisher: Medical Information Science Reference, Pages: 998-1003, ISBN: 9781599048895
Poher V, Grossman N, Kennedy GT, et al., 2008, Micro-LED arrays: a tool for two-dimensional neuron stimulation, Journal of Physics D: Applied Physics, Vol: 41, Pages: 094014-094023, ISSN: 0022-3727
Grossman N, Nikolic K, Degenaar P, 2008, The neurophotonic interface: stimulating neurons with light, Neuromorphic Engineer
Nikolic K, Marinkovic P, Cvetic J, 2008, Physics: solved problems (in serbian: Fizika - Zbirka resenih zadataka), 4th edition, Belgrade, Publisher: DN Centar, ISBN: 9788683239047
Degenaar P, Hankins MW, Drakakis E, et al., 2007, Retinal Prosthetic Devices
Nikolic K, Murugesan M, Forshaw M, et al., 2007, Self-Assembly of Nanoparticles on the Surface of Ionic Crystals: Structural Properties, SURFACE SCIENCE, Vol: 601, Pages: 2730-2734
Nikolic K, Grossman N, Yan H, et al., 2007, A non-invasive retinal prosthesis - testing the concept., Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference, Pages: 6365-6368, ISSN: 1557-170X
We have developed a testing platform for a novel type of retinal prosthesis. Our system uses an array of light sources as non-contact stimulators. The platform consists of an imaging system based on a CMOS camera, PC based image processing, and a stimulation address system carried out on a Field Programmable Gated Array which addresses a matrix array of LEDs. Special optics are used to focus the light from the LED array onto light sensitized cells.
Nikolic K, Grossman N, Yan H, et al., 2007, A Non-Invasive Retinal Prosthesis - Testing the Concept, 29th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBS), Publisher: IEEE, Pages: 6364-6367, ISSN: 1557-170X
Nikolic K, 2006, New imaging devices and image processing challenges, La Rivista del Nuovo Cimento, Vol: 29, Pages: 1-51
Nikolic K, Degenaar P, Toumazou C, 2006, Modeling and engineering aspects of ChannelRhodopsin2 system for neural photostimulation, 28th Annual International Conference of the IEEE-Engineering-in-Medicine-and-Biology-Society, Publisher: IEEE, Pages: 651-654
Yan Huang, Emmanuel Drakakis, Chris Toumazou, et al., 2006, An Optoelectronic Platform for Retinal Prosthesis, IEEE BioCAS, Biomedical Circuits and Systems Conference, Publisher: IEEE, Pages: 110-113
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