References of "Ignatenko, Andrew 50002022"
     in
Bookmark and Share    
Full Text
See detailROS homeostasis in a dynamic model: How to save PD neuron?
Kolodkin, Alexey UL; Ignatenko, Andrew UL; Sangar, Vineet et al

Poster (2014, December)

Detailed reference viewed: 92 (14 UL)
See detailSimulation, control and optimisation for the model of ROS management system
Ignatenko, Andrew UL

Presentation (2014, November 06)

Detailed reference viewed: 25 (3 UL)
Full Text
Peer Reviewed
See detailComparison of ODE-based models for reactive oxygen species regulation system
Ignatenko, Andrew UL; Kolodkin, Alexey UL; Peters, Bernhard UL et al

in Proceedings of ICCSA 2014 (2014, June)

Reactive oxygen species (ROS) play important role in the functioning of any cell and especially in the lifecycle of mitochondria. Since the action of ROS can be both positive and negative then the ... [more ▼]

Reactive oxygen species (ROS) play important role in the functioning of any cell and especially in the lifecycle of mitochondria. Since the action of ROS can be both positive and negative then the remarkable role can be played by ROS regulation system. We constructed three different ODE based kinetic models of different complexity for the ROS management system and shown the difference in the dynamics of these systems under different conditions. Using results of numerical simulation we showed that extraction of some subsystems can make the model more unstable. We also introduced the objective function for comparison of the models with structure of different complexity [less ▲]

Detailed reference viewed: 128 (34 UL)
See detailROS-activated signaling network: dynamic modelling and design principles study
Kolodkin, Alexey UL; Ignatenko, Andrew UL; Sangar, Vineet et al

Poster (2014, June)

Detailed reference viewed: 116 (11 UL)
See detailDynamic modelling of ROS management and ROS-induced mitophagy
Kolodkin, Alexey UL; Ignatenko, Andrew UL; Sangar, Vineet et al

Poster (2014, June)

Detailed reference viewed: 92 (16 UL)
See detailODE-based model for ROS management system
Ignatenko, Andrew UL

Presentation (2013, October 24)

Detailed reference viewed: 23 (2 UL)
Full Text
See detailDesign principles study of ROS management and ROS-induced mitophagy with a kinetic model
Kolodkin, Alexey UL; Ignatenko, Andrew UL; Sangar, Vineet et al

Poster (2013, September 27)

In vivo evidence demonstrates three fundamental interconnected adaptive survival mechanisms , which protect against excessive ROS that is generated during mitochondrial dysfunction: (i) autophagy ... [more ▼]

In vivo evidence demonstrates three fundamental interconnected adaptive survival mechanisms , which protect against excessive ROS that is generated during mitochondrial dysfunction: (i) autophagy/mitophagy, (ii) adaptive antioxidant response and (iii) NFkB signaling in cancer and neurodegeneration. We have been expanding a kinetic model which recapitulates the consensus understanding of the mechanisms responsible for cellular ROS – management system and performed modular analysis to analyze emergent behavior. We started with the simplest model and added stepwise new modules. We identify the qualitative role (certain emergent behavior) attributed to each module and thus understand the design principles of the system. We propose a detailed, mechanistic, kinetic model for studying how mutations relevant for diseases such as PD and cancer affect the emergent behavior of ROS management network. [less ▲]

Detailed reference viewed: 239 (11 UL)
Peer Reviewed
See detailModeling cellular ROS defense in mitochondrial-related diseases
Simeonidis, Vangelis UL; Kolodkin, Alexey UL; Ignatenko, Andrew UL et al

Poster (2013, July 22)

Reactive Oxygen Species (ROS) generation is an unavoidable background process during normal cellular function. The main contributor to ROS production is the electron transport chain, which reduces oxygen ... [more ▼]

Reactive Oxygen Species (ROS) generation is an unavoidable background process during normal cellular function. The main contributor to ROS production is the electron transport chain, which reduces oxygen to water. Some incompletely-reduced oxygen species escape and oxidize a variety of organic molecules, leading to molecular dysfunction and initiating a positive feedback loop of ever increasing active radical production. The increased concentration of ROS damages the mitochondria, therefore further elevating the rate of ROS generation. Healthy cells manage ROS enzymatically and by mitophagy of damaged mitochondria. The precise tuning of the latter mechanism is crucial for cell survival and is controlled by a ROS-induced regulatory network. We have built a set of kinetic models of varying complexity, based on the current understanding of the mechanism of cellular ROS defense. Our models allow simulation of various patho-physiological scenarios related to mitochondrial dysfunction and the failure of the system of ROS regulation in human cells. We employ the models we have constructed to simulate the effects of diseases related to mitochondrial dysfunction and excessive ROS generation, such as Parkinson’s disease, Huntington’s disease and cancer. Experimental evidence is used for model fitting, and we propose model improvements based on incorporation of single-cell experimental measurements. Finally, we discuss the perspective of integrating our kinetic models with genome-scale, constraint-based, tissue-specific models of metabolism, in order to study the effect of ROS misregulation on metabolic phenotype. [less ▲]

Detailed reference viewed: 112 (5 UL)
Full Text
See detailROS-induced regulation of mitophagy and its failure in Parkinson’s disease
Kolodkin, Alexey UL; Ignatenko, Andrew UL; Simeonidis, Vangelis UL et al

Poster (2013, May)

Reactive Oxygen Species (ROS) generation is an unavoidable background process in the normal functioning of the cell. The greatest contributor to ROS production is the electron transport chain (ETC) where ... [more ▼]

Reactive Oxygen Species (ROS) generation is an unavoidable background process in the normal functioning of the cell. The greatest contributor to ROS production is the electron transport chain (ETC) where O2 is reduced to H2O. Some incompletely-reduced oxygen species escape and oxidize a variety of organic molecules (e.g. proteins and lipids in the mitochondrial membrane), leading to molecular dysfunction and initiating a positive feedback loop leading to generation of even more active radicals. Increased ROS concentration damages mitochondria and further increases ROS generation. Healthy cells manage ROS enzymatically with superoxide dismutase and other enzymes, various antioxidants, and ultimately through increased mitophagy of damaged mitochondria. The precise tuning of the latter mechanism is crucial for cell survival and is controlled in the cell by a ROS-induced regulatory network, which consists of many components such as Nrf2, Keap1, Parkin and p62 with a rather complicated cross-talk (Figure 1). In many diseases (cancer, Parkinson’s disease (PD), Huntington’s disease (HD), etc.), various components of the ROS management network are altered. Deconstructing the molecular mechanisms underlying or resulting from these alterations might contribute to better understanding of the dynamics of related pathophysiological processes. We have built a kinetics-based model which recapitulates the consensus understanding of the mechanism responsible for cellular ROS – managing system. [less ▲]

Detailed reference viewed: 125 (10 UL)
Full Text
Peer Reviewed
See detailData pattern tomography: reconstruction with an unknown apparatus
Ignatenko, Andrew UL; Mogilevtsev, Dmitry; Maloshtan, Alexander et al

in New Journal of Physics (2013), 15

We propose a scheme for the reconstruction of the quantum state without a priori knowledge about the measurement setup. Using the data pattern approach, we develop an iterative procedure for obtaining ... [more ▼]

We propose a scheme for the reconstruction of the quantum state without a priori knowledge about the measurement setup. Using the data pattern approach, we develop an iterative procedure for obtaining information about the measurement which is sufficient for an estimation of a particular signal state. The method is illustrated with the examples of reconstruction with on/off detection and quantum homodyne tomography. [less ▲]

Detailed reference viewed: 40 (6 UL)
Full Text
Peer Reviewed
See detailEfficient single-photon generator based on entanglement between the emitter and field in a photonic crystal near the band edge
Mogilevtsev, Dmitri; Maloshtan, Alexander; Ignatenko, Andrew UL et al

in Optics & Spectroscopy (2010), 108(3), 425-432

The possibility of using the long-lived entangled state between the emitter and field near the band edge of the density of states of a photonic crystal to create an efficient generator of single photons ... [more ▼]

The possibility of using the long-lived entangled state between the emitter and field near the band edge of the density of states of a photonic crystal to create an efficient generator of single photons is considered. The generator can be efficiently excited by incoherent pumping, excludes simultaneous generation of two photons, and ensures a high probability of extracting the photon into a specified mode. [less ▲]

Detailed reference viewed: 36 (0 UL)
Full Text
Peer Reviewed
See detailQuantum dynamics of interaction of elementary detector with single-mode multiphoton states of electromagnetic field
Ignatenko, Andrew UL; Kilin, Sergei

in Optics & Spectroscopy (2010), 108(3), 412-416

The dynamics of the elementary photoelectric conversion in the interaction of a single-mode electromagnetic field with an arbitrary photon number distribution and a bound electron in a 1D rectangular ... [more ▼]

The dynamics of the elementary photoelectric conversion in the interaction of a single-mode electromagnetic field with an arbitrary photon number distribution and a bound electron in a 1D rectangular potential well is considered. It is shown that if the frequency of the coherent field exceeds the frequency corresponding to the electron work function, the photoexcitation of this electron is incomplete. [less ▲]

Detailed reference viewed: 25 (0 UL)
Full Text
Peer Reviewed
See detailQuantum dynamics of single-photon detection
Ignatenko, Andrew UL; Kilin, Sergei

in Optics & Spectroscopy (2007), 103(1), 121-128

Dynamics of the elementary photoelectric conversion upon interaction of a single-photon mode with a bound electron in a one-dimensional rectangular potential well is considered. The spatial and temporal ... [more ▼]

Dynamics of the elementary photoelectric conversion upon interaction of a single-photon mode with a bound electron in a one-dimensional rectangular potential well is considered. The spatial and temporal dynamics of the wave packet corresponding to a free photoelectron is investigated. [less ▲]

Detailed reference viewed: 27 (0 UL)