Parameter Estimation for Biochemical Reactions in Phototransduction
نویسنده
چکیده
Vision begins when photons are captured by rhodopsin molecules in photoreceptor cells in the back of the retina. Activation of rhodopsin instigates a cascade of biochemical reactions, which eventually results in reduction of the steady (dark) current across the photoreceptor plasma membrane. This is the photoreceptor response, the signal that propagates to the brain enabling vision. Employing an existing model for the biochemical cascade and the response, expressed as a system of ordinary differential equations involving 16 parameters, we present an approach based on statistical sensitivity/uncertainty analysis and optimization, to find parameters that produce a response matching experimental data. AMS (MOS) Subject Classification. 92C45, 90C31, 62J02.
منابع مشابه
Parameter estimation for stochastic models of biochemical reactions
Parameter estimation is very important for the analysis of models in systems biology. Computational modeling is a central approach in systems biology, for studying increasingly complex biochemical systems. Progress in experimental techniques, e.g. the possibility to measure small numbers of molecules in single cells [1], highlights the need for stochastic modeling approaches. Simulation methods...
متن کاملThe probabilistic cell: implementation of a probabilistic inference by the biochemical mechanisms of phototransduction.
When we perceive the external world, our brain has to deal with the incompleteness and uncertainty associated with sensory inputs, memory and prior knowledge. In theoretical neuroscience probabilistic approaches have received a growing interest recently, as they account for the ability to reason with incomplete knowledge and to efficiently describe perceptive and behavioral tasks. How can the p...
متن کاملScalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks
Mechanistic mathematical modeling of biochemical reaction networks using ordinary differential equation (ODE) models has improved our understanding of small- and medium-scale biological processes. While the same should in principle hold for large- and genome-scale processes, the computational methods for the analysis of ODE models which describe hundreds or thousands of biochemical species and ...
متن کاملNumerical modeling for nonlinear biochemical reaction networks
Nowadays, numerical models have great importance in every field of science, especially for solving the nonlinear differential equations, partial differential equations, biochemical reactions, etc. The total time evolution of the reactant concentrations in the basic enzyme-substrate reaction is simulated by the Runge-Kutta of order four (RK4) and by nonstandard finite difference (NSFD) method. A...
متن کاملSBMLSimulator: A Java Tool for Model Simulation and Parameter Estimation in Systems Biology
The identification of suitable model parameters for biochemical reactions has been recognized as a quite difficult endeavor. Parameter values from literature or experiments can often not directly be combined in complex reaction systems. Nature-inspired optimization techniques can find appropriate sets of parameters that calibrate a model to experimentally obtained time series data. We present S...
متن کامل