Stochastic simulation
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McGraw-Hill serie in industrial engineering and management science
321 s.
Cell cycle is controlled by the activity of protein family of cyclins and cyclin-dependent kinases that are periodically expressed during cell cycle and that are conserved among different species. Genome-wide location analysis found that cyclins are controlled by a small number of transcription factors that form closed network of genes controlling each other. To investigate gene expression dynamics of this network, we developed a general procedure for stochastic simulation of gene expression process. Using the binding data, we simulated gene expression of all genes of the network for all possible combinations of regulatory interactions and by statistical comparison with experimentally measured time series excluded those interactions that formed gene expression temporal profiles significantly different from the measured ones. These experiments led to a new definition of the cyclins regulatory network coherent with the binding experiments which are kinetically plausible. Level of influence of individual regulators in control of the regulated genes is defined. Simulation results indicate particular mechanism of regulatory activity of protein complexes involved in the control of cyclins.
Modeling and simulation in science, engineering and technology
ix, 343 s. ; 24 cm
- MeSH
- časové faktory MeSH
- stochastické procesy MeSH
- teoretické modely MeSH
- věda MeSH
- Publikační typ
- monografie MeSH
- Konspekt
- Statistika
- NLK Obory
- statistika, zdravotnická statistika
This article presents a stochastic model of binaural hearing in the medial superior olive (MSO) circuit. This model is a variant of the slope encoding models. First, a general framework is developed describing the elementary neural operations realized on spike trains in individual parts of the circuit and how the neurons converging onto the MSO are connected. Random delay, coincidence detection of spikes, divergence and convergence of spike trains are operations implemented by the following modules: spike generator, jitter generator, and coincidence detector. Subsequent processing of spike trains computes the sound azimuth in the circuit. The circuit parameters that influence efficiency of slope encoding are studied. In order to measure the overall circuit performance the concept of an ideal observer is used instead of a detailed model of higher relays in the auditory pathway. This makes it possible to bridge the gap between psychophysical observations in humans and recordings taken of small rodents. Most of the results are obtained through numerical simulations of the model.
- MeSH
- akční potenciály fyziologie MeSH
- akustická stimulace metody MeSH
- lidé MeSH
- modely neurologické * MeSH
- nervová síť * fyziologie MeSH
- nucleus olivaris caudalis * fyziologie MeSH
- sluchová dráha * fyziologie MeSH
- stochastické procesy MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Interaural time differences (ITDs), the differences of arrival time of the sound at the two ears, provide a major cue for low-frequency sound localization in the horizontal plane. The first nucleus involved in the computation of ITDs is the medial superior olive (MSO). We have modeled the neural circuit of the MSO using a stochastic description of spike timing. The inputs to the circuit are stochastic spike trains with a spike timing distribution described by a given probability density function (beta density). The outputs of the circuit reproduce the empirical firing rates found in experiment in response to the varying ITD. The outputs of the computational model are calculated numerically and these numerical simulations are also supported by analytical calculations. We formulate a simple hypothesis concerning how sound localization works in mammals. According to this hypothesis, there is no array of delay lines as in the Jeffress' model, but the inhibitory input is shifted in time as a whole. This is consistent with experimental observations in mammals.
- MeSH
- akustická stimulace MeSH
- lidé MeSH
- lokalizace zvuku MeSH
- neurony fyziologie MeSH
- savci MeSH
- sluchová dráha fyziologie MeSH
- stochastické procesy MeSH
- teoretické modely MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- zvířata MeSH
- Publikační typ
- práce podpořená grantem MeSH
In the nervous system, the representation of signals is based predominantly on the rate and timing of neuronal discharges. In most everyday tasks, the brain has to carry out a variety of mathematical operations on the discharge patterns. Recent findings show that even single neurons are capable of performing basic arithmetic on the sequences of spikes. However, the interaction of the two spike trains, and thus the resulting arithmetic operation may be influenced by the stochastic properties of the interacting spike trains. If we represent the individual discharges as events of a random point process, then an arithmetical operation is given by the interaction of two point processes. Employing a probabilistic model based on detection of coincidence of random events and complementary computer simulations, we show that the point process statistics control the arithmetical operation being performed and, particularly, that it is possible to switch from subtraction to division solely by changing the distribution of the inter-event intervals of the processes. Consequences of the model for evaluation of binaural information in the auditory brainstem are demonstrated. The results accentuate the importance of the stochastic properties of neuronal discharge patterns for information processing in the brain; further studies related to neuronal arithmetic should therefore consider the statistics of the interacting spike trains.
- MeSH
- akční potenciály fyziologie MeSH
- lidé MeSH
- modely neurologické MeSH
- nervová síť fyziologie MeSH
- nervový útlum fyziologie MeSH
- neurony fyziologie MeSH
- počítačová simulace MeSH
- stochastické procesy MeSH
- teorie pravděpodobnosti MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Dynamic modeling of biological systems is essential for understanding all properties of a given organism as it allows us to look not only at the static picture of an organism but also at its behavior under various conditions. With the increasing amount of experimental data, the number of tools that enable dynamic analysis also grows. However, various tools are based on different approaches, use different types of data and offer different functions for analyses; so it can be difficult to choose the most suitable tool for a selected type of model. Here, we bring a brief overview containing descriptions of 50 tools for the reconstruction of biological models, their time-course simulation and dynamic analysis. We examined each tool using test data and divided them based on the qualitative and quantitative nature of the mathematical apparatus they use.
- MeSH
- biologické modely * MeSH
- datové soubory jako téma MeSH
- genové regulační sítě MeSH
- lidé MeSH
- počítačová simulace MeSH
- software * MeSH
- stochastické procesy MeSH
- systémová biologie metody MeSH
- ukládání a vyhledávání informací MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- přehledy MeSH
