Search results for "Biological system"
showing 10 items of 319 documents
Individual Variability and Average Reliability in Parallel Networks of Heterogeneous Biological and Artificial Nanostructures
2013
We simulate the collective electrical response of heterogeneous ensembles of biological and artificial nanostructures whose individual threshold potentials show a significant variability. This problem is of current interest because nanotechnology is bound to produce nanostructures with a significant experimental variability in their individual physical properties. This diversity is also present in biological systems that are however able to process information efficiently. The nanostructures considered are the ion channels of biological membranes, nanowire field-effect transistors, and metallic nanoparticle-based single electron transistors. These systems are simulated with canonical models…
Probing dynamics of dense suspensions: three-dimensional cross-correlation technique
1997
We describe the realization of a novel three-dimensional (3D) cross-correlation scheme, which provides the possibility to measure dynamic structure factors of highly concentrated colloidal samples without contributions of multiply scattered light. The apparatus is easier to align and more compact than the two-colour cross-correlation apparatus, which is commercially available. This should make the 3D cross-correlation set-up more convenient for routine applications, for example in industrial laboratories. We describe the set-up and discuss some special features of the optical components.
Multilayer perceptron neural networks and radial-basis function networks as tools to forecast accumulation of deoxynivalenol in barley seeds contamin…
2011
The capacity of multi-layer perceptron artificial neural networks (MLP-ANN) and radial-basis function networks (RBFNs) to predict deoxynivalenol (DON) accumulation in barley seeds contaminated with Fusarium culmorum under different conditions has been assessed. Temperature (20-28 °C), water activity (0.94-0.98), inoculum size (7-15 mm diameter), and time were the inputs while DON concentration was the output. The dataset was used to train, validate and test many ANNs. Minimizing the mean-square error (MSE) was used to choose the optimal network. Single-layer perceptrons with low number of hidden nodes proved better than double-layer perceptrons, but the performance depended on the training …
Sorting of Single Biomolecules based on Fourier Polar Representation of Surface Enhanced Raman Spectra
2016
AbstractSurface enhanced Raman scattering (SERS) spectroscopy becomes increasingly used in biosensors for its capacity to detect and identify single molecules. In practice, a large number of SERS spectra are acquired and reliable ranking methods are thus essential for analysing all these data. Supervised classification strategies, which are the most effective methods, are usually applied but they require pre-determined models or classes. In this work, we propose to sort SERS spectra in unknown groups with an alternative strategy called Fourier polar representation. This non-fitting method based on simple Fourier sine and cosine transforms produces a fast and graphical representation for sor…
A Method of Three-Dimensional Visualization of Molecular Processes of Apoptosis
2014
Apoptosis or programmed cell death plays an important role in many physiological states and diseases. Detection of apoptotic cells, tracing the development of apoptosis, drug development and regulation of apoptosis are an important parts of basic research in medicine. A large number of models have been developed that are based on the differential equations of the chemical kinetics, and can be expressed in a uniform notation using some XML-based languages, such as SBML and CellML. We describe the CellML and the simulation environment OpenCell herein. These tools can display models schematically and output results in the form of graphs showing time dependencies of component concentrations. Ho…
Improving light propagation Monte Carlo simulations with accurate 3D modeling of skin tissue
2008
In this paper, we present a 3D light propagation model to simulate multispectral reflectance images of large skin surface areas. In particular, we aim to simulate more accurately the effects of various physiological properties of the skin in the case of subcutaneous vein imaging compared to existing models. Our method combines a Monte Carlo light propagation model, a realistic three-dimensional model of the skin using parametric surfaces and a vision system for data acquisition. We describe our model in detail, present results from the Monte Carlo modeling and compare our results with those obtained with a well established Monte Carlo model and with real skin reflectance images.
Are simple striate cells analysers of visual signals both in spatial position as well as in spatial frequency?
1984
According to a modern view, simple cells of the cat striate cortex are considered to operate as apart of Fourier analysis system thus leading to the idea that the operational mechanism of the visual cortex is concerned with the analysis of spatial frequencies. Nevertheless if simple cells are really concerned only with the analysis of spatial frequencies there should exist a strict relationship between their spatial frequency selectivity and the spatial organization of their receptive fields. This is because it is the spatial organization of the spatial frequency detector i.e. the cell's receptive field that determines the cell's spatial frequency selectivity. Since the quantitative analysi…
Burst analysis tool for developing neuronal networks exhibiting highly varying action potential dynamics
2012
In this paper we propose a firing statistics based neuronal network burst detection algorithm for neuronal networks exhibiting highly variable action potential dynamics. Electrical activity of neuronal networks is generally analyzed by the occurrences of spikes and bursts both in time and space. Commonly accepted analysis tools employ burst detection algorithms based on predefined criteria. However, maturing neuronal networks, such as those originating from human embryonic stem cells (hESC), exhibit highly variable network structure and time-varying dynamics. To explore the developing burst/spike activities of such networks, we propose a burst detection algorithm which utilizes the firing s…
Quantification and automatized adaptive detection of in vivo and in vitro neuronal bursts based on signal complexity.
2015
In this paper, we propose employing entropy values to quantify action potential bursts in electrophysiological measurements from the brain and neuronal cultures. Conventionally in the electrophysiological signal analysis, bursts are quantified by means of conventional measures such as their durations, and number of spikes in bursts. Here our main aim is to device metrics for burst quantification to provide for enhanced burst characterization. Entropy is a widely employed measure to quantify regularity/complexity of time series. Specifically, we investigate the applicability and differences of spectral entropy and sample entropy in the quantification of bursts in in vivo rat hippocampal meas…
Protein data condensation for effective quaternary structure classification
2007
Many proteins are composed of two or more subunits, each associated with different polypeptide chains. The number and the arrangement of subunits forming a protein are referred to as quaternary structure. The quaternary structure of a protein is important, since it characterizes the biological function of the protein when it is involved in specific biological processes. Unfortunately, quaternary structures are not trivially deducible from protein amino acid sequences. In this work, we propose a protein quaternary structure classification method exploiting the functional domain composition of proteins. It is based on a nearest neighbor condensation technique in order to reduce both the porti…