Excellence in Research and Innovation for Humanity

International Science Index

Commenced in January 1999 Frequency: Monthly Edition: International Paper Count: 6

Biological, Biomolecular, Agricultural, Food and Biotechnological Engineering

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  • 6
    Stochastic Simulation of Reaction-Diffusion Systems

    Reactiondiffusion systems are mathematical models that describe how the concentration of one or more substances distributed in space changes under the influence of local chemical reactions in which the substances are converted into each other, and diffusion which causes the substances to spread out in space. The classical representation of a reaction-diffusion system is given by semi-linear parabolic partial differential equations, whose general form is ÔêétX(x, t) = DΔX(x, t), where X(x, t) is the state vector, D is the matrix of the diffusion coefficients and Δ is the Laplace operator. If the solute move in an homogeneous system in thermal equilibrium, the diffusion coefficients are constants that do not depend on the local concentration of solvent and of solutes and on local temperature of the medium. In this paper a new stochastic reaction-diffusion model in which the diffusion coefficients are function of the local concentration, viscosity and frictional forces of solvent and solute is presented. Such a model provides a more realistic description of the molecular kinetics in non-homogenoeus and highly structured media as the intra- and inter-cellular spaces. The movement of a molecule A from a region i to a region j of the space is described as a first order reaction Ai k- → Aj , where the rate constant k depends on the diffusion coefficient. Representing the diffusional motion as a chemical reaction allows to assimilate a reaction-diffusion system to a pure reaction system and to simulate it with Gillespie-inspired stochastic simulation algorithms. The stochastic time evolution of the system is given by the occurrence of diffusion events and chemical reaction events. At each time step an event (reaction or diffusion) is selected from a probability distribution of waiting times determined by the specific speed of reaction and diffusion events. Redi is the software tool, developed to implement the model of reaction-diffusion kinetics and dynamics. It is a free software, that can be downloaded from http://www.cosbi.eu. To demonstrate the validity of the new reaction-diffusion model, the simulation results of the chaperone-assisted protein folding in cytoplasm obtained with Redi are reported. This case study is redrawing the attention of the scientific community due to current interests on protein aggregation as a potential cause for neurodegenerative diseases.

    Decision Support System for Farm Management
    The emergence of information technology has resulted in an ever-increasing demand to use computers for the efficient management and dissemination of information. Keeping in view the strong need of farmers to collect important and updated information for interactive, flexible and quick decision-making, a model of Decision Support System for Farm Management is developed. The paper discusses the use of Internet technology for the farmers to take decisions. A model is developed for the farmers to access online interactive and flexible information for their farm management. The workflow of the model is presented highlighting the information transfer between different modules.
    Predicting Protein Function using Decision Tree
    The drug discovery process starts with protein identification because proteins are responsible for many functions required for maintenance of life. Protein identification further needs determination of protein function. Proposed method develops a classifier for human protein function prediction. The model uses decision tree for classification process. The protein function is predicted on the basis of matched sequence derived features per each protein function. The research work includes the development of a tool which determines sequence derived features by analyzing different parameters. The other sequence derived features are determined using various web based tools.
    Clustering Protein Sequences with Tailored General Regression Model Technique
    Cluster analysis divides data into groups that are meaningful, useful, or both. Analysis of biological data is creating a new generation of epidemiologic, prognostic, diagnostic and treatment modalities. Clustering of protein sequences is one of the current research topics in the field of computer science. Linear relation is valuable in rule discovery for a given data, such as if value X goes up 1, value Y will go down 3", etc. The classical linear regression models the linear relation of two sequences perfectly. However, if we need to cluster a large repository of protein sequences into groups where sequences have strong linear relationship with each other, it is prohibitively expensive to compare sequences one by one. In this paper, we propose a new technique named General Regression Model Technique Clustering Algorithm (GRMTCA) to benignly handle the problem of linear sequences clustering. GRMT gives a measure, GR*, to tell the degree of linearity of multiple sequences without having to compare each pair of them.
    A New Automatic System of Cell Colony Counting
    The counting process of cell colonies is always a long and laborious process that is dependent on the judgment and ability of the operator. The judgment of the operator in counting can vary in relation to fatigue. Moreover, since this activity is time consuming it can limit the usable number of dishes for each experiment. For these purposes, it is necessary that an automatic system of cell colony counting is used. This article introduces a new automatic system of counting based on the elaboration of the digital images of cellular colonies grown on petri dishes. This system is mainly based on the algorithms of region-growing for the recognition of the regions of interest (ROI) in the image and a Sanger neural net for the characterization of such regions. The better final classification is supplied from a Feed-Forward Neural Net (FF-NN) and confronted with the K-Nearest Neighbour (K-NN) and a Linear Discriminative Function (LDF). The preliminary results are shown.
    Inferring the Dynamics of “Hidden“ Neurons from Electrophysiological Recordings
    Statistical analysis of electrophysiological recordings obtained under, e.g. tactile, stimulation frequently suggests participation in the network dynamics of experimentally unobserved “hidden" neurons. Such interneurons making synapses to experimentally recorded neurons may strongly alter their dynamical responses to the stimuli. We propose a mathematical method that formalizes this possibility and provides an algorithm for inferring on the presence and dynamics of hidden neurons based on fitting of the experimental data to spike trains generated by the network model. The model makes use of Integrate and Fire neurons “chemically" coupled through exponentially decaying synaptic currents. We test the method on simulated data and also provide an example of its application to the experimental recording from the Dorsal Column Nuclei neurons of the rat under tactile stimulation of a hind limb.