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Drinking Water Distribution Systems (DWDSs) play a key role in sustainable development of modern society. They are classified as critical infrastructure systems. This imposes a large set of highly demanding requirements on the DWDS operation and requires dedicated algorithms for on-line monitoring and control to tackle related problems. Requirements on DWDS availability restrict the usability of the real plant in the design phase. Thus, a proper model is crucial. Within this paper a DWDS multi-species...
In this paper we present the extension of the kinetic logic proposed by René Thomas for analysis of genetic regulatory gene networks. We consider the case with a Gaussian noise added to the regulation function and propose a method of analyzing the resulting model with a discrete time Markov model.
The HP model is one of the most popular discretized models for attacking the protein folding problem,
i.e., for the computational prediction of the tertiary structure of a protein from its amino acid
sequence. It is based on the assumption that interactions between hydrophobic amino acids are the main
force in the folding process. Therefore, it distinguishes between polar and hydrophobic amino acids only and
tries to embed the amino acid sequence into a two- or three-dimensional grid lattice...
We analyze and suggest improvements to a recently developed approximate continuum-electrostatic model for proteins. The model, called BIBEE/I (boundary-integral based electrostatics estimation with interpolation), was able to estimate electrostatic solvation free energies to within a mean unsigned error of 4% on a test set of more than 600 proteins¶a significant improvement over previous BIBEE models. In this work, we tested the BIBEE/I model for its capability to predict residue-by-residue interactions...
The following is an expository article meant to give a simplified introduction to applications of topology to DNA.
The problem of assessing the reliability of clusters patients identified by clustering algorithms is crucial to estimate
the significance of subclasses of diseases detectable at bio-molecular level, and more in general to support bio-medical discovery
of patterns in gene expression data.
In this paper we present an experimental analysis of the reliability of clusters discovered in lung tumor patients
using DNA microarray data.
In particular we investigate if subclasses of lung adenocarcinoma...
The paper is devoted to the method of computer simulation of protein interactions taking
part in photosynthetic electron transport reactions. Using this method we have studied
kinetic characteristics of protein-protein complex formation for four pairs of proteins
involved in photosynthesis at a variety of ionic strength values. Computer simulations
describe non-monotonic dependences of complex formation rates on the ionic strength as the
result of...
We analyze three simple genetic circuits which involve transcriptional regulation and feedback: the autorepressor, the switch and the repressilator, that consist of one, two and three genes, respectively. Such systems are commonly simulated using rate equations, that account for the concentrations of the mRNAs and proteins produced by these genes. Rate equations are suitable when the concentrations of the relevant molecules in a cell are large and fluctuations are negligible. However, when some...
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