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A biochemical multi-species quality model of a drinking water distribution system for simulation and design

Krzysztof Arminski, Tomasz Zubowicz, Mietek A. Brdys (2013)

International Journal of Applied Mathematics and Computer Science

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...

A model for gene activation.

Oppenheimer, Seth F., Fan, Ruping, Pruett, Stephan (2009)

Electronic Journal of Differential Equations (EJDE) [electronic only]

A stochastic extension of R. Thomas regulatory network modelling

Bartek Wilczyński (2008)

Banach Center Publications

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.

A weighted HP model for protein folding with diagonal contacts

Hans-Joachim Böckenhauer, Dirk Bongartz (2007)

RAIRO - Theoretical Informatics and Applications

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...

Analysis of fast boundary-integral approximations for modeling electrostatic contributions of molecular binding

Amelia B. Kreienkamp, Lucy Y. Liu, Mona S. Minkara, Matthew G. Knepley, Jaydeep P. Bardhan, Mala L. Radhakrishnan (2013)

Molecular Based Mathematical Biology

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...

Applications of topology to DNA

Isabel Darcy, De Sumners (1998)

Banach Center Publications

The following is an expository article meant to give a simplified introduction to applications of topology to DNA.

Characterization of lung tumor subtypes through gene expression cluster validity assessment

Giorgio Valentini, Francesca Ruffino (2006)

RAIRO - Theoretical Informatics and Applications

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 can be detected with high reliability at bio-molecular level. To this end we apply cluster validity measures based on random projections recently proposed by Bertoni and coworkers. The results show that at least two subclasses of lung adenocarcinoma can be detected with relatively high reliability, confirming and extending previous findings reported in the literature.

Computer Simulation of Protein-Protein Association in Photosynthesis

I.B. Kovalenko, A.M. Abaturova, A.N. Diakonova, O.S. Knyazeva, D.M. Ustinin, S.S. Khruschev, G.Yu. Riznichenko, A.B. Rubin (2011)

Mathematical Modelling of Natural Phenomena

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...

Deterministic and stochastic simulations of simple genetic circuits

Ofer Biham, Nathalie Q. Balaban, Adiel Loinger, Azi Lipshtat, Hagai B. Perets (2008)

Banach Center Publications

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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