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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.

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