http://www.hindawi.com The latest articles from Hindawi Publishing Corporation © 2013 , Hindawi Publishing Corporation . All rights reserved. Wed, 08 May 2013 14:51:15 +0000 http://www.hindawi.com/journals/cbj/2013/263973/ Biochemical networks are not only complex but also extremely large. The dynamic biological model of great complexity resulting in a large number of parameters is a main difficulty for optimization and control processes. In practice, it is highly desirable to further simplify the structure of biological models for the sake of reducing computational cost or simplification for the task of system analysis. This paper considers the S-system model used for describing the response of biochemical networks. By introducing the technique of singular value decomposition (SVD), we are able to identify the major state variables and parameters and eliminate unimportant metabolites and the corresponding signal transduction pathways. The model reduction by multiobjective analysis integrates the criteria of reactive weight, sensitivity, and flux analyses to obtain a reduced model in a systematic way. The resultant model is closed to the original model in performance but with a simpler structure. Representative numerical examples are illustrated to prove feasibility of the proposed method. Yen-Chang Liu, Chun-Liang Lin, and Chia-Hua Chuang Copyright © 2013 Yen-Chang Liu et al. All rights reserved. Thu, 11 Apr 2013 16:49:58 +0000 http://www.hindawi.com/journals/cbj/2013/562767/ Sparse-grid interpolation provides good approximations to smooth functions in high dimensions based on relatively few function evaluations, but in standard form it is expressed in Lagrange polynomials. Here, we give a block-diagonal factorization of the basis-change matrix to give an efficient conversion of a sparse-grid interpolant to a tensored orthogonal polynomial (or gPC) representation. We describe how to use this representation to give an efficient method for estimating Sobol' sensitivity coefficients and apply this method to analyze and efficiently approximate a complex model of T-cell signaling events. Gregery T. Buzzard Copyright © 2013 Gregery T. Buzzard. All rights reserved. Wed, 03 Apr 2013 13:33:01 +0000 http://www.hindawi.com/journals/cbj/2013/938169/ Cystic fibrosis is one of the most common inherited diseases and is caused by a mutation in a membrane protein, the cystic fibrosis transmembrane conductance regulator (CFTR). This protein serves as a chloride channel and regulates the viscosity of mucus lining the ducts of a number of organs. Although much has been learned about the consequences of mutations on the energy landscape and the resulting disrupted folding pathway of CFTR, a level of understanding needed to correct the misfolding has not been achieved. The most common mutations of CFTR are located in one of two nucleotide binding domains, namely, the nucleotide binding domain 1 (NBD1). We model NBD1 using a nested graph model. The vertices in the lowest layer each represent an atom in the structure of an amino acid residue, while the vertices in the mid layer each represent the residue. The vertices in the top layer each represent a subdomain of the nucleotide binding domain. We use this model to quantify the effects of a single point mutation on the protein domain. We compare the wildtype structure with eight of the most common mutations. The graph-theoretic model provides insight into how a single point mutation can have such profound structural consequences. Debra J. Knisley, Jeff R. Knisley, and Andrew Cade Herron Copyright © 2013 Debra J. Knisley et al. All rights reserved. Thu, 10 Jan 2013 17:06:45 +0000 http://www.hindawi.com/journals/cbj/2013/807592/ Density functional theory has been used to calculate harmonic normal mode vibrational frequencies for unlabeled and isotope-labeled ubisemiquinones in both the gas phase and in several solvents. It is shown that four methoxy group conformations are likely to be present in solution at room temperature. Boltzmann weighted infrared and Raman spectra for the four conformers were calculated, and composite spectra that are the sum of the Boltzmann weighted spectra were produced. These composite spectra were compared to experimental FTIR and resonance Raman spectra, and it is shown that the calculated band frequencies, relative band intensities, and and isotope-induced band shifts are in excellent agreement with experiment. The calculations show that the C=O and C=C modes of ubisemiquinone strongly mix with methoxy methyl CH bending vibrations, and that the degree of mixing is altered upon isotope labeling, resulting in complicated changes in mode frequencies, intensities, and composition upon isotope labeling. Upon consideration of the calculated potential energy distributions of the normal modes of ubisemiquinone, and how they change upon isotope labeling, an explanation of some puzzling features in previously published Raman spectra is provided. Hari P. Lamichhane and Gary Hastings Copyright © 2013 Hari P. Lamichhane and Gary Hastings. All rights reserved.