An updated genome-scale reconstruction of the metabolic network in Escherichia coli K-12 MG1655 is presented. This updated metabolic reconstruction includes: (1) an alignment with the latest genome annotation and the metabolic content of EcoCyc leading to the inclusion of the activities of 1260 ORFs, (2) characterization and quantification of the biomass components and maintenance requirements associated with growth of E. coli and (3) thermodynamic information for the included chemical reactions. The conversion of this metabolic network reconstruction into an in silico model is detailed. A new step in the metabolic reconstruction process, termed thermodynamic consistency analysis, is introduced, in which reactions were checked for consistency with thermodynamic reversibility estimates. Applications demonstrating the capabilities of the genome-scale metabolic model to predict high-throughput experimental growth and gene deletion phenotypic screens are presented. The increased scope and computational capability using this new reconstruction is expected to broaden the spectrum of both basic biology and applied systems biology studies of E. coli metabolism.

We analyzed the glassy-state structural relaxation of polymers near surfaces and interfaces by monitoring fluorescence in multilayer films. Relative to that of bulk, the rate of structural relaxation of poly(methyl methacrylate) is reduced by a factor of 2 at a free surface and by a factor of 15 at a silica substrate interface; the latter exhibits a nearly complete arresting of relaxation. The distribution in relaxation rates extends more than 100 nanometers into the film interior, a distance greater than that over which surfaces and interfaces affect the glass transition temperature.

Owing to the improvement of properties including conductivity, toughness and permeability, polymer nanocomposites are slated for applications ranging from membranes to fuel cells. The enhancement of polymer properties by the addition of inorganic nanoparticles is a complex function of interfacial interactions, interfacial area and the distribution of inter-nanofiller distances. The latter two factors depend on nanofiller dispersion, making it difficult to develop a fundamental understanding of their effects on nanocomposite properties. Here, we design model poly(methyl methacrylate)-silica and poly(2-vinyl pyridine)-silica nanocomposites consisting of polymer films confined between silica slides. We compare the dependence of the glass-transition temperature (Tg) and physical ageing on the interlayer distance in model nanocomposites with the dependence of silica nanoparticle content in real nanocomposites. We show that model nanocomposites provide a simple way to gain insight into the effect of interparticle spacing on Tg and to predict the approximate ageing response of real nanocomposites.

A new form of metabolic flux analysis (MFA) called thermodynamics-based metabolic flux analysis (TMFA) is introduced with the capability of generating thermodynamically feasible flux and metabolite activity profiles on a genome scale. TMFA involves the use of a set of linear thermodynamic constraints in addition to the mass balance constraints typically used in MFA. TMFA produces flux distributions that do not contain any thermodynamically infeasible reactions or pathways, and it provides information about the free energy change of reactions and the range of metabolite activities in addition to reaction fluxes. TMFA is applied to study the thermodynamically feasible ranges for the fluxes and the Gibbs free energy change, Delta(r)G', of the reactions and the activities of the metabolites in the genome-scale metabolic model of Escherichia coli developed by Palsson and co-workers. In the TMFA of the genome scale model, the metabolite activities and reaction Delta(r)G' are able to achieve a wide range of values at optimal growth. The reaction dihydroorotase is identified as a possible thermodynamic bottleneck in E. coli metabolism with a Delta(r)G' constrained close to zero while numerous reactions are identified throughout metabolism for which Delta(r)G' is always highly negative regardless of metabolite concentrations. As it has been proposed previously, these reactions with exclusively negative Delta(r)G' might be candidates for cell regulation, and we find that a significant number of these reactions appear to be the first steps in the linear portion of numerous biosynthesis pathways. The thermodynamically feasible ranges for the concentration ratios ATP/ADP, NAD(P)/NAD(P)H, and H(extracellular)(+)/H(intracellular)(+) are also determined and found to encompass the values observed experimentally in every case. Further, we find that the NAD/NADH and NADP/NADPH ratios maintained in the cell are close to the minimum feasible ratio and maximum feasible ratio, respectively.

A new, to our knowledge, group contribution method based on the group contribution method of Mavrovouniotis is introduced for estimating the standard Gibbs free energy of formation (Delta(f)G'(o)) and reaction (Delta(r)G'(o)) in biochemical systems. Gibbs free energy contribution values were estimated for 74 distinct molecular substructures and 11 interaction factors using multiple linear regression against a training set of 645 reactions and 224 compounds. The standard error for the fitted values was 1.90 kcal/mol. Cross-validation analysis was utilized to determine the accuracy of the methodology in estimating Delta(r)G'(o) and Delta(f)G'(o) for reactions and compounds not included in the training set, and based on the results of the cross-validation, the standard error involved in these estimations is 2.22 kcal/mol. This group contribution method is demonstrated to be capable of estimating Delta(r)G'(o) and Delta(f)G'(o) for the majority of the biochemical compounds and reactions found in the iJR904 and iAF1260 genome-scale metabolic models of Escherichia coli and in the Kyoto Encyclopedia of Genes and Genomes and University of Minnesota Biocatalysis and Biodegradation Database. A web-based implementation of this new group contribution method is available free at http://sparta.chem-eng.northwestern.edu/cgi-bin/GCM/WebGCM.cgi.