An improved multi-parametric programming algorithm for flux balance analysis of metabolic networks

Flux balance analysis has proven an effective tool for analyzing metabolic networks. In flux balance analysis, reaction rates and optimal pathways are ascertained by solving a linear program, in which the growth rate is maximized subject to mass-balance constraints. A variety of cell functions in response to environmental stimuli can be quantified using flux balance analysis by parameterizing the linear program with respect to extracellular conditions. However, for most large, genome-scale metabolic networks of practical interest, the resulting parametric problem has multiple and highly degenerate optimal solutions, which are computationally challenging to handle. An improved multi-parametric programming algorithm based on active-set methods is introduced in this paper to overcome these computational difficulties. Degeneracy and multiplicity are handled, respectively, by introducing generalized inverses and auxiliary objective functions into the formulation of the optimality conditions. These improvements are especially effective for metabolic networks because their stoichiometry matrices are generally sparse; thus, fast and efficient algorithms from sparse linear algebra can be leveraged to compute generalized inverses and null-space bases. We illustrate the application of our algorithm to flux balance analysis of metabolic networks by studying a reduced metabolic model of Corynebacterium glutamicum and a genome-scale model of Escherichia coli. We then demonstrate how the critical regions resulting from these studies can be associated with optimal metabolic modes and discuss the physical relevance of optimal pathways arising from various auxiliary objective functions. Achieving more than five-fold improvement in computational speed over existing multi-parametric programming tools, the proposed algorithm proves promising in handling genome-scale metabolic models.Comment: Accepted in J. Optim. Theory Appl. First draft was submitted on August 4th, 201

Sustainable diets in the UK—developing a systematic framework to assess the environmental Impact, cost and nutritional quality of household food purchases

Sustainable diets should not only respect the environment but also be healthy and affordable. However, there has been little work to assess whether real diets can encompass all three aspects. The aim of this study was to develop a framework to quantify actual diet records for health, affordability and environmental sustainability and apply this to UK food purchase survey data. We applied a Life Cycle Assessment (LCA) approach to detailed food composition data where purchased food items were disaggregated into their components with traceable environmental impact data. This novel approach is an improvement to earlier studies in which sustainability assessments were based on a limited number of “food groups”, with a potentially high variation of actual food items within each group. Living Costs and Food Survey data for 2012, 2013 and 2014 were mapped into published figures for greenhouse gas emissions (GHGE, taking into account processing, transport and cooking) and land use, a diet quality index (DQI) based on dietary guidelines and food cost, all standardised per household member. Households were classified as having a ‘more sustainable’ diet based on GHGE, cost and land use being less than the median and DQI being higher than the median. Only 16.6% of households could be described as more sustainable; this rose to 22% for those in the lowest income quintile. Increasing the DQI criteria to >80% resulted in only 100 households being selected, representing 0.8% of the sample. The framework enabled identification of more sustainable households, providing evidence of how we can move toward better diets in terms of the environment, health, and costs

Development of Improved Rhenium Coatings for Fluorine Engine Thrust Chambers

Coating trials were undertaken to evaluate the application of rhenium to carbon-carbon composite sheet by plasma spraying. Optimum spray parameters and coating thickness were identified for production of coatings free from continuous defects and with adequate adherence to the substrate. A tungsten underlayer was not beneficial and possibly detracted from coating integrity. Stress calculations indicated that the proposed operating cycle of the rocket engine would not cause spalling of the rhenium coating. Calculations indicated that permeation of gases through the coating would not be significant during the expected life of the thrust chamber. The feasibility of applying rhenium coatings by laser melting was also studied. Poor wetting of the composite surface by the liquid rhenium precluded production of uniform coatings. Borate/carborate fluxes did not improve wetting characteristics

Casimir Friction Force Between Polarizable Media

This work is a continuation of our recent series of papers on Casimir friction, for a pair of particles of low relative particle velocity. Each particle is modeled as a simple harmonic oscillator. Our basic method, as before, is the use of quantum mechanical statistical mechanics, involving the Kubo formula, at finite temperature. In this work we begin by analyzing the Casimir friction between two particles polarizable in all spatial directions, this being a generalization of our study in EPL 91, 60003 (2010), which was restricted to a pair of particles with longitudinal polarization only. For simplicity the particles are taken to interact via the electrostatic dipole-dipole interaction. Thereafter, we consider the Casimir friction between one particle and a dielectric half-space, and also the friction between two dielectric half-spaces. Finally, we consider general polarizabilities (beyond the simple one-oscillator form), and show how friction occurs at finite temperature when finite frequency regions of the imaginary parts of polarizabilities overlap.Comment: 13 pages latex, no figure

Optimal Computation of Avoided Words

The deviation of the observed frequency of a word $w$ from its expected frequency in a given sequence $x$ is used to determine whether or not the word is avoided. This concept is particularly useful in DNA linguistic analysis. The value of the standard deviation of $w$, denoted by $std(w)$, effectively characterises the extent of a word by its edge contrast in the context in which it occurs. A word $w$ of length $k>2$ is a $\rho$-avoided word in $x$ if $std(w) \leq \rho$, for a given threshold $\rho < 0$. Notice that such a word may be completely absent from $x$. Hence computing all such words na\"{\i}vely can be a very time-consuming procedure, in particular for large $k$. In this article, we propose an $O(n)$-time and $O(n)$-space algorithm to compute all $\rho$-avoided words of length $k$ in a given sequence $x$ of length $n$ over a fixed-sized alphabet. We also present a time-optimal $O(\sigma n)$-time and $O(\sigma n)$-space algorithm to compute all $\rho$-avoided words (of any length) in a sequence of length $n$ over an alphabet of size $\sigma$. Furthermore, we provide a tight asymptotic upper bound for the number of $\rho$-avoided words and the expected length of the longest one. We make available an open-source implementation of our algorithm. Experimental results, using both real and synthetic data, show the efficiency of our implementation

Green's Dyadic Approach of the Self-Stress on a Dielectric-Diamagnetic Cylinder with Non-Uniform Speed of Light

We present a Green's dyadic formulation to calculate the Casimir energy for a dielectric-diamagnetic cylinder with the speed of light differing on the inside and outside. Although the result is in general divergent, special cases are meaningful. It is pointed out how the self-stress on a purely dielectric cylinder vanishes through second order in the deviation of the permittivity from its vacuum value, in agreement with the result calculated from the sum of van der Waals forces.Comment: 8 pages, submitted to proceedings of QFEXT0

Tidally Triggered Star Formation in Close Pairs of Galaxies: Major and Minor Interactions

We study star formation in a sample of 345 galaxies in 167 pairs and compact groups drawn from the original CfA2 Redshift Survey and from a follow-up search for companions. We construct our sample with attention to including pairs with luminosity contrast |\Delta m_R| >= 2. These 57 galaxies with |\Delta m_R| >= 2 provide a set of nearby representative cases of minor interactions, a central feature of the hierarchical galaxy formation model. Here we report the redshifts and positions of the 345 galaxies in our sample, and of 136 galaxies in apparent pairs that are superpositions. In the pairs sample as a whole, there are strong correlations between the equivalent width of the H\alpha emission line and the projected spatial and the line-of-sight velocity separation of the pair. For pairs of small luminosity contrast, |\Delta m_R| < 2, the member galaxies show a correlation between the equivalent width of H\alpha and the projected spatial separation of the pair. However, for pairs with large luminosity contrast, |\Delta m_R| >= 2, we detect no correlation between the equivalent width of H\alpha and the projected spatial separation. The relative luminosity of the companion galaxy is more important in a gravitational tidal interaction than the intrinsic luminosity of the galaxy. Central star formation across the entire pairs sample depends strongly on the luminosity ratio, |\Delta m_R|, a reasonable proxy for the mass ratio of the pair; pairs composed of similarly luminous galaxies produce the strongest bursts of star formation. Pairs with |\Delta m_R| >= 2 rarely have EW(H\alpha) >~ 70 Ang.Comment: Minor revisions following journal proof

3-dimensional Rules for Finite-Temperature Loops

We present simple diagrammatic rules to write down Euclidean n-point functions at finite temperature directly in terms of 3-dimensional momentum integrals, without ever performing a single Matsubara sum. The rules can be understood as describing the interaction of the external particles with those of the thermal bath.Comment: 12 pages, 4 figures, to appear in Physics Letters