Mass conserved elementary kinetics is sufficient for the existence of a non-equilibrium steady state concentration

Living systems are forced away from thermodynamic equilibrium by exchange of mass and energy with their environment. In order to model a biochemical reaction network in a non-equilibrium state one requires a mathematical formulation to mimic this forcing. We provide a general formulation to force an arbitrary large kinetic model in a manner that is still consistent with the existence of a non-equilibrium steady state. We can guarantee the existence of a non-equilibrium steady state assuming only two conditions; that every reaction is mass balanced and that continuous kinetic reaction rate laws never lead to a negative molecule concentration. These conditions can be verified in polynomial time and are flexible enough to permit one to force a system away from equilibrium. In an expository biochemical example we show how a reversible, mass balanced perpetual reaction, with thermodynamically infeasible kinetic parameters, can be used to perpetually force a kinetic model of anaerobic glycolysis in a manner consistent with the existence of a steady state. Easily testable existence conditions are foundational for efforts to reliably compute non-equilibrium steady states in genome-scale biochemical kinetic models.Comment: 11 pages, 2 figures (v2 is now placed in proper context of the excellent 1962 paper by James Wei entitled "Axiomatic treatment of chemical reaction systems". In addition, section 4, on "Utility of steady state existence theorem" has been expanded.

The Yale Lar TPC

In this paper we give a concise description of a liquid argon time projection chamber (LAr TPC) developed at Yale, and present results from its first calibration run with cosmic rays.Comment: 4 pages, 3 figures, NuInt07 Conference Proceeding

Interacting staggered domain wall fermions

The behavior of staggered domain wall fermions in the presence of gauge fields is presented. In particular, their response to gauge fields with nontrivial topology is discussed.Comment: Lattice2002(Chiral) proceedings, LaTeX, 3 pages 2 eps figure

MetaboTools: A comprehensive toolbox for analysis of genome-scale metabolic models

Metabolomic data sets provide a direct read-out of cellular phenotypes and are increasingly generated to study biological questions. Our previous work revealed the potential of analyzing extracellular metabolomic data in the context of the metabolic model using constraint-based modeling. Through this work, which consists of a protocol, a toolbox, and tutorials of two use cases, we make our methods available to the broader scientific community. The protocol describes, in a step-wise manner, the workflow of data integration and computational analysis. The MetaboTools comprise the Matlab code required to complete the workflow described in the protocol. Tutorials explain the computational steps for integration of two different data sets and demonstrate a comprehensive set of methods for the computational analysis of metabolic models and stratification thereof into different phenotypes. The presented workflow supports integrative analysis of multiple omics data sets. Importantly, all analysis tools can be applied to metabolic models without performing the entire workflow. Taken together, this protocol constitutes a comprehensive guide to the intra-model analysis of extracellular metabolomic data and a resource offering a broad set of computational analysis tools for a wide biomedical and non-biomedical research community

Conditions for duality between fluxes and concentrations in biochemical networks

Mathematical and computational modelling of biochemical networks is often done in terms of either the concentrations of molecular species or the fluxes of biochemical reactions. When is mathematical modelling from either perspective equivalent to the other? Mathematical duality translates concepts, theorems or mathematical structures into other concepts, theorems or structures, in a one-to-one manner. We present a novel stoichiometric condition that is necessary and sufficient for duality between unidirectional fluxes and concentrations. Our numerical experiments, with computational models derived from a range of genome-scale biochemical networks, suggest that this flux-concentration duality is a pervasive property of biochemical networks. We also provide a combinatorial characterisation that is sufficient to ensure flux-concentration duality. That is, for every two disjoint sets of molecular species, there is at least one reaction complex that involves species from only one of the two sets. When unidirectional fluxes and molecular species concentrations are dual vectors, this implies that the behaviour of the corresponding biochemical network can be described entirely in terms of either concentrations or unidirectional fluxes

Multiparticle States and the Hadron Spectrum on the Lattice

The Clebsch-Gordan decomposition is calculated for direct products of the irreducible representations of the cubic space group. These results are used to identify multiparticle states which appear in the hadron spectrum on the lattice. Consideration of the cubic space group indicates how combinations of both zero momentum and non-zero momentum multiparticle states contribute to the spectrum.Comment: v2) Little groups for lattice momenta corrected. Includes a more consistent labeling scheme. (13 pages

Pion Interactions in the X(3872)

We consider pion interactions in an effective field theory of the narrow resonance X(3872), assuming it is a weakly bound molecule of the charm mesons D^{0} \bar D^{*0} and D^{*0} \bar D^{0}. Since the hyperfine splitting of the D^{0} and D^{*0} is only 7 MeV greater than the neutral pion mass, pions can be produced near threshold and are non-relativistic. We show that pion exchange can be treated in perturbation theory and calculate the next-to-leading-order correction to the partial decay width \Gamma[X \to D^0 \bar D^{0} \pi^0].Comment: 26 pages, 11 figures, revtex4, to appear in Phys. Rev.