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Robert A Alberty – One of the best experts on this subject based on the ideXlab platform.

  • thermodynamics of Biochemical reactions
    , 2003
    Co-Authors: Robert A Alberty
    Abstract:

    Preface. Chapter 1. Introduction to Apparent Equilibrium Constants. Chapter 2. Structure of Thermodynamics. Chapter 3. Chemical Equilibrium in Aqueous Solutions. Chapter 4. Thermodynamics of Biochemical Reactions at Specified pH. Chapter 5. Matrices in Chemical and Biochemical Thermodynamics. Chapter 6. Systems of Biochemical Reactions. Chapter 7. Thermodynamics of Binding of the Ligands by Proteins. Chapter 8. Phase Equilibrium in Aqueous Systems. Chapter 9. Oxidation-Reduction Reactions. Chapter 10. Calorimetry of Biochemical Reactions. Chapter 11. Use of Semigrand Partition Functions. Glossary. References.

  • Biochemical thermodynamics.
    Biochimica et biophysica acta, 1994
    Co-Authors: Robert A Alberty
    Abstract:

    Biochemists need two types of reaction equations, chemical equations in terms of species and Biochemical equations in terms of reactants at specified pH and concentrations of free metal ions that are bound by reactant species. Both types of reaction equations have corresponding equilibrium constants, K for chemical reactions and K’ for Biochemical reactions. When the pH is specified you enter a whole new world of thermodynamics. There are new thermodynamic properties, new names (transformed thermodynamic properties), and new values, which are quite different, especially for the standard transformed Gibbs energy. This raises nomenclature problems because it is important to be able to distinguish between chemical equations and Biochemical equations at a glance. It is also important to distinguish between the standard thermodynamic properties calculated from K and its temperature coefficient and the standard transformed thermodynamic properties calculated from K’ and its temperature coefficient.

  • Equilibrium compositions of solutions of Biochemical species and heats of Biochemical reactions.
    Proceedings of the National Academy of Sciences of the United States of America, 1991
    Co-Authors: Robert A Alberty
    Abstract:

    Equilibrium compositions of solutions of Biochemical species can be calculated by use of general equilibrium computer programs that minimize the Gibbs energy. The standard Gibbs energies of formation and standard enthalpies of formation of the species in a Biochemical system can be calculated by Gaussian reduction of the augmented transpose of the stoichiometric number matrix for the system. The conservation matrix, which is also needed for the calculation of the equilibrium composition, can be obtained in two ways. The hydrolysis of adenosine 5′-triphosphate in solutions containing magnesium ions can be treated by considering 17 species. The equilibrium composition and enthalpy are calculated before and after adding ATPase. This makes it possible to calculate DeltapH, DeltapMg, and the heat of reaction when ATPase is added.

Bernhard O. Palsson – One of the best experts on this subject based on the ideXlab platform.

  • The underlying pathway structure of Biochemical reaction networks
    Proceedings of the National Academy of Sciences of the United States of America, 1998
    Co-Authors: Christophe H. Schilling, Bernhard O. Palsson
    Abstract:

    Bioinformatics is yielding extensive, and in some cases complete, genetic and Biochemical information about individual cell types and cellular processes, providing the composition of living cells and the molecular structure of its components. These components together perform integrated cellular functions that now need to be analyzed. In particular, the functional definition of Biochemical pathways and their role in the context of the whole cell is lacking. In this study, we show how the mass balance constraints that govern the function of Biochemical reaction networks lead to the translation of this problem into the realm of linear algebra. The functional capabilities of Biochemical reaction networks, and thus the choices that cells can make, are reflected in the null space of their stoichiometric matrix. The null space is spanned by a finite number of basis vectors. We present an algorithm for the synthesis of a set of basis vectors for spanning the null space of the stoichiometric matrix, in which these basis vectors represent the underlying Biochemical pathways that are fundamental to the corresponding Biochemical reaction network. In other words, all possible flux distributions achievable by a defined set of Biochemical reactions are represented by a linear combination of these basis pathways. These basis pathways thus represent the underlying pathway structure of the defined Biochemical reaction network. This development is significant from a fundamental and conceptual standpoint because it yields a holistic definition of Biochemical pathways in contrast to definitions that have arisen from the historical development of our knowledge about Biochemical processes. Additionally, this new conceptual framework will be important in defining, characterizing, and studying Biochemical pathways from the rapidly growing information on cellular function.

  • Biochemical production capabilities of escherichia coli
    Biotechnology and Bioengineering, 1993
    Co-Authors: Amit Varma, Brian W. Boesch, Bernhard O. Palsson
    Abstract:

    Microbial metabolism provides at mechanism for the conversion of substrates into useful Biochemicals. Utilization of microbes in industrial processes requires a modification of their natural metabolism in order to increase the efficiency of the desired conversion. Redirection of metabolic fluxes forms the basis of the newly defined field of metabolic engineering. In this study we use a flux balance based approach to study the biosynthesis of the 20 amino acids and 4 nucleotides as Biochemical products. These amino acids and nucleotides are primary products of biosynthesis as well as important industrial products and precursors for the production of other Biochemicals. The biosynthetic reactions of the bacterium Escherichia coli have been formulated into a metabolic network, and growth has been defined as a balanced drain on the metabolite pools corresponding to the cellular composition. Theoretical limits on the conversion of glucose, glycerol, and acetate substrates to biomass as well as the Biochemical products have been computed. The substrate that results in the maximal carbon conversion to a particular product is identified. Criteria have been developed to identify metabolic constraints in the optimal solutions. The constraints of stoichiometry, energy, and redox have been determined in the conversions of glucose, glycerol, and acetate substrates into the Biochemicals. Flux distributions corresponding to the maximal production of the Biochemicals are presented. The goals of metabolic engineering are the optimal redirection of fluxes from generating biomass toward producing the desired Biochemical. Optimal biomass generation is shown to decrease in a piecewise linear manner with increasing product formation. In some cases, synergy is observed between Biochemical production and growth, leading to an increased overall carbon conversion. Balanced growth and product formation are important in a bioprocess, particularly for nonsecreted products.

Jin-soo Hwang – One of the best experts on this subject based on the ideXlab platform.

  • furfural hemicellulose xylosederived Biochemical
    Biofuels Bioproducts and Biorefining, 2008
    Co-Authors: Ajit S. Mamman, Jong-min Lee, Yeong-cheol Kim, In Taek Hwang, No-joong Park, Young Kyu Hwang, Jong-san Chang, Jin-soo Hwang
    Abstract:

    Hemicellulose, the second, most common polysaccharide in nature constitutes approximately 20—35% of lignocellulosic biomass. Effective utilization of biomass, hitherto underutilized, is gaining tremendous importance for the production of energy, fuels, and chemicals. Amongst the vast array of chemicals derived from lignocellulosics, furfural is the key chemical that finds wide applications in oil refining, plastics, pharmaceutical and agrochemical industries. There is no synthetic route for the production of furfural. A few conventional technologies currently in practice for its separation and subsequent isolation are appropriately reviewed. Major disadvantages associated with processes currently used for the production of furfural based on acid-catalyzed hydrhydrolysis have been discussed. A need to develop a process which is devoid of all the shortcomings associated with conventional process is emphasized. Several important aspects of chemistry underlying the acid hydrolysis of xylose are discussed. The importance of myriad pre-treatment steps involved to surmount the physical and chemical barriers and to liberate xylose from the confines of acid-resistant layer of lignin has been emphasized. New developments in the production of furfural from cyclodehydration of xylose using solid acid catalysts in the recent past have been reviewed appropriately in present communication. Finally, the production of furfural and furfuryl alcohol, their domestic market and export in China deserve some coverage and therefore have appropriately been discussed as well. © 2008 Society of Chemical Industry and John Wiley & Sons, Ltd

  • Furfural: Hemicellulose/xylosederived Biochemical
    Biofuels Bioproducts and Biorefining, 2008
    Co-Authors: Ajit S. Mamman, Jong-min Lee, Yeong-cheol Kim, In Taek Hwang, No-joong Park, Young Kyu Hwang, Jong-san Chang, Jin-soo Hwang
    Abstract:

    Hemicellulose, the second, most common polysaccharide in nature constitutes approximately 20—35% of lignocellulosic biomass. Effective utilization of biomass, hitherto underutilized, is gaining tremendous importance for the production of energy, fuels, and chemicals. Amongst the vast array of chemicals derived from lignocellulosics, furfural is the key chemical that finds wide applications in oil refining, plastics, pharmaceutical and agrochemical industries. There is no synthetic route for the production of furfural. A few conventional technologies currently in practice for its separation and subsequent isolation are appropriately reviewed. Major disadvantages associated with processes currently used for the production of furfural based on acid-catalyzed hydrhydrolysis have been discussed. A need to develop a process which is devoid of all the shortcomings associated with conventional process is emphasized. Several important aspects of chemistry underlying the acid hydrolysis of xylose are discussed. The importance of myriad pre-treatment steps involved to surmount the physical and chemical barriers and to liberate xylose from the confines of acid-resistant layer of lignin has been emphasized. New developments in the production of furfural from cyclodehydration of xylose using solid acid catalysts in the recent past have been reviewed appropriately in present communication. Finally, the production of furfural and furfuryl alcohol, their domestic market and export in China deserve some coverage and therefore have appropriately been discussed as well. © 2008 Society of Chemical Industry and John Wiley & Sons, Ltd

Timothy C. Elston – One of the best experts on this subject based on the ideXlab platform.

  • Biochemical Network Stochastic Simulator (BioNetS): software for stochastic modeling of Biochemical networks.
    BMC bioinformatics, 2004
    Co-Authors: David Adalsteinsson, David R. Mcmillen, Timothy C. Elston
    Abstract:

    Intrinsic fluctuations due to the stochastic nature of Biochemical reactions can have large effects on the response of Biochemical networks. This is particularly true for pathways that involve transcriptional regulation, where generally there are two copies of each gene and the number of messenger RNA (mRNA) molecules can be small. Therefore, there is a need for computational tools for developing and investigating stochastic models of Biochemical networks. We have developed the software package Biochemical Network Stochastic Simulator (BioNetS) for efficientlyand accurately simulating stochastic models of Biochemical networks. BioNetS has a graphical user interface that allows models to be entered in a straightforward manner, and allows the user to specify the type of random variable (discrete or continuous) for each chemical species in the network. The discrete variables are simulated using an efficient implementation of the Gillespie algorithm. For the continuous random variables, BioNetS constructs and numerically solvesthe appropriate chemical Langevin equations. The software package has been developed to scale efficiently with network size, thereby allowing large systems to be studied. BioNetS runs as a BioSpice agent and can be downloaded from http://www.biospice.org . BioNetS also can be run as a stand alone package. All the required files are accessible from http://x.amath.unc.edu/BioNetS . We have developed BioNetS to be a reliable tool for studying the stochastic dynamics of large Biochemical networks. Important features of BioNetS are its ability to handle hybrid models that consist of both continuous and discrete random variables and its ability to model cell growth and division. We have verified the accuracy and efficiency of the numerical methods by considering several test systems.

Richard John – One of the best experts on this subject based on the ideXlab platform.

  • Ferricyanide mediated Biochemical oxygen demand – development of a rapid Biochemical oxygen demand assay
    Analytica Chimica Acta, 2001
    Co-Authors: Kristy Nicole Morris, Kylie Patricia Catterall, Huijun Zhao, Neil Pasco, Richard John
    Abstract:

    Abstract The use of an artificial electron acceptor in microbial respiration was investigated with a view to developing a rapid assay for Biochemical oxygen demand (BOD). The use of ferricyanide resulted in a significant increase in the rate of the Biochemical reaction and allowed for biodegradative conversion efficiencies similar to the 5-day BOD assay to be achieved in 1 h. The extent and rate of the ferricyanide mediated microbial reaction was determined by monitoring the concentration of the microbially produced ferrocyanide during or after incubation of microorganisms in the presence of ferricyanide and organic substrate. Spectrophotometry, potentiometry and amperometry using microelectrodes were evaluated as detection methods, with the latter providing the most convenient, stable and reproducible results. Experimental parameters investigated included incubation time, incubation temperature, microbial concentration, ferricyanide concentration and substrate concentration. In all cases, the results obtained were analogous to that expected in conventional aerobic microbial oxidation of organic material, with the major difference being the considerable increase in rate. The microorganisms used in this study were Escherichia coli and Pseudomonas putida . Results showed that while E. coli could successfully catabolise a standard BOD solution containing glucose and glutamic acid, its use for other substrates was limited. Preliminary investigations into the use of P. putida , however, showed significantly improved performance and demonstrated the promise of this approach for rapid BOD determinations.