Modeling of DNAPL-Dissolution,Rate-Limited Sorption and Biodegradation Reactions in Groundwater Systems

This article presents an approach for modeling the dissolution process of single component dense non-aqueous phase liquids (DNAPL), such as tetrachloroethene and trichloroethene, in a biologically reactive porous medium. In the proposed approach, the overall transport processes are conceptualized as three distinct reactions. Firstly, the dissolution (or dissolving) process of a residual DNAPL source zone is conceptualized as a mass-transfer limited reaction. Secondly, the contaminants dissolved from the DNAPL source are allowed to partition between sediment and water phases through a rate-limited sorption reaction. Finally, the contaminants in the solid and liquid phases are allowed to degrade by a set of kinetic-limited biological reactions. Although all of these three reaction processes have been researched in the past, little progress has been made towards understanding the combined effects of these processes. This work provides a rigorous mathematical model for describing the coupled effects of these three fundamental reactive transport mechanisms. The model equations are then solved using the general-purpose reactive transport code RT3D (Clement, 1997).     

Modeling of a Field Experiment on Bioremediation of Chlorobenzenes in Groundwater

The aquifer below an abandoned chemical plant in Hamburg, Germany, is heavily contaminated with chlorinated aromatic compounds, mainly chlorobenzenes. Preliminary evaluations made evident that pump-and-treat remediation of the site would be inefficient due to adsorption of the contaminants and the possible presence of dense nonaqueous phase liquid (DNAPL) in the aquifer. Other preliminary studies indicated that benzenes with a low degree of chlorination, which account for the bulk of the contamination in the aquifer, were aerobically degradable. Thus, in situ bioremediation using dissolved oxygen as an oxidant was proposed as an alternative to pump-and-treat remediation.

To assess the feasibility of bioremediation at this site, a pilot study was conducted on a 55 m x 30 m test plot that was equipped with two injection wells, six extraction wells, and 18 observation wells. Water saturated with oxygen using pure oxygen gas was injected for a period of 433 days.

Application of the three-dimensional reactive transport model, Transport, Biochemistry, and Chemistry (TBC), allowed the distinction between transport and reactive processes and the evaluation of oxygen consuming processes. Preliminary mass balance considerations had indicated that a significant portion of the injected oxygen was used for oxidation of inorganic compounds instead of the contaminants. The model calculations allowed quantification of these effects. Simulation results suggested that in situ bioremediation occurred at the site, but with an unacceptably low efficiency. Only 2% of the injected oxygen was used for contaminant degradation, while 63% was consumed by inorganic reductants, presumably mainly pyrite. Approximately 32% of the injected oxygen was extracted by the extraction wells and approximately 3% remained in the aquifer after the pilot study was completed.     

Development of a Distributed Watershed Contaminant Transport,Transformation, and Fate (CTT&F) Sub-model

CTT&F is a physically based, spatially distributed watershed contaminant transport, transformation, and fate sub-model designed for use within existing hydrological modeling systems. To describe the fate of contaminants through landscape media as well as spatial variations of contaminant distributions, physical transport and transformation processes in CTT&F are simulated for each cell in the model and routed to the watershed outlet. CTT&F simulates contaminant erosion from soil and transport across the land surface by overland flow. The model also simulates contaminant erosion from stream bed sediment and transport through channels in addition to transport of contaminants inputs by overland flow. CTT&F can simulate solid (granular) contaminant transport and transformation, including partitioning between freely dissolved, dissolved organic carbon (DOC) bound, and particle-sorbed phases. To demonstrate model capabilities, CTT&F was coupled with an existing distributed hydrologic model and was tested and validated to simulate RDX and TNT transport using two experimental plots. These experiments examined dissolution of solid contaminants into the dissolved phase and their subsequent transport to the plot outlet. Model results were in close agreement with measured data. Such a model provides information for decision makers to make rational decisions relevant to the fate of toxic compounds.     

Non-standard numerical methods applied to subsurface biobarrier formation models in porous media

Biofilm forming microbes have complex effects on the flow properties of natural porous media. Subsurface biofilms have the potential for the formation of biobarriers to inhibit contaminant migration in groundwater. Another example of beneficial microbial effects is the biotransformation of organic contaminants to less harmful forms, thereby providing an in situ method for treatment of contaminated groundwater supplies. Mathematical models that describe contaminant transport with biodegradation involve a set of coupled convection-dispersion equations with non-linear reactions. The reactive solute transport equation is one for which numerical solution procedures continue to exhibit significant limitations for certain problems of groundwater hydrology interest. Accurate numerical simulations are crucial to the development of contaminant remediation strategies. A new numerical method is developed for simulation of reactive bacterial transport in porous media. The non-standard numerical approach is based on the ideas of the ‘exact’ time-stepping scheme. It leads to solutions free from the numerical instabilities that arise from incorrect modeling of derivatives and reaction terms. Applications to different biofilm models are examined and numerical results are presented to demonstrate the performance of the proposed new method.     

Kinetic modeling of enzyme-catalysed reactions with participation of activators applied to ATP hydrolysis by Mg2+- ATPase

Theoretical investigation of the model of reaction of ATP hydrolysis by "basal" Mg2+-ATPase has been carried out. It has been assumed that during the reaction each of three reacting substances (Mg2+, ATP, enzyme) can combine into complexes in couples with other participants of this process. Then the third component can associate with formed complexes producing the ternary complex of enzyme-activator-substrate. Such approach allowed to take into account all possible interactions in the chosen system, to investigate overall process in detail avoiding any simplifications and to find such peculiar properties of the process which will allow to understand the reaction mechanism and to explain observed experimental data. All possible pathways of the ATP hydrolysis process have been examined separately and as a whole. It is shown that if the reaction proceeds via two or three possible pathways then maximums are observed on plots of initial reaction rate on concentration ATP or magnesium. In addition maximums are also observed when enzyme concentration is increased. It is qualitatively new result that does not follow from the existing theories. The obtained results permit to explain some experimental data of ATP hydrolysis, active ion transport and some other reactions in a new fashion. The studied model and obtained results may be applied to another enzyme-catalysed reactions which proceed in the activator presence.     

Mitochondrial free radical generation, oxidative stress, and aging

Mitochondria have been described as "the powerhouses of the cell" because they link the energy-releasing activities of electron transport and proton pumping with the energy conserving process of oxidative phosphorylation, to harness the value of foods in the form of ATP. Such energetic processes are not without dangers, however, and the electron transport chain has proved to be somewhat "leaky." Such side reactions of the mitochondrial electron transport chain with molecular oxygen directly generate the superoxide anion radical (O2*-), which dismutates to form hydrogen peroxide (H2O2), which can further react to form the hydroxyl radical (HO*). In addition to these toxic electron transport chain reactions of the inner mitochondrial membrane, the mitochondrial outer membrane enzyme monoamine oxidase catalyzes the oxidative deamination of biogenic amines and is a quantitatively large source of H2O2 that contributes to an increase in the steady state concentrations of reactive species within both the mitochondrial matrix and cytosol. In this article we review the mitochondrial rates of production and steady state levels of these reactive oxygen species. Reactive oxygen species generated by mitochondria, or from other sites within or outside the cell, cause damage to mitochondrial components and initiate degradative processes. Such toxic reactions contribute significantly to the aging process and form the central dogma of "The Free Radical Theory of Aging." In this article we review current understandings of mitochondrial DNA, RNA, and protein modifications by oxidative stress and the enzymatic removal of oxidatively damaged products by nucleases and proteases. The possible contributions of mitochondrial oxidative polynucleotide and protein turnover to apoptosis and aging are explored.     

Effect of unstirred layers on binding and reaction kinetics at a membrane surface

The effects of solution unstirred layers on the time course of chemical reactions and transport processes at a membrane surface are determined. A set of equations which describes non-steady-state diffusion through an unstirred layer coupled with chemical reaction at a membrane surface or transport through a membrane is developed. A numerical solution to the equations is obtained by uncoupling diffusive and chemical processes in an iterative manner. The diffusive process is solved by the Crank-Nicolson method; the chemical process is solved by integrating the differential equations describing the kinetics. Diffusive processes in one dimension, in three dimensions, and in the presence of an arbitrary potential near the membrane surface are solved. General characteristics of the calculated reaction time course are discussed using surface binding and membrane transport examples. Small, neglected, unstirred layers are shown to sometimes yield erroneous values of rate parameters for a surface reaction and to simulate competitive reaction kinetics. Experimental approaches for measuring unstirred layer thickness are reviewed.     

Simple dissolution-reaction model for enzymatic conversion of suspension of solid substrate

Although reactions in substrate suspension are employed in industry for several bioconversion processes, there appears to be no quantitative model available in the literature to rationalize the optimization of these processes. We present a simple model that incorporates the kinetics of substrate dissolution and a simultaneous enzymatic reaction. The model was tested in the alpha-chymotrypsin-catalyzed hydrolysis of an aqueous suspension of dimethyl benzylmethylmalonate to a homogeneous solution of enantiomerically pure monoester. This reaction occurs in the bulk phase, so catalysis by enzyme absorbed at the solid-liquid interface plays no role. The value of the parameters in the model (i.e., the mass transfer coefficient of substrate dissolution (k(L)), the substrate solubility, and the rate constant for the enzymatic reaction) were determined in separate experiments. Using these parameter values, the model gave a good quantitative prediction of the rate of the overall dissolution-reaction process. When the particle size distribution is known, k(L) may also be calculated instead. The model seems to be applicable also for other poorly soluble substrates, other enzymes, and other solvents. (c) 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 56: 433-440, 1997.     

Understanding the effect of adsorption on activated processes using molecular theory and simulation

Most chemical reactions of practical interest are catalysed by porous materials, which can improve reaction rates and equilibrium yields through various interactions with the reacting mixture. Nucleation, another kind of activated process, can also be substantially affected by the presence of a surface or by the confinement within a porous material. There are several different effects that can influence such activated processes, such as the reduced dimensionality of the porous space or the adsorbed layer, physical or chemical interactions with the adsorbate and transport limitations. This paper presents a unifying perspective on the influence of each of these effects on chemical reactions and crystallisation processes through the discussion of selected examples from the literature. The common aspects and the differences between these two different kinds of activated processes are considered in the context of each effect. Finally, some of the important issues that could benefit from the development of new molecular simulations methods are discussed.     

Three-Dimensional Multifluid Flow and Transport at the Brooklawn Site near Baton Rouge,LA: A Case Study

Disposal quantities of organic wastes at the Brooklawn Site in Louisiana are suspected to equal nearly 1.45 × 10⁸Kg, making this site one of the most contaminated dense nonaqueous phase liquid (DNAPL) sites in the world. Remedial activities at the site include groundwater and DNAPL extraction from recovery wells. DNAPL recovery has markedly declined in recent years, with many of the peripheral wells showing negligible recovery of organic liquids. Three-dimensional simulations of DNAPL movement in the subsurface were conducted using the STOMP simulator, including a new coupled-well model. The objectives of this modeling effort were to (1) determine the fate and transport of infiltrated DNAPL, and (2) measure the effects of active recovery through DNAPL pumping. A detailed three-dimensional geologic model of the Brooklawn primary DNAPL disposal area was developed and used as the framework for DNAPL simulations. Additionally, site-specific data were obtained to determine the most important hydraulic properties of the subsurface related to DNAPL movement and formation of entrapped DNAPL in the laboratory. In addition to a simulation using the best available subsurface information, several sensitivity simulations were conducted to assess the effects on DNAPL migration. These simulations include DNAPL pumping, well screen extension, an alternative geology, increased DNAPL density, lower DNAPL viscosity, and more-permeable sand and silt deposits.

Results of the simulations were compared to field data that define the extent of DNAPL movement based on where DNAPL has been extracted in the site recovery wells. The model simulations show that pumping has a negligible effect on subsurface DNAPL saturations and movement. Pumped DNAPL volumes diminish rapidly due to the limited radius of influence of the wells and movement of the DNAPL out of the zone of influence of the wells with a maximum radius of influence of about 6 m. The numerical analysis also demonstrates that it is impractical to extend existing wells or install new wells to retrieve enough DNAPL to affect the overall extent of DNAPL movement.     

Pseudomorphic Transformation of Interpenetrated Prussian Blue Analogs into Defective Nickel Iron Selenides for Enhanced Electrochemical and Photo‐Electrochemical Water Splitting

A significant methodology gap remains in the construction of advanced electrocatalysts, which has collaborative defective functionalities and structural coherence that maximizes electrochemical redox activity, electrical conductivity, and mass transport characteristics. Here, a coordinative self‐templated pseudomorphic transformation of an interpenetrated metal organic compound network is conceptualized into a defect‐rich porous framework that delivers highly reactive and durable photo(electro)chemical energy conversion functionalities. The coordinative‐template approach enables previously inaccessible synthesis routes to rationally accomplish an interconnected porous conductive network at the microscopic level, while exposing copious unsaturated reactive sites at the atomic level without electronic or structural integrity trade‐offs. Consequently, porous framework, interconnected motifs, and engineered defects endow remarkable electrocatalytic hydrogen evolution reaction and oxygen evolution reaction activity due to intrinsically improved turnover frequency, electrochemical surface area, and charge transfer. Moreover, when the hybrid is coupled with a silicon photocathode for solar‐driven water splitting, it enables photon assisted redox reactions, improved charge separation, and enhanced carrier transport via the built‐in heterojunction and additive co‐catalyst functionality, leading to a promising photo(electro)chemical hydrogen generation performance. This work signifies a viable and generic approach to prepare other functional interconnected metal organic coordinated compounds, which can be exploited for diverse energy storage, conversion, or environmental applications.     

Biphasic mini-reactor for characterization of biocatalyst performance

Biphasic reaction media are extending the scope of technical biocatalysis. Thorough investigation of the factors affecting catalyst performance under these conditions is of key importance for the successful implementation of catalytic processes. Here, we present a reactor setup suitable for comprehensive systematic characterization and optimization of biocatalyzed reactions in biphasic systems with distinct phases. It is distinguished by small volumes allowing reproducible experimentation with minimum amounts of solvent and catalyst. The interfacial area is kept constant and independent stirring of both phases is allowed in order to minimize superimposing effects. Evaporation of low-volatile organic solvents is prevented by use of airtight construction. The broad applicability of this mini-reactor is demonstrated with regard to determination of mass transfer, enzyme productivity, and enzyme stability in both batch and continuous mode.     

Low-reactive free radicals inhibiting nonbranched chain processes of addition

The kinetics of inhibition of nonbranched chain processes of addition of reactive free radicals at double bonds O=O, C=O, and C=C of molecules in liquid homogeneous binar systems from saturated and unsaturated components by low-reactive free radicals (o-CH3C6H4CH2O*4, HO*4; HC=O; CH2=C(CH3)CH2, and CH2=CHCHOH) was studied. It was assumed that as the concentration of the unsaturated component (as a source of low-reactive free radicals) increases (after the optimum concentration is attained, which corresponds to the maximum rate of the process) the phenomena of increasing inhibition of these processes may act as the elements of self-regulation of similar processes in nature, which returns them into the stationary state. The energetics of the key radical-molecular gas phase reactions was analyzed. The thermal effects of total dissociation reactions of simple alkylperoxyl (exo effect) and alkoxyl (endo effect) reactive free radicals in the gas phase were compared. The kinetic equations (with one to three parameters being directly determined), obtained by the quasi-steady-state treatment, are presented, which make it possible to describe nonmonotonic (with a maximum) dependencies of the rates of formation of molecular 1:1-adducts on the concentration of the unsaturated component.     

Schiff-Type Reagents in Cytochemistry. 2. Detection of Primary Amine Dye Impurities In Pyronin B and Pyronin Y(G)

Many batches of pyronin B (C.I. 45010), pyronin Y or G (C.I. 45005), and acridine red (C.I. 45000) produce positive Feulgen or PAS reactions when their 0.25% solutions are saturated with SO₂ and used on acid-hydrolyzed or periodate-oxidized tissue sections. These dyes behave as Schiff-type reagents and stain aldehyde-containing structures orange, brown, pink, red, or violet, depending on the particular batch used. The most frequent contaminants are violet and are nonfluorescent. Aldehyde groups are stained by these dyeSO₂ solutions as is shown by using unhydrolyzed controls in the Feulgen reaction and unoxidized controls in the PAS reaction, and by dye solutions lacking SO₂. Other procedures included reactions with aldehyde-blocking reagents, treatment with deoxyribonuclease and diastase, and extraction of nudeic acids with trichloroaeetic acid. The standard Schiff reagent was used in the Same procedures as a basis for comparing results. Since the Schiff-aldehyde reaction requires a dye with a primary amine group and since true pronins contain only secondary or tertiary amines, the positive histochemical results are evidently caused by dye contaminants possessing primary amine groups. The PAS reaction is more sensitive than the Feulgen reaction in detecting dye contaminants. Tissues used were chiefly formalin-fixed mouse intestine and ascites cells. Seventy-five commercial pyronins were studied from 21 different firms. Among 19 batches of pyronin B, 14 were found to contain primary amine dye contaminants. Among 39 batches of pyronin Y(G), 19 contained similar primary amine dye contaminants. Of the 8 batches of acridine red tested, 7 were found to contain primary amine dye contaminants. Nine commercial mixtures of methyl green-pyronin were studied and 4 were found to be likewise contaminated, but these reactive dye contaminants in them are apparently not associated with methyl green. A tabulated summary of the pyronin batches containing primary amine contaminants, and a list of sources and distributors of pyronin dyes are included.     

Structural interaction between DsrE-DsrF-DsrH proteins involved in the transport of electrons in the dsr operon

Biological redox reactions of inorganic sulfur compounds are important for the proper maintenance of environmental sulfur balance. These reactions are mediated by phylogeneticaly diverse set of microorganisms. The protein complex that is involved in such redox reactions of sulfur compounds is the complex encoded by dsr operon. The ecological and industrial importance of these microorganisms led us to investigate the structural details of the mechanism of the process of electron transport during such redox reactions performed by the dsr operon. Among the gene products of the operon, the proteins DsrE, DsrF, and DsrH are small soluble cytoplasmic proteins acting as alpha2beta2gamma2 heterohexamer and are involved in the process of electron transport in these ecologically as well as industrially important microorganisms. Since no structural details of the proteins were available we employed homology modeling to construct the three-dimensional structures of the DsrE, DsrF, and DsrH from Chlorobium tepidum. The putative three dimensional structures of the proteins were predicted from the models. Since DsrE, DsrF, and DsrH proteins act as a hetero-hexameric complex, the modeled proteins were subjected to molecular docking analyses to generate the model of the biochemically active complex. This allowed us to predict the probable binding modes of the proteins as well as the biochemical and the structural basis of the mechanism of the electron transport process by this complex. The hexamerization of the proteins would help to bring the Cys residues in close proximity, which enables the complex to actively take part electron transport process.     

Kinetic analysis of the assembly of the outer membrane protein LamB in Escherichia coli mutants each lacking a secretion or targeting factor in a different cellular compartment

Outer membrane beta-barrel proteins in gram-negative bacteria, such as Escherichia coli, must be translocated from their site of synthesis in the cytoplasm to the periplasm and finally delivered to the outer membrane. At least a dozen proteins located in the cytoplasm, the periplasm, and both the inner and outer membranes are required to catalyze this complex assembly process. At normal growth temperatures and conditions the transport and assembly processes are so fast that assembly intermediates cannot be detected. Using cells grown at a low temperature to slow the assembly process and pulse-chase analysis with immunodetection methods, we followed newly synthesized LamB molecules during their transit through the cell envelope. The quality and reproducibility of the data allowed us to calculate rate constants for three different subassembly reactions. This kinetic analysis revealed that secB and secD mutants exhibit nearly identical defects in precursor translocation from the cytoplasm. However, subsequent subassembly reaction rates provided no clear evidence for an additional role for SecD in LamB assembly. Moreover, we found that surA mutants are qualitatively indistinguishable from yfgL mutants, suggesting that the products of both of these genes share a common function in the assembly process, most likely the delivery of LamB to the YaeT assembly complex in the outer membrane.     

Structural Interaction Between DsrE-DsrF-DsrH Proteins Involved in the Transport of Electrons in the dsr Operon

Abstract

Biological redox reactions of inorganic sulfur compounds are important for the proper maintenance of environmental sulfur balance. These reactions are mediated by phylogeneticaly diverse set of microorganisms. The protein complex that is involved in such redox reactions of sulfur compounds is the complex encoded by dsr operon. The ecological and industrial importance of these microorganisms led us to investigate the structural details of the mechanism of the process of electron transport during such redox reactions performed by the dsr operon. Among the gene products of the operon, the proteins DsrE, DsrF, and DsrH are small soluble cytoplasmic proteins acting as α₂β₂γ₂ heterohexamer and are involved in the process of electron transport in these ecologically as well as industrially important microorganisms.

Since no structural details of the proteins were available we employed homology modeling to construct the three-dimensional structures of the DsrE, DsrF, and DsrH from Chlorobium tepidum. The putative three dimensional structures of the proteins were predicted from the models. Since DsrE, DsrF, and DsrH proteins act as a hetero-hexameric complex, the modeled proteins were subjected to molecular docking analyses to generate the model of the biochemically active complex. This allowed us to predict the probable binding modes of the proteins as well as the biochemical and the structural basis of the mechanism of the electron transport process by this complex. The hexamerization of the proteins would help to bring the Cys residues in close proximity, which enables the complex to actively take part electron transport process.     

Kinetic modeling of lipase‐catalyzed esterification reaction between oleic acid and trimethylolpropane: A simplified model for multi‐substrate multi‐product ping–pong mechanisms

Kinetic models are among the tools that can be used for optimization of biocatalytic reactions as well as for facilitating process design and upscaling in order to improve productivity and economy of these processes. Mechanism pathways for multi‐substrate multi‐product enzyme‐catalyzed reactions can become very complex and lead to kinetic models comprising several tens of terms. Hence the models comprise too many parameters, which are in general highly correlated and their estimations are often prone to huge errors. In this study, Novozym^®435 catalyzed esterification reaction between oleic acid (OA) and trimethylolpropane (TMP) with continuous removal of side‐product (water) was carried out as an example for reactions that follow multi‐substrate multi‐product ping‐pong mechanisms. A kinetic model was developed based on a simplified ping‐pong mechanism proposed for the reaction. The model considered both enzymatic and spontaneous reactions involved and also the effect of product removal during the reaction. The kinetic model parameters were estimated using nonlinear curve fitting through unconstrained optimization methodology and the model was verified by using empirical data from different experiments and showed good predictability of the reaction under different conditions. This approach can be applied to similar biocatalytic processes to facilitate their optimization and design. © 2013 American Institute of Chemical Engineers Biotechnol. Prog., 29:1422–1429, 2013