Biodegradation modelling reactions

Solute transport with biodegradation modelled as an "instantaneous" biodegradation reaction (approach used by BIOPLUME models). 

Models of chemical reactions of trace pollutants in groundwater must be based on experimental analysis of the kinetics of possible pollutant interactions with earth materials, much the same as smog chamber studies considered atmospheric photochemistry. Fundamental research could determine the surface chemistry of soil components and processes such as adsorption and desorption, pore diffusion, and biodegradation of contaminants. Hydrodynamic pollutant transport models should be upgraded to take into account chemical reactions at surfaces. 

In a final example, we consider a similar problem in two dimensions. Water containing 1 mg kg-1 benzene leaks into an aquifer for a period of two years, at a rate of 300 m3 yr-1. Once in the aquifer, which is 1 m thick, the benzene migrates with the ambient flow, sorbs, and biodegrades. We model flow and reaction over 10 years, within a 600 m x 60 m area, assuming a dispersivity ay along the flow of 30 cm, and a-y across flow of 10 cm. All other parameters, including the flow velocity, remain the same as in the previous calculation. 

Many wastewater flows in industry can not be treated by standard aerobic or anaerobic treatment methods due to the presence of relatively low concentration of toxic pollutants. Ozone can be used as a pretreatment step for the selective oxidation of these toxic pollutants. Due to the high costs of ozone it is important to minimise the loss of ozone due to reaction of ozone with non-toxic easily biodegradable compounds, ozone decay and discharge of ozone with the effluent from the ozone reactor. By means of a mathematical model, set up for a plug flow reactor and a continuos flow stirred tank reactor, it is possible to calculate more quantitatively the efficiency of the ozone use, independent of reaction kinetics, mass transfer rates of ozone and reactor type. The model predicts that the oxidation process is most efficiently realised by application of a plug flow reactor instead of a continuous flow stirred tank reactor. 

The compound formaldehyde is biodegrading in several systems simultaneously (1) a lake, modeled as a complete mix reactor (2) an estuary, modeled as three complete mixed reactors in series (3) a large river, modeled as 10 complete mixed reactors in series, and a small stream, modeled as a plug flow reactor. What is the nondimensional reaction/residence time, k p, that is required for each of these systems to reach a degradation of 50%, 90%, 99%, and 99.9% ... 

Polycondensation reactions in oriented monolayers and bilayers proceed without catalysis, and simply occur due to the high packing density of the reactive groups and their orientation in these layers. Bulk condensation of the a-amino acid esters at higher temperatures does not lead to polypeptides but to 2,5-diketopiperazines. No diketopiperazines are found in polycondensed monolayers or liposomes. Polycondensation in monolayers and liposomes leading to oriented polyamides represents a new route for stabilizing model membranes under mild conditions. In addition, polypeptide vesicles may be cleavable by enzymes in the blood vessels. In this case, they would represent the first example of stable but biodegradable polymeric liposomes. 

The fundamentals and background of QSAR modeling and predictions have been detailed previously (e.g., Nendza, 1998). Regarding the different physicochemical bases of transformation processes, different approaches to their estimation have been taken. The intention should always be to use process-related models. Thermodynamic principles underlie the relationships between abiotic one-step reaction rates and physicochemical descriptors of the structures. Mechanistic modeling is much more intricate for multistep biodegradations, where the (varying) rate-limiting... 

BIOPLUME III is a public domain transport code that is based on the MOC (and, therefore, is 2-D). The code was developed to simulate the natural attenuation of a hydrocarbon contaminant under both aerobic and anaerobic conditions. Hydrocarbon degradation is assumed due to biologically mediated redox reactions, with the hydrocarbon as the electron donor, and oxygen, nitrate, ferric iron, sulfate, and carbon dioxide, sequentially, as the electron acceptors. Biodegradation kinetics can be modeled as either a first-order, instantaneous, or Monod process. Like the MOC upon which it is based, BIOPLUME III also models advection, dispersion, and linear equilibrium sorption [67]. 

In the RT3D simulation, advective/dispersive transport of each contaminant is assumed. Sorption is modeled as a linear equilibrium process and biodegradation is modeled as a first-order process. Due to the assumed degradation reaction pathways (Fig. 2) transport of the different compounds is coupled. In the study, four reaction zones were delineated, based on observed geochemistry data. Each zone (two anaerobic zones, one transition zone, and one aerobic zone) has a different value for the biodegradation first-order rate constant for each contaminant. For example, since PCE is assumed to degrade only under... 

In ambient air, the primary removal mechanism for acrolein is predicted to be reaction with photochemically generated hydroxyl radicals (half-life 15-20 hours). Products of this reaction include carbon monoxide, formaldehyde, and glycolaldehyde. In the presence of nitrogen oxides, peroxynitrate and nitric acid are also formed. Small amounts of acrolein may also be removed from the atmosphere in precipitation. Insufficient data are available to predict the fate of acrolein in indoor air. In water, small amounts of acrolein may be removed by volatilization (half-life 23 hours from a model river 1 m deep), aerobic biodegradation, or reversible hydration to 0-hydroxypropionaldehyde, which subsequently biodegrades. Half-lives less than 1-3 days for small amounts of acrolein in surface water have been observed. When highly concentrated amounts of acrolein are released or spilled into water, this compound may polymerize by oxidation or hydration processes. In soil, acrolein is expected to be subject to the same removal processes as in water. 

In this section the environmental distribution of PCAs will be estimated using Mackay s Equilibrium Criterion (EQC) level III fugacity model [79]. Level III refers to a steady state, nonequilibrium system among soil, air, and water compartments, with the chemical undergoing reactions or inputs and removal processes (advection, volatilization, deposition, photolysis, hydrolysis, and biodegradation). 

Oh M, Yamada T, Eiattori M, Goto S, Kanehisa M. Systematic analysis of enzyme-catalyzed reaction patterns and prediction of microbial biodegradation pathways. J. Chem. Inf Model 2007 47 1702-1712. 

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