[1] A generalized formulation for kinetically controlled reactions has been developed and incorporated into a multicomponent reactive transport model to facilitate the investigation of a large variety of problems involving inorganic and organic chemicals in variably saturated media. The general kinetic formulation includes intra-aqueous and dissolution-precipitation reactions in addition to geochemical equilibrium expressions for hydrolysis, aqueous complexation, oxidation-reduction, ion exchange, surface complexation, and gas dissolution-exsolution reactions. The generalized approach allows consideration of fractional order terms with respect to any dissolved species in terms of species activities or in terms of total concentrations, which facilitates the incorporation of a variety of experimentally derived rate expressions. Monod and inhibition terms can be used to describe microbially mediated reactions or to limit the reaction progress of inorganic reactions. Dissolution-precipitation reactions can be described as surface-controlled or transport-controlled reactions. The formulation also facilitates the consideration of any number of parallel reaction pathways, and reactions can be treated as irreversible or reversible processes. Two groundwater contamination scenarios, both set in variably saturated media but with significantly different geochemical reaction networks, are investigated and demonstrate the advantage of the generalized approach. The first problem focuses on a hypothetical case study of the natural attenuation of organic contaminants undergoing dissolution, volatilization, and biodegradation in an unconfined aquifer overlaid by unsaturated sediments. The second problem addresses the generation of acid mine drainage in the unsaturated zone of a tailings impoundment at the Nickel Rim Mine Site near Sudbury, Ontario, and subsequent reactive transport in the saturated portion of the tailings.

https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2001WR000862

Multicomponent reactive transport modeling in variably saturated porous media using a generalized formulation for kinetically controlled reactions

This paper presents a three-dimensional, MODFLOW/MT3DMS-based reactive multicomponent transport model for saturated porous media. Based on a split-operator technique, the model, referred to as PHT3D, couples the transport simulator MT3DMS and the geochemical modeling code PHREEQC-2. Through the flexible, generic nature of PHREEQC-2, PHT3D can handle a broad range of equilibrium and kinetically controlled reactive processes, including aqueous complexation, mineral precipitation/dissolution, and ion exchange. The diversity of potential applications is demonstrated through simulation of five existing literature benchmarks and a new three-dimensional sample problem. The model might be applied to simulate the geochemical evolution of pristine and contaminated aquifers as well as their cleanup. The latter problem class includes the natural and enhanced attenuation/remediation schemes of a wide range of organic and inorganic contaminants. Processes/reactions not included in the standard PHREEQC-2 database but typical for this type of application (e.g., NAPL dissolution, microbial growth/decay) can be defined and included via the extensible PHREEQC-2 database file.

MODFLOW/MT3DMS‐Based Reactive Multicomponent Transport Modeling

Module-oriented modeling of reactive transport with HYTEC

The two isoforms cyclooxygenase-1 and -2 catalyze the initial step in the formation of prostaglandins in a variety of pathophysiological processes. More recently their role in carcinogenesis has become more evident. They seem to influence apoptosis, angiogenesis, and invasion, and play a role in the production of carcinogens. Usually, a high level of COX-2 expression is found in cancer cells. However, low COX-2 expression is observed in some cancers like prostate or breast cancer. This phenomenon is quite surprising and should influence on clinical trial designs. Large epidemiological trials studying users and non-users of aspirin have shown that cyclooxygenase (COX) inhibitors and non-steroidal anti-inflammatory drugs (NSAIDs) could be of benefit against the development and growth of malignancies. Moreover, clinical trials in patients with familial adenomatosis polyposis syndrome have shown too the efficacy of non-selective COX inhibitors and recently also of selective COX-2 inhibitors in the reduction of the number and the size of colorectal polyps. However, a primary chemopreventive effect has not been demonstrated yet. NSAIDs are also supposed to have a preventive and growth inhibitory effect in extra-colonic epithelial malignancies. Several preclinical studies show promising results with combination treatments of either chemotherapy or radiotherapy with COX inhibitors. Preclinical studies with the simultaneous use of inhibitors of the epidermal growth factor receptor and COX-2 inhibitors have shown also promising results. Encouraging results with the first clinical trials combining chemotherapy with COX-2 inhibitors in patients with cancer in the advanced and neoadjuvant setting have recently been reported. However, NSAIDs effects in cancer cells are mediated not only by COX enzymes but also by interactions with downstream effectors of COX-2. Hence, we can state that targeting the COX-2 pathway is a promising strategy in the prevention and treatment of solid tumors. Ongoing trials are expected to answer - at least partly - the remaining questions concerning COX-2 and cancer.

Cyclooxygenase-2 as a target for anticancer drug development.

From laboratory experiments it is known that bacterial biomass is able to influence the hydraulic properties of saturated porous media, an effect called bioclogging. To interpret the observations of these experiments and to predict possible bioclogging effects on the field scale it is necessary to use transport models, which are able to include bioclogging. For these models it is necessary to know the relation between the amount of biomass and the hydraulic conductivity of the porous medium. Usually these relations were determined using bundles of parallel pore channels and do not account for interconnections between the pores in more than one dimension. The present study uses two-dimensional pore network models to study the effects of bioclogging on the pore scale. Numerical simulations were done for two different scenarios of the growth of biomass in the pores. Scenario 1 assumes microbial growth in discrete colonies clogging particular pores completely. Scenario 2 assumes microbial growth as a biofilm growing on the wall of each pore. In both scenarios the hydraulic conductivity was reduced by at least two orders of magnitude, but for the colony scenario much less biomass was needed to get a maximal clogging effect and a better agreement with previously published experimental data could be found. For both scenarios it was shown that heterogeneous pore networks could be clogged with less biomass than more homogeneous ones.

Influence of Microbial Growth on Hydraulic Properties of Pore Networks

Simulation of reactive processes related to biodegradation in aquifers: 1. Structure of the three-dimensional reactive transport model

Simulation of reactive processes related to biodegradation in aquifers. 2. Model application to a column study on organic carbon degradation

http://www.talkingcells.org/pdf/Ziemann_2002_mdr1b-cox.pdf

Dirk Schäfer

Papers

Simulation of reactive processes related to biodegradation in aquifers: 1. Structure of the three-dimensional reactive transport model

Simulation of reactive processes related to biodegradation in aquifers. 2. Model application to a column study on organic carbon degradation

The cyclooxygenase system participates in functional mdr1b overexpression in primary rat hepatocyte cultures