A pore-scale model for permeable biofilm: numerical simulations and laboratory experiments

In this paper we derive a pore-scale model for permeable biofilm formation in a two-dimensional pore. The pore is divided in two phases: water and biofilm. The biofilm is assumed to consist of four components: water, extracellular polymeric substances (EPS), active bacteria, and dead bacteria. The flow of water is modeled by the Stokes equation whereas a diffusion-convection equation is involved for the transport of nutrients. At the water/biofilm interface, nutrient transport and shear forces due to the water flux are considered. In the biofilm, the Brinkman equation for the water flow, transport of nutrients due to diffusion and convection, displacement of the biofilm components due to reproduction/dead of bacteria, and production of EPS are considered. A segregated finite element algorithm is used to solve the mathematical equations. Numerical simulations are performed based on experimentally determined parameters. The stress coefficient is fitted to the experimental data. To identify the critical model parameters, a sensitivity analysis is performed. The Sobol sensitivity indices of the input parameters are computed based on uniform perturbation by $\pm 10 \%$ of the nominal parameter values. The sensitivity analysis confirms that the variability or uncertainty in none of the parameters should be neglected

Microfluidic study of effects of flow velocity and nutrient concentration on biofilm accumulation and adhesive strength in the flowing and no-flowing microchannels

Biofilm accumulation in porous media can cause pore plugging and change many of the physical properties of porous media. Engineering bioplugging may have significant applications for many industrial processes, while improved knowledge on biofilm accumulation in porous media at porescale in general has broad relevance for a range of industries as well as environmental and water research. The experimental results by means of microscopic imaging over a T-shape microchannel clearly show that increase in fluid velocity could facilitate biofilm growth, but that above a velocity threshold, biofilm detachment and inhibition of biofilm formation due to high shear stress were observed. High nutrient concentration prompts the biofilm growth; however, the generated biofilm displays a weak adhesive strength. This paper provides an overview of biofilm development in a hydrodynamic environment for better prediction and modelling of bioplugging processes associated with porous systems in petroleum industry, hydrogeology and water purification.acceptedVersio

Antibacterial and Anticancer Drugs - Interaction with DNA

This thesis is concerned with the interactions of drugs with DNA mediated by metal ions. The interactions of two types of drugs were investigated: fluoroquinolone antibacterial agents, represented by ciprofloxacin (cipro), levofloxacin (levo) and ofloxacin (oflo), and the anticancer drug cis-[Pt(NH3)2Cl2] (cisplatin). Fluoroquinolones are highly effective antibacterial agents of which some can be administered orally, thereby having major pharmaeconomical advantages over other antibiotics. Cipro and levo are the most widely prescribed fluoroquinolones and are used against a variety of bacterial infections including treatment of infections of the gastrointestinal, respiratory and urinary tracts, selected sexually transmitted diseases and infections in bones, joints, skin and soft tissues. The primary target for fluoroquinolones is DNA and cellular death is caused by irreversible formation of a ternary fluoroquinolone – DNA – DNA Gyrase complex. However, the molecular mechanisms of action are still largely unknown. Does fluoroquinolone bind preferentially to single-stranded (ss) or double-stranded (ds) DNA ? What is the role of the essential divalent magnesium ion ? What is the binding mode for fluoroquinolones to DNA ? This work attempts to improve the knowledge of this interaction by investigating cipro and levo interactions with DNA in the presence and absence of Mg(II) as well as shedding light on the physico-chemical properties of fluoroquinolones. In paper I, hydrothermal complexes of [Mg(R-oflo)(S-oflo)(H2O)2]·2H2O and [Mg(S-oflo)2(H2O)2]·2H2O were synthesized and studied by x-ray crystallography and NMR. In both structures the anionic fluoroquinolone ligands were coordinated through the keto and carboxylate oxygens forming 1:2 Mg:oflo complexes. The two structures were practically identical, except for the orientation of the oxazine methyl group which lead to shorter distance between layers for the Mg(S-oflo)2 complex. The complexes showed different solution behaviour both in the preparation of and the solvation of the crystals, indicating that the orientation of the oxacine methyl group plays a significant role for the solution behaviour, e.g. selfassociated stacking. In the first high-resolution study of a fluoroquinolone-DNA interaction (paper II), the influence of divalent Mg-ions on the ciprofloxacin affinity for ds-DNA and subsequent implications for the binding mode were investigated. The results showed that ciprofloxacin binds to DNA in both the presence and absence of Mg(II)-ions. In the absence of Mg(II), both major and minor groove binding were observed, while in the presence of Mg(II), the preferred binding site was the minor groove as evident from several cipro-DNA NOE cross-peaks. The Mg(II)-mediated interaction of levofloxacin with two different ds-DNAs was investigated in paper III. Contrary to the observations for ciprofloxacin, levo did not bind to either of the oligomers in the absence of Mg(II). However, in the presence of physiological concentration of Mg(II), levo was found to bind to both oligomers as evident from several NOE cross-peaks. Non-specific binding to both the major and minor groove and interaction with the terminal base pair was observed for both oligomers. Restrained molecular dynamics simulation showed that the minor groove conformation was particularly favourable due to the perfect fit of levo in the minor groove, in accord with the molecular docking results for ciprofloxacin (paper II). One of the oligomers showed levo intercalation between a central GpG step at higher ratios of levo to DNA. The last part of the thesis is concerned with the interaction of the antitumor agent cisplatin with DNA. Cisplatin is the world's most used metal-based anticancer drug and has been in clinical use since 1978. For the first time a structural characterisation of a cisplatin adduct to a ds-DNA containing a GGG sequence has been undertaken. The cisplatin-DNA adduct was investigated using NMR and molecular modelling. The initial G*G*G adduct transformed to a GG*G* adduct through a reversible isomerization reaction. This enabled a comparison of the effects of guanine flanking bases on both the 3´ and the 5´ side of the G*G* cross-link and pyrimidine flanking bases. The results showed that a 3´ flanking guanine has little influence on the G*G* cross-link, while a 5´ flanking guanine induces significant structural perturbations. The context -GG*G*T- was basically similar in structure to the general -pyG*Gpy- context, however the 5´ XpG* step was different in both structure and dynamics. The fact that the isomerization reaction took place suggests that the cisPt - GN7 bond is labile. This would imply that the current models used to describe protein interaction with cisplatin-DNA cross-links should be re-evaluated

Polymer Injectivity: Investigation of Mechanical Degradation of Enhanced Oil Recovery Polymers Using In-Situ Rheology

Water soluble polymers have attracted increasing interest in enhanced oil recovery (EOR) processes, especially polymer flooding. Despite the fact that the flow of polymer in porous medium has been a research subject for many decades with numerous publications, there are still some research areas that need progress. The prediction of polymer injectivity remains elusive. Polymers with similar shear viscosity might have different in-situ rheological behaviors and may be exposed to different degrees of mechanical degradation. Hence, determining polymer in-situ rheological behavior is of great significance for defining its utility. In this study, an investigation of rheological properties and mechanical degradation of different partially hydrolyzed polyacrylamide (HPAM) polymers was performed using Bentheimer sandstone outcrop cores. The results show that HPAM in-situ rheology is different from bulk rheology measured by a rheometer. Specifically, shear thickening behavior occurs at high rates, and near-Newtonian behavior is measured at low rates in porous media. This deviates strongly from the rheometer measurements. Polymer molecular weight and concentration influence its viscoelasticity and subsequently its flow characteristics in porous media. Exposure to mechanical degradation by flow at high rate through porous media leads to significant reduction in shear thickening and thereby improved injectivity. More importantly, the degraded polymer maintained in-situ viscosity at low flow rates indicating that improved injectivity can be achieved without compromising viscosity at reservoir flow rates. This is explained by a reduction in viscoelasticity. Mechanical degradation also leads to reduced residual resistance factor (RRF), especially for high polymer concentrations. For some of the polymer injections, successive degradation (increased degradation with transport length in porous media) was observed. The results presented here may be used to optimize polymer injectivity

Polymer Injectivity: Investigation of Mechanical Degradation of Enhanced Oil Recovery Polymers Using In-Situ Rheology

Water soluble polymers have attracted increasing interest in enhanced oil recovery (EOR) processes, especially polymer flooding. Despite the fact that the flow of polymer in porous medium has been a research subject for many decades with numerous publications, there are still some research areas that need progress. The prediction of polymer injectivity remains elusive. Polymers with similar shear viscosity might have different in-situ rheological behaviors and may be exposed to different degrees of mechanical degradation. Hence, determining polymer in-situ rheological behavior is of great significance for defining its utility. In this study, an investigation of rheological properties and mechanical degradation of different partially hydrolyzed polyacrylamide (HPAM) polymers was performed using Bentheimer sandstone outcrop cores. The results show that HPAM in-situ rheology is different from bulk rheology measured by a rheometer. Specifically, shear thickening behavior occurs at high rates, and near-Newtonian behavior is measured at low rates in porous media. This deviates strongly from the rheometer measurements. Polymer molecular weight and concentration influence its viscoelasticity and subsequently its flow characteristics in porous media. Exposure to mechanical degradation by flow at high rate through porous media leads to significant reduction in shear thickening and thereby improved injectivity. More importantly, the degraded polymer maintained in-situ viscosity at low flow rates indicating that improved injectivity can be achieved without compromising viscosity at reservoir flow rates. This is explained by a reduction in viscoelasticity. Mechanical degradation also leads to reduced residual resistance factor (RRF), especially for high polymer concentrations. For some of the polymer injections, successive degradation (increased degradation with transport length in porous media) was observed. The results presented here may be used to optimize polymer injectivity

Qualification of New Methods for Measuring In-Situ Rheology of Non-Newtonian Fluids in Porous Media

Pressure drop (ΔP) versus volumetric injection rate (Q) data from linear core floods have typically been used to measure in situ rheology of non-Newtonian fluids in porous media. However, linear flow is characterized by steady-state conditions, in contrast to radial flow where both pressure and shear-forces have non-linear gradients. In this paper, we qualify recently developed methods for measuring in situ rheology in radial flow experiments, and then quantitatively investigate the robustness of these methods against pressure measurement error. Application of the new methods to experimental data also enabled accurate investigation of memory and rate effects during polymer flow through porous media. A radial polymer flow experiment using partially hydrolyzed polyacrylamide (HPAM) was performed on a Bentheimer sandstone disc where pressure ports distributed between a central injector and the perimeter production line enabled a detailed analysis of pressure variation with radial distance. It has been suggested that the observed shear-thinning behavior of HPAM solutions at low flux in porous media could be an experimental artifact due to the use of insufficiently accurate pressure transducers. Consequently, a generic simulation study was conducted where the level of pressure measurement error on in situ polymer rheology was quantitatively investigated. Results clearly demonstrate the robustness of the history match methods to pressure measurement error typical for radial flow experiments, where negligible deviations from the reference rheology was observed. It was not until the error level was increased to five-fold of typical conditions that significant deviation from the reference rheology emerged. Based on results from pore network modelling, Chauveteau (1981) demonstrated that polymer flow in porous media may at some rate be influenced by the prior history. In this paper, polymer memory effects could be evaluated at the Darcy scale by history matching the pressure drop between individual pressure ports and the producer as a function of injection rate (conventional method). Since the number of successive contraction events increases with radial distance, the polymer has a different pre-history at the various pressure ports. Rheology curves obtained from history matching the radial flow experiment were overlapping, which shows that there is no influence of geometry on in-situ rheology for the particular HPAM polymer investigated. In addition, the onset of shear-thickening was independent of volumetric injection rate in radial flow

Qualification of New Methods for Measuring In-Situ Rheology of Non-Newtonian Fluids in Porous Media

Pressure drop (ΔP) versus volumetric injection rate (Q) data from linear core floods have typically been used to measure in situ rheology of non-Newtonian fluids in porous media. However, linear flow is characterized by steady-state conditions, in contrast to radial flow where both pressure and shear-forces have non-linear gradients. In this paper, we qualify recently developed methods for measuring in situ rheology in radial flow experiments, and then quantitatively investigate the robustness of these methods against pressure measurement error. Application of the new methods to experimental data also enabled accurate investigation of memory and rate effects during polymer flow through porous media. A radial polymer flow experiment using partially hydrolyzed polyacrylamide (HPAM) was performed on a Bentheimer sandstone disc where pressure ports distributed between a central injector and the perimeter production line enabled a detailed analysis of pressure variation with radial distance. It has been suggested that the observed shear-thinning behavior of HPAM solutions at low flux in porous media could be an experimental artifact due to the use of insufficiently accurate pressure transducers. Consequently, a generic simulation study was conducted where the level of pressure measurement error on in situ polymer rheology was quantitatively investigated. Results clearly demonstrate the robustness of the history match methods to pressure measurement error typical for radial flow experiments, where negligible deviations from the reference rheology was observed. It was not until the error level was increased to five-fold of typical conditions that significant deviation from the reference rheology emerged. Based on results from pore network modelling, Chauveteau (1981) demonstrated that polymer flow in porous media may at some rate be influenced by the prior history. In this paper, polymer memory effects could be evaluated at the Darcy scale by history matching the pressure drop between individual pressure ports and the producer as a function of injection rate (conventional method). Since the number of successive contraction events increases with radial distance, the polymer has a different pre-history at the various pressure ports. Rheology curves obtained from history matching the radial flow experiment were overlapping, which shows that there is no influence of geometry on in-situ rheology for the particular HPAM polymer investigated. In addition, the onset of shear-thickening was independent of volumetric injection rate in radial flow

Qualification of New Methods for Measuring In Situ Rheology of Non-Newtonian Fluids in Porous Media

Pressure drop (ΔP) versus volumetric injection rate (Q) data from linear core floods have typically been used to measure in situ rheology of non-Newtonian fluids in porous media. However, linear flow is characterized by steady-state conditions, in contrast to radial flow where both pressure and shear-forces have non-linear gradients. In this paper, we qualify recently developed methods for measuring in situ rheology in radial flow experiments, and then quantitatively investigate the robustness of these methods against pressure measurement error. Application of the new methods to experimental data also enabled accurate investigation of memory and rate effects during polymer flow through porous media. A radial polymer flow experiment using partially hydrolyzed polyacrylamide (HPAM) was performed on a Bentheimer sandstone disc where pressure ports distributed between a central injector and the perimeter production line enabled a detailed analysis of pressure variation with radial distance. It has been suggested that the observed shear-thinning behavior of HPAM solutions at low flux in porous media could be an experimental artifact due to the use of insufficiently accurate pressure transducers. Consequently, a generic simulation study was conducted where the level of pressure measurement error on in situ polymer rheology was quantitatively investigated. Results clearly demonstrate the robustness of the history match methods to pressure measurement error typical for radial flow experiments, where negligible deviations from the reference rheology was observed. It was not until the error level was increased to five-fold of typical conditions that significant deviation from the reference rheology emerged. Based on results from pore network modelling, Chauveteau (1981) demonstrated that polymer flow in porous media may at some rate be influenced by the prior history. In this paper, polymer memory effects could be evaluated at the Darcy scale by history matching the pressure drop between individual pressure ports and the producer as a function of injection rate (conventional method). Since the number of successive contraction events increases with radial distance, the polymer has a different pre-history at the various pressure ports. Rheology curves obtained from history matching the radial flow experiment were overlapping, which shows that there is no influence of geometry on in-situ rheology for the particular HPAM polymer investigated. In addition, the onset of shear-thickening was independent of volumetric injection rate in radial flow.publishedVersio