Computational fluid dynamics (CFD) simulation of velocity and concentration profiles in the vicinity of immobilized Acidithiobacillus ferrooxidans cells

Computational fluid dynamics simulation was used to estimate the flow and ferric iron concentration profiles around a single cell or pairs of cells of A. ferrooxidans, immobilized on the surface of a sulfide crystal. It has been shown that there are significant concentration gradients of ferric iron concentration between the surface of the crystal and the liquid bulk. The difference between the bulk and surface ferric ions concentrations can reach several hundred mg/L. These results can explain the difference between the chemical and biological oxidation rates of metal sulfides in liquid media containing iron ions.     

The Shape of the Urine Stream — From Biophysics to Diagnostics

We develop a new computational model of capillary-waves in free-jet flows, and apply this to the problem of urological diagnosis in this first ever study of the biophysics behind the characteristic shape of the urine stream as it exits the urethral meatus. The computational fluid dynamics model is used to determine the shape of a liquid jet issuing from a non-axisymmetric orifice as it deforms under the action of surface tension. The computational results are verified with experimental modelling of the urine stream. We find that the shape of the stream can be used as an indicator of both the flow rate and orifice geometry. We performed volunteer trials which showed these fundamental correlations are also observed in vivo for male healthy volunteers and patients undergoing treatment for low flow rate. For healthy volunteers, self estimation of the flow shape provided an accurate estimation of peak flow rate (). However for the patients, the relationship between shape and flow rate suggested poor meatal opening during voiding. The results show that self measurement of the shape of the urine stream can be a useful diagnostic tool for medical practitioners since it provides a non-invasive method of measuring urine flow rate and urethral dilation.     

Effect of particle-particle shearing on the bioleaching of sulfide minerals

The biological leaching of sulfide minerals, used for the production of gold, copper, zinc, cobalt, and other metals, is very often carried out in slurry bioreactors, where the shearing between sulfide particles is intensive. In order to be able to improve the efficiency of the bioleaching, it is of significant importance to know the effect of particle shearing on the rate of leaching. The recently proposed concept of ore immobilization allowed us to study the effect of particle shearing on the rate of sulfide (pyrite) leaching by Thiobacillus ferrooxidans. Using this concept, we designed two very similar bioreactors, the main difference between which was the presence and absence of particle-particle shearing. It was shown that when the oxygen mass transfer was not the rate-limiting step, the rate of bioleaching in the frictionless bioreactor was 2.5 times higher than that in a bioreactor with particle friction (shearing). The concentration of free suspended cells in the frictionless bioreactor was by orders of magnitude lower than that in the frictional bioreactor, which showed that particle friction strongly reduces the microbial attachment to sulfide surface, which, in turn, reduces the rate of bioleaching. Surprisingly, it was found that formation of a layer of insoluble iron salts on the surface of sulfide particles is much slower under shearless conditions than in the presence of particle-particle shearing. This was explained by the effect of particle friction on liquid-solid mass transfer rate. The results of this study show that reduction of the particle friction during bioleaching of sulfide minerals can bring important advantages not only by increasing significantly the bioleaching rate, but also by increasing the rate of gas-liquid oxygen mass transfer, reducing the formation of iron precipitates and reducing the energy consumption. One of the efficient methods for reduction of particle friction is ore immobilization in a porous matrix.     

The Preparation of Electrohydrodynamic Bridges from Polar Dielectric Liquids

Horizontal and vertical liquid bridges are simple and powerful tools for exploring the interaction of high intensity electric fields (8-20 kV/cm) and polar dielectric liquids. These bridges are unique from capillary bridges in that they exhibit extensibility beyond a few millimeters, have complex bi-directional mass transfer patterns, and emit non-Planck infrared radiation. A number of common solvents can form such bridges as well as low conductivity solutions and colloidal suspensions. The macroscopic behavior is governed by electrohydrodynamics and provides a means of studying fluid flow phenomena without the presence of rigid walls. Prior to the onset of a liquid bridge several important phenomena can be observed including advancing meniscus height (electrowetting), bulk fluid circulation (the Sumoto effect), and the ejection of charged droplets (electrospray). The interaction between surface, polarization, and displacement forces can be directly examined by varying applied voltage and bridge length. The electric field, assisted by gravity, stabilizes the liquid bridge against Rayleigh-Plateau instabilities. Construction of basic apparatus for both vertical and horizontal orientation along with operational examples, including thermographic images, for three liquids (e.g., water, DMSO, and glycerol) is presented.     

Foam separation of microbial cells

Batch foam separation has been employed to separate Saccharomyces carlsbergensis cells from their broth without the use of any external surface-active agent. A model has been developed to predict the foamate cell concentration as well as the variation of cell concentration in the bulk liquid in the foam column as a function of time. The model assumes a linear equilibrium relation between the cell concentrations at the interface and the bulk. The foam has interface as well as interstitial liquid. The interface is assumed to be in equilibrium with the interstitial liquid, which in turn is assumed to have the same concentration as the bulk. The interfacial area is calculated by assuming the foam bubbles to be pentagonal dodecahedral in shape. The model has been found to explain the results of foam separation of cells quite well, particularly with respect to the effect of bubble size and aeration rate.     

Critical temperature estimation of bulk and confined atomic fluid using vapour−liquid interfacial free energy

The critical temperatures of bulk and confined atomic fluids are investigated using values of the vapour?liquid interfacial free energy of coexistence obtained from grand-canonical transition-matrix Monte Carlo simulations using a histogram reweighting technique. The temperature corresponding to zero interfacial free energy of coexistence is the estimated critical temperature for the system under investigation. Slit width of confined atomic fluid for this investigation is varied from 40 to 1 fluid particle diameter. The obtained critical temperatures have shown nonlinear monotonic trend with inverse of slit width. Moreover, five different linear regimes of critical temperature are observed in the studied range of slit width. Interestingly, in the slit width range of less than two fluid particle diameters, the critical temperature approaches two-dimensional value and remains approximately indifferent with a decrease in slit width up to one fluid particle diameter. This investigation also reveals that the critical temperature of bulk and confined atomic fluid estimated using the vapour?liquid interfacial free energy of coexistence is within reasonable accuracy with that obtained using the simplified form of scaling law.     

Intraparticle diffusion alters the dynamic response of immobilized cell/enzyme columns

The effect of intra-particle tracer diffusion on the transient response of a fixed-bed column containing porous Ca-alginate beads is investigated experimentally. Dynamic response experiments are carried out using acetone solutions as tracer, whose concentration in the effluent stream is monitored on-line using a UV analyzer. Comparison of the response of such columns for two particle sizes (radii of 2 and 1?mm) to that of otherwise identical beds filled with solid glass particles of equal size reveals a substantial difference, mainly characterized by a trailing of the effluent concentration-vs-time curves at longer times. This cannot be explained by assuming a change in the effective porosity of the system, nor a change in the hydrodynamic dispersion. Following independent experimental determination of the pertinent physical parameters, a model based on the tanks-in-series concept [1,?2] is implemented on a personal computer and its predictions are compared to the experimental data. The essential assumption of the model is that tracer convection in the bulk liquid is substantially faster than intra-particle diffusion and, as a result, a bead is always surrounded by fluid of uniform (albeit time-dependent) concentration. In the absence of external mass transfer resistances and assuming that the porous nature of the Ca-alginate beads does not substantially alter the hydrodynamic dispersion in the column, the agreement between model and experiment is remarkably good. This leads to the suggestion that the observed response can be explained as the combined result of (fast) tracer convection in the bulk liquid and (slower) tracer diffusion from the bulk liquid to the beads.     

A model for oxygen supply in fixed bed reactors with immobilized hybridoma cells

In fixed bed reactors with animal cells immobilized in macroporous carriers sufficient oxygen supply is a critical parameter. For modelling of the oxygen consumption and the oxygen profile in a fixed bed oxygen gradients within the porous carriers and along the length of the fixed bed have to be considered. For the complex geometry of the fixed bed a model structure was assumed, that allows the calculation of the oxygen profile. The model for oxygen supply of the immobilized cells included the transport resistance from the bulk fluid into the carriers and diffusion within the carriers. The model was compared with experimental data obtained with a hybridoma cell line for production of monoclonal antibodies. Model calculations and experimental data agree rather well. The mean volume-specific oxygen uptake rate as an indicator for the cell activity increased with the superficial flow velocity of the bulk liquid flow, and did not depend on the length of the fixed bed in the range tested. This indicates, that the convective transport from the bulk liquid flow between the carriers to the outer surface of the carriers is a dominating transport resistance besides the diffusive oxygen supply within the carriers.     

Non‐homogeneous biofilm modeling applied to bioleaching processes

A two‐dimensional non‐homogeneous biofilm model is proposed for the first time to study chemical and biochemical reactions at the microorganism scale applied to biological metal leaching from mineral ores. The spatial and temporal relation between these reactions, microorganism growth and the morphological changes of the biofilm caused by solid inorganic precipitate formation were studied using this model. The model considers diffusion limitations due to accumulation of inorganic particles over the mineral substratum, and allows the study of the effect of discrete phases on chemical and microbiological mineral solubilization. The particle‐based modeling strategy allowed representation of contact reactions between the microorganisms and the insoluble precipitates, such as those required for sulfur attack and solubilization. Time‐dependent simulations of chemical chalcopyrite leaching showed that chalcopyrite passivation occurs only when an impervious solid layer is formed on the mineral surface. This mineral layer hinders the diffusion of one kinetically determinant mineral‐attacking chemical species through a nearly irreversible chemical mechanism. Simulations with iron and sulfur oxidizing microorganisms revealed that chemolithoautotrophic biofilms are able to delay passivation onset by formation of corrosion pits and increase of the solid layer porosity through sulfur dissolution. The model results also show that the observed flat morphology of bioleaching biofilms is favored preferentially at low iron concentrations due to preferential growth at the biofilm edge on the surface of sulfur‐forming minerals. Flat biofilms can also be advantageous for chalcopyrite bioleaching because they tend to favor sulfur dissolution over iron oxidation. The adopted modeling strategy is of great interest for the numerical representation of heterogeneous biofilm systems including abiotic solid particles. Biotechnol. Bioeng. 2010;106: 660–676. © 2010 Wiley Periodicals, Inc.     

Effects of key parameters in recycling of metals from petroleum refinery waste catalysts in bioleaching process

Environmental laws concerning spent catalysts disposal have become increasingly more severe in recent years. Due to the toxic nature of spent catalysts, their disposal can pollute the environment. The recovery of heavy metals decreases the environmental impact of the waste catalysts and the recycled product can be further used for industrial purposes. Bio-hydrometallurgical approaches, such as bioleaching, appear to offer good prospects for recovering valuable metals from spent refinery catalysts. Currently, identifying and modifying the parameters that influenced the efficiency of bioleaching is important for industrial sector. The biological system can be further improved through optimizing the bioleaching parameters, such as the nutrient culture media, amount of oxygen and carbon dioxide, pH, temperature, inoculum, metal resistance of microorganisms, chemistry of solid waste, particle size of solid waste, solid liquid ratio, bioleaching period, size of substrate, shaking speed, and also the development of more effective bioleaching microorganisms. In our previous review (Asghari et al. in J Ind Eng Chem 19:1069–1081, 2013), information available in the literature on the bioleaching fundamentals of spent catalysts with a focus on recent developments was reviewed in detail. In this study, the effects of most important factors that influence an efficient bioleaching process of spent refinery catalysts with the hope that these valuable and useful data can help determine the most efficient process will be discussed. The details of metals recovery with a focus on the effects of different variables in the bioleaching such as reaction time, pulp density, initial pH, particle size, nutrient concentration, temperature and buffer will also be presented.     

Mesoscopic dynamics of colloids simulated with dissipative particle dynamics and fluid particle model

We report results of numerical simulations of complex fluids, using a combination of discrete-particle methods. Our molecular modeling repertoire comprises three simulation techniques: molecular dynamics (MD), dissipative particle dynamics (DPD), and the fluid particle model (FPM). This type of model can depict multi-resolution molecular structures (see the Figure) found in complex fluids ranging from single micelle, colloidal crystals, large-scale colloidal aggregates up to the mesoscale processes of hydrodynamical instabilities in the bulk of colloidal suspensions. We can simulate different colloidal structures in which the colloidal beds are of comparable size to the solvent particles. This undertaking is accomplished with a two-level discrete particle model consisting of the MD paradigm with a Lennard-Jones (L-J) type potential for defining the colloidal particle system and DPD or FPM for modeling the solvent. We observe the spontaneous emergence of spherical or rod-like micelles and their crystallization in stable hexagonal or worm-like structures, respectively. The ordered arrays obtained by using the particle model are similar to the 2D colloidal crystals observed in laboratory experiments. The micelle shape and its hydrophobic or hydrophilic character depend on the ratio between the scaling factors of the interactions between colloid–colloid to colloid–solvent. Unlike the miscellar arrays, the colloidal aggregates involve the colloid–solvent interactions prescribed by the DPD forces. Different from the assumption of equilibrium growth, the two-level particle model can display much more realistic molecular physics, which allows for the simulation of aggregation for various types of colloids and solvent liquids over a very broad range of conditions. We discuss the potential prospects of combining MD, DPD, and FPM techniques in a single three-level model. Finally, we present results from large-scale simulation of the Rayleigh–Taylor instability and dispersion of colloidal slab in 2D and 3D. Electronic supplementary material to this paper can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s00894-001-0068-3.Electronic Supplementary Material available.     

Target delivery in a microfluidic immunosensor

A study is presented that examines the effect of microfluidic mixing elements on direct and sandwich assays performed in microchannels. Patterned grooves were embossed in the top of microchannels made in PDMS using soft lithography. The grooves redirected the fluid flowing in the channel, enhancing delivery of the target from the bulk fluid to the surface and preventing the formation of a depletion layer at the surface. Comparing assays in grooved and plain channels demonstrated that the mixers improved assay results by 26-46%. A computational flow analysis showed that the grooves caused virtual particles in the bulk flow to come close to the surface ( approximately 11 microm) which is consistent with the signal increase seen experimentally. Direct assays for several concentrations of CY5-labeled biotin were performed in the microchannels. The mixers also improved signal intensity in sandwich assays for botulinum toxin which required mixing of the reagents as well as the direction of the target to the surface.     

Spatial and temporal resolution of shear in an orbiting petri dish

It is well documented that physiological and morphological properties of anchored cells are influenced by fluid shear stress. Common orbital shakers provide a means of simultaneously applying shear stress to cells for tens to hundreds of cases by loading the shaker with multiple dishes. However, the complex flow in orbiting dishes is amenable to analytical solution for resolving shear created by the fluid motion only for simplified conditions. The only existing quantification of shear in this flow is an equation that estimates a constant scalar value of shear for the entire surface of the dish. In practice, wall shear stress (WSS) will be oscillatory rather than steady due to the travelling waveform and will vary across the surface of the dish at any instant in time. This article presents a computational model that provides complete spatial and temporal resolution of WSS over the bottom surface of a dish throughout the orbital cycle. The model is reasonably well validated by the analytical solution, with resultant WSS magnitudes that are within 0.99 ± 0.42 dyne/cm(2) . The model results were compared to tangential WSS magnitudes obtained using one-dimensional optical velocimetry at discreet locations on the bottom of an orbiting dish. The experimental minimum and maximum WSS at 1 mm from the center of the dish were 6 and 7 dyne/cm(2) , respectively, whereas WSS generated from the computational model ranged from 0.5 to 8.5 dyne/cm(2) . The experimental minimum and maximum WSS at 12 mm from the center of the dish were 6 and 16 dyne/cm(2) , respectively, whereas WSS generated from the computational model ranged from 0.5 to 14 dyne/cm(2) . Discrepancies between the experimental and computational data may be attributed to a sparse sampling rate for the experimental probe, a sharp gradient at the sample area which could cause the unidirectional probe to be inaccurate if its location were not precise, and too few particles to track and a scattering of the signal by the free surface when the liquid is shallow.     

Modelling of pyrolysis of large wood particles

A fully transient mathematical model has been developed to describe the pyrolysis of large biomass particles. The kinetic model consists of both primary and secondary reactions. The heat transfer model includes conductive and internal convection within the particle and convective and radiative heat transfer between the external surface and the bulk. An implicit Finite Volume Method (FVM) with Tridiagonal Matrix Algorithm (TDMA) is employed to solve the energy conservation equation. Experimental investigations are carried out for wood fines and large wood cylinder and sphere in an electrically heated furnace under inert atmosphere. The model predictions for temperature and mass loss histories are in excellent agreement with experimental results. The effect of internal convection and particle shrinkage on pyrolysis behaviour is investigated and found to be significant. Finally, simulation studies are carried out to analyze the effect of bulk temperature and particle size on total pyrolysis time and the final yield of char.     

Apparent zero-order kinetics of phenol biodegradation by substrate-inhibited microbes at low substrate concentrations

The reaction kinetics for phenol biodegradation at low substrate concentrations can be estimated based on the analysis of changes in the dissolved oxygen concentration in the bulk liquid during biodegradation. The measured oxygen concentration changes with an interesting behavior as biodegradation proceeds. The oxygen concentration in the bulk liquid decreases rapidly in the early stages of degradation and subsequently decreases linearly and then rapidly recovers to the initial saturated level. Taking into account the oxygen transfer rate between gas and liquid phases and oxygen consumption rate by microbes, the change in the dissolved oxygen concentration can be simulated with an unsteady state mass balance equation and three kinetic models for the rate of phenol metabolism: a substrate-inhibited model; a zero-order model; and a combined model. In the combined model, it is assumed that, at phenol concentrations above 10 mg/L, the degradation rate is expressed by a substrate-inhibited model; whereas at concentrations below 10 mg/L the zero-order model is applied. It was found that the characteristics of the change in the dissolved oxygen concentration, especially the rapid increase at the end of degradation, can only be described by the combined kinetic model. This result suggests that conventional Haldane-type kinetics would be unsuitable for estimating the phenol consumption rate at low phenol concentrations, in particular, at concentrations less than 10 mg/L. (c) 1996 John Wiley & Sons, Inc.     

Single-step stereolithography of complex anatomical models for optical flow measurements

Transparent stereolithographic rapid prototyping (RP) technology has already demonstrated in literature to be a practical model construction tool for optical flow measurements such as digital particle image velocimetry (DPIV), laser doppler velocimetry (LDV), and flow visualization. Here, we employ recently available transparent RP resins and eliminate time-consuming casting and chemical curing steps from the traditional approach. This note details our methodology with relevant material properties and highlights its advantages. Stereolithographic model printing with our procedure is now a direct single-step process, enabling faster geometric replication of complex computational fluid dynamics (CFD) models for exact experimental validation studies. This methodology is specifically applied to the in vitro flow modeling of patient-specific total cavopulmonary connection (TCPC) morphologies. The effect of RP machining grooves, surface quality, and hydrodynamic performance measurements as compared with the smooth glass models are also quantified.     

Direct observation of intraparticle equilibration and the rate-limiting step in adsorption of proteins in chromatographic adsorbents with confocal laser scanning microscopy

The adsorption of different proteins in a single biospecific and hydrophobic adsorbent particle for preparative protein chromatography has been observed directly by confocal laser scanning microscopy as a function of time at a constant bulk concentration c(b). The bulk concentration was in the non-linear part of the adsorption isotherm. At all times the concentration of free protein at the particle surface was almost equal to the bulk content indicating that external mass transfer resistance is not rate limiting for the adsorption under these conditions. Inside the particles a distinct maximum in adsorbed and free protein concentration that moved inside to a distance of approximately 0.2 R (R particle radius) from the particle surface, was observed. This is due to a decreasing solid-phase density and adsorptive capacity in the particle between 0.8 R and R indicating that the fraction of macropores (or void space) is larger in the outer than in the inner part of the adsorbent particles. By increasing the bulk concentration by a factor of 10 the equilibration time was reduced by about the same magnitude. This is in agreement with the concentration dependence of the effective pore diffusion coefficient D(p,eff)=D(p)/[epsilon(p)[1+nK/(K +c)(2)]] derived from the mass conservation relations describing the adsorption process. The time dependence protein adsorption up to approximately 90% of the equilibration value q* could be described by a bilinear free driving force model. The rapid equilibration in the outer part of the particle with a half-life time of approximately 100 s in the studied systems accounted for 0.3-0.4 q*. The slower equilibration with a up to ten times longer half-life time, was the adsorption in the inner part of the particle that outside 0.5 R accounts for 0.5-0.6 q*. These data were compared with literature data for batch adsorption of proteins in biospecific, hydrophobic and ion-exchange adsorbents. They could also be described by a bilinear free driving force model, with about the same quantitative results as obtained for similar conditions in the single particle experiments. The static adsorption parameters, maximum binding site concentration n, and dissociation constant for the protein binding to a binding site K, were determined from Scatchard plots. For the same protein-adsorbent system the plots changed from linear to non-linear with increasing n. This change occurred when the average distance between adjacent binding sites become of the same order of magnitude as the size of the binding site or adsorbed protein. This causes a shielding of free binding sites increasing with n and the concentration of adsorbed protein, yielding a concentration dependence in K. These results show that for a high throughput and rapid adsorption in preparative chromatography, the adsorption step should be carried out in the non-linear part of the adsorption isotherm with concentrations up to c(b) where q*/c(b)>/=10 to obtain high protein recoveries. To avoid tailing due to the flow of adsorbed proteins in the inner part of the particles further into the particles at the start of the desorption, and to speed up desorption rates, protein adsorption in the particle within 0.5 R from the particle center should be avoided. This requires the further development of suitable pellicular particles for preparative protein chromatography that meet this requirement.     

Modeling micropatterned antigen-antibody binding kinetics in a microfluidic chip

The reaction kinetics of antigen-antibody binding in the electrokinetically controlled microfluidic heterogeneous immunoassays has been investigated by numerical simulations. A two-dimensional computational model was employed to include the mass transport (convection and diffusion) and binding reaction between the antigen in the bulk flow and the immobilized antibody at the channel surface. The influence of the bulk velocity, the concentrations of the antibody and antigen, and the geometry of the microchips was studied for a variation of conditions and the guidance for designing of microfluidic immunoassay was provided. The model also shows that electrokinetically driven immunoassays have better reaction kinetics than pressure-driven ones, resulting from the plug-like velocity profile. Finally, a multi-patch immunoassay chip was analyzed and the reaction kinetics was optimized by rearranging the reaction patches at the channel surfaces.     

Effects of biofilm structures on oxygen distribution and mass transport

Aerobic biofilms were found to have a complex structure consisting of microbial cell clusters (discrete aggregates of densely packed cells) and interstitial voids. The oxygen distribution was strongly correlated with these strutures. The voids facilitated oxygen transport from the bulk liquid through the biofilm, supplying approximately 50% of the total oxygen consumed by the cells. The mass transport rate from the bulk liquid is influenced by the biofilm structure; the observed exchange surface of the biofilm is twice that calculated for a simple planar geometry. The oxygen diffusion occurred in the direction normal to the cluster surfaces, the horizontal and vertical components of the oxygen gradients were of equal importance. Consequently, for calculations of mass transfer rates a three-dimensional model is necessary. These findings imply that to accurately describe biofilm activity, the relation between the arrangement of structural components and mass transfer must be undrstood. (c) 1994 John Wiley & Sons, Inc.     

Pressure effects on mechanisms of charge transport across bilayer membranes

Ion transport across diphytanoylphosphatidylcholine/decane bilayer membranes was measured as a function of hydrostatic pressure over the range 0.1-100 MPa (1-1000 atm). Carrier-mediated K+ conductance decreased with increasing pressure, yielding positive activation volumes of 45 A3 per complex for valinomycin mediated transport, and 74 A3 per complex in the case of nonactin. Comparison with the known pressure dependence of the viscosity of bulk alkane liquids supports the view that the rate limiting step for carrier-mediated transport is the translocation of the carrier-cation complex across an essentially fluid hydrocarbon membrane core. The parameters characterizing transient conductance by the hydrophobic anions, dipicrylaminate and tetraphenylborate, by contrast, were found to be insensitive to pressure over the range available. This was also the case for the steady-state conductance observed at elevated concentrations of both tetraphenylborate and the hydrophobic cation, tetraphenylarsonium. The quasi-stationary conductance observed at elevated concentrations of dipicrylaminate did, however, decrease significantly with increasing pressure, indicating a positive activation volume of 20 A3 per ion. Alternative explanations of this more complex response of hydrophobic ions to pressure are considered. Ancillary measurements of specific membrane capacitance revealed an increase of about 10% with an increase of pressure to 100 MPa, yielding an estimated membrane compressibility on the order of 10(-9) m2 X N-1, comparable to that of bulk liquid hydrocarbons.