Residence time distribution of liquid phase in an external-loop airlift bioreactor

The residence time distribution analysis was used to investigated the flow behaviour in an external-loop airlift bioreactor regarded as a single unit and discriminating its different sections. The experimental results were fitted according to plug flow with superimposed axial dispersion and tank-in-series models, which have proved that it is reasonable to assume plug flow with axial dispersion in the overall reactor, in riser and downcomer sections, as well, while the gas separator should be considered as a perfectly mixed zone. Also, the whole reactor could be replaced with 105-30 zones with perfect mixing in series, while its separate zones, that is the riser with 104-27, the downcomer with 115-35 and the gas separator with 25-5 perfectly mixed zones in series, respectively, depending on gas superficial velocity, A_D/A_R ratio and the liquid feed rate.List of Symbols A _D cross sectional area of downcomer (m²) - A _R cross sectional area of riser (m²) - A ₁ A ₂ length of connecting pipes (m) - Bo Bodenstein number (Bo=vL·L/D _ax (-) - C concentration (kg m^–3) - C residence time distribution function - C ₀ coefficientEquation (12) - C _r dimensionless concentration - D _D diameter of downcomer (m) - D _R diameter of riser column (m) - D _ax axial dispersion coefficient (m²s^–1) - H _d height of gas-liquid dispersion (m) - H _L height of clear liquid (m) - i number of complete circulations - L length of path (m) - m order of moments - N _eq number of perfectly mixed zones in series - n _c circulating number - Q _c recirculating liquid flow rate (m³ s^–1) - q _F liquid feed flow rate (m³s^–1) - Q _G gas flow rate (m³s^–1) - Q _T total liquid flow rate (m³s^–1) - r recycle factor - s exponent inEquation (12) regarded as logarithmic decrement of the oscillating part of RTD curve - t time (s) - t _C circulation time (s) - t _s mean residence time (s) - t ₉₉ time necessary to remove 99% of the tracer concentration (s) - V _A volume of connecting pipes (m³) - V _D volume of downcomer (m³) - V _L liquid volume in reactor (m³) - V _R volume of riser (m³) - V _LD linear liquid velocity in downcomer (m s^–1) - V _LR linear liquid velocity in riser (m s^–1) - V _SLD superficial liquid velocity in downcomer (m s^–1) - V _SLR superficial liquid velocity in riser (m s^–1) - x independent variable inEquation (1) - ¯x mean value of x - z axial coordinate - _GR gas holdup in riser - _m(x) central moment of m order - ² variance - dimensionless time     

Computational modeling of the arterial wall based on layer-specific histological data

Arterial walls typically have a heterogeneous structure with three different layers (intima, media, and adventitia). Each layer can be modeled as a fiber-reinforced material with two families of relatively stiff collagenous fibers symmetrically arranged within an isotropic soft ground matrix. In this paper, we present two different modeling approaches, the embedded fiber (EF) approach and the angular integration (AI) approach, to simulate the anisotropic behavior of individual arterial wall layers involving layer-specific data. The EF approach directly incorporates the microscopic arrangement of fibers that are synthetically generated from a random walk algorithm and captures material anisotropy at the element level of the finite element formulation. The AI approach smears fibers in the ground matrix and treats the material as homogeneous, with material anisotropy introduced at the constitutive level by enhancing the isotropic strain energy with two anisotropic terms. Both approaches include the influence of fiber dispersion introduced by fiber angular distribution (departure of individual fibers from the mean orientation) and take into consideration the dispersion caused by fiber waviness, which has not been previously considered. By comparing the numerical results with the published experimental data of different layers of a human aorta, we show that by using histological data both approaches can successfully capture the anisotropic behavior of individual arterial wall layers. Furthermore, through a comprehensive parametric study, we establish the connections between the AI phenomenological material parameters and the EF parameters having straightforward physical or geometrical interpretations. This study provides valuable insight for the calibration of phenomenological parameters used in the homogenized modeling based on the fiber microscopic arrangement. Moreover, it facilitates a better understanding of individual arterial wall layers, which will eventually advance the study of the structure–function relationship of arterial walls as a whole.     

Concentric-tube airlift bioreactors

Gas holdup investigations were performed in three concentric-tube airlift reactors of different scales of operation (RIMP: 0.070 m³; RIS-1: 2.5 m³; RIS-2: 5.2 m³; nominal volumes). The influences of the top and bottom clearances and the flow resistances at the downcomer entrance were studied using tap water as liquid phase and air as gaseous phase, at atmospheric pressure. It was found that the gas holdup in the individual zone of the reactor: riser, downcomer and gas-separator, as well as that in the overall reactor is affected by the analyzed geometrical parameters in different ways, depending on their effects on liquid circulation velocity. Gas holdup was satisfactorily correlated with Fr, Ga, bottom spatial ratio (B), top spatial ratio (T), gas separation ratio (Y) and downcomer flow resistance ratio (A _d /A _R ). Correlations are presented for gas holdup in riser, downcomer, gas separator and for the total gas holdup in the reactor. All the above stressed the importance of the geometry in dynamic behaviour of airlift reactors.     

BiNChE: A web tool and library for chemical enrichment analysis based on the ChEBI ontology

Background

Ontology-based enrichment analysis aids in the interpretation and understanding of large-scale biological data. Ontologies are hierarchies of biologically relevant groupings. Using ontology annotations, which link ontology classes to biological entities, enrichment analysis methods assess whether there is a significant over or under representation of entities for ontology classes. While many tools exist that run enrichment analysis for protein sets annotated with the Gene Ontology, there are only a few that can be used for small molecules enrichment analysis.

Results

We describe BiNChE, an enrichment analysis tool for small molecules based on the ChEBI Ontology. BiNChE displays an interactive graph that can be exported as a high-resolution image or in network formats. The tool provides plain, weighted and fragment analysis based on either the ChEBI Role Ontology or the ChEBI Structural Ontology.

Conclusions

BiNChE aids in the exploration of large sets of small molecules produced within Metabolomics or other Systems Biology research contexts. The open-source tool provides easy and highly interactive web access to enrichment analysis with the ChEBI ontology tool and is additionally available as a standalone library.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-015-0486-3) contains supplementary material, which is available to authorized users.     

Hydrodynamics in external-loop airlift bioreactors with static mixers

Liquid circulation superficial velocity and gas holdup behaviours were investigated in an external-loop airlift bioreactor of 0.170?m³ liquid volume in gas-induced and forced-circulation-loop operation modes, in the presence of static mixers made of corrugated stainless steel pieces, resulting in packets with the height-to-diameter ratio equal to unity and using non-Newtonian starch solutions as liquid phase. The static mixers were disposed in the riser in three blocks, each with three mixing packets, successively turned 90° to the adjacent mixing element. It was found that in the presence of static mixers and forced-loop operation mode, liquid circulation superficial velocity in the riser section was significantly diminished, while gas holdup increased in a great measure. It was considered that static mixers split the fluid into individual streams and break up the bubbles, resulting in small bubble sizes with a relative homogeneous bubble distribution over riser cross section. They act as supplementary resistances in liquid flow, reducing riser cross sectional area, equivalent with A _D /A _R area ratio diminishing.     

Stochastic modelling of axial dispersion in external-loop airlift bioreactors

The paper presents a model of the motion of a particle subjected to several transport processes in connection with mixing in two phase flow. A residence time distribution technique coupled with a one-dimensional dispersion model was used to obtain the axial dispersion coefficient in the liquid phase, D_ax. The proposed model of D_ax for an external-loop airlift bioreactor is based on the stochastic analysis of the two-phase flow in a cocurrent bubble column and modified for the specific flow in the airlift reactor. The model takes into account the riser gas superficial velocity, the riser liquid superficial velocity, the Sauter bubble diameter, the riser gas hold-up, the downcomer-to-riser cross sectional area ratio. The proposed model can be applied with an average error of ᆨ.     

Effects of downcomer-to-riser cross sectional area ratio on operation behaviour of external-loop airlift bioreactors

Experiments performed in two external-loop airlift bioreactors of laboratory and pilot scale, (1.880–1.189) · 10^–3 m³ and (0.170-0.157)m³, respectively, are reported. The A _D /A _R ratio was varied between 0.111–1.000 and 0.040–0.1225 in the laboratory and pilot contractor respectively.Water and solutions of different coalescence (2-propanol 2% vol, 1 M Na (glucose 50% wt/vol) and rheological behaviour (non-Newtonian starch solutions with consistency index K=0.061–3.518 Pas ⁿ and flow behaviour index n=0.86-0.39), respectively, were used as liquid phase. Compressed air at superficial velocities v _SGR =0.016–0.178 ms^–1 in the laboratory contactor and v _SGR =0.010–0.120 ms^–1 in the pilot contactor, respectively was used as gaseous phase.The A _D /A _R ratio affect gas-holdup behaviour as a result of the influence of A _D /A _R on liquid circulation velocity.Experimental results show that A _D /A _R ratio affect circulation liquid velocity by modifying he resistence to flow and by varying the fraction of the total volume contained in downcomer and riser. A _D /A _R ratio has proven to be the main factor which determines the friction in the reactor. Mixing time increases with increasing of the reactor size and decreases with A _D /A _R decreasing.The volumetric gas-liquid mass transfer coefficient increases with A _D /A _R ratio decreasing, as a result of variations of the liquid velocity with A _D /A _R , which affect interfacial areas.Correlations applicable to the investigated contactors have been presented, together with the fit of some experimental data to existing correlation in literature.List of Symbols A _D downcomer cross sectional area (m²) - A _R riser cross sectional area (m²) - a coefficient in Eq. (9) (-) - a _L gas-liquid interfacial area per unit volume (m^–1) - b coefficient in Eq. (9) (-) - C tracer concentration (kg m^–3) - C tracer concentration at the state of complete mixing (kg m^–3) - c coefficient in Eq. (12) - c _S coefficient in Eq. (5) - D _D downcomer diameter (m) - D _R riser diameter (m) - d _B bubble size (m) - H _D downcomer height (m) - H _d dispersion height (m) - H _L gas-free liquid height (m) - H _R riser height (m) - I inhomogeneity (-) - K consistency index (Pa s ⁿ ) - k _L a volumetric gas-liquid oxygen mass transfer coefficient (s^–1) - m exponent in Eq. (12) (-) - n flow behaviour index (-) - P _G power input due to gassing (W) - t _M mixing time (s) - V _A connecting pipe volume (m³) - V _D downcomer volume (m³) - V _d volume of dispersion (m³) - V _R riser volume (m³) - V _T total reactor liquid volume (m³) - v _SGR riser gas superficial velocity (m s^–1) - _GR riser gas holdup (-) - shear rate (m s^–1) - _app apparent viscosity (Pa s) - shear stress     

Hydrodynamics of non-Newtonian liquids in external-loop airlift bioreactors

In order to obtain further information on the behaviour and optimal design of external-circulation-loop airlift bioreactors, the liquid circulating velocity was studied using highly viscous pseudoplastic solutions of starch and antibiotic biosynthesis liquids of Penicillium chrysogenum, Streptomyces griseus, Streptomyces erythreus, Bacillus licheniformis and Cephalosporium acremonium. Measurements of liquid circulation velocity were made in laboratory and pilot plant external-loop airlift bioreactors, under various conditions concerning gas flow rate, riser liquid height at constant downcomer height, A _D /A _R ratio, using the impulse-response technique. It has been found that these parameters had a significant effect on liquid circulation velocity together with the apparent viscosity and dry weight of the solid phase in the biosynthesis liquids. For the tested liquids, the superficial liquid velocity in the riser section of an external-loop airlift bioreactor may be described by the following equation: where the exponents and the constant c take different values depending on the liquid phase properties and flow regime.     

Modelling mixing parameters in concentric-tube airlift bioreactors

The mixing behaviour of the liquid phase in concentric-tube airlift bioreactors of different scale (RIMP: V_L=0.070 m³; RIS-1: V_L=2.50 m³; RIS-2: V_L=5.20 m³) in terms of mixing time was investigated. This mixing parameter was determined from the output curves to an initial Dirac pulse, using the classical tracer response technique, and analyzed in relation to process and geometrical parameters, such as: gas superficial velocity, x_SGR; top clearance, h_S; bottom clearance, h_B, and ratio of the resistances at downcomer entrance, A_d/A_R. A correlation between the mixing time and the specified operating and geometrical parameters was developed, which was particularized for two flow regimes: bubbly and transition (x_SGRА.08 m/s) and churn turbulent flow (x_SGR> 0.08 m/s) respectively. The correlation was applied in bioreactors of different scale with a maximum error of ᆲ%.     

Performance of industrial scale bioreactors with modified RUSHTON turbine agitators

The data presented here with respect to the behaviour of industrial scale stirred tank bioreactors equipped with modified RUSHTON turbine agitators in the biosynthesis processes of antibiotics are valid for that case that the power consumption is the same as it is in standard RUSHTON turbine agitators. Each modified RUSHTON turbine agitator was obtained through the variation of the blade surface by adding perforations so that the ratio between the perforation surface area and the full surface area (or the surface fraction of the perforations) is 0.36. In the fermentations of Streptomyces aureofaciens, Streptomyces rimosus and Penicillium chrysogenum producing tetracycline, oxytetracyline and penicillin, respectively, in bioreactors equipped with modified RUSHTON turbine agitators, the relative antibiotic production is increased by more than 30% compared to standard bioreactors.