[Show abstract][Hide abstract] ABSTRACT: Transcription of genes coding for xylanolytic and cellulolytic enzymes in Aspergillus niger is controlled by the transactivator XlnR. In this work we analyse and model the transcription dynamics in the XlnR regulon from time-course data of the messenger RNA levels for some XlnR target genes, obtained by reverse transcription quantitative PCR (RT-qPCR). Induction of transcription was achieved using low (1 mM) and high (50 mM) concentrations of D-xylose (Xyl). We investigated the wild type strain (Wt) and a mutant strain with partial loss-of-function of the carbon catabolite repressor CreA (Mt).
An improved kinetic differential equation model based on two antagonistic Hill functions was proposed, and fitted to the time-course RT-qPCR data from the Wt and the Mt by numerical optimization of the parameters. We show that perturbing the XlnR regulon with Xyl in low and high concentrations results in different expression levels and transcription dynamics of the target genes. At least four distinct transcription profiles were observed, particularly for the usage of 50 mM Xyl. Higher transcript levels were observed for some genes after induction with 1 mM rather than 50 mM Xyl, especially in the Mt. Grouping the expression profiles of the investigated genes has improved our understanding of induction by Xyl and the according regulatory role of CreA.
The model explains for the higher expression levels at 1 mM versus 50 mM in both Wt and Mt. It does not yet fully encapsulate the effect of partial loss-of-function of CreA in the Mt. The model describes the dynamics in most of the data and elucidates the time-dynamics of the two major regulatory mechanisms: i) the activation by XlnR, and ii) the carbon catabolite repression by CreA.
Full-text · Article · Dec 2015 · BMC Systems Biology
[Show abstract][Hide abstract] ABSTRACT: Tubular photobioreactors (PBR) have great potential for microalgae cultivation due to its high productivity compared with open ponds. However, the energy uptake for fluid circulation and mixing is significant, impacting the operation and production costs. In this work, we investigate by CFD simulation the effect of wall turbulence promoters, i.e. profiles at the inner tube wall, at low flow velocities (0.1–0.3 m/s). The use of these wall turbulence promoters is compared to the mixing behaviour in standard tubular PBRs at flow velocity of 0.5 m/s. It was found that the wall turbulence promoters have at flow velocities of 0.2–0.25 m/s better mixing behaviour as in standard PBRs while the energy uptake is 60–80% lower.
[Show abstract][Hide abstract] ABSTRACT: Energy requirements for resource transport of algae cultivation are unknown. This work describes the quantitative analysis of energy requirements for water and CO2 transport. Algae cultivation models were combined with the quantitative logistic decision model ‘BeWhere’ for the regions Benelux (Northwest Europe), southern France and Sahara. For photobioreactors, the energy consumed for transport of water and CO2 turns out to be a small percentage of the energy contained in the algae biomass (0.1–3.6%). For raceway ponds the share for transport is higher (0.7–38.5%). The energy consumption for transport is the lowest in the Benelux due to good availability of both water and CO2. Analysing transport logistics is still important, despite the low energy consumption for transport. The results demonstrate that resource requirements, resource distribution and availability and transport networks have a profound effect on the location choices for algae cultivation.
No preview · Article · Mar 2015 · Bioresource Technology
[Show abstract][Hide abstract] ABSTRACT: Environmental impact is an essential aspect for the introduction of algae production systems. As information of large scale algae production is hardly available, process simulation is the only way to evaluate environmental sustainability in an early phase of process design. Simulation results allow the evaluation of production and design scenarios, and reveal the potential to improve the Life Cycle Performance of algae production systems. In this work, we discuss how choices in the process design of algae production systems (cultivation, biorefinery and the supply chain) advance LCA-results.
[Show abstract][Hide abstract] ABSTRACT: This work concerns the degradation of the nutritional compounds glucoraphanin (GR) and vitamin C (Vc), and the inactivation of the enzyme myrosinase (MYR) in broccoli (Brassica oleracea var. italica) during drying with air temperatures in the range of 30–60 °C. Dynamic optimization is applied to find the optimized temperature trajectories that minimize degradation and inactivation. Simulation and experimental results for optimized temperature trajectories are compared to constant inlet air temperature drying at 40 and 50 °C. The results show that with the optimized temperature trajectories the retention of GR, MYR and Vc improved significantly. Moreover, the experiments show that degradation and inactivation during drying is slower than expected from kinetic studies. The deviation is explained from the difference in the physical state of the samples used in the drying experiments, i.e. original plant tissue versus the grounded state of the plant tissue used in the experiments for the kinetic studies. The results indicate that besides temperature and moisture content the physical state is also an important aspect in the degradation of nutritional compounds and enzymes.
Full-text · Article · Nov 2014 · Lebensmittel-Wissenschaft und-Technologie
[Show abstract][Hide abstract] ABSTRACT: The analyses of algae biorefinery performance are commonly based on fixed performance data for each processing step. In this work, we demonstrate a model-based combinatorial approach to derive the design-specific upstream energy consumption and biodiesel yield in the production of biodiesel from microalgae. Process models based on mass and energy balances and conversion relationships are presented for several possible process units in the algae processing train. They allow incorporating the effects of throughput capacity and process conditions, which is not possible in the data-based approach. Therefore, the effect of choices in the design on the overall performance can be quantified. The process models are organised in a superstructure to evaluate all combinations of routings. First, this is done for selected fixed design conditions, which is followed by optimisation of the process conditions for each route by maximising the net energy ratio (NER), based on upstream energy consumption and biodiesel yield. A scenario based on current energy production and state-of-the art techniques for algae processing is considered. The optimised process conditions yield NER values which are up to about 30% higher than those for fixed process conditions. In addition, the approach allows a quantitative bottleneck analysis for each process route. The model-based approach proves to be a versatile tool to guide the design of efficient microalgae processing systems.
[Show abstract][Hide abstract] ABSTRACT: In this work, the Flory Huggins Free Volume theory is used to interpret the sorption isotherms of broccoli from its composition and using physical properties of the components. This theory considers the mixing properties of water, biopolymers and solutes and has the potential to describe the sorption isotherms for varying product moisture content, composition and temperature. The required physical properties of the pure components in food became available in recent years and allow now the prediction of the sorption isotherms with this theory. Sorption isotherm experiments have been performed for broccoli florets and stalks, at two temperatures. Experimental data shows that the Flory Huggins Free Volume (FHFV) theory represents the sorption isotherm of fresh and blanched broccoli samples accurately. The results also show that blanching affects the sorption isotherm due to the change of composition via leaching solutes and the change of interaction parameter due to protein denaturation.
[Show abstract][Hide abstract] ABSTRACT: This work concerns the combined optimization of the retention of bioactive components and energy efficiency during drying of broccoli. Kinetics for the degradation of glucosinolates, vitamin C and drying of broccoli are used to calculate optimal drying trajectories for the control variables air flow rate and temperature. It is shown from plots of the optimal drying trajectories in moisture-temperature state diagrams with degradation and drying rates, that areas with high degradation rates are circumvented. The optimized drying strategies result in significant improvement of energy efficiency (65%) and vitamin C retention of 55%.
No preview · Article · Feb 2014 · Journal of Food Engineering
[Show abstract][Hide abstract] ABSTRACT: This work presents an approach to compute dryer energy efficiency using air flowrate step responses and establish a link between drying energy efficiency and process controllability. The approach is based on the temperature drop between the dryer inlet and outlet air under adiabatic conditions and so decouples water evaporation from heat loss and product heating effects on dryer temperature drop. As such, the computation is accurate even for dryers with significant heat losses where the traditional use of actual temperature drop measurements is grossly inaccurate. The approach is tested and verified on two experimental case studies involving significant heat losses: the first, a continuous fluidized-bed dryer (from literature); the second, a conventional and zeolite wheel-assisted batch dryer designed in the current study.
No preview · Article · Dec 2013 · Drying Technology
[Show abstract][Hide abstract] ABSTRACT: This work establishes a relationship between dryer energy performance and controllability using energy balances and process resiliency analysis. It is shown that using the process gain matrix, the dryer energy efficiency can be reliably calculated with conditions for simultaneous controllability improvement established. By incorporating a drying rate modifying system such as a desiccant dehumidifier as an add-on, these conditions are shown to be achievable due to the extra dehumidification which can be manipulated using the additional degrees of freedom introduced by the sorption system. Due to the adsorbent regulation properties which are enhanced by high-temperature regeneration, the resilience of energy performance to disturbances is significantly improved compared to conventional dryers. Also, a desiccant system performance indicator, the "adsorber-regenerator net energy efficiency ARNEE" is introduced and it is shown that energy efficiency improvement is possible only if the ARNEE is greater than the energy efficiency of the stand-alone dryer.
No preview · Article · Dec 2013 · Computers & Chemical Engineering
[Show abstract][Hide abstract] ABSTRACT: To evaluate microalgae production in large scale open ponds under different climatologic conditions, a model-based framework is used to study the effect of light conditions, water temperature and reactor design on trends in algae productivity. Scenario analyses have been done for two algae species using measured weather data of the Netherlands and Algeria. The effects of temperature control, photo-inhibition and using monthly or yearly fixed biomass concentrations are estimated by a sensitivity analysis. The calculation-based results show that climate conditions such as solar irradiation and temperature dynamics play an important role in open raceway ponds. In moderate climate zones low and high temperatures over a season suppress growth. At high latitudes this effect is important as light levels vary much during the day and between seasons. Optimal biomass concentrations in ponds depend on location, pond depth and algae species. Pond design, location and algae species interact and productivity cannot be based solely on general or assumed efficiencies. It is essential to select algae species that have a suitable growth rate, light absorption coefficient and the ability to grow over a broad temperature range. The presented approach gives a framework to validate specific cultivation systems.
[Show abstract][Hide abstract] ABSTRACT: Microalgae productivity in tubular photobioreactors depends on algae species, location, tube diameter, biomass concentration, distance between tubes and for vertically stacked systems, the number of horizontal tubes per stack. A simulation model for horizontal and vertically stacked horizontal tubular reactors was made to quantify the effect of these decision variables on production yield. The model uses reactor dimensions, dynamic sunlight patterns over the day and year, and growth characteristics of algae species as inputs. Scenario studies were done to study the effect of decision variables on reactor performance in The Netherlands, France and Algeria. Results indicate that the areal biomass productivity in vertically stacked photobioreactors is 25–70% higher than in plain horizontal systems. Reactor design is location specific because light conditions differ. In The Netherlands, the best horizontal distance between tubes is 0.05 m for horizontal and 0.25 m for vertical systems. For France and Algeria, the best horizontal distance between vertical systems is 0.20 m and 0.15 m respectively. System performance can be improved further by using light reflection materials on the ground surface. Improving the transparency properties of tube material does not significantly affect areal productivity.
[Show abstract][Hide abstract] ABSTRACT: This work presents a mixed integer nonlinear programming method for the design of energy efficient multistage adsorption dryers within product temperature and moisture constraints. The aim is to find the adsorbent type and properties that minimize specific energy consumption. The results show that the adsorbents chosen in each stage have highest sorption capacities for corresponding drying air conditions. Heat requirements are matched so, zero utility energy is spent regenerating the second stage adsorbent. The adsorbent flow speeds are such that the first stage is optimized for dehumidification and the second for heat recovery. Overall, the optimal system reduces specific energy consumption by about 64% compared to a conventional system at the same drying temperature. Also, drying capacity is improved which permits the use of smaller dryers.
No preview · Article · Dec 2012 · Computer Aided Chemical Engineering
[Show abstract][Hide abstract] ABSTRACT: This work shows from energy balances and process resiliency analysis, the relationship between dryer controllability and energy performance. It is shown that using the process gain matrix, the dryer temperature drop and hence, energy efficiency can be reliably calculated. Conditions necessary for simultaneous energy efficiency and controllability improvement are established. By pre-conditioning the drying air using a desiccant adsorption system, such conditions are shown to be achievable for the same input choice as a conventional dryer. Also, extra degrees of freedom introduced by the desiccant system promote controllability with the advantage best exploited using full multivariable control. Energy efficiency disturbance resilience is also improved.
No preview · Article · Dec 2012 · Computer Aided Chemical Engineering
[Show abstract][Hide abstract] ABSTRACT: Cells react to various forms of physical phenomena that promote and maintain the formation of tissues. The best example of this are cells of musculoskeletal origin, such as mesenchymal stem cells (MSCs), which consistently proliferate or differentiate under cues from hydrostatic pressure, diffusive mass transport, shear stress, surface chemistry, mechanotransduction, and molecular kinetics. To date, no other cell type shows greater receptiveness to macroscopic and microscopic cues, highlighting the acute sensitivity of MSCs and the importance of physical principles in tissue homeostasis. In this review, we describe the literature that has shown how physical phenomena govern MSCs biology and provide insight into the mechanisms and strategies that can spur new biotechnological applications with tissue biology.
No preview · Article · Sep 2012 · Trends in Biotechnology
[Show abstract][Hide abstract] ABSTRACT: This work presents a mixed integer nonlinear programming (MINLP) formulation for the design of energy-efficient multistage adsorption dryers within constraints on product temperature and moisture content. Apart from optimizing temperatures and flows, the aim is to select the most efficient adsorbent per stage and product to air flow configuration. Superstructure models consisting of commonly used adsorbents such as zeolite, alumina, and silica-gel are developed and optimized for a two-stage, low-temperature, adsorption drying system. Results show that the optimal configuration is a hybrid system with zeolite as the first-stage adsorbent and silica-gel as the second-stage adsorbent in counter-current flow between drying air and product. A specific energy consumption of 2,275 kJ/kg is achieved, which reduces to 1,730 kJ/kg with heat recovery by a heat exchanger. Compared to a conventional two-stage dryer at the same drying temperature, this represents a 59% reduction in energy consumption. The optimal system ensures the exhaust air temperature of the first-stage regenerator is high enough to regenerate the second-stage adsorbent so no utility energy is spent in the second stage. A higher second-stage adsorbent wheel speed favors energy performance as it becomes optimized for energy recovery while the first is optimized for dehumidification. Although this work considers three candidate adsorbents in a two-stage system, the same reasoning can be applied to systems with more stages and adsorbents. The developed superstructure optimization methodology can, by extension, be applied to optimize multistage hybrid drying systems in general for any objective.
No preview · Article · Jun 2012 · Drying Technology
[Show abstract][Hide abstract] ABSTRACT: One of the challenges in genetic network reconstruction is finding experimental designs that maximize the information content in a data set. In this work, the information value of mRNA transcription time course experiments was used to compare experimental designs. The study concerns the dynamic response of genes in the XlnR regulon of Aspergillus niger, with the goal to find the best moment in time to administer an extra pulse of inducing D-xylose. Low and high D-xylose pulses were used to perturb the XlnR regulon. Evaluation of the experimental methods was based on simulation of the regulon. Models that govern the regulation of the target genes in this regulon were used for the simulations. Parameter sensitivity analysis, the Fisher Information Matrix (FIM) and the E-modified criterion were used to assess the design performances. The results show that the best time to give a second D-xylose pulse is when the D-xylose concentration from the first pulse has not yet completely faded away. Due to the presence of a repression effect the strength of the second pulse must be optimized, rather than maximized. The results suggest that the modified E-criterion is a better metric than the sum of integrals of absolute sensitivity for comparing alternative designs.
No preview · Article · Apr 2012 · IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM