Conceptual and Experimental Tools to Understand Spatial Effects and Transport Phenomena in Nonlinear Biochemical Networks Illustrated with Patchy Switching

Many biochemical systems are spatially heterogeneous and exhibit nonlinear behaviors, such as state switching in response to small changes in the local concentration of diffusible molecules. Systems as varied as blood clotting, intracellular calcium signaling, and tissue inflammation are all heavily influenced by the balance of rates of reaction and mass transport phenomena including flow and diffusion. Transport of signaling molecules is also affected by geometry and chemoselective confinement via matrix binding. In this review, we use a phenomenon referred to as patchy switching to illustrate the interplay of nonlinearities, transport phenomena, and spatial effects. Patchy switching describes a change in the state of a network when the local concentration of a diffusible molecule surpasses a critical threshold. Using patchy switching as an example, we describe conceptual tools from nonlinear dynamics and chemical engineering that make testable predictions and provide a unifying description of the myriad possible experimental observations. We describe experimental microfluidic and biochemical tools emerging to test conceptual predictions by controlling transport phenomena and spatial distribution of diffusible signals, and we highlight the unmet need for in vivo tools.

Kinetics and Mechanisms of Saccharomyces boulardii Release from Optimized Whey Protein-Agavin-Alginate Beads under Simulated Gastrointestinal Conditions

Encapsulation is a process in which a base material is encapsulated in a wall material that can protect it against external factors and/or improve its bioavailability. Among the different encapsulation techniques, ionic gelation stands out as being useful for thermolabile compounds. The aim of this work was to encapsulate Saccharomyces boulardii by ionic gelation using agavins (A) and whey protein (WP) as wall materials and to evaluate the morphostructural changes that occur during in vitro gastrointestinal digestion. Encapsulations at different levels of A and WP were analyzed using microscopic, spectroscopic and thermal techniques. Encapsulation efficiency and cell viability were evaluated. S. boulardii encapsulated at 5% A: 3.75% WP (AWB6) showed 88.5% cell survival after the simulated gastrointestinal digestion; the bead showed a significantly different microstructure from the controls. The mixture of A and WP increased in the survival of S. boulardii respect to those encapsulated with alginate, A or WP alone. The binary material mixture simultaneously allowed a controlled release of S. boulardii by mostly diffusive Fickian mechanisms and swelling. The cell-release time was found to control the increment of the Damköhler number when A and WP were substrates for S. boulardii, in this way allowing greater protection against gastrointestinal conditions.

Experimental determination of nonequilibrium transport parameters reflecting the competitive sorption between Cu and Pb in slag-sand column

Competitive sorption and resulting nonequilibrium transport of Cu and Pb were investigated using slag as a primary sorbent. A series of estimation models were applied based on the equilibrium, and nonequilibrium sorption respectively, and finally calibrated by incorporating the experimentally determined batch kinetic data. When applied individually, the behavior of metals in slag-sand column were well predicted by both equilibrium and nonequilibrium models in CXTFIT code. However, coexisting Cu and Pb exhibited competition for sorption sites, generating an irregular breakthrough curves such as overshoot (higher concentration in effluent than the feed concentration) of Cu and corresponding earlier peak of Pb followed by gradual re-rising. Although two-site nonequilibrium model further considers coupled hydrochemical process, desorption of the Cu from competition made the model prediction inaccurate. However, the parameter estimation could be improved by incorporating the experimentally determined mass transfer rate, ωexp from batch kinetics. Based on the calibrated model, the fraction of instantaneous retardation, βexp of Pb decreased from 0.41 in the single system to 0.30 in the binary system, indicating the shift from equilibrium to nonequilibrium state, where which of Cu increased from 0.39 to 0.94, representing the shift towards equilibrium. The modified results were also compared with five-step sequential extraction data, confirming that the shift of particular metal fractions from the competition triggered the nonequilibrium transport.

Scaling up adsorption media reactors for copper removal with the aid of dimensionless numbers

Adsorption media may be used to sorb copper in an aquatic environment for pollution control. Effective design of adsorption media reactors is highly dependent on selection of the hydraulic residence time when scaling up a pilot-scale reactor to a field-scale reactor. This paper seeks to improve scaling-up technique of the reactor design process through the use of the Damköhler and Péclet numbers via a dimensional analysis. A new scaling-up theory is developed in this study through a joint consideration of the Damköhler and Péclet numbers for a constant media particle size such that a balance between transport control and reaction control can be harmonized. A series of column breakthrough tests at varying hydraulic residence times revealed a clear peak adsorption capacity at a Damköhler number of 2.74. The Péclet numbers for the column breakthrough tests indicated that mechanical dispersion is an important effect that requires further consideration in the scaling-up process. However, perfect similitude of the Damköhler number cannot be maintained for a constant media particle size, and relaxation of hydrodynamic similitude through variation of the Péclet number must occur.

A study of the optimum injection rate of carbonic acid during matrix acidizing of carbonate reservoirs: Implications for reducing CO2 emissions

This study investigates the process of optimizing the injection rates of carbonic acid during matrix acidizing in carbonate formations, highlighting its impact on wormhole formation, dissolution, and the changes in rock petrophysical properties. Indiana limestone core samples, with porosity ranging from 14 % to 16 % and permeability from 7 to 12 mD, were flooded using diffrent injection rates (0.5, 1, 2, and 5 cm³/min) to determine the optimal injection velocity. The carbonic acid is prepared by mixing 70 % fresh water with 30 % sc-CO2 at 1500 psi and room temperature. A micro-CT scan was employed to visualize the wormhole patterns, measure its size, and calculate the optimum Damköhler Number. Moreover, inductively coupled plasma (ICP) was used to measure the calcium concentrations from effluents collected at different intervals. Two models were used to ascertain the optimum injection rate; the first model based on PVBT as a function of injection rate, indicated that 2 cm³/min is the optimum injection rate with 22 pore volumes to breakthrough (PVBT). The second model considered the relationship between PVBT and interstitial velocity (Vi), leading to an optimum injection rate of 1.7 cm³/min, corresponding to an interstitial velocity of 1 cm/min. Calculations of the optimum Damkhöler number reveal a value significantly different from the 0.29 proposed by Fredd and Fogler. This study provides valuable insights into the utilization of CO2 to enhance well productivity as a replacement for conventional acids.

Effect of vane angle on turbulence-chemistry interactions, temperature, flow field, burnout, and NOx emissions in swirling flames fueled by semicoke mixtures

To enhance the combustion efficiency and reduce NOx emissions in large-scale semicoke and bituminous coal blends, an extensive numerical study was conducted. The focus of this study was to optimize the quaternary air vane angle (αv) through detailed analysis of the temperature and flow fields, turbulence-chemistry interactions, char burnout, and NOx formation in a carefully scaled 1:5 dual-swirl burner. The results showed that with increasing αv, the high-temperature flame region was narrowed and the peak temperature was reduced along with the broadened inner recirculation zone and the shrunken external recirculation zone due to better pulverized fuel-oxidant blending and reinforced convective heat transfer. The peak turbulent Damköhler number Dat evidently increased from 197.5 to 496 with increasing αv, which implied a strengthened homogeneous combustion. Additionally, the corresponding mixing time scales increased while the chemical kinetics time scales decreased, which denoted that an intense diffusing flame was generated with a strong turbulent intensity. The peak heterogeneous Damköhler number Das-O2 showed a reduction from 2.54 to 2.27, while the peak values of Das-CO2 and Das-H2O decreased from 0.1 to 0.077 and from 0.02 to 0.015, respectively. The char-O2 reaction was controlled by diffusion/kinetics; both char-CO2 and char-H2O reactions were determined by kinetics, and all gas‒solid reactions showed a kinetically controlled regime. With increasing αv, the enlarged inner recirculation region increased the residence time, and a higher dilution level lessened the peak temperature, which led to reductions in fuel-NOx and the thermal-NOx. The αv range of 30-45° (or swirl number Sn = 0.55-0.95) was suggested by taking the high burnout and low-NOx formation into account.