Functional studies of synthetic gramicidin hybrid ion channels in CHO cells

The function of a gramicidin hybrid ion channel in living Chinese hamster ovary (CHO) cells was investigated by the patch clamp method. The synthetic ion channel 1 consists of two cyclohexyl ether amino acids that link two mini-gramicidin strands. With 1 at a concentration of 1.0 microM, an increase in the whole-cell membrane conductance was observed after 1.37 min. The conductance showed larger currents when Cs(+) was used as charge carrier than when Na(+) and K(+) were used. In single-channel recordings with Cs(+) as charge carrier, the substance showed comparable single-channel amplitudes in the membrane of living cells and artificial black lipid bilayers. In addition to functioning as a cation channel, compound 1 appeared to be a water channel. Exposure of the CHO cells to an extracellular hypoosmotic solution did not substantially change the cell volume. Extracellular hypoosmotic conditions in the presence of 1 increased the cell size to 146.5 % that of the control. Thus, the synthetic hybrid channel 1 can function as a cation channel with some Cs(+) specificity, and as a water channel in CHO cells.     

Computational studies of the primary phototransduction event in visual rhodopsin

This Account addresses recent advances in the elucidation of the detailed molecular rearrangements due to the primary photochemical event in rhodopsin, a prototypical G-protein-coupled receptor (GPCR) responsible for the signal transmission cascade in the vertebrate vision process. The reviewed studies provide fundamental insight on long-standing problems regarding the assembly and function of the individual residues and bound water molecules that form the rhodopsin active site, a center that catalyzes the 11-cis/all-trans isomerization of the retinyl chromophore in the primary step of the phototransduction mechanism. Emphasis is placed on the authors' recent computational studies, based on state-of-the-art quantum mechanics/molecular mechanics (QM/MM) hybrid methods, addressing the structural refinement of the retinyl chromophore binding site in high-resolution X-ray structures of bovine visual rhodopsin, the energy storage mechanism, and the molecular origin of spectroscopic changes due to the primary photochemical event.     

Computational studies of turbulent premixed flame based dump combustor

The present work reports the computational studies of turbulent premixed flame based dump combustor. The effects of various flow parameters such as inlet Reynolds number, inlet turbulence intensity and expansion ratio on important flow quantities like axial velocity, turbulent kinetic energy and turbulent dissipation rate have been studied extensively. It was found out that the axial velocities and the radial velocities within the flowfield are many times higher as compared to the cold flow case due to the heat release and volumetric expansion. The reattachment length for the reacting flow case is found to be lower than that of the cold flow cases due to higher recirculation velocities. A maximum reduction of 64.6% compared to the cold flow reattachment length was observed in the case of turbulence intensity, I = 10%, equivalence ratio,  = 1.00 with an expansion ratio of 2. In contrast, minimum of 41.51% reduction in recirculation length was observed in the case of I = 5%,  = 0.5 for the same expansion ratio. This reduction was quite significant at higher inlet turbulence intensities and at higher equivalence ratios.     

Computational prediction of PVC degradation during injection molding in a rectangular channel

A computational model has been developed to calculate the degradation of PVC during injection molding. The results in this work are for the flow in a rectangular geometry. The effects of the injection speed, melt temperature, and material properties were examined. It was determined that the principal factor influencing PVC degradation is the injection speed. Very good agreement between computational and experimental results was obtained. Furthermore, it was calculated that the materials are more thermally sensitive during processing, with activation energy of 65 kcal/mol. Finally, it was calculated that the degradation becomes significant when the melt temperature is above 250°C, independent of the material studied. The model could be used to design the process to avoid degradation. Polym. Eng. Sci. 44:1295–1312, 2004. © 2004 Society of Plastics Engineers.     

Computational studies on the diffusion behaviour of alkylaromatics in large pore zeolites

Alkylation of aromatics over solid acid catalysts such as zeolites, has emerged in the recent past as a viable alternative to conventional Friedel–Crafts alkylation over environmentally hostile catalysts. We studied the diffusion behaviour of ethylbenzene (EB), isobutylbenzene (IBB), o-, m- and p-isobutylethylbenzene (IBEB) in various zeolites such as offretite (OFF), cancrinite (CAN), ZSM-12 (MTW) and ZSM-18 (MEI) by computational procedures. The periodic variations of interaction energy between the molecules and zeolite framework in the calculated diffusion energy profiles are used to predict the energy barrier for diffusion. We analyzed the results to understand the product selectivity in the formation of IBEB in the transalkylation/disproportionation reaction between IBB and EB. The results indicated that the zeolites with channel-like pores are more suitable than those with cage-like pores to achieve better selectivity. The zeolites with channels whose diameters are close to the dimensions of the molecules and those which do not have intersecting channels are better selective catalysts. The efficiency of shape selective production of p-IBEB in these zeolites will be in the order MEI < OFF ∼ MTW < CAN as predicted from their diffusion energy barriers. The detailed analysis of the configurations of the molecules in the most favourable and unfavourable adsorption location, indicate that the p-IBEB has favourable interaction energy in all the four zeolites with different pore architecture, compared to o- and m-IBEB except for MEI. It could be concluded that the pore architecture plays a dominant role in controlling the adsorption and diffusion characteristics of these molecules. The actual values of interaction energy themselves are indication of their adsorption behaviour inside the pores of the zeolite. This revised version was published online in June 2006 with corrections to the Cover Date.     

Computational studies of the activation of lipases and the effect of a hydrophobic environment

We have investigated the activation pathway of three wild type lipases and three mutants using molecular dynamics techniques combined with a constrained mechanical protocol. The activation of these lipases involves a rigid body hinge-type motion of a single helix, which is displaced during activation to expose the active site and give access to the substrate. Our results suggest that the activation of lipases is enhanced in a hydrophobic environment as is generally observed in experiments. The energy gain upon activation varies between the different lipases and depends strongly on the distribution of the charged residues in the activating loop region. In a low dielectric constant medium (such as a lipid environment), the electrostatic interactions between the residues located in the vicinity of the activating loop (lipid contact zone) are dominant and determine the activation of the lipases. Calculations of the pKas qualitatively indicate that some titratable residues experience significant pK shifts upon activation. These calculations may provide sufficient details for an understanding of the origin and magnitude of a given electrostatic effect and may provide an avenue for exploring the activation pathway of lipases.      

Computational studies of nonadiabatic effects in gas—surface encounters

Model studies are presented, each of which employs a different approach to solving the problem of nonadiabatic dynamics occurring at a solid surface. The jumping wave packet-type approach involving dynamics on two potential energy surfaces punctuated by Franck—Condon transitions was applied to the dynamics of CO desorbed from Ru following energetic electron bombardment. Classical dynamics was also employed in this system to gain a more detailed understanding of the factors important to the final molecular state distribution. To study charge transfer from an alkali-halide surface to a scattering atom, we have used full multi-surface quantum dynamics. A simple, but effective, analysis method was used to make a more detailed connection between the potential energy surfaces and the dynamics. To study the fate of the transferred electron and to model how this depends on substrate and projectile species, we have used a four-dimensional wave packet implementation in which two of the dimensions explicitly account for the electron dynamics. Finally, we consider the famous electron—hole pair excitation problem, from a density functional theory perspective. Spin nonadiabaticity is found to be a new important feature in gas—metal surface interactions.     

Experimental studies of ventilated cavities in a channel

Ventilated cavities are characterized by the cavity shape, size, inception mechanism, cavity pressure with drag reduction, re-entrant jet and bubble breakoff from the cavity tip. All these characteristics are dependent upon each other. The aim of the present work is to study these aspects in an integrated way. Ventilated cavity formation was studied in a transparent acrylic channel by sparging gas behind straight blades. Clinging, partial, full and large cavity shapes were observed. Cavity transitions are correlated with the Froude and aeration numbers. Other cavities such as slug, and emulsion cavity were also observed. Bubble breakoff from the cavities is found to be dependent on the cavity type. Typically, large bubbles breakoff from slug cavities while smaller bubble sizes are observed breaking off from emulsion cavities. Other cavity shapes show a mixed breakoff pattern of varying proportion of large and small bubbles. Change in drag force on the blade is found to be dependent on the cavity shape and size. The cavity pressure is correlated with the liquid velocity over the blade and the superficial gas velocity. Negative and positive cavity pressure is found to be associated with the presence and absence of re-entrant jet.     

Computational and experimental studies of electrohydrodynamic atomization for pharmaceutical particle fabrication

Electrohydrodynamic atomization (EHDA) is a promising method for the fabrication of micro‐ and nanosized particles with narrow‐size distribution and better morphologies in comparison to conventional methods of particle fabrication. A computational model was developed in this study to simulate the fluid and particle dynamics in an EHDA chamber, and thereby providing a means of predicting particle collection efficiencies at various operating conditions. Experiments were also conducted using a new design of the EHDA chamber. It was found that nitrogen flow rate, solution flow rate and voltage difference between the nozzle and ring can significantly affect the particle collection efficiency of the EHDA process. Electric field and electric potential profiles in the chamber were significantly affected by the combined voltages of the nozzle and ring. In general, a good qualitative agreement in particle collection efficiencies was obtained from experiments and simulations. The computational model developed in this study provided a means of understanding the various processes involved in micro‐ and nano‐sized particle fabrication using the EHDA methodology. © 2012 American Institute of Chemical Engineers AIChE J, 2012     

Computational and experimental studies of electrospray deposition process in pharmaceutical micro-pattern formation

Electrospray deposition on a substrate through a mask is a simple (single-step) yet versatile and robust approach to generate biodegradable polymeric particle patterns. Different methods including photolithography, soft lithography and ink jetting have been employed for automated micro-pattern fabrication; however, most of them are limited to the investigation of material properties of substrates with high-cost and complex procedures. In the present work, two slightly different experimental setups were used to investigate the effect of different operational parameters in electrospray particle deposition on both mask and substrate. The sample consists of an aqueous solution of polymer, solvent and drug. In addition to the experimental section, a mathematical model was developed to track the particle trajectories and focusing effect in electrospray deposition process on the substrate.The final results confirm that the clearest particle pattern and the best focusing effect on the substrate can be achieved with long distance between the nozzle and the substrate, high voltage difference between the nozzle and the mask, short process time and low solution flow rate. On the contrary, a smooth and integrated layer on the mask can be formed with a short distance between the nozzle and substrate in which no clear pattern can be recognized. Furthermore, micro-fibers can be observed on the mask when the voltage difference between the nozzle and substrate is not high.     

Hydrodynamic characteristics of valve tray: Computational fluid dynamic simulation and experimental studies

In order to better understand the hydrodynamics of valve trays, air-water operation in an industrial scale tower with 1.2 m of diameter, consisting of two 14% valve trays, was studied. Experimental results of clear liquid height, froth height, average liquid holdup, dry pressure drop, total pressure drop, weeping and entrainment were investigated, and empirical correlations were presented. Then, a three-dimensional computational fluid dynamics (CFD) simulation in an Eulerian framework for valve tray with ANSYS CFX software was done. The drag coefficient, which was used in the CFD simulations, was calculated from the data obtained in the experiments. The simulation results were found to be in good agreement with experimental data at this industrial scale. The objective of the work was to study the extent to which experimental and CFD simulations must be used together as a prediction and design tool for industrial trays.     

Computational fluid dynamics studies of dry and wet pressure drops in structured packings

Computational fluid dynamics was used to study the hydrodynamic of structured packings. The results showed that the k–ω was a suitable turbulence model for analyzing the flows in structured packings. A simple method was proposed for evaluating the liquid holdup based on the Iliuta and Larachi (2001) model [25], the calculated liquid film thickness in 2D framework, and the empirical correlation of Brito et al. (1994) [26]. The presented method can be used for estimating the wet pressure drop in 3D structured packings for loading region with good accuracy as well as computational economy. The process of liquid film formation was also discussed.     

Computational and experimental studies of mercury adsorption on unburned carbon present in fly ash

Unburned carbon (UBC) present in fly ash has been shown to adsorb mercury. In this work mercury adsorption onto the surface of UBC particles was investigated by using both computational and experimental methods. The UBC surfaces were assumed to be similar to that of graphene (single-layer graphite). The theoretical predictions using the Hartree–Fock method found that the zigzag edge of the carbonaceous cluster (C₂₅H₉) used provides stronger forces to attract mercury compared to the armchair edge (C₂₄H₈), probably resulting in greater mercury removal from flue gases. The adsorption of mercury on the simulated UBC surface (C₂₅H₉) was found to be a chemical process, with the predicated adsorption energy of 288.632 kJ/mol at room temperature. Furthermore, as temperature increases the adsorption energy slightly raises. The experimental studies showed that decreasing the particle size of UBC particles resulted in higher mercury uptake. Increasing the bed length resulted in higher mercury uptakes. Particle size can affect the sorbent capacity, and in this study UBC particles with size ranging between 125 and 250 μm seem to be more effective for mercury adsorption.     

Computational simulation of gas separation using nonporous polymeric membranes: Experimental and theoretical studies

In this study, preparation and simulation of polydimethylsiloxane (PDMS) membranes for gas separation is carried out. The membranes are synthesized by solution‐casting method via silicon oil as precursor. Gas permeation experiments for single gases of CH₄ and N₂ were conducted at different feed pressures (2–10 bars). PDMS membrane as a rubbery polymer showed that are more permeable toward more condensable gases, i.e., CH₄ compared to N₂. It was indicated that increasing feed pressure enhances permeability of CH₄ through the membrane slightly, but the permeability of nitrogen was almost constant over enhancement of feed pressure. Moreover, a mathematical model was developed to predict the permeation of gases across PDMS membrane. The model is based on solving conservation equations for gases in the membrane phase. Finite element analysis was utilized for numerical simulation of the governing equations. The simulation results were used to predict the concentration of gases inside the membrane. POLYM. ENG. SCI., 55:54–59, 2015. © 2014 Society of Plastics Engineers