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PubMed2003

Large-scale simulations of concentrated emulsion flows.

Applications of the newly developed hybrid of the boundary integral and economical multipole techniques to large-scale dynamical simulations of concentrated emulsion flows of deformable drops are considered. For N = O(10(2)-10(3)) drops in a periodic cell with O(10(3)) boundary elements per drop, the method has two to three orders of magnitude gain over a standard boundary-integral method at each time-step, thus making long-time large-scale dynamical simulations feasible. In the steady shear flow, large systems N >/= O(10(2)) are imperative for convergence at high drop volume fractions c >/= 0.5. At high concentrations, most of the shear thinning occurs for nearly non-deformed drops; at c approximately 0.55 and small capillary numbers, phase transition is observed in dynamical simulations. In sedimentation of deformable drops from a homogeneous initial state, even larger N >/= O(10(3)) are required to accurately describe the Koch-Shaqfeh type of instability in a wide time range with N up to 1200 and ensemble averaging over the initial conditions. The dynamics of the average sedimentation rate is studied versus concentration c for matching viscosities lambda = 1; for a Bond number of 1.75, systems with c approximately 0.25 are found to be most unstable. Additionally, a low drop-to-medium-viscosity ratio system, lambda = 0.1, is more unstable than those with lambda = 0.25 and lambda = 1. In the third application, buoyancy- or gravity-driven motion of a large bubble/drop through a concentrated emulsion of neutrally buoyant drops is studied by simulations. For a size ratio of two, convergent (box-size independent) results for the bubble/drop settling velocity are obtained in simulations with N </= 800.

Algorithms↗

PubMed2005

A microfabricated electrical SPLITT system.

A growing need for methods to analyze and prepare monodisperse nanoparticles on an industrial scale exists and may be solved by the application of split flow thin fractionation (SPLITT) at the microscale. Microfluidic systems of this type have the ability to separate nanoparticles with high precision in a continuous manner. A miniaturized SPLITT system can be fabricated using standard microfabrication technologies, works in a continuous mode, and can be used as a sample preparation instrument in a micro-total-analysis-system (micro-TAS). In this paper, a miniaturized electrical SPLITT system, which separates particles continuously based on electrophoretic mobility, has been characterized. The advantages of miniaturization have been elucidated. The various aspects of the micro SPLITT system discussed in this paper can be broadly classified into: micro SPLITT system design, fluidics modeling to refine the splitter arrangements, and experimental characterization of the SPLITT system. The design of the micro SPLITT system has been elucidated focusing on the two designs that were implemented. Fluid modeling, used to arrive at a new SPLITT design, was done using a commercially available CFD package to investigate behavior of the fluid in the microchannel with various splitter arrangements. Testing was done with nanoparticles of varying diameter and electrophoretic mobilities to verify the modeling results and demonstrate functionality of the SPLITT system. Particles eluted from both outlets of the SPLITT system were characterized using AFM and SEM to verify the function of the system.

Chemical Fractionation↗

PubMed2006

Comparative study of biological nutrient removal (BNR) processes with sedimentation and membrane-based separation.

A membrane-enhanced biological phosphorus removal (MEBPR) process was operated in parallel with a conventional EBPR (CEBPR) process under challenging operating conditions to uncover fundamental differences in their ability to remove chemical oxygen demand (COD), nitrogen (N), and phosphorus (P) from municipal wastewater. Both systems exhibited the same potential to achieve excellent soluble-P removal when a favorable COD to P ratio was maintained in the influent. The MEBPR train generated a superior effluent quality when measured as total P. The CEBPR effluent contained significantly lower levels of nitrates due to the extra denitrification occurring in the sludge blanket of the secondary clarifier. The observed sludge yield in the MEBPR system was estimated to be between 0.23 and 0.28 g VSS/g COD, and this was 15% lower than the CEBPR sludge yield. When the influent volatile fatty acids (VFAs) became limiting, the CEBPR train exhibited better performance in the removal of soluble-P, due to the higher observed sludge yield and an overall greater denitrification activity that led to a more efficient use of VFAs in the anaerobic zone. After experiencing a severe deterioration of the biological P activity in both processes, the MEBPR train exhibited faster recovery than the CEBPR side. In this experimental work, it was demonstrated that an MEBPR process can sustain long-term satisfactory bio-P performance at HRTs as low as 7 h. However, the lower sludge yield and the reduced denitrification capacity are two important factors that impact the design of high rate membrane-assisted biological nutrient removal (BNR) processes.

Biotechnology↗

PubMed2004

Biotechnological applications of bioluminescence and chemiluminescence.

Recent progress in molecular biology has made available several biotechnological tools that take advantage of the high detectability and rapidity of bioluminescence and chemiluminescence spectroscopy. These developments provide inroads to in vitro and in vivo continuous monitoring of biological processes (e.g. gene expression, protein-protein interaction and disease progression), with clinical, diagnostic and drug discovery applications. Furthermore, combining luminescent enzymes or photoproteins with biospecific recognition elements at the genetic level has led to the development of ultrasensitive and selective bioanalytical tools, such as recombinant whole-cell biosensors, immunoassays and nucleic acid hybridization assays. The high detectability of the luminescence analytical signal makes it appropriate for miniaturized bioanalytical devices (e.g. microarrays, microfluidic devices and high-density-well microtiter plates) for the high-throughput screening of genes and proteins in small sample volumes.

Animals↗

PubMed2003

Ionic interactions play a role in the regulatory mechanism of scallop heavy meromyosin.

Heavy meromyosin from scallop (scHMM) striated muscle is regulated by calcium binding to the essential light chain. The regulation can be modeled with a calcium-dependent equilibrium between on and off scHMM conformations. The observed rate constant for mant-ADP dissociation from scHMM is calcium dependent, and we show here that it can be used to define the equilibrium constant (K(eq)) between on and off conformations. The data show that K(eq) is markedly ionic strength dependent, with high salt (>/=200 mM) abolishing the off state even in the absence of calcium and low salt (<50 mM) favoring the off state even in the presence of calcium. Debye-Huckel plots of the equilibrium constant (K(eq)) for the on and off forms gave parallel slopes (5.94 +/- 0.33 and 6.36 +/- 0.17 M(-0.5)) in the presence and absence of calcium. The presence of an equilibrium mixture of two conformations was confirmed by sedimentation data and the effects of ADP, calcium and ionic strength were in qualitative agreement. Thus scHMM exists in two conformations that can be distinguished in sedimentation profiles and by the rate of release of mant-ADP. Increasing salt concentrations biases the system toward the on state, suggesting a role for ionic interactions in stabilizing the off state.

Adenosine Diphosphate↗

PubMed2003

Sedimentation velocity analysis of flexible macromolecules: self-association and tangling of amyloid fibrils.

A novel bead modeling technique has been developed for the analysis of the sedimentation velocity behavior of flexible fibrils. The method involves the generation of a family of bead models representing a sample of the conformations available to the molecule and the calculation of the sedimentation coefficients of these models by established techniques. This approach has been used to investigate the size distribution of amyloid fibrils formed by human apolipoprotein C-II (apoC-II). ApoC-II fibrils have a simple and homogeneous ribbon morphology with no evidence of amorphous aggregation. Freshly prepared apoC-II forms fibrils with systematically larger sedimentation coefficients upon increasing protein concentration (modes of 100, 300, and 800 for apoC-II concentrations of 0.3, 0.7, and 1.0 mg/mL, respectively). The sedimentation coefficient distributions are not affected by rotor speed, and are not significantly changed by dilution once the fibrils are formed. The kinetics of aggregation (1 mg/mL apoC-II) as assessed using thioflavin T and preparative pelleting assays reveal that monomeric apoC-II is depleted after approximately 12 h incubation at room temperature. In contrast, the sedimentation coefficient distribution of fibrils continues to grow larger over a period of 48 h to an average value of 800 S. Calculations using the bead modeling procedure suggest maximum sedimentation coefficients for individual apoC-II fibrils to be around 100 S. The larger experimentally observed sedimentation coefficients for apoC-II fibrils indicate an extensive and time-dependent tangling or association of the fibrils to form specific networks.

Amyloid beta-Peptides↗

PubMed2002

A straight interpretation of the solids flux theory for a three-layer sedimentation model.

One-dimensional settling models based on the conservation law calculate the flux of particles via discrete horizontal layers. Commonly at least 10 of these spatial elements with constant volume are considered in order to achieve a satisfying fit with data. This paper deals with a conceptual approach of a simplified layer model, its theoretical confirmation and its applicability. The model differs three layers with variable volume--clarification-, hindered settling- and compression zone--which are not derived from numerical requirements but from the basic principles of solids flux theory for batch sedimentation. In accordance to the three types of propagation velocities of solids flux theory--hindered settling, signal speed and propagation of concentration discontinuities--three density layers of settling particles of a suspension have been defined. Model development has focused on a reduction of model complexity for on-line control purpose and for coupling with a biokinetic model. Another intention was the model's universal applicability to both batch and continuous settling in order to compare different types of activated sludge strategies. The model has been evaluated against the analytical solution of the flux function and against data from full-scale SBR experiments and from a secondary clarifier under hydraulic overload.

Fractionation, Field Flow↗

PubMed2003

The contribution of particles washed from rooftops to contaminant loading to urban streams.

Rooftops are both a source of and a pathway for contaminated runoff in urban environments. To investigate the importance of particle-associated contamination in rooftop runoff, particles washed from asphalt shingle and galvanized metal roofs at sites 12 and 102 m from a major expressway were analyzed for major and trace elements and PAHs. Concentrations and yields from rooftops were compared among locations and roofing material types and to loads monitored during runoff events in the receiving urban stream to evaluate rooftop sources and their potential contribution to stream loading. Concentrations of zinc, lead, pyrene, and chrysene on a mass per mass basis in a majority of rooftop samples exceeded established sediment quality guidelines for probable toxicity of bed sediments to benthic biota. Fallout near the expressway was greater than farther away, as indicated by larger yields of all contaminants investigated, although some concentrations were lower. Metal roofing was a source of cadmium and zinc and asphalt shingles a source of lead. The contribution of rooftop washoff to watershed loading was estimated to range from 6 percent for chromium and arsenic to 55 percent for zinc. Estimated contributions from roofing material to total watershed load were greatest for zinc and lead, contributing about 20 and 18 percent, respectively. The contribution from atmospheric deposition of particles onto rooftops to total watershed loads in stormwater was estimated to be greatest for mercury, contributing about 46 percent.

Air Pollutants↗

PubMed2006

Solution formation of Holliday junctions in inverted-repeat DNA sequences.

The structure of Holliday junctions has now been well characterized at the atomic level through single-crystal X-ray diffraction in symmetric (inverted-repeat) DNA sequences. At issue, however, is whether the formation of these four-stranded complexes in solution is truly sequence dependent in the manner proposed or is an artifact of the crystallization process and, therefore, has no relevance to the behavior of this central intermediate in homologous recombination and recombination-dependent cellular processes. Here, we apply analytical ultracentrifugation to demonstrate that the sequence d(CCGGTACCGG), which crystallizes in the stacked-X form of the junction, assembles into four-stranded junctions in solution in a manner that is dependent on the DNA and cation concentrations, with an equilibrium established between the junction and duplex forms at 100-200 microM DNA duplex. In contrast, the sequence d(CCGCTAGCGG), which has been crystallized as B-DNA, is seen to adopt only the double-helical form at all DNA and salt concentrations that were tested. Thus, the ACC trinucleotide core is now shown to be important for the formation of Holliday junctions in both crystals and in solution and can be estimated to contribute approximately -4 kcal/mol to stabilizing this recombination intermediate in inverted-repeat sequences.

Crystallography, X-Ray↗

PubMed2006

Functional and structural analysis of the photosynthetic apparatus of Rhodobacter veldkampii.

In the widely studied purple bacterium Rhodobacter sphaeroides, a small transmembrane protein, named PufX, is required for photosynthetic growth and is involved in the supramolecular dimeric organization of the core complex. We performed a structural and functional analysis of the photosynthetic apparatus of Rhodobacter veldkampii, a related species which evolved independently. Time-resolved optical spectroscopy of R. veldkampii chromatophores showed that the reaction center shares with R. sphaeroides spectral and redox properties and interacts with a cytochrome bc(1) complex through a Q-cycle mechanism. Kinetic analysis of flash-induced cytochrome b(561) reduction indicated a fast delivery of the reduced quinol produced by the reaction center to the cytochrome bc(1) complex. A core complex, along with two light-harvesting LH2 complexes significantly different in size, was purified and analyzed by sedimentation, size exclusion chromatography, mass spectroscopy, and electron microscopy. A PufX subunit identified by MALDI-TOF was found to be associated with the core complex. However, as shown by sedimentation and single-particle analysis by electron microscopy, the core complex is monomeric, suggesting that in R. veldkampii, PufX is involved in the photosynthetic growth but is unable to induce the dimerization of the core complex.

Amino Acid Sequence↗

PubMed2003

Microfluidic sorting in an optical lattice.

The response of a microscopic dielectric object to an applied light field can profoundly affect its kinetic motion. A classic example of this is an optical trap, which can hold a particle in a tightly focused light beam. Optical fields can also be used to arrange, guide or deflect particles in appropriate light-field geometries. Here we demonstrate an optical sorter for microscopic particles that exploits the interaction of particles-biological or otherwise-with an extended, interlinked, dynamically reconfigurable, three-dimensional optical lattice. The strength of this interaction with the lattice sites depends on the optical polarizability of the particles, giving tunable selection criteria. We demonstrate both sorting by size (of protein microcapsule drug delivery agents) and sorting by refractive index (of other colloidal particle streams). The sorting efficiency of this method approaches 100%, with values of 96% or more observed even for concentrated solutions with throughputs exceeding those reported for fluorescence-activated cell sorting. This powerful, non-invasive technique is suited to sorting and fractionation within integrated ('lab-on-a-chip') microfluidic systems, and can be applied in colloidal, molecular and biological research.

Capsules↗

PubMedDate not supplied

Histologic comparison of autologous fat processing methods.

PURPOSE: To perform a quantitative analysis of adipocyte viability after fat processing during autologous fat transfer, comparing the processing methods of washing, centrifuging, and sedimentation. METHODS: An experimental study was conducted in which 24 fat samples were obtained after processing from 22 patients undergoing autologous fat transfer. Histologic analysis of periodic acid-Schiff-stained specimens was then performed. RESULTS: Cell counts per high-powered field of intact adipocytes and nucleated adipocytes and adipocyte cross-sectional area were significantly greater in samples processed by sedimentation, compared with those by centrifuging or washing. CONCLUSIONS: Of the various processing techniques currently used during autologous fat transfer, sedimentation appears to yield a higher proportion of viable adipocytes than does washing or centrifuging.

Adipocytes↗

PubMed2006

Crystallohydrodynamics of protein assemblies: Combining sedimentation, viscometry, and x-ray scattering.

Crystallohydrodynamics describes the domain orientation in solution of antibodies and other multidomain protein assemblies where the crystal structures may be known for the domains but not the intact structure. The approach removes the necessity for an ad hoc assumed value for protein hydration. Previous studies have involved only the sedimentation coefficient leading to considerable degeneracy or multiplicity of possible models for the conformation of a given protein assembly, all agreeing with the experimental data. This degeneracy can be considerably reduced by using additional solution parameters. Conformation charts are generated for the three universal (i.e., size-independent) shape parameters P (obtained from the sedimentation coefficient or translational diffusion coefficient), nu (from the intrinsic viscosity), and G (from the radius of gyration), and calculated for a wide range of plausible orientations of the domains (represented as bead-shell ellipsoidal models derived from their crystal structures) and after allowance for any linker or hinge regions. Matches are then sought with the set of functions P, nu, and G calculated from experimental data (allowing for experimental error). The number of solutions can be further reduced by the employment of the D max parameter (maximum particle dimension) from x-ray scattering data. Using this approach we are able to reduce the degeneracy of possible solution models for IgG3 to a possible representative structure in which the Fab domains are directed away from the plane of the Fc domain, a structure in accord with the recognition that IgG3 is the most efficient complement activator among human IgG subclasses.

Computer Simulation↗

PubMed2001

Flow fractionation of microparticles under a dielectrophoretic field in a quadrupole electrode capillary.

A technique of fractionation for microparticles was proposed that utilized a unique combination of a dielectrophoretic (DEP) field generated by a quadrupole electrode and a laminar flow in a capillary of 82.5 microm in radius. The fabricated capillary possessed four platinum wires in its inside wall as a quadrupole electrode. In a nonuniform electric field generated by the quadrupole electrode, microparticles, such as polystyrene and carbon, in water experienced DEP forces in the radial direction. When a sample solution was pumped in, an ideal laminar flow perpendicular to the DEP force was formed inside the capillary. The microparticles dynamically migrated by the DEP force across the laminar flow while they were carried by the flow. A theoretical model taking the DEP force and the laminar flow pattern into account predicted the elution profiles of the single microparticles quantitatively. The elution times of the microparticles depended on the dielectric properties and the sizes of the microparticles, as well as the voltage and frequency of the applied alternating current.

Journal Article↗

PubMed2004

Effect of flow development region and fringing magnetic force field on annular split-flow thin fractionation.

Split-flow thin (SPLITT) fractionation devices have been widely used to separate macromolecules, colloids, cells and particles. Recently, the quadrupole magnetic flow sorter (QMS) has been reported in the literature as another family of SPLITT fractionation device. However, the separation performance observed in the experimental measurements is generally found to deviate from the ideal behaviour. Possible causes such as hydrodynamic lift force, high particle concentration and imperfect geometries have been extensively examined. However, the effects of flow development regions and fringing magnetic force field at the separation channel inlet and outlet, which are ignored by the theory, have not been investigated. The error introduced by ignoring these effects need to be rigorously studied so that the theory can be used to optimise operation flow rates with confidence. Indeed, we find in this paper that these ignored effects are responsible to the discrepancy between the experimental data and the theoretical predictions. A new theory has been proposed for optimisation of device operation.

Algorithms↗

PubMedDate not supplied

Preparative concentration and size fractionation of DNA by porous media using a combination of flow and low electric field strength.

The retention of DNA by porous media during chromatography with an applied axial electric field was investigated. DNA was retained by negative electric fields in columns packed with Sephadex G-75 and G-25. A negative field was defined as the electric field orientation in which the direction of electrophoresis was opposing the direction of buffer flow (positive electrode at the column inlet). A positive field was not effective at retaining the DNA. The electric field strength required to retain the DNA was dependent upon the buffer flow rate. The retention of DNA using Sephadex G-25, a gel filtration medium with a higher degree of cross-linking, required higher electric fields than the more porous Sephadex G-75. A dilute DNA solution was concentrated at the inlet of the chromatography bed by an electric field. Mixtures of DNA restriction fragments were used to determine size-dependent retention. DNA was size-fractionated by varying the electric field strength and flow rate. At a given electric field strength and flow rate, the lower molecular weight DNA fragments were not as strongly retained as the higher molecular weight fragments. Decreasing the flow rate or increasing the electric field strength resulted in increased retention of the lower molecular weight DNA fragments. In this manner, by selecting a specific set of conditions (packing material, flow rate, and electric field strength), the molecular weight of DNA fragments retained by the column can be adjusted. Efficient separation of high molecular weight DNA from bovine serum albumin, a protein with high electrophoretic mobility, was demonstrated using a field of 2 V/cm in a column packed with Sephadex G-75.

Animals↗

PubMedDate not supplied

Three-dimensional numeric simulation of flow through an aortic bileaflet valve in a realistic model of aortic root.

A three-dimensional, realistic model of an aortic mechanical heart valve and Valsalva sinuses was developed to predict, by means of a numerical time dependent simulation, the flow field during a fraction of the systolic period. The numeric simulation was performed upon a model of valve similar to a Carbomedics 27 mm placed in a physiologic aortic root shaped model, in which no symmetry planes were exploited to reach a more realistic level. Input data for the simulation have been acquired during an experimental session on the same valve, according to the guidelines of testing protocol for prosthetic heart valves. Flow was assumed to be Newtonian and laminar at low regime and the leaflets fixed in the fully open position. The forward flow of the systolic phase was investigated, and a comparison with experimental results was performed at peak systole, the most representative point of the cardiac cycle. The results of this simulation furnished a reasonable indication (in terms of fluid dynamics) parameters downstream of the prosthetic device, especially in Valsalva sinuses, the role of which is proven to affect the valve's performance.

Aortic Valve↗

PubMed2006

Analytical and preparative applications of magnetic split-flow thin fractionation on several ion-labeled red blood cells.

BACKGROUND: Magnetic Split-flow thin (SPLITT) fractionation is a newly developed technique for separating magnetically susceptible particles. Particles with different field-induced velocities can be separated into two fractions by adjusting applied magnetic forces and flow-rates at inlets and outlets. METHODS: Magnetic particles, Dynabeads, were used to test this new approach of field-induced velocity for susceptibility determination using magnetic SF at different magnetic field intensities. Reference measurements of magnetic susceptibility were made using a superconducting quantum interference device (SQUID) magnetometer. Various ion-labeled red blood cells (RBC) were used to study susceptibility determination and throughput parameters for analytical and preparative applications of magnetic SPLITT fractionation (SF), respectively. Throughputs were studied at different sample concentrations, magnetic field intensities, and channel flow-rates. RESULTS: The susceptibilities of Dynabeads determined by SPLITT fractionation (SF) were consistent with those of reference measurement using a superconducting quantum interference device (SQUID) magnetometer. Determined susceptibilities of ion-labeled RBC were consistent within 9.6% variations at two magnetic intensities and different flow-rates. The determined susceptibilities differed by 10% from referenced measurements. The minimum difference in magnetic susceptibility required for complete separation was about 5.0 x 10(-6) [cgs]. Sample recoveries were higher than 92%. The throughput of magnetic SF was approximately 1.8 g/h using our experimental setup. CONCLUSION: Magnetic SF can provide simple and economical determination of particle susceptibility. This technique also has great potential for cell separation and related analysis. Continuous separations of ion-labeled RBC using magnetic SF were successful over 4 hours. The throughput was increased by 18 folds versus early study. Sample recoveries were 93.1 +/- 1.8% in triplicate experiments.

Journal Article↗