Motion of a doublet of two cylinders in contact in a narrow channel flow.

The motion of two rigid circular cylinders in contact immersed in an incompressible Newtonian fluid in a channel is examined numerically in the zero Reynolds number limit, for various values of the cylinder radius/channel width ratio. Analyses of the time courses of the lateral position and the orientation of the doublet showed that, depending on the initial condition and the doublet/channel size ratio, the doublet exhibit one of the three types of motion: a continuous rotation in the same direction during a period, and a rotation changing its direction at every half period with a large or a small variation of the orientation.     

Stability of elliptical cylinders in two-dimensional channel flow

The flow around rigid cylinders of elliptical cross section placed transverse to Poiseuille flow between parallel plates was simulated to investigate issues related to the tumbling of red blood cells and other particles of moderate aspect ratio in the similar flow in a Field Flow Fractionation (FFF) channel. The torque and transverse force on the cylinder were calculated with the cylinder freely translating, but prevented from rotating, in the flow. The aspect ratios (long axis to short axis) of the elliptical cylinders were 2, 3, 4, and 5. The cylinder was placed transversely at locations of y0/H = 0.1, 0.2, 0.3, and 0.4, where y0 is the distance from the bottom of the channel and H is the height of the channel, and the orientation of the cylinder was varied from 0 to 10 deg with respect to the axis of the channel for a channel Reynolds number of 20. The results showed that equilibrium orientations (indicated by a zero net torque on the cylinder) were possible for high-aspect-ratio cylinders at transverse locations y0/H < 0.2. Otherwise, the net torque on the cylinder was positive, indicating that the cylinder would rotate. For cylinders with a stable orientation, however, a transverse lift forced existed up to about y0/H = 0.25. Thus, a cylinder of neutral or low buoyancy might be lifted with a stable orientation from an initial position near the wall until it reached y0/H < 0.2, whereupon it would begin to tumble or oscillate. The dependence of lift and torque on cylinder orientation suggested that neutral or low-buoyancy cylinders may oscillate in both transverse location and angular velocity. Cylinders more dense than the carrier fluid could be in equilibrium both in terms of orientation and transverse location if their sedimentation force matched their lift force for a location y0/H < 0.2.     

High-current plasma channel produced with a narrow gas column

A new method for creating high-current plasma channels is developed. The method uses a narrow gas column formed by the leading particles of a nonsteady gas jet outflowing into a vacuum. An electric discharge device with a system for the formation of a narrow gas column is experimentally studied. The parameters of emission from the plasma channel are measured.     

Hinge-bending motions in the pore domain of a bacterial voltage-gated sodium channel

Computational methods and experimental data are used to provide structural models for NaChBac, the homo-tetrameric voltage-gated sodium channel from the bacterium Bacillus halodurans, with a closed and partially open pore domain. Molecular dynamic (MD) simulations on membrane-bound homo-tetrameric NaChBac structures, each comprising six helical transmembrane segments (labeled S1 through S6), reveal that the shape of the lumen, which is defined by the bundle of four alpha-helical S6 segments, is modulated by hinge bending motions around the S6 glycine residues. Mutation of these glycine residues into proline and alanine affects, respectively, the structure and conformational flexibility of the S6 bundle. In the closed channel conformation, a cluster of stacked phenylalanine residues from the four S6 helices hinders diffusion of water molecules and Na(+) ions. Activation of the voltage sensor domains causes destabilization of the aforementioned cluster of phenylalanines, leading to a more open structure. The conformational change involving the phenylalanine cluster promotes a kink in S6, suggesting that channel gating likely results from the combined action of hinge-bending motions of the S6 bundle and concerted reorientation of the aromatic phenylalanine side-chains.     

Pulsatile flow in a constricted channel.

A nonuniform channel is used as a simple model of a constricted arterial vessel. Flow patterns have been calculated for pulsatile flow with both sinusoidal and nonsinusoidal flow rates for a range of Reynolds number, Re, and Strouhal number, St. The results show that even for relatively low frequency flows a strong vortex wave will be generated with a complex wall shear stress distribution and peak values much greater than those found in steady or unsteady parallel flow. The vortex wave increases in strength with increasing Re and St, with its total length and wavelength independent of Re but inversely proportional to St. The form of the imposed flow rate is found to have an important effect on the flow and the shear stress distribution.     

Dimensions of the narrow portion of a recombinant NMDA receptor channel.

Glutamate-activated single-channel and ensemble currents were recorded from Xenopus laevis oocytes and HEK 293 cells expressing a recombinant NMDA receptor, assembled from NR1 and NR2A subunits. Cesium was the main charge carrier, and organic cations were used to determine the presence of vestibules of this channel and to estimate its pore diameter. The large organic cations tris-(hydroxymethyl)-aminomethane (Tris), N-methyl-glucamine (NMG), arginine (NMG), arginine (Arg), choline, and tetramethylammonium (TMA), when added in millimolar concentrations to the extracellular or cytoplasmic side, produced a voltage-dependent blockade of single-channel Cs+ currents. These molecules behaved as impermeant ions that only partially traverse the channel from either side. The smaller cations trimethylammonium (TriMA) and dimethylammonium (DMA) produced a small and nearly voltage-independent reduction in current amplitude, suggesting that they are permeant. In biionic experiments with Cs+ as the reference ion, the large blocking cations NMG, Arg, Tris, TMA, choline, hexamethonium (Hme), triethylammonium (TriEA), and tetraethylammonium (TEA) showed no measurable permeability. TriMA and smaller ammonium derivatives were permeant. Both the permeability and single-channel conductance of organic cations, relative to Cs+, decreased as the ion size increased. The results suggest that the NMDA receptor has extracellular and cytoplasmic mouths that can accommodate large cations up to 7.3 A in mean diameter. The narrow portion of the pore is estimated to have a mean diameter of 5.5 A.     

Effects of particle characteristics on magnetic immunoassay in a thin channel

The effects of size and porosity of particles on magnetic immunoassay in a thin channel were studied. Experimental parameters were investigated and compared using a model immunoassay complex of carcinoembryonic antigen (CEA)/anti-CEA. The rate constant for the affinity reaction between functional particles increased as the size of magnetic nanoparticles (800-80 nm) decreased. The affinity reaction between functional particles had no significant effect on the sizes of microparticles (1.0-4.4 μm) at commonly used thin channel flow-rates of 0.001-0.025 ml/min. Competitive and sandwich reactions of CEA/anti-CEA were studied for CEA detection. Microparticles of different porosities produced similar linear ranges of detection and limits of detection. The limits of detection for CEA were 0.29 pg/ml and 0.21 pg/ml for competitive and sandwich reactions, respectively. The linear ranges of detection were from 0.49 pg/ml to 4.9 ng/ml for both competitive and sandwich reactions. The detection limits were lower, and the linear ranges were wider than those of literature. There was a 9% difference in CEA detection measurements between competitive and sandwich magnetic immunoassay. The measurements of two magnetic immunoassays differed by less than 13% from the ELISA reference measurements. The running time was less than 30 min. Magnetic immunoassay in a thin channel has great potential for biochemical analysis and immunoassay-related applications.     

Waveform dependence of pulsatile flow in a stenosed channel

Bloodflow in arteries often shows a rich variety of vortical flows, which are dominated by the complex geometry of blood vessels, the dynamic pulsation of blood flow, and the complicated boundary conditions. With a two-dimensional model of unsteady flow in a stenosed channel, the pulsatile influence on such vortical fluid dynamics has been numerically studied in terms of waveform dependence on physiological pulsation. Results are presented for unsteady flows downstream of the stenosed portion with variation in the wavefiorms of systole and diastole. Overall, a train of propagating vortex waves is observed for all the cases, but it shows great sensitivity to the waveforms. The generation and development of the vortex waves may be linked to the presence of an adverse pressure gradient within a specific interval between two points of inflection of the systolic waveform. The adverse pressure gradient consists of a global pressure gradient that is found to be closely related to the dynamnics of' the pulsation, and a local pressure gradient, which is obsented to be dominated by the nonlinear vortex dynamics.     

Inferred motions of the S3a helix during voltage-dependent K+ channel gating

The gating of voltage-dependent potassium channels is controlled by conformational changes in voltage sensor domains. Previous studies have shown that the S1 and the S2 helices of the voltage sensor are static with respect to motion across the membrane, while the voltage sensor paddle consisting of the C-terminal half of S3 (S3b) and the charge-bearing S4 is mobile. The mobile component is attached to S1 and S2 via the S2-S3 turn and the N-terminal half of S3 (S3a). In this study, we analyze KvAP, an archaebacterial voltage-dependent potassium channel, to study the mobility with respect to translation across the membrane of S3a. We utilize an assay based on attachment of tethered biotin and its site-specific accessibility to avidin. Our results reveal that the S3a helix does not move appreciably across the membrane in association with gating. The static behavior of S3a constrains the conformations available to the voltage sensor when it closes and suggests that a set of negative countercharges within the membrane's inner leaflet remains intact in the closed conformation.     

An approximation diffusion equation for a long narrow channel with varying cross-sectional area

The diffusion equation for long narrow channels which lie parallel to a rectangular coordinate and have varying cross-sectional areas may be approximated by an equation which involves only one space variable and the average concentration at each value of this space variable. This equation is derived and is discussed along with its assumptions.     

Low Reynolds number equi-bifurcation flow in a two-dimensional channel

The fluid flow in some physiological vessels such as the blood flow in blood vessels and the air flow through bronchi and bronchioles in the lungs undergoes a large number of bifurcations. The understanding of the bifurcation flow is of importance for a better comprehension of its effect in the blood and the air circulatory systems of the living body. The Reynolds number of flow in large blood vessels and bronchi is high and fluid inertia plays a dominant role in the bifurcation flow in such vessels. In small caliber blood vessels such as arterioles and capillaries, and bronchioles, the Reynolds number of flow is quite low and the effect of fluid inertia is negligible compared to the pressure and shear forces. In order to have a quantitative understanding of the bifurcation flow at low Reynolds numbers, the low Reynolds number equi-bifurcation flow in a two-dimensional channel at zero bifurcation angle is studied based on the Stokes approximation. The solution of the problem is posed as an infinite series, where the truncated version is used in numerical calculations. The results of this analysis is discussed in connection with the bifurcation flow of blood in small caliber blood vessels and that of the air in bronchioles in the lung.     

Cytoplasmic motions, rheology, and structure probed by a novel magnetic particle method

The motions of magnetic particles contained within organelles of living cells were followed by measuring magnetic fields generated by the particles. The alignment of particles was sensed magnetometrically and was manipulated by external fields, allowing non-invasive detection of particle motion as well as examination of cytoplasmic viscoelasticity. Motility and rheology data are presented for pulmonary macrophages isolated from lungs of hamsters 1 d after the animals had breathed airborne gamma-Fe2O3 particles. The magnetic directions of particles within phagosomes and secondary lysosomes were aligned, and the weak magnetic field produced by the particles was recorded. For dead cells, this remanent field was constant, but for viable macrophages, the remanent field decreased rapidly so that only 42% of its initial magnitude remained 5 min after alignment. A twisting field was applied perpendicular to the direction of alignment and the rate at which particles reoriented to this new direction was followed. The same twisting was repeated for particles suspended in a series of viscosity standards. Based on this approach, the low-shear apparent intracellular viscosity was estimated to be 1.2-2.7 X 10(3) Pa.s (1.2-2.7 X 10(4) poise). Time-lapse video microscopy confirmed the alignment of ingested particles upon magnetization and showed persistent cellular motility during randomization of alignment. Cytochalasin D and low temperature both reduced cytoplasmic activity and remanent-field decay, but affected rheology differently. Magnetic particles were observed in association with the microtubule organizing center by immunofluorescence microscopy; magnetization did not affect microtubule distribution. However, both vimentin intermediate filaments and f-actin reorganized after magnetization. These data demonstrate that magnetometry of isolated phagocytic cells can probe organelle movements, rheology, and physical properties of the cytoskeleton in living cells.     

Transient relative motion of two cells in a channel flow

The hydrodynamic interaction of a red blood cell and a white blood cell in microvessels is studied, by use of a two-dimensional numerical model. The red blood cell, modeled as a small rigid circular cylinder, and the white blood cell, modeled as a larger rigid circular cylinder, are immersed in an incompressible Newtonian fluid in a two-dimensional channel. It is assumed that no external force or moment acts on the model cells, and the effect of inertia forces on the motion of the fluid and the cells is neglected. The velocity field of the suspending fluid and the instantaneous velocities of the two model cells are computed by the finite element method. Using the translational velocities of the model cells obtained, the trajectories of their relative motion are determined, for various initial positions. It is shown that the cells may or may not pass each other or separate, depending on the initial positions. The present results compare well to the experimental results.     

The intracellular calcium dynamics in a single vascular endothelial cell being squeezed through a narrow microfluidic channel

Biomechanics and Modeling in Mechanobiology - Revealing the mechanisms underlying the intracellular calcium responses in vascular endothelial cells (VECs) induced by mechanical stimuli contributes...     

Forced gating motions by a substituted titratable side chain at the bundle crossing of a potassium channel

Numerous inwardly rectifying potassium (Kir) channels possess an aromatic residue in the helix bundle crossing region, forming the narrowest pore constriction in crystal structures. However, the role of the Kir channel bundle crossing as a functional gate remains uncertain. We report a unique phenotype of Kir6.2 channels mutated to encode glutamate at this position (F168E). Despite a prediction of four glutamates in close proximity, Kir6.2(F168E) channels are predominantly closed at physiological pH, whereas alkalization causes rapid and reversible channel activation. These findings suggest that F168E glutamates are uncharged at physiological pH but become deprotonated at alkaline pH, forcing channel opening due to mutual repulsion of nearby negatively charged side chains. The potassium channel pore scaffold likely brings these glutamates close together, causing a significant pK(a) shift relative to the free side chain (as seen in the KcsA selectivity filter). Alkalization also shifts the apparent ATP sensitivity of the channel, indicating that forced motion of the bundle crossing is coupled to the ATP-binding site and may resemble conformational changes involved in wild-type Kir6.2 gating. The study demonstrates a novel mechanism for engineering extrinsic control of channel gating by pH and shows that conformational changes in the bundle crossing region are involved in ligand-dependent gating of Kir channels.     

Bacterial chemotaxis transverse to axial flow in a microfluidic channel

Swimming bacteria sense and respond to chemical signals in their environment. Chemotaxis is the directed migration of a bacterial population toward increasing concentrations of a chemical that they perceive to be beneficial to their survival. Bacteria that are indigenous to groundwater environments exhibit chemotaxis toward chemical contaminants such as hydrocarbons, which they are also able to degrade. This phenomenon may facilitate bioremediation processes by bringing bacteria into closer proximity to these contaminants. A microfluidic device was assembled to study chemotaxis transverse to advective flow. Using a T-shaped channel design (T-sensor), two fluid streams were brought into contact by impinging flow. They then flowed adjacent to each other along a transparent channel. An advantage to this design is that it allows real-time visualization of bacterial distributions within the channel. Under laminar flow conditions a chemotactic driving force was created perpendicular to the direction of flow by diffusion of the chemical attractant from one input stream to the other. A comparison of the chemotactic band behavior in the absence and presence of flow showed that fluid velocity did not significantly impede chemotactic migration in the transverse direction.