Electro-hydrodynamic extraction of DNA from mixtures of DNA and bovine serum albumin.

We report separation of genomic DNA (48 kbp) from bovine serum albumin (BSA) by the electro-hydrodynamic coupling between a pressure-driven flow and a parallel electric field. Electro-hydrodynamic extraction exploits this coupling to trap DNA molecules at the entrance of a microfluidic contraction channel, while allowing proteins and salts to be flushed from the device. Samples (10 µL) containing λ-DNA (1 ng) and BSA (0.3 mg) were injected directly into the device and convected to the contraction channel entrance by a flowing buffer solution. The DNA remains trapped in this region essentially indefinitely, while proteins and salts are eluted. The effectiveness of the concept has been assessed by fluorescence measurements of DNA and BSA concentrations. Electro-hydrodynamic extraction in a single-stage device was found to enhance the concentration of DNA 40-fold, while reducing the BSA concentration by four orders of magnitude. The relative concentrations of DNA to BSA at the contraction channel entrance can be as large as 1.5 : 1, corresponding to an A260/280 ratio of 1.9. The maximum yield of DNA from a salt-free solution is 50%, while salted (150 mM) solutions have a lower yield (38%).

Trapping DNA with a high throughput microfluidic device.

Long strands of DNA can be trapped and concentrated near the inlet of a microfluidic channel by applying a pressure gradient and an opposing electric field. The mechanism for trapping involves a migration of DNA perpendicular to both the fluid flow and the electric field. Migration leads to a highly nonuniform distribution of DNA within a cross section of the channel, with the bulk of the DNA concentrated in a thin (10 µm) layer next to the walls of the channel. This highly concentrated layer generates an electrophoretic flux toward the inlet to the device, despite the much larger fluid flow in the opposite direction. In this paper, the extent to which DNA can be trapped and concentrated by this means has been characterized by fluorescence measurements. At short times (<2 hours) nearly all the incoming DNA remains trapped within the device until the electric field is turned off. The DNA largely accumulates near the inlet, but after 30-60 minutes additional DNA starts to accumulate deeper into the channel. Eventually DNA leaks from the device itself, but ≈80% of the incoming DNA can be retained for up to 5 hours. Optimizing the electric field strength can increase the amount of DNA that can be trapped, but the efficiency is not affected by the channel cross-section.

Inverse Saffman-Taylor Experiments with Particles Lead to Capillarity Driven Fingering Instabilities.

Using air to displace a viscous fluid contained in a Hele-Shaw cell can create a fingering pattern at the interface between the fluids if the capillary number exceeds a critical value. This Saffman-Taylor instability is revisited for the inverse case of a viscous fluid displacing air when partially wettable hydrophilic particles are lying on the walls. Though the inverse case is otherwise stable, the presence of the particles results in a fingering instability at low capillary number. This capillary-driven instability is driven by the integration of particles into the interface which results from the minimization of the interfacial energy. Both axisymmetric and rectangular geometries are considered in order to quantify this phenomenon.

Electro-hydrodynamic concentration of genomic length DNA.

We report a method of concentrating genomic length DNA within a microfluidic device, using a novel mechanism that combines polyelectrolyte migration with electrophoretic recirculation. Suitable combinations of geometry, pressure and voltage will trap long DNA molecules (>10 kbp) within a small volume (approximately 1 nL), amplifying the local concentration at rates in excess of 1000 fold per minute. The rate at which DNA accumulates is length dependent, while charged particles of similar size pass freely through the device. Experimental observations confirm that the rapid accumulation of DNA at the inlet is caused by an outward migration of the polyelectrolyte towards the capillary boundaries, followed by electrophoresis of DNA within the stagnant fluid layer next to the wall.

Transverse migration of polyelectrolytes in microfluidic channels induced by combined shear and electric fields.

If a dilute solution of a polyelectrolyte such as DNA is forced through a microcapillary by an electric field, while simultaneously driven by a pressure gradient, then the polymer will migrate in directions transverse to the field lines. Here we investigate the sharp increase in concentration in the center of the channel that arises when the flow and electric field drive the polymer in the same direction. We report the first systematic investigation of the effects of flow velocity, electric field, and ionic strength on the degree of migration. Our experiments show that migration increases with increasing shear and electric field as predicted by kinetic theory [Butler et al., Phys. Fluids, 2007, 19, 113101], but eventually saturates as suggested by computer simulations [Kekre et al., Phys. Rev. E: Stat., Nonlinear, Soft Matter Phys., 2010, 82, 050803(R)]. The addition of salt reduces the strength of the migration, consistent with a screening of long-range hydrodynamic flow fields by added salt. However, increasing the ionic strength of a Tris-acetate-EDTA buffer solution has much less effect on the degree of migration.

Gelation and large thermoresponse of cranberry-based xyloglucan.

Cranberry waste contains potentially valuable components, such as proanthocyanidins, flavanols, and xyloglucan. Highly-purified xyloglucan (XG) from cranberries were studied through steady and oscillatory shear rheology at various concentrations and temperatures. At room temperature, an apparent yield stress is observed and the storage modulus exceeds the loss modulus ( [Formula: see text] ) for concentrations of 0.5 wt% and higher, indicating that the XG solution has formed a physical hydrogel. Thermoresponsive gelation is observed with a five-order of magnitude increase in shear moduli as it undergoes a weak to strong gel transition around 52 °C. The gelation time was 5 min with an observed storage moduli up to 3500 Pa. Cranberry-based XG exhibits thermoresponsive behavior at concentrations as low as 0.1 wt% (w/v), which is significantly lower than prior gelation studies of XG from other sources. The formation of a weak gel at room temperature and large storage moduli observed at room temperature is likely associated with the low level of impurities and small amount of galactose present in the XG chains.

Estimating Kinetic Rate Parameters for Enzymatic Degradation of Lyophilized Silk Fibroin Sponges.

Sponge-like biomaterials formed from silk fibroin are promising as degradable materials in clinical applications due to their controllable breakdown into simple amino acids or small peptides in vivo. Silk fibroin, isolated from Bombyx mori silkworm cocoons, can be used to form sponge-like materials with a variety of tunable parameters including the elastic modulus, porosity and pore size, and level of nanocrystalline domains. These parameters can be independently tuned during formulation resulting in a wide parameter space and set of final materials. Determining the mechanism and rate constants for biomaterial degradation of these tunable silk materials would allow scientists to evaluate and predict the biomaterial performance for the large array of tissue engineering applications and patient ailments a priori. We first measured in vitro degradation rates of silk sponges using common protein-degrading enzymes such as Proteinase K and Protease XIV. The concentration of the enzyme in solution was varied (1, 0.1, 0.01 U/mL) along with one silk sponge formulation parameter: the level of crystallinity within the sponge. Additionally, two experimental degradation methods were evaluated, termed continuous and discrete degradation methods. Silk concentration, polymer chain length and scaffold pore size were held constant during experimentation and kinetic parameter estimation. Experimentally, we observed that the enzyme itself, enzyme concentration within the bulk solution, and the sponge fabrication water annealing time were the major experimental parameters dictating silk sponge degradation in our experimental design. We fit the experimental data to two models, a Michaelis-Menten kinetic model and a modified first order kinetic model. Weighted, non-linear least squares analysis was used to determine the parameters from the data sets and Monte-Carlo simulations were utilized to obtain estimates of the error. We found that modified first order reaction kinetics fit the time-dependent degradation of lyophilized silk sponges and we obtained first order-like rate constants. These results represent the first investigations into determining kinetic parameters to predict lyophilized silk sponge degradation rates and can be a tool for future mathematical representations of silk biomaterial degradation.

Interfacial polymerization of a thin film on contact lenses for improving lubricity.

HYPOTHESIS: A large number of contact lens wearers drop out each year due to end of day discomfort, which could possibly be reduced by designing lenses with highly lubricious surfaces. We hypothesize that polymerizing a thin film of dimethyl acrylamide (DMA) on the surface of the lenses will improve lubricity. EXPERIMENTS: The thin film is polymerized by loading a commercial contact lens (1-DAY ACUVUE® TruEye®) with N,N,N',N'-Tetramethylethane-1,2-diamine (TEMED) and soaking it in a solution of DMA and ammonium per sulfate (APS). The two components of the redox couple (APS and TEMED) mix near the surface of the lens due to diffusion and react rapidly to form free radicals. The free radicals lead the polymerization of the DMA monomer near the surface resulting in the formation of the thin hydrogel layer that is attached to the lens matrix through activation of unreacted vinyl groups or possibly through formation of entanglements with the lens polymer. FINDINGS: The thickness of the layer is controlled by the polymerization time which is limited to 30 s to create a layer of DMA only at the surface. The presence of the DMA layer is confirmed through measurements of Fourier-transform infrared spectroscopy (FTIR) spectra in total internal reflection mode. The layer is determined to be about 3-5 µm thick with a water content of about 285%. The presence of the layer significantly improves lubricity as is evident through the qualitative rubbing test and quantitative measurement of the friction coefficient. A preliminary one-week safety study in rabbits show that lens wear does not cause any toxicity.

Long-term improvements to photoluminescence and dispersion stability by flowing SDS-SWNT suspensions through microfluidic channels.

Shearing single-walled carbon nanotubes (SWNTs) coated with sodium dodecyl sulfate in microfluidic channels significantly increases the photoluminescence (PL) intensity and dispersion stability of SWNTs. The PL quantum yield (QY) of SWNTs improves by a factor of 3 for initially bright suspensions; on the other hand, SWNT QYs in a "poor" suspension improve by 2 orders of magnitude. In both cases, the QYs of the sheared suspensions are approximately 1%. The increases in PL intensity persist for months and are most prominent in larger diameter SWNTs. These improvements are attributed to surfactant reorganization rather than disaggregation of SWNTs bundles or shear-induced alignment. The results also highlight potential opportunities to eliminate discrepancies in the PL intensity of different suspensions and further improve the PL of SWNTs by tailoring the surfactant structure around SWNTs.

Transverse migration and microfluidic concentration of DNA using Newtonian buffers.

We present experimental evidence that DNA can be concentrated due to an electrohydrodynamic coupling between a pressure-driven flow and a parallel electric field. The effects of buffer properties on the process were measured in a microfluidic channel. The concentration rates and the efficiency of trapping DNA were quantified as functions of the ion and polymer concentrations of the buffer solution. Buffers with large ion concentrations hindered the ability to trap DNA, reducing the short-time efficiency of the concentration process from nearly 100% to zero. Importantly, DNA was trapped in the microfluidic channel even when the buffer solution lacked any measurable viscoelastic response. These observations indicate that electrohydrodynamic migration drives the concentration of DNA. We found no evidence of viscoelastic migration in these experiments.

Improving the effectiveness of interfacial trapping in removing single-walled carbon nanotube bundles.

Single-walled carbon nanotube (SWNT) bundles are selectively removed from an aqueous dispersion containing individually suspended carbon nanotubes coated with gum Arabic via interfacial trapping. The suspensions are characterized with absorbance, fluorescence, and Raman spectroscopy as well as atomic force microscopy (AFM) and rheology. The resulting aqueous suspensions have better dispersion quality after interfacial trapping and can be further improved by altering the processing conditions. A two-step extraction process offers a simple and fast approach to preparing high-quality dispersions of individual SWNTs comparable to ultracentrifugation. Partitioning of SWNTs to the liquid-liquid interface is described by free energy changes. SWNT bundles prefer to reside at the interface over individually suspended SWNTs because of greater free energy changes.

Cross-stream migration in dilute solutions of rigid polymers undergoing rectilinear flow near a wall.

Kinetic theory is used to investigate cross-stream migration of a rigid polymer undergoing rectilinear flow in the vicinity of a wall. Hydrodynamic interactions between the polymers and the boundary result in a cross-stream migration. In simple shear flow, polymers migrate away from the wall, creating a depletion layer in the vicinity of the wall which thickens as the flow strength increases relative to the Brownian force. In pressure-driven flow, an off-center maximum in the center-of-mass distribution occurs due to a competition between hydrodynamic interactions with the wall and the anisotropic diffusivity induced by the inhomogeneous flow field.

Irreversibility and chaos: role of lubrication interactions in sheared suspensions.

We investigate non-Brownian particles suspended in a periodic shear-flow using simulations. Following Metzger and Butler [Phys. Rev. E 82, 051406 (2010)], we show that the chaotic dynamics arising from lubrication interactions are too weak to generate an observable particle dispersion. The irreversibility observed in periodic flow is dominated by contact interactions. Nonetheless, we show that lubrication interactions must be included in the calculation to obtain results that agree with experiments.

Irreversibility and chaos: role of long-range hydrodynamic interactions in sheared suspensions.

Non-Brownian particles suspended in an oscillatory shear flow are studied numerically. In these systems it is often assumed that chaos (due to the long-range nature of the hydrodynamic interaction between particles) plus noise (contact or roughness) lead to irreversible behavior. However, we demonstrate that the long-range hydrodynamic interactions are not a source, nor even a magnifier, of irreversibility when coupled with nonhydrodynamic interactions. Additionally, analysis reveals that the apparent anisotropy of the particle diffusion is due to coupling of the shear flow and transverse diffusion.

Role of hydrodynamic interactions in the migration of polyelectrolytes driven by a pressure gradient and an electric field.

Experiments have shown that DNA molecules in capillary electrophoresis migrate across field lines if a pressure gradient is applied simultaneously. We suggest that this migration results from an electrically driven flow field around the polyelectrolyte, which generates additional contributions to the center-of-mass velocity if the overall polymer conformation is asymmetric. This hypothesis leads to a coarse-grained polymer model, without explicit charges, that quantitatively explains the experimentally observed migration. The simulations contradict the widely held notion that charge neutrality eliminates the effects of hydrodynamic interactions in electrically driven flows of polyelectrolytes. We predict a measurable increase in the electrophoretic velocity of a sheared polyelectrolyte that depends on chain length.

Comparison of lattice-Boltzmann and brownian-dynamics simulations of polymer migration in confined flows.

This paper compares results from lattice-Boltzmann and brownian-dynamics simulations of polymer migration in confined flows bounded by planar walls. We have considered both a uniform shear rate and a constant pressure gradient. Lattice-Boltzmann simulations of the center-of-mass distribution agree quantitatively with brownian-dynamics results, contradicting previously published results. The mean end-to-end distance of the extended polymer is more sensitive to grid resolution Δx and time-step Δt. Nevertheless, for sufficiently small Δx and Δt, convergent results for the polymer stretch are obtained which agree with brownian dynamics within statistical uncertainties. The brownian-dynamics simulations incorporate a mobility matrix for a confined polymer that is both symmetric and positive definite for all physically accessible configurations.

Comparison of the static and dynamic properties of a semiflexible polymer using lattice Boltzmann and Brownian-dynamics simulations.

The aim of this paper is to compare results from lattice Boltzmann and Brownian-dynamics simulations of linear chain molecules. We have systematically varied the parameters that may affect the accuracy of the lattice Boltzmann simulations including grid resolution, temperature, polymer mass, and fluid viscosity. The effects of the periodic boundary conditions are minimized by an analytic correction for the different long-range interactions in periodic and unbounded systems. Lattice Boltzmann results for the diffusion coefficient and Rouse mode relaxation times were found to be insensitive to temperature, which suggests that effects of hydrodynamic retardation are small. By increasing the resolution of the lattice Boltzmann grid with respect to the polymer size, convergent results for the diffusion coefficient and relaxation times were obtained; these results agree with Brownian dynamics to within 1%-2%.

Transverse migration of a confined polymer driven by an external force.

We demonstrate that a polymer confined to a narrow channel migrates towards the center when driven by an external force parallel to the channel walls. This migration results from asymmetric hydrodynamic interactions between polymer segments and the confining walls. A weak pressure-driven flow, applied in the same direction as the external force, enhances the migration. However, when the pressure gradient and the external force act in opposite directions the polymer can migrate towards the boundaries. Nevertheless, for sufficiently strong forces the polymer always migrates towards the center. A dumbbell kinetic theory explains these results qualitatively. A comparison of our results with experimental measurements on DNA suggests that hydrodynamic interactions in polyelectrolytes are only partially screened. We propose new experiments and analysis to investigate the extent of the screening in polyelectrolyte solutions.

Simulations of concentrated suspensions of rigid fibers: relationship between short-time diffusivities and the long-time rotational diffusion.

Brownian dynamics simulations of the behavior of suspensions of fibers demonstrate that the scaling of the rotational diffusivity with respect to the number density (nL3) is a sensitive function of the thickness and the parameter L2D(R0)/D(T0), where D(R0) is the rotational diffusivity at infinite dilution, D(T0) is the average center-of-mass diffusivity at infinite dilution, and L is the fiber length. Existing theories for the long-time rotational diffusivities of rigid fibers in the semidilute and concentrated regimes fail to accurately account for the relationship with the dilute values of the rotational and translational diffusivities of the various physical models used to simulate the fibers. The concentration regime studied in this work ranges from a number density of nL3 approximately 0-150, which is below the transition from an isotropic to nematic state. The effect of the fiber thickness was studied by performing simulations of rods with aspect ratios (fiber length over diameter) of 25, 50, and 500, as well as performing projections for infinitely thin fibers. The excluded volume of the rods was enforced through the use of short-range potentials. For a rod with an aspect ratio of 50 with a parameter of L2D(R0)/D(T0)=9, which corresponds to a slender-body model of the individual fibers, the rotational diffusivity (D(R)) scales as D(R)/D(R0) approximately (nL3)(-1.9) in the concentration regime of 70 < or = nL3 < or = 150. Similarly with a parameter of L2D(R0)/D(T0)=4, corresponding to a rigid-dumbbell model, the rotational diffusivity scales as D(R)/D(R0) approximately (nL3)(-1.1) over the same range of concentrations. For rods with aspect ratios of 25, it is observed that a difference in the scaling is seen for L2D(R0)/D(T0) approximately < 8, with higher values of this ratio exhibiting essentially the same scaling. Additional values of the ratio L2D(R0)/D(T0) were investigated to determine the overall behavior of the suspension dynamics with respect to this parameter. These findings resolve discrepancies between simulation results for rotational diffusivities reported by previous investigators and provide new insights for the development of an accurate theory for the diffusivity of rigid rods suspended in solution.

Large-scale streamers in the sedimentation of a dilute fiber suspension.

We experimentally characterize structures formed during the sedimentation of rigid fibers of high aspect ratio at small Reynolds number using particle image velocimetry. Measurements show the existence of large-scale streamers during early stages of the sedimentation process, consistent with previously published theory and numerical simulations. At longer times, the cell-wide inhomogeneities evolve into smaller-scale streamers. Measurements of spatially averaged fiber velocities and velocity fluctuations are also presented.