Sumita Pennathur

Nanofluidic technology for biomolecule applications: a critical review

In this review, we present nanofluidic phenomena, particularly as they relate to applications involving analysis of biomolecules within nanofabricated devices. The relevant length scales and physical phenomena that govern biomolecule transport and manipulation within nanofabricated nanofluidic devices are reviewed, the advantages of nanofabricated devices are presented, and relevant applications are cited. Characteristic length scales include the Debye length, the Van der Waals radius, the action distance of hydrogen bonding, the slip length, and macromolecular dimensions. On the basis of the characteristic lengths and related nanofluidic phenomena, a nanofluidic toolbox will be assembled. Nanofluidic phenomena that affect biomolecule behavior within such devices can include ion depletion and enrichment, modified velocity and mobility, permselectivity, steric hindrance, entropy, adsorption, and hydrodynamic interaction. The complex interactions and coupled physics of such phenomena allow for many applications, including biomolecule separation, concentration, reaction/hybridization, sequencing (in the case of DNA) and detection. Examples of devices for such applications will be presented, followed by a discussion of near-term challenges and future thoughts for the field.

Distinct Conformations of DNA-Stabilized Fluorescent Silver Nanoclusters Revealed by Electrophoretic Mobility and Diffusivity Measurements

Silver-DNA nanoclusters (Ag:DNAs) are novel fluorophores under active research and development as alternative biomolecular markers. Comprised of a few-atom Ag cluster that is stabilized in water by binding to a strand of DNA, they are also interesting for fundamental explorations into the properties of metal molecules. Here, we use in situ calibrated electrokinetic microfluidics and fluorescence correlation spectroscopy to determine the size, charge, and conformation of a select set of Ag:DNAs. Among them is a pair of spectrally distinct Ag:DNAs stabilized by the same DNA sequence, for which it is known that the silver cluster differs by two atoms. We find these two Ag:DNAs differ in size by ∼30%, even though their molecular weights differ by less than 3%. Thus a single DNA sequence can adopt very different conformations when binding slightly different Ag clusters. By comparing spectrally identical Ag:DNAs that differ in sequence, we show that the more compact conformation is insensitive to the native DNA secondary structure. These results demonstrate electrokinetic microfluidics as a practical tool for characterizing Ag:DNA.

Streaming current and wall dissolution over 48 h in silica nanochannels

We present theoretical and experimental studies of the streaming current induced by a pressure-driven flow in long, straight, electrolyte-filled nanochannels. The theoretical work builds on our recent one-dimensional model of electro-osmotic and capillary flow, which self-consistently treats both the ion concentration profiles, via the nonlinear Poisson-Boltzmann equation, and the chemical reactions in the bulk electrolyte and at the solid-liquid interface. We extend this model to two dimensions and validate it against experimental data for electro-osmosis and pressure-driven flows, using eight 1-μm-wide nanochannels of heights varying from 40 nm to 2000 nm. We furthermore vary the electrolyte composition using KCl and borate salts, and the wall coating using 3-cyanopropyldimethylchlorosilane. We find good agreement between prediction and experiment using literature values for all parameters of the model, i.e., chemical reaction constants and Stern-layer capacitances. Finally, by combining model predictions with measurements over 48 h of the streaming currents, we develop a method to estimate the dissolution rate of the silica walls, typically around 0.01 mg/m(2)/h, equal to 45 pm/h or 40 nm/yr, under controlled experimental conditions.

Surface-dependent chemical equilibrium constants and capacitances for bare and 3-cyanopropyldimethylchlorosilane coated silica nanochannels

We present a combined theoretical and experimental analysis of the solid-liquid interface of fused-silica nanofabricated channels with and without a hydrophilic 3-cyanopropyldimethylchlorosilane (cyanosilane) coating. We develop a model that relaxes the assumption that the surface parameters C(1), C(2), and pK(+) are constant and independent of surface composition. Our theoretical model consists of three parts: (i) a chemical equilibrium model of the bare or coated wall, (ii) a chemical equilibrium model of the buffered bulk electrolyte, and (iii) a self-consistent Gouy-Chapman-Stern triple-layer model of the electrochemical double layer coupling these two equilibrium models. To validate our model, we used both pH-sensitive dye-based capillary filling experiments as well as electro-osmotic current-monitoring measurements. Using our model we predict the dependence of ζ potential, surface charge density, and capillary filling length ratio on ionic strength for different surface compositions, which can be difficult to achieve otherwise.

Separation of ions in nanofluidic channels with combined pressure-driven and electro-osmotic flow.

Separation of ionic species with the same electrophoretic mobility but different valence in electrolyte systems can occur within nanometer-scale channels with finite electrical double layers (EDLs). This is because EDL thicknesses are a significant fraction of slit height in such channels and can create transverse analyte concentration profiles that allow for unique separation modalities when combined with axial fluid flow. Previous work has shown such separation to occur using either pressure-driven flow or electro-osmotic flow separately. Here, we develop a Poisson-Boltzmann model to compare the separation of such ions using the combination of both pressure-driven and electro-osmotic flow. Applying a pressure gradient in the opposite direction of electro-osmotic flow can allow for zero or infinite retention of analyte species, which we investigate using three different wall boundary conditions. Furthermore, we determine conditions in fused silica nanochannels with which to generate optimal separation between two analytes of different charge but the same mobility. We also give simple rules of thumb to achieve the best separation efficacy in nanochannel systems.

Multiphase flow in lab on chip devices: a real tool for the future?

Many applications for lab on a chip (LOC) devices require the use of two or more fluids that are either not chemically related (e.g. oil and water) or in different phases (e.g. liquid and gas). Utilizing multiphase flow in LOC devices allows for both the fundamental study of multiphase flow and the development of novel types of pumping, mixing, reaction, separation, and detection technologies. Current examples of multiphase LOC applications include inkjet printers, separation of biochemical samples, manipulation of biomolecules, bio-sensing, enhanced mixing for bio-sample reactions, biomolecule detection, microelectronic cooling, drug delivery devices, explosives detection, dairy analysis, bubble computing and analysis of emulsions, foams, and bubble coalescence. In this focus article, we will briefly review the basics of multiphase flow with reference to microfluidic systems, describe some of the most promising flow control methods for multiphase fluid systems, and discuss our thoughts about future directions of microfluidic multiphase flow.

Improving fluorescence detection in lab on chip devices.

Fluorescence is the workhorse for analysis in many of today’s lab-on-chip (LOC) devices. However, LOC fluorescence detection is limited in both spatial resolution and sensitivity, due primarily to sub-optimal light collection. More sensitive, higher resolution LOC devices would enable novel structural and functional biomolecule studies, as well as improve chip-based bioanalytical assays by orders of magnitude. In this focus article, we consider the possible avenues for performing high-sensitivity and high-resolution fluorescence detection within LOC devices.

Efficiently accounting for ion correlations in electrokinetic nanofluidic devices using density functional theory

The electrokinetic behavior of nanofluidic devices is dominated by the electrical double layers at the device walls. Therefore, accurate, predictive models of double layers are essential for device design and optimization. In this paper, we demonstrate that density functional theory (DFT) of electrolytes is an accurate and computationally efficient method for computing finite ion size effects and the resulting ion-ion correlations that are neglected in classical double layer theories such as Poisson-Boltzmann. Because DFT is derived from liquid-theory thermodynamic principles, it is ideal for nanofluidic systems with small spatial dimensions, high surface charge densities, high ion concentrations, and/or large ions. Ion-ion correlations are expected to be important in these regimes, leading to nonlinear phenomena such as charge inversion, wherein more counterions adsorb at the wall than is necessary to neutralize its surface charge, leading to a second layer of co-ions. We show that DFT, unlike other theories that do not include ion-ion correlations, can predict charge inversion and other nonlinear phenomena that lead to qualitatively different current densities and ion velocities for both pressure-driven and electro-osmotic flows. We therefore propose that DFT can be a valuable modeling and design tool for nanofluidic devices as they become smaller and more highly charged.

Field-amplified sample stacking and focusing in nanofluidic channels

Nanofluidic technology is gaining popularity for bioanalytical applications due to advances in both nanofabrication and design. One major obstacle in the widespread adoption of such technology for bioanalytical systems is efficient detection of samples due to the inherently low analyte concentrations present in such systems. This problem is exacerbated by the push for electronic detection, which requires an even higher sensor-local sample concentration than optical detection. This paper explores one of the most common preconcentration techniques, field-amplified sample stacking, in nanofluidic systems in efforts to alleviate this obstacle. Holding the ratio of background electrolyte concentrations constant, the parameters of channel height, strength of electric field, and concentration are varied. Although in micron scale systems, these parameters have little or no effect on the final concentration enhancement achieved, nanofluidic experiments show strong dependencies on each of these parameters. Further,...

Quantitative characterization of the colloidal stability of metallic nanoparticles using UV-vis absorbance spectroscopy.

Plasmonic nanoparticles are used in a wide variety of applications over a broad array of fields including medicine, energy, and environmental chemistry. The continued successful development of this material class requires the accurate characterization of nanoparticle stability for a variety of solution-based conditions. Although many characterization methods exists, there is an absence of a unified, quantitative means for assessing the colloidal stability of plasmonic nanoparticles. We present the particle instability parameter (PIP) as a robust, quantitative, and generalizable characterization technique based on UV-vis absorbance spectroscopy to characterize colloidal instability. We validate PIP performance with both traditional and alternative characterization methods by measuring gold nanorod instability in response to different salt (NaCl) concentrations. We further measure gold nanorod stability as a function of solution pH, salt, and buffer (type and concentration), nanoparticle concentration, and concentration of free surfactant. Finally, these results are contextualized within the literature on gold nanorod stability to establish a standardized methodology for colloidal instability assessment.