Nanofluidic Confinement Research Articles

Fabrication of a hybrid device for the integration of light-triggered proton pumps

Biological ion pumps, such as bacteriorhodopsin (bR), utilize photons to move ions against concentration gradients, offering energy harvesting and spatiotemporal control of chemical gradients. This capability goes far beyond the capabilities of today's synthetic devices, suggesting a hybrid approach to embed bRs in synthetic devices in order to direct the proton flow towards useful system applications. In this study, a hybrid silicon-based nanochannel network with integrated purple membranes (PM) containing bR was fabricated. The fabrication method combines thermal scanning probe lithography, etching techniques, atomic layer deposition, plasma-enhanced chemical vapor deposition, and photolithography to create devices with buried nanochannels on silicon substrates. PM patches were deposited onto specified sites by a tunable nanofluidic confinement apparatus. The resulting device holds the potential for locally controlling directed ion transport in micrometer scale devices, a first step towards applications, such as locally affected proton catalyzed chemical reaction networks. Furthermore, this fabrication strategy, employing a maskless overlay, is a tool for constructing intricate nanofluidic network designs which are mechanically robust and straightforward to fabricate.

Placement of Biological Membrane Patches in a Nanofluidic Gap With Control Over Position and Orientation

AbstractPurple membranes from the archaeon Halobacterium salinarum consist of 2D crystals of the light‐driven proton pump bacteriorhodopsin, which convert photons into a proton gradient across the cell membrane. This functional feature and the structural rigidity make them appealing candidates for integration into biomimetic devices. To this end, and in order to carry out their function, purple membranes must be positioned in the correct orientation at the position of interest. Precise placement and control over the orientation of nanoscale objects still constitutes a formidable challenge. Here, it is shown that isolated purple membrane patches can be transported and positioned at predefined locations in nanofluidic confinement, with control over their orientation at the target sites. The transport is achieved through a rocking Brownian motor scheme, while the controlled deposition of the membranes is realized by engineering the surface potential of a fluid‐filled nanofluidic slit. This controlled manipulation of purple membrane patches outlines a new pathway toward the integration of biological or other delicate supramolecular structures into top–down‐fabricated patterns, for the assembly of nanoscale hybrid devices that serve as a light‐driven source of (chemical) energy.

Superfluid Optomechanics With Phononic Nanostructures

In quantum optomechanics, finding materials and strategies to limit losses has been crucial to the progress of the field. Recently, superfluid 4He was proposed as a promising mechanical element for quantum optomechanics. This quantum fluid shows highly desirable properties (e.g. extremely low acoustic loss) for a quantum optomechanical system. In current implementations, superfluid optomechanical systems suffer from external sources of loss, which spoils the quality factor of resonators. In this work, we propose a new implementation, exploiting nanofluidic confinement. Our approach, based on acoustic resonators formed within phononic nanostructures, aims at limiting radiation losses to preserve the intrinsic properties of superfluid 4He. In this work, we estimate the optomechanical system parameters. Using recent theory, we derive the expected quality factors for acoustic resonators in different thermodynamic conditions. We calculate the sources of loss induced by the phononic nanostructures with numerical simulations. Our results indicate the feasibility of the proposed approach in a broad range of parameters, which opens new prospects for more complex geometries.

Electrochemiluminescence reaction pathways in nanofluidic devices.

Nanofluidic electrochemical devices confine the volume of chemical reactions to femtoliters. When employed for light generation by electrochemiluminescence (ECL), nanofluidic confinement yields enhanced intensity and robust luminescence. Here, we investigate different ECL pathways, namely coreactant and annihilation ECL in a single nanochannel and compare light emission profiles. By high-resolution imaging of electrode areas, we show that different reaction schemes produce very different emission profiles in the unique confined geometry ofa nanochannel. The confrontation of experimental results with finite element simulation gives further insight into the exact reaction ECL pathways. We find that emission strongly depends on depletion, geometric exclusion, and recycling of reactants in the nanofluidic device.

Energy from the Nanofluidic Transport of Water through Nanochannels between Packed Silica Spheres

Efficient harvesting of electrokinetic-streaming-potential requires a trade-off between high flow-rate and nanofluidic confinement. To attain the best out of these parameters, we have developed a p...

The nanofluidic confinement apparatus: studying confinement-dependent nanoparticle behavior and diffusion.

The behavior of nanoparticles under nanofluidic confinement depends strongly on their distance to the confining walls; however, a measurement in which the gap distance is varied is challenging. Here, we present a versatile setup for investigating the behavior of nanoparticles as a function of the gap distance, which is controlled to the nanometer. The setup is designed as an open system that operates with a small amount of dispersion of ≈20 μL, permits the use of coated and patterned samples and allows high-numerical-aperture microscopy access. Using the tool, we measure the vertical position (termed height) and the lateral diffusion of 60 nm, charged, Au nanospheres as a function of confinement between a glass surface and a polymer surface. Interferometric scattering detection provides an effective particle illumination time of less than 30 μs, which results in lateral and vertical position detection accuracy ≈10 nm for diffusing particles. We found the height of the particles to be consistently above that of the gap center, corresponding to a higher charge on the polymer substrate. In terms of diffusion, we found a strong monotonic decay of the diffusion constant with decreasing gap distance. This result cannot be explained by hydrodynamic effects, including the asymmetric vertical position of the particles in the gap. Instead we attribute it to an electroviscous effect. For strong confinement of less than 120 nm gap distance, we detect the onset of subdiffusion, which can be correlated to the motion of the particles along high-gap-distance paths.

Chemical reactions under the nanofluidic confinement of reconstructed lamellar membranes

The nanochannel network of reconstructed vermiculite clay is employed here to study the effects of nanofluidic confinement on chemical reactions.

In situ contrast calibration to determine the height of individual diffusing nanoparticles in a tunable confinement

We study the behavior of charged spherical Au nanoparticles in a nanofluidic slit as a function of the separation of the symmetrically charged confining surfaces. A dedicated setup called the nano-fluidic confinement apparatus allows us to parallelize the two confining surfaces and to continuously approach them down to direct contact. Interferometric scattering detection is used to measure the particle contrast with 2 ms temporal resolution. We obtain the confinement gap distance from the interference signal of the glass and the oxide-covered silicon wafer surface with nanometer accuracy. We present a three parameter model that describes the optical signal of the particles as a function of particle height and gap distance. The model is verified using nanoparticles immobilized at the glass and the substrate surface. For freely diffusing particles, the envelope of the particle signal as a function of gap distance and the known particle height at tight confinement is used to calibrate the particle signal in situ and obtain all free model parameters. Due to the periodic contrast variation for large gap distances, we obtain a set of possible particle heights for a given contrast value. For a range of small gap distances, this assignment is unique, and the particle height can be measured directly with high accuracy. The high temporal resolution allows us to measure the height occupation probability, which provides a direct link to the free-energy landscape the particles are probing via the Boltzmann distribution. Accordingly by fitting the results to a physical model based on the linear superposition approximation, the physical parameters governing the particle-glass interaction are quantified.

Direct optical mapping of transcription factor binding sites on field-stretched λ-DNA in nanofluidic devices.

Mapping transcription factor (TF) binding sites along a DNA backbone is crucial in understanding the regulatory circuits that control cellular processes. Here, we deployed a method adopting bioconjugation, nanofluidic confinement and fluorescence single molecule imaging for direct mapping of TF (RNA polymerase) binding sites on field-stretched single DNA molecules. Using this method, we have mapped out five of the TF binding sites of E. coli RNA polymerase to bacteriophage λ-DNA, where two promoter sites and three pseudo-promoter sites are identified with the corresponding binding frequency of 45% and 30%, respectively. Our method is quick, robust and capable of resolving protein-binding locations with high accuracy (∼ 300 bp), making our system a complementary platform to the methods currently practiced. It is advantageous in parallel analysis and less prone to false positive results over other single molecule mapping techniques such as optical tweezers, atomic force microscopy and molecular combing, and could potentially be extended to general mapping of protein–DNA interaction sites.

Recessed Ring–Disk Nanoelectrode Arrays Integrated in Nanofluidic Structures for Selective Electrochemical Detection

Arrays of recessed ring-disk (RRD) electrodes with nanoscale spacing fabricated by multilayer deposition, nanosphere lithography, and multistep reactive ion etching were incorporated into nanofluidic channels. These arrays, which characteristically exhibit redox cycling leading to current amplification during cyclic voltammetry, can selectively analyze electroactive species based on differences in redox reversibility, redox potential, or both. Using Ru(NH3)6(3+) and ascorbic acid (AA) as model reversible and irreversible redox species, the selectivity for electrochemical measurement of Ru(NH3)6(3+) against a background of AA improves from ∼10, for an array operated in a fluidically unconstrained geometry, to ∼70 for an array integrated within nanofluidic channels. RRD arrays were also used for the detection of dopamine in the presence of AA by cyclic voltammetry. A linear response ranging from 100 nM to 1 mM with a detection limit of 20 nM was obtained for dopamine alone without nanofluidic confinement. In nanochannel-confined arrays, AA was depleted by holding the ring electrodes at +0.5 V versus Ag/AgCl, allowing interference-free determination of dopamine at the disk electrodes in the presence of a 100-fold excess of AA. For selective detection of electrochemically reversible interfering species on an RRD array without nanochannel confinement, a ring potential can be chosen such that one species exhibits exclusively cathodic (anodic) current, allowing the other species to be determined from its anodic (cathodic) current. This approach for selective detection is demonstrated in a mixture of Ru(NH3)6(3+) and Fe(CN)6(3-), which have resolved redox potentials. The same principle was successfully applied to differentiate species with overlapping redox potentials, such as dopamine/Fe(CN)6(3-) and ferrocenemethanol/Fe(CN)6(4-).

Force-fluctuation physics of confined DNA: probing the breakdown of the Marko-Siggia law


 
 
 Introduction: The study of polymers in nanofluidic systems such as nanopores and nanochannels is an important avenue of research in the physical and life sciences today. Complex nanofluidic devices containing varying topography are ideal for quantifying the behaviour of polymers under confinement. This study investigates the Marko-Siggia force-extension relationship under confinement. We measure the transverse fluctuations of deoxyribonucleic acid (DNA) confined between two pits in a nanofluidic slit to measure the potential breakdown of this model.
 Methods: We took images of fluorescently tagged single DNA molecules in the nanopit array with video- fluorescence microscopy and analyzed the standard deviation of the peak position along the direction of the molecular extension.
 Results: We were able to measure the parabolic relation between position and the strength of transverse fluctuations. By examining the peak variance as a function of slit height, our results indicate that the two dimensional version of the force-fluctuation relationship may be appropriate in the limit of strong confinement. However, we could not consistently measure the absolute length of the DNA stretched between two pits, which prevented us from fully exploring the force-extension and force-fluctuation relationships of confined DNA.
 Conclusions: These experiments further demonstrate that nanofluidic confinement serves as a useful tool for testing the extreme properties of polymers, and our results suggest further investigation into the breakdown of the Marko-Siggia force law.
 
 
 
 
 
 
 
 
 
 

Probe Pattern Transitions in Bacterial Oscillating System using Palm Imaging and Nanofluidic Confinement

Faithful cell division of bacterium E. coli relies on remarkable oscillations of the MinCDE system to perform accurate and symmetric septation. Perturbing this bio-oscillator by disrupting minB locus or altering MinDE expressions is known to cause mini-celling and otherwise filamentous phenotypes. Recent reports suggested MinE plays a pivotal role in spatiotemporal pattern formation of MinDE cohorts; yet it remains elusive if their pattern transitions led to changes in cell morphology, and vice versa.In the present study, the coupling dynamics of MinDE interplays is investigated by time-lapse microscopy. We used multicolor fluorescence imaging to detail the mode transitions in distinct MinDE pattern formations, and photoactivated localization microscopy (PALM) to probe the nanoscale fine structures of the MinDE filaments/patterns in living cells. Despite E-ring capping has been viewed as a drive of pole-to-pole MinD oscillations, we found peculiar expression signatures in MinD and MinE spatiotemporal distributions, corresponding to MinDE patterns other than the E-ring type, correlate to their relative expression levels. Alternatively, bacteria were cultured and confined in micro/nanofluidic devices, to mimic various curvature changes of cell peripherals. Interestingly, under strong nanoslit confinement of 400 nm depth, bacteria are able to proliferate, but show irregular pancake-like morphology and intermittent oscillation episodes were observed in MinDE dynamics. The transitions between intermittent episodes display period-doubling signature of bifurcation by analyzing image series via spatial time-frequency method.Our results indicate MinDE pattern fluctuations / transitions correspond to aberrancy in septation and morphology. The study synergizes the join merits of in vivo imaging, single cell analysis, and nanofluidics to grasp the insight of noisedriven pattern transitions and phenotypic changes in bacteria.

Rapid Prototyping of Nanofluidic Systems Using Size‐Reduced Electrospun Nanofibers for Biomolecular Analysis

Biomolecular transport in nanofluidic confinement offers various means to investigate the behavior of biomolecules in their native aqueous environments, and to develop tools for diverse single-molecule manipulations. Recently, a number of simple nanofluidic fabrication techniques has been demonstrated that utilize electrospun nanofibers as a backbone structure. These techniques are limited by the arbitrary dimension of the resulting nanochannels due to the random nature of electrospinning. Here, a new method for fabricating nanofluidic systems from size-reduced electrospun nanofibers is reported and demonstrated. As it is demonstrated, this method uses the scanned electrospinning technique for generation of oriented sacrificial nanofibers and exposes these nanofibers to harsh, but isotropic etching/heating environments to reduce their cross-sectional dimension. The creation of various nanofluidic systems as small as 20 nm is demonstrated, and practical examples of single biomolecular handling, such as DNA elongation in nanochannels and fluorescence correlation spectroscopic analysis of biomolecules passing through nanochannels, are provided.