-
[show abstract]
[hide abstract]
ABSTRACT: An aluminum bow-tie nano-antenna is combined with the resonance Raman effect in the deep ultraviolet to dramatically increase the sensitivity of Raman spectra to a small volume of material, such as benzene used here. We further demonstrate gradient-field Raman peaks for several strong infrared modes. We achieve a gain of [Formula: see text] in signal intensity from the near field enhancement due to the surface plasmon resonance in the aluminum nanostructure. The on-line resonance enhancement contributes another factor of several thousands, limited by the laser line width. Thus, an overall gain of hundreds of million is achieved.
Applied Physics Letters 09/2012; 101(11):113116. · 3.84 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: We observe the formation of heaps of repulsive microspheres, created by
flowing a colloidal microsphere suspension towards a flat-topped ridge placed
within a quasi two-dimensional microfluidic channel. This configuration allows
for both shear and normal forces on the microspheres in contact with the ridge.
The heaps, which form against the ridge, are characterized by two distinct
phases: a solid-like bulk phase in the interior, and a highly-fluctuating,
liquid-like state which exists along its leading edge. We observe that heaps
only form above a critical flow velocity, (v_c), and that they are destroyed by
thermal rearrangements when the flow ceases. We monitor the dynamics of heap
formation using fluorescence video microscopy, measuring the heap volume and
the angle of repose in response to microsphere deposition and erosion
processes. We find that the steady-state angle of repose, (\theta_f), increases
as a function of inflow velocity, (v_\infty), with a functional form (\theta_f
\propto \sqrt{v_\infty - v_c}).
07/2012;
-
[show abstract]
[hide abstract]
ABSTRACT: We report an experimental investigation of the magnitude of length and density fluctuations in DNA that has been stretched in nanofluidic channels. We find that the experimental data can be described using a one-dimensional overdamped oscillator chain with nonzero equilibrium spring length and that a chain of discrete oscillators yields a better description than a continuous chain. We speculate that the scale of these discrete oscillators coincides with the scale at which the finite extensibility of the polymer manifests itself. We discuss how the measurement process influences the apparent measured dynamic properties, and outline requirements for the recovery of true physical quantities.
Journal of Applied Physics 01/2012; 111(2):24701-247018. · 2.17 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: We report the profiling of the 5-methyl cytosine distribution within single genomic-sized DNA molecules at a gene-relevant resolution. This method linearizes and stretches DNA molecules by confinement to channels with a dimension of about 250×200 nm(2). The methylation state is detected using fluorescently labeled methyl-CpG binding domain proteins (MBD), with high signal contrast and low background. DNA barcodes consisting of methylated and non-methylated segments are generated, with both short and long concatemers demonstrating spatially resolved MBD binding. The resolution of the technique is better than 10 kbp, and single-molecule read-lengths exceeding 140 kbp have been achieved.
Biomicrofluidics 09/2011; 5(3):34106-341068. · 3.37 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: DNA confined to rigid nanotubes shows density fluctuations around its stretched equilibrium conformation. We report an experimental investigation of the length-scale dependent dynamics of these density fluctuations. We find that for highly elongated molecules a Rouse description is consistent with observations at sufficiently large length scales. We further find that for strongly fluctuating molecules, or short length scales, such Rouse modes cannot be detected due to strong mixing of fluctuation modes.
Applied Physics Letters 06/2011; 98(25):253704. · 3.84 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: We report that double-stranded DNA collapses in the presence of ac electric fields at frequencies of a few hundred Hertz, and does not stretch as commonly assumed. In particular, we show that confinement-stretched DNA can collapse to about one quarter of its equilibrium length. We propose that this effect is based on finite relaxation times of the counterion cloud, and the subsequent partitioning of the molecule into mutually attractive units. We discuss alternative models of those attractive units.
Physical Review Letters 06/2011; 106(24):248103. · 7.37 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: DNA molecules under good solvent conditions condense when subjected to strong AC electrical fields. It is shown that AC electrical fields couple charge fluctuations to molecular shape fluctuations, which produces a non-equilibrium noise source that can dominate over equilibrium thermal noise in the long-wavelength limit. The field-induced excess charge fluctuations amplify the Asakura-Oosawa fluctuation attraction force between neighboring chains, providing a mechanism for field-induced DNA condensation.
ChemPhysChem 11/2009; 10(16):2871-5. · 3.41 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Upconverting nanoparticles (UCNPs) when excited in the near-infrared (NIR) region display anti-Stokes emission whereby the emitted photon is higher in energy than the excitation energy. The material system achieves that by converting two or more infrared photons into visible photons. The use of the infrared confers benefits to bioimaging because of its deeper penetrating power in biological tissues and the lack of autofluorescence. We demonstrate here sub-10 nm, upconverting rare earth oxide UCNPs synthesized by a combustion method that can be stably suspended in water when amine modified. The amine modified UCNPs show specific surface immobilization onto patterned gold surfaces. Finally, the low toxicity of the UCNPs is verified by testing on the multi-cellular C. elegans nematode.
Nanotechnology 10/2009; 20(40):405701. · 3.98 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: We present a method for the stretching of chromatin molecules in nanofluidic channels width a cross-section of about 80 x 80 nm(2), and hundreds of microns long. The stretching of chromatin to about 12 basepairs/nm enables location-resolved optical investigation of the nucleic material with a resolution of up to 6 kbp. The stretching is based on the equilibrium elongation that polymers experience when they are introduced into nanofluidic channels that are narrower than the Flory coil corresponding to the whole chromatin molecule. We investigate whether the elongation of reconstituted chromatin can be described by the de Gennes model. We compare nanofluidic stretching of bare DNA and chromatin of equal genomic length, and find that chromatin is 2.5 times more compact in its stretched state.
Lab on a Chip 10/2009; 9(19):2772-4. · 5.67 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Nanochannels offer a way to align and analyze long biopolymer molecules such as DNA with high precision at potentially single basepair resolution, especially if a means to detect biomolecules in nanochannels electronically can be developed. Integration of nanochannels with electronics will require the development of nanochannel fabrication procedures that will not damage sensitive electronics previously constructed on the device. We present here a near-room-temperature fabrication technology involving parylene-C conformal deposition that is compatible with complementary metal oxide semiconductor electronic devices and present an analysis of the initial impedance measurements of conformally parylene-C coated nanochannels with integrated gold nanoelectrodes.
Biomicrofluidics 01/2009; 3(3):31101. · 3.37 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Zero-Mode Waveguides were first introduced for Fluorescence Correlation Spectroscopy at micromolar dye concentrations. We show that combining zero-mode waveguides with fluorescence correlation spectroscopy in a continuous flow mixer avoids the compression of the FCS signal due to fluid transport at channel velocities up to approximately 17 mm/s. We derive an analytic scaling relationship [equation: see text] converting this flow velocity insensitivity to improved kinetic rate certainty in time-resolved mixing experiments. Thus zero-mode waveguides make FCS suitable for direct kinetics measurements in rapid continuous flow.
Optics Express 08/2008; 16(14):10077-90. · 3.59 Impact Factor
-
Robert Riehn,
Walter Reisner,
Jonas O. Tegenfeldt,
Yan Mei Wang,
Chih-Kuan Tung,
Shuang-Fang Lim,
Edward Cox,
James C. Sturm,
Keith Morton,
Steven Y. Chou,
Robert H. Austin
[show abstract]
[hide abstract]
ABSTRACT: This review will discuss the theory of confined polymers in nanochannels and present our experiments, which test the theory
and explore use of nanochannels for genomic analysis. Genomic length DNA molecules contained in nanochannels, which are less
than one persistence length in diameter, are highly elongated. Thus, nanochannels can be used to analyze genomic length DNA
molecules with very high linear spatial resolution. Also, nanochannels can be used to study the position and dynamics of proteins
such as transcription factors that bind to DNA with high specificity. In order to realize these goals not only must nanochannels
be constructed whose radius is less than the persistence length of DNA, but it is also necessary to understand the dynamics
of polymers within nanochannels and develop experimental tools to study the dynamics of polymers in such confined volumes,
tools which we review here.
03/2008: pages 151-186;
-
[show abstract]
[hide abstract]
ABSTRACT: We present a metamaterial consisting of a two-dimensional, asymmetric lattice of crossed nanochannels in fused silica, with channel diameters of 80 nm to 140 nm. When DNA is introduced, it is stretched and linearized. We show that the asymmetry in channel dimensions gives rise to a preferred direction for DNA orientation and a preferred direction for transport under dc electrophoresis. Interestingly, the preferred axis of orientation and transport can be switched by 90 degrees through application of an ac voltage. We explain the results in terms of an energy landscape for polyelectrolytes that consists of entropic and dielectrophoretic contributions and whose strength and sign can be tuned by changing the ac field strength.
Nano Letters 10/2006; 6(9):1973-6. · 13.20 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: We consider the diffusive motion of a localized knot along a linear polymer chain. In particular, we derive the mean diffusion time of the knot before it escapes from the chain once it gets close to one of the chain ends. Self-reptation of the entire chain between either end and the knot position, during which the knot is provided with free volume, leads to an L^3 scaling of diffusion time; for sufficiently long chains, subdiffusion will enhance this time even more. Conversely, we propose local ``breathing'', i.e., local conformational rearrangement inside the knot region (KR) and its immediate neighbourhood, as additional mechanism. The contribution of KR-breathing to the diffusion time scales only quadratically, L^2, speeding up the knot escape considerably and guaranteeing finite knot mobility even for very long chains. Comment: 7 pages, 2 figures. Accepted to Europhys. Lett
EPL (Europhysics Letters) 09/2006; · 2.17 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: We describe a method for wetting micro- and nanofluidic devices with water or any other pure liquid. The process is performed by enclosing the fluidic device in a liquid-filled cell, heating the cell to a temperature above the critical point of the liquid, and subsequent cooling of the cell to room temperature. Because the process liquid is essentially a gas during wetting, arbitrary shapes can be wetted. We demonstrate wetting of micro- and nanostructures in a fused-silica device with only a single inlet. The process is low-cost, fast, safe, and very reliable.
Analytical Chemistry 09/2006; 78(16):5933-4. · 5.86 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Separation of blood cells by native susceptibility and by the selective attachment of magnetic beads has recently been demonstrated on microfluidic devices. We discuss the basic principles of how forces are generated via the magnetic susceptibility of an object and how microfluidics can be combined with micron-scale magnetic field gradients to greatly enhance in principle the fractionating power of magnetic fields. We discuss our efforts and those of others to build practical microfluidic devices for the magnetic separation of blood cells. We also discuss our attempts to integrate magnetic separation with other microfluidic features for developing handheld medical diagnostic tools.
Journal of Applied Physics 05/2006; · 2.17 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: We show here that upconversion phosphors can be imaged both by infrared excitation and in a scanning electron microscope. We have synthesized and characterized for this work up-converting phosphor nanoparticles nonaggregated nanocrystals of size range 50-200 nm. We have investigated the optical properties of 50-200 nm nanoparticles and found a square dependence of the emitted visible fluorescence on the infrared excitation and verified that under electron excitation similar narrow band emission spectra can be obtained as is seen with IR upconversion. The viability of the nanoparticles for biological imaging was confirmed by imaging the digestive system of the nematode worm Caenorhabditis elegans, and we have confirmed using energy-dispersive X-ray analysis that the up-conversion nanoparticles can be identified in a scanning electron microscope at high spatial resolution.
Nano Letters 03/2006; 6(2):169-74. · 13.20 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: We have performed restriction mapping of DNA molecules using restriction endonucleases in nanochannels with diameters of 100-200 nm. The location of the restriction reaction within the device is controlled by electrophoresis and diffusion of Mg2+ and EDTA. We have successfully used the restriction enzymes SmaI, SacI, and PacI, and have been able to measure the positions of restriction sites with a precision of approximately 1.5 kbp in 1 min using single DNA molecules.
Proceedings of the National Academy of Sciences 08/2005; 102(29):10012-6. · 9.68 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: The successful design of nanofluidic devices for the manipulation of biopolymers requires an understanding of how the predictions of soft condensed matter physics scale with device dimensions. Here we present measurements of DNA extended in nanochannels and show that below a critical width roughly twice the persistence length there is a crossover in the polymer physics.
Physical Review Letters 06/2005; 94(19):196101. · 7.37 Impact Factor
-
Jonas O Tegenfeldt,
Christelle Prinz,
Han Cao,
Steven Chou,
Walter W Reisner, Robert Riehn,
Yan Mei Wang,
Edward C Cox,
James C Sturm,
Pascal Silberzan,
Robert H Austin
[show abstract]
[hide abstract]
ABSTRACT: We show that genomic-length DNA molecules imaged in nanochannels have an extension along the channel that scales linearly with the contour length of the polymer, in agreement with the scaling arguments developed by de Gennes for self-avoiding confined polymers. This fundamental relationship allows us to measure directly the contour length of single DNA molecules confined in the channels, and the statistical analysis of the dynamics of the polymer in the nanochannel allows us to compute the SD of the mean of the extension. This statistical analysis allows us to measure the extension of lambda DNA multimers with a 130-nm SD in 1 min.
Proceedings of the National Academy of Sciences 08/2004; 101(30):10979-83. · 9.68 Impact Factor
