2015

Publications

K. Kistrup, C.E. Poulsen, M.F. Hansen, A. Wolff, Ultrasonic welding for fast bonding of self-aligned structures in lab-on-a-chip systems, Lab Chip 15, 1988-2001 (2015).

Abstract: Ultrasonic welding is a rapid, promising bonding method for the bonding of polymer chips; yet its use is still limited. We present two lab-on-a-chip applications where ultrasonic welding can be preferably applied: (1) Self-aligned gapless bonding of a two-part chip with a tolerance of 50 um; (2) bonding of a large area shallow chamber (1.8 cm^2 X 150 um). Using injection moulding combined with ultrasonic welding we achieved a total production and bonding time of 60 s per chip, and a batch of chips could be produced within a day going from design to finished chips. We believe that the technical solutions offered here can significantly help bridge the gap between academia and industry, where the differences in production methods and materials pose a challenge when transferring technology.

Agentoft Feidenhans, Poul-Erik Hansen, Lukas Pilny, Morten Hannibal Madsen, Giuliano Bissacco, Jan C. Petersen, Rafael Taboryski, Comparison of optical methods for surface roughness characterization, Meas. Sci. Technol. 26 (2015) 085208 (10pp).

Abstract: We report a study of the correlation between three optical methods for characterizing surface roughness: a laboratory scatterometer measuring the bi-directional reflection distribution function (BRDF instrument), a simple commercial scatterometer (rBRDF instrument), and a confocal optical profiler. For each instrument, the effective range of spatial surface wavelengths is determined, and the common bandwidth used when comparing the evaluated roughness parameters. The compared roughness parameters are: the root-mean-square (RMS) profile deviation (Rq), the RMS profile slope (Rdq), and the variance of the scattering angle distribution (Aq). The twenty-two investigated samples were manufactured with several methods in order to obtain a suitable diversity of roughness patterns.

Our study shows a one-to-one correlation of both the Rq and the Rdq roughness values when obtained with the BRDF and the confocal instruments, if the common bandwidth is applied. Likewise, a correlation is observed when determining the Aq value with the BRDF and the rBRDF instruments.

Furthermore, we show that it is possible to determine the Rq value from the Aq value, by applying a simple transfer function derived from the instrument comparisons. The presented method is validated for surfaces with predominantly 1D roughness, i.e. consisting of parallel grooves of various periods, and a reflectance similar to stainless steel. The Rq values are predicted with an accuracy of 38% at the 95% confidence interval.

Morten Hannibal Madsen, Poul-Erik Hansen, Maksim Zalkovskij, Mirza Karamehmedovic, Jørgen Garnæs, Fast Characterization of Moving Samples with Nano-Textured Surfaces, Vol. 2, Issue 4, pp. 301-306 (2015).

Abstract: Characterization of structures using conventional optical microscopy is restricted by the diffraction limit. Techniques such as atomic force and scanning electron microscopy can investigate smaller structures but are very time consuming. We show that using scatterometry, a technique based on optical diffraction, integrated into a commercial light microscope we can characterize nano-textured surfaces in a few milliseconds. The adapted microscope has two detectors, a CCD camera used to easily find an area of interest and a spectrometer for the measurements. We demonstrate that the microscope has a resolution in the nanometer range for the topographic parameters—height, width, and sidewall angle of a periodic grating—even in an environment with many vibrations, such as a production facility with heavy equipment.

Pétur G. Hermannsson, Kristian T. Sørensen, Christoph Vannahme, Cameron L.C. Smith, Jan J. Klein, Maria-Melanie Russew, Gabi Grützner, and Anders Kristensen, All-polymer photonic crystal slab sensor, Vol. 23, Issue 13, pp. 16529-16539 (2015).

Abstract: An all-polymer photonic crystal slab sensor is presented, and shown to exhibit narrow resonant reflection with a FWHM of less than 1 nm and a sensitivity of 31 nm/RIU when sensing media with refractive indices around that of water. This results in a detection limit of 4.5 × 10−6 RIU when measured in conjunction with a spectrometer of 12 pm/pixel resolution. The device is a two-layer structure, composed of a low refractive index polymer with a periodically modulated surface height, covered with a smooth upper-surface high refractive index inorganic-organic hybrid polymer modified with ZrO2-based nanoparticles. Furthermore, it is fabricated using inexpensive vacuum-less techniques involving only UV nanoreplication and polymer spin-casting, and is thus well suited for single-use biological and refractive index sensing applications.

K. Kistrup, K.S. Sørensen, A. Wolff, M.F. Hansen, Liquid carry-over in an injection moulded all-polymer chip system for immiscible phase magnetic bead-based solid-phase extraction, J. Magn. Magn. Mater. 380, 191-196 (2015).

Abstract: We present an all-polymer, single-use microfluidic chip system produced by injection moulding and bonded by ultrasonic welding. Both techniques are compatible with low-cost industrial mass-production. The chip is produced for magnetic bead-based solid-phase extraction facilitated by immiscible phase filtration and features passive liquid filling and magnetic bead manipulation using an external magnet. In this work, we determine the system compatibility with various surfactants. Moreover, we quantify the volume of liquid co-transported with magnetic bead clusters from Milli-Q water or a lysis-binding buffer for nucleic acid extraction (0.1 (v/v)% Triton X-100 in 5 M guanidine hydrochloride). A linear relationship was found between the liquid carry-over and mass of magnetic beads used. Interestingly, similar average carry-overs of 1.74(8) nL/µg and 1.72(14) nL/µg were found for Milli-Q water and lysis-binding buffer, respectively.

Marco Matteucci, Marco Triches, Giovanni Nava, Anders Kristensen, Mark R Pollard, Kirstine Berg-Sørensen, Rafael Taboryski, Fiber-Based, Injection-Molded Optofluidic Systems: Improvements in Assembly and Applications, Micromachines, 6 (2015) 1971-1983.

Abstract: We present a method to fabricate polymer optofluidic systems by means of injection molding that allow the insertion of standard optical fibers. The chip fabrication and assembly methods produce large numbers of robust optofluidic systems that can be easily assembled and disposed of, yet allow precise optical alignment and improve delivery of optical power. Using a multi-level chip fabrication process, complex channel designs with extremely vertical sidewalls, and dimensions that range from few tens of nanometers to hundreds of microns can be obtained. The technology has been used to align optical fibers in a quick and precise manner, with a lateral alignment accuracy of 2.7 ± 1.8 μm. We report the production, assembly methods, and the characterization of the resulting injection-molded chips for Lab-on-Chip (LoC) applications. We demonstrate the versatility of this technology by carrying out two types of experiments that benefit from the improved optical system: optical stretching of red blood cells (RBCs) and Raman spectroscopy of a solution loaded into a hollow core fiber. The advantages offered by the presented technology are intended to encourage the use of LoC technology for commercialization and educational purposes.

Vannahme, C., Dufva, M., & Kristensen, A., High frame rate multi-resonance imaging refractometry with distributed feedback dye laser sensor, Science & Applications, 4(4), e269.

Abstract: High frame rate and highly sensitive imaging of refractive index changes on a surface is very promising for studying the dynamics of dissolution, mixing and biological processes without the need for labeling. Here, a highly sensitive distributed feedback (DFB) dye laser sensor for high frame rate imaging refractometry without moving parts is presented. DFB dye lasers are low-cost and highly sensitive refractive index sensors. The unique multi-wavelength DFB laser structure presented here comprises several areas with different grating periods. Imaging in two dimensions of space is enabled by analyzing laser light from all areas in parallel with an imaging spectrometer. With this multi-resonance imaging refractometry method, the spatial position in one direction is identified from the horizontal, i.e., spectral position of the multiple laser lines which is obtained from the spectrometer charged coupled device (CCD) array. The orthogonal spatial position is obtained from the vertical spatial position on the spectrometer CCD array as in established spatially resolved spectroscopy. Here, the imaging technique is demonstrated by monitoring the motion of small sucrose molecules upon dissolution of solid sucrose in water. The omission of moving parts improves the robustness of the imaging system and allows a very high frame rate of up to 12 Hz.

Peter Friis Østergaard, Joanna Lopacinska-Jørgensen, Jonas Nyvold Pedersen, Niels Tommerup, Anders Kristensen, Henrik Flyvbjerg, Asli Silahtaroglu, Rodolphe Marie, Rafael Taboryski, Optical mapping of single-molecule human DNA in disposable, mass-produced all-polymer devices, J. Micromech. Microeng. 25 (2015) 105002 (8pp).

Abstract: We demonstrate all-polymer injection molded devices for optical mapping of denaturation–renaturation (DR) patterns on long, single DNA-molecules from the human genome. The devices have channels with ultra-low aspect ratio, only 110 nm deep while 20 μm wide, and are superior to the silica devices used previously in the field. With these polymer devices, we demonstrate on-chip recording of DR images of DNA-molecules stretched to more than 95% of their contour length. The stretching is done by opposing flows Marie et al (2013 Proc. Natl Acad. Sci. USA 110 4893–8). The performance is validated by mapping 20 out of 24 Mbp-long DNA fragments to the human reference genome. We optimized fabrication of the devices to a yield exceeding 95%. This permits a substantial economies-of-scale driven cost-reduction, leading to device costs as low as 3 USD per device, about a factor 70 lower than the cost of silica devices. This lowers the barrier to a wide use of DR mapping of native, megabase-size DNA molecules, which has a huge potential as a complementary method to next-generation sequencing.

M Calaon,MH Madsen, J Weirich, HN Hansen, G Tosello, P E Hansen, J Garnaes and P T Tang, Replication fidelity assessment of large area sub-μmstructured polymer surfaces using scatterometry, Surf. Topogr.: Metrol. Prop. 3 (2015) 045005.

Abstract: The present study addresses one of the key challenges in the product quality control of transparent structured polymer substrates, the replication fidelity of sub-μm structures over a large area. Additionally the work contributes to the development of new techniques focused on in-line characterization of large nanostructured surfaces using scatterometry. In particular an approach to quantify the replication fidelity of high volume manufacturing processes such as polymer injection moulding is presented. Both periodic channels and semi-spherical structures were fabricated on nickel shims used for later injection moulding of Cyclic-olefin-copolymer (COC) substrate were the sub-μm features where ultimately transferred. The scatterometry system was validated using calibrated atomic force microscopy measurements and a model based on scalar diffraction theory employed to calculate the expected angular distribution of the reflected and the transmitted intensity for the nickel surfaces and structured COC and, respectively.

Kristian Tølbøl Sørensen, Joanna M. Lopacinska, Niels Tommerup, Asli Silahtaroglu, Anders Kristensen, and Rodolphe Marie, Automation of a single-DNA molecule stretching device, Review of Scientific Instruments 86, 063702 (2015).

Abstract: We automate the manipulation of genomic-length DNA in a nanofluidic device based on real-time analysis of fluorescence images. In our protocol, individual molecules are picked from a microchannel and stretched with pN forces using pressure driven flows. The millimeter-long DNA fragments free flowing in micro- and nanofluidics emit low fluorescence and change shape, thus challenging the image analysis for machine vision. We demonstrate a set of image processing steps that increase the intrinsically low signal-to-noise ratio associated with single-molecule fluorescence microscopy. Furthermore, we demonstrate how to estimate the length of molecules by continuous real-time image stitching and how to increase the effective resolution of a pressure controller by pulse width modulation. The sequence of image-processing steps addresses the challenges of genomic-length DNA visualization; however, they should also be general to other applications of fluorescence-based microfluidics.

 Henrik Flyvbjerg, Kim I. Mortensen, Sifting noisy data for truths about noisy systems Comment on “Extracting physics of life at the molecular level: A review of single-molecule data analyses” by W. Colomb and S.K.Sarkar, Phys Life rev, 2015, Vol. 13, 2015, p. 141-143.

Yu Chen, Ezra S. Abrams, T. Christian Boles, Jonas N. Pedersen, Henrik Flyvbjerg, Robert H. Austin, and James C. Sturm, Concentrating Genomic Length DNA in a Microfabricated Array, Phys. Rev. Lett. 114, 198303 – Published 15 May 2015.

Abstract: We demonstrate that a microfabricated bump array can concentrate genomic-length DNA molecules efficiently at continuous, high flow velocities, up to 40 μm/s, if the single-molecule DNA globule has a sufficiently large shear modulus. Increase in the shear modulus is accomplished by compacting the DNA molecules to minimal coil size using polyethylene glycol (PEG) derived depletion forces. We map
out the sweet spot, where concentration occurs, as a function of PEG concentration and flow speed using a combination of theoretical analysis and experiment. Purification of DNA from enzymatic reactions for
next-generation DNA-sequencing libraries will be an important application of this development.

Conferences