| 51. |
- Ström, Oskar E., et al.
(författare)
-
DNA concentration wave formation in pillar arrays
- 2020
-
Ingår i: MicroTAS 2020 - 24th International Conference on Miniaturized Systems for Chemistry and Life Sciences. - 9781733419017 ; , s. 240-241
-
Konferensbidrag (refereegranskat)abstract
- High throughput in particle and molecular sorting schemes is an important performance indicator and can be realized through increased volumetric processing rates or increased concentrations. Here we investigate the effect of increased concentration of high-molecular weight DNA in micropillar arrays for deterministic lateral displacement (DLD). We find that the array imposes regular fluctuations in the concentration of the DNA if the sample concentration and flow rates exceed respective threshold values. We characterize the resulting concentration waves and study their influence on microsphere trajectories in the device. We expect our results to be relevant e.g. for sample preparation of cell lysates which can often be complicated by the release of chromosomal DNA.
|
|
| 52. |
- Ström, Oskar E., et al.
(författare)
-
Geometry-Dependent Elastic Flow Dynamics in Micropillar Arrays
- 2024
-
Ingår i: Micromachines. - 2072-666X. ; 15:2
-
Tidskriftsartikel (refereegranskat)abstract
- Regular device-scale DNA waves for high DNA concentrations and flow velocities have been shown to emerge in quadratic micropillar arrays with potentially strong relevance for a wide range of microfluidic applications. Hexagonal arrays constitute another geometry that is especially relevant for the microfluidic pulsed-field separation of DNA. Here, we report on the differences at the micro and macroscopic scales between the resulting wave patterns for these two regular array geometries and one disordered array geometry. In contrast to the large-scale regular waves visible in the quadratic array, in the hexagonal arrays, waves occur in a device-scale disordered zig-zag pattern with fluctuations on a much smaller scale. We connect the large-scale pattern to the microscopic flow and observe flow synchronization that switches between two directions for both the quadratic and hexagonal arrays. We show the importance of order using the disordered array, where steady-state stationary and highly fluctuating flow states persist in seemingly random locations across the array. We compare the flow dynamics of the arrays to that in a device with sparsely distributed pillars. Here, we observe similar vortex shedding, which is clearly observable in the quadratic and disordered arrays. However, the shedding of these vortices couples only in the flow direction and not laterally as in the dense, ordered arrays. We believe that our findings will contribute to the understanding of elastic flow dynamics in pillar arrays, helping us elucidate the fundamental principles of non-Newtonian fluid flow in complex environments as well as supporting applications in engineering involving e.g., transport, sorting, and mixing of complex fluids.
|
|
| 53. |
- Ström, Oskar E., et al.
(författare)
-
High-Throughput Separation of Long DNA in Deterministic Lateral Displacement Arrays
- 2022
-
Ingår i: Micromachines. - : MDPI AG. - 2072-666X. ; 13:10
-
Tidskriftsartikel (refereegranskat)abstract
- Length-based separation of DNA remains as relevant today as when gel electrophoresis was introduced almost 100 years ago. While new, long-read genomics technologies have revolutionised accessibility to powerful genomic data, the preparation of samples has not proceeded at the same pace, with sample preparation often constituting a considerable bottleneck, both in time and difficulty. Microfluidics holds great potential for automated, sample-to-answer analysis via the integration of preparatory and analytical steps, but for this to be fully realised, more versatile, powerful and integrable unit operations, such as separation, are essential. We demonstrate the displacement and separation of DNA with a throughput that is one to five orders of magnitude greater than other microfluidic techniques. Using a device with a small footprint (23 mm × 0.5 mm), and with feature sizes in the micrometre range, it is considerably easier to fabricate than parallelized nano-array-based approaches. We show the separation of 48.5 kbp and 166 kbp DNA strands achieving a significantly improved throughput of 760 ng/h, compared to previous work and the separation of low concentrations of 48.5 kbp DNA molecules from a massive background of sub 10 kbp fragments. We show that the extension of DNA molecules at high flow velocities, generally believed to make the length-based separation of long DNA difficult, does not place the ultimate limitation on our method. Instead, we explore the effects of polymer rotations and intermolecular interactions at extremely high DNA concentrations and postulate that these may have both negative and positive influences on the separation depending on the detailed experimental conditions.
|
|
| 54. |
- Ström, Oskar E., et al.
(författare)
-
Integrated on-chip system for DNA purification, labelling and surface stretching
- 2018
-
Ingår i: 22nd International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2018. - 9781510897571 ; 2, s. 1177-1180
-
Konferensbidrag (refereegranskat)abstract
- We report a simplified, integrated and more efficient way of preparing DNA for analysis. We have developed a microfluidic platform that can purify DNA and subsequently label and stretch it on a surface. We have successfully extracted DNA from a gel-filled microfluidic channel using electrophoresis and subsequently stretched the DNA linearly by absorption to either a hydrophobic or a positively-charged surface. To our knowledge, DNA has not previously been stretched on to a surface while being moved using an electric field in this way. We have also labelled DNA after stretching with intercalating dyes. The intention, following stretching and labelling, is to analyze the DNA with optical mapping.
|
|
| 55. |
- Ström, Oskar E., et al.
(författare)
-
KÁRMÁN VORTEX CITY OF DNA STRANDS
- 2021
-
Ingår i: MicroTAS 2021 - 25th International Conference on Miniaturized Systems for Chemistry and Life Sciences. - 9781733419031 ; , s. 13-14
-
Konferensbidrag (refereegranskat)abstract
- Kármán vortex streets are repeating patterns of swirling vortices, appearing when a fluid passes an obstacle at Re>50. We present an array of interacting vortices, a Kármán vortex city, that arises when a DNA solution flows through an array of micro posts at Re <0.5. Above thresholds in concentration and flow rate, the vortices formed behind posts interact, leading to concentration fluctuation waves. We explore the effect of lattice structure, polymer length and salt and relate the wave formation to the overlap concentration. Our work will allow us to optimize high-concentration DNA manipulation and sorting of DNA in microfluidic arrays.
|
|
| 56. |
- Ström, Oskar E., et al.
(författare)
-
Long DNA isolation and imaging using lateral displacement arrays integrated with DNA combing
- 2019
-
Ingår i: 23rd International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2019. - 9781733419000 ; , s. 771-772
-
Konferensbidrag (refereegranskat)abstract
- We demonstrate proof of principle of an efficient and simple method combining sample preparation and stretching of DNA in a single device that can be used as basis for an integrated portable system for optical DNA mapping. An important bottleneck for DNA mapping, as well as for other methods, is the isolation of long DNA molecules from a background of contaminants such as shorter DNA fragments, dyes, and lysate. We demonstrate the isolation of longer (48.5 kbp or 166 kbp) from shorter (<10 kbp) DNA strands using Deterministic Lateral Displacement (DLD), followed by surface-stretching of the sorted DNA for mapping.
|
|
| 57. |
- Ström, Oskar E., et al.
(författare)
-
Short and long-range cyclic patterns in flows of DNA solutions in microfluidic obstacle arrays
- 2023
-
Ingår i: Lab on a Chip. - : Royal Society of Chemistry (RSC). - 1473-0197 .- 1473-0189. ; 23, s. 1779-1793
-
Tidskriftsartikel (refereegranskat)abstract
- We observe regular patterns emerging across multiple length scales with high-concentration DNA solutions in microfluidic pillar arrays at low Reynolds numbers and high Deborah numbers. Interacting vortices between pillars lead to long-range order in the form of large travelling waves consisting of DNA at high concentration and extension. Waves are formed in quadratic arrays of pillars, while randomizing the position of the pillar in each unit cell of a quadratic array leads to suppression of the long-range patterns. We find that concentrations exceeding the overlap concentration of the DNA enables the waves, and exploring the behavior of the waves as a function of flow rate, buffer composition, concentration and molecular length, we identify elastic effects as central to the origin of the waves. Our work may not only help increase the low throughput that often limits sample processing in microfluidics, it may also provide a platform for further studies of the underlying viscoelastic mechanisms.
|
|
| 58. |
- Tegenfeldt, Jonas O., et al.
(författare)
-
Label-free cytometry - Novel sorting parameters and opportunities
- 2014
-
Ingår i: 18th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2014. - 9780979806476 ; , s. 242-245
-
Konferensbidrag (refereegranskat)abstract
- The inherent properties of cells and micro-organisms is an under-explored source of specificity for particle sorting. In contrast to standard immunolabeling it allows us to perform fractionation without any chemical preparation of the sample. This improves the accessibility and affordability of the technology. Our contribution in the field is to extend the scope of deterministic lateral displacement (DLD) from merely a very powerful size-based sorting scheme so that it is used to sort with respect to several other physical parameters. We have explored parameters such as shape, deformability, dielectric properties, secretion and density with potential applications in bacteriology, parasitology and oncology.
|
|
| 59. |
- Tran, Si Hoai Trung, et al.
(författare)
-
Open channel deterministic lateral displacement for particle and cell sorting
- 2017
-
Ingår i: Lab on a Chip - Miniaturisation for Chemistry and Biology. - : Royal Society of Chemistry (RSC). - 1473-0197. ; 17:21, s. 3592-3600
-
Tidskriftsartikel (refereegranskat)abstract
- We present the use of capillary driven flow over patterned surfaces to achieve cheap and simple, but powerful separation of biologically relevant particle systems. The wide use of microfluidics is often hampered by the propensity for devices to clog due to the small channel sizes and the inability to access the interior of devices for cleaning. Often the devices can only be used for a limited duration and most frequently only once. In addition the cost and power requirements of flow control equipment limits the wider spread of the devices. We address these issues by presenting a simple particle- and cell-sorting scheme based on controlled fluid flow on a patterned surface. The open architecture makes it highly robust and easy to use. If clogging occurs it is straightforward to rinse the device and reuse it. Instead of external mechanical pumps, paper is used as a capillary pump. The different fractions are deposited in the paper and can subsequently be handled independently by simply cutting the paper for downstream processing and analyses. The sorting, based on deterministic lateral displacement, performs equivalently well in comparison with standard covered devices. We demonstrate successful separation of cancer cells and parasites from blood with good viability and with relevance for diagnostics and sample preparation. Sorting a mixture of soil and blood, we show the potential for forensic applications.
|
|
| 60. |
- Tran, Si Hoai Trung, et al.
(författare)
-
Particle separation and diffusion based limitation
- 2016
-
Ingår i: 20th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2016. - 9780979806490 ; , s. 1545-1546
-
Konferensbidrag (refereegranskat)abstract
- Deterministic lateral displacement (DLD) is a promising method for particle separation in the micrometer range, the proof of principle of which has been demonstrated to be successful in fields such as biomedicine and physics [1]. However, the enhanced particle dispersion (Figure 1 & 2) arising when separating very small particles (such as viruses and proteins) constitutes the main functional barrier of DLD-based devices. In this study theoretical predictions made by [2, 3] have been experimentally observed, the relation of the dispersion effect with the construction parameters of the bumper arrays has been investigated, and a strategy for dispersion reduction is suggested.
|
|
