arXiv subjects

Jonas O. Tegenfeldt

Publications and source records attributed to Jonas O. Tegenfeldt.

8 recordsLinked to original sources

arXiv2026

Programmatically Generated Microparticles Using SUEX Dry-Film Epoxy Resist

We present a lithographic method for fabricating free-standing microparticles directly from SUEX dry-film epoxy resist. Unlike conventional SU-8 particle fabrication, which requires patterning on solid substrates followed by sacrificial-layer release, our approach eliminates substrate use entirely and produces particles with near 100% yields. The process supports a wide design space of in-plane geometries, including high-aspect-ratio and highly complex shapes. To enable large-scale particle libraries, we integrate the method with the Nazca Python library, allowing programmatic generation of tens of thousands of parametrically defined particle designs. This combination of substrate-free fabrication and automated design provides a scalable route to custom microparticles for materials science, microfluidics, and soft-matter applications.

physics.app-ph↗

arXiv2023

Short and Long-range cyclic patterns in flows of DNA solutions in microfluidic obstacle arrays

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. 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.

physics.flu-dyn↗

arXiv2023

Broken Symmetries in Microfluidic Pillar Arrays are Reflected in a Flowing DNA Solution across Multiple Length Scales

Unlike Newtonian fluids, viscoelastic fluids may break time-reversal symmetry at low Reynolds numbers resulting in elastic turbulence. Furthermore, under some conditions, instead of the chaotic turbulence, large-scale regular waves form, as has been shown for DNA flowing in microfluidic pillar arrays. We here demonstrate how the symmetry of the individual pillars influences the symmetry of these waves, thereby contributing to the understanding of the origin of the waves and opening up for better control of the waves with relevance to applications such as microfluidic sorting and mixing. The onset of waves occurs at different Deborah numbers for flow in different directions through the same array. Because the onset of waves leads to an increase in flow rate for a given driving pressure, we observe an increase in diodicity within this range.

physics.flu-dyn↗

arXiv2020

Stochastic unfolding of nanoconfined DNA: experiments, model and Bayesian analysis

Nanochannels provide means for detailed experiments on the effect of confinement on biomacromolecules, such as DNA. We here introduce a model for the complete unfolding of DNA from the circular to linear configuration. Two main ingredients are the entropic unfolding force as well as the friction coefficient for the unfolding process, and we describe the associated dynamics by a non-linear Langevin equation. By analyzing experimental data where DNA molecules are photo-cut and unfolded inside a nanochannel, our model allows us to extract values for the unfolding force as well as the friction coefficient for the first time. In order to extract numerical values for these physical quantities, we employ a recently introduced Bayesian inference framework. We find that the determined unfolding force is in agreement with estimates from a simple Flory type argument. The estimated friction coefficient is in agreement with theoretical estimates for motion of a cylinder in a channel. We further validate the estimated friction constant by extracting this parameter from DNA's center-of-mass motion before and after unfolding, yielding decent agreement.

physics.bio-ph↗

arXiv2019

Sorting of particles suspended in whole blood

An important step in diagnostics is the isolation of specific cells and microorganisms of interest from blood. Since such bioparticles are often present at very low concentrations, throughput needs to be as high as possible. In addition, to ensure simplicity, a minimum of sample preparation is important. Therefore, sorting schemes that function for whole blood are highly desirable. Deterministic lateral displacement (DLD) has proven to be very precise and versatile in terms of a wide range of sorting parameters. To better understand how DLD performs for blood as the hematocrit increases, we have performed measurements and simulations for spherical particles in the micrometer range moving through DLD arrays for different flow velocities and hematocrits ranging from pure buffer to whole blood. We find that the separation function of the DLD array is sustained, even though blood cells introduce a shift in the trajectories and a significant dispersion for particles that are close to the critical size in the device. Simulations qualitatively replicate our experimental observations and help us identify fundamental mechanisms for the effect of hematocrit on the performance of the DLD device.

cond-mat.soft↗

arXiv2015

How nanochannel confinement affects the DNA melting transition within the Poland-Scheraga model

When double-stranded DNA molecules are heated, or exposed to denaturing agents, the two strands get separated. The statistical physics of this process has a long history, and is commonly described in term of the Poland-Scheraga (PS) model. Crucial to this model is the configurational entropy for a melted region (compared to the entropy of an intact region of the same size), quantified by the loop factor. In this study we investigate how confinement affects the DNA melting transition, by using the loop factor for an ideal Gaussian chain. By subsequent numerical solutions of the PS model, we demonstrate that the melting temperature depends on the persistence lengths of single-stranded and double-stranded DNA. For realistic values of the persistence lengths the melting temperature is predicted to decrease with decreasing channel diameter. We also demonstrate that confinement broadens the melting transition. These general findings hold for the three scenarios investigated: namely 1. homo-DNA, i.e. identical basepairs along the DNA molecule; 2. random sequence DNA, and 3. "real" DNA, here T4 phage DNA. We show that cases 2 and 3 in general give rise to broader transitions than case 1. Case 3 exhibits a similar phase transition as case 2 provided the random sequence DNA has the same ratio of AT to GC basepairs. A simple analytical estimate for the shift in melting temperature is provided as a function of nanochannel diameter. For homo-DNA, we also present an analytical prediction of the melting probability as a function of temperature.

q-bio.BM↗

arXiv2015

A fast and scalable kymograph alignment algorithm for nanochannel-based optical DNA mappings

Optical mapping by direct visualization of individual DNA molecules, stretched in nanochannels with sequence-specific fluorescent labeling, represents a promising tool for disease diagnostics and genomics. An important challenge for this technique is thermal motion of the DNA as it undergoes imaging; this blurs fluorescent patterns along the DNA and results in information loss. Correcting for this effect (a process referred to as kymograph alignment) is a common preprocessing step in nanochannel-based optical mapping workflows, and we present here a highly efficient algorithm to accomplish this via pattern recognition. We compare our method with the one previous approach, and we find that our method is orders of magnitude faster while producing data of similar quality. We demonstrate proof of principle of our approach on experimental data consisting of melt mapped bacteriophage DNA.

q-bio.QM↗

arXiv2008

Multi-directional sorting modes in deterministic lateral displacement devices

Deterministic lateral displacement (DLD) devices separate micrometer-scale particles in solution based on their size using a laminar microfluidic flow in an array of obstacles. We investigate array geometries with rational row-shift fractions in DLD devices by use of a simple model including both advection and diffusion. Our model predicts novel multi-directional sorting modes that could be experimentally tested in high-throughput DLD devices containing obstacles that are much smaller than the separation between obstacles.

physics.flu-dyn↗