Research

Nanotechnology spans a range of length scales that overlap with the length scales on which the most fundamental biological processes take place. Using nanotechnology we aim at investigating the basis for biology by making tools for measurements on the nanoscale and by creating artificial environments that mimic nature on a molecular level.

Currently, we focus on developing devices and tools for handling and analysis of biomolecules and cells using particle sorting and by stretching DNA in nanoscale channels.

If you would like to work in our group you will need access to one or more of the following lab facilities. The links are directed to information about contact persons and procedures to obtain training and access.

Lund Nano Lab - advanced micro and nanofabrication

BioPL Lab - two microscopy labs adapted to microfluidics and low light level imaging

PDMS Lab - soft lithography lab

Biochemistry lab - wet-lab for standard biochemistry

STED Lab - STED microscope setup for super resolution microscopy

 

 

Separation science

Dr Jason Beech, Researcher

Esra Yilmaz, PhD student

Elham Akbari, PhD student

Enrico Turato, PhD student

Key objectives: develop label-free sorting schemes based on physical properties of cells for parasitology and oncology. In addition, develop techniques for sample preparation for genomics.

We add further functionalities to a powerful microfluidic particle sorting approach based on deterministic lateral displacement (DLD) (originally developed at Princeton University: Huang et al in Science 2004). The feature size in the post array determines the scale of the particles to be separated. See Youtube video describing the basic idea. We use that fact that the effective size is dependent on the shear rate for deformable particles and of the orientation for non-spherical particles. The objective is to develop fractionation schemes based on inherent physical properties of cells as well as enrichment of rare molecules and particles with important relevance for the improving the sensitivity of bioanalytical assays and preparations.

We have added the following functionalities to deterministic lateral displacement: shape, deformability, dielectric properties, density and secretion.

For a recent review paper on sorting of trypanosomes, please click here.

Key publications

Viscoelastic instabilities

During an attempt to purify DNA at high concentration and high flow rate, we observed fascinating waves. Understanding these viscoelastic instabilities in detail will help us designing microfluidic devices for transport of viscoelastic fluids, for enhanced mixing in microfluidics, and finally for sorting and purification of DNA in microfluidics devices.

 

Beech, J.P., O.E. Ström, E. Turato, and J.O. Tegenfeldt, Using symmetry to control viscoelastic waves in pillar arrays. RSC Advances 13(45): p. 31497-31506 (2023) Abstract

A symmetry breaking of the pillars in the array causes the waves to break their symmetry. This suggests a strong connection between the shape of the pillars on the 10µm scale and the waves on the 1mm scale. Specifically, we show proof of principle of three potential applications of symmetry breaking: (1) fluidic diode, (2) enhanced mixing, (3) suppressed mixing.

 

Ström, O. E., Beech, J. P., Tegenfeldt, J. O., "Short and Long-range cyclic patterns in flows of DNA solutions in microfluidic obstacle arrays", Lab on a Chip, 23 1779-1793 (2023) Abstract

The viscoelastic wave phenomena is described in detail. The waves consist of regions of high concentration and highly oriented DNA molecules.  The waves appear in the flow in regular quadratic arrays of pillars for high DNA concentrations, high flow speeds, long DNA moleculkes.

 

Ström, O. E., Beech, J. P., Tegenfeldt, J. O., "High-throughput separation of long DNA in deterministic lateral displacement arrays", Micromachines 13 (10), 1754 (2022) Abstract

Motivated by the need for long DNA of high purity for gene sequencing applications we employed deterministic lateral displacement for DNA sorting at high concentrations and high flow rates. We found that the throughput of the sorting is limited by wave-like instabilities in the flow.

 

Deformability and morphology sorting

Jason P. Beech, Stefan Holm, Kalle Adolfsson, Jonas O. Tegenfeldt, “Sorting cells by size, shape and deformability”, Lab on a Chip, 12, 1048-1051 (2012) Abstract
Shear causes deformation of the particles passing through the device, thereby decreasing their effective size. Running a DLD at different flow speeds gives information on the deformability of the particles.

 

Jason P. Beech, Bao Dang Ho, Geneviève Garriss, Vitor Oliveira, Birgitta Henriques Normark, Jonas O. Tegenfeldt, “Separation of Pathogenic Bacteria by Chain Length”, Analytica Chimica Acta (2018) 1000, 223-231 Abstract

The shape of bacteria is beleived to couple to their virulence. Here we have developed a scheme to separate different shapes of S. pneumoccocus into different fractions.

 

Stefan H. Holm, Jason P. Beech, Michael P. Barrett, Jonas O. Tegenfeldt, “Simplifying Microfluidic Separation Devices towards Field-Detection of Blood Parasites” Analytical Methods 8, 3291-3300 (2016) Abstract Cover

Stefan Holm*, Jason P. Beech*, Michael P. Barrett, and Jonas O. Tegenfeldt, “Separation of parasites from human blood using deterministic lateral displacement”, Lab Chip, 11, 1326-1332 (2011) Abstract
The morphological differences between the parasites and the red blood cells are accentuated through the shape sensitive sorting. The key to obtain a shape sensitive DLD is to control the orientation of the particles. Here the orientation is controlled through the variation of the depth of the device.
Collaboration with Prof Michael Barrett at Glasgow University.

 

Electrokinetic DLD

“Active Posts in Deterministic Lateral Displacement Devices”, Jason P. Beech, Kevin Keim, Bao Dang Ho, Carlotta Guiducci, Jonas O. Tegenfeldt, Advanced Materials Technologies, (2019) 1900339 Abstract

By making the posts in the DLD array conducting and connecting them to an external voltage source, we can apply the electric field locally between the rows of posts. Collaboration with Prof Guiducci at EPFL.

 

Jason P. Beech, Peter Jönsson, and Jonas O. Tegenfeldt, “Tipping the balance with dielectrophoresis – electrical deterministic lateral displacement”, Lab Chip, 9, 2698 - 2706 (2009) Abstract
A dielectrophoretic force is applied to influence the trajectories of particles in a DLD device.

 

Fundamentals of DLD

“Particle sorting in erythrocyte suspensions”, Stefan H. Holm, Zunmin Zhang, Jason P. Beech, Gerhard Gompper, Dmitry A. Fedosov and Jonas O. Tegenfeldt, Physical Review Applied, volume 12(1), 014051 Abstract

DLD is quite remarkable in its capability to provide high-resolution sorting even at very high hematocrit. Here we characterize in detail the performance of DLD at different hematocrits.

 

Brian R. Long, Martin Heller, Jason P. Beech, Heiner Linke, Henrik Bruus, Jonas O Tegenfeldt, “Diffusion and novel sorting modes in deterministic lateral displacement”, Physical Review E, 78(4), 046304 (2008) Abstract
Anomalous trajectories in DLD are demonstrated through simulation. Normally for DLD there are just two trajectories: one for particles with size greater than the critical size and one for particles with size smaller. However, here we show that for arrays with non-integer periodicities up to four different trajectories are possible.
Collaboration with Prof Henrik Bruus at the Technical University of Denmark. The concept was developed independently by the Tegenfeldt and the Bruus groups. Eventually we decided to copublish.

 

Trung S. H. Tran, Bao D. Ho, Jason P. Beech, Jonas O. Tegenfeldt, “Open Channel Deterministic Lateral Displacement for Particle and Cell Sorting”, Lab on a Chip (2017) 17 (21), 3592 - 3600 Abstract

We demonstrate several examples of DLD sorting on a patterned surface (without a cover) where the liquid is pulled along the surface using a simple capillary pump. The approach alows straightforward cleaning of the device and is especially promising for complex samples where clogging is a problem.

 

Jason P. Beech & Jonas O. Tegenfeldt, “Tuneable separation in elastomeric microfluidics devices”, Lab on a Chip, 8(5), 657-659 (2008) Abstract
Benefiting from the fact that PDMS is an elastic material we make an adjustable DLD device. As the device is stretched the critical size is increased accordingly.

 

DNA analysis with nanofluidics

Senior team member:

Dr Jason Beech, Researcher

Junior team member:

Oskar Ström, PhD student


Key objectives: develop simple techniques for coarse-grained labeling of DNA on the single-molecule and single-cell level with applications in bacterial identification and characterization of structural variations.

Direct visualization of DNA stretched in nanofluidic channels was pioneered a decade ago (Tegenfeldt et al. PNAS2004), opening up the possibility of directly reading out much of the information contained in the genomes of single cells. Using standard fluorescent probes for genetic variations and for regulatory modifications, we aim to complement conventional bioanalytical techniques for e.g. genetic mapping, SNP detection and epigenetic profiling with a technology that does not require any DNA amplification nor any cell culturing.

See our review paper in Chemical Society Reviews for an overview of the field.
 

Within the projects NanoDiaBac, funded through EuroNanoMed, and BeyondSeq, funded by Horizon2020 of "personalized healthcare" the main theme is genetically based diagnostics. Here we will work with the entire chain of clinical samples for analysis of DNA. The analysis takes place on single DNA molecules, which means no cell culture or DNA amplification is needed, which in turn opens up significantly faster diagnosis of infectious and genetic diseases than before, while obtaining unique information about the genetic variations between individual cells. We will work in close collaboration between academia, industry and clinics and develop advanced diagnostic tools of relevance in infectious medicine, hematology, oncology and genetic diseases.

To simplify the analysis we are currently working on cellphone-based microscopy for imaging of stretched DNA in a project funded by the Swedish Research Council.

 

 

Key publications

C. Freitag, C. Noble, J. Fritzsche, F. Persson, M. Reiter-Schad, A. N. Nilsson, A. Graneli, T. Ambjörnsson, K. U. Mir and Jonas O. Tegenfeldt, “Visualizing the entire DNA from a chromosome in a single frame”, Biomicrofluidics, 9, 044114 (2015) Abstract

A meandering channel allows a chromosomal length DNA to be fit within one single field of view.

Charleston Noble, Adam N. Nilsson, Camilla Freitag, Jason P. Beech, Jonas O. Tegenfeldt, Tobias Ambjörnsson, “A fast and scalable kymograph alignment algorithm for nanochannel-based optical DNA mappings”, PLoS ONE 10(4): e0121905 (2015) Abstract

A fast alignment algorithm for data analysis.

Mohammadreza Alizadehheidari, Erik Werner, Charleston Noble, Michaela Reiter-Schad, Lena K. Nyberg, Joachim Fritzsche, Bernhard Mehlig, Jonas O. Tegenfeldt, Tobias Ambjörnsson, Fredrik Persson and Fredrik Westerlund, “Nanoconfined circular and linear DNA – equilibrium conformations and unfolding kinetics”, Macromolecules, 48 (3), pp 871–878 (2015) Abstract

Experimental and theoretical comparison of biopysics of circular and linear DNA.

Erik Werner, Fredrik Westerlund, Jonas O. Tegenfeldt, Bernhard Mehlig "Density profile of DNA, Macromolecules 46(16), 6644–6650 (2013) Abstract
Collaboration with Prof Bernhard Mehlig at University of Gothenburg.

Eric Werner, Fredrik Persson, Fredrik Westerlund, Jonas O. Tegenfeldt, Bernhard Mehlig, “Orientational effects on confined DNA”, Physical Review E, 86(4), 041802 (2012) Abstract
The failure of using a powerlaw to describe the dependence of the extension as a function of channel diameter is explained by a model based on a biased random walk.
Collaboration with Prof Bernhard Mehlig at University of Gothenburg.

Fredrik Persson, Joachim Fritzsche, Kalim U Mir, Mauro Modesti, Fredrik Westerlund, Jonas O. Tegenfeldt, “Lipid-based passivation in nanofluidics”, Nano Letters, 12 (5), 2260-2265 (2012) Abstract
A passivation scheme based on a lipid bilayer opens up for studies of protein-DNA interactions with a minimum of non-specific adhesion to the nanochannels walls.

J. Lin, F. Persson, Joachim Fritzsche, J. O. Tegenfeldt, O. A. Saleh, “Bandpass filtering of DNA elastic modes using confinement and tension” Biophysical Journal, 102(1), 96-100 (2012) Abstract
First demonstration of tweezers combined with nanochannels. Lateral fluctuation modes are selectively suppressed by confinement
Collaboration with Prof Omar Saleh at UCSB.

Lena K Nyberg, Fredrik Persson, Johan Berg, Johanna Bergström, Emelie Fransson, Linnea Olsson, Moa Persson, Antti Stålnacke, Jens Wigenius, Jonas O Tegenfeldt, Fredrik Westerlund, “A single-step competitive binding assay for mapping of single DNA molecules” Biochemical and Biophysical Research Communications, 417, 404-408 (2012) Abstract
First demonstration of a labeling scheme based on competitive binding.
Collaboration with Prof Fredrik Westerlund at Chalmers Technical University.

 Fredrik Persson, Pit Bingen, Thorsten Staudt, Johann Engelhardt, Jonas O. Tegenfeldt, Stefan W. Hell “Fluorescence nanoscopy of single DNA molecules using STED”, Angewandte Chemie 50 (24), 5581-5583 (2011) Abstract
First demonstration of STED of DNA on a surface.
Collaboration with Prof Stefan Hell.

Walter W. Reisner, Niels B. Larsen, Asli Silahtaroglu, Anders Kristensen, Niels Tommerup, Jonas O. Tegenfeldt*, Henrik Flyvbjerg* “Single-Molecule Denaturation Mapping of Genomic DNA in Nanofluidic Channels”, Proceedings of the National Academy of Sciences USA 107 (30), 13294-13299 (2010) Abstract
Simple mapping scheme based on local melting of DNA. The resulting pattern is the result of the difference in binding and quantum yield of an intercalating dye along ds and ss DNA.
Collaboration with Technical University of Denmark (primarily Prof Henrik Flyvbjerg and Prof Anders Kristensen)

Fredrik Persson, Fredrik Westerlund, Jonas O. Tegenfeldt, Anders Kristensen, “Local Conformation of Confined DNA Studied Using Emission Polarization Anisotropy”, Small, 5(2), 190-193 (2009) Abstract
Direct monitoring of the local conformation of the DNA. The intercalating dye is such that the emitted light is polarized perpendicular to the backbone of the DNA.
Collaboration with Prof Anders Kristensen at the Technical University of Denmark.

Walter W. Reisner, Jason P. Beech, Niels B. Larsen, Henrik Flyvbjerg, Anders Kristensen, and Jonas O. Tegenfeldt, “Nanoconfinement-enhanced conformational response of single DNA molecules to changes in ionic environment”, Physical Review Letters, 99, 058302 (2007) Abstract
One of the first investigations of the effect of salt on the confirmation of confined DNA.
Collaboration with the Technical University of Denmark.

 

Nanoscale injection needles

 

Key objective: develop tools to directly access the cytosol of single cells.

To access the cytosol chemically in real time for perturbation and analysis, we develop arrays of hollow nanowires that can be used as nanoinjection needles for single cells. In this way we will be able to perturb large numbers of individual cells in parallel with a minimal variation in the perturbation and with a minimal mechanical disturbance to the cells. Any heterogeneity within the cell population will then be readily observable.

 

Key publications

 

Henrik Persson, Zhen Li, Jonas O. Tegenfeldt, Stina Oredsson, and Christelle N. Prinz, “From immobilized cells to motile cells on a bed-of-nails: effects of vertical nanowire array density on cell behaviour”, Scientific Reports 5, 18535 (2015) Abstract

Henrik Persson, Jason P. Beech, Lars Samuelson, Christelle N. Prinz, Jonas O. Tegenfeldt, “Vertical oxide nanotubes connected by subsurface microchannels”, Nano Research 5(3), 190–198 (2012) Abstract

Niklas Sköld, Waldemar Hällström, Henrik Persson, Lars Montelius, Martin Kanje, Lars Samuelson, Christelle N. Prinz, Jonas O. Tegenfeldt, “Nanofluidics in hollow nanowires” Nanotechnology 21(15), 155301 (2010) Abstract