Diffusion Fundamentals (E-Journal)

Kühn, Ingolf

The Open-Access Journal for the Basic Principles of Diffusion Theory, Experiment and Application
Drivers and impacts of the spread of alien species in Europe
Ingolf Kühn
Helmholtz Center for Environmental Research – UFZ, Halle, Germany
ingolf.kuehn@ufz.de
Species occurring outside their natural range due to human facilitation are called alien (synonyms: non-
native, exotic). While most of these species integrate into native ecosystems without causing (major)
problems, some of them can have considerable impacts on native biodiversity, ecosystems, human
infrastructure and/or health, thus causing environmental or economic harm [1].
During my talk, I will specifically review the situation in Europe with a focus on plant species. Most
of the plant species in Europe were introduced intentionally (e.g., as agricultural crop or forestry tree
or for ornamental purposes [2] and then escaped [3]. Exchange across biogeographic barriers largely
increased with human travel, transport and trade. Several environmental factors are related to spread
of these species, such as rivers and canals, roads and railways. Furthermore, habitat disturbance and
climate change are now known to increase invasibility [4, 5].
From an ecological point of view, this spread is most interesting and there are several methods to model
spread under static and dynamic conditions. During my talk I will therefore provide an overview on
the variety of model. Some of these models are based on ecological processes such as meta-population
dynamics, colonization and extinction probability related to habitat characteristics, dispersal abilities
related to species traits or using physical principles based on diffusion models [e.g., 6].
References
[1] M. Vila et al.: How well do we understand the impacts of alien species on ecosystem services?
A pan-European, cross-taxa assessment. Frontiers in Ecology and the Environment 8, 135–144
(2010)
[2] P.P. Pyšek et al.: Alien vascular plants of Europet. In: The handbook of alien species in Europe,
DAISIE (Editor). Springer: Dordrecht. p. 43–61 (2009)
[3] P.E. Hulme et al.: Grasping at the routes of biological invasions: A framework for integrating
pathways into policy. Journal of Applied Ecology 45, 403–414 (2010)
[4] M. Chytry et al.: Habitat invasions by alien plants: A quantitative comparison among mediter-
ranean, subcontinental and oceanic regions of Europe. Journal of Applied Ecology 45, 448–458
(2008)
[5] G.-R. Walther et al.: Alien species in a warmer world – Risks and opportunities. Trends in Ecology
& Evolution 24, 686–693 (2009)
[6] M.G. Smolik et al.: Integrating species distribution models and interacting particle systems to
predict the spread of an invasive alien plant. Journal of Biogeography 37, 411–422 (2010)


English

Drivers and impacts of the spread of alien species in Europe

Pearce, Daniel John Gaythorne

Rowlands, George

Turner, Matthew Simon

The Open-Access Journal for the Basic Principles of Diffusion Theory, Experiment and Application
Dynamics in social fluids
Dan J.G. Pearce, George Rowlands, Matthew S. Turner∗
University of Warwick, Coventry, UK
m.s.turner@warwick.ac.uk
Bird flocks, insect swarms and fish shoals resemble fluids made up of many individuals where the
controlling interactions are social rather than physical in character [1]. Some progress has been made
reverse-engineering candidates for these interactions that are local in space, either in a metric-based
[2] or topological sense [3, 4]. A question that has been largely overlooked is whether the interactions
should be expected to be local at all. We discuss the evidence for them having a non-local character
and, furthermore, that there is a natural choice for this that is consistent with the cognitive limitations
of a bird’s vision. This leads us to propose a non-local hybrid-projection model. We study the global
character of the flocks that emerge from this model and their various phenotypes. Most significantly,
an emergent state arises in which the probability that a typical bird can see out (sky) in any direction
divided by the probability that its view is blocked by other bird(s) is O(1). We refer to this as marginally
opaque, see Fig. 1. We present experimental data on bird flocks that confirm this prediction. Finally,
we discuss how these models may naturally be associated with evolutionary fitness, as well as being
physiologically plausible.
Figure 1: The centre panel is an image of a real flock of Starlings. It is marginally opaque. The left and right
panels show the same image artificially doctored so as to resemble states that would have a very low (1) or a
very high (≈1) opacity, respectively.
References
[1] I. Giardina: Collective behaviour in animal groups: Theoretical models and empirical studies.
HFSP Journal 2, 205–219 (2008)
[2] T. Vicsek, A. Cziroók, E. Ben-Jacob, I. Cohen, O. Shochet: Novel type of phase transition in a
system of self-driven particles. Phys. Rev. Lett. 75, 1226–1229 (1995)
[3] A. Cavagna, A. Cimarelli, I. Giardina, G. Parisi, R. Santagati, F. Stefanini, M. Viale: Scale-free
correlations in starling flocks. PNAS 107, 11865–11870 (2010)
[4] M. Ballerini, N. Cabibbo, R. Candelier, A. Cavagna, E. Cisbani, I. Giardina, A. Orlandi, G. Parisi,
A. Procaccini, M. Viale, V. Zdravkovic: Empirical investigation of starling flocks: A benchmark
study in collective animal behaviour. Anim. Behav. 76, 201–215 (2008)


Dynamics in social fluids

Lamura, Antonio

Winkler, Roland G.

The Open-Access Journal for the Basic Principles of Diffusion Theory, Experiment and Application
Two-dimensional semiflexible polymers under external fields
Antonio Lamura1∗, Roland G. Winkler2
1IAC CNR, Bari, Italy
2IAS, Forschungszentrum Juelich, Germany
∗a.lamura@ba.iac.cnr.it
The non-equilibrium structural and dynamical properties of semiflexible polymers confined to
two dimensions are investigated by molecular dynamics simulations. Three different scenarios are
considered: The force-extension relation of tethered polymers, the relaxation of an initially stretched
semiflexible polymer, and semiflexible polymers under shear flow. We find quantitative agreement with
theoretical predictions for the force-extension relation and the time dependence of the entropically
contracting polymer. The semiflexible polymers under shear flow exhibit significant conformational
changes at large shear rates, where less stiff polymers are extended by the flow, whereas rather stiff
polymers are contracted. In addition, the polymers are aligned by the flow, thereby the two-dimensional
semiflexible polymers behave similarly to flexible polymers in three dimensions. The tumbling times
display a power-law dependence at high shear rate rates with an exponent comparable to the one of
flexible polymers in three-dimensional systems.
References
[1] A. Lamura, R.G. Winkler: Semiflexible polymers under external fields confined to two dimensions.
J. Chem. Phys. 137, 244909 (2012)


Two-dimensional semiflexible polymers under external fields

Fritzsche, Siegfried

Schierz, Philipp

Janke, Wolfhard

Hannongbua, Supot

Saengsawang, Oraphan

Chmelik, Christian

The Open-Access Journal for the Basic Principles of Diffusion Theory, Experiment and Application
Diffusion investigation for hydrogen guest molecules in an adapted force
field for ZIF-11
Siegfried Fritzsche1∗, Philipp Schierz1, Wolfhard Janke1, Supot Hannongbua2,3,
Oraphan Saengsawang2,3, Christian Chmelik4
1Universität Leipzig, Institute for Theoretical Physics, Leipzig, Germany
2Chulalongkorn University, Computational Chemistry Unit Cell (CCUC),
Department of Chemistry, Bangkok, Thailand
3Chulalongkorn University, Center of Innovative Nanotechnology, Bangko, Thailand
4Universität Leipzig, Institute for Experimental Physics I, Leipzig, Germany
∗fritzsche@itp.uni-leipzig.de
The large family of Metal Organic Frameworks, to which ZIF-11 belongs, demands for the possibility
to predict properties regarding adsorption and diffusion behavior from their crystal structure.
Therefore, as a first step, it is important to find good parameters to describe some members of the MOF
family and to try in a second step to draw conclusions to other materials from the gained experience.
In this work the structure of ZIF-11 was investigated and a force field was found that was able to repro-
duce experimental adsorption behavior [1]. The force field was based on the AMBER [2] parameters
and was adapted to get good agreement with measured properties. Connections between adjacent cav-
ities were identified and a way has been described to deal with uncertainties in the provided X-Ray
structures [1].
Afterwards longer simulations runs have been performed to get estimates for the behavior of the diffu-
sion coefficient.
Figure 1: The temperature dependence of the diffusion coefficient for hydrogen in ZIF-11 together with a linear
fit
References
[1] K.S. Park, Z. Ni, A.P. Côté, J.Y. Choi, R. Huang: Exceptional chemical and thermal stability of
zeolitic imidazolate frameworks. Proceedings of the National Academy of Sciences 103, 10186–
10191 (2006)
[2] Y. Duan, C. Wu, S. Chowdhury, M.C. Lee, G. Xiong, W. Zhang, R. Yang, P. Cieplak, R. Luo,
T. Lee, J. Caldwell, J. Wang, P. Kollman: A point-charge force field for molecular mechanics
simulations of proteins based on condensed-phase quantum mechanical calculations. J. Comp.
Chem. 24, 1999–2012 (2003)


Diffusion investigation for hydrogen guest molecules in an adapted force field for ZIF-11

Furó, István

Fernandes, Ricardo

Shtein, Michael

Bar, Ilan Pri

Regev, Oren

Marques, Eduardo F.

The Open-Access Journal for the Basic Principles of Diffusion Theory, Experiment and Application
Surface diffusion of polymers on carbon nanotubes
István Furó1∗, Ricardo Fernandes1,2, Michael Shtein3, Ilan Pri Bar3,
Oren Regev3, Eduardo F. Marques2
1Division of Applied Physical Chemistry, Department of Chemistry,
KTH Royal Institute of Technology, Stockholm, Sweden
2Centro de Investigação em Quı́mica, Department of Chemistry and Biochemistry,
University of Porto, Porto, Portugal
3Department of Chemical Engineering and the Ilse Katz Institute for Nanotechnology,
Ben-Gurion University of the Negev, Beer-Sheva, Israel
∗furo@kth.se
Carbon nanotubes (CNTs) are emerging materials with a wealth of applications in different areas,
ranging from molecular devices and sensors to drug delivery. However, pristine CNTs tend to bundle
into strongly bound aggregates due to van der Waals interactions. This is a drawback, since many
applications require individually dispersed CNTs. One possibility to overcome this problem is to use
non-covalent dispersants such as surfactants or polymers, which can exfoliate and stabilize CNTs in
aqueous solutions. However, non-covalent dispersion is still poorly understood at molecular level [1].
In what concerns polymers as dispersants, two main qualitative models on the polymer-CNT interaction
are wrapping where polymers coat the CNT in a tight contact and loose adsorption where a weaker
interaction between the polymer and the CNT takes place, so that the bound polymer remains almost
like in its natural state in a good solvent, i.e. a random coil [2].
Figure 1: 1H pulsed-field-gradient spin-echo decays of Pluronic R© F127 recorded with different diffusion times
in aqueous solutions containing single walled carbon nanotubes.
We have studied by 1H NMR diffusometry the exchange and translational dynamics of triblock
copolymers Pluronic R© in aqueous solution containing single walled nanotubes (SWNT). The 1H
pulsed-field-gradient spin-echo decay (Fig. 1) was nonexponential for all investigated polymers and
changed character upon changing the diffusion time ∆, which indicates a situation where there is
exchange of the polymer between its free and adsorbed states and where the exchange time lies in the
100 ms range [3] set by the experimental time scale (∆). Within the framework of the well-known
Kärger model, the self-diffusion coefficient of the polymers in their CNT-adsorbed state can also be
obtained. For Pluronic R© F127 we found that the surface diffusion coefficient is in the order of 2.2 ×
10−12 m2s−1, ca 30-fold smaller than that obtained for the unbound polymer in water (5.9 × 10−11
m2s−1). This result seems to support the “loose adsorption” model for Pluronic-CNT interaction.
References
[1] H. Wang: Dispersing carbon nanotubes using surfactants. Curr. Opin. Colloid Interface Sci. 14,
364–371 (2009)
[2] M. Granite, A. Radulescu, W. Pyckhout-Hintzen, Y. Cohen: Interactions between block copoly-
mers and single-walled carbon nanotubes in aqueous solutions: A small-angle neutron scattering
study. Langmuir 27, 751–759 (2011)
[3] A.E. Frise, G. Pages, M. Shtein, I. Pri Bar, O. Regev, I. Furó: Polymer binding to carbon nan-
otubes in aqueous dispersions: Residence time on the nanotube surface as obtained by NMR
diffusometry. J. Phys. Chem. B 116, 2635–2642 (2012)


Surface diffusion of polymers on carbon nanotubes

Pilvar, Pooneh

Caro, Jürgen

The Open-Access Journal for the Basic Principles of Diffusion Theory, Experiment and Application
Molecular dynamics investigation of the transport of hydrogen in ZIF-7
Pooneh Pilvar1∗, Siegfried Fritzsche1, Jürgen Caro2, Wolfhard Janke1
1Universität Leipzig, Institute for Theoretical Physics,
Leipzig, Germany
2Leibniz University Hannover, Institute of Physical Chemistry and Electrochemistry,
Hannover, Germany
∗p.pilvar@gmail.com
The importance of hydrogen-based clean energy systems due to the global climate change, air pollu-
tion and energy security has lead to several studies of hydrogen production, separation and storage in
industry and science [1, 2].
In the current study, we have investigated the diffusion of hydrogen within a novel Zeolitic imidazolate
framework (ZIF-7, Figure 1a). ZIFs are a subfamily of porous metal-organic frameworks (MOFs) [3, 4].
For investigating diffusion behavior of hydrogen in this lattice, we have applied Molecular Dynamics
(MD) simulations. At the studied temperatures in a series of MD simulations performed with a rigid
lattice, no diffusion of any gas was observed in ZIF-7. The same behavior has been reported by A.
Battisti et al. [5]. Applying the flexibility to the framework, the measured diffusion coefficient for
hydrogen was about 2.7× 10−9 m2 s−1 while nearly no diffusion was observed for any other studied gas
in ZIF-7. These results clearly elucidate the molecular sieving behavior of this material for hydrogen
reported by Caro et al. and represent it as a promising membrane in this domain which is due to its very
small pore structure and window size (0.3 nm) that is close to the kinetic size of the hydrogen molecule
[1].
Figure 1: ZIF-7 unit cell (a). The main six-member window of ZIF-7 (b); Top view (left), side view (right).
References
[1] Y. Li, F. Liang, H. Bux, W. Yang, J. Caro: Zeolitic imdazolate framework ZIF-7 based molecular
sieve membrane for hydrogen separation. Journal of Membrane Science 354, 48–54 (2010)
[2] B. Assfour, S. Leoni, G. Seifert: Hydrogen adsorption sites in zeolite imidazolate frameworks
ZIF-8 and ZIF-11. Journal of Physical Chemistry C 2010 114, 13381–13384 (2010)
[3] S.L. James: Metal-organic frameworks. Chemical Society Review 32, 276–288 (2003)
[4] A.W. Thornton, D. Dubbeldam, M.S. Liu, B.P. Ladewig, A.J. Hill, M.R. Hill: Feasibility of ze-
olitic imidazolate framework membranes for clean energy application. Energy & Environmental
Science 5, 7637–7616 (2012)
[5] A. Battisti, S. Taioli, G. Garberoglio: Zeolitic imidazolate frameworks for separation of binary
mixtures of CO2, CH4, N2 and H2: A computer simulation investigation. Microporous and Meso-
porous Materials 143, 46–53 (2011)


Molecular dynamics investigation of the transport of hydrogen in ZIF-7

Petrov, Eugene P.

Herold, Christoph

Schwille, Petra

The Open-Access Journal for the Basic Principles of Diffusion Theory, Experiment and Application
Translational and rotational diffusion of semiflexible DNA polymers
and rod-like fd virus particles on weakly charged freestanding cationic
lipid membranes
Eugene P. Petrov1∗, Christoph Herold2, Petra Schwille1
1Max Planck Institute of Biochemistry, Department of Cellular and Molecular Biophysics,
Martinsried, Germany
2Biophysics, BIOTEC, Technische Universität Dresden, Dresden, Germany
∗petrov@biochem.mpg.de
Diffusion and conformational dynamics of single semiflexible and flexible macromolecules and col-
loids adhereing to freestanding lipid membranes is a challenging problem both from the experimental
and theoretical standpoint. Using cationic supergiant unilamellar vesicles [1] as an experimental plat-
form for mimicking freestanding lipid membrane in combination with single-molecule fluorescence
video microscopy, we have previously discovered that local interaction of single DNA molecules with
moderately and strongly charged freestanding lipid membranes can lead to interesting unexpected ef-
fects [2]. In the present contribution, using the same experimental technique, we investigate the diffu-
sion behavior of semiflexible DNA polymers and much more rigid negatively charged colloidal parti-
cles, fd viruses [3], upon their electrostatic binding to weakly charged freestanding cationic lipid mem-
branes. The wide range of contour lengths of DNA macromolecules (5–48.5 kbp) and fd virus particles
(0.88–9.7 µm), allowed us to observe the crossover from the stiff-rod to semiflexible (fd virus) and
from semiflexible to flexible (DNA) behavior which is accompanied by a crossover in the diffusion be-
havior of membrane-attached particles – from the 2D membrane-controlled to 3D bulk fluid-controlled
diffusion dynamics. We compare the obtained experimental results on translational and rotational diffu-
sion of DNA and fd virus particles with the predictions of hydrodynamics-based theories of membrane
diffusion [4–8] and determine their ranges of applicability.
This work was supported by the DFG (FOR 877).
References
[1] C. Herold, G. Chwastek, P. Schwille, E.P. Petrov: Efficient electroformation of supergiant unil-
amellar vesicles containing cationic lipids on ITO-coated electrodes. Langmuir 28, 5518–5521
(2012)
[2] C. Herold, P. Schwille, E.P. Petrov: DNA condensation at freestanding cationic lipid bilayers.
Phys. Rev. Lett. 104, 148102 (2010)
[3] S. Fraden, Z. Dogic, In: Soft Matter 2: Complex Colloidal Suspensions. Eds. G. Gompper, M.
Schick, Wiley-VCH, Weinheim, 1–86 (2006)
[4] B.D. Hughes, B.A. Pailthorpe, L.R. White: The translational and rotational drag on a cylinder
moving in a membrane. J. Fluid Mech. 110, 349–372 (1981)
[5] E.P. Petrov, R. Petrosyan, P. Schwille: Translational and rotational diffusion of micrometer-sized
solid domains in lipid membranes. Soft Matter 8, 7552–7555 (2012)
[6] S. Ramachandran, S. Komura, K. Seki, G. Gompper: Dynamics of a polymer chain confined in a
membrane. Eur. Phys. J. E 34, 11046 (2011)
[7] A.J. Levine, T.B. Liverpool, F.C. MacKintosh: Dynamics of rigid and flexible extended bodies in
viscous films and membranes. Phys. Rev. Lett. 93, 038102 (2004)
[8] T.M. Fischer: The drag on needles moving in a Langmuir monolayer. J. Fluid Mech. 498, 123–137
(2004)


Translational and rotational diffusion of semiflexible DNA polymers and rod-like fd virus particles on weakly charged freestanding cationic lipid membranes

Dikic, Jasmina

Kostiuk, Georgij

Siksnys, Virginijus

Seidel, Ralf

The Open-Access Journal for the Basic Principles of Diffusion Theory, Experiment and Application
Protein diffusion on DNA
Jasmina Dikic1, Georgij Kostiuk2, Virginijus Siksnys2, Ralf Seidel1∗
1Institute for Molecular Cell Biology, University of Münster, Münster, Germany
2Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
∗ralf.seidel@uni-muenster.de
Diffusion is a major transport mechanism within living systems. Protein diffusion along elongated
cellular structures (e.g. cytoskeletal filaments or DNA), often termed one-dimensional diffusion, has
recently gained increasing interest. This is because confinement of the diffusion path can enhance the
success rate of localizing a target on the particular structure. Here we focus on a new aspect, namely
that protein diffusion along DNA can be itself a central part of an enzymatic reaction. Using magnetic
tweezers and fluorescence techniques we provide single-molecule observations of the monomeric re-
striction enzyme BcnI which needs to turn on DNA to cut both strands of the helix. We reveal on one
hand the orientation of the enzyme bound to its target site, and on the other hand the one-dimensional
diffusion of the enzyme along DNA under different ionic conditions. Both observations provide evi-
dence for a mechanism of the enzyme where indeed a monomer cuts both DNA strands in a sequential
manner.
This work was supported by the DFG (FOR 877).


Protein diffusion on DNA

Shakhov, Alexander

Kärger, Jörg

Valiullin, Rustem

The Open-Access Journal for the Basic Principles of Diffusion Theory, Experiment and Application
Tracing molecular propagation in dextran solution by pulsed
field gradient NMR
Alexander Shakhov∗, Jörg Kärger, Rustem Valiullin
Faculty of Physics and Earth Sciences, Universität Leipzig, Leipzig, Germany
∗alexander.shakhov@uni-leipzig.de
Molecular self-diffusion in biological systems plays an important role by not only providing a mech-
anism of matter transport, but also by determining the rates and patterns of bio-chemical reactions
in cells [1]. In recent years, fluorescence correlation spectroscopy (FCS) has emerged as a powerful
technique for studying transport processes in biological systems on a spatial scale up to hundreds of
nanometers [2]. The data obtained by this technique reveal that in most cases diffusion of tracer dye
molecules under these conditions shows anomalous behavior, i.e., the mean square displacements grow
not linearly with time, but as a power law with the exponent α < 1 [3]. This finding, which is typically
associated with molecular crowding effect, has far reaching consequences, among which reformulation
of the concepts of bio-chemical reactions in life matter is currently under discussion. However, there
are much experimental evidences of normal diffusion in highly crowded media. Therefore, experimen-
tal exploration of the origins of anomalous diffusion observed in the FCS experiments is of immediate
importance for life sciences.
Figure 1: Schematic representation of diffusion patterns of tracer molecules obtained in model crowded media
mimicking biological cells using fluorescence correlation spectroscopy and pulsed field gradient NMR.
In the present work, we have used potentials of pulsed field gradient NMR to extend the time- and
space scales for the diffusion processes in the same system already probed by the FCS technique [4].
Notably, the latter technique revealed that in the aqueous solutions of dextran mixtures, mimicking
crowded media in bio-cells, on the time scale up to 500 nm diffusion has shown subdiffusive behavior
with the anomality exponent being a function of the solvent concentration and of the dextran molecular
mass and the mixture composition [5, 6]. By choosing an optimal system with still pronounced
anomality, but simultaneously providing reliable NMR signals for diffusion studies, we have traced
self-diffusivities of two dextrans of 40 kDa and 640 kDa molecular mass in the mixture in deuterated
water. The results obtained have provided clear evidence that for the lighter dextan, being an analogue
for the probe molecule in the FCS experiments, there should be a crossover to normal diffusion on
the spatial scale between 500 nm and 1200 nm. Bridging the gap between these two values in order
to validate the existence of the crossover or to demonstrate that these two types of experimental
approaches providing ensemble-averaged quantities (NMR) and operating with finite number of
tracers (FCS) may yield differing data is among of our current activities.
References
[1] A.P. Minton: The influence of macromolecular crowding and macromolecular confinement on
biochemical reactions in physiological media. J. Biol. Chem. 276, 10577–10580 (2001)
[2] J. Ries, P Schwille: Fluorescence correlation spectroscopy. BioEssays 34, 361–368 (2012)
[3] M. Hellmann, J. Klafter, D.W. Heermann, M. Weiss: Challenges in determining anomalous diffu-
sion in crowded fluids. J. Phys.: Condens. Matter 23, 234113–234120 (2011)
[4] A. Shakhov, R. Valiullin, J. Kärger: Tracing molecular propagation in dextran solutions by pulsed
field NMR. J. Phys. Chem. Letters 3, 1854–1857 (2012)
[5] M. Weiss, M. Elsner, F. Kartberg, T. Nilsson: Anomalous subdiffusion is a measure for for cyto-
plasmic crowding in living cells. Biophys. J. 87, 3518–3524 (2004)
[6] D.S. Banks, C. Fradin: Anomalous diffusion of proteins die to molecular crowding. Biophys. J.
89, 2960–2971 (2005)


Tracing molecular propagation in dextran solution by pulsed field gradient NMR

Simmert, Steve

Schäffer, Erik

The Open-Access Journal for the Basic Principles of Diffusion Theory, Experiment and Application
Interference reflection microscopy to visualize sub-diffraction limited
objects in 3D
Steve Simmert1∗, Erik Schäffer2
1Biotechnology Center, TU Dresden, Dresden, Germany
2Center for Plant Molecular Biology (ZMBP), Universität Tübingen, Tübingen, Germany
∗steve.simmert@biotec.tu-dresden.de
The visualization of objects smaller than the diffraction limit has become a broad field, especially in
life science. However, current technologies often require a fluorescent label and/or complicated optical
setups. Here, we report the observation of single, non-labeled microtubules with interference reflection
microscopy (IRM) using a light emitting diode for illumination. IRM can visualize sub-diffraction-
limited objects, provides three-dimensional (3D) information with nanometer resolution in the axial
direction, and a superior signal-to-noise ratio compared to differential interference contrast (DIC)
microscopy. In comparison to other techniques such as DIC microscopy, IRM does not require any
(expensive) polarizing optics, is independent of the object orientation, and can easily be implemented
into conventional inverted microscopes. Also, IRM provides free access to the upper side of the sample
and can be combined with other optical techniques such as fluorescence microscopy and optical
tweezers.


Interference reflection microscopy to visualize sub-diffraction limited objects in 3D

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