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OnderzoekZernike (ZIAM)OnderwijsTop Master Program in Nanoscience

NS194. Small research project-- available projects for 2010 [now obsolete]

The following small research projects have been proposed by the research groups.

1. Research group Polymer chemistry and bio-engineering (Prof. Andreas Herrmann)

1.1. DNA nanotubes with well defined length

DNA is well known as one of the most promising materials for future nanotechnologies. Its unique self-recognition properties and structural strength have been used to design a staggering array of beautiful self-assembled nanostructures, from tetrahedral building blocks to extended functionalizable sheets to smiley faces. A major obstacle to working with such nanostructures, though, is the prohibitively large number of sequences generally required. A stunning exception is a sequence reported by the Mao group1, a 52-base DNA strand which can self-assemble into well-defined nanotubes of up to 60 microns in length. However impressive these materials may be, their potential for future applications is limited until it is possible to control their length, which will be the focus of this small project. By hybridizing this sequence in a well-defined confined volume, for instance within an emulsion, it should be possible to greatly reduce the resulting nanotube length. The student will also have the opportunity to study the controlled self-assembly of nanotubes using the DNA hybrid materials which are the specialty of this group. This should result in a hydrophobic polymer core, which would in turn enable dyes, drugs and other hydrophobic materials to be loaded into these novel nanocontainers. Through this project the student will become well-versed in basic DNA handling and three of the most important characterization techniques in nanoscience – AFM, TEM and fluorescence correlation spectroscopy.

1) Liu et al., Angew. Chem. Int. Ed. 45, 1942

1.2. Slippery DNA

Surface immobilized polymers have long been known for their lubricating properties, particularly in aqueous environments. They are studied both for their obvious practical applications and to gain a greater understanding of the fundamental principles of lubrication - shedding light, for example, on extremely effective biological lubrication systems. It has been shown that performance depends strongly on polymer branching, length, charge and surface attachment strength, which can often be difficult to independently study in polymeric systems. In this project, the student will synthesize and characterize a novel lubricant system based on DNA. This molecule combines high charge density with the potential to introduce precisely controlled branching, sample various attachment chemistries and even alter the physical properties of the molecule. Not only does this material have the potential for high performance, it offers the opportunity to independently study the effect of individual material properties. During the course of this project, the student will become proficient in basic DNA handling, surface characterization with IR and X-ray spectroscopy and cutting-edge AFM force measurement techniques.

2. Research group Bio-inspired polymer chemistry (Prof. Katja Loos)

2.1 Starch granule surface imaging with atomic force microscopy (AFM)

Starch is the bulk carbohydrate source in human foods. It is easily digestible in its processed form which causes undesirably high glycemic index of starch containing foods; that leads to fast increasing of blood glucose level causes diabetes type II. Starch interaction with other components is one of the possibilities to diminish starch digestibility. These compounds protect starch to some extent not to be easily in access of alpha-amylase.

It may be expected that the surface of the starch granules has major influence on the properties of the whole granules (influence on granule hydration, enzyme attack and interaction with other components).

Atomic Force Microscopy (AFM) seems the most appropriate technique to study the surface of starch granules because of high resolution and unique sample preparation. AFM is a well recognized surface probe microscopy technique in which a very fine crystal tip is rastered over the sample, allowing acquisition of a three-dimensional image of the sample surface topology.

Of interest in this project is defining the sample preparation technique (dry and wet). Studying the surface of starch granules with different origins and assess the potential interactions of protein and / or fatty acids with surface of starch granules which is observable with AFM.


Baldwin P.M.Starch granule surface imaging using low-voltage scanning electron microscopy and atomic force microscopy. International Journal of Biological Macromolecules 21 (1997) 103-107

Neethirajan S. Characterization of the Surface Morphology of Durum Wheat Starch Granules Using Atomic Force Microscopy. Microscopy Research and Technique 71 (2008) 125-132

Starch Granule Surface Imaging. Cyber starch.

2.2 Enzymatic hydrolyzation of water insoluble proteins and investigation of interaction process by AFM

Starch is a macro constituent of many foods and its properties and interactions with other constituents are of interest to the food industry and for human nutrition. Being able to predict functionality from knowledge of the structure and explain how starch interacts with other major food constitutes remain significant challenges in food science and nutrition.

An important property of starch is its ability to absorb water, resulting in gelatinization and loss of granular organization. While starch granules are swollen, they are at the high risk of enzyme attack which leads to digestibility. Protein is one of the constituents protecting starch granules against enzymatic digestibility in case of protein solubility in water.

Wide range of proteins are applied which some are water insoluble. The project was led to apply enzymatic hydrolyzation for the water insoluble proteins till particular break down, achieving solubility of these proteins in water.

Atomic Force Microscopy (AFM) is proposed to investigate the interaction between wheat starch granules and hydrolyzed proteins according to the purpose of the project, investigation the interaction possibilities and functionality of hydrolyzed proteins to compare with the water soluble proteins.  AFM is a lens-less microscopy technique, in which a sample surface is brought into such close proximity with a fine crystal tip mounted on a flexible cantilever, that atomic interaction forces between the tip and the sample cause the cantilever to bend.


A. Mannheim, M. Cheryan; 1993; Water-Soluble Zein by Enzymatic Modification in Organic Solvents; Cereal Chemistry; Vol. 70 (2); P. 115 – 121

Die Grundlagen der Atomkraftmikroskopie (AFM)

L. Copeland, J. Blazek, H. Salman, M. Chiming Tang; 2009; Form and functionality of starch; Food Hydrocolloids; Vol. 23; P. 1527 – 1534

R. P. Goncalves, S. Scheuring; 2006; Manipulating and imaging individual membrane proteins by AFM; Surface and Interface Analysis; Vol. 38; P. 1413 – 1418

2.3 Inclusion complex betweenthree arms polytetrahydrofuran-block-amylose and fatty acids

Amylose is able to form inclusion complex with fatty acids, such as lauric or palmitic acids, by providing cavity for its guest molecules to be included via hydrophobic interaction. This ability to form inclusion complex can be used to form more advanced structure, by attaching amylose as the second block into three arms polytetrahydrofuran. Functionalized three arms polytetrahydrofuran (PTHF) can be prepared via cationic ring opening polymerization, followed by reductive amination to attach maltoheptaose as the primer for enzymatic polymerization of glucose-1-phosphate. The enzyme (potato phosporylase) transfers a glucose unit from glucose-1-phosphate to non-reducing end of maltoheptaose forming alpha-(1a4) glycosidic linkages in amylose chain. The growing amylose chain includes fatty acids into its helix. The characterization of the product includes GPC (gel permeation chromatoghraphy), 1H-NMR (nuclear magnetic resonance), FTIR (Fourier transform infra red spectroscopy), UV/VIS spectroscopy, and X-Ray diffraction.

3. Research group Optical condensed-matter physics (Prof. van Loosdrecht)

3.1 Hybrid materials

Organic/Inorganic hybrid materials combine the versatility of organic materials with the robust electronic properties of inorganic materials. These highly tunable materials, with an alternating organic/inorganic self organized nanostructure, may show multifunctional behavior, making them promising for applications. Furthermore, it is expected that the magnetic and optical properties of these materials are highly switchable using short optical pulses, leading for instance to a bi-stability behavior.
This short project is devoted to the study of the dynamical properties of one class of these materials which members show 1, 2 and 3 dimensional (quantum) magnetic behavior. The experimental methods used in this project are (time resolved) optical spectroscopy and micro-Raman spectroscopy at cryogenic temperatures.

3.2 Quantum magnetic heat transport

Low dimensional quantum magnetic materials show an unusually high unidirectional thermal conductivity. Theoretically, the magnetic heat transport is predicted to be fully dissipationless, though in practice this will be limited by lattice defects and scattering from other excitations in the materials. Still, the fact that these materials are electrically insulating, while having heat transport coefficients comparable to metals makes them highly promising for heat management applications in modern microelectronic devices.
This project focuses on studying and visualizing the heat transport in these materials using time and place resolved optical techniques. The experimental methods used in this project are fluorescence thermal microscopy imaging as well as a novel real time laser based heat diffusion method.

4. Research group Micro mechanics (Prof. Erik van der Giessen, Prof. Patrick Onck)

4.1 Bio-inspired design of an artificial nanoswimmer
Externally-controlled swimmers at the micron- and nanoscale can find many applications in medical science, such as diagnosis on lab-on-chip biosensors, intricate drug delivery systems and nanosurgery. As the length of the swimmer decreases, the dynamics of  swimming becomes more and more dominated by viscous forces while the inertia forces become negligible. The design strategies for swimmers at this scale are therefore very different from those used for swimmers observed in day-to-day life, which are mostly inertia driven. Viscous-force-driven swimming demands a time-irreversible motion, also known as non-reciprocal motion, to achieve a net propulsion. Microorganisms found in nature, such as spermatozoa and bacteria, make use of ATP-driven motor proteins to achieve such a non-reciprocal motion. The present project will draw inspiration from these biological strategies used by the microorganisms. The aim of this project is to design an artificial micro-swimmer under magnetic actuation. The main challenge lies in achieving the non-reciprocal motion under such externally controlled actuation. A coupled problem of fluid, solid and magnetic interaction has to be used to find a prescription for that external magnetic field that can drive the swimmer leading to directional control and optimal swimming velocity.
Researchers involved: Sandeep Namdeo and Patrick Onck
4.2  A ctin network dynamics through cross-link unbinding

Supervisor: Prof. Erik van der Giessen.

Click here for a project description in PDF-format.

5. Research group Functional Nanomaterials-Solid State Chemistry (Prof. B. Noheda)

5.1 Atomically flat surfaces for layer-by-layer growth

[For a project description including figures, please click here. For technical reasons, the figures are not present in the description below.]

Oxide materials, in particular the perovskite family, are a very active subject of research because of the number of interesting functional properties that they display: superconductivity, ferroelectricity, frustrated magnetism, etc. and the possibility to tune these properties with very small changes in the composition or external stimuli. Nowadays, a lot of effort is dedicated to the epitaxial growth these materials. The advantage of thin films versus the bulk materials is obvious when thinking of device miniaturization or energy efficiency, but epitaxial growth brings additional benefits. The most important one in the possibility to modify the materials’ structure with the epitaxial strain that is induced in the film by a substrate with similar structure but slightly different lattice parameters. In this way, crystal symmetries that are not allowed in bulk can be stabilized. Since the fundamental dipolar and magnetic interactions are largely dependent on the atomic distances and angular distortions, strain engineering can be utilized to modify the materials’ responses.

In order to do that, the films have to be grown with atomic control and the substrate has to be atomically flat. In this respect, one of the best substrates to grow perovskites oxides is SrTiO3. With a proper chemical and thermal treatment, the (001) surface of SrTiO3 crystals can become atomically flat, with perfectly flat terraces of 200 nm or larger, depending of the miscut angle (the angle between the main crystalline planes and the crystal surface).

In the figure, a 3D atomic force microscopy (AFM) image of the surface of a SrTiO3 crystal displays a step-terrace morphology. A 2D image of a smaller area of the same surface shows that the terraces are ~200nm wide. A linear scan along the green line, confirms that the step height is ~0.4nm, corresponding to 1 unit cell.

In this project, the treatment and AFM imaging of SrTiO3 and other useful perovskite substrates will be performed. Different surfaces will be investigated and insight will be obtained on the energetics and the kinetic processes that give rise to atomically flat surfaces.

6. Research group Theory of Condensed Matter (Prof. Knoester;  daily supervisor Thomas la Cour Jansen)

6.1 Exciton transfer in systems with dynamic disorder

[For a project description including figures, please click here. For technical reasons, the figures are not present in the description below.]

Energy transfer between molecules plays a crucial role in natural light harvesting systems, artificial solar cells and light emitting diodes. While there are large expectations for organic solar cells due to the expected low production cost and flexibility, the efficiency is still too low. A better understanding of the energy transfer in such systems is crucial for the improving the design to maximize the efficiency. In this study a model will be constructed to describe the transfer of an excitation along a chain of coupled chromophores. Each chromophore will be coupled to an overdamped harmonic oscillator to account for the local disorder. The model will contain three parameters: the interaction strength between neighboring molecules J, the magnitude of the bath interaction D and the rate at which the local overdamped oscillator can respond to a local excitation G . When the bath interaction is small compared to the interaction ( D <J) one expect to observe coherent (ballistic) transport along the chain. If the bath coupling is strong the transport can become incoherent (diffusive) and depending on the time scale the bath self-trapping might occur. This detailed dependence of the interplay between these parameters will be investigated by calculating the mean square displacement <r2> of an excitation along the chain as a function of the relative bath coupling D /J and bath rate G /J. The transport parameters will be determined using that <r2> µ v2 t2 + 2Dt, where the ballistic velocity v and the diffusion constant are connected with different time dependence of the transport. As a starting point D /J is varied with G =J. If time allows G /J is varied as well. For the static case ( G =0) no self-trapping takes place.

[Please see Dr. La Cour Jansen for a project description including figures; these are not available from the web site.]
7. Research group Physics of Nano-Devices (Prof. Caspar van der Wal)
7.1 Optical pump-probe studies of suppressed spin dephasing for electron ensembles in semiconductor devices

Optical time-resolved Kerr rotation measurements allow for preparing and detecting the spin states of electron ensembles in GaAs with very high (subpicosecond) time resolution. We use this project to study how electron spin states evolve and dephase while they are localized or transported in small semiconductor channels. The spin signals in GaAs typically decay fast due to spin-orbit interactions. The central question in this project is whether one can engineer devices which automatically suppress or counter-act this relaxation mechanism for spins, by guiding the electron orbitals with respect to the spin-orbit fields. Even more exciting is that such a mechanism can in principle be switched on at off with an electrostatic gate, such that spin signals in devices can be switched between 0 and 1.
Your task is to participate in this research effort. In the Spring of 2010 a new generation of devices will be nano-fabricated in the Zernike cleanroom.
The control with electrostatic gates needs to be tested. The setup for time-resolved Kerr readout is currently improved and you can learn much optics from carrying out several test experiments. In addition, the goal is of course that you participate in, and report on taking Kerr data on the new device structures.

7.2 Quantum optics with electron spins in semiconductor nanodevices

This experimental project explores whether quantum information that is carried by an optical pulse can be stored in a memory element that is formed
by an electron-spin ensemble in a semiconductor. This work is relevant for developing quantum-computation and quantum-communication systems with
solid-state devices, and for research on the foundations of quantum theory.
In the Spring of 2010 this project will look for the first time into obtaining spin-resolved photo-luminescence signals from ensembles of donor-bound electron spins in ultra pure GaAs samples with very low Si doping. Your task is to participate in this research effort. In particular, you should collect data and report on the magnetic field dependence of spin splittings in the optical transitions. This is crucial for identifying the optical transitions that can be operated with a new quantum-optical control scheme.

8 Research group Theoretical Chemistry (Prof. Ria Broer) 8.1 and 8.2 (Joint project for two topmaster students) Effect of dimerisation on the band structure of (EDO-TTF)2PF6.

For technical reasons, the figures are not present in the description below.] EDO-TTF is a planar molecule with a p-electron system that extends above and below the plane of the molecule. In the crystalline material, EDO-TTF molecules stack to form columns. The p-MO’s of different molecules overlap to form p-bands.

The project entails the calculation of the band structure of the (EDO-TTF)2PF6 crystal at high and low temperatures. At high temperature the material is a metal, whereas at low temperature the material is an insulator. At high T one unit cell contains 2 planar EDO-TTF molecules and one PF6 molecule. At low T, the unit cell doubles, while two EDO-TTF molecules remain planar and and form a dimer, whereas the other two molecules become bent.

It is interesting to compare this system to polyacetylene (PA): (CH=CH-)n. In PA the p system extends along the molecular chain. One electron is being donated to the p system by each carbon atom. A possible geometry of PA is one where all carbon bonds are equal, somewhere between being double and single. Such a PA structure can be written as (CH)n with one carbon atom per unit cell. There is one half filled p MO per molecule and that gives rise to one half filled p band in the crystal. Therefore (CH)n would be a metal. But PA is not a metal. Dimerisation occurs and the carbon bonds are alternating, close to double C-C bonds and close to single C-C bonds. The unit cell doubles and it contains 2 carbon atoms. (Note the parallel with (EDO-TTF)2PF6 at low temperature here.) Now there are two p electrons in two p MO’s. In the crystal these form two p bands of which the lowest band is completely filled and the higher band is empty. This is the reason why PA is not a metal.

Calculations on the free molecule are in progress in the group, a first paper has been submitted for publication.

It would be interesting to find the band structures of (EDO-TTF)2PF6 at both temperatures. Can we find the a similar effect as in PA? What happens when we increase or decrease the dimerisaton in the low temperature crystal? These questions will be addressed with the B3LYP-DFT approach, using the CRYSTAL package.

One student would focus on the high T crystal. Can we explain the metallic phase? This student would also do some calculations on PA, for comparison.

One student would focus on the low T crystal. Does dimerisation occur? Does charge separation of bent and planar EDO-TTF molecules in the crystal, as suggested in the literature, indeed take place?

9 Research group Synthetic organic chemistry (Prof. Ben Feringa)

9.1 Molecular motors

[a project description including figures]

9.2 Molecular switches

[a project description including figures.]

10. Research group Single-Molecule Biophysics (Prof. Antoine van Oijen)

10.1. Watching proteins move on DNA

The Single-Molecule Biophysics group is a new group at Groningen University and focuses on the development and use of single-molecule tools to understand how proteins work. One of our goals is to study the interactions between proteins and DNA and how these interactions underlie a variety of important biological processes, such as DNA replication, repair, and recombination.

In this project, you will use state-of-the art fluorescence imaging techniques to visualize how individual, fluorescently tagged proteins move along stretched DNA molecules. In particular, you will study how proteins involved in gene expression are able to very rapidly locate specific sequences on the DNA (so-called promotors) by sliding along the DNA. By chemically modifying DNA molecules, you will be able to couple them at one end specifically to a glass surface. By combining this surface-coupling technology with microfluidics, you will be able to use hydrodynamic flow to stretch the DNA molecules. Fluorescently tagged proteins can now be introduced into the flow cell, excited by laser illumination, and their fluorescence emission visualized by a microscope and CCD camera. Analyzing the protein movement along the DNA will allow you to characterize the diffusional properties of the protein and its ability to search large portions of the DNA for the correct sequence. This project will allow you get hands-on experience with the many different experimental aspects of single-molecule biophysics: laser optics, microfluidics, fluorescence microscopy, image analysis, etc.

11. Research Group Physics of Nanodevices (Dr. Tamalika Banerjee)
Spintronics is an emerging field of science and technology that utilizes the electron spin for significantly enhanced or fundamentally new device functionality. Our current research focus is to investigate spin dependent transport and magnetism at the nanoscale in hithertho unexplored material systems. Half-metallic ferromagnetic materials will be probed as they exhibit almost complete or nearly 100% spin polarization and are interesting because of their exceptional electron correlation effects.

Our research combines exploratory fundamental studies of spin transport at the nanoscale in novel material systems using local probe techniques and solid state functional devices by:

-Harnessing the functional properties of oxide ferromagnetic materials and designing epitaxial oxide heterostructures

-Probing spin transport and spin torque induced magnetization dynamics in such epitaxial heterostructures

-Implementing Nano-fabrication and nano-characterization tools

11.1. Metal Spintronics
This experimental project is aimed to probe spin dependent transport in metallic spin valves using the unique capabilities and the local technique of Ballistic Electron Magnetic Microscopy. The student will have hands-on experience in the growth and fabrication of nanodevices using the state-of-art cleanroom facilities at the NanoLab Groningen. Magnetic imaging at the nanoscale along with spin dependent transport studies will yield valuable insight into theelastic and inelastic scattering andinterface contributions to spin dependent transmission in such metallic spin valves.

11.2. Oxide Spintronics

Here, new complex oxide material systems will be used to probe, for the first time, spin transport and spin torque induced non-equlibrium magnetization dynamics in them. This will be done by tuning the compositional and structural parameters as well as epitaxial strain in material system as La0.67Sr0.33MnO 3and their heterostructures. The student will use the clean room facilities at the NanoLab Groningen to fabricate spin transfer torque devices,both giant magnetoresistive and tunnel magnetoresitive nanopillars.

11.3. Graphite Spintronics
Here, graphite (few layers of graphene) will be used as a model system to fabricate spin valves to study spin transport properties in a direction perpendicular to the weakly bonded graphene sheets using the technique of Ballistic Electron Magnetic Microscopy. Recent successful demonstration of perfect spin transmission in a graphite nanostructure without any measurable loss of spin information has opened up differentinteresting avenues to study spin transport in this new material system.

11.4. Nanomagnetism
In this research project, the student will study magnetic properties of nanoscale magnetic elements fabricated using e-beam lithography and using Magnetic Force Microscopy. The effect of shape and size of magnetic elements on their magnetic configuration and the magnetostatic interaction between them will be studied. Nanoscale magnetic elements are of practical importance because of their possible applications in patterned recording media, spin transfer torque devices and Magnetic Random Access Memories (MRAM’s).

12. Research group Thin films and surfaces (Prof. Petra Rudolf)
12.1. Graphene - new production methods (making and characterizing)  more chemistry oriented
12.2. Graphene - new surface assembly methods (making and characterizing) - more physics oriented
12.3. organic-inorganic hybrids (making and characterizing) - see also talk by Paul Van Loosdrecht at Zernike Institute quarterly meeting on
Feb 2nd - more physics oriented
12.4. organic molecules on surfaces (deposition and STM study) - more physics oriented
12.5. molecular motors and switches on surfaces (grafting, excitation with light to reveal movement or switching) - - more chemistry oriented

Last modified:17 November 2017 5.21 p.m.