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OnderzoekZernike (ZIAM)OnderwijsTop Master Program in Nanoscience

NS194. Small research project -- projects for 2013 [now obsolete]

The available small research projects for 2013 are listed here. Please contact the supervisor mentioned in case you are interested in a project. First come, first served...

For contact information on all mentioned professors and groups see

1 Group: Micromechanics

Project 1.1

Supervisor: Prof. Patrick Onck

Nanoporous actuators

Nanoporous actuators can provide voltage-induced deformations of 0.1% strain at much lower voltages (1V) than conventional piezoelectric actuators (> 100V).
Because of the low voltage operating capability and small weight, nanoporous actuators can find application in precision manufacturing and medical devices.
The high surface to volume ratio of nanoporous metals is exploited to electrochemically inject charge on the metal surface. The injected charge changes the electronic distribution on the surface atoms, which results in an increase in atomic bond length, eventually giving rise to macroscopic deformation of the metal. The objective of this small research project is to predict the charge-induced strain in ordered nanoporous structures using molecular dynamics simulations, and to study morphological and topological effects on the overall voltage-induced deformation.

Project 1.2

Supervisor: Prof. Patrick Onck

Molecular modeling of transport through the Nuclear Pore Complex

The nuclear pore complex (NPC) is a large protein complex that is embedded in the membrane envelope surrounding the nucleus and transports hundreds of
proteins and nucleic acids in a selective manner. Despite its important biological role, the mechanism of selective transport of the NPC is not yet understood. A wide variety of different theories exists based on experimental observations regarding the interactions between central FG-Nup domain and transport factors. In the current work, we use coarse-grained molecular dynamics simulations to study the deformation of individual FG-nups as a function of their amino-acid sequence. The goal of this small research project is to study the collective behavior of the FG-nups when they are anchored to a substrate, forming thin polymer brushes.

2 Group: Photophysics and opto-electronics

Project 2.1

Supervisor: Prof. Maria Loi

Room-temperature synthesis of ZnO nanowire anodes for quantum-dots sensitized solar cells

Recently, a 12.3% solar energy conversion efficiency was achieved by zinc porphyrin dye sensitized mesoporouse TiO2 [1]. Mesoporous TiO2 is a well-known photoanode materials for dye-sensitized and quantum dots-sensitized solar cells, since TiO2 nanoparticle provides large surface area for dye and quantum dots adsorption [2] . However, low electron mobility and large amount of surface defects of TiO2 result in serious energy loss[3-4]. ZnO nanowires attracts much attention owing to their superior electron transport properties. Recently, ZnO NWs and hierarchical nanostructures ZnO NWs were successfully grown by chemical bath deposition (CBD) at room-temperature[5-6]. The excellent carrier transport properties and large surface area for dye absorption make nanostructures ZnO NWs be promising materials for quantum dots sensitized solar cells (QDSSCs). Therefore, in this work chemical bath synthesis of ZnO nanostructures are proposed as anodes for PbS quantum dots sensitized solar cells.

3 Group: Surfaces and thin films

Project 3.1

Supervisor: M. Stöhr

Surface-supported molecular nanoporous networks

The quest for miniaturization especially in microelectronics and magnetic data storage together with steadily increasing fabrication costs for devices built by the conventional “top-down” approach stimulates the search for alternative routes for the fabrication of ever smaller devices. The employment of synthetic supramolecular structures is such a possible alternative. In general, supramolecular structures are based on the self-assembly of molecular building blocks equipped with recognition moieties. The molecules interact via non-covalent interactions through these recognition moieties and in this way, the envisaged structure is formed.

In the present project, 2D supramolecular structures will be fabricated on metallic supports. The aim is the structural characterization of these molecular structures. In addition, the conditions, under which nanoporous structures are formed, shall be identified. All experiments will be conducted under ultrahigh vacuum conditions. The molecules are sublimed onto metallic single crystals (Au(111) or Cu(111)) and the structural investigations will be carried out by scanning tunneling microscopy and low energy electron diffraction.

4 Group: Optical physics of condensed matter

Project 4.1

Supervisor: Ron Tobey

Surface plasmon polaritons in superconducting oxides

Surface Plasmon Polaritons (SPP) are propagating electromagnetic excitations that are localized to the interface of a dielectric and a conductor. These modes are coupled electromagnetic waves and the plasma oscillations of free electrons in the metal. In conventional noble metals such as silver and gold, excitation can be readily achieved in the visible spectral regime, and can propagate for distances that are limited by the complex portion of the metal dielectric constant.

In this proposed short project, we will lay the groundwork for SPP generation in high Tc superconducting copper oxides where we try to couple the electromagnetic wave to the bath of condensed electrons. The project will proceed along several parallel paths:

  1. Experimental –

The student will construct a device for measuring SPP dispersion in the noble metals silver, gold and platinum. The device will be massively parallelized and acquire the entire spectrum and SPP dispersion relation in a single exposure.

  1. Modeling –

a.                   The student will calculate/model using Matlab the dispersion relation for SPPs in silver and gold and compare to that observed in the experiment above.

b.                 Once the modeling is proven successful, the student will input the dielectric functions of several copper oxide superconductors and predict an appropriate geometry for their generation and detection.

Project 4.2

Supervisor: Ron Tobey

The Graphene Auston Switch

Photoconductivity is the process by which an electrical current can be produced when photons strike a material. Under specific conditions, ultrafast pulses of electrical current can be generated by using ultrafast pulses of radiation. This device is called an Auston switch and can be used to generate fast pulses of current and far infrared radiation (Terahertz radiation).   For the past 20 years, Auston switches have relied on structures manufactured from gallium arsenide and gold.

However, new materials now open the possibility for fabricating Auston switches with ever better properties. In particular, the incorporation of Graphene into a switch device could open the door to increased current capacity, increased electron speed and mobility, and low dispersion, allowing us to propagate the current without distortions to the pulse shape.  

In the proposed short project, the student will construct a basic photoconductive switch based on Graphene and test the switch’s dispersive properties.   The project is largely technical in nature with the potential to fabricate a novel device. The student will learn photolithography techniques and ultrafast optics. They will subsequently test the device characteristics such as current carrying capacity and dispersion properties.

5 Group: Single-molecule biophysics

Project 5.1

Supervisor: Dr. Thorben Cordes (

Observing chemical reactions one molecule at a time (Spectroscopy, Chemistry & Photophysics)

Our group uses single-molecule fluorescence microscopy as a tool to monitor unsynchronized chemical reactions in real-time. In such a system, fluorescent molecules report on the state of a chemical substrate or catalyst. In this project, you will develop a novel assay to monitor a DNA-based catalytic chemical reaction. Here, the “reporter-dye” will only be fluorescent during the periods of chemical conversion. With the use of single molecule fluorescence techniques it is possible to monitor the reaction in real time and reveal subpopulations, which are otherwise hidden by ensemble averaging. Such an approach gives a direct access to the duration of the chemical process and hence provides unique insights into the studied catalytic reaction. Your task in the project will be the preparation, surface immobilization and spectroscopic characterization of the active catalyst/reporter-complex. Additionally, you will monitor single turn-over events in the presence of the reactive species using state-of-the-art single-molecule fluorescence microscopy. For this interdisciplinary research we expect a keen interest in laser-microscopy, single-molecule detection, and the will to perform some wet-lab work, i.e., surface chemistry & sample preparation.

Project 5.2

Supervisor: Dr. Thorben Cordes (

Closing upon binding or binding upon closing? – A single-molecule investigation of the substrate binding protein of OpuA (Spectroscopy, Biology & Biophysics)

ABC (ATP Binding Cassette) transporters are ubiquitous in cells of all three domains of life and represent the most abundant and diverse family of known transport proteins. Despite their importance we still lack a fundamental understanding of the dynamic conformational changes occurring in these molecular motors upon substrate binding and subsequently their transport. In this project you will contribute to our efforts to study the conformational equilibrium (open vs. closed state) of the substrate-binding domain of the bacterial membrane transporter OpuA, which is responsible for cell-volume regulation. You will also extend your study to other classes of substrate binding domains to investigate if there is a common mechanism in trapping substrates. To accomplish that you will develop novel single-molecule assays based on fluorophore quenching and Förster resonance energy transfer to monitor different conformational states. We offer a multidisciplinary project and expect a motivated student with a keen interest on biology that is willing to combine laser-microscopy and single-molecule detection with biochemical work.

Project 5.3

Supervisor:  Dr. Thorben Cordes (

Measuring multiple distances in protein complexes (Subjects: Optics, Programming & Spectroscopy)

Förster resonance energy transfer (FRET) is a powerful tool to study distance changes (at the range of 2-10 nm) in biological systems such as proteins, DNA or RNA. Our group is interested to identify conformational states of substrate-binding proteins of membrane transporters and also to characterize their relevance for the transport process. In this project you will setup a confocal microscope with multicolor excitation/detection to simultaneously monitor, up to three distances in a single protein complex. Your main tasks are (i) to built a confocal microscope with multi-color excitation (488/532/640 nm) and detection, (ii) to establish a software for alternating laser-excitation, i.e., rapid switching of laser excitation for three different colors on the µs-time-scale, and (iii) to test this method on fluorophore-labelled double-stranded DNA and proteins. We are looking for a student with interest in a highly interdisciplinary research project with a focus on optics built-up and lab-view programming with final test experiments on biological samples.

6 Group: Molecular dynamics

Project 6.1

Supervisor: Prof. Siewert-Jan Marrink

Computer simulation of gating of mechano-sensitive membrane channels

Mechanosensitive channels are small membrane proteins that sense the tension in the cell membrane. Once the tension gets above a certain threshold, the channels open. By this mechanism, bacterial cells protect themselves against hypoosmotic shocks. In this project you will use a state-of-the-art computer simulation technique, multi-scale molecular dynamics, to unravel the molecular details of this process. Everything in-silico, no need to clean up afterwards!

7 Group: Systems chemistry

Project 7.1

Supervisor: Prof. Sijbren Otto

Photo-controlling self-replication in dynamic combinatorial library

Self-replication and self-organization are often considered as the hallmarks of living systems. Self-replicating molecules are likely to have played an important role in the origin of life. To create de-novo life, one key step is the emergence of self-replicators from complex mixtures, a process that is still not understood. Dynamic Combinatorial Chemistry (DCC) provides us an opportunity to shed some light on this intriguing process. In a Dynamic Combinatorial Library (DCL), a mixture of continuously interconverting molecules is formed in a combinatorial way by linking building blocks together through reversible chemical bonds. All these library species will compete with each other for building blocks required for their own formation. The concentration of the various library members is governed by a thermodynamic equilibrium. Those species that have a lower energy level will be present in a larger concentration. If one of the library species can bind to copies of itself, this species will self-assemble and the equilibrium will be shifted, amplifying its concentration. In this way, the self-assembling library members are essentially self-replicating. The result is a self-assembling material that is also self-synthesizing, as the assembly process promotes the synthesis of the very molecules that assembl.1 From our previous studies we know that self-replication can be affected by environment changes. For example, controlling the strength of mechanic agitation may lead to the emergence of different self-replicators.2

In this project, we will study the influence of light on self-replication by irradiating the DCL under UV light. The library will be made from photo-switchable building blocks. On one hand, irradiation at different wavelengths will allow us to switch the building blocks between two isomers, increasing the species diversity of the library. On the other hand, this system may create a platform of producing self-synthesizing materials whose macroscopic morphology and mechanic properties may be precisely tuned by light. This will open a door of exploring novel materials.

The student is encouraged to contribute his/her own ideas to this project as it progresses. He/she will be trained in Chemical synthesis, 1H NMR measurement, HPLC-MS analysis, UV-irradiation equipment set-up and UV-vis measurements. Possible training on further experimental skills will depend on the results.

[1] J. Li, J. M. A. Carnall, M. C. A. Stuart, S. Otto Angew. Chem. Int. Ed. 2011, 50, 8384.

[2] J. M. A. Carnall, C. A. Waudby, A. M. Belenguer, M. C. A. Stuart, J. J.-P. Peyralans, S. Otto Science 2010, 327, 1502.

Project 7.2

Supervisor: Prof. Sijbren Otto

A self-assembled, unidirectional walker molecule

Synthetic molecular motors have experienced a well deserved rapid surge in popularity among scientist in recent years. Despite noticeable achievements in the field, extracting useful work from the motion of a molecular motor still poses a big challenge for nanotechnology. In contrast to chemistry, biology can do that efficiently: proteins like kinesin can efficiently transport cargo while moving along cytoskeleton, bacteria can sense chemical gradients and follow them thanks to flagella motors, Usain Bolt can complete a 100 m sprint in less than 9.6 s using actin and myosin proteins. In order to address nature's challenge, nanomotors have to be coupled to a track they can follow, their movement should be unidirectional and has to be controlled and powered by simple stimuli that do not require oscillatory changes in chemical composition of the environment.

In this project the walker molecule will constitute of a macrocycle self-assembled around the polymeric track. In order to move, the macrocycle will be equipped with peptide chains containing azobenzene moieties, conjugated with aldehyde groups. Aldehydes can react with amines on the polymer in a reversible manner, forming imine bonds. Azobenzenes substituted with imines exhibit different spectroscopic properties than the ones substituted with aldehydes, therefore it should be possible to isomerize them into shortened Z form while on the track and to the E form while detached, making the macrocycle "pull" the polymer. Over the course of the project, the student will complete a short organic synthesis, a peptide synthesis with an automated synthesizer, analyze switching properties of aldehyde- and imine-substituted azobenzenes and study the movement of the self-assembled peptidic macrocycle along the polymer using spectroscopic techniques.

8 Group: Physics of nanodevices

Project 8.1

Supervisor: Dr. Tamalika Banerjee (

Hot electron transport across a Graphene/Silicon Schottky interface

We have fabricated Graphene/Silicon Schottky interface and study vertical transport in graphene. Such studies go beyond the demonstrated lateral charge and spin transport in graphene and reveal new transport characteristics intrinsic to graphene and sheds light on the influence of extrinsic parameters as charge puddles to vertical transport in graphene. The current focus is on studying vertical transport in graphene using hot electrons at higher energies where transport can be markedly different from that close to the Dirac point. These studies will also be done at the nanoscale in addition to probing transport in macroscopic junctions.

The student is expected to join the current research efforts to extensively study local scale transport in such novel device schemes where hithertho unexplored transport characteristics in graphene are expected to emerge. There is a possibility to gain hands-on experience in the growth and fabrication of such nanodevices using the facilities available at NanoLab Groningen (evaporation, sputtering, UV and e-beam lithography) and at the Physics of Nanodevices group (BEEM and standard magnetotransport measurements) in this small research project.

Project 8.2  

Supervisor: Dr. Tamalika Banerjee (

Spin transport in all-oxide heterojunctions

After the successful demonstration of electron transport in a strongly correlated material as LaSrMnO3 and the extraction of relevant transport parameters, we are now embarking on yet another challenging topic viz. of studying spin transport in LSMO in oxide spin valves. Our study is expected to yield fundamental insights into the physics of spin transport in such spin valves and the influence of strong correlation to spin transport in such half metals. Further, our work has now been successfully extended to other oxide systems as ruthenates (Strontium ruthenate) and multiferroics (BiFeO3) where the growth parameters are tuned to carry out magnetic field and temperature dependent studies in oxide devices.

The student will work closely with the Ph.D student(s) involved in this project which is also done in collaboration with the SSME group at the Zernike Institute. The growth and fabrication infrastructure and device fabrication tools available at NanoLab Groningen will be made available as will be the characterization and measurement techniques needed for this small research project.

Project 8.3

Supervisor: Dr. Tamalika Banerjee (

Spin transport in topological insulator materials

A new research direction where the thrust is on studying spin transport in topological insulators of Bi2Se3 and Bi2Te3. The samples are obtained from collaboration with the Rutgers University, USA. The non-local scheme will be used to study charge and spin transport in these materials with the aim to estimate the spin diffusion length in the surface states of these materials. The surface states in the TI are immune to any surface impurities, thus tunnelling contacts will be used to inject non-equlibrium carriers, without modifying their transport characteristics.

The student will work closely with the current research team and this work will be done in collaboration with the OCMS group. The relevant fabrication infrastructure and measurement techniques exist within the NanoLab Groningen and the Zernike Institute for Advanced Materials.

Project 8.4 and 8.5
Supervisor: Prof. C.H. van der Wal (c.h.van.der.wal@rug)

Quantum optics with electron spins in semiconductor nanodevices
(2 topmaster projects)

These projects are in an experimental research effort that explores the fundamental physics of how quantum information in an optical pulse can be stored in a quantum memory. This memory 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. For the spring of 2013 we look for student participation in these two experiments:

1) Optical characterization of a micro-photonic device for use as a quantum memory

The transient nature of photons poses a challenge for the next generation of optical communication devices that operate according to
quantum mechanical principles. Fortunately, the invention of optical quantum memory devices ensures that photons can be coherently stored and manipulated. We have developed a highly novel platform to meet this challenging goal, which is based on the storage of photons in an
ensemble of electron spins in pure semiconductor (Silicon-doped GaAs).
Furthermore, since this type of quantum memory is fabricated in an optical waveguide on a microchip it is both miniature and compatible
with other microchip devices, such as photo detectors and lasers. You will be responsible for the detailed optical characterization of these
waveguides. In particular, the light propagation of higher transverse modes through the waveguide will be studied experimentally and numerically.

2) Laser cooling of nuclear spins to milli-Kelvin temperatures

The interaction of nuclear spins with electron spins has recently become an important focus for the ever-growing field of quantum optics with
solid-state physics. We use a material system that exploits the spin states of an electron that is bound to a donor atom in a very pure
semiconductor (Silicon-doped GaAs). The preservation of long-lived spin states (e.g., spin up and spin down states) is a challenging goal due to the uncontrolled effects of noisy nuclear-electron spin coupling. This coupling limits the generation of coherent quantum superpositions of
these two spin states, and thus makes the operation of quantum memories inefficient. In the context of your TopMaster project, you will
participate in our first experiments to cool nuclear spins to milli-Kelvin temperatures such that their coupling to the electron spins
is negligible. In particular, the cooling scheme will employ three state-of-the-art laser systems to control both electron and nuclear spin

9 Group: Solid state materials for electronics

Project 9.1

Supervisors: Prof. Thomas Palstra and Dr. Graeme Blake

Structural, magnetic and dielectric properties of organic-inorganic hybrid materials

Organic-inorganic hybrid materials consist of transition metal halide layers separated by organic molecules. The two components are held together by hydrogen bonding. These hybrids combine the robust electronic and magnetic properties of inorganic materials with the structural flexibility of organics. They are of interest in various fields of research such as multiferroics and highly anisotropic magnetic systems. Some of the most interesting compounds in this class of materials are those based on perovskite-like MCl4 layers where M = Cr, Mn, Fe and Ni. The type of organic ligand appears to give rise to large differences in the magnetic and dielectric behavior, for reasons that are not yet understood.

This project aims to provide insight into the correlation between structure, magnetic and dielectric properties and will involve the following aspects:

-Crystal growth from solution.

-Powder and single-crystal X-ray diffraction as a function of temperature to determine precise details of crystal structures and phase transitions, in conjunction with differential scanning calorimetry.

-Measurement of the magnetic and dielectric properties as a function of temperature and applied magnetic field to study magnetic ordering and possible ferroelectric order.

Project 9.2

Supervisors: Prof. Thomas Palstra and Dr. Graeme Blake

Synthesis, structural, magnetic and dielectric properties of potential new multiferroic materials

Multiferroic materials, in which magnetism and ferroelectricity coexist and are intimately coupled, have the potential to form the basis of future high-speed information storage technology as well as smart devices such as magnetoelectric sensors. The goal of research in this area is to realize multifunctional materials in which electric and magnetic moments can be manipulated by magnetic and electric fields, respectively. However, there are still rather few multiferroics known and the magnetoelectric (ME) coupling in many of them is weak. It is therefore necessary to search for new families of materials that exhibit multiferroic properties.

In this project crystals of potential new multiferroic materials will be grown in which the magnetic cations are arranged on a triangular network. Such an arrangement is predicted to give strong ME coupling [1]. We will focus on compounds that contain mixed-valent iron cations [2]. The chemical synthesis will be carried out hydrothermally, where crystals are grown from aqueous solution under elevated temperature and pressure. The structures of the crystals will be investigated by X-ray diffraction. Both the magnetic and dielectric properties will be studied as a function of temperature and applied magnetic field. This project will provide hands-on experience of many of the experimental aspects of solid-state chemistry and condensed matter physics.

[1] K.T. Delaney, M. Mostovoy, and N.A. Spaldin, Phys. Rev. Lett. 102, 157203 (2009).

[2] G. Paul, A. Choudhury, E.V. Sampathkumaran, and C.N.R. Rao, Angew. Chem. Int. Ed. 41, 4297 (2002).

Project 9.3

Supervisors: Prof. Thomas Palstra and Dr. Graeme Blake

Potential new antiferromagnetic half-metals

Spintronics applications, where information is carried by the spins of electrons, require materials in which there is metallic conduction for only one spin channel, while the other is insulating. Such materials are known as half metals. Useful half metals are rather scarce because ferromagnetic ordering above room temperature is generally required. However, a new class of half metals has been theoretically predicted in which there should be antiferromagnetic ordering above room temperature. These materials have composition (Cu1-xMx)AlS2, where M is another transition metal.

In this project attempts will be made to synthesise powder or single crystal samples of materials with the chemical compositions predicted to be half-metallic. Both their magnetic and electrical transport properties will then be studied as a function of temperature and composition x.

Project 9.4

Supervisors: Prof. Thomas Palstra and Dr. Graeme Blake

Thermopower of thermoelectric delafossite material

Thermoelectric materials potentially play an important role in waste heat recovery applications in a resource-limited world, especially when a significant amount of waste energy is in thermal form. Thermoelectrics can directly convert thermal energy into electrical energy without moving parts. CuCrO2 delafossite has hexagonal layered structure in which Cu+ layers and CrO2 triangular layers are alternatively stacked along c-axis. This layer structure leads to high electrical conductivity s and high Seebeck coefficient S, resulting in large thermopower sS 2. Increasing thermopower of thermoelectric materials is one of the targets of thermoelectric research. The project aims to study thermopower of CuCrO2 at different crystallite and particle sizes. It will cover the following aspects:

-         Improving Labview measurement program

-         Scanning electron microscopy to image the particle shape and size

-         Measurements of electrical conductivity and Seebeck coefficient as a function of temperature.

Project 9.5

Supervisor: Prof. Thomas Palstra

Interplay of heat and spin: Spin seebeck effect

Electron has two degrees of freedom: charge and spin; the flow of spin angular momentum is known as a spin current. The spin current can flow in ferromagnetic metals as well as in insulators where the charge current cannot flow due to absence of free electrons. Recently discovered application of “pure spin currents” is the spin seebeck effect where electrons have shown to not play a role in the spin conduction. In this effect, heat gradients transform into electrical power [1], have the potential to form the basis of future magnetic heat engines and can be used for energy harvesting. When a ferromagnet is heated, a spin current is generated in a certain direction and can propagate through several millimeter length scales in a ferromagnet. These spin currents transfer the angular moment and create an electrical voltage due to the inverse spin Hall effect in the Pt layer deposited on top of the ferromagnet. The goal of research in this area is to realize suitable materials in which heat can efficiently couple to the spin currents and thermopower can be improved. However, there are still rather few materials known in which spin seebeck effect have been realized. It is therefore necessary to search for new families of materials that exhibit spin seebeck effect.

In this project low dimensional spin ladder compound will be used and spin seebeck effect would be studied in different device geometry: longitudinal [2] and transverse [3] configurations. The deposition of metals on ladder compound and other device fabrication steps will be carried out in clean-room and the physical properties measurement system (PPMS) will be used to perform room temperature and low-temperature measurements at various fields. Both in-plane and out-of-plane response of sample as a function of thermal gradient would be checked. This project will provide hands-on experience of many of the experimental aspects of device fabrication and condensed matter physics.

[1]. G. E. W. Bauer, E. Saitoh, B. J. van Wees, Nature Mater. 11, 391, (2012).

[2]. K. Uchida, H. Adachi, T. Ota, H. Nakayama, S. Maekawa, E. Saitoh, Appl. Phys. Lett. 97, 172505, (2010).

[3]. K. Uchida, S. Takahashi, K. Harii, J. Ieda, W. Koshibae, K. Ando, S. Maekawa, E. Saitoh, Nature, 455, 778, (2008).

Project 9.6

Supervisor: Prof. dr. B. Noheda (Solid State Materials for Electronics)
Daily supervisor: Dr. Sylvia Matzen

Atomically flat surfaces for layer-by-layer growth

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. This limits the amount of crystals that one can use as substrates for epitaxial growth of the best quality, since only those crystals whose surfaces can be made atomically flat are interesting. Devising methods to attain this in different materials is, therefore, of much importance. In this respect, the best substrates to grow perovskite oxides onto are SrTiO3 and DyScO3 . With a proper chemical and thermal treatment, the (001) surface of these crystals can become atomically flat.

In this project, the treatment and AFM imaging of SrTiO3 and DyScO3  substrate crystals will be performed. Different surfaces will be investigated. The goal of the project is to obtain insight on the energetics and the kinetic processes that give rise to atomically flat surfaces in different materials. That rarionale should help to propose and implement chemical and/or thermal treatments for other interesting crystals for which the treatment is currently unknown.

10 Group: Biomolecular chemistry

Project 10.1

Supervisor: Prof. Gerard Roelfes (; web:

A detection platform for small molecules based on a synthetic protein channel

Small molecules are omnipresent in biology, and mediate communication between all kingdoms of life. Understanding the distribution of these molecules with respect to space and time is needed to decipher the environment a cell experiences, which can explain why a cell acts in a certain way. Current techniques in biology cannot be used to detect a wide range of small molecules with high spatiotemporal resolution, without labeling the molecules in question. Previously, we have developed a concept that enables the detection of a wide range of neurotransmitters using biological nanopores. The neurotransmitters are observed on the single-molecule level, and multiple different compounds can be followed. Because proteins are not easy to modify and are as a result less modular, an equivalent synthetic pore is required that can surpass the successful concept of analyte detection with biological nanopores. In this project, a synthetic designer peptide that can form transient pores will be modified so that it will form open stable pores. In the next stage, analyte interacting groups will be incorporated in the pore. Upon binding the analyte within the pore, a read-out is generated in a planar lipid bilayer set-up. Skills that will be acquired during this project are peptide and organic synthesis, hplc, mass spectrometry, and biophysical techniques such as planar lipid bilayers.

11 Group: Polymer chemistry

Project 11.1

Supervisors: Dr. Kamlesh Kumar (, 050-3636444 ) and Prof. Katja Loos

Synthesis of P2VP-block-amylose copolymer

Novel rod-coil copolymers with amylose moieties will be synthesized by a combination of 'traditional' synthetic approaches and enzymatic polymerization. Due to hydrophobic cavity, amylose is able to form inclusion complexes with a wide variety of hydrophobic guest molecules. This ability to form inclusion complex of amylose can be combined with self-assembly of block copolymers to obtain more advanced structure, by attaching amylose as the second block with poly(2-vinyl pyridine). Maltoheptaose, which acts as a recognition unit for the enzymatic synthesis of amylose, can be covalently attached to poly(2-vinyl pyridine) via reductive amination. The resulting product, poly(2-vinyl pyridine)-b-maltoheptaose, can be used as a primer for the subsequent enzymatic polymerization of amylose using glucose-1- phosphate (G1P) as a monomer. The enzyme (potato phosphorylase) transfers a glucose unit from glucose-1-phosphate to non-reducing end of maltoheptaose forming alpha-(1→4) glycosidic linkages in amylose chain. The characterization of the product includes GPC (gel permeation chromatography), 1H-NMR (nuclear magnetic resonance), FTIR (Fourier transform infrared spectroscopy), UV/VIS spectroscopy, and XRD (X-Ray diffraction). Period (        Research Plan        
15.02.13 - 28.2.13

(15 days)        Acquainting laboratory apparatus        
01.03.13 - 30.04.13

(2 months)        Synthesis and characterization of P2VP-block-amylose copolymer        
01.05.13 - 31.05.13

(1 months)        Data analysis, discussions and writing of the results    

12 Group: Theoretical chemistry

Project 12.1

Supervisors: Msc. H. de Gier, Prof. R. Broer and Dr. R.W.A. Havenith

Excited state dipoles

Organic photovoltaics have distinct advantages over inorganic ones. However, at the moment, organic photovoltaics are not very efficient. One bottleneck in organic photovoltaics is the generation of free charge carriers from excitons (bound electron-hole pair). Recently, it has been suggested that a better electron-hole separation in the excited state facilitates charge separation [1,2]. A probe for this charge separation is the change in dipole moment upon excitation. This change in dipole moment can be very dependent on the ground state conformation of the polymer. In this project, the change in dipole moment for a set of molecules (Scheme 1) will be calculated as a function of conformation, together with the exciton binding energy. The study will reveal whether this correlation indeed exists, and will show its dependence on conformation.

[1] B. S. Rolczynski, J. M. Szarko, H. J. Son, Y. Liang, L. Yu, L. X. Chen, J. Am. Chem. Soc. 134 (2012), 4142-4152.

[2] B. Carsten, J. M. Szarko, H. J. Son, W. Wang, L. Lu, F. He, B. S. Rolczynski, S. J. Lou, L. X. Chen, L. Yu, J. Am. Chem. Soc. 133 (2011), 20468-20475.

Project 12.2

Supervisors: Andrii Rudavskyi, Ria Broer

Extracting the HS-LS energy splitting in spin crossover materials by combining experimental and theoretical techniques

Spin crossover materials are transition metal based molecular systems that may remain in both a high spin (HS) and a low spin (LS) state for sufficiently long times. HS-LS energy splitting is one of the main parameter that determines lifetimes of the two states, so in order to control lifetimes of the metastable states one has to be able to control energy difference between the two states.

Experimentally the HS-LS splitting parameter is not always available. Moreover, it is also hard to predict the HS-LS energy splitting using a computationally feasible method such as density functional theory. Expensive wave function based methods give better results but they are still quite sensitive to the chosen geometry of the systems.

HS-LS energy difference can also be extracted from temperature dependence of the HS-LS relaxation rate. It has been shown 1 that in the single mode approximation the transition rate depends on the thermally averaged Frank-Condon factor, a second order spin-orbit coupling matrix element 2 1 .

The single mode approximation does not always work, thus one has to develop similar procedure for the case when many modes participate in a transition process. By using a time-dependent formalism to evaluate the Fermi Golden rule expression for the intersystem crossing transition rate one is able to derive an analytical expression for the rate 3 . The latter contains readily available information about the system, such as equilibrium geometries and vibrational frequencies for initial and final states, as well as adiabatic energy difference between the states. The expression for the transition rate takes into account all vibrational modes of the system and thus it goes beyond single-mode approximation. Within the latest version of the program, thermal averaging over the vibrational modes of the initial electronic state became possible. Thus by investigating temperature dependence of the calculated transition rate and comparing it to the experimental data it will now be possible to extract HS-LS energy splitting for those systems for which single-mode approximation is not valid. The goal of the project is to perform for the first time such calculations for a relevant spin crossover compound.

          (1)       Hauser, A.; Enachescu, C.; Dakua, M. L.; Vargas, A. Coord. Chem. Rev. 2006, 250, 1642.

          (2)       Buhks, E.; Navon, G.; Bixon, M.; Jortner, J. J. Am. Chem. SOC 1980, 102.

          (3)       Marian, C. M. Advanced Review 2011, 00, 1.

Project 12.3

Supervisor: Dr. R.W.A. Havenith

Möbius aromaticity

The presence of an odd number of out-of-phase overlaps in delocalised p orbitals of cyclically conjugated, closed shell systems, inverts the Hückel 4n/4n+2 rule: a system with 4n electrons would be stabilised (aromatic), whereas the 4n+2 system would be destabilised (anti-aromatic). This effect was related to the Möbius strip topology. An organic system that is supposed to be Möbius aromatic is the C9H9 + cation [1]. Other molecules that show possible Möbius aromaticity are metallacycles (Scheme 1). The latter molecules may become Möbius aromatic depending on which d-orbitals are involved in the π-electron delocalisation. In this project, the aromaticity of the C9H9 + ion and metallacycles will be studied. One defining property for aromaticity is the ability of a molecule to sustain a diatropic ring current induced by an external magnetic field. Therefore, the induced current density by an external magnetic field will be calculated for these systems, and a detailed analysis of this induced current density in terms of orbital contributions will show whether these systems show Möbius aromaticy and it will reveal the role of the d-electrons in this delocalisation.

[1] M. Mauksch, V. Gogonea, H. Jiao, P. von R. Schleyer, Angew. Chem. Int. Ed. 37 (1998), 2395-2397.

[2] M. Mauksch, S. B. Tsogoeva, Chem. Eur. J. 16 (2010), 7843-7851

13 Group: Polymer chemistry and bio-engineering

Descriptions of the following three projects, all supervised by Prof. Herrmann, are available directly from him.

Projct 13.1

Selection of short peptides as asymmetric catalysts by phage display

Project 13.2

A DNA origami ion channel

Project 13.3

Fabrication of new antibiotics with the help of aptamer shields

Last modified:17 November 2017 1.59 p.m.