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OnderzoekZernike (ZIAM)OnderwijsTop Master Program in Nanoscience

NS194. Small research project -- projects for 2015

Last update 30 Jan. 2015, 17:45 hrs (maybe very few extra projects will still come with some delay)

The available small research projects for 2015 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 the Zernike Institute web site.

1 Group: Computational Physics

Project 1.1

Supervisor(s): Profs H.A. DeRaedt and D.G. Stavenga

Nanophotonics of bird feathers

Background: The feathers of many birds, particularly birds of paradise and hummingbirds, are colored by nanophotonics. Photonic crystals consisting of stacks of melanin rodlets, often with an air core, are periodically arranged to create extreme iridescence.

Project: The aim is to explain the feather’s photonic and spectral properties from the structuring of the feathers, which strongly depends on the bird species. The experimental methods involve microspectrophotometry, imaging scatterometry, angle-dependent reflection measurements, and Jamin-Lebedeff-interference microscopy. The data are interpreted with computational methods, specifically matrix-transfer methods and the FDTD (Finite-Difference Time-Domain) method.

Literature :

Wilts BD, Michielsen K, De Raedt H, Stavenga DG (2014) Sparkling feather reflections of a bird-of-paradise explained by finite-difference time-domain modelling. Proc Natl Acad Sci USA 111, 4363-4368

Stavenga DG (2014) Thin film and multilayer optics cause structural colors of many insects and birds. Mat Today Proc 1S:109-121

Stavenga DG, Leertouwer HL, Osorio DC, Wilts BD (2014) High refractive index of melanin in shiny occipital feathers of a bird of paradise. LSA, in press

2 Group: Theory of Condensed Matter

Project 2.1

Supervisor(s): Dr. Thomas la Cour Jansen and Ana V. Cunha

Dynamics in Perovskite solar cell materials

Background: Perovskite solar cells have emerged as a promising new possibility for converting sunlight into electric power. These materials are hybrid materials containing interacting inorganic and organic components. The organic ions have recently been demonstrated to rotate on two different timescales using non-linear optical experiments [1]. Modeling in our group has confirmed the experimental findings, however, this modeling rely on expensive ab initio molecular dynamics simulations. This method is computationally too demanding for studying the role that the organic ion rotation may play in the solar cell. A new model needs to be established to allow such research.

Project: A classical molecular dynamics model will be developed, tested and possibly improved to allow a description of the findings in the non-linear optical experiments and previous high-level ab initio molecular dynamics simulations. The new description of the organic ion dynamics in hybrid solar cells will allow simulating a large number (>100) of unit cells as compared to ~8 unit cells in previous models. These new simulations will enable the study of collective organic ion dynamics and may in the future be used to study the role of the organic ions in the solar cells.

Further Information e-mail:


[1] Bakulin et al. Real-Time Observation of Organic Cation Motion in Methylammonium Lead Iodide Perovskites, in preparation

3 Group: Membrane Enzymology

Project 3.1

Supervisors: Prof. Bert Poolman and Dr. Christoffer Åberg (daily)

Anomalous Motion in the Bacterial Membrane

The Brownian motion paradigm (originally pioneered by Einstein, Smoluchowski, Langevin and others) has dominated the thinking on molecular motion within the physical sciences for a long time, and is now routinely applied also in the life sciences [1]. While Brownian behavior is in a sense typical (a statement that may be made quite precise mathematically), there are a number of systems which exhibit anomalous behavior. It is now emerging that motion within the bacterial cell may be one of them [2,3], though a clear consensus is yet to be reached.

The aim of the present project is to investigate the type of motion in the plasma membrane of Escherichia coli, using fluorescently-labeled membrane proteins. Time-lapse fluorescence microscopy of cells can be utilized to follow single proteins, and observables such as mean square displacements allows the identification of the type of motion. Moderate computational analysis of the resulting data will be required.

Potential extensions include testing other proteins in the same bacterium; another type of bacterium or microorganism; or studying how the type of motion is modulated by control parameters such as osmotic stress, metabolic activity [3] or growth phase.


1.   Frey, E. & Kroy, K. Brownian motion: a paradigm of soft matter and biological physics. Annalen der Physik 14, 20–50 (2005).
2.   Golding, I. & Cox, E. C. Physical nature of bacterial cytoplasm. Phys. Rev. Lett. 96, 098102 (2006).
3.   Parry, B. R. et al. The bacterial cytoplasm has glass-like properties and is fluidized by metabolic activity. Cell 156, 183–194 (2014).

Project 3.2

Supervisors: Prof. Bert Poolman and Dr. Christoffer Åberg (daily)

Diffusion-Limited Reactions in Confined Geometries

The cell depends on the existence of a vast and complex network of chemical reactions to sustain life. The analysis of such biochemical reactions is based upon structurally simple rate equations, whose constants are typically taken from experiments. The fundamental theoretical understanding was initiated by Smoluchowski over a century ago, and in its present state describes the reaction rate in terms of an intrinsic rate modulated by the diffusional motion of the reactants towards each other [2]. Recently, it has been shown that in some cases diffusion not only modifies the rate constants, but also the actual reaction scheme[1].

The aim of the present project is to investigate how these recent results are modified when the diffusional transport occurs within a confined geometry, such as a living cell. Exemplar reaction schemes and geometries of increasing complexity will be investigated, and key limits taken to identify simple and transparent results.

This is a theoretical project and would be investigated using a combination of analytical approaches coupled to numerical calculations. Simple numerical simulations may be needed for extending the results to more complicated cases.

Potential extensions include investigating how the results are modulated if the diffusional transport is anomalous, considering how the presence of interactions among the reactants transform the rates or applying the formalism to a specific experimental system.

1.   Gopich, I. V. & Szabo, A. Diffusion modifies the connectivity of kinetic schemes for multisite binding and catalysis. PNAS 110, 19784–19789 (2013).
2.   Keizer, J. Diffusion effects on rapid bimolecular chemical reactions. Chemical Reviews 87, 167–180 (1987).

Project 3.3

Supervisors: Prof. Bert Poolman and Paul Schavemaker (

Protein diffusion and surface properties and their relation to the physical chemistry of biological cells

Biological machineries that are present in cells are influenced in their properties by the nature of the cytoplasm. A well-known example of such influence is the excluded volume effect (or macromolecular crowding). The cytoplasm is full of macromolecules that occupy a certain volume of the space. So if you want to put another macromolecule in you have less space to do so. This has consequences for the thermodynamic and kinetic properties of these biological machineries.

In the past two unexplained observations have been made that have possible implications for our understanding of the cytoplasm. (1) Escherichia coli cells that are exposed to high salt concentrations expel water and as a result the relative excluded volume increases. This leads to a decrease in protein diffusion rates. If these same cells however are slowly exposed to higher salt concentrations the relative excluded volume is also increased but the diffusion coefficient is not decreased. (2) The diffusion coefficient of proteins drops more rapidly with relative cell volume in Lactococcus lactis than in Escherichia coli.

We want to find out whether interactions between macromolecules have anything to do with these phenomena. At the moment we are studying the effect of surface charge on the diffusion coefficient of a fluorescent protein GFP. We have various variants of GFP with differences in surface charge. We express these variants in E. coli cells and determine the diffusion coefficients by fluorescence recovery after photobleaching (FRAP).

In this project we will measure diffusion coefficients under variety of physiological conditions that impact the composition of the cytoplasm (including the macromolecular crowding). In addition we will think about (1) the relation between surface properties and the two phenomena mentioned (for example whether the rapid drop of diffusion coefficient in L. lactis is due to a higher stickiness of the L. lactis proteins as compared to E. coli proteins), (2) whether something else is giving rise to these strange observations and (3) whether mistakes have been made in the experiments that revealed the two phenomena.

Konopka MC et al. (2009) Journal of Bacteriology, Vol. 191, No. 1, p. 231-237.
Mika JT, Schavemaker PE et al. (2014) Molecular Microbiology, Vol. 94, Iss. 4, p. 857-870.

Project 3.4

Supervisor(s): Paul Schavemaker ( or Bert Poolman (

Single-molecule studies on the in vivo assembly of ABC transporters

NOTE, this is in fact a 45 EC project, discuss the 13 EC options with the supervisors
BC transporters are protein complexes that are present in all domains of life. They transport molecules over membranes in an ATP-dependent manner. They generally consist of two transmembrane domains and two nucleotide-binding domains (NBDs) on the cytoplasmic side of the membrane. Some of these transporters also have a substrate-binding domain on the outside of the membrane. In this project, we want to study the assembly of these protein complexes in the membrane. More specifically, we are going to look at the rate of binding of the nucleotide binding domains to the transmembrane part. Questions are: What is the time between the binding events of the two NBDs? What is the time between membrane insertion of the transmembrane domains and the binding of NBDs? We want to look at these events on the level of single molecules and complexes. We will strategically label the various ABC protein domains with fluorescent proteins so we can observe their behaviour in live cells by fluorescence microscopy. (Experimental) Techniques - Molecular cloning to introduce fluorescent tags - Cultivation of cells - Fluorescence microscopy on single molecules in cells - Semi-automated analysis of microscopy images - Uptake assays to measure transport activities

The biological system of interest: Slotboom DJ (2014) Structural and mechanistic insights into prokaryotic energy-coupling factor transporters. Nature Reviews Micobiology.
Example of single molecule fluorescence microscopy: Yu J, Xiao J, Ren X, Lao K, Xie XS (2006) Probing Gene Expression in Live Cells, One Protein Molecule at a Time. Science.

4 Group: Solid State materials for Electronics (SSME)

Project 4.1

Supervisor(s): Prof. Thom Palstra, daily supervisor Machteld Kamminga

Chemical tuning of organic-inorganic hybrid materials; crystal structure and dielectric properties.

Organometal halide perovskites, such as CH3NH3PbI3, have recently attracted great attention as they are promising for highly efficient and easily processable solar cells. Implementation of CH3NH3PbI3 as the absorber material has obtained high power-to-electrical conversion efficiencies of over 19% in simplified planar heterojunction solar cell devices [1]. However, most of current research has mainly been done via an engineering approach with the focus on device physics, while the working principle is still unknown. Therefore, we focus on the organometal halide perovskite materials from a solid state chemistry point of view.

These organometal halide perovskites are hybrid structures that contain inorganic metal halides and organic ligands that are held together by hydrogen bonding. These hybrids combine the robust electronic properties of inorganic materials with the structural flexibility of the organics. Changing the chemical composition of these hybrid materials will change its structural parameters, such as distances and angles that define the perovskite structure.

This project aims to gain insight into the correlation between the crystal structure and dielectric properties and will involve the following aspects:
·         Crystal growth of various hybrid materials.
·         Single-crystal X-ray diffraction as a function of temperature to determine the crystal structures in detail, accompanied by differential scanning calorimetry to determine phase transitions.
·         Measurement of the dielectric properties as a function of temperature.

[1]       Zhou et al., Science, 345 (6196), 542-546 (2014).

Project 4.2

Supervisor(s): Dr. Graeme Blake

Synthesis and characterization of an environmentally benign thermoelectric material

Thermoelectric (TE) materials are attracting increasing attention as a means of converting waste heat to electricity. Unfortunately the best performing TE materials generally contain toxic or scarce elements such as lead and tellurium. Therefore the search for environmentally benign and abundant TE materials is of great importance.

Mg2Si is a promising TE candidate and is comprised of non-toxic and abundant elements. The energy conversion efficiency of TE materials is directly related to the thermoelectric figure of merit zT, which is given by the equation =S^2 Tσ/κ , where S is the Seebeck coefficient, σ is the electrical conductivity and κ is the thermal conductivity. The creation of TE materials with nanoporous / mesoporous structures offers a route to decrease κ by scattering long wavelength phonons. In this project, attempts to synthesise mesoporous Mg2Si will be made. This has not yet been reported in the literature so there will be an emphasis on developing novel chemical synthesis routes. The structure and purity of the resulting samples will first be characterized by X-ray diffraction. The pore size and chemical composition will be analyzed by SEM/TEM and EDX. Finally, the temperature dependence of the thermoelectric parameters will be investigated.

Project 4.3

Supervisor(s): Dr. Graeme Blake

High-performance thermoelectric materials

Thermoelectric (TE) materials are of interest for both the conversion of waste heat to electrical power and in solid-state cooling systems. However, the efficiency of current TE devices is not good enough to be cost effective for widespread commercial applications. Improvements in the TE properties of basic materials are still necessary.

Some of the best performing TEs are derived from group IV-VI semiconductors such as GeTe and PbTe. It has recently been reported in the scientific literature that incorporating small concentrations (1-2%) of magnetic rare-earth elements such as Ce, Yb and Dy in IV-VI semiconductors can result in a remarkable improvement in their TE properties. The reasons for this are still unclear and we are carrying out systematic studies of the effects of such substitutions.

We are also investigating the potential of more earth-abundant selenium as a replacement for the scarce element tellurium. GeSe is particularly promising but thus far has not been studied much in the scientific literature regarding its TE properties.

This project will initially involve the chemical synthesis of powder and single crystal samples of various promising group IV-VI semiconductor TEs derived from GeTe and GeSe. X-ray diffraction will be used to determine their crystal structures and will be complemented by high-resolution electron microscopy. The TE properties will be characterized by means of electrical resistivity, thermopower and thermal conductivity measurements. This project will provide hands-on experience of many of the experimental aspects of solid-state chemistry.

Project 4.4

Supervisor(s): Dr. Graeme Blake, Prof. Thomas Palstra

Synthesis of novel room temperature magnetic insulator

Magnetic insulators have the unique property of being able to generate pure spin currents due to the absence of free electrons [1]. They have great potential for not only transport [2] but also for magnetic storage spintronics devices. However, there are very few room temperature magnetic insulators. Cu2OSeO3 (Tc = 64 K) has attracted considerable attention due to the coexistence of ferromagnetic and ferroelectric orders. It has been predicted that by changing the growth conditions of Cu2OSeO3, the structure can be modified to form a new compound with room temperature magnetism.

In this project, the chemical vapour transport method will be used to grow single crystals of the new room-temperature magnetic compound related to Cu2OSeO3. The quality and structure of the crystals will be determined using single crystal X-ray diffraction. The magnetic behaviour of the crystals will be studied using a SQUID magnetometer. The electrical properties of the crystals will be analyzed using the physical properties measurement system (PPMS) as a function of temperature in various magnetic fields. This project will provide hands-on experience of many of the experimental aspects of crystal growth and various characterization techniques.

[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).

5 Group: (Bio)Organic Materials and Devices

Project 5.1

Supervisor(s): Prof. Ryan Chiechi

Electrolyte Gating Molecular Electronic Devices

Molecular Electronic devices in which single molecule or molecular monolayers are utilized as active electronic components is promising for the construction of miniaturization and integration of electronic devices. To realize the molecular electronics, the critical step is fabricating the three terminal field-effect molecular transistor. In past decades, many attempts were carried out. However, only few of them were successful. Recently, our group developed a simple method to fabricate self-assembled, addressable nanogap (STAN) electrodes by nanoskiving. Based on this technique, in order to construct high performance three terminal devices, ionic liquids-room temperature molten salts will be applied to gate these molecular junctions.

The research comprises two parts:

1) Synthesize a series of alkyl dithiol (1,12-dodecanedithiol; 1,14-tetradecanedithiol; 1,16-hexadecanedithiol). The synthetic route has already been investigated.

2) Construct the molecular junctions and characterize by electrical measurements.

You can expect to learn about:

·         Organic synthesis of alkyl dithiol and self-assembling.

·         Working in the clean room, fabricating STAN electrodes.

·         Nanoskiving

·         Electron microscopy.

Project 5.2

Supervisor(s): Prof. Ryan Chiechi

Investigate Rectification in Molecular Tunneling Junctions: Terthiophene-Terminated n-Alkanethiolates

Molecular rectification is a particularly attractive phenomenon which shows the variety in charge transport across the same molecular Junctions but opposite direction. This is important in studying structure–property relationships in charge transport across molecular junctions. Eutectic Gallium Indium (EGaIn)-liquid metal at room temperature is introduced as top contact to form molecular junctions which is well developed by our group. In this project, we designed a new organic molecular rectifier: a molecular junction having the structure AgTS/S(CH2)n-terthiophene//Ga2O3/EGaIn and the rectification need to be studied by electrical measurements.

The research comprises two parts:

1) Synthesize a series of Terthiophene-Terminated n-Alkanethiol. A three steps routine has already been designed.

2) Characterize by EGaIn measurements.

You can expect to learn about:

·         Organic synthesis of Terthiophene-Terminated n-Alkanethiol and self-assembling.

·         Metal deposition by vacuum technology.

·         EGaIn molecular junctions.

·         Working with flow-box.

Project 5.3

Supervisor(s): Prof. Ryan Chiechi and Olga E. Castañeda

Soft Device Fabrication comprising Photosystem I

The goal of this project is the fabrication of devices comprising the biological complex photosystem I (PSI) by incorporating it into microfluidic channels (formed using soft lithography) making use of the self-aligning liquid metal contacts made from eutectic Ga-In (EGaIn).

This research will focus on finding an anode material (porous/nanocrystalline, transparent, conducting oxides, etc.) that will contact the photosystem I and complete the circuit of the device. The ultimate goal is to create a "self-fabricating" photovoltaic device similar to a dye-sensitized cell with reverse electron-flow. The work function of EGaIn (around –4 eV), will ideally ensure a higher open-circuit potential than is possible with conventional electrode materials.

You will learn about microfluidic devices (including fabrication), self-assembled monolayers, sol-gel and/or nano-particle synthesis.

Project 5.4

Supervisor(s): Prof. Ryan Chiechi and Olga E. Castañeda

Fabrication and Light effect studies on solid-state devices of Photosystem I

Photosystem I (PSI) is nature’s perfect solar cell. With its 100% internal efficiency, it’s the only complex able to take in all photons and convert them in to energy.

Our research group has developed PSI solid state devices which we can interrogate with a liquid metal tip (made from eutectic Ga-In) to find out information about the electric properties of arrays of these complexes (junctions of about 25µm2). The idea of the proposed research project is to fabricate a type of device where we can study these complexes under the influence of light to study its effect on the electrical properties of oriented PSI.
You can expect to learn about fabricating solid-state devices, creating Self Assembled Monolayers (SAMs), depositing metals by vacuum technology, and conducting electrical measurements with EGaIn.

6 Group: Surfaces and Thin films

Project 6.1

Supervisor(s): Prof. Dr. Petra Rudolf and Dr. Régis Gengler

Large area deposition of single layer dichalcogenides materials

The graphene era has triggered an enormous interest in inorganic atomically thin materials with unique electrical, optical and chemical properties. The major disadvantage of graphene is the absence of a band gap limiting its use in electronic applications. Transition metal dichalcogenides are layered materials with very strong in plane bonding but weak out-of plane interaction, just like graphite. However, most of them are semiconductors with direct or indirect bandgaps. In this short project the student will focus on a surface chemistry approach, namely the Langmuir Blodgett (LB) technique, to deposit large areas of single layer dichalcogenides material. The main task of the student will be the surface deposition (LB) , and characterization by surface microscopy (atomic force microscopy) and spectroscopy ( x-ray photoemission spectroscopy).

Project 6.2

Supervisor(s): Prof. Dr. Petra Rudolf and Dr. Régis Gengler

High quality deposition of organic material for atomic exploration

Ultrafast electron diffraction (UED) is a brand new technique mastered only by a few groups around the globe. This technique aims at characterizing atomic motion with picosecond time resolution. The understanding of organic material dynamics is of major importance for the future since these materials become more and more part of real life applications like LED’s, solar cells, etc. The student will make use of the Langmuir-Blodgett method to prepare highly ordered organic thin films for UED investigation.

7 Group: Photophysics and opto-electronics

Project 7.1

Supervisor(s): Dr. Jan Anton Koster and Solmaz Torabi, MSc

The effect of topological variations on the capacitance of thin film capacitors

The presence of roughness at metal-insulator or metal-semiconductor interfaces has a detrimental role in the function of scaled down electronic devices. A great deal of effort is underway to understand the electrical properties of devices influenced by such microstructural imperfections. Some investigated properties which are known as being strongly influenced by surface roughness include the local electric field hence the breakdown field strength, electrical conductivity, leakage current, electronic energy levels and electric capacitance.

A few experimental reports and many theoretical and simulation studies, specifically, have proved that the increased roughness at the film-electrode interface will increase the capacitance of the thin film capacitors. Nevertheless, no quantitative connection between experimental studies and theoretical predictions have been established yet.

Project: a wide range of capacitors will be designed with varied film roughness. The fabricated capacitors will be electrically characterized. The roughness profiles will be scanned with atomic force microscopy and analyzed topographically. Ultimately the effective capacitance will be formulated in terms of roughness parameters. The outcome will be of great interest in many applications from storage capacitors for random access memories, organic electroluminescent devices to transistors and solar cells.

8 Group: Systems Chemistry

Project 8.1

Supervisor(s): Prof. Sijbren Otto ( ); d aily guidance by Dávid Komáromy ( )

Dynamic combinatorial approach to self-replication based on hydrophobic interactions

In dynamic combinatorial chemistry, small organic molecules containing functional groups which are capable of reversible covalent bond formation (i.e. thiols) are reacted with each other to give complex equilibrium mixtures of macrocyclic compounds called dynamic combinatorial libraries (DCLs). Upon careful design of the building blocks, self-replicating macrocycles can emerge from the DCL formed [1,2]. Until now, self-replicating behavior could be observed among building blocks peptide side chains constructed from containing alternating polar and apolar amino acids. In this project, we attempt to synthesize and study an aromatic dithiol building block, which is expected to be capable of self-replication in water, based solely on hydrophobic interactions. That is, hydrophobic interactions are expected to promote the stacking of one or another type of macrocycle molecules on each other, leading to self-replicatory behavior.

The project begins with the 4-step synthesis of the molecule, the first step of which is literature-known procedure, while for the other ones our group has developed well-established procedures. Once the building block is synthesized, the formation of the DCLs can be monitored by UPLC and LC-MS. If self-replication is observed, seeding experiments are needed to further corroborate the self-replicatory behavior. Finally, if time is sufficient, TEM experiments can be carried out to study the morphology of the aggregates formed by self-replication.

[1] J. M. A. Carnall, C. A. Waudby, A. M. Belenguer, M. C. A. Stuart, J. J.-P. Peyralans, S. Otto Science 2010, 327, 1502-1506
[2] M. Malakoutikhah, J.J-P. Peyralans, M. Colomb-Delsuc, H. Fanlo-Virgos, M. C. A. Stuart, S. Otto J. Am. Chem. Soc. 2013, 135, 49, 18406-18417.

Project 8.2

Supervisor(s): Prof. Sijbren Otto ( ); d aily guidance by Giulia Leonetti ( )

Guest-triggered self-replication

This project combines molecular recognition and self-replication in dynamic combinatorial libraries (DCLs). Molecular recognition is a process where several molecules interact selectively and spontaneously via non-covalent binding, leading to the formation of a supramolecular complex. Self-replication is the ability of a single molecule to produce multiple copies of itself in presence of its building blocks. These two themes have been developed in our laboratory over the last years:

-         Molecular recognition in a DCL: it has been shown that guest molecules change the composition of DCLs by interacting with one of their component . For example, a library made of a naphthalene-based building block, that in absence of a guest molecule contains mostly catenanes, changes its composition when an adamantane derivative is added, leading to the presence of only tetramers, which binds to the adamantane guest.1

-         Self-replication emerging from a DCL: oxidation of peptide based building blocks containing two thiol groups can lead to the formation of macrocycles. When stacking of one of the macrocycles can occur due to weak interactions of their side chains, fibres are formed, and they can catalyse the formation of similar macrocycles. Therefore, self-replication is observed.2

A logical development now would be to combine these two features in a single system. This can be achieved by setting up DCLs that contains two types of buildings blocks (BBs): i) some that have already shown the ability to lead to a host-guest complex when a given substrate is added and ii) others that are already known to form replicators. Both will be thiol-based so as to allow their mutual interaction. Preliminary results have already shown that when mixing these two types of BBs no replication will take place initially. However, if the right guest is added to the library, the BBs involved in molecular recognition should combine together in order to create the right receptor. This will leave only the replicating BBs available, and they should then combine to form the replicating species. Therefore it would be a way to trigger self-replication by the addition of a guest molecule.

1.       Hamieh S.; Saggiomo V.; Nowak P.; Mattia E.; Ludlow R. F.; Otto S. Angew. Chem. Int. Ed. 2013, 52, 12368–12372
2.       Carnall J. M. A.; Waudby C. A.; Belenguer A. M.; Stuart M. C.A.; Peyralans J. J.-P.; Otto S. Science 2010, 327, 1502−1506

9 Group: Physics of Nanodevices (Quantum Devices subgroup)

Project 9.1

Supervisor(s): Prof. Caspar van der Wal and Olger Zwier

Optical Control of Electron Spins in a Semiconductor

Background: The possibility to store optical information in electron spins is important for classical and quantum communication . Quantum communication holds promise for an internet in which eavesdropping is fundamentally impossible. However information in present-day communication networks obeys the laws of classical physics. Towards this goal, a very recent research development in the group of Prof. Caspar van der Wal has shown that ensembles in a semiconductor can be very homogeneous and show a quantum optical phenomenon. This phenomenon is Electromagnetically Induced Transparency (EIT) and relies on three-level quantum systems with two low-energy spin states that both have an optical transition to a common excited state.

Project: We plan to explore the physics of Coherent Population Trapping (CPT, which is similar to EIT) in a collection of electronic spins in Silicon Carbide (SiC) in the context of using it as a quantum memory . In parallel, this project will investigate the role of unavoidable inhomogeneities leading to dephasing, which has been an obstacle for state-of-the-art semiconductor systems to date. The project will employ laser beams to appropriately couple the ground and excited states of atom-like divacancies in SiC. This includes techniques such as photoluminescence spectroscopy and single-photon counting.

Further information:

Project 9.2

Supervisor(s): Prof. Caspar van der Wal, Danny O'Shea and Jakko de Jong

Optical Manipulation of Gallium Arsenide Spins

Background: This project is 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.

Project: 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 a challenge for research. In the context of your project, you will participate in our experiments to measure and enhance the spin relaxation and decoherence times of donor-bound electrons in gallium arsenide. Additionally, the experimental scheme will employ three state-of-the-art laser systems to measure and control both electron and nuclear spins.

Further information:

10 Group: Theoretical Chemistry

Project 10.1

Supervisor(s): Katalin Barta and Dr. Remco Havenith

Computational studies on the acid catalysed cleavage of the β-O-4 ether bond in lignin

A future sustainable society requires the use of renewable carbon sources for the production of commodity chemicals. Lignocellulosic biomass and specifically discarded inedible plant material harbour great potential for this purpose.[1][2] One of the main components of lignocellulosic biomass is lignin, which would be ideal for the production of aromatic chemicals. [3] However, depolymerisation of lignin faces challenges. Selective cleavage of the most common β -O-4 ether linkage (up to 50%) is the key to effective depolymerisation towards aromatic subunits. In our group, we are developing new methodologies that enable cleavage of this bond. Initial results show, that triflic acid is very efficient in cleavage of several model compounds containing the β -O-4 ether linkage. It was also found, that temperature and the solvent play a significant role in the rate of these processes. It is assumed based on literature, that cleavage proceeds through specific intermediates, which also lead to recondensation and low product yields. Catalytic and stoichiometric methodologies that trap these intermediates enable high product yields. A more in-depth understanding of the reaction pathways at this stage is highly desired.

The project will consist of:

-ab initio calculations to uncover mechanistic details of possible cleavage pathways
-synthesis of a model compounds mirroring the beta-O-4 linkage
-catalytic acidolysis of these models to determine the effect of various reaction parameters on cleavage efficiency.
-trapping the reactive intermediates formed upon acid catalysis by formation of acetals with biomass derived alcohols
-mechanistic insight into dehydration pathways

Depending on the interest of the student, the project can be more focused on theory or experiment. The results are expected to support future methodology development to enable lignin as renewable feedstock for our chemical industry.

[1]       Ragauskas, A. J., Williams, C. K., Davison B. H., Britovsek, G., Cairney, J., Eckert, C. A., Frederick Jr., W. J., Hallett, J. P., Leak, D. J., Liotta, C. L., Mielenz, J. R., Murphy, R., Templer, R. and Tschaplinski, T., Science, 311 (2006), 484
[2]       Deuss, P. J., Barta, K., de Vries, J. G., Catal. Sci. Technol., 4 (2014), 1174
[3]       Bruijnincx, A., Jongerius, A. L. and Weckhuysen, B. M., Chem Rev., 110 (2010), 3552

11 Group: Nanostructured Materials and Interfaces

Project 11.1

Supervisor(s): Prof. Bart Kooi

SeAsTe phase-change alloys studied by ultrafast differential scanning calorimetry (DSC)

Phase-change materials (PCMs) are currently investigated intensely, mainly to replace in the near future the popular Flash-type memory, which is used in e.g. mobile phones, tablet computers, USB memory sticks etc.. PCMs already have been applied successfully in optical recording, well-known from the rewritable CD, DVD and Blu-Ray Disk formats. Phase-change memories can be switched reversibly more than a million times between amorphous and crystalline states and exploit the large differences in optical reflectivity or electrical resistance of the two states.

Recently we were the first in the world to study the reversible amorphous-crystalline phase change in a chalcogenide model PCM material using ultrafast DSC, which allows heating rates up to 40000 K/s and cooling rates down to -4000 K/s. The chalcogenide model PCM was SeTe where we studied a large composition range between 15 and 60 at.% Te. For this small research project we want to extend this work by analyzing the ternary SeAsTe alloy. Measurements in the ultrafast DSC involve rapidly cooling (with various rates) a melt into an amorphous state and then measuring the glass transition and crystallization peak during heating with various heating rates allowing determination of the activation energies of the transitions. Important outcome will be the effect of the addition of As on the properties of SeTe.

12 Group: Micromechanics

Project 12.1

Supervisor(s): P.R. Onck and E. van der Giessen

Computational design of a biomolecular crowding sensor in living cells

Cells are highly crowded by macromolecules which influences essential biomolecular processes such as transport, diffusion and folding. Measurements of crowding can be performed by using Fluorescence Resonance Energy Transfer of genetically encoded proteins. The sensitivity of these FRET-sensors depends strongly on their molecular architecture. In this project we use a recently developed one-bead-per-amino-acid molecular dynamics model to test the sensitivity of existing sensors and to design new genetically engineered constructs that show an optimal FRET output for typical crowding densities in living cells. This project will be carried out in collaboration with groups in the Groningen Biomolecular Sciences and Biotechnology Institute (GBB).

13 Group: Spintronics in functional materials (Prof. Tamalika Banerjee)

Spintronics entails phenomena that exploits the magnetic moments of the electrons in addition to their spins, in different materials and their heterostructures. Currently we are looking into new materials and spintronic devices, with the aim to manipulate the transport of spins in them using new mechanisms. The research projects mentioned below can be specifically designed for both a short and long research project. For specific details please contact the supervisors listed.

Project 13.1

Supervisor(s): Prof. Tamalika Banerjee and Eric de Vries (daily supervisor)

Spin momentum locking in Topological Insulators

Topological insulators (TIs) are electrically insulating in the bulk and have metallic surface states that originate due to spin-orbit coupling. This special property is expected to make TIs interesting for spintronic applications. We have successfully demonstrated the characteristic spin-momentum locking of the surface states in thin TI films of Bi2Se3 (20 QL). We are currently extending our studies to design new device geometries that allows us to rule out extraneous mechanism that can influence such transport. For these studies, we plan to use thin flakes of different TI’s as well as thin films of Bi2Se3 capped with different tunneling barriers, which assist in designing robust detection contacts with uniform contact resistances. Such devices will allow us to address the gate dependence of the spin voltage which is expected to resolve the intriguing question on the exact origin of the observed bias and temperature dependence of the spin voltage. The student will work in the NanoLab Groningen for the fabrication (using Electron Beam Lithography, Deep UV Lithography various deposition tools) of the different device geometries and will acquire hands-on experience on the transport measurements. Further supporting characterization tools such as the Atomic Force Microscopy and Scanning Tunneling Microscopy will be used for the project. For further details, please contact one of us.

Project 13.2

Supervisor(s): Prof. Tamalika Banerjee and Roald Ruiter (daily supervisor)

Spin and charge transport in graphene on high k dielectrics (oxides)

In spite of the exceptional charge transport properties in graphene, the origin and mechanisms that limit spin transport in graphene, is a topic actively pursued by researchers, using different routes. Quite recently, we have demonstrated the first results on spin transport in graphene on a high k dielectric substrates such as SrTiO3, using metallic ferromagnetic contacts. SrTiO3 has a dielectric constant of 300 that increases to 104, in a non-linear manner, with decreasing temperature. This arises due to ferroelectric instability in such materials and is commonly attributed to phonon dynamics at such temperatures. Presently, we are active in studying the role of dielectric enhanced screening, long range charge interactions as well as electron-phonon interactions at the substrate-graphene interface to spin transport. This task is quite challenging task as minimizing the presence and role of surface adsorbates and defects intrinsic to graphene (devices) can equally mask the influence of the effects described above to spin transport. We plan to study this using two different design geometries that differ primarily in the nature and spin transport properties of the injection contacts and using new approaches to ensure a clean graphene surface. The student will join the daily supervisor in the actual fabrication of the device using the facilities at NanoLab Groningen (Electron Beam Lithography, transfer of graphene using established and new protocols) and using different deposition tools ranging from thermal evaporation to Pulsed Laser Deposition. Besides, the student will be involved in the measurements and analyses of spin transport in such devices using the non-local geometry in a varying temperature and magnetic field set-up. For further details, please contact one of us.

Last modified:17 November 2017 4.58 p.m.