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OnderzoekZernike (ZIAM)OnderwijsTop Master Program in Nanoscience

NS194. Small research project -- projects for 2016

Last update 19 Feb 2016, 09:50 hrs

The available small research projects for 2016 are listed here. Please contact the supervisor mentioned in case you are interested in a project. First come, first served...

The students with a Tata Steel Scholarship must contact Caspar van der Wal for being guided to projects (at least 12) that match the requirements that come with this scholarship.

For contact information on all mentioned professors and groups see [ the most complete listing with (nearly) ALL staff ]
and also [ list of Zernike staff without the associate members - use the above if possible ]


1 Group: Polymer Chemistry and Bioengineering

Project 1.1 (already one student admitted to this project, in exceptional cases more students can be admitted, contact the supervisor)

Bio- and nanomaterials for clinical applications

Supervisor: Dr. ir. B.J. Crielaard

Cell-targeted nanoparticles for cancer therapy

Anti-cancer therapeutics generally are highly toxic for cancer cells, but unfortunately also for healthy cells, which explains the serious side-effects associated with chemotherapy (anemia, hair loss). Targeted therapies aim to prevent, or at least limit, such off-target toxicity. For example, in some forms of cancer, tumor cells express high amounts of specific membrane receptor(s) that can be exploited for attacking these target cells while sparing the healthy cells that don’t express these receptors.

This project involves the development of nanosized particles and drug carriers functionalized with DNA aptamers (1) that target the HER receptor family, members of which are overexpressed by some forms of breast and lung cancer (2) . There is evidence that targeting multiple receptors at the same time, such as by a nanoparticle with multiple binding ligands, the growth of these cells can be inhibited more strongly than by using only a single binding ligand. Another way to achieve anti-cancer efficacy is to load a drug into a nanocarrier, such as a liposome, that is functionalized with aptamers to enhance cancer cell-specific uptake. In this project, nanoparticles (DNA nanostructures, DNA micelles) and nanocarriers (liposomes) that target HER-family receptors will be prepared and characterized (DLS, TEM), and their uptake by, as well as cytotoxic activity against, breast cancer cells will be evaluated (cell culture, XTT assay, confocal microscopy, flow cytometry).

[1] Keefe AD, Pai S, Ellington A. Aptamers as therapeutics. Nat Rev Drug Discov. 2010 Jul;9(7):537–50.

[2] Chong CR, Jänne PA. The quest to overcome resistance to EGFR-targeted therapies in cancer. Nat Med. 2013 Nov;19(11):1389–400.

2 Group Membrane enzymology

Project 2.1

Poolman group, Biochemistry

Supervisors: Dr. Arnold Boersma, Dr. Matteo Gabba, prof. Bert Poolman

Determination of the heterogeneity in crowding in cells by fluorescence lifetime imaging

Cells are highly crowded by macromolecules (~20 – 40 % w/w), which influences essential biomolecular processes such as aggregation, conformational changes, diffusion and protein folding. Measurements of crowding can be performed in vivo by using Fluorescence Resonance Energy Transfer (FRET) of a recently developed genetically encoded sensor.1

Crowding theories predict a non-homogeneous distribution of biopolymers, which should influence the functioning and physiology of the cell. However, we have not been able to image heterogeneities because we determined FRET by fluorescence intensities in confocal microscopy. The alternative is fluorescence lifetime imaging microscopy (FLIM) of the FRET sensors: The advantages of lifetime over intensity based imaging are: (1) the contrast, that improves the discrimination of variations (this may allow discrimination of the heterogeneities that in the intensity based measurements are hidden in the noise) and (2) the possibility to discriminate multiple states by fitting the decays with multiple components.

In this project we will be the first to determine the heterogeneity of crowding cells directly. We will image yeast cells by fluorescence lifetime imaging microscopy (FLIM) of the FRET sensors. Upon successful lifetime-based imaging of the sensors in yeast we will explore the implementation of superresolved lifetime imaging (STED-FLIM) as a final step.

[1]  Boersma, A. J.; Zuhorn, I. S.; Poolman, B. Nat. Methods, 2015, 12, 227.

Project 2.2

Following the Motion of Nanoparticles inside Cells – Towards Optimising Nanomedicines

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

Nanomedicine, the utilization of nano-sized delivery vehicles to combat diseases, is currently under intense development. Nevertheless, success in the clinic has so far been limited.1 Part of the problem is likely that a mechanistic understanding of how nano-sized objects are internalized into cells and subsequently transported inside is largely lacking2 – at all levels: from the molecular to the mesoscopic. In particular, it is currently unknown how nano-sized objects exactly move inside cells, information arguably crucial for optimising the release of a drug at the right time and place.

This project is focussed on understanding the processes by which nano-sized objects are transported inside human cells. Simply exposing living cells to model nanoparticles, the nanoparticles are rapidly taken up by the cells. Using fluorescently labelled nanoparticles, it is thereby possible to image the nanoparticles inside the cells using fluorescence microscopy. Subsequent image analysis will allow extracting the positions of the nanoparticles in time, thereby building up the trajectories they follow. The trajectories will be studied within the framework of random motion, originally developed by Einstein, von Smoluchowski and others to describe Brownian motion, and nowadays generalized to much more complicated type of motion.

The motion of nano-sized objects inside cells will ultimately determine to which locations the objects go inside cells – and how quickly they get there. This project may thereby contribute to the development of “smarter” nanomedicines.

[1] Park, K. Facing the truth about nanotechnology in drug delivery. ACS Nano 7, 7442–7447 (2013).

[2] Time to deliver. Nature Biotechnology 32, 961–961 (2014).

3. Group: Photophysics and OptoElectronics

Project 3.1

Supervisors: Sampson Adjokatse, Bart Groeneveld, Prof. dr. Maria A. Loi ( e-mail: , )

Fabrication, Optimization and Characterization of Novel Organometal Halide Perovskite Materials For Opto-electronic Applications

Organic-inorganic halide perovskite materials have become pre-eminent in electronic and opto-electronic technologies due to properties such as direct band gap, long carrier diffusion length, long carrier lifetimes and high light-harvesting capabilities demonstrated in hybrid perovskite materials such as methylammonium lead halide perovskites, MAPbX3 (X = Cl, Br, I). Although the first perovskite-sensitized solar cell was reported only in mid-2009, having power conversion efficiency of 3.8%, the past four years have witnessed an unprecedented rapid progress with energy conversion efficiencies exceeding 20%. Nonetheless, this technology is still suboptimal with several pressing issues such as lack of control of crystallization and morphology of the perovskite thin films, lack of efficient interfacial or transport layers, material and device instability etc. Beside these issues, there is also the need for design of new perovskite materials with improved capabilities or properties.

Note that, perovskites are a class of materials that adopt the same crystal structure as calcium titanate (CaTiO3) with the generic chemical formula, ABX3 where the A and B sites usually accommodate inorganic cations of various valence and ionic radius and the X site accommodates anions (halogen or oxygen). However, replacing the A cations with suitable organic species creates organic-inorganic hybrid materials. The most commonly used perovskites in solar cells are the organolead halide perovskites, where the organic species are CH3NH3 + (MA) or HC(NH2)2 + (FA) and X is halogen, typically Cl, Br or I.

The goal for this research project is in two-fold. The first part is focused on the design and fabrication of new organolead halide perovskites by replacing MA and FA species with novel organic species. On the other hand, the second part is focused on the design and fabrication of lead-free hybrid perovskite compounds with analogous or improved optical and electrical properties as organolead halide perovskites. To achieve these, several characterization techniques such as microscopy and spectroscopy techniques in combination with other structural and electrical characterization methods will be employed to study and understand the physical properties of these novel hybrid perovskites.

The two topics under this research project can be investigated mutually exclusively. Hence, due to the time limitation for the topmaster small projects, the topics can be studied independently.

Project 3.2

Supervisors: T. Sherkar and Dr. L.J.A. Koster

Hybrid Perovskite Solar Cells: Charge recombination at interfaces between electron (hole) transport layer and the perovskite absorber

Perovskite solar cells (PSC) have recently attracted great interest which has led to increase in their power conversion efficiency from 3.8% in 2008 to 20% in 2015. The role of the electron and hole transport layers (ETL/HTL) in PSCs is to efficiently transport the photogenerated electrons (and holes) in the perovskite toward the extracting electrodes. However, because of the presence of traps at interfaces between the ETL (HTL) and the perovskite layer, photogenerated charges recombine with traps and this leads to poor solar cell performance. Therefore, a thorough understanding of the charge dynamics at these interfaces is necessary in order to improve the solar cell performance.

A simulation model has the power to imitate the real-world device operation and study microscopic phenomenon which are difficult to quantify experimentally. Our drift diffusion simulation is able to represent the key characteristics or behaviors of a solar cell such as, charge generation, transport and recombination. The aim of this project is to study the charge recombination via traps at the interfaces between the ETL (HTL) and the perovskite absorber, and quantify its effect on the performance of perovskite solar cells. The student needs to have knowledge of the fundamental concepts of programming. The results from this simulation can then be complemented with experimental results to provide a detailed picture for the basis of understating the recombination in perovskite solar cells.

Project 3.3

Supervisor: Dr. L.J.A. Koster

Characterisation of traps in organic semiconductors

Organic semiconductors have in the last few decades been extensively investigated not only due to their applicability as electronic devices such as polymer light emitting diodes (PLEDs), field effect transistors (FETs), and organic solar cells (OSCs) but also due to their low cost processing from solution . It became clear that in order to make efficient and stable devices, charge transport in conjugated polymers is an important phenomenon to understand. These charges, especially electrons can be trapped in these materials.

Trap states can have a significant influence on the performance of organic solar cells, as they act as recombination centers, lower mobility, disturb the internal field distribution and reduce the power conversion efficiency (PCE). Furthermore, induced trap states by oxygen exposure can have a high impact on the long term stability of organic photovoltaic devices1.

Therefore, detailed information about the trap states in the active materials used for solar cells, their densities and energetic levels as well as their origins are an important prerequisite for enhancing PCE and operating stability of OSCs.

It is generally accepted that the density of state (DOS) is a Gaussian distribution, and the states in the tail act as trapped states2. The use of thermally stimulated current (TSC) is a direct way of determining the density and energy distribution of trap states. Traps in a material can be filled by white light excitation (e.g. 150 W halogen light) at low temperature; the voltage is then reversed and the temperature is increased linearly by means of a controlled heat input. The current is then measured as a function of temperature, which yields a map of the energetic distribution of traps.

We propose TSC to probe the trap states in our new set of conjugated donor polymers and PCBM fullerene acceptor. The aim of the short project is to perform the first set of measurements on [70]PCBM. This will set the ground for the main research project.

For more info contact:

[1] J. Schafferhans et al., PhD Thesis, 2011

[2] A.J. Campbell et al., J. Appl. Phys. , 1997, 82, 6326-6342

[3] J. Schafferhans et al., 2008, arXiv:0810.3534

4. Group: Surfaces and Thin Films

Project 4.1

Supervisor: Prof. M.A. Stöhr

Graphene growth on metal oxides

Due to its overwhelming electronic properties, graphene is considered to be used in future electronic devices transcending conventional silicon-based electronics. However, the prerequisite - a one-step growth process on a non-interacting substrate resulting in high quality graphene with its intrinsic properties preserved – is a difficulat task to be realized. When graphene is grown via chemical vapour deposition (CVD) on metals, a transfer step onto a non-interacting substrate is needed. This is known to introduce defects and contaminations. On the other hand, the direct growth on metal oxides often results in reduced graphene quality. In our recent work, we could demonstrate the possibility to grow graphene directly on a metal oxide surface – oxidized Cu(111) – via a one-step growth process [1]. Moreover, the graphene was found to exhibit the properties of freestanding graphene.

In the present project, instead of using an oxidized Cu surface graphene should be grown on the surface of bulk metal oxide. For this a Cu2O single crystal will be employed. The graphene growth will be done under vacuum conditions using either methane or ethylene as carbon precursor. It is the aim to determine the right graphene growth conditions with respect to pressure of the precursor, temperature of the Cu2O single crystal and growth time. The grown graphene will be investigated in situ with low energy electron diffraction and scanning tunneling microscopy to determine the structural properties on a global as well as very local scale.

[1] S. Gottardi et al., Nano Lett. 15 (2015) 917

Further information:

Project 4.2

Supervisor: Petra Rudolf

Design and development of novel and hybrid 2D materials

Students are invited to contact Prof. Petra Rudolf. In her team, projects are available in the area of field-induced chemistry to convert CO2 into two different carbonaceous materials (carbon black and graphene), doping of graphene-based materials with high surface area and surface functionalities for cost-effective and safe applications, and the design and development of novel layered nanostructured hybrid materials for environmental, medical and catalytic applications.

5. Group: Optical Condensed Matter Physics

Project 5.1

Ultrafast Molecular Dynamics subgroup

Supervisors: Björn Kriete and Dr. Maxim S. Pchenitchnikov

Self-Assembled Nanotubes

Self-assembly as a “bottom-up” approach to fabricate nanoscale structures has become vital to various fields of science ranging from biomedical engineering to nanoelectronics. [1] This approach is tantalizing as in principal the assembly of complex structures does not require any human intervention once a detailed understanding of all molecular building blocks and associated dynamics has been obtained. Nature provides inspiration for highly successful self-assembled structures such as the light-harvesting systems of photosynthetic bacteria and plants.

This small project aims for spectroscopic investigations of self-assembled molecular aggregates of the cyanine dye C8S3, where the main focus is on understanding the aggregate morphology, exciton dynamics and their interplay.[2] First the student has to become familiar with the system in general and master the sample preparation in particular. Due to the involved self-assembly process the preparation itself is in principal simple, but has to be executed carefully and requires some practice. For the next step, the actual characterization using optical spectroscopy, different options are available, i.e. (1) absorption spectroscopy in conjunction with microfluidics to unravel the assembly dynamics of such aggregates, (2) low temperature absorption and fluorescence spectroscopy to elucidate disorder and (3) ultrafast time-resolved fluorescence spectroscopy to understand exciton dynamics. Finally, the acquired data has to be evaluated, interpreted and discussed.

During the project, the students will develop the following central skills:

- Familiarization with various optical spectroscopic techniques

- Application of these spectroscopic techniques for nanoassembly characterization

- Acquisition and assessing experimental data

- Drawing scientific conclusions from results and discussing/defending these

- Preparing a scientific presentation (on the results of the project)

[1] G. M. Whitesides and B. Grzybowski, “Self-Assembly at All Scales”, Science 295, 2418-2421 (2002).

[2] C. Didraga et al., “Structure, Spectroscopy, and Microscopic Model of Tubular Carbocyanine Dye Aggregates”, J. Phys. Chem. B 108, 14976-14985 (2004).

Project 5.2

Ultrafast Molecular Dynamics subgroup

Supervisors: Oleg Kozlov and Dr. Maxim S. Pchenitchnikov

Exciton diffusion in novel organic semiconductors

Organic electronics is an emerging field of science and technology that represents a promising alternative to conventional electronics. Organic electronic devices are based on organic semiconductors, which combine attractive properties of organic materials with semiconducting behavior. The elementary excitation in these materials is a so-called “exciton” – a strongly bound pair of negative (electron) and positive (hole) charges. As a result, organic electronics essentially rely on exciton dynamics that have to be controlled and observed to ensure the development of high-efficient organic devices [1].

The aim of this experimental project is to understand the exciton diffusion in novel organic semiconductors at ultrafast timescales. The research involves sample preparation and their thorough spectroscopic characterization, including ultrafast photoluminescence measurements [2]. During the project implementation the student will learn underlying photophysical processes in organic electronic devices and acquire valuable skills and expertise in fields of “soft” condensed matter and (ultrafast) optical spectroscopy.

[1] O. Mikhnenko et al., “Exciton diffusion in organic semiconductors”, Energy Environ. Sci.8, 2015

[2] J. Lin et al., “Systematic study of exciton diffusion length in organic semiconductors by six experimental methods”, Material Horizons 1(2), 2014

Group 6: Solid State Materials for Electronics

Project 6.1

(Already one student admitted to this project, when more students are interested, please contact the supervisor)

Supervisor: Dr. Graeme Blake

Enhanced thermoelectric materials for waste heat recovery

Thermoelectric (TE) materials are of interest for the conversion of waste heat to electrical power. This principle can be used for example to make factories more energy efficient. The construction of an efficient energy-harvesting TE module requires both p- and n-type semiconductors that have high electrical conductivity, high thermopower (Seebeck coefficient) and low thermal conductivity. Furthermore, the semiconductor materials should be cheap to produce, environmentally friendly, and stable at high operating temperatures.

This project will involve joining the development team for a prototype thermoelectric module to be placed in Tata’s steel factory. The materials research will be carried out in close collaboration with RGS Development, who produce the component materials using tape casting technology which involves the casting of a liquid silicide on a solid substrate. The aim of the project is to improve the thermoelectric properties of existing silicon-based semiconductors by for example adding nanoparticles to the melt and optimizing process parameters. The work will be carried out partly in the Solid State Materials for Electronics group and partly at the RGS facility in Broek op Langedijk (near Alkmaar).

Project 6.2

Supervisors: Dr. Graeme Blake and Prof. T.T.M. Palstra

Novel magnetic insulators for spintronics

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 not for only spin transport [2] but also for magnetic storage spintronics devices. However, very few room temperature magnetic insulators are known. Copper oxyselenides are a promising family of ferromagnetic insulator materials. In particular, Cu2OSeO3 (Tc = 64 K) has attracted considerable attention due to the coexistence of ferromagnetic and ferroelectric orders, as well as the existence of a skyrmion phase (vortex-like spin order) under applied magnetic field. The manipulation of skyrmions is a potential new method of controlling thermal transport using spin, a field known as spin caloritronics. Preliminary experiments in our group have suggested that by changing the growth conditions of Cu2OSeO3, the structure can be modified to form novel insulating compounds with much higher magnetic ordering temperatures.

In this project, the chemical synthesis of single crystals of new magnetic compounds related to Cu2OSeO3 will be explored. The structure of the crystals will be determined using single crystal X-ray diffraction. The magnetic behaviour of the crystals will then be studied using SQUID magnetometry. Measurements of the response to an applied magnetic field along different crystal directions will provide insight into magnetic exchange pathways between the copper ions. This will allow the identification of structural features that give rise to strong magnetic exchange interactions, with the aim of designing insulating copper oxyselenides that are magnetic at higher temperature.

[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).

Group 7: Systems Chemistry

Project 7.1

Supervisors: Prof. Sijbren Otto, Andreas Hussain and Piotr Nowak

Macroscopic Self-Replication: Darwinian evolution with 3D-printed building blocks

In this project you will study Darwinian and Lamarckian evolution of a system of macroscopic objects. For that you will design and 3D-print building blocks incorporating small neodymium magnets and study their self-assembly [1]. With proper geometry and placement of the magnets, the self-assembled structures should be able to self-replicate and transfer hereditary information, similarly to DNA in living systems.
Your research will be aimed towards two goals: extension of biological and chemical concepts to the macroscopic world and the visual readout of information without sophisticated, expensive, and often unreliable techniques used in molecular biology and chemistry.
The basic design guidelines will closely mimic a synthetic chemical self-replicating system developed in our group [2]. We found out that dithiols equipped with short peptides form cyclic structures which then stack together forming long fibers. Upon shear stress the fibers break and replicate. If two different building blocks are mixed, the molecular information is transferred to the progeny. Mutations occur spontaneously leading to the formation of abiotic ‘species’ [3].
We want you to extend the principles which gave origin to life to macroscopic systems, based on magnetism and simple mechanics, rather than chemical interactions. As such systems are easy to design, manipulate, and analyze, they will be able to provide more insight into basic evolutionary and prebiotic processes, providing inspiration to both biologists and chemists. Furthermore, your research can pave the way for self-synthesizing materials optimized by Darwinian evolution.
Apart from performing intellectually stimulating research bridging concepts from physics, chemistry, and biology, you will learn the basics of computer aided design (CAD) and various techniques and materials used in additive manufacturing (3D-printing) and molding. Later on you might want to use image analysis particle tracking tools to analyze your system and computer simulations to model the physical behavior of the blocks.

[1] A. J. Olson, Y. H. E. Hu, E. Keinan Proc. Natl. Acad. Sci. USA 2007, 104, 20731–20736 (accompanying video: ).
[2] J. M. A. Carnall, C. A. Waudby, A. M. Belenguer, M. C. A. Stuart, J. J.-P. Peyralans, S. Otto Science 2010, 327, 1502–1506.
[3] J. W. Sadownik, E. Mattia, P. Nowak, S. Otto Nature Chem. 2016, ASAP. doi:10.1038/nchem.2419. (accompanying video: )

Project 7.2

Supervisors: Prof. Sijbren Otto, Prof. Siewert-Jan Marrink and Dr. Pim Frederix

Structural and optical properties of peptide macrocycles

Peptides functionalised by aromatic dithiols can undergo reversible covalent bond formation to form mixtures of various sizes of macrocycles [1]. Depending on the functionalities presented on the peptide side chains, different sizes of these macrocycles can nucleate and self-assemble, therefore driving the reaction to induce exponential self-replication of one of the species in the reaction mixture as shown in this video . The macrocycles typically aggregate into long, one-dimensional nanostructures that can be observed by electron microscopy. However, we do not know what happens on the molecular level to enable the self-assembly process for one type of macrocycle, but not for the other.
In the Otto group we routinely synthesize and analyse libraries of these self-replicating macrocycles. We want to expand our knowledge on their molecular architecture by doing theoretical work and spectroscopic analysis of the self-assembled structures. The applicant will learn how to perform Infrared (IR) absorption and circular dichroism (CD) spectroscopy. In collaboration with the Molecular Dynamics (MD) group in the GBB and the Theory of Condensed Matter group in the Zernike institute, the applicant will perform MD simulations of the nanostructures and subsequently employ semi-empirical quantum chemical methods to calculate the IR and CD spectra of the nanostructures. Comparison of the theoretical spectra and experimental spectra should give the required insight into the structure of the self-replicating assemblies.
Depending on the choice of the applicant, the project can be weighted more towards the synthesis, the spectroscopy or the modelling of the system.

[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.

Project 7.3

Supervisors: Prof. Sijbren Otto and Yigit Altay

Self-Replication of Peptides in Protocells

Peptides functionalised with aromatic disulfides can form mixtures of compounds that can interconvert through reversible linkages between constituent building blocks in water. If the system is under thermodynamic control, the concentration of each compound will be determined by its relative stability. When one of the molecules in such a network can stabilise copies of itself through intermolecular non-covalent interactions, it can nucleate and start to self-assemble. This self-assembly then drives the system to produce more copies of the self-assembling molecule: self-replication [1,2]. This self-replication process is illustrated in this video .
Until now self-replicating systems, that are developed and analysed in the Otto group, are based on the replicator behaviour in bulk media. Compartmentalisation, on the other hand, is one of the essential characteristics of life. We are aiming to study the self-replication behaviour of peptides in a confined space. Liposomes are good candidates for that purpose because of their well-defined structures, encapsulation abilities, available synthesis and analysis methods. The student will learn how self-replicating peptides from dynamic combinatorial libraries work. Furthermore, you will develop a novel protocell with preparation of large unilamellar vesicles from phospholipids and optimisation of liposomal encapsulation of the peptide replicators. In the course of the project you will develop strong analytical skills in liquid chromatography, mass spectrometry and dynamic light scattering.

[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] J. W. Sadownik, E. Mattia, P. Nowak, S. Otto Nature Chem. 2016, ASAP. doi:10.1038/nchem.2419. (accompanying video: )

Group 8: Theory of Condensed Matter

Project 8.1

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 improved to allow a description of the findings in new unpublished non-linear optical experiments and 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 will in the future be used to study the functional role of the organic ions in the solar cells. At the end of the project you should be able to answer the question if the organic ion rotation dynamics is collective as proposed in recent studies or not.

Tools: You will be running extensive molecular dynamics simulations on our computer cluster and develop a small analysis program for interpreting the results.

Further Information e-mail:



[1] Bakulin et al. Real-time observation of organic cation reorientation in methylammonium lead iodide perovskites, J. Phys. Chem. Lett. 6:3663 (2015)

Project 8.2

Supervisor(s): Dr. Thomas la Cour Jansen

Molecular Motors driven only by Light

Background: Molecular motors are an active research area. Molecular motors are nano-machines that may be driven by chemical reactions or light. Great successes have already been achieved in this area for example leading to synthetic light-driven monodirectional molecular motors [1]. Still all existing rotational motors require thermalisation steps to overcome small potential energy barriers limiting the number of rotations to about 1 1/ms. Eliminating the thermal steps should allow much higher operational speeds down to 1 1/ns.

Project: A quantum-classical model will be developed describing the time-evolution of a molecular motor excited by light. This will allow the study of the interaction between the electronic excitation behaving quantum mechanically, the rotational coordinate behaving classically and other degrees of freedom that accept excess energy. The model will be implemented in a computer program to evaluate the performance to the molecular motor. The parameter space in which an acceptable behaviour is observed will be determined and used to propose a molecular structure for a prototype.

Tools: You will develop your own program for solving coupled quantum-classical motion.

Further Information e-mail:


[1] B. L. Feringa et al. Light-driven monodirectional molecular motor, Nature  401  152  (1999)

Group 9: Nanostructured materials and interfaces

Project 9.1

Supervisor: prof. dr. B.J. Kooi

TEM analysis of extremely air sensitive photocathode thin films of image intensifier tubes

Photocathodes are a crucial element in image intensifier tubes (IITs), where incoming photons are amplified by a factor of about 104-105, in order to produce discernable images at very low illumination level. Research on the photocathodes is strongly hampered, because they completely degrade in air within seconds and are therefore during production directly sealed in ultra-high vacuum conditions in the IITs.In previous research our group showed that, opening the IITs in a glove box and then using a specially developed transfer holder, photocathode layers can be analyzed in their proper state in a scanning electron microscope. In a next, more difficult step we now want to perform analyses on a more local scale in a transmission electron microscope (TEM). Also here a methodology has been developed including a special sample holder that has to be tested. This testing and the subsequent analysis is the subject of the small research project proposed here. Photocathode films will be deposited in UHV on 20 nm thick silicon-nitride membranes and then sealed in IITs. These IITs have to be opened in a glove box in which directly a thin (10 nm) film of Al is deposited on the photocathode layers. After this protection, the TEM specimen can be taken out of the glove box and then directly analyzed with TEM. This type of analysis has to contribute to a better understanding of the structure and performance of the photocathodes and to improve their production process.

Project 9.2

Supervisor: prof. dr. B.J. Kooi

Extraction replicas for analyzing nanoscale precipitates in grain oriented electrical steels

Energy loss in power transformers constitute a significant fraction of the worldwide losses in the electricity distribution networks and research aiming to reduce this is therefore highly relevant. An important component of transformers is the core that is made from grain oriented electrical steels (GOES). These steels have extraordinary microstructures consisting of centimeter sized grains of body-centered-cubic iron with the crystal lattice having the so-called Goss orientation: <001> axis is parallel to the rolling direction and the {110} planes parallel to the rolling plane . This microstructure with sharp crystallographic texture results in soft (easy) magnetization and low magnetic hysteresis losses. A crucial role in achieving this extraordinary microstructure and texture is played by nanoscale (MnS, CuS, AlN) precipitates. Despite the empirical improvements that have been achieved, fundamental understanding and extensive nanoscale information is lacking concerning the whole process of texture selection and microstructure formation. This hampers further well-directed developments of these steels towards lower losses.

Therefore, together with Tata Steel we started a project to understand the complex precipitation process that is critical for the development of the special texture in GOES. The focus of the research is on the evolution of the precipitation during the heat treatment where the anomalous grain growth occurs that selects the Goss-oriented crystals. In this small research project first experiments will be conducted to produce TEM specimen based on carbon-film extraction replicas, where the precipitates are taken out of the magnetic matrix in order to remove its detrimental effect on the TEM imaging and to produce TEM specimen with large transparent areas allowing analysis of the precipitates with excellent statistics.

Project 9.3

Supervisor: prof. dr. G. Palasantzas

Control capillary forces via surface roughening

When two bodies are separated by a small distance surface roughness starts to play an important role in the interaction between the bodies, their adhesion, and friction. Control of this short-distance interaction is crucial for micro and nanoelectromechanical devices, microfluidics, and for micro and nanotechnology. Because of the very small sizes involved in micro and nanoelectromechanical systems (MEMS/NEMS), surface forces are dominant, and they can generate a malfunction some of the devices or making fabrication impossible. The problem is spontaneous stiction between separate device elements. This is an important limitation in bringing MEMS to the broader market. MEMS structures are typically made by forming a layer of material on top of a sacrificial layer above another material with the following wet etching of the sacrificial layer. Drying after rinsing is the final fabrication step can collapse such microstructures resulting in permanent adherence. Strong capillary forces pull the surfaces together but when the liquid is dried out the surfaces can stuck permanently due to presence of the dispersion forces.

Moreover, when two surfaces approach too close to each other (< 5 nm) during the device operation, surface forces (capillary, electrostatic, Casimir/van der Waals) or inertial forces (shock, rapid air flow) can lead to stiction (irreversible adhesion) due to jump to contact. Atomic force microscopy measurements (in the sphere-plate geometry [1]) have shown that the capillary force can change by more two orders in magnitude by a change of only less than 10 nm of the surface roughness [2]. Moreover, coating with different materials the components and environmental aging can influence the adhesion.

The goal of the project will be to describe capillary force data versus surface roughness using extreme value statistical analysis of the corresponding topographies (obtained by AFM) used also for the force measurements.

[1] V. B. Svetovoy and G. Palasantzas, Influence of surface roughness on dispersion forces (Review Article), Advances in Colloid and Interface Science 216, 1-19 (2015). See refs. therein.

[2] P. J. van Zwol, G. Palasantzas, Influence of roughness on capillary forces between hydrophilic surfaces , Phys. Rev. E 78, 031606 (2008).

Group 10: Physics of Nanodevices

Project 10.1

Supervisor: Prof. dr. Tamalika Banerjee (Supervisor)

Graphene-Silicon interfaces at the nanoscale using Ballistic Electron Emission Microscopy

One of the challenges in Spintronics is to integrate memory and logic in one device architecture. Towards this end, the search is constantly on to look for new methods to realize devices and functionalities with new materials. Necessary metrology to study and characterize such new devices and their interfaces are needed and the technique of Ballistic Electron Emission Microscopy (BEEM) is particularly useful. In this project, the student will be involved in the fabrication of a vertical device stack of Gr on Si in the NanoLab and investigate this interface using BEEM. The proposition is to study the following i) the effect of intrinsic doping in graphene on the band alignment at the Graphene on Si interface while probing local regions of the device, ii) realization of ballistic transport of electrons and holes in a clean interface of graphene/Si, iii) consequences of a vanishing density of states at the charge neutrality point to energy dependence of charge transport and iv) the factors that limit transport across such interfaces at the nanoscale using BEEM. The student will acquire hands-on experience in the operation of the BEEM and will carry out characterization of such interfaces for the studies listed above.

Further research projects and possibilities also exist and the interested student is encouraged to mail for details.

Project 10.2

Supervisor(s): Prof. Bart van Wees and team

Physics and technology of graphene and graphene based and related materials

Students are invited to contact Prof. Bart van Wees for information on projects on the physics and technology of graphene and graphene based and related materials. Projects are available on the following topics: Science and technology of graphene spintronics and graphene magnetism; Development and study of new 2D layered materials; Development and study of graphene based devices, including potential applications for graphene based sensors and optoelectronic devices; Science and technology of vertical graphene based devices.

Further information:

Project 10.3

Quantum Devices subgroup

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

Optical and microwave control of electron spins in a semiconductor at high temperatures

We plan to explore the physics of controlling and reading out electronic spins of lattice defects in Silicon Carbide (SiC) at room temperature, in the context of using this for magnetometry. While we will build on recent results from our team that demonstrated how all-optical control and readout can be realized with lasers and the material below a temperature of 10 K, extending this technique to room temperature probably requires the addition of control with microwaves. In this project you will contribute to measurements that explore the physics of spin-selective optical transitions at higher temperatures than 10 K, and the design of devices and materials that allow for adding microwave control of spins.

Further information:

Group 11: Micromechanics

Project 11.1

Supervisors: Sander Boonstra MSc (daily), prof. Patrick Onck and prof. Erik van der Giessen

Influenza viral fusion: dynamics and pH sensitivity of the hinge peptide

Replication of enveloped viruses only occurs after the viral RNA has been delivered to the cell nucleus by merging of the viral and cell membranes. Membrane fusion is thermodynamically favorable, but has a high kinetic barrier. Viral fusion proteins, like the influenza hemagglutinin (HA), deliver the energy required to overcome the barrier and fuse the membranes [1].

HA is triggered by acidification, after which a hydrophobic fusion peptide at the end of the protein is exposed and inserts into the target membrane. The putative ‘extended intermediate’ that is formed this way bridges the two membranes. Subsequent collapse of the extended intermediate transforms the protein into a lever that is supposed to pull the membranes together. The conventional hypothesis is that only triggering is influenced by the low pH, but recent work has indicated that the hinge region is pH sensitive as well [2].

The goal of this project is to elucidate the role of pH during the conformational changes in the hinge region. To explore the conformational space of the hinge peptide, you will implement an enhanced sampling method for molecular dynamics in GROMACS [3]. You will test the validity of this implementation by comparing your results with experiments on reference peptides from literature. Once you have established the method, you will use it to study the dynamics of the hinge peptide at different pH.

In the process, you will learn about the mechanics of biophysical phenomena like protein folding and membrane fusion. You will work with molecular dynamics simulations and a High Performance Computing (HPC) facility for fast parallel calculations, in a group that is highly experienced in the modeling of micro- and nanoscale mechanical phenomena.

[1] Harrison, S.C. Viral membrane fusion. Virology 479-480, 498-507 (2015)

[2] Kalani, M.R. et al. Characterizing a histidine switch controlling pH-dependent conformational changes of the influenza virus hemagglutinin. Biophysical Journal 105, 993-1003 (2013)

[3] Terakawa, T. On easy implementation of a variant of the replica exchange with solute tempering in GROMACS. J. Comput. Chem. 32 1228–1234 (2011)

Group 12: Molecular Biophysics

Project 12.1

Supervisor(s): Prof. dr. Wouter H. Roos and Dr. Sourav Maity

Nanoindentation measurements on M13 Bacteriophage

Single-molecule techniques, such as Atomic Force Microscopy (AFM), are increasingly widely applied to explore the physical properties of biological assemblies. Recently developed atomic force microscopy (AFM) nanoindentation experiments have been successfully implemented to investigate the material properties of single viral particles [1,2], including their Young’s modulus, breaking force, and resistance to material fatigue. This information is essential to understand the physico-chemical and mechanical properties of viral nanoparticles. AFM experiments reveal a surprising diversity of mechanical properties of biological particles. These properties have been shown to correlate with local conformational dynamics of the capsid structure and to contribute to events such as receptor binding, genome uncoating and capsid maturation, crucial steps in different viral infectious cycles.

The aim of this project is to investigate the mechanical properties of M13 bacteriophage nano-particles using AFM imaging and nanoindentation measurements. M13 is a filamentous bacteriophage (virus infecting bacteria) composed of circular single stranded DNA encapsulated in a rod-like structure of the major coat protein P8 . In collaboration with the group of Prof. Andreas Herrmann we study wild type particles as well as mutant particles that have elastin sequences incorporated. We expect the latter to be more flexible and the student will investigate this. The project includes training of state-of-the-art AFM techniques including high-resolution imaging, nanoindentation and single molecule force spectroscopy, as well as experiments on complex bio-nanoparticles.

[1] Roos WH, Bruinsma R, Wuite GJL, Physical virology Nature Physics (2010) 6:733–743.

[2] Snijder J, Uetrecht C, Rose R, Sanchez R, Marti G, Agirre J, Guerin DM, Wuite GJ, Heck AJR, Roos WH, Probing the biophysical interplay between a viral genome and its capsid, Nature Chemistry (2013) 5:502-509

Group 13: Nanostructures of Functional Oxides

Project 13.1

Supervisors: M. Salverda, B. Noheda

Dielectric behavior of CoCr2O4 spinel: a ferroelectric and magnetic insulator

CoCr2O4 is one of the rare materials in which long range ferroelectric order (spontaneous polarization) and long range ferrimagnetic order (spontaneous magnetization) coexist. The coupling between these two properties is also strong and, thus, the magnetization can be driven by both magnetic and an electric fields, which is of much interest in spintronic applications. So far, there are only a handful of reports on the properties of CoCr2O4 and the magnetic structure is still controversial, mainly due to difficulties in synthesizing good quality samples. In our lab, Jeroen Heuver has managed, as part of his PhD thesis, to grow excellent quality thin films[1,2], which are arising great interest in the field. During this project the student will investigate the dielectric properties of these films and will search for signatures of magnetoelectric coupling.

[1] Strain-induced magnetic anisotropy in epitaxial thin films of the spinel CoCr2O4, J. A. Heuver, A. Scaramucci, Y. Blickenstorfer, S. Matzen, N. A. Spaldin, C. Ederer, and B. Noheda. Phys. Rev. B 92, 214429 (2015)

[2] Spin-Hall magnetoresistance and spin Seebeck effect in spin-spiral and paramagnetic phases of multiferroic CoCr2O4 films, A. Aqeel, N. Vlietstra, J. A. Heuver, G. E. W. Bauer, B. Noheda, B. J. van Wees, and T. T. M. Palstra, Phys. Rev. B 92, 224410 (2015)

Last modified:17 November 2017 1.59 p.m.