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OnderzoekZernike (ZIAM)OnderwijsTop Master Program in Nanoscience

NS194. Small research project -- projects for 2017

The available small research projects for 2017 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 ]

Group 1: Physics of Nanodevices

Project 1.1
Supervisor: prof. dr. T. (Tamalika) Banerjee

Spin orbit coupling induced new phenomena in devices between complex oxides and two dimensional materials

The effects of spin-orbit coupling at interfaces between complex oxides, two dimensional materials and their hybrids give rise to new phenomena which is studied in our research team. We tailor material interfaces for this and have demonstrated that electric fields at such interfaces can tune spin transport across them at room temperature. We are currently extending the work to the study of new material interfaces with the aim to exploit and enhance the effects of spin orbit coupling at the interfaces of a spin injection device. In this project the student will join the team of researchers to design new material interfaces using Pulsed Laser Deposition and contribute to the design of spin devices using the fabrication suite at Nanolab Groningen. Spin transport studies will be carried out in variable magnetic fields and temperature.

In another project a hybrid device of two dimensional material on a complex oxide interface will be fabricated with the aim to study the effects of spin orbit coupling on the spin transport and specifically around the ferroelectric phase transition temperature of the material. Recent studies in our team underpins the role of the electric field due to the surface dipoles to spin transport in such two dimensional materials. The student joining this project will participate in the device design, fabrication to spin transport studies in such hybrid devices.

Project 1.2
Supervisor(s): Prof. Caspar van der Wal, Tom Bosma

Waveguides in silicon carbide

Coherent spin states in defects in silicon carbide allow for quantum optical applications, such as magnetometry and quantum communication. However, to observe these phenomena at high temperatures, high intensity laser fields are required. Therefore, it is proposed to construct waveguides within silicon carbide to confine high laser power to small areas. Initial devices consist of an intrinsic layer of 4H-SiC, encapsulated between two n-type doped layers, which possibly creates the necessary contrast in refractive index to enable wave guiding. However, at this stage the physics of these effects still needs further studies. In this project you will contribute to optical experiments on several waveguide samples at both low temperatures (1.8K), and room temperature. This way, you will measure the quality of these samples, and consecutively make improvements to the device design. The experimental studies can or will be combined with studies of quantum-optical control of electronic spins in this material.

project 1.3
Supervisor(s): Xu Yang, Prof. Caspar van der Wal, Prof. Bart van Wees

Molecularly functionalized graphene nano opto-electronics

As the thinnest material on earth, graphene has attracted intense research interests in fields such as electronics, energy, surface sciences, bio-engineering and even medicine. In our group we use graphene as transport channels to build nano spintronic and electronic devices. However due to the lack of a bandgap graphene does not exhibit any optical reaction. In this project the student will try to introduce a self-assembled monolayer (SAM) of optically-active molecules onto graphene surfaces, in order to functionalize graphene for opto-electronic applications. The project starts with the preparation and optimization of SAMs, followed by single-molecular characterizations using various scanning probe microscopic (SPM) techniques. The student will be working with a strong and friendly team and will be able to use facilities in the Nanolab cleanroom and some chemistry labs. This is an interdisciplinary research that brings the topmaster core module knowledge together and puts it into practice.

Group 2: Membrane Enzymology group

Project 2.1
Supervisors: Dr. Aditya Iyer and prof. Bert Poolman

Biophysical characterization of a structural protein involved in cell volume regulation

Bacterial cells such as Escherichia coli (E. coli) are frequently exposed to osmotic challenges in osmotically diverse environments ranging from salty waters to the human gut. Their survival in such environments necessitates the presence of mechanisms such as cell-volume regulation. In fact, the regulation of cell-volume is an important mechanism not only to their survival but also for growth. This is because cells will otherwise lose control of their internal crowding and osmolarity, and may ultimately lyse or plasmolyse. How bacterial cells cope with osmotically diverse and dynamic environments is not well understood. Existing studies in literature suggest the role of an osmotically inducible protein Y (OsmY) that is expressed only under hyperosmotic stress in E. coli but the role and precise function of this protein remains unknown.

The protein OsmY is proposed to link the inner and outer membrane, and hence control the cellular volume. But the secondary structure of OsmY and the details of OsmY-membrane interaction have not been investigated yet. Knowledge of this information will be crucial for ongoing studies in the lab pertaining to regulatory mechanisms underlying survival of bacterial cells under (extreme) osmotic stress.

In this project, the student will carry out a comprehensive biophysical characterization of purified OsmY protein. From E.coli cells overexpressing the OsmY protein, the student will purify using established protein purification and analysis techniques. Thereafter, the secondary structure of OsmY will be investigated using circular dichroism (CD) spectroscopy and light scattering techniques. Additionally, phospholipid membrane binding studies will be carried out using isothermal calorimetry (ITC). If time permits, the student will learn how to engineer single point mutations in the OsmY protein that will be useful for fluorescent labelling.

Project 2.2
Supervisors: Wojciech M. Śmigiel, prof. Bert Poolman

Single molecule studies of membrane protein insertion rates in cells

Biological cells have many proteins in their membranes, carrying out for example transport of nutrients and energy conversion. Membrane protein production requires an insertion step, in addition to the transcription and translation steps common to all proteins. Translation and insertion of a single membrane protein happen simultaneously but staggered in time. Multiple proteins can be made from a single mRNA.

We want to measure the time between subsequent translation/insertions of proteins from a single mRNA inside growing and dividing bacterial cells. The traditional method for measuring the dynamics and kinetics of protein production is to fuse the protein of interest with a fluorescent protein. The presence of the fluorescent protein can be visualized in a fluorescence microscope. The problem with this is that it takes on the order of 10 min for a fluorescent protein to become fluorescent, whereas it takes 10’s of seconds for proteins to be produced and only a few minutes before mRNAs are degraded.

The solution we came up with is to visualize membrane protein production by localization of a fluorescent protein, which is present in the cytoplasm, to the membrane. This fluorescent protein is already fluorescent so the time it takes to visualize the insertion event is limited by the fluorescent protein finding the membrane protein, which it does in seconds. We can see the localization because membrane proteins diffuse 100 times slower than cytoplasmic proteins. This means that we can pick the exposure time of the camera such that the fluorescent cytoplasmic proteins look like a haze and the fluorescent membrane proteins look like clearly defined dots.

More specifically we have the membrane protein LacSΔIIA fused with multiple copies of the proteinprotein interaction domains Suntag or Synzip2 expressed in the bacterium Lactococcus lactis. In these same cells we have the fluorescent protein mNeongreen fused to the protein-protein interaction domains scFv or Synzip1. A similar setup is present in the bacterium Escherichia coli with the membrane protein LacY. We are also trying to visualize the insertion events of the protein OpuABC in Lactococcus lactis by labelling it from the outside of the cell with organic dyes attached to protein-protein interaction domains. Your contribution will be to try these methods out on a single molecule-sensitive fluorescence microscope and to tune the systems to make them work.


Review on single molecule studies of protein production in bacterial cells:
Li G. and Xie X.S. (2011) Central dogma at the single-molecule level in living cells. Nature

Single molecule studies on protein production:

Yu J., Xiao J., et al. (2006) Probing Gene Expression in Live Cells, One Protein Molecule at a Time. Science
Yan X., Hoek T.A., et al. (2016) Dynamics of Translation of Single mRNA Molecules In Vivo. Cell

Group3: Surfaces and Thin Films

project 3.1
Supervisor: Prof. M.A. Stöhr

Supramolecular networks from phthalocyanine derivatives at the solid-liquid interface

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 from phthalocyanine derivatives having alkoxy side chains on HOPG (highly oriented pyrolytic graphite). The samples will be studied by scanning tunneling microscopy at the solid-liquid interface. It shall be investigated which effect the side chains have on the structural arrangement of the molecules. In addition, the influence of both the solvent used and the molecular concentration on the outcome of the self-assembly process will be studied. Finally, binary mixtures of the two molecules will be investigated with the aim to unravel if intermixing or phase separation occurs.

Further information:

Group 4: Solid State Materials for Electronics

Project 4.1
Supervisor: Dr. Graeme Blake

Enhanced thermoelectric materials for waste heat recovery

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 thermoelectrics are derived from IV-VI semiconductors such as GeTe, PbTe and PbSe. Preliminary experiments in our group have suggested that incorporating small concentrations (about 1%) of magnetic transition metal or rare-earth elements such as Mn, V, Ce and Gd in IV-VI semiconductors can result in a remarkable improvement in their thermoelectric properties approaching record literature values. However, no systematic study of the effects of such substitutions has been carried out yet.

This project will initially involve the chemical synthesis of powder and single crystal samples of various promising group IV-VI TE materials derived from GeTe and possibly also GeSe. X-ray diffraction will be used to determine their crystal structures and will be complemented by scanning electron microscopy to examine their nanostructures. 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 4.2:
Supervisor: Dr. Graeme Blake

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, using methods such as chemical vapour transport and hydrothermal synthesis. 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 5: Micromechanics

Project 5.1
Supervisors: Sander Boonstra, Patrick R. Onck and Erik van der Giessen

Mechanics of influenza viral fusion: Evaluating free energy differences between hemagglutinin subtypes

Replication of 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

We are using confinement free energy molecular dynamics simulations to estimate the free energy that HA (virus subtype H3) can generate during its conformational rearrangements.2,3 However, HA constantly changes its appearance through mutations, thus creating new subtypes such as H1, H2 and H5, evading the existing antiviral drugs.
You will build models of the H1 intermediate and postfusion states, based on the H3 pre- and postfusion structures.4 From these, you will use confinement free energy simulations to estimate the free energy available in H1 and compare it to H3.

In the process, you will learn about the mechanics of biophysical phenomena like protein folding and membrane fusion. You will carry out molecular dynamics simulations on 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. Blijleven, J.S. et al. Mechanisms of influenza viral membrane fusion. Seminars in Cell and Developmental Biology 60, 78-88 (2016)
2. Cecchini, M. et al. Calculation of free-energy differences by confinement simulations. J Phys Chem B. 113(29), 9728-40 (2009)
3. Ovchinnikov, V. et al. A Simplified Confinement Method (SCM) for Calculating Absolute Free Energies and Free Energy and Entropy Differences. J Phys Chem B. 117(3), 750-762 (2013)
4. Arnold K. et al. The SWISS-MODEL Workspace: A web-based environment for protein structure homology modelling. Bioinformatics 22,195-201 (2006)

Group 6: Nanostructured Materials and Interfaces

Project 6.1
Supervisors: Paul Vermeulen Msc., Prof. Bart Kooi

Controlling the growth of 2D-chalcogenide superlattices using pulsed laser deposition

The challenge of present-day materials science lies in probing and exploiting the physics in materials with confined dimensions. 2D-chalcogenides, specifically the group V-VI materials, such as (Sb,Bi)2(Se,Te)3 naturally occur in quasi-2D layered structures bonded by van der Waals forces. They are intensively studied in bulk form for their remarkable functional properties as thermoelectrics, phase change materials, and topological insulators. Their exceptional bonding state allows us to build designer heterostructures, where successive material layers are stacked as if they were nanometer-thick Lego blocks, to optimize their functional properties. 1,2

In this project, you will grow your own samples of Sb2Te3 using a Pulsed Laser Deposition (PLD) setup. While this technique shows great promise in delivering stoichiometric and monolayer accuracy with short deposition times, the present challenge is to also control crystallographic structure and texture. The aim is to understand the physics governing growth of these materials. To this end, you will be trained to work with and interpret the data from a number of common analysis tools you will encounter in your future studies, e.g. SEM, TEM, AFM,XRD. The final goal of the project will be to combine your knowledge with that of a PhD student to grow a superlattice structure consisting of alternating layers of Sb2Te3/Bi2Te3.

1. Geim, a K.; Grigorieva, I. V. Nature 2013, 499 (7459), 419–425.
2. Snyder, G.; Toberer, E. Nat. Mater. 2008, 7 (February), 105–114.  

Group 7: Macromolecular Chemistry and New Polymeric Materials

Project 7.1
Supervisors: Jin Xu, Prof. Katja Loos

Polymer-templated chemical solution deposition of multiferroic nanocomposites

Multiferroic nanocomposites combine ferroelectric and ferromagnetic materials at the nanoscale. Various nanocomposite systems have demonstrated magnetoelectric coupling between the two ferroic phases [1], which makes them great candidates for applications such as four-state memory devices and magnetic field sensors. The previously studied multiferroic nanocomposites are predominately fabricated via pulsed laser deposition [2, 3], which requires expensive equipments and is unsuitable for large-scale manufacture.

The aim of this project is to fabricate ordered multiferroic nanocomposites via a low-cost chemical solution deposition approach, using nanostructured polymer thin films as templates. You will prepare the nanocomposites and measure their surface morphology with atomic force microscope. Film thickness determination with x-ray reflectivity will also be included. Once the nanocomposites are obtained, multiferroic properties will be investigated as well.

1. W. Eerenstein, N. D. Mathur, J. F. Scott, Nature 442, 759 (2006).
2. F. Zavaliche, H. Zheng, L. Mohaddes-Ardabili, S. Y. Yang, Q. Zhan, P. Shafer, E. Reilly, R. Chopdekar, Y. Jia, P. Wright, D. G. Schlom, Y. Suzuki, R. Ramesh, Nano Lett. 5(9), 1793 (2005).
3. X. Gao, B. J. Rodriguez, L. Liu, B. Birajdar, D. Pantel, M. Ziese, M. Alexe, D. Hesse, ACS Nano 4(2), 1099 (2010).

Group 8: Molecular Biophysics

Project 8.1
Supervisor(s): Prof. dr. Wouter H. Roos and Guus van der Borg

Nanoindentation measurements on healthy and cancerous cells

In addition to bulk measurements, single-particle techniques are increasingly widely applied to explore the physical properties of biomaterials, as such experiments directly give information of particle to particle heterogeneity. For instance, recently developed atomic force microscopy (AFM) nanoindentation experiments have been successfully implemented to investigate the material properties of bioassemblies. Using our existing expertise in AFM nanoindentation [1,2] the student will set-up a study of cell stiffness measurements for a variety of cells. In particular, we will use AFM to evaluate stiffness of healthy and cancerous cells. It is proposed that cancerous cells are more easily deformed, which would facilitate migration to the blood circulation, but opposing models are at hand as well. The student will scrutinize what the difference in material properties is between healthy and cancerous cells. If time permits, at the end of the project we will use primary cells from our collaborator at the UMCG.

[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

Project 8.2
Supervisor(s): Prof. dr. Wouter H. Roos and Pedro Buzón

Studying DNA-intercalator interaction by single-molecule techniques

DNA intercalators are widely used as fluorescent probes in molecular biology studies to visualize DNA by fluorescence microscopy. In addition, these compounds can be potentially used as precursors of anticancer drugs, since their strong interaction with DNA can perturb DNA stability and structure, which can in turn impede DNA replication. Even though DNA intercalators are well-known compounds, the binding mechanism of some of these molecules still remain uncharacterized.

For the study of DNA-intercalator interaction we will combine Optical Tweezers and Fluorescence Microscopy techniques [1]. This approach allows us to isolate and manipulate a single molecule of DNA, and look at single binding events simultaneously. This project will involve the performance of experiments at different intercalator concentrations, in order to fully describe the process in thermodynamic and kinetic terms. Thermodynamic information can be obtained by force spectroscopy measurement, following the changes in the mechanical properties of DNA molecules, while kinetics can be resolved by identifying and measuring fluorescence intensity of individual binder versus time. Studying one molecule at the time, we will be able to describe new molecular properties of these compounds that are unachievable by ensemble experiment.

We propose in this project the study of the interaction between DNA and intercalator compounds by applying force and fluorescence spectroscopy techniques at the single-molecule level, with the aim to unravel the mechanisms involved in DNA-intercalator interaction.

[1] M. Hashemi Shabestari, A.E.C. Meijering, W.H. Roos, G.J.L. Wuite, E.J.G. Peterman. Recent Advances in Biological Single-Molecule Applications of Optical Tweezers and Fluorescence Microscopy. (2017) Methods in Enzymology. Vol. 582, p85-119

Group 9: Synthetic Organic Chemistry

Project 9.1
Supervisors: Andreas Hussain, Guillermo Monreal Santiago, Piotr Nowak & Sijbren Otto

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 9.2
Supervisors: Guillermo Monreal Santiago, Andreas Hussain & Sijbren Otto

Insight in the replication mechanism of a synthetic molecule by isotopic labelling and mass spectrometry

Self-replication is one of the main characteristics of life. However, it remains unclear how this behavior could emerge in prebiotic systems. Synthetic self-replicators are relevant as a model to study this emergence, and also some other mechanisms that are found in living systems (competition, adaptation, Darwinian evolution…) [1]

In the Otto group, we have described how self-replicators can emerge from a dynamic combinatorial library of peptides functionalized with aromatic thiols [2]. These molecules self-assemble forming fibers, and achieve exponential growth by an elongation-fragmentation mechanism of such fibers (as illustrated in this video )

We have studied these fibers in very different contexts, ranging from materials science to mutation and evolution [3,4]. We have also obtained some insight into their replication mechanism via kinetic data and modelling [5], but the precise details for fiber fragmentation (one of the key events of the replication process) remain unknown.

In this project, you will prepare self-replicators using deuterated and non-deuterated peptides, and alternate both of them in supramolecular block co-fibers. Analysis of these fibers with chemical reduction and LC-MS should provide information of the composition of their fiber ends, and by analyzing them before and after mechanical fragmentation we are expecting to obtain information on the mechanism of this process. During the course of the project, you will gain experience with supramolecular chemistry, analytical techniques such as UPLC-MS or TEM, and mathematical models. You will also contribute significantly to our knowledge of the mechanism of this self-replication process.

1. Ruiz-Mirazo, K.; Briones, C.; de la Escosura, A. Chem. Rev. 2014, 114, 285
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.
3. A. Pal, M. Malakoutikhah, G. Leonetti, M. Tezcan, M. Colomb-Delsuc, V. D. Nguyen, J. van der Gucht, S. Otto. Angew. Chem. Int. Ed. 2015, 54, 7852.
4. J. W. Sadownik, E. Mattia, P. Nowak, S. Otto. Nature Chem. 2016, 8, 264.
5. M. Colomb-Delsuc, E. Mattia, J. W. Sadownik, S. Otto. Nat. Commun. 2015, 6, 7427

Project 9.3
Supervisors: Jim Ottelé & Sijbren Otto

Kinetic analysis of a self-replicating system

Self-replication, the ability to construct more copies of oneself, is a requirement for life de novo. To create synthetic life, a chemical system must at least have three major functions; it must self-replicate, it must have a metabolism and it must be compartmentalized [i] . In 2010, Sijbren Otto et al. reported [ii] a chemical system in which two types of self-replicating molecules emerge from a dynamic mixture of interchanging molecules.

Recently, a new method has been developed to determine kinetic parameters of these systems using UPLC (Ultra Performance Liquid Chromatography) and a Couette cell. This has been successfully applied to one of the model mixtures. We are now looking to expand this method to other systems and other parameters.

This project involves the identification of unknown parameters of various known replicators, such as growth rate, probability of breakage and temperature dependence. As a student, you will learn how to work with a glovebox, how to operate a Couette cell and how to prepare, perform and analyse UPLC samples. If the student is interested in modelling, these parameters can be used to do stochastic simulations of these self-replicating systems.

1. B.H. Patel, C. Percivalle, D.J. Ritson, C.D. Duffy, J. D. Sutherland, Common Origins of RNA, Protein and Lipid Precursors in a Cyanosulfidic Protometabolism, Nat. Chem., 2015, pp 301-307
2. J. M. A. Carnall, C. A. Waudby, A. M. Belenguer, M. C. A. Stuart, J. J.-P. Peyralans, S. Otto, "Mechanosensitive Self-Replication Driven by Self-Organisation", Science, 2010, pp 1502-1506

Project 9.4
Supervisors: Charalampos G. Pappas, Bin Liu and Prof. Sijbren Otto

Self-replicating peptide nucleic acids

The conditions that led to the formation of the first organisms and the way that life originates from a lifeless chemical soup several billion years ago are poorly understood, but scientists have considered that there is a close linkage between amino acids and genetic code that may extend to the origin of life. There's still a lot we do not understand about how nucleotides and those 20 simple amino acids worked together to promote chemical structure and function. The collaboration between RNA and peptides may give rise to life-like behavior even with simple fully synthetic building blocks.

We have discovered that small peptides can organize themselves into rings and subsequently form stacks. Each stack can grow from the end and after reaching a certain length can be broken by mechanical agitation into smaller stacks.2 The processes lead to self-replicating molecules-molecules that are able to make copies of themselves. Furthermore, we have recently observed diversification in these systems, where molecular information splits into two lineages.3

Now we would like to extend these principles and combining peptides and nucleobases into one building block. You will first investigate the role of the nucleobases and amino acids on the replication process and study the behavior of mixtures of building blocks containing complementary nucleobases (Adenine-Thymine and Guanine-Cytosine). Additionally, templating effects (by single nucleobases or oligonucleotides) will be explored in order to promote the formation of specific compounds in the dynamic molecular network.

This research project spans of a number of disciplines, including analytical chemistry, supramolecular and systems chemistry and origin of life research and builds an important new bridge to the hitherto unconnected discipline of evolutionary biology. Apart from performing exciting research, you will develop strong analytical skills in liquid chromatography, mass and circular dichroism spectroscopy.

1. W. Gilbert, Origin of Life - the RNA World. Nature, 1986, 319, 618.
2. J. M. Carnall, C. A. Waudby, A. M. Belenguer, M. C. Stuart, J. J. Peyralans and S. Otto, Science, 2010, 327, 1502-1506.
3. J. W. Sadownik, E. Mattia, P. Nowak and S. Otto, Nat. Chem., 2016, 8, 264-269 (accompanying video: )

Group 10: Theory of Condensed Matter

Project 10.0
Supervisor(s): Dr. Thomas la Cour Jansen

Ferroelectricity on the nanoscale in Hybrid Perovskite 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. For methylammonium containing materials, the organic ions have recently been demonstrated to rotate on two different timescales using non-linear optical experiments [1,2]. Modeling in our group has confirmed the experimental findings. However, the use of alternative organic ions holds interesting prospect for example for inducing ferroelectricity on the nanoscale.

Project: A classical molecular dynamics model will be developed for perovskite materials with alternative organic ions in combination with methylammonium.  The structural ordering and dynamics of the different ions will be studied both in the presence of an external electric field and without a field present. These new simulations will enable the study of collective organic ion dynamics and the emergence of nanoscale ferroelectric domains.

Further Information e-mail:


1. Jansen et al. Real-Time Observation of Organic Cation Motion in Methylammonium Lead Iodide Perovskites, J. Phys. Chem. Lett. 6: 3663 (2015)
2. Jansen et al. Organic Cation Rotation and Immobilisation in Pure and Mixed Methylammonium Lead-Halide Perovskites, J. Am. Chem. Soc. (submitted)

Project 10.2
Supervisor(s): Dr. Thomas la Cour Jansen

Sensing Stress by Light

Background: Dye molecules in close proximity of each other interact resulting in changes of the overall absorption of the systems [1]. When stress is applied to a system with interacting dye molecules the arrangement of these will be altered and the optical response changed [2]. This mechanochromic effect can be exploited to sense mechanical stress using light. While color changes in materials are apparent in experiments, the details of the mechanisms are poorly understood preventing the design of materials capable of distinguishing normal and sheer stress. Such materials will be useful for early detection of problems for example plane wings.

Project: The goal is to identify and explain the difference of the effect of normal and shear stress on the optical response of dye molecule stacks. A coarse-grained coupled spring model will be used to model the mechanical properties. Assuming a Frenkel exciton model the absorption spectra will be modeled under different stress conditions. By varying the applied stress and monitoring the resulting spectral changes a fundamental understanding of the stress-spectral relationship will be established and ideas for more efficient dye arrangements will be considered.

Collaboration with: Francesco Picchioni

Further Information e-mail:

1. Exciton mobility control throughsub−Å packing modifications in molecular crystals N. J. Hestand and R. Tempelaar and J. Knoester and T. L. C. Jansen and F. C. Spano, Physical Review B  91    (2015)
2. Approaches to polymeric mechanochromic materials C. Calvino and L. Neumann and C. Weder and S. Schrettl Journal of Polymer Science Part A: Polymer Chemistry  55  640–652  (2016)

Project 10.3
Supervisor(s): Dr. Thomas la Cour Jansen

Molecular Motors driven only by Light

Background: The 2016 Nobel prize was awarded in for the development of Molecular motors. 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: The goal is to identify candidate molecules that follow a new design principle for light-driven molecular motors. Using electronic structure calculations the energy landscape for the proposed molecules will be explored and suitable molecules will be tested using quantum-classical calculations to study their dynamics under working conditions.

Further Information e-mail:

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

Group 11: Optical Condensed Matter Physics

Project 11.1
Supervisor(s): Björn Kriete and Dr. Maxim S. Pchenitchnikov

Nanoconfinement in Self-Assembled Molecular Aggregates

Inspired by the success of natural photosynthetic complexes, self-assembled molecular aggregates have garnered considerable interest as promising candidates for artificial light-harvesting systems. Specifically, in aqueous solution the cyanine dye C8S3 autonomously assembles into highly uniform nanotubes of ~15 nm diameter and μm’s lengths [Nature Chemistry 4, 655 (2012)]. These nanotubes are composed of many thousands of energetically coupled molecules giving rise to highly delocalized excited state wavefunctions [NanoLetters 16, 6808 (2016)]. Physically truncating the nanotube at 100’s nm lengths leads to localization/confinement of the excited state wavefunction, in close analogy to the size dependence of quantum dots.

The current project aims for combined spectroscopy/microscopy investigation of the nanoconfinement effect in the self-assembled nanotubes. The main focus of the project is on the fluorescence signature of the single nanotubes. First, the student becomes acquainted with the sample preparation, which specifically means inducing the aggregation and subsequently embedding the aggregates in a sugar matrix at different growth stages to truncate the length. As a next step, the student will use optical microscopy with diffraction-limited spatial resolution to characterize the size distribution of the nanotubes and record their fluorescence spectra. Finally, the acquired data will be evaluated, interpreted and discussed. The project will be benefit from theoretical support from and close collaboration with the Molecular Dynamics and the Theory of Condensed Matter groups of the Zernike Institute.   

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

- Familiarization with optical microscopy and related spectroscopic techniques
- Application of these techniques to investigate nanoconfinement in nanotubes
- Acquisition and assessing experimental data
- Drawing scientific conclusions from results and discussing/defending these
- Preparing a scientific presentation on the results of the project

Project 11.2
Supervisor(s): Oleg Kozlov and Dr. Maxim S. Pchenitchnikov

Small Molecular Semiconductors: Effect of Molecular Design on Ultrafast Photophysics

Small semiconducting molecules are nowadays the most promising class of organic photovoltaic materials due to their high stability, excellent reproducibility and outstanding flexibility in molecular design. The latter is of great importance: even slight variations of the molecular chemical structure may lead to unexpected changes in photophysical properties of the material. Therefore, understanding the structure-properties relationship in small molecules is one of the primary goals of material science.

This experimental project aims at revealing the effect of molecular design on ultrafast photophysics of novel star-shaped small molecules [Organic Electronics 32, 157 (2016)]. The research involves manufacturing of the samples and their spectroscopic characterization, including ultrafast photoluminescence measurements. During the project, the student will learn underlying photophysical processes in organic electronic devices. He/she will acquire skills and expertise in fields of “soft” condensed matter and (ultrafast) optical spectroscopy.

Group 12: Chemistry of (Bio)Molecular Materials and Devices

Project 12.1
Supervisor(s): Prof. Ryan Chiechi and Marco Carlotti

Exploring Quantum Interference in Tunneling Junctions: an Interdisciplinary Approach to Molecular Electronics

The aim of molecular electronics is to make use of single molecules (or single molecular arrays) as active elements in the field of electronics. Compared to silicon-based technologies, when dealing with entities on the nanometer scale, the quanto-mechanical nature of matter is relevant and might confer to the devices properties that are not possible to obtain otherwise.

In our research group we are interested in the planning, the design, and the synthesis of organic molecules with an interesting electronic structure which might show peculiar transport properties. A simple and easy-to-use experimental setup is then used to investigated the electrical properties of large area tunneling junctions comprising Self-Assembled Monolayers (SAMs) of the compounds we prepared.

In one of our recent studies (Carlotti et al., Nature Communications, 2016, 7, 13904) we highlighted the possible correlation between the molecular geometry and destructive Quantum Interference (QI), a phenomenon that can change the conductivity of tunneling junctions by several order of magnitude. In this project: new compounds will be synthesized which present different electronic and/or steric characteristics; SAMs of these latter will be grown on atomically flat Au or Ag surfaces, and characterized by different techniques; and, finally, the performances of the different SAMs as active element in molecular junctions will be studied in large-area tunneling junctions using a non-Newtonian liquid metal alloy (EGaIn, Ga and In at their eutectic composition) as top electrode in order to gain better insight on the role of dipoles, bond alternation, and molecular geometry on QI and the electric properties of large area tunneling junctions.

Project 12.1
Supervisor(s): Prof. Ryan Chiechi and Marco Carlotti

Exploring Quantum Interference in Tunneling Junctions: an Interdisciplinary Approach to Molecular Electronics

In order to extent the Moore's law, new methods to fabricate smaller feature sizes of transistors are required since the limitation of tradition photo lithography technologies. Bottom-up methods provide an approach to minimize the dimensions of channel of transistors which is decided by a monolayer of molecules (1-2nm). In this project, you will learn how to prepare reduced graphene oxide(rGO), fabricate molecular transistors by our nanofabrication method called nanoskiving and characterize their electrical performance.

These devices are based on SAM-templated nanogaps as described here: ACS Nano 2012, 6 (6), 5566. In this project, you will add a third electrode to function as a gate. At first, working with rGO as a proof-of-concept and then (time permitting) by introducing molecules into the gap and attempting to gate them.

Group 13: Quantum Interactions and Structural Dynamics

Project 1 3.1
Supervisor(s): Prof. Dr. Ronnie Hoekstra and Dr. Thomas Schlathölter

EUV sources for nanolithography

Next generation nanolithography machines will use EUV light at 13.5 nm for “writing”. To generate intense beams of 13.5-nm light micrometer size tin droplets are irradiated with a powerful infrared laser, creating an exploding plasma ball of tin ions which produces the EUV light. The energetic Sn ions may damage plasma facing material and equipment. To protect the equipment against damage hydrogen gas is used to stop the Sn ions.

The aim of the project is to perform the first experiments of energy and charge-state selected Sn ions colliding with H2 gas. These experiments should unveil whether the H2 molecules stay intact or fragment into two energetic hydrogen atoms or ions, which in their turn may damage plasma facing optics.

Last modified:15 December 2017 3.31 p.m.