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OnderzoekZernike (ZIAM)OnderwijsTop Master Program in Nanoscience

NS194. Small research project -- projects for 2012 [now obsolete]

The available small research projects for 2012 are listed here. Please contact the supervisor mentioned in case you are interested in a project. First come, first served...

1 Group: Micromechanics

Project 1.1

Supervisor: Prof. Patrick Onck

Nanoporous actuators

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

Project 1.2

Supervisor: Prof. Patrick Onck

Molecular modeling of transport through the Nuclear Pore Complex

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

2 Group: Polymer thin film and surface science

Project 2.1

Supervisor: Prof. Arend Jan Schouten

Cell-polymer surface interactions

Tissue regeneration is the technology to grow new tissue in situ in vivo supported by a synthetic scaffold. Scaffold materials include mostly (semi)synthetic polymers processed into a suitable system to support and enhance cell growth and tissue regeneration.This can be a hydrogel, foam or woven and non-woven fabric. Ultimately the polymeric system has to be resorbed by the body leaving newly formed tissue. Successful systems from our lab include polyurethanes based on butanediisocyanate and oligoesters. Not much is known about the fundamental interactions and processes occurring at the interface between the adhering cells and polymer surface. Also differences between different cells and the polymers are not studied so far.

The project is about the fundamental study of the interaction between cells and polymer surfaces, both from a materials point of view and a biological point of view and will be carried out in close collaboration with the medical department.

Polymers have to be synthesized, processed into suitable substrates and covered with different cells. After growth and proliferation cell behaviour will be studied as well as the surface of the polymeric substrates. Polymers include polyurethanes 1 mentioned above and amylose-derived polymers.

1.Heijkants, R. G. J. C.; van Calck. R. V.; van Tienen, T. G.; de, Groot. J. H.; Pennings, A. J.; Buma, P.; Veth, R. P. H.; Schouten, A. J., Polyurethane scaffold formation via a combination of salt leaching and thermally induced phase separation. J. Biomed. Mater. Res., Part A 2008, 87A, 921-932.

3 Group: Single-molecule biophysics

Project 3.1

Supervisor:  Dr. Thorben Cordes (

) DNA-based catalysis one molecule at a time (Spectroscopy, Chemistry & Optics)

Our group uses single-molecule fluorescence microscopy as a tool to monitor unsynchronized (bio)chemical reactions in real-time. In such systems, fluorescent molecules report on the state of a (bio)chemical substrate or catalyst. In this project, you will develop a novel assay to monitor chemical reactions occurring at a DNA-based catalyst. Here, the “reporter-dye” will only be fluorescent during the periods of chemical conversion. This gives a direct access to the duration of the chemical processes and hence provides unique insights into the studied reaction. Your task in the project will be the preparation, surface immobilization and spectroscopic characterization of the active catalyst/reporter-complex. Finally, you will monitor single turn-over events in the presence of substrates using state-of-the-art single-molecule fluorescence microscopy. For this interdisciplinary research we expect a keen interest (but not necessarily expertise) in laser-microscopy, single-molecule detection, and wet-lab work, i.e., surface chemistry & sample preparation.

Project 3.2

Supervisor:  Dr. Thorben Cordes (

Monitoring molecular transport molecule by molecule (Spectroscopy, Biophysics & Optics)

ABC (ATP Binding Cassette) transporters are ubiquitous in cells of all three domains of life and represent the most abundant and diverse family of known transport proteins. Despite their importance we still lack a fundamental understanding of the dynamical conformational changes in these proteins that occur upon transport of a substrate. In this project it is your aim to pave the way for a single-molecule assay that monitors transport-associated conformational changes in dimeric protein domains with high distance resolution <2nm. You will therefore characterize the distance dependence of the self-quenching process of two (identical) organic fluorophores. By testing different single-molecule compatible fluorophores using ensemble and single-molecule methods (fluorescence spectroscopy & microscopy) you will identify suitable dyes, which can be used for protein labeling later on, for the transport-assay. This project has a focus on the spectroscopic investigation of fluorophores and the self-quenching processes. We expect a motivated student that is willing to work on laser-microscopy, single-molecule detection and to perform wet-lab work in order to prepare samples.

Project 3.3

Supervisor:  Dr. Thorben Cordes (

Measuring distances at the nanoscale (Subjects: Programming, Spectroscopy & Biophysics)

Förster resonance energy transfer (FRET) is a powerful tool to study distance changes (2-10 nm) in biological systems such as proteins, DNA or RNA. In this project you will contribute to our efforts to study the conformational equilibrium (open vs. closed form) of the substrate-binding domain of the bacterial membrane transporter OpuA, which is responsible for cell-volume regulation. Your main task is to design a software that allows to combine single-molecule detection in a confocal microscope with distance measurements in proteins via FRET. You will (i) establish a software for alternating laser-excitation, i.e., rapid switching of laser excitation from green to red on the µs-time-scale, and (ii) test this method on fluorophore-labelled double-stranded DNA or labelled proteins. We are looking for a student with interest in a highly interdisciplinary research project that has the major focus on lab-view programming and experimental realization of single-molecule FRET measurements; only minor parts of the project will involve wet-lab work.

4 Group: Physics of nanodevices

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

These projects are in an experimental research effort that explores whether quantum information that is carried by an optical pulse can be stored in a memory element that is formed by an electron-spin ensemble in a semiconductor. This work is relevant for developing quantum-computation and quantum-communication systems with solid-state devices, and for research on the foundations of quantum theory.
For the Spring of 2012 we look for student participation in these two experiments:

Project 4.1

Supervisor: Prof. C.H. van der Wal

High resolution spectroscopy of donor-bound exciton states

Our quantum memory uses the spin states of an electron that is bound at a donor atom in a very pure semiconductor (GaAs). Optical interaction with these states is implemented via transitions that create a bound exciton (electron-hole pair) at the donor site. Despite 50 years of research, there is no consensus on the energy level structure of this system, but detailed knowledge of this is key for future work. You will participate in optical spectroscopy experiments with ultra-high resolution that can unravel the energy level structure.

Project 4.2

Supervsior: Prof. C.H. van der Wal

Driving nuclear magnetic resonance in quantum-optical devices

The spin states of an electron that is bound to a donor atom in a very pure semiconductor (GaAs) form the 0 and the 1 state of the quantum memory that we develop. We need control over long-lived coherent quantum superpositions of these two spin states. Loss of quantum coherence is dominated by weak interactions with nuclear spins in the sample. You will participate in our first experiments that use nuclear-magnetic-resonance (NMR) techniques for bringing the nuclear spins in a state where they do not harm the quantum coherence of the electron spin.

Project 4.3

Supervisor: Dr. T. Banerjee

Spin transport in metallic spin valves using an epitaxial Schottky interface

The possibility of fabricating epitaxial interfaces of Cu on Si(100) using an unique fabrication protocol has enabled us to study spin transport in metallic spin valves. We have recently demonstrated exciting features in the spin dependent transport of metallic spin valves with increasing energy. For this, we use the technique of Ballistic Electron Magnetic Microscopy (BEMM). The features in spin transport are correlated to the location of the energy bands in the bulk semiconductor and the efficiency of the epitaxial Schottky interface to act as an effective momentum filter. Besides, using the technique of BEMM, we have been successful in resolving magnetic domains over a lateral extent of 16 nm which sets a new high to the resolution of this technique. We are actively pursuing extensions of this work to unravel the unknown contributions of different scattering mechanisms to spin dependent transport in diverse spin valves.

The student will have hands-on experience in the growth and fabrication of such nanodevices using the facilities available at NanoLab Groningen (evaporation, sputtering, UV and e-beam lithography) and at the Physics of Nanodevices group (BEEM and standard magnetotransport measurements).

Further information on the published work and experimental details can be obtained from Subir Parui ( )

Project 4.4

Supervsior: Dr. T. Banerjee

Spin transport in all-oxide heterojunctions

Novel devices of an epitaxial ferromagnetic oxide on an oxide semiconducting substrate have been fabricated and their electron transport, at the nanoscale, and at different energies investigated. Such studies, done for the first time in an intrinsically phase separated correlated oxide system, have revealed several important features in electron transport not only at Room Temperature but also at low temperatures and with applied magnetic field. The thrust is on understanding the scattering processes that govern the transport parameters (time and length scales) in such oxide systems, in all-oxide heterostructures, at the nanoscale. A futuristic goal is to study the spin transport of electrons in an all oxide spin valve involving half-metals. Further, local imaging done on such heterostructures, with the technique of Ballistic Electron Emission Microscopy (BEEM) has revealed anisotropic conduction in the epitaxial films – a direction which is being currently pursued.

The student will work closely with the Ph.D student(s) involved in this project and will have access to the growth and fabrication infrastructure available at NanoLab Groningen (evaporation, sputtering, UV and e-beam lithography) and at the Physics of Nanodevices group (BEEM and standard magnetotransport measurements)

Further information on the ongoing/published work and experimental details can be obtained from Gaurav Rana ( )

5 Group: Nanostructured materials and interfaces

Project 5.1

Supervsiors: O. Ergincan, Dr. G. Palasantzas, Prof. B.J. Kooi

Influence of crystalline-amorphous phase transition onresonatingproperties of micro cantilevers

To investigate how the amorphous-to-crystalline transition in thin films deposited onto microcantilevers affects the quality factoras a function of pressure and surface morphology.This will be accomplished with noise measurements from high vacuum to air in a dedicated atomic force microscope assembled to allow evacuation down to 10-6 mbar.

Project 5.2

Supervisor: Dr. G. Palasantzas

Surface patch potentials contribution on contact potential: An surface scanning potential microscopy (SSPM) study with application to Casimir force

Although the surface electric forces can be minimized during a Casimir force measurement, they cannot be completely nullified and the presence of the so called contact potential is manifested in Casimir force measurement. The presence of such a long-ranged force can be heavily pronounced in materials preventing the experiment to distinguish among different theoretical models describing the thermal Casimir force. Moreover, it represents an obstacle in search of new forces beyond the standard model since the Casimir effect is a possible probe in this strange world. The situation is rather complex since the contact potential varies with separation distance due to surface patch potentials (areas with different work functions). Therefore, studies with AFM based surface scanning potential microscopy (Kelvin probe microscopy) is a tool to augment our understanding of surface potential variation with surface roughness and if possible to obtain further information for patch potential distributions.

Project 5.3

Supervisors: G. Krishnan, Dr. G. Palasantzas, Prof. B.J. KooiCore shell nanoparticles

AFM analysis of size distributions of core-shell nanoparticles produced via gas phase high pressure magnetron sputtering in combination with a unique magnetron coater of a beam of nanoparticles. Comparisons of the particle coating technique to core shell nanoparticles produced using joinedmetal targets will be performed. Comparison with results from TEM will also be performed. The work will be done under the supervision of  G. Krishnan, G. Palasantzas, and B. J. Kooi.

6 Group: Optical condensed matter physics

van Loosdrecht/Pchenitchnikov/Tobey

The optical condensed matter physics group focuses on the physical properties of materials with intriguing electromagnetic functionalities (magnetism, ferroelectricity, charge separation, etc. etc.). Below are some examples of short projects within the current research lines investigated within the group. For more information please contact the person mentioned or the group leader Prof. Paul van Loosdrecht ( ). For the projects related to photovoltaics one may also contact Dr. MaximPchenitchnikov ( ). More information can be found on the OCMP website ( )

Project 6.1

Hybrid materials: Coupling of low energy excitations to ferroelectric and ferromagnetic order

Hybrid materials combine the intriguing electronic properties of inorganic matter with the versatility of organic matter. Recently our institute discovered that some members of this class of materials exhibit a simultaneous magnetic and polar order. This opens the potential to use these materials in magneto-electric applications. The goal of this project is to investigate the coupling of low energy modes with the ferroelectric and ferromagnetic transitions in these materials. The project comprises a temperature dependent study of low energy excitations using state-of-the-art time domain femtosecond THz spectroscopy.

Contact: Toni Caretta ( )

Project 6.2

Optical signatures of photogenerated charges

Conjugated polymers are one of the perspective classes of materials for application as light-absorbing and charge-transporting components in potentially inexpensive and mechanically flexible organic photovoltaics (OPV). The efficiency of these materials is largely determined by their charge photogeneration properties. The aim of the project is to detect and assign the charge-associated absorption bands in the novel polymers by (ultrafast) optical spectroscopy.  

Contact: Vlad Pavelyev (

Project 6.3

Energy and charge dynamics at organic interfaces

The project aims at understanding of fundamental photophysical processes at the interfaces of photovoltaic related organic materials. It is primarily focused on the initial processes in material after light is absorbed, namely energy and charge transfer dynamics. The knowledge gained from research is essential step in understanding possibilities to manipulate the processes in favor for innovative devices, in example: organic photovoltaics, organic light emitting diodes, organic optoelectronics, etc. Dynamics will be observed using ultrafast laser systems. Additional characterization of materials will be done with absorption and fluorescence spectrometers and other equipment.

Contact: Almis Serbenta (

Project 6.4

Optical control of Spin-Peierls transition in CuGeO3

The insulating low dimensional quantum magnet CuGeO3 has a spin chain structure characterized by a spin-Peierls transition at low temperature, i.e.a spontaneous pairing of neighbouring spins along the chain, accompained by a structural distortion. This makes this system an archetypical material to investigate the interplay between the magnetic (magnons), electronic (zhang-rice singlets) and vibrational (phonons) degrees of freedom in low dimensional quantum magnets. This phase transition can be observed – and potentially controlled – by time resolved optics using short coherent pulses in the Therahertzfrequency region.

Contact: Ekaterina Khadikova ( )

Project 6.5

Non-equilibrium heat transport in low dimensional quantum magnets at small length scales.

In low dimensional quantum magnets heat transport is controlled by the subtle interplaybetween the magnetic excitationsand other degrees of freedom, like crystal vibrations (phonons). This dynamics mainly unfolds at short length scales.The aim of the project is to use ultrafast laser systems, cryomicroscopy, and various nonlinear optical techniques to make time resolved transport experiments with high spatial resolution to extractinformation about the magnon-phonon interaction dynamics.

Contact: Matteo Montagnese (

Project 6.6

Dynamical thermal conductivity in bulk magnetic materials

To measure heat conductivties in low dimensional quantum magnet in a dynamical way we have developed a new approach to measure the dynamic heat conductivity of materials using particular fluorescent molecules as temperature sensors. This allows us to explore the non-equilibrium transport dynamics of different materials in a flexible and controlled way.The aim of the project is to apply this method to a well-known class of bulk magnetic materials in the fluoride and garnets family, to validate the technique and to investigate the magnon-phonon interplay in these well studied materials.

Contact: Matteo Montagnese ( )

Project 6.7

Characterization and optimization of a low dimensional magnetic thermal rectifier

The junction between two materials with different thermal conductivities can result in a thermal rectifier, a device resembling the diode semiconductor p-n junction in electronic devices. Such rectifiers are considered to be key elements in the development of caloritronics. Low dimensional quantum magnets are interesting candidates to be used in a thermal rectifier. The aim of the project is to simulate and build a rectifying junction with low dimensional quantum magnets and subsequently characterize it by the time of flight method.

Contact: Matteo Montagnese ( )

7 Group: Polymer chemistry & bioengineering

Details about the following three projects can be obtained from Prof. Andreas Herrmann directly.

Project 7.1

Supervisor: Prof. A. Herrmann

Nanodiagnostics: Virus-DNAzyme hybrid detection assays

Project 7.2

Supervisor: Prof. A. Herrmann

Slippery DNA

Project 7.3 [No longer available: chosen by Eric de Vries]

Supervisor: Prof. A Herrmann

Optically active SWNTs-FET-sensors for detection of chiral molecules

8 Group: Surfaces and Thin Films

Project 8.1

Supervisor: Dr. M. Stöhr

On-surface polymerization

The implementation of one- and two-dimensional organic polymers as active materials in nanoelectronic devices is a promising alternative to conventional silicon-based materials. Advantages are much lower fabrication costs and tunable properties. With the extremely high charge carrier mobility of graphene in mind, the prospect to achieve similar values for conjugated two-dimensional polymers is very stimulating for performing research towards their controlled fabrication.

The aim of the project is to create one-dimensional polymers on a substrate surface and to perform a detailed characterization regarding structural properties. In a first step, the starting molecular building blocks (monomers), from which the polymeric material will be fabricated, need to be characterized with respect towards intermolecular and molecule substrate interactions. This will be done with scanning tunneling microscopy under ultrahigh vacuum conditions at either room or low temperature. In retrospect, this information will help to understand the underlying principles for polymer formation on surfaces like diffusion and / or pre-organization of the monomers. In a second step, the chemical reaction leading to the polymer formation will be initiated. This will be done by heating up the sample. The obtained polymeric material will be characterized in a similar way as the monomers were already characterized. A careful analysis of all the data will result in a better understanding of the various parameters controlling on-surface reactions.

Project 8.2

Supervisor: Prof. Dr. P. Rudolf

Daily supervisor: Oleksii Ivashenko

Molecular switching in the self-assembled monolayers

Nano-engines and molecular motors are at the heart of practically all biological processes. In contrast to nature’s approach to achieving complex tasks, manmade technology functions exclusively through the static and/or equilibrium properties. It is therefore to be anticipated that the controlled movement of molecules or parts of molecules, offers unprecedented technological possibilities for the future. This project seeks to step forward in this direction by utilizing the effects of mechanical motion at the molecular level to induce changes in physical properties at the macroscopic level. Self–assembled monolayers of various organic switchable molecules (diarylethenes, spiropyrans, azobenzenes, rotaxanes, ruthenium complexes) will be prepared. Their composition and changes which occur in the monolayer upon applying photo-, electrochemical stimuli will be studied by X-rays photoelectron spectroscopy and contact angle measurements.

Project 8.3

Supervisor: Prof. Dr. P. Rudolf

Daily supervisor: Naureen Akhtar

Multifunctional organic-inorganic hybrid films

The field of organic-inorganic hybrids aims at combining the novel properties of these two classes into a single material. The focus of the present work is to combine the versatility of organic conducting materials with the intriguing magnetic properties of inorganic materials. Such hybrids could provide a potential for applications in cheap and printable single-use electronics that require both data storage and data processing.

In the first step, thin hybrid films composed of conducting organic molecules and photoswitchable single-molecule magnets will be fabricated in layer by layer fashion by employing the Langmuir-Blodgett technique. In the next step, thin films will characterized for crystal structure and composition analysis using X-ray diffraction and X-ray photoelectron spectroscopy respectively. Fourier transform infrared and electron paramagnetic resonance spectroscopy will be done to quantify the molecular orientation and photoswitchable properties of the organic and inorganic molecules.

Project 8.4

Supervisor: Dr. M. A. Stöhr

Daily supervisor: Stefano Gottardi

Study of graphene production by CVD on Cu(111) and copper foil
Graphene, a single layer of carbon atoms positioned in a honeycomb fashion is a very promising new material for applications in electronics, spintronics, sensor development, photovoltaics as transparent electrodes and many more. Chemical vapour deposition (CVD) of methane is one of the widely used production methods for this material but the details on what exactly determines the grapheme properties as a function of production protocol are not known yet. This project aims at understanding these issues and clarifying the role of oxygen on the growth process and its contribution to the modification of the morphology of graphene/copper. Photoemission spectroscopy, scanning tunneling microscopy and atomic force microscopy will be employed to characterize grapheme.

9 Group: Solid state materials for electronics

Project 9.1

Supervisors: Prof. Thomas Palstra and Dr. Graeme Blake

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

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

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

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

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

Project 9.2

Supervisors: Prof. Thomas Palstra and Dr. Graeme Blake

Structural and magnetic properties of organic-inorganic hybrid materials

Organic-inorganic hybrid materials consist of transition metal halide layers separated by organic molecules; the two components are held together by hydrogen bonding. These hybrids combine the robust electronic and magnetic properties of inorganic materials with the structural flexibility of organics. They are of interest in various fields of research such as multiferroics, energy storage and highly anisotropic magnetic systems. Some of the most interesting compounds in this class of materials are the family of nickel chloride-based hybrids, which form one-dimensional chains of Ni2+ cations along which the strongest magnetic interactions are found. The resulting spin chains that are formed at low temperature give way on further cooling to a magnetic ground state that is still unclear - either a Haldane gap opens or three-dimensional magnetic ordering sets in due to weak inter-chain interactions. The type of organic ligand and especially its conjugation give rise to large differences in the magnetic behavior, for reasons that are not yet understood.

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

-Crystal growth from aqueous solution.

-Powder X-ray diffraction as a function of temperature and differential scanning calorimetry to determine any structural phase transitions that are present.

-Single crystal X-ray diffraction to determine precise details of the structures of hybrids containing different organic ligands.

-Measurement of the magnetic properties as a function of temperature and applied magnetic field for hybrids containing different organic ligands.

10 Group: Synthetic organic chemistry

Project 10.1

Supervisor: Dr. S. Otto

Responsive materials that make themselves

Dynamers are defined as "dynamic combinatorial polymers" and are a unique type of material that can change its chemical composition in response to changes in its environment. Thus, dynamers can undergo changes in their physical and chemical properties as a result of an external stimulus. Objective of this project is to expand the family of dynamers with a new type of architecture: dynatubes, which are dynamic nanotubes. Using the extensive expertise on dynamic combinatorial chemistry within the Otto group we aim to build dynamic nanotubes through linking stacks of simple macrocycles. The macrocycles are, under specific conditions, able to stack on top of each another forming nanotubes. Under other conditions, the nanotube may be switched back to the macrocycles.

During the course of the project the student will synthesize a building block and investigate the conditions for nanotube formation.

Project 10.2

Supervisor: Dr. S. Otto

Instructable silica nanoparticles for biomolecule recognition

Surface recognition plays an essential role in biological systems; the process is responsible for selective interactions of biomacromolecules in cell cycle regulation, gene expression, signalling, immune responses, etc. The enormous complexity and plasticity of the surfaces involved in such binding renders the design of synthetic materials targeting them a huge challenge. However, if such materials are built from a mixture of small building blocks reacting reversibly with each other (Dynamic Combinatorial Chemistry), the target biomolecule can be added as a template to direct the functionalization of the surface by self-assembly. Because thousands of possible surface patterns can be formed from even a small set of building blocks, there is a large probability of that some of these are good binders of the target molecule. When surface functionalization is performed under using a reversible reaction, the various surface patterns are in equilibrium with each other. The pattern that best matches the biomolecule surface will bind to it and will thereby be stabilized and become the dominant pattern in the system. Hence, the optimum surface functionalization can be achieved in a one simple step, provided that appropriate building blocks are present.

Most biological targets (proteins, DNA) are a few nanometers in size; therefore a scaffold of comparable dimension has to be used. Spherical nanoparticles of tuneable size are ideally suited for this purpose. Silica nanoparticles can be easily coated with organic ligands which can be subsequently functionalized to form nanoparticles with aldehyde groups on their surfaces. Aldehydes and amines form imines reversibly. Imine formation is unfavorable in water, unless the pattern formed is able to bind the template (no nanoparticles with the wrong patterns should be produced). In this way, the biomolecule instructs the nanoparticles how to recognize it. Next, in order to fix the recognition sites, imines can be reduced to amines, so that the nanoparticles permanently memorize the information from the template. Nanoparticles obtained in such way can be used as for sensing and imaging purposes or as drugs altering cellular processes.

Techniques used in this project will include chemical synthesis, HPLC, TEM, electrophoresis, ITC, NMR, MS.

Further reading: P. T. Corbett et al., Chem. Rev. 106, 3652 (2006).

11 Group: Materials science

Project 11.1

Supervisor: Dr. W. van Dorp or Prof. J.Th.M. De Hosson

Writing SiO2 on the nanoscale with a new type of lithography

Focused electron beam induced deposition (FEBID) is a new type of lithography. Well-known lithographic techniques such as optical lithography and electron beam lithography need photo-sensitive layers to define and transfer patterns. In contast, with FEBID material can be deposited directly, without any additional processing steps. The strong point of FEBID is its high resolution: 15 nm wide lines are feasible with our setup.

One of the materials we deposit with FEBID is SiO2. Preliminary experiments indicate that it has good insulating properties, which makes it promising for use in nanoelectronics. But how good is it exactly? In this project, you will characterize the electrical properties of the SiO2, as well its composition and morphology. Along the way you will be introduced to advanced techniques such as scanning and/or transmission electron microscopy.

Project 11.2

Supervisor: Dr. W. van Dorp or Prof. J.Th.M. De Hosson

A new precursor for electron-induced physics and chemistry

A promising lithography technique for future nanotechnology is focused electron beam induced deposition (FEBID). In FEBID, gaseous precursor molecules are introduced in a vacuum system and they adsorb on the surface of the sample. The precursor molecules carry the material that the operator wants to deposit (for instance gold). When the precursor molecules are exposed to electrons, they dissociate and form the desired deposit on the surface. The main advantages of FEBID are that it is a one-step process and that a high resolution can be obtained: we have written features as small as 1 nm.

A major limitation of FEBID is currently the purity of the deposit. The dissociation of existing precursors is generally incomplete, so that (unwanted) fragments of the molecule are included in the deposit. In this project, you will test a new gold compound that is expected to perform much better than existing precursors. You will do this with X-ray photoelectron spectroscopy, a characterization method that uses monochromated X-rays to measure subtle changes in the precursor. Along the way you will be introduced to the use of ultrahigh vacuum techniques.

Project 11.3

Supervisor: Dr. W. van Dorp or Prof. J.Th.M. De Hosson

Cutting graphene with the electron beam

Graphene is a material that attracts great attention from scientists and engineers because of its unique electrical, optical and mechanical properties. But creating arbitrary circuits with graphene is not so straightforward, because how do you cut or pattern the graphene? Standard patterning approaches rely on photosensitive resists or ion beams, both of which can create unwanted damage to the graphene.

In this project, you will attempt to pattern graphene with the electron beam in a scanning electron microscope, in the presence of water. The water will act as the etchant gas, which is locally activated by the electron beam. At room temperature there is little interaction between the graphene, making the etching slow and inefficient. We expect that the etch rate increases significantly if the sample is cooled. Your goal is to explore this approach with sample cooling, which, if successful, potentially has a high impact.

Project 11.4

Supervisors: Dr. W. van Dorp (Materials Science Group) and Dr. R. Havenith (Theoretical Chemistry group)

Modelling electron-induced chemistry

Chemistry induced by slow electrons is all around us. Examples are the damage to DNA by high energy radiation that causes cancer, the treatment of cancer with X-rays, the depletion of ozone in the outer layer of the earths atmosphere, the formation of complex biomolecules in interplanetary environments, the processing of hazardous chemical waste. All these processes are the result of reactions that are induced by slow electrons (0-100eV). Such reactions also play an important role in nanolithography. The technique focused electron beam induced deposition (FEBID) relies on the reaction between electrons and adsorbed organometallic molecules. As a result of this reaction, the organometallic molecule dissociates and leaves a residue on the surface of the sample. Because electron beams can be focussed to a small spot (< 1 nm) it is possible to write very small features (< 1nm) with FEBID. That makes it a promising candidate for future nanolithography.

But first we need to understand what happens when electrons interact with an organometallic molecule. What molecular orbital does the electron occupy? How does the molecule respond to this extra electron? And how important is the energy of the electron? Using (time-dependent) density functional theory, you will be among the first to study how electrons induce chemistry in organometallic molecules.

12 Group: Theory of condensed matter

Project 12.1

Supervisor: Dr. Thomas la Cour Jansen

Nonlinear spectroscopy of alcohols

The alcohol group is present in many organic and biological systems, with carbohydrates, DNA and proteins as the most prominent examples. The alcohol group can therefore potentially be used as a reporter on structure and dynamics in such systems. In particular the hydrogen bond formation and dynamics should be possible to study. The aim of this project is to develop a map for the OH stretch vibration of alcohols to test it by applying it to calculate the linear and two-dimensional spectrum of alcohol in solution. The map will be constructed using electronic structure calculations of an alcohol unit in different point charge environments mimicking a solvent and a fitting procedure to correlate the vibrational frequency with the local electric field. The solvated alcohol will be simulated using molecular dynamics simulations that will be used to determine how the electric field generated by the solvent behaves. Finally, the spectra will be calculated by combining the electronic structure map and the molecular dynamics simulation according to the spectral simulation protocol developed in the group [1]. The spectra will be compared with experimental spectra [2] and with observations in other hydrogen bonding systems [3,4,5].

[1] Jansen and Knoester, Acc. Chem. Res. 42:1405 (2009)
[2] Farwaneh, Yarwood, Cabaco, and Besnaro, J. Mol. Liquids 56:317 (1993)
[3] Kim and Hochstrasser, J. Phys. Chem. B 110:8531 (2006)
[4] Jansen, Cringus, and Pshenichnikov, J. Phys. Chem. A 113:6260 (2009)
[5] Knop, Jansen, Lindner, and Vohringer, Phys. Chem. Chem. Phys. (2011) DOI: 10.1039/C0CP02143A

Last modified:17 November 2017 1.59 p.m.