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OnderzoekZernike (ZIAM)OnderwijsTop Master Program in Nanoscience

Small research project (NS194)

Introduction

In the second semester of the first year, each student will carry out a small research project around an already defined problem. This course is designed to provide a first taste of scientific research. Properly keeping a lab journal, and presenting it at the end, is an important part of this course (see guidelines below). Additionally, each student should give an oral presentation on her/his research project. The students will organize a scientific symposium at the end of the semester where they all give their oral presentations.

Impotant: the small research project needs to be performed in a different group from the master thesis project (NS200). Moreover, it is required that students that have the intention to do the master project on a physics topic do the short research project on a chemistry (or bio-chemistry/physics), and vice versa.

All learning objectives, teachers, assesments and the time schedule can be found on Ocasys, all additional information can be found on this page.


Organization

Research groups in the Zernike Institute for Advanced Materials submit brief (half A4, no pictures or equations) proposals, which are collected in a list of available projects: you find the available projects for 2018 at the bottom of this page. Futhermore, for reference or inspiration, the lists of available projects of the years 2010-2017 are also archived at the bottom of this page). Each prospective supervisor can submit up to two proposals, with a maximum of five per research group.

The student selects a topic from the list of available projects and discusses this with her/his mentor, before contacting the project supervisor. Selection has to be completed by early February (exact date will be announced in time), while the actual working on the project should start per 1 March at the latest.

Note: students should not feel restricted to the listing, when a student has an idea for a small project of her/his own, she/he is always welcome to approach a prospective supervisor with the idea for asking whether it can be carried out.


Guidelines

Here you can find a file with all guidelines for top master Nanoscience students and supervisors on individually supervised course units


Guidelines on lab journal keeping

The pdf document at this link provides the instructions that must be followed for keeping a lab jounral during the NS194 course.



Guidelines on symposium

Each student should give an oral presentation on her/his research project. The students will organize a scientific symposium at the end of the semester where they all give their oral presentations. Find the programme of June 2018 on www.nanosymposium.nl.

The presentations should be aimed at an audience of fourth and fifth year students of physics or chemistry; staff members of the Zernike Institute will also be present. Each presentation should take approximately 15 minutes, plus 5 minutes for questions and discussion.

Use of modern audio-visual presentation techniques is encouraged. It is the student's responsibility to avail him/herself of advice on scientific presentation skills, if needed. There is a wealth of literature on this topic. The supervisor will assist the student by paying special attention to presentation skills during the preparation period and especially during trial presentations.

In addition, NS194 foresees in providing lectures and tutorials on oral presentation skills (by Dr. Maxim Pchenitchnikov).


Evaluation

The small research project is reported individually as well as collectively:

  • each student must present the progress and results of his/her research to the supervisor in the form of a log-book (note that a thesis-like report is not required as output to pass NS194; however, upon mutual agreement between a student and a supervisor documenting the results in a report can be part of the student's task).

  • all students belonging to the same cohort jointly organize a symposium in which everyone gives an oral presentation.

One overall mark will be given to each individual participant. A proposed final grade is formed by averaging a grade for the symposium presentation (weight 1/3), and a grade by the supervisor reflecting the research project's quality (incl. the log-book keeping) as performed in the research group (weight 2/3). The supervisor is asked to use a standard form for the assessment. The grade for the symposium presentation is the average grade from at least 2 (typically 4, incl. the coordinator) staff members who use a standard form for the assessment. The coordinator will define the final grade from moderating the proposed final grades, by comparing the various student cases and by accounting for the quality of the student's contribution to the organization of the symposium.


Time schedule

Selection of a project: early February (exact date will be announced in time)

Start actually working on a project: around 15 February, per 1 March at the latest. Students and supervisors must plan a workload of 13 ECTS (13 x 28 hours) in the period up to the symposium (including the symposium presentation), in parallel with the other study tasks.

The symposium should be held before 1 July.


Current projects

The available small research projects for 2018 are listed below. Please contact the supervisor mentioned in case you are interested in a project. Keep in mind that these projects are meant as inspiration. You may design a project together with a supervisor from the ZI-NRC list below or adapt one from the list below in discussion with the supervisor. First come, first served...

For contact information on all mentioned professors and groups see
www.rug.nl/research/zernike/research/zi-nrc [ the most complete listing with (nearly) ALL staff ]
and also
www.rug.nl/research/zernike/research/people [ list of Zernike staff without the associate members - use the above if possible ]
www.rug.nl/research/zernike/research/labs

Group 1: Molecular Biophysics

Project 1.1
Supervisor(s): Prof. dr. Wouter H. Roos and Ignacio de Blas

Nanoindentation measurements on viruses
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 to unravel the mechanical properties of viruses. In particular, we will use AFM to evaluate stiffness of viruses with different amounts of genomic content, in order to scrutinize the influence of cargo on structural and functional properties of these natural nanoparticles.

[1] M. Baclayon, G. K. Shoemaker, C. Uetrecht, S. Crawford, M. K. Estes, B. Prasad, A. J. Heck, G. J. Wuite, W. H. Roos, Pre-stress strenghtens the shell of Norwalk Virus Nanoparticles Nano Letters (2011) Vol. 11, 4865-4869. [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 2) Supervisor(s): Prof. dr. Wouter H. Roos and Pedro Buzón

Project 1.2
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 novel molecular properties of these compounds that are unachievable by ensemble experiments.

[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

Project 1.3
Supervisor(s): Prof. Erik Van der Giessen (in collaboration with Jiawen Chen from the Feringa lab)

Understanding the operation of artificial supramolecular muscles through computational modelling
Mid-december 2017, a group of researchers in and around Feringa's lab appeared in the news with artificial muscle fibers. In a paper in Nature Chemistry [1] they presented a unique artificial supramolecular muscle, composed of 95% water, formed by hierarchical self-assembly of a photo-responsive molecular motor. Both in water and in air, photoactivation of the 300-micron thick fiber induces a bending motion which can lift small objects and perform mechanical work in the range of micro-Joules.

It is not clear, however, how the rotary motion of the motors stacked in nanofibers is amplified up the macroscopic scale and where it is that work is actually being generated. While SAXS experiments provide support for the hypothesized assembly of the motors into a nanofiber, there is only circumstantial evidence for the structural change in the nanofibers by light-induced rotation of the motor molecules. The amplification across length scales is likely to be the reason behind the fact that the muscle fibers respond within tens of seconds, while the switching of a single motor is almost instantaneous.

The objective of this project is to develop a hierarchical computational model that is able to simulate macroscopic bending from the rotary motion of the molecules at the smallest scale. Considering the size of the system, it will be necessary to develop a coarse-grained molecular model (for instance of the type used in [2]).

[1] J. Chen, F.K.C. Leung, M.C.A. Stuart, T. Kajitani, T. Fukushima, E. van der Giessen, B.L. Feringa (2017). Artificial Muscle-Like Function from Hierarchical Supramolecular Assembly of Photoresponsive Molecular Motors. Nature Chemistry DOI: 10.1038/NCHEM.2887. [2] D. Bochicchio, G.M. Pavan (2017). From Cooperative Self-Assembly to Water-Soluble Supramolecular Polymers Using Coarse-Grained Simulations. ACS Nano 11, 1000 DOI: 10.1021/acsnano.6b07628.

Project 1.4
Supervisor(s): Profs. Erik Van der Giessen and Patrick Onck

Computational modelling of mechanotransduction in cancer
Cancer is the outcome of genetic modifications, but develops by altering its own physical context. Mechanical forces are central in this. Mechanotransduction has been identified to be the essential link from the physical surroundings of a cell towards signalling pathways inside the cell such as differentiation, migration and apoptosis. In turn, these signals can modify the cellular and even extracellular structure. In healthy physiological conditions, the mechanosensitive feedback loop is well balanced, but in cancer it leads to a vicious cycle of enhanced matrix stiffening and mechanosensing. The latter provides the biomechanical support for the tendency of cancer cells to spread and invade surrounding tissues.

Among the various adhesion molecules found in nature, integrins play an important role in functioning as transmembrane linkers between cytoskeleton and extra cellular matrix, and in sensing the forces that are involved. The subtype integrin a6 is particularly important because it is especially sensitive to the hypoxic conditions often found in tumors. Even though quite some qualitative biochemical information is available on the signalling pathways that can be activated by integrins, quantitative biophysical understanding of how this happens.

This project is aimed towards a molecular model that enables the understanding of how integrin a6 proteins actually sense force and activate a remodelling pathway. The model will be a key component in a computational biochemical/biophysical study of ‘Cancer as a Materials Science Problem’ (a.k.a. ‘Physics of Cancer’).

Group 2: Photophysics and OptoElectronics

Project 2.1
Supervisor(s): Dima Bederak and prof. Maria A. Loi

Colloidal quantum dots ink
PbS colloidal quantum dots (CQDs) are solution-processable semiconductors, which have been used to fabricate solar cells, photodetectors and field effect transistors. The properties of this material are size-dependent and can also be tuned by the surface ligands.

As synthesized PbS CQDs are capped with long and insulating oleic acid ligands. It is necessary to replace these native ligands to enable electronic coupling between the individual quantum dots. Preparation of colloidal inks is a powerful strategy for the one-step device fabrication and it was employed for making state-of- the-art CQDs solar cells.

In this project, new ink formulations with different perovskite-like ligands will be prepared and used for the device fabrication. Thin film field-effect transistors will be fabricated in order to characterize the transport properties of the material. This project is focused on optimization of the ink formulation (such as solvents, concentration, ligands) and deposition parameters for obtaining high- quality films. An optimized ink formulation and deposition method will be tested for solar cells fabrication. During this project, you will develop skills and gain knowledge about the chemistry of the ligands, the ink preparation, fabrication and characterization of field-effect transistors and solar cells.


Project 2.2
Supervisor(s): prof. Maria A. Loi

Composition engineering in mixed tin and lead perovskite solar cells
Organic inorganic metal-halide perovskites have been attracting much attention in recent years as promising photovoltaic materials due to their unique photovoltaic properties. The power conversion efficiency (PCE) of perovskite solar cells (PSCs) has been remarkably boosted from 3.8% to 22.1%. A proven concept for further enhancing the efficiency of PSCs beyond the Shockley-Queisser limit for single- junction solar cells is to fabricate tandem solar cells, which consist of a wide-bandgap top cell and a low- bandgap bottom cell. Device modelling has shown that for efficient two-junction monolithic tandem cells, the top cell should have a bandgap of 1.7-1.9 eV, whereas the bottom cell should have a bandgap of 0.9-1.2 eV. Lead (Pb) and tin (Sn) halide perovskites exhibit excellent bandgap tunability. Pb mixed iodide (I) and bromine (Br) perovskites cover the bandgap range from 1.58 (pure I) to 2.20 eV (pure Br), while mixed Sn and Pb iodide perovskites exhibit bandgaps from 1.17 (50% Sn and 50% Pb) to 1.58 eV (pure Pb), making them suitable for the top- and bottom-cell, respectively. Additionally, the possibility to process both devices at low-temperature is an important added advantage, which makes the fabrication of all-perovskite tandem cells feasible. However, the state-of- art of mixed tin and lead perovskite solar cells has a record PCE of about 17%, much lower than the 22% of the pure lead based perovskite solar cells.

Goal of the project In this short project, we aim to improve the PCE of the mixed tin-lead perovskite solar cells by engineering the molar composition of Sn and Pb in the mixed tin-lead perovskite film. After the optimization of the Sn and Pb ratio, if the time will be sufficient, other important quantities, such as the amount of reducing agent will be optimized.

Group 3: Chemistry of (Bio)organic Materials and Devices

Project 3.1
Supervisor(s): Ryan Chiechi, M. Carlotti

New Molecules for Old Ideas in Molecular Electronics
In Molecular Electronics (ME) we study the use of single molecules and molecular assemblies as active elements in electrical components. Still far from being able to compete with Si on traditional technologies, circuit elements with dimensions on the molecular scale can display interesting functionality due to their quanto-mechanic nature that would not be readily obtainable otherwise.

In one of the first and most iconic papers on ME, Aviram and Ratner theorized a molecule, characterized by an electron donor and an electro acceptor separated by an alkyl bridge, that would act as a current rectifier when placed between two electrodes (A. Aviram, M.A. Ratner, Chemical Physics Letters, 1974, 29, 277-283). According to their model, this effect arises from the different alignment of the molecular orbitals of the two termini of the molecule compared to the electrodes.

In this project, we will investigate the tunneling properties of molecular junctions comprising Self Assembled Monolayers (SMAs) of a series of these compounds.

We will design and synthesize a library of donors and acceptors that we will connect with a bicyclo[1.1.1]pentane unit as rigid spacer. With those compounds at hand, we will form Self- Assembled Monolayers on different ultra-flat metal substrates and investigate their electrical properties in tunneling junctions: this will be done using different techniques such as conductive probe AFM and large area junctions realized using a liquid metal top electrode (made from a Ga-In alloy at its eutectic composition).

This project will involve both synthesis and measurements, and therefore is aimed to students who would like to challenge themselves with both synthesis and applications.


Project 3.2
Supervisor(s): prof. Ryan Chiechi, Viktor Ivasyshyn

Synthesis and Optimization of Hominal Bis(gem-CF 2 ) Fragment
A short project will involve synthesis of hominal bis(gem-CF 2 ) fragment including procedure and yield optimization, possibility to explore influence of protecting groups on the outcome and implementing one-pot synthesis. Student will have a possibility to learn numerous new skills and techniques (e.g. 19 FNMR analysis, deoxofluorination, desulfurative fluorination, hydrogenation in autoclave) while improving already known ones (e.g. oxidation, epoxidation, metalorganic chemistry, etc.) and to become involved in an interesting, challenging and rare branch of organic chemistry.

During the course of the project student is encouraged to show initiative, to suggest and implement his ideas. Depending on the student performance, project might be extended to include attachment of the obtained synthon to the substrate of choice and further polymerization and characterization of the product obtained.

Project 3.3
Supervisor(s): prof. Ryan Chiechi, Yong Ai &amp

Single-molecule Junction for Molecular Electronic devices
According to the Moore's law and the development trend of electronic devices, the size of a single component on a chip continuously decreasing during the past decades. In the foreseen future it will be reduced to the scale of a few molecules or even a single molecule. It is our dream to utilize molecules as a basic component performing special functions in digital electronic devices. Functional organic molecules can act as molecular wires, molecular switches, molecular rectifiers, etc. When device size is reduced to below 10 nm, quantum effects will be detected. Namely, charge transport properties change from the classical regime (Ohm's law) to the quantum regime. Understanding the electron transport on molecular scale is one of the main goals in Molecular electronic devices. To investigate charge transport through molecular electronic devices, we need to find a way to wire molecules between the electrodes, for instance, constructing the Metal/Molecule/Metal (MMM) junctions. Scanning Tunneling Microscope break junction (STM-BJ)is a technique widely used for the in- situ formation of a single molecular junction. It starts with a metallic STM tip located a few Ångström above the substrate electrode. Then the tip is precisely driven by the piezo, leading to a repeated construction and break of a contact with the substrate. During such movements, the molecules may bridge the gap between the tip and the substrate electrodes. Meanwhile, current versus tip travel time (I-s) curves are recorded when tip is driven up until the junctions are broken. Single molecular conductance is usually determined by the last plateau on the current versus displacement plot as well as the conductance histogram constructed from large number of individual events.

In this project, the student will construct a single molecular device and carry out the conductance measurement using a well-developed STM-BJ technique. Quantum interference in molecular charge transport is interesting. Anthraquinone derivatives are consistent with destructive quantum interference in molecular junctions. We have designed and synthesized a series of anthraquinone substitute molecules for this study. Furthermore, molecules exhibit unbalanced conduction under reversed bias will be discussed, concerning molecular rectification towards diodes. Additionally, all of those interesting effect at single molecular level will also be compared with that in larger area molecular devices, such as EGaIn and CP-AFM set up.

[1] Guédon, Constant M., et al. "Observation of quantum interference in molecular charge transport." Nature nanotechnology 7.5 (2012): 305-309. [2] Carlotti, Marco, et al. "Conformation-driven quantum interference effects mediated by through-space conjugation in self-assembled monolayers." Nature communications 7 (2016).

Group 4: Theory of Condensed Matter

Project 4.1
Supervisor(s)Dr. Thomas la Cour Jansen

Interfaces 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 highly mobile organic components [1,2]. A key challenge is, however, the stability if these materials especially towards for example water moisture. It has been suggested that covering the surface with an appropriate layer of hydrophobic organic molecules can circumvent this problem.

Project: A classical molecular dynamics model will be developed for perovskite materials with a protective layer of different organic ions and water. The efficiency of the protecting layer will be examined for the different ions will be studied. These new simulations will allow proposing new, better, or simpler molecules to use in real devices.

Further Information e-mail: t.l.c.jansen@rug.nl
Literature: [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. 139:4068-4074  (2017)


Project 4.2
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: t.l.c.jansen@rug.nl
Literature: [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)

Group 5: Micromechanics

Project 5.1
Supervisor(s) Prof.dr.ir. Patrick R. Onck and Hamidreza Jafarinia

Coarse-grained molecular dynamics simulations of disease-related mutations in the unfolded domain of RNA-binding proteins
In our aging society, more and more people are affected by neurodegenerative diseases. However, the underlying molecular mechanisms governing the development of these diseases are not understood. It has recently been discovered that the misregulation of RNA-binding proteins (RBPs) might play a very important role. Many RBPs have distinctive sequence architectures, including so-called unfolded low- complexity domains (LCDs), which are often the central players for neuronal disorders. The pathology of RBP-related diseases are frequently linked with abnormal LCD-mediated liquid-liquid phase separation (LLPS) which has recently become an intriguing and popular area of research in molecular biophysics. In recent studies some mutations in the gene encoding LCDs have been observed in ALS, FTD, and MSP disease cases which can affect RBP function [1].

In this project you will conduct molecular dynamics simulations to study changes in biophysical properties of disease-related mutants with respect to the wild-type LCDs. Next you will compare the collective/aggregation/LLPS behavior of the mutants and wild-type LCDs to find how these changes can contribute to the disease pathway. During the project you will learn advanced simulation techniques and carry out your simulations based on a coarse-grained model for disordered proteins developed in our group [2,3].

For each part of the project, your results will be compared with available in vivo and in vitro data in the literature. In addition, it is possible to benefit from our experimental collaborators’ expertise at the UMCG (group of Dr. Veenhoff). It will be very interesting to find any correlation between the type and location of the mutations and physical properties of the mutants. If successful, the results can be used as a basis for new treatment approaches.

[1] A. F. Harrison, et al., Biochemical Journal (2017) [2] A. Ghavami et al., Biophysical Journal (2014) [3] A. Ghavami et al., PLoS ONE (2016)

Project 5.2
Supervisor(s) Prof.dr.ir. Patrick R. Onck and Henry de Vries

Developing a coarse-grained model of Kap- centric transport in Nuclear Pore Complexes
The nuclear pore complex (NPC) is a very large (1.2×10^8 Da) protein complex that forms a highly selective gate between the nucleus and the cytoplasm in a cell. Small cargo is allowed to pass the NPC, but large molecules need to be bound to transport proteins (’Kaps’) that shuttle the cargo through the NPC. The mechanism behind this selectivity has been puzzling scientists for the last two decades: our current understanding is that Kaps interact with unfolded proteins in the NPC, which contain many phenylalanine-glycine (FG) repeats. Debate still exists on the dominant mechanism in facilitating size-selective transport, and various transport models have been proposed [1]. Biomolecular modeling would be an excellent tool for studying the mechanisms behind NPC selectivity, but due to the size of the NPC it is impossible to perform molecular dynamics (MD) simulations on the NPC at the atomistic scale. To overcome this limitation we have developed a coarse-grained model [2,3], through which we can probe the unfolded FG- repeat proteins in the NPC at single amino acid resolution.

In this project, you will derive a coarse-grained model for Kap proteins, and investigate the effect of Kap concentration on the spatial organization of NPCs. To do so, you will derive a coarse-grained structure of Kap proteins, together with effective Kap-protein interaction potentials, based on experimental data. You will then combine your coarse-grained Kap with our earlier work on NPCs and experimental NPC mimics (in collaboration with the group of prof. Cees Dekker at TU Delft) to investigate the effect of Kap concentration on structuring of NPC-type systems.

If successful, your results will play an important role in determining the correct NPC transport model, as it will be the first computational model to both include Kaps as well as the complete amino acid sequence information of NPC proteins. Furthermore, this project will provide you with a thorough introduction to molecular dynamics simulation techniques and the advanced topic of coarse-graining. You will perform your simulations on state-of-the-art high-performance computing (HPC) infrastructures.

More information on NPCs and our coarse-grained model can be found in the following references: 1. R. Hayama et al., Curr Opin Cell Biol 46: 110-118 (2017) 2. A. Ghavami et al., Biophys J. 107 (6): 1393-402 (2014) 3. A. Ghavami et al., PLoS ONE 11(2): e0148876 (2016).

Group 6: Theoretical Chemistry

Project 6.1
Supervisor(s) Prof. Dr. Shirin Faraji

Theoretical study on light-induced electron transfer in DNA photorepair
DNA photolyases are highly efficient enzymes utilizing UV/blue light to eliminate UV- derived photoproducts that are the major source of skin cancer. The enzymatic repair occurs in three sequential steps: (i) photo-induced electron transfer from the catalytic cofactor, reduced flavine adenine dinucleotide (FADH − ) to the lesion; (ii) electron- induced splitting of the lesion; (iii) back electron transfer to FADH . . The initial steps of the repair mechanism, i.e., light absorption, energy transfer and generation of the catalytic electron, are now well understood from both experimental and theoretical point of views. However, despite their importance (recognized by the Chemistry Nobel Prize 2015), this is a very complex subject that led to numerous controversies in the field, which motivate this project. For example, the fate of the generated electron and the underlying transfer mechanism is still unclear. For example, we cannot discriminate between one-step direct electron transfer vs. multi-step electron hopping. Contradictory experimental and theoretical findings exist. For example, our previous studies suggested that residue His365 serves as an intermediate in the electron transfer that further induces proton transfer from His365 to the lesion. This contradicts experimental findings, in which the electron is transferred to the lesion first and the proton from His365 follows. Here you will develop a reliable protocol to fully understand electron transfer processes, by performing hybrid quantum mechanics/molecular mechanics (QM/MM) simulations to validate the feasibility of various electron transfer mechanisms by means of Marcus theory. The goal is to perform quantum dynamical simulations on a simplified model system, which will provide a quantitative understanding of the open questions regarding spectral information of the intermediate electron acceptors, electron transfer rates, and to ultimately shed more light on the nature of electron transfer dynamics initiating the DNA-repair.

During this project you will be familiarized with i) theoretical description of proton- coupled electron transfer reaction mechanism, ii) Marcus theory in various flavor, iii) hybrid quantum/classical dynamics simulations, and iv) QChem and Gromacs software.

[1] S. Faraji, A. Dreuw (2017), “Insights into light-driven DNA repair by Photolyases: challenges and opportunities for electronic structure theory", Photochem. Photobiol., 93(1), 37-50. [2] S. Faraji, Dongping Zhong, A. Dreuw (2016), “Characterization of the Intermediate in and Identification of the Repair Mechanism of (6-4) Photolesions by Photolyases", Angew. Chem. Int. Ed., 55(17), 5175-8.

Project 6.2
Supervisor(s) Prof. Dr. Shirin Faraji

Theoretical study on the photochemistry of far-red/near infrared biomarkers/biosensors
In life sciences, optical technologies use light to visualize, detect, and control biological processes in living tissues. These techniques include genetically encoded fluorescent proteins, biosensors, and optogenetics. The optical transparency window of mammalian tissues spans the near-infrared range, where the combined absorption of hemoglobin, melanine, and water is minimal. This limits the utility of the green fluorescent protein (GFP) and its derivatives. The recently developed near-infrared FPs (iRFPs) from Bacterial Phytochrome Photoreceptors (BphPs) offers a new twist to the conventional FPs, which are relevant to deep-tissue in vivo imaging and development of optogenetic tools. They use chromophore biliverdin (BV), an intermediate of heme metabolism ubiquitous in mammalian tissues. Experimental and theoretical studies investigated various aspects of the excited-state processes involved in the GFP photocycle. However, experimental studies of the excited-state dynamics of the iRFPs are still very scarce, and the mechanism of their photo-activations and signaling has yet to be established. An important practical question is how to block unwanted excited-state processes, such as excited-state proton transfer and cis-trans isomerization, to increase the fluorescence efficiency, which is the most essential concern in the design of optical imaging tools. In this project you will study excited-state dynamics of RFPs and will demonstrate how theory can contribute towards molecular-level understanding of chromophores photochemistry. Your research will provide molecular-level insights into the spectral shifts in iRFP and the role of crucial amino acids, which will allow researchers to design new BphP-based probes with desired spectral properties matching specific application in optogenetic technology.

During this project you will be familiarized with i) various ground and excited-state electronic structure theories, ii) excited-state dynamics beyond Born-Oppenheimer approximation, iii) hybrid quantum/classical dynamics simulations, and iv) QChem and Gromacs software.

[1] Vladislav V. Verkhusha et al (2017), “Designing brighter near-infrared fluorescent proteins: insights from structural and biochemical studies”, Chem. Sci., 8, 4546-56. [2] S. Faraji, S. Matsika, A. I. Krylov (2018), Calculation of non-adiabatic couplings within equation- of-motion coupled-cluster framework: Theory, implementation, and validation against multi- reference methods. J. Chem. Phys. 148, 21-38. [3] S. Faraji, A. I. Krylov (2015), On the nature of an extended Stokes shift in mPlum fluorescent protein", J. Phys. Chem. B, 119, 41, 13052-13062.

Group 7: Synthetic Organic Chemistry

Project 7.1
Supervisor(s) Jim Ottelé (j.ottele@rug.nl) & Sijbren Otto


Kinetic analysis of a self-replicating system
The de-novo synthesis of life is one of the grand challenges in contemporary science. To create life de-novo, a chemical system must at least have three major functions; it must self-replicate, it must have a metabolism and it must be compartmentalized . In 2010, the Otto group discovered  a chemical system in which self-replicating molecules emerge spontaneously from a dynamic mixture of interchanging molecules. In this project you will investigate the mechanism of self-replication, which relies on the assembly of replicators into fibers and a fiber growth-breakage mechanism.

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

Project 7.2
Guillermo Monreal Santiago (g.monreal.santiago@rug.nl) & Sijbren Otto

Proto-metabolism in synthetic replicators
Self-replication, the ability of an entity to create copies of itself, is one of the main characteristics of life. However, it is not the only one. Living beings interact with their environment, using energy to catalyse chemical reactions and create favorable conditions for their replication.
In our group, we have developed the first examples of synthetic self-replicating molecules that can trigger other reactions. By activating a photooxidation catalyst through supramolecular interactions, our synthetic replicators can use light to induce the formation of their own precursors, and therefore replicate more efficiently.

Your project will explore the possible behaviours that can be achieved using this effect. You will mainly focus in two directions:
1)    Find conditions where the precursors of a replicator are not stable, but can be temporarily formed by the photooxidation process indicated above. In that way, your goal will be to achieve out-of-equilibrium replication fueled by light.
2)    Study to which extent different replicators can activate the photooxidation catalyst. If a suitable pair of replicators is found (i.e. one that induces oxidation and another one that does not) that could lead to complex “ecological” behaviours, such as competition or parasitism.
During the project, you will be trained in the use of UPLC systems to analyse the molecular composition of the systems of replicators. You will also work with supramolecular chemistry, photochemistry, and out-of-equilibrium concepts. The project is not focused on synthesis.

Group 8: Biomedical Engineering

Project 8.1
Supervisor(s) Dr. Patrick van Rijn

Telling viral structures how to assemble
The highly infectious nature of viruses are threatening lives worldwide everyday but can also be used for good. Viral structures composed of several smaller protein sub-units (capsids) assembled around an RNA- or DNA-strand are used in the formation of new bio- compatible materials, as delivery vehicles and nano-containers/reactors. Nature provides a limited number of virus morphologies which is of great consequence for the properties of the virus. Influencing the morphology of the viral assembly with high accuracy will provide more control over the viral properties. Here an approach is presented where the capsid is dynamicly attached to a small DNA-linker and coordinated onto a synthetic template varying in shape and size e.g. cyclic, helical and random coils containing complementary DNA-linkers. The viral infectious properties are now fine-tuned to control size, shape and cellular interaction e.g. the cell infiltration, location inside the cell and structure stability. Viral structures take specific shapes mainly due to the inter-protein interactions. By artificially directing the viral capsids it will become clearer how the overall arrangement and packing of the capsids affects the shape, rigidity, stability and ultimately function.

Interactions between capsids and template can be varied by varying the length of the DNA-linkers and thereby influencing the artificial virus’ stability and dynamics. Incorporating responsive linkages between the template and the DNA-linker binding-site also allows for a controlled release of the capsids from the template allowing for the structures to be used as intra-cellular delivery vessels with controlled release of active viral sub-units or template-confined molecules.

The newly developed viral systems will revolutionize virus-based formulations in medicine since the approach here can be extrapolated to many different types of viruses and by introducing morphology control as well as control over the disassembly of the structures, a broad spectrum delivery agents and bio-makers will result from this.

Group 9: Surfaces and Thin Films

project 9.1
Supervisor(s) Prof. dr. M.A. Stöhr and Prof. dr. B. Noheda

Detecting of conduction paths in nickelates by Scanning Tunneling Microscopy
Neuromorphic computing that mimics synaptic functions has received much attention for its potential in improving power-efficiency and parallel computation in electronics. Recently, materials having a history-dependent resistance, named memristors, have been regarded as promising candidates for neuromorphic computing.

In this project, epitaxial rare-earth nickelate (RENiO 3 , RE= rare earth cation) films deposited by pulsed laser deposition (PLD) will be utilized as memristors because their metal-insulator transition - and thus their resistance - can be tuned by factors such as the RE radius, temperature, epitaxial strain and oxygen vacancies. We aim to construct conducting paths in RENiO 3 by selectively inducing the metallic phase around the domain walls in an insulating film (or vice versa). The construction of these conducting paths and the modulation of their resistance will enable to build a neuromorphic system in just one film!

In this project, these films will be investigated on the atomic scale using scanning tunneling microscopy (STM). The metallic and insulating areas will be investigated to characterize local differences in band gap and structure and to correlate these finding. The thin films are provided by the group of Beatriz Noheda and the research will be performed in the group of Meike Stöhr.

Group 10: Spintronics of Functional Materials

Project 10.1
Supervisor(s) Prof Tamalika Banerjee

Designing technologically important magnetic materials by enhancing magnetic anisotropy at material interfaces with large spin orbit coupling.
Magnetic anisotropy provides directionality and stability to magnetization and has enabled the realization of nanomagnets in conventional transition ferromagnetic materials in proximity with heavy metals. In this project a different route will be adopted by using complex oxide material interfaces. In few recent works we have shown the onset and control of large perpendicular magnetic anisotropy across ruthenates on titanates.

This work will be extended to other oxide (anti)ferromagnets interfaces where tailoring the strain state by choosing appropriate substrates and film thickness is expected to give rise to new magnetic textures which will be probed by electrical transport schemessuch as the inverse spin hall effect. The thin films will be grown and optimized using the Pulsed Laser Deposition system (Nanolab/Zernike) and the devices will be patterned at Nanolab Groningen for spin transport measurements.

The student will work under the daily supervision of a PhD researcher.

Project 10.2
Supervisor(s) Prof Tamalika Banerjee

Device designs and their characterization for brain inspired computing.
The von Neuman architecture used in computing and thus connecting devices for Internet of Things will lead to an unsustainable rise in energy consumption and an interesting alternative that is actively researched is that inspired by the human brain. Different materials their devices and mechanisms have been studied in this context and memristors have gained rapid momentum. A memristor is a passive two terminal nonlinear device capable of exhibiting atleast two level non volatile resistive state.

Very recently we demonstrated (Scientific Reports 2018) that carefully engineering the potential landscape across the interface between SrTiO_3 and 3d transition ferromagnetsresults in the emergence of a new spintronics phenomena known as tunneling anisotropic magnetoresistance which coexists with the two resistance states in such a ‘spin- memristor’. In this project we will continue investigating the underlying physics and look for strategies to use them for specific cognition capabilities of the human brain. We will work together with researchers at Artificial Intelligence for this while the (new) device design and architecture will be carried out at the Nanolab Groningen.

The student(s) will have access to all experimental facilities and will work in an interdisciplinary consortium (this project is more suitable for a longer research).

Group 11: Nanostructures of Functional Oxides

Project 11.1
Supervisor(s) Prof.Dr. Beatriz Noheda , Silang Zhou (s.zhou@rug.nl) and Mart Salverda

A novel phase transition with domain doubling/halving behaviour in BaTiO 3 thin films
BaTiO 3 is a ferroelectric material that displays spontaneous electric polarization that can be switched by applying electric field. In ferroelectrics, like in other types of materials, proximity to phase transitions enhances the dielectric and piezoelectric responses. One way of engineering phase transitions in materials is by using strain engineering. In our group, thin films of BaTiO 3 have been grown epitaxially on NdScO 3 substrates, which provide less than 1% strain to the BaTiO3 lattice. Two types of new phases, so called a/b and a/c phases with periodic ferroelectric domains were found. The two phases can be transformed into each other by applying electric field or changing temperature. At room temperature, the thin films are in the a/b phase and they transform into the a/c phase, at about 50 Celsius[1].

The periodic domains of the two phases are characterized by differently oriented domain walls with similar periodicities. It was found that the a/b and a/c domains evolve into each other in a unique way, by what it looks like periodicity doubling/halving cascades, a phenomenon that may have reminiscences of order-to- chaos phases transitions. In this project, the student is expected to capture high quality images of the phase transition with the Piezo-Force Microscopy (PFM) mode of an Atomic Force Microscope (AFM). The student will learn about ferroelectrics, domain formation, phase transition, strain engineering, etc. If time allows, the student can also do some dielectric measurements and in-plane switching by PFM.

[1] A. S. Everhardt, S. Matzen, N. Domingo, G. Catalan & B. Noheda, "Ferroelectric Domain Structures in Low-Strain BaTiO 3 ", Advanced Electronic Materials 2, 1500214 (2015)


Project 11.2
Supervisor(s) Prof.Dr. Beatriz Noheda and Silang Zhou (s.zhou@rug.nl)

Characterization of Si x Ge 1-x O 2 thin films
Quartz (SiO 2 ) is one of the first crystals which was found to be piezoelectric. It has numerous applications such as sensors, frequency stabilizers, etc. in all kinds of areas. However, the further application is limited due to its low piezo response and synthesis difficulties. Because the energy of the crystalline quartz and the amorphous silica glass are nearly equal, it is very difficult to crystallize quartz unless reaching the melting point, which is about 1600 Celsius. In 2003, nanocrystals of quartz were first synthesized successfully by hydrothermal method. However, they are polycrystalline; while for piezoelectric applications, a single crystal or, at least, an oriented polycrystal, is needed. Currently the group is trying to make Si x Ge 1-x O 2 thin films by pulsed laser deposition. Substitution of Si by Ge will generate a complex phase diagram with those compositions being closer to phase boundaries being highly responsive and, hopefully increasing the piezoelectric response significantly. So far, single crystal GeO 2 with unique crystal distortion was successfully grown on quartz substrate for the first time. At this moment, we are trying to crystallize the whole composition range. We have learned that the Si-rich compositions have an increased tendency to be amorphous. One trick we can play is by adding some melting agent, such as Cs.

During this project, the student will work together with the daily supervisor (PhD student in charge of this project) and have a taste of real research. The films will be grown by the daily supervisor and the student will characterize the film properties by XRR (X-ray Reflectivity), X-ray RSM (Reciprocal Space Mapping), RHEED (reflection high energy electron diffraction) and AFM (atomic force microscope). By these techniques, the student is expected to tell the quality of the film, such as roughness, thickness, composition, the structure relationship between the substrate and film, and so on. This feedback will help the daily supervisor crystallize the stubborn SiO 2 hopefully.

Project 11.3
Supervisor(s) Dr. S. Farokhipoor, Prof. dr. B. Noheda

Domain walls (DWs) in multiferroic thin films are nanoscale regions presenting different properties compared to the adjacent domains.
This distinct behavior originates from the broken crystal symmetry and intense strain gradients around the walls. Therefore, engineering and controlling the properties of DWs in different types of functional materials, in particular in complex oxides, can become a promising path to design and tailor novel nano-electronic and spintronic devices. In this project you will be working on TbMnO 3 in thin film form. in bulk form TbMnO 3 is an antiferromagnetic orthorhombic perovskite, in thin film form the properties are altered. Ferroelastic DWs in TbMnO 3 thin films can be formed in a very controlled way, with densities that increase inversely proportional to the film thickness. Back in 2014, we have found that these DWs, display a net magnetic moment that originates in a unique chemical environment: a novel Mn coordination has been locally induced due to the local stress present at the DWs [S. Farokhipoor, et al., Nature (2014)]. For your project, we provide the thin films and you will investigate the magnetoelectric properties of these DWs. You will gain/develop your expertise in working with transport measurement setups in the absence and/or presence of magnetic field. You will learn how to interpret the DW nanoscale behavior from your macroscopic measurements. At the end, you can also study various magnetoelectric mechanisms and analyze your model system data. Hence, getting a well-understood insight on the origin of the behavior of this specific DWs. Ultimately, in this project you will help us to take one step further towards nano-scale device fabrication based on DWs.

Project 11.4
Supervisor(s) Q. Guo, Dr. S. Farokhipoor, Prof. dr. B. Noheda

Perovskite rare-earth nickelates (RENiO 3 ) displays a sharp paramagnetic metal-to- antiferromagnetic insulator transition, accompanied by an orthorhombic-to- monoclinic phase transition. This family has been regarded as a remarkable example of materials for fundamental physics studies of the interdependence between structural, electronic and magnetic properties. Interestingly, the transition in RENiO 3 can also be tuned by the RE radius, growth temperature, epitaxial strain, vacancy content, etc. All these factors have made the RENiO 3 a focus point in oxide electronics community in recent years.

Recently, we have already found an inverse dependence of the resistivity of the films with their thickness, for one particular composition, which is interestingly different from the previous reports. In this project, you will be provided with epitaxial RENiO 3 (RE=Nd, Sm, or Nd 0.6 Sm 0.4 ) thin films with different thickness (1 nm -300 nm), grown by pulsed laser deposition (PLD). You will help us to investigate the influence of the rare-earth atom (composition) and thickness on the transport properties, including resistance, metal-insulator transition temperature and hysteresis between heating up and cooling down process. You will get familiar about how to make the right electrical contacts and use the right measurement geometry to perform transport measurements of the provided thin films. You will also acquire/mature your expertise to choose the right setup measurement system between the ones available in our physics lab.

Finally, you will analyze the transport properties based on your data as the main focus of your project. The final objective of this project is to get a deep insight into the origin of the physical mechanism of metal-insulator transition in RENiO 3 , which is essential and instructive for their further application in electronic devices.

Project 11.5
Supervisor(s): Prof. Dr. Beatriz Noheda, Mart Salverda (m.salverda@rug.nl)

Synthesis and Pulsed Laser Deposition of SrO in order to measure domain wall networks
In neuromorphic computing, lessons are taken from the biological brain, which can learn, recognize patterns easily and which is quite energy efficient in doing so: whereas the human brain consumes only about 20W, a comparable supercomputer is estimated to need MW to GW in power to operate.

We know from computer science and artificial intelligence research that these features (learning and pattern recognition) are very useful in handling (categorizing) large amounts of input data (Big Data). This is useful not only for social media, but also for research and other fields in which more and more data is produced that needs to be analyzed, for example in autonomous vehicles.

To reduce the power consumption of neuromorphic computing, which currently is only simulated in software running on conventional hardware, we look for neuromorphic hardware to reduce the power consumption.

In our group, we make use of self-assembled networks of (in this project) conducting domain walls in thin films of the oxide perovskite BiFeO 3 . Vacancies are responsible for the conductivity and can be manipulated by external electrical stimuli. This has already been shown for a single domain wall in vertical geometry, but not yet for domain wall networks in lateral geometry, which resembles more a neural network. We focus on the latter.

In this project you will synthesize a target of SrO for Pulsed Laser Deposition and use it to deposit and characterize an atomically thin layer on a substrate of SrTiO 3 . On top of this layer, the BiFeO 3 will be grown which can then be used for measurements of the lateral domain wall network. Techniques that will be used are solid-state synthesis, powder X-ray diffraction, Pulsed Laser Deposition (PLD), Reflective High Energy Electron Diffraction (RHEED) and Atomic Force Microscopy (AFM). If time allows, also the characterization of the BiFeO 3 film can be performed with Piezoresponse Force Microscopy (PFM), Conductive-AFM and electrical measurements.

[1] S. Farokhipoor and B. Noheda, Phys. Rev. Lett. 107 (2011)

Archive

Archive of the advertised student projects (as listed before the start of the project) are listed below. Note: these project are no longer valid, but merely listed for inspiration.


Last modified:26 February 2018 11.25 a.m.