TECHNISCHE PHYSICA Vereniging Voor Technische Physica

RESEARCH GROUP GUIDE 2016

VERENIGING VOOR TECHNISCHE PHYSICA Vereniging voor Technische Physica

Lorentzweg 1 Kamer A109 2628 CJ Delft

(015) 278 612 20 [email protected] www.vvtp.tudelft.nl Table of Contents

BioNanoscience Aubin-Tam Lab 4 Beaumont Lab 5 Cees Dekker Lab 7 Dogterom Lab 8 Idema Lab 9 Meyer Lab 10 Nynke Dekker Lab 11 Fluid Flow and Transport Phenomena Atmospheric Physics 13 Fluid Mechanics 14 Transport Phenomena 15 Imaging Physics Acoustical Wavefield Imaging 18 Charged Particle Optics 19 Optics 21 Quantitative Imaging 23 Systems and Control (DCSC) 25 Quantum Nanoscience High Resolution Electron Microscopy 27 Kavli Nanolab 28 Molecular Electronics & Devices 30 Quantum Transport 32 Theoretical Physics 35 Radiation Science and Technology Radiation and Health for Isotopes 38 Radiation Detection and Medical Imaging 38 Nuclear Energy and Radiation Applications 39 Neutron & Positron Methods in Materials 39 Fundamental Aspects of Materials and Energy 40

3 BioNanoscience Aubin-Tam Lab

Aubin-Tam group

We are developing biophysical tools that allow real-time control over single biomolecules and single cells. We are also exploiting the unique properties of some proteins to design novel bio- and nano materials.

Freestanding membrane in microdevice à tudies s on protein-induced membrane deformation Master project: Pulling membrane tubes from freestanding membranes with optical tweezers

In biology, we can find several example of membrane tubes. One important question is the role 75µm of proteins in shaping membranes. One step towards these interesting studies is to create networks of membrane tubes. In the Aubin-Tam A microfluidic device is custom-designed in your group in order to form group, we have the technology that could enable stable freestanding membranes. Picture of the membrane(right). this highly novel way of creating artificial membrane a b networks. Collaborator for theory: Timon Idema

Koster et al. PNAS 2003 a. Membrane tube pulled from a vesicle with optical tweezers. b. In this project, a tube will be pulled from a freestanding membrane.

Production of biomimetic materials with the use of microorganisms Biomaterials in the natural world provide an abundant source of Bachelor project: C urli biofilms towards artificial nacre inspiration for the design of novel high-performance materials. production Nacre consists of stacked layers of calcium carbonate In this project, the student will engineer bacteria to (CaCO3) separated by thin 20nm layers of sticky elastic biopolymer. This layered confers exceptional mechanical fabricate nacre-like material. CaCO3 crystallization will properties. Our approach is to exploit synthetic biology to self- be induced by bacteria. The organic layer of this novel assemble artificial nacre with reprogrammed bacteria. artificial nacre material will be biofilms made of reprogrammed curli proteins. Mechanical characterization will be performed.

! Collaborator: Anne Meyer Nacre multilayered structure. CaCO3 platelets are “glued” ! together with biopolymers. Scale bar = 20mm.

Flagellar biolocomotion at microscale Collaborator in Fluid Dynamics: Daniel Tam

Bachelor or Master Project: E xternal perturbations on a single cell of Chlamydomonas to study flagellar biolocomotion

The ability of flagella to manipulate and transport fluid relies on their capacity to spontaneously beat and synchronize with one another. Identifying the physical mechanisms leading to flagellar synchronization has been the subject of intense investigations in recent years. The algae Chlamydomonas is a model system used is most of these studies. External perturbations on Chlamydomonas will be imposed to identify what causes its two flagella to beat in sync. This project is at the intersect between cell biology, biophysics and fluid mechanics. Single cell of the algae Chlamy- domonas is recorded will an ultrafast camera.

For more information, please contact us: [email protected]

4 RESEARCH GROUP GUIDE 2016 BioNanoscience Beaumont Lab Evolution, biophysics and synthetic biology in the Beau- Evolutionary gear shifting in a bacterial nanomotor mont Lab Cells are alive because of interactions between thousands of Biological evolution has generated nanomachines of a nanoscopic machines that perform critical processes. Some complexity far greater than any man-made devices of this size. of these molecular machines are built from protein parts that Research in the Beaumont lab is inspired by the question of interact to give rise to a higher-order function. Modern biology how the molecular machines of the cell evolved their complex has a very good theory that explains how such complex multi- functionality. Using three different model systems, we seek component systems can have been generated by evolution. All to understand the mechanisms by which evolution assembles evidence suggests that they evolved by the step-wise joining of them from protein building blocks and fine-tunes their function. protein parts that already existed and played a role in different Our multidisciplinary research strategy combines methods cellular processes. We study how such components can be from biophysics, synthetic biology, nanotechnology and real- modified by evolution in order to function in a new complex. time laboratory evolution. This work has begun to illuminate We do this in real-time laboratory evolution experiments. These the functioning and evolution of our model systems, a first step experiments make use of genetically engineered bacteria in toward discovering the engineering principles needed to build which one component of their flagellar motor—a rotary motor bionanomachines with novel functions. We have MSc and BSc that comprises 25 different parts that is used by bacteria to projects available for curious and driven students on three swim—has been replaced with a an incompatible component. topics. Contact Bertus Beaumont ([email protected]) Next, we study how evolution integrates this component, yielding for more information. a fully functional motor and cells capable of swimming. These experiments have successfully captured this process. So far, our work has identified the underlying mutations. We are now studying how these mutations achieve component integration by reconstructing them in different combinations and studying how they change the motor, the cellular behavior and fitness. The project uses a broad range of methods including video-tracking microscopy (to study how the capability to swim re-evolves), mutation reconstruction (synthetic biology tools to study the effects of the mutations we identified on the motor and on cell swimming), competition assays (to measure the fitness effects of the mutations) and single-motor experiments (to analyze the effects of mutations at the level of a single flagellar motor). We are also doing experiments that use synthetic biology and experimental evolution to introduce a new component into the flagellar motor that is essential for function (i.e. that is required for the new, more complex motor to spin). Together, these lines of research will shed light on the evolutionary mechanisms that enabled the evolution of complex bionanomachines and begin to reveal engineering principles that are needed to engineer molecular machines with novel functions.

RESEARCH GROUP GUIDE 2016 5 BioNanoscience Beaumont Lab Reprogramming anti-bacterial protein nanomachines Nanodevices that kill bacteria by mechanically puncturing their membrane could end the ongoing battle against bacteria that have become resistant to conventional antibiotics. Bacteriophages and pyocins are biological molecular machines made from protein components that are capable of puncturing and killing specific bacteria. Recently, it has been demonstrated that their target specificity can be reprogrammed using a synthetic biology approach; however, owing to a lack of fundamental understanding of the underlying molecular mechanisms, this process is very inefficient. We have devised a novel strategy that exploits the power of synthetic biology, experimental evolution and single molecule fluorescence microscopy to rapidly generate reprogrammed phages/pyocins and discover the underlying engineering principles. In this project, we will implement a gene-shuffling based chimeric phage/pyocin evolutionary selection procedure that will allow Multi-level biophysics of conductive bacterial nanowires rapid reprogramming in order to alter the target specificity. All life forms must get rid of waste electrons from their In parallel we will develop two single phage/pyocin-particle metabolism. Humans use oxygen, but bacteria can use a broad microscopy approaches that capable of detecting all key events range of other chemicals for this purpose. One organism, in their mode of attack in real time under the microscope. Next, Geobacter sulfurreducens, has evolved a unique strategy that we will combine these two capabilities in a highly innovative allows it to transfer its excess electrons to rust particles (iron approach to gain the much-needed insight into the engineering oxide) outside of the cell. It does this using specialized nanowires principles that underlie phage/pyocin reprogramming. that self-assemble from protein building blocks. How it is possible for protein molecules to conduct electricity and what the electrical properties of these nanowires are is still mysterious. Moreover, it is unknown what type of cellular behaviors the wires enable. How does a single cell make contact with a rust particle and how does the electrical network formed by the nanowires allow interconnected populations of cells to grow? In this project, we are studying these questions at different levels of biological organization using a multidisciplinary approach that features methods from quantum nanophysics, single-cell biology and bacterial ecology. We have isolated protein nanowires and developed methods to measure their electrical properties using custom-made nanochips with gold electrodes. In parallel, we have developed tools to study the growth of single cells and populations of cells under the microscope in the presence of iron-oxide particles and potentiated artificial electrodes. With these tools, and using genetically modified strains that do not produce nanowires or produce wires that are less conductive, we will explore the multi-level physics, physiology and ecology of conductive nanowires and the cells that use them. The work will deliver fundamental new insights into electron transport by proteins, reveal the secret life of G. sulfurreducens and paving the way for future technological applications of conductive proteins.

6 RESEARCH GROUP GUIDE 2016 BioNanoscience Cees Dekker Lab Come do your MSc/BSc project at the Cees Dekker Lab!

DNA bio-physics at the crossroads of nanotechnology, physics and biology Here’s some examples of our cutting-edge research where you could step in:

Studying DNA at the single-molecule level Our nanopore research leads us to the

The physical structure of frontiers of new technology and science DNA is of paramount Our group pioneered the use importance in cells. We of nanopores for detection of investigate the interactions single DNA molecules, now between DNA and its aiming at DNA sequencing. structuring proteins, with We currently expand into many special emphasis on DNA exciting new directions: supercoiling (a la the detecting and sequencing annoying knots in your single proteins, using exciting headphone cords). We use new materials like graphene sophisticated instruments and DNA origami, adding laser (some unique at world excitation and plasmonics. Will level), like high-speed AFM, you contribute to tomorrows optical and magnetic next sensing technology? tweezers combined with Mechanism of homology recognition in DNA recombination Resolved in dual-molecule experiments fluorescence. Artist impression of graphene nanopore

We engineer bacteria into totally novel We aim to create de novo synthetic cells shapes and understand their biophysics For many years, people dreamed We explore bacterial cells in about creating life. Today this microfabricated structures dream begins to come within on chip, to examine the reach. In our group we develop biophysical value of bacterial new microfluidic technologies and shape. Side-by-side with it use them to control the division we use state-of-the-art and growth of simple model cells fluorescence microscopy in (vesicles with proteins). Combining real-time to study the physics and biology, we study how dynamics of homology DNA and proteins are spatially search during DNA repair in organized, for example to control living bacterial cells. where such vesicles will divide. Bacterial communities, their You have the opportunity to join ecology and dynamic is also this exciting adventure to realize one of our main interests. synthetic cells, an effort that until

recently was merely a dream Production of liposomes on chip Bacteria in a nanoslit (top) Bacteria shaped into TUDELFT shape (bottom)

What is it like to do a Bsc or Msc graduation project in our group? When you start your project here, you will work in close collaboration with your direct supervisor. Projects vary in content: some are more physics-, some more bio-like. You will immediately be involved in the cutting-edge science conducted at our group.

Our group at a group While doing research, you will be given freedom excursion to Iceland!! to explore interesting opportunities for your project. You will be fascinated to see that the theory you have learned in courses is brought to action in the lab. It will be a great learning experience in a fun (!) and energetic environment! Visit our website: www.ceesdekkerlab.tudelft.nl or contact Amanda van der Vlist to make an appointment: [email protected]

RESEARCH GROUP GUIDE 2016 7 BioNanoscience Dogterom Lab The assembly, force generation and organization of cytoskeletal polymers lie at the basis of many cellular processes. The research objective of the Marileen Dogterom lab is to gain a quantitative understanding of the physics behind these cytoskeleton-based processes. Several approaches are being employed, but all follow a bottom-up synthetic-biology approach to understand the function of individual components in an artificial in vitro system. Using simplified physically- and biochemically-controlled microfabricated environments, we can investigate the involvement of pushing and pulling forces generated by microtubules and motor proteins in the positioning of centrosomes, a key process behind chromosome separation during mitosis. The latest fluorescence microscopy techniques capable of imaging single molecules allow the characterization of regulatory proteins responsible for controlling these cytoskeletal dynamics. Together with novel techniques to control the activation of these proteins with light, we strive to build a controllable artificial system for studying complex cytoskeletal processes. The following projects are available: • Mitotic spindle positioning in emulsion droplets • Light-activated control of cytoskeletal dynamics • Force generation at microtubule ends Highly-motivated Bachelor and Master students are encouraged to apply for one of our projects!

8 RESEARCH GROUP GUIDE 2016 BioNanoscience Idema Lab Biology is often highly nonlinear, which is good news for life: Nematic order and defects in bacterial colonies many actors together can accomplish what a few cannot, not Many bacteria have rod-like shapes, which extend as they grow, just for lack of individual strength, but because the whole really and are halved when they divide. Due to both these shapes is more than the sum of its parts. In our group, we study how and the growth process, a bacterial colony becomes an active collective dynamics of many particles, from protein inclusions material with interesting topological properties, including such in the membrane to growing and dividing cells in colonies, affect features as head-to-tail linking lines and orientational defects. the function and behaviour of the living system they are part of. We study these defects both experimentally and in simulations. Membrane-mediated interactions When you put two balls on a mattress, they attract, because they deform the mattress. Two (or more) proteins in a membrane experience similar interactions because of the deformations they impose. Unlike electrostatic interactions, these membrane- mediated interactions are not additive, and can even change sign due to the presence of multiple proteins. Moreover, many membranes in living systems are naturally curved, creating a nontrivial energy landscape that depends on the relative curvature of the membrane and the imposed curvature of the protein. We study the patterns and shapes these membrane/ protein compounds form using analytical and numerical tools.

From single to multicellular behaviour Individual cells and animals behave differently on their own than in a group. Being part of a group is often useful, for protection against outside factors like the weather or predators, or because together cells can achieve more than any single one could alone. We study the collective behaviour of self-propelled soft particles as a model for these systems, looking for a minimal set of rules that allows the cells to exhibit complex patterns together.

RESEARCH GROUP GUIDE 2016 9 BioNanoscience Meyer Lab Project 1: Engineering bacteria to produce improved biomaterials The Meyer lab is using synthetic biology techniques to redesign and reprogram bacterial genetic circuitry in order to synthesize bio-inspired materials with improved properties. This approach has the potential to replace traditional chemical approaches that require extreme environmental conditions, expensive equipment, and the generation of hazardous waste. We have targeted bacterial production of artificial nacre, a layered biomineralized material lining seashells with exceptional mechanical toughness. We are also using engineered bacteria to synthesize graphene. A third project combines the expression of silica- precipitating enzymes with functionalizable biofilms to produce targeted microlens arrays for bio-imaging applications. The use of light to induce biomaterial production will allow for the application of light patterns to produce micropatterned materials. Expression of the responsible enzymes in bacteria will allow for precise control over the production of our biomaterials, in order to create products with tunable material properties.

Project 2: The role of biocrystallization in survival Striking microscopy has revealed that bacteria respond to conditions of extreme stress by condensing their DNA into a crystalline lattice (see figure). The protein responsible for creating these structures is Dps, which becomes one of the most abundant components of prokaryotic cells in times of stress and is absolutely required for bacteria to survive in damaging environments. Little is known about how Dps binds to and organizes DNA, or why this behavior can protect cells from damage. Currently we are developing novel biophysical and biochemical tools to measure the interaction of Dps with DNA, and its ability to oxidize and store iron. Why are these activities so important for bacteria to survive in damaging environments? How do they differ between individual cells? We welcome highly motivated Bachelor’s and Master’s students to join us on these projects. Depending on student interests, project activities will involve multiple techniques in areas including biophysics, biochemistry, directed evolution, genetic modification of bacteria, cell biology, chemistry, synthetic biology, or state-of- the-art microscopy. We highlyvalue students who are interested in thinking independently and creatively to solve problems. Contact: Anne Meyer, [email protected].

10 RESEARCH GROUP GUIDE 2016 BioNanoscience Nynke Dekker Lab The Nynke Dekker Lab The Nynke Dekker Lab is a single-molecule focused Biophysics research lab and is one of the most established laboratories at in the Department of Bionanoscience in TU Delft. This vibrant and growing new department is dedicated to research at the interface between nanoscience, synthetic biology and cell biology. It focuses on the functioning of single cells in all their complexity down to the single molecule level. Understanding the fundamental molecular processes is of crucial importance for diverse developments and applications involved in targeted therapeutics, biomedicine, diagnostics and alternative energy sources, among others. • Having experience with Matlab. Research • Applying mathematics to learn about biological pro Our research group focusses on the study of the biomolecules cesses. (DNA, RNA, and proteins) relevant to cellular key processes • Learning cutting edge experimental techniques with such as transcription, replication, and genome compaction. living organisms. Our studies on the behavior of individual biological molecules are conducted both in vitro and in vivo, which allows us to • Eager to learn and develop one’s own ideas. quantitatively characterize enzymes individually and in the Then a project within the Live Cell Imaging subgroup will be awe- cellular environment. To do so, we continuously develop and some for you! Feel free to ask questions through email, or come employ several cutting-edge single molecule techniques, over for some coffee and a chat. such as magnetic and optical tweezers, flow-stretched DNA curtains and super-resolution fluorescence on living cells, using Contact nanostructures and microfluidics. Studying molecular processes MSc. Roy de Leeuw using these techniques requires broad expertise; our lab is Dept. of Bionanoscience, TU Delft composed of a multidisciplinary team of international scientists with backgrounds ranging from cell biology, biochemistry, Room F062, Tel: +31-(0)15 2785394 biophysics and engineering. There are always opportunities for Email: [email protected] exciting and challenging BEP and MEP projects in the field of fundamental and applied life sciences in our lab! DNA Compaction: Single Molecule Studies of Eukaryotic Histones Guidance The meters of DNA present in eukaryotic systems, ranging Students are fully integrated in our multidisciplinary team, from yeast to humans, are densely packed into a hierarchical gaining a unique experience at the frontier of research. The structure called chromatin in order to fit in the tiny nucleus. Its projects include all aspects of practical lab work, experiments basic unit is a DNA-protein complex termed nucleosome which and analysis. Every student will grow in their his or her skills and essentially comprises a core of so-called histone proteins with become independent to a level where they he or she can make a a small piece of DNA wrapped around it. Besides packaging DNA, real contribution to research at the cutting edge of science, often nucleosomes also play an essential role in the regulation of the including a publication in an international scientific journal. genome during key nuclear processes such as transcription, Current BEP and MEP Projects replication and repair by controlling DNA accessibility and, hence, are a burning topic of fundamental research! We study Looking at shiny single proteins within living cells the structure and dynamics of nucleosomes at single-molecule Proteins have specific unique behaviors within the cell. For level using magnetic tweezers. example, they can exist in large numbers or small, become BEP and MEP projects DNA bound or float freely, fluctuate at high speeds from pole to pole, etc. To address and quantify these types of behaviors We are looking for students who are interested in joining our we are developing specific image processing algorithms. One of current efforts in investigating the assembly and dynamics of the main problems is accurately tracking the proteins over time, nucleosomes containing artificially modified histones using regardless of its behavior i.e. one has to be sure that blob A in different magnetic tweezers techniques. There are different frame 1 is still blob A in frame 2. This method is essential to possibilities to contribute to this research: determining the properties of the proteins you are looking at. • Designing and developing an assay to study the cha This process requires a sophisticated mathematical approach racteristics of certain nucleosomes. that uses probability and combinatorics to make decisions on • Taking measurements based on an already establi spot localizations. In doing so it is also essential to develop shed experimental design to obtain statistical data. methods and criteria of spot recognition to distinguish one from another. Do you resonate with the following statements? • Analyzing large single-molecule data involving fitting and calculation of different parameters of interest.

RESEARCH GROUP GUIDE 2016 11 BioNanoscience Nynke Dekker Lab Contact MSc. Orkide Ordu Contact Dept. of Bionanoscience, TU Delft Dr. Mariana Köber Room F086, Tel: +31-152781025 Dept. of Bionanoscience, TU Delft Email: [email protected] Room F090, Tel: +31-152783552 Email: [email protected] DNA Transcription: Function of RNA Polymerase Trans- cription Factors RNA polymerases (RNAP) are a main target for the regulation of gene expression and thus a possible target for antibiotics and vaccines. RNAP are highly conserved across different organisms And the RNA chain elongation is stochastic and highly dynamic, interrupted by pauses that represent a gene regulatory feature; they facilitate the timely interaction of regulatory factors and the synchronization with the subsequent translation. We characterize the transcription mechanism and related pausing events during RNA chain elongation of E. coli RNA polymerase on a single-molecule level as model system. The RNAP dynamics are probed under different experimental conditions, e.g. we study the force and nucleotide concentration dependencies, as well as the effects of the nucleotide analogue inosine to the proofreading mechanism, and the role and impact of the most DNA Replication: Single Molecule Studies of Eukaryotic important transcription elongation factors that are expressed Helicases in the cell. Each time a cell divides, the entire genome has to be copied. In BEP and MEP projects this process, a helicase separates double-stranded DNA, allowing Students will be involved in projects creating a mechanistic each strand to be copied individually. The misregulation of DNA kinetic model of the regulation of gene expression and determine replication is recognized as a significant source for chromatin further the impact of transcription factors. The selected changes leading to genome instability in tumors. By means of transcription factors correspond to fundamental mechanisms Magnetic Tweezers we characterize the dynamics of helicases such as proofreading, recuperation from arrested states, DNA- that work in eukaryotic cells. Our final goal is to elucidate some repair process, virulence and anti-termination. of the physical and molecular mechanisms involved in chromatin replication, and therefore contribute to identify sources that • Studying the impact of the virulence factor RfaH to the may lead to cancer. transcription process. RfaH is considered as major target for novel antibiotics. . BEP and MEP projects • Characterize the influence of RNA cleavage factors and DNA • Which mechanism does the helicase use for unwin repair factors on RNAP dynamics and processivity. ding? Does it actively break the base pairs or is it ra ther opportunistic, waiting for a transient opening of • Probing the transcription dynamics under macromolecular the double helix due to thermal fluctuations? crowding conditions, simulating as such the cellular environment. In this project you will build on a working assay, so you can directly go to the lab to see how the enzyme reacts when you Contact vary one of the following parameters: the amount of energy you Dr. Richard Janissen supply to the helicase, the force to destabilize the DNA double helix, or the temperature. If lab work is not yours, you can also Dept. of Bionanoscience, TU Delft choose to be rather involved in the data analysis and modelling part. • What happens if the helicase encounters a nucleoso me? How is the unwinding of DNA affected? Does the nucleosome disassemble? In our lab we are in the exceptional position to have expertise on single-molecule experiments with both nucleosomes and helicases. In this exploratory project you will add the missing link and combine both.

12 RESEARCH GROUP GUIDE 2016 Fluid Flow Atmospheric Physics The Atmospheric Physics (Clouds and Climate) group studies Radiative transfer through clear and cloud-topped turbulence and clouds in the atmosphere. We are particularly atmospheres: Observations and modelling interested in the transport of heat, momentum, moisture and chemical species, but also in the life cycle of clouds as Clouds reflect a large fraction of the downwelling solar radiation their presence strongly affects the radiative properties of the back to space. At the same time they emit radiation as a atmosphere, which is relevant in the context of weather as blackbody thereby increasing the amount of infrared radiation well as climate. As a practical example, we are performing high towards the ground surface. Observations of vertically integrated resolution simulations of clouds and wind to provide detailed cloud liquid water, radiative fluxes, and other key quantities are information about the expected amount of energy from renewable collected at the KNMI measurement platform Cabauw. In this energy sources. Many students have performed their MSc or BSc project radiative transfer calculations will be performed with project with use of the Dutch Atmospheric Large Eddy Simulation the Rapid Radiative Transfer Model for Global models (RRTMG), model, while some have developed conceptual models to better and the results will be compared with observations. The aim is understand physical processes in the atmosphere. We are also to test the skill of the radiation model to compute solar and interested in the analysis of observations. infrared fluxes at the ground surface. In principle we always have projects available for both BSc and Urban Energy Budget: Solar and infrared radiation MSc students. Every project proposal can be performed for a calculations with a Monte Carlo approach short BSc project as well as for a full MSc thesis project. The temperature in (big) cities develops differently than its Group members: Prof. Dr. Harm J. J. Jonker, Prof. Dr. A. Pier rural surroundings. As a reason, buildings absorb solar radiation Siebesma, Dr. Stephan R. de Roode and Bas van de Wiel more efficiently during the day, and loose infrared radiation more slowly during the night as compared to a flat terrain. This Solar and wind energy predictions with a large-eddy si- effect can be modelled with the Monte Carlo technique, with mulation model which photons are randomnly ‘shot’ into the urban canyon. The Low clouds like stratocumulus are poorly represented by current absorption, and the direction of reflection of the photon are state-of-the art weather forecast models. Previous MSc student treated with simple probability functions. The question is which projects have shown promising results of cloud predictions urban geometry, as measured by the height-to-width ratio of the with a Large-Eddy Simulation model. In this project the surface buildings, most efficiently traps radiation? boundary condition used by the LES model will be considered, in Development of a conceptual model for low clouds particular the role of soil moisture on evaporation, and, in turn, its effect on the temporal development of low clouds. The mixed-layer model is a simple conceptual model which is based on the premise that turbulence stirs the lower part of the We have recently implemented wind turbines in the LES atmosphere towards a vertically well mixed state. To study the model. The high-resolution results pave the way to improve its evolution of this layer one only needs to specify the bottom and representation in coarse-resolution weather forecast models. In top fluxes, in addition to possible source terms like radiation this project the effect of atmospheric stability and turbulence or precipitation. The mixed-layer model has been developed by on the wake structure will be studied. students during the last couple of years. In this project it will be Large-eddy simulation of deep convective clouds explored whether the model can be used to study the evolution of a solid cloud deck towards a broken structure. Deep convective clouds are characterized by strong turbulence and a strong precipitation. In this project the role of the surface temperature and the mean vertical stability of the atmosphere on the development of deep convection will be explored. Observations and modelling of fog During calm and clear weather conditions fog may occur. In this project observations will be used to assess the conditions during which fog develops. Selected cases will be modelled with the large-eddy simulation model.

RESEARCH GROUP GUIDE 2016 13 Fluid Flow Fluid Mechanics Experimental and computational studies are made of systems at different scales, from lab-scale to industrial scale. Detailed investigations are made using laser diagnostic techniques (such as particle image velocimetry, laser-induced fluorescence, and other spectroscopic methods) and using advanced computational models, such as large-eddy simulation and direct numerical simulation. Information on completed, current and available projects can be found at http://delftpe.nl/Education/MScProjects or by

The section Fluid Mechanics is part of the Department Process and Energy of the Faculty 3mE. Fluid mechanics is an essential part of physics and especially students following the track “Fluid Flow and Transport Phenomena” of the Master Applied Physics, can find interesting research opportunities for a graduation project among the topics investigated at the section. Thesis supervisor can be prof. dr. ir. J. Westerweel, prof. dr. DJEM Roekaerts, prof.dr.ir. RAWM Henkes, Dr. ir. C. Poelma and other

staff members. 1cm The research in the section concerns fundamental aspects of flows, but always with a clear connection to a practical application or process in industry, environment or other sectors of society (e.g. sports). contacting the staff members. Important themes are: Contact information • Complex flows (multiphase, microfluidic, biological, reacting) http://delftpe.nl • Detailed measurements and modeling of turbulence Prof. dr. ir. J. Westerweel - [email protected] • Turbulent combustion dr. ir. C. Poelma - [email protected] • Turbulence and energy transfer Prof. dr. D.J.E.M. Roekaerts - [email protected] The research program responds to a substantial drive from society and industry, for example for more environmentally friendly combustion processes avoiding the formation of Secretariat: NOx and particulates (soot) in industrial combustion systems C. Legierse (furnaces, gas turbines, engines), and for the development of energy efficient processes (e.g., through drag reduction). [email protected] The activities in microfluidic flows aim at the investigation of Building 34; Room : 5B-1-30 small-scale cardiovascular flows, flow geometries with complex boundary conditions (such as micro-flagellae), and micro-scale multiphase flows.

14 RESEARCH GROUP GUIDE 2016 Fluid Flow Transport Phenomena Department Chemical Engineering, www.cheme.nl The Research Groups “Transport Phenomena (TP)” and “Product and Process Engineering (PPE)” in the Department of Chemical Engineering offer BSc and MSc graduation projects for physics students in the field of fluid flow, transport phenomena and soft matter physics. Although our groups are in the ChemE department, our research has very strong physics components. Many of the professors and students in our groups are physicists by education. We publish a large fraction of our work in physics journals, such as Physics of Fluids, Physical Review Letters, Journal of Applied Physics and Physical Review E. Our BSc projects are often inspired by questions from society and industry, with applications in energy conversion, advanced materials processing, and health. Many projects are being executed in collaboration with companies such as Shell, ASMI, DSM, Friesland Campina, Tata Steel and NAM, as well as the academic hospitals LUMC and EMC. The dimensions of the systems that we study range from microns to tens of meters and we want to understand and control them. The fun thing about most of our work is that you can observe the relevant phenomena with your own eyes and that the relevance of what you do is obvious even to your laymen family. An MSc in either PPE or TP is an excellent preparation for your future career. The majority of our graduates easily find jobs in the (process) industry or in research institutions. Many of our best graduates continue their scientific career by doing a PhD. In TP and PPE, we study multiphase fluid dynamics and transport phenomena in Labs-on-Chips simulations to understand processes that are too difficult to study experimentally. Examples of what we are currently studying are: fluid dynamics in labs-on-chips, multiphase pattern formation in nanofluidics, aerosol drug transport in human lungs, blood flow and magnetic drug targeting in arteries, atmospheric dispersion of pollution, magneto-hydrodynamics in metallurgy, and multiphase flow in bio fermenters. In TP, together with researchers from the LUMC academic hospital, we study the influence arterial plaque on blood flow in the carotic artery.

Section Product and Process Engineering, www.cheme. nl/ppe Section Transport Phenomena, www.cheme.nl/tp (Dr. Pouyan Boukany, Prof. Michiel Kreutzer, Dr. Ruud van Ommen, (Prof. Harry van den Akker, Prof. André de Haan, Dr. Sasa Kenjeres, Dr. Volkert Van Steijn) Prof. Chris Kleijn, Prof. Rob Mudde, Dr. Luis Portela) The Product and Process Engineering (PPE) group studies The Transport Phenomena group studies the exiting and fluid flow and transport phenomena in chemical processes complex dynamics of liquid and gas flows, in industry, in the aimed at creating novel (bio)chemical and biomedical devices, environment, and in living organisms. Our research revolves processes and products. With expertise in reaction engineering, around the Navier-Stokes equations, which might well be the fluid mechanics and transport phenomena, the group creates mathematically most challenging equations in physics. We study solutions for soft-matter, nanotechnology, energy, and lab-on- the interaction between macroscopic fluid flow phenomena chip applications, often together with chemistry, physics and and molecular phenomena that occur around (gas-liquid, gas- life-science groups; we love interdisciplinary projects. For us, solid and liquid-solid) interfaces in complex liquids such as engineering implies out-of-the-box thinking and design, from a foams and suspensions. We use optical and X-ray techniques sound basis in natural sciences with mathematical rigor. to look inside flowing media, and massively parallel computer Examples of what we are currently studying are: bio- laboratories-

RESEARCH GROUP GUIDE 2016 15 Fluid Flow Transport Phenomena on-chip, organs-on-a-chip, pattern formation in multiphase ([email protected]), Prof. Rob Mudde (r.f.mudde@tudelft. porous media flows, synthesis of core-shell nanoparticles, nl) photocatalysis for energy conversion, flow of granular matter, • Mass transfer in a gas-liquid-liquid system, experimental MSc Nanofluidics for Drug/Gene Delivery, Nano-chips for detection project, ir. Manas Mandalahalli ([email protected]), of biomolecules, molecular rheology and rheo-physics of DNA. Prof. Rob Mudde ([email protected]) In PPE, we study Atomic Layer Deposition in a fluidized bed as a • Reactive extraction of HMF (5-hydroxymethylfurfural) from novel technique for atomic precision coating of nanoparticles, aqueous solution in the presence of ionic liquid and organic e.g. for application in Li-ion batteries. solvent, computational and experimental MSc project, ir. Saidah Altway ([email protected]), prof. André de Haan ([email protected] ) Flow and transport phenomena in biomedical applications • Extracting a heartbeat from the light scattered by red blood cells in motion, BSc or MSc computational and theoretical project, also suited for TWN double degree students, joint project between ChemE/TP and ImPhys/Optics, ir. Kevin van As ( [email protected] ), Dr. Sasa Kenjeres (s.kenjeres@tudelft. nl) • Experimental studies of pulsating blood flow in a realistic patient specific artery model, Experimental MSc project, Dr. Sasa Kenjeres ([email protected]) • Experimental studies of the magnetic deposition efficiency in micro-vessels, Experimental MSc project, Dr. Sasa Kenjeres ([email protected]) • Computer simulations of blood separation process, Computational MSc project, Dr. Sasa Kenjeres (s.kenjeres@ tudelft.nl) • Numerical modeling of aerosol distribution in a realistic lung geometry, computational BSc or MSc project, also suited for TWN double degree students, Dr. Sasa Kenjeres (s.kenjeres@ tudelft.nl) • Numerical modeling and computer simulations of atherosclerosis, computational BSc or MSc project, also suited for TWN double degree students , Dr. Sasa Kenjeres ([email protected]) Available projects in the Transport Phenomena group • Numerical simulations of blood flow and magnetic particle (February 2016) deposition in realistic arteries including fluid-structure- The following BSc and MSc projects are available for physics interactions, computational BSc or MSc project, also suited for students as per February 1, 2016. For each project we indicate TWN double degree students, Dr. Sasa Kenjeres (s.kenjeres@ whether it is a BSc or MSc project, whether it is an experimental, tudelft.nl) computational or theoretical project, and the name and e-mail Environmental flow and transport phenomena of the contact persons. • Air flow and turbulent dispersion of pollutants in urban areas, For several projects it is indicated that the project is also suited computational BSc or MSc project, also suited for TWN double for BSc TWN double degree students. degree students, Dr. Sasa Kenjeres ([email protected]) Multiphase flow and transport phenomena in Flow and transport phenomena in materials processing bioprocessing • Numerical simulations and modeling of MHD transient and • Gas-liquid flows stirred fermentors, computational turbulent flows, Computational MSc project, Dr. Sasa Kenjeres MSc project, ir. Cees Haringa ([email protected]), ([email protected]) Prof. Rob Mudde ([email protected]) • Modeling rarefied gas jets in Physical Vapor Deposition, • Mass transfer and interaction dynamics from Rising, Computational BSc project, also suited for TWN double degree computational BSc or MSc Project, also suited for students, ir. Chirag Khalde ([email protected]), prof. Chris TWN double degree students, ir. Siddhartha Mukherjee Kleijn ([email protected])

16 RESEARCH GROUP GUIDE 2016 Fluid Flow Transport Phenomena • Modeling of Atomic Layer Deposition of nanofilms inside Soft matter nanopores, Computational BSc or MSc project, joint project • Transport phenomena of emulsion droplets, MSc project, Dr. with the PPE section, ir. Wenjie Jin ([email protected]), prof. Volkert Van Steijn ([email protected]) Chris Kleijn ([email protected]) • Mixed convection flow in porous media, Experimental BSc or Nanomaterials processing MSc project, ir. Iman Ataei Dadavi ([email protected]), • Modelling of nanoparticle agglomeration and fluidization, MSc prof. Chris Kleijn ([email protected]) project, Dr. Ruud van Ommen ([email protected] ) • The interplay between interparticle forces and nanoparticle flow – an experimental study, Experimental MSc project, Dr. Flow and transport phenomena in energy conversion Ruud van Ommen ([email protected] ) • Modelling multicomponent mass transfer in nanofluidic • A microfluidic spraydryer for controlled manufacturing of multiphase flows, computational BSc or MSc Project, joint nanocrystals, Experimental MSc project, Dr. Ruud van Ommen, project with the PPE section, also suited for TWN double degree [email protected], Dr. Volkert van Steijn ( V.vanSteijn@ students, ir. Hrushikesh Pimpalgaonkar (H.G.Pimpalgaonkar@ tudelft.nl) tudelft.nl), prof. Chris Kleijn ([email protected]) • Atomic layer deposition in a fluidized bed for making medical • Simulating Fischer-Tropsch synthesis in nanopores, isotopes, BSc or MSc project, computational BSc or MSc Project, joint project with the PPE section, also suited for TWN double degree students, ir. • Dr. Josette Moret ( [email protected]), Dr. Ruud van Hrushikesh Pimpalgaonkar ([email protected]), Ommen ([email protected]) prof. Chris Kleijn ([email protected]) • The interplay between flow and chemistry in atomic layer • Implementing an equation of state in the phase field method, deposition - modelling & experiments, MSc project, ir. Fabio computational BSc or MSc Project, joint project with the PPE Grillo ([email protected]); Dr. Hao Bui ([email protected]), Dr. section, also suited for TWN double degree students, ir. Ruud van Ommen ([email protected]) Hrushikesh Pimpalgaonkar ([email protected]), prof. Chris Kleijn ([email protected]) Gas solid flows • Developing the optimum tracer particle for single-photon • Modeling and simulation of multi-phase multi-component emission computed tomography (SPECT), MSc project, Dr. systems, computational BSc or MSc Project, joint project with Ruud van Ommen ([email protected]), Prof. Rob Mudde the PPE section, also suited for TWN double degree students, ([email protected]) ir. Hrushikesh Pimpalgaonkar ([email protected]), prof. Chris Kleijn ([email protected]) Other projects More information can be found on www.cheme.nl/ppe. You can also come and talk personally to the interim head of the group, • Solving the mysteries of the Feynman Sprinkler, computational Dr. Ruud van Ommen, [email protected] and theoretical BSc or MSc Project, also suited for TWN double degree students, prof. Chris Kleijn ([email protected]), Prof. Rob Mudde ([email protected]) • Fluid dynamics in a fruit juice sterilizer, experimental MSc project, prof. Chris Kleijn ([email protected]) • More information can be found on www.cheme.nl/tp. You can also come and talk personally to the head of the group, prof. Chris Kleijn, [email protected]. Available projects in the Product and Process Engineering group (February 2016) The following BSc and MSc projects are available for physics students as per February 1, 2016. For each project we indicate whether it is a BSc or MSc project, and the name and e-mail of the contact persons. Nanofluidics • Dynamic pattern formation at the nanoscale, MSc project, joint project with the TP section, ir. Hrushikesh Pimpalgaonkar ([email protected]), Dr. Volkert Van Steijn ([email protected]) • Nanofluidic gun for gene therapy, BSc or MSc project, Dr. Pouyan Boukany ( [email protected])

RESEARCH GROUP GUIDE 2016 17 Imaging Physics Acoustical Wavefield Imaging The research within the research group Acoustical Wavefield Imaging (AWI) is geared towards using (ultra)sound waves for non- destructive imaging at sub-wavelength resolution. The applications range from a very large scale for creating seismic images of the interior of the earth’s subsurface to a much smaller scale for ultrasonic diagnosis of tumors or cardiovascular diseases. Developments in medical acoustics and seismics go very fast. Because we want to provide students with actual topics, we do not provide a list over here, but we refer to our website for an actual overview of Bachelor and Master projects. When you plan to do your bachelor or master project within our section, the best approach is to make an appointment with one or – preferably – more staff members ahead of time. They can provide you with an overview of the most recent projects and can define a project suited to your interest and preferences. Usually, you can choose to perform experimentally-oriented research or work with a more theoretical/numerical character that is often based on computer simulations using existing or new software. The thesis work is often coupled to a PhD student or a staff member. This person will help you with your work on a daily basis. The group has connections with various industries (oil-related, ultrasonic inspection, medical and research institutes) for doing an internship or do part of the thesis work: Erasmus MC (Rotterdam), TNO (Delft, Utrecht, Den Haag), Oldelft (Delft), Netherlands Forensic Institute (Rijswijk), Shell (Rijswijk), Total (Pau), BP (London, Houston), CGG (Paris), ConocoPhillips (Houston), PGS (Leiden), Schlumberger (Houston), Statoil (Oslo, Trondheim), Philips (Eindhoven), RTD-Applus (Rotterdam), Karlsruhe Institute of Technology.

Opto-acoustic probe on a membrane (red dot) Supervision: [email protected], D.J.Verschuur@tudelft. nl, [email protected], [email protected]

18 RESEARCH GROUP GUIDE 2016 Imaging Physics Charged Particle Optics The ambition of the Charged Particle Optics Group (CPO) is to develop new instruments to look at the microscopic world and to invent new methods to create structures down to nanometer size. We design innovative, sometimes revolutionary instruments operating with beams of electrons, photons, ions, or combinations thereof. All projects are focused on applications in industry, and often involve the use of our Scanning Electron Microscopes (SEM) and/ or our Focused Ion Beam instruments (FIB). Secondary electron detection in the multi-beam Scanning Electron Microscope The group has a unique electron microscope to speed up imaging by a factor >100. The secondary electrons from 196 beams are projected onto a fluorescent screen. The student is asked to design, build and test an optical transfer system for bringing the signal to a detector.

Supervision: [email protected] , [email protected] the nanometer scale. The student is asked to make 3D-patterns and measure their size and shape, using electron microscopy and atomic force microscopy. The final goal is characterize the process such that well-defined patterns can be fabricated in a controlled way. Supervision: [email protected] , [email protected] Sub-10 nm pattern transfer In a European project we develop methods to fabricate single- nanometer devices. A necessary step in that is the transfer of patterns into an underlying layer using masks. The goal is to write the masks using electron beam induced deposition (EBID) and use plasma etching for the pattern transfer. The student is asked to make these masks, inspect them and inspect the patterns after etching, using electron microscopy and atomic force microscopy. Supervision: [email protected], [email protected] Focused ion beam nanofabrication Size and shape control over nanometer deposits In a cooperation with FEI Company the group is developing a new ion Electron beam induced deposition (EBID) is a technique in which a source. At the core of this source is a nanostructure with 50 nm thin focused electron beam dissociates precursor molecules adsorbed foils in which we drill 100nm holes. Within this gas cell electrons create to a substrate into a solid deposit attached to the substrate and a ions. The student is asked to design and create (using the focused volatile fragment. The technique allows to make patterns down to ion beam machine) a new version of this structure with a closed top aperture of variable thickness to decelerate the electrons. Supervision: [email protected], [email protected] Secondary electron yield measurements In a cooperation with NIKHEF the group is developing methods to determine the secondary electron yield (SEY) of materials exposed to a primary electron beam. This will be applied to ultra-thin dynodes of a future particle detector. These dynodes consist mainly of SiN now, but perhaps can be made of diamond just as well. The student is asked to further develop the methods and do experiments to measure the SEY of various materials. Supervision: [email protected] and [email protected] Nanopatterning biomolecules using Electron Beam Induced Deposition (EBID) By exposing poly-ethylene-glycol (PEG) layers to electrons the properties of the PEG change such that fluorescent biomolecules

RESEARCH GROUP GUIDE 2016 19 Imaging Physics Charged Particle Optics can be attached to the PEG layer. The group wants to use this to processes using extremely short (~20 fs) laser and electron pulses. make biofunctionalized nanopatterns. The student is asked to do However, resolution with the laser pulses is limited by diffraction to experiments to unravel the mechanism of the electron induced ~300nm. We want to switch certain parts of the diffraction-limited changes to the PEG layer, and to make the smallest possible spot “off” using the ~5nm focused electron beam to, increase laser biofunctionalized patterns. microscopy resolution. The student is asked to design and do proof- of-principle experiments. Supervision: [email protected], [email protected], [email protected] Finding the size limit for nanoparticle x-ray analysis When a high-energy electron-beam hits a material x-rays are emitted that are material-characteristic. We want to use a novel, highly-sensitive x-ray spectrometer to identify nanoparticles in liquids and biological materials. The student is asked to do experiments to determine the smallest size of nanoparticles that can still be detected (different types of particles under different conditions). Supervision: [email protected], [email protected], [email protected], [email protected] Timing escape times of photons Supervision: [email protected], [email protected] The group has built a unique microscope that can determine the time it takes for photons to escape from a material. The photons 3D-Electron Beam Induced Deposition (3D-EBID) are generated when an electron beam hits a (nano)particle. The EBID is a technique in which a focused electron beam dissociates escape time bears unique knowledge about the particle and its local precursor molecules adsorbed to a substrate into a solid deposit environment. The student is asked to do experiments to measure attached to the substrate and a volatile fragment. The technique photon escape times from nanoparticles in different environments. allows to make 3D structures down to the nanometer scale. The student is challenged to make an attractive 3-dimensional structure at the nanometer scale, using our electron microscopes. That structure will be used to demonstrate to the world the capabilities of EBID as a 3D nanofabrication technique. Supervision: [email protected], [email protected] Shot-noise limit in lithography As electronic devices become smaller and smaller, the requirements for the lithography necessary to make the devices become more and more demanding. Line-widths have to be defined within a few nanometers and the line-edge roughness has to stay within strict limits. Supervision: [email protected] , [email protected] The group is investigating the fundamental limits of lithography, such as the shot-noise limit. The student will fabricate patterns in electron Light microscopy with electrons beam resist, using our electron microscopes, that can be characterized A major challenge in microscopy is to perform light microscopy with in terms of line-edge-roughness and line-width-roughness. a resolution equal to molecular dimensions. Electron beams can be routinely focused to nanometer length scale. We want to use electrons Supervision: [email protected], [email protected], T.Verduin@ to generate light microscopy signals at few nanometers resolution. tudelft.nl Students are asked to operate SEM and light microscope, write control Ultrafast Microscopy software, do experiments, and analyse results. The group is developing a new microscope to image ultrafast Supervision: [email protected] Deadly snapshots on living specimen. For long, electron microscopy on living biological cells was not possible due to the needed vacuum environment and the huge dose delivered to the cell when imaging. We are developing technology to keep cells alive inside an electron microscope and we try to answer the question ‘how deadly is a single electron snapshot if we can direct it at exactly the right moment and exactly the right location?’ Students are asked to design and perform experiments and perform biological cell culture.

20 RESEARCH GROUP GUIDE 2016 Imaging Physics Optics Scatterometry for applications in inspection in lithography Dimensional metrology of small structures is a basic subject, which is important for applications within a wide variety of areas, mainly in the semiconductor and optical industries, but also in mechanical engineering (length and angle encoders), biological and medical industries. Dimensional metrology of high-end laterally structured surfaces is a constant challenge due to the progressive minimisation of structures combined with an increasing impact of feature details on the functionality of these surfaces. The development of advanced lithography in particular requires metrology methods with state of the art low measurement uncertainty for the metrology of the 3D structures. For critical parameters, like the pitch or the width of the structures, values for the measurement uncertainty of well below one nanometre are necessary. In this project the student will help to design and built a laser scatterometer equipped with an interferometer arm to obtain Trace gas molecule detection for Environmental data that will be used to reconstruct the parameters of the monitoring or medical diagonistics object being measured. We do cavity enhanced trace gas absorption spectroscopy The project is mainly experimental. to look for molecules which are present as contaminants in For more information, please contact Silvania Pereira the environment or as biomarkers for disease in the breath of [email protected] people. Students can join in working on the experimental setup or simulations which are done for this project. Contact: [email protected] Refractive Index of Air Accurate determination of refractive index of air is necessary for many measurement systems like for example length measurements. To know the refractive index one has to know the environmental parameters. For this we are developing spectroscopic temperature, humidity and CO2 measurement tools. In this project there is experimental work and simulation work to be done. Contact: [email protected] Terahertz generation via plasmonics We are currently developing a new way of generating terahertz waves. This technique make use of near-infrared plasmon created by gratings of nanometric size. We focus a 800nm femtosecond laser beam on our nanostructures, increasing the absorption of the near-infrared light. In response, we generate in a nanothick layer above the gratings a strong Terahertz pulse (over 100 µm in wavelength). For this project, we need to model the nano-gratings with FDTD software, fabricate in the clean room the structures and measure their optical and terahertz properties in our laboratory. This project involves both modeling and experimental side. Contact: Dr. Aurèle Adam, Optics Group Room E006. a.j.l.adam@ tudelft.nl Study the aging of painting using Terahertz waves Our group has a good research record on studying paint layer using THz Layer. Here we plan to study these layers for the

RESEARCH GROUP GUIDE 2016 21 Imaging Physics Optics is based on a direct application of Terahertz Time Domain Spectrosocopy to be implemented in a factory line. The work consist on an experimental part and on a theoretical part. Implementations of the findings will lead to a future prototype by the company. Due to confidentiality reasons, more informations about the project can be requested directly to Dr. Aurèle Adam, Optic Group Room E006. [email protected] Terahertz Hyperbolic media Hyperbolic media are theoretical object with optical properties as amazing as the negative refraction. Waveguide made of the media would have infinite number of modes possible. The diffraction limit would also be beaten while using a material made of this media. Unfortunately, fabricate this object hasn’t been achieved yet. We are working on developing such a media for the terahertz frequencies and demonstrate the extraordinary painting industry. The drying and the aging of this layer, their effects that are expected by the theory. The project involves resistance to weather condition will be investigated with THz both a theoretical side and a more experimental side. and compared to results using other optical techniques. Contact: Dr. Aurèle Adam, Optic Group Room E006. a.j.l.adam@ This work is in collaboration with the Aerospace department of tudelft.nl TUDelft. Imaging system with Quantum Cascade Lasers Contact: Dr. Aurèle Adam, Optic Group Room E006. a.j.l.adam@ With the recent development of laser working in the mid-infrared tudelft.nl region (7-12µm), new possibilities for imaging are in reach. In Near Field Set-up for fiber measurement at THz our lab, we have acquired a tunable Quantum Cascade laser frequencies operating in pulse mode from 7 µm to 12 µm. We are planning to build an imaging set-up which consist on a far-field and in a A new set-up has to be build in order to perform near-field microscopy configuration. Various biological and non biological measurement of field inside THz plastic fiber. The idea is to use samples would be studied using the set-ups. This project a fiber coupled femto-second laser to generate and detect near requires mainly experimental skills. field emerging from new designed fiber made in Denmark by our collaborators. The set-up required knownledge in optics and in Contact: Dr. Aurèle Adam, Optic Group Room E006. a.j.l.adam@ electronics. It is mainly experimental. tudelft.nl or [email protected] This work is in collaboration with the Copenhagen University Design of gratings for new LED illumination (Denmark) More and more light bulb will be designed using LEDs. One draw Contact: Dr. Aurèle Adam, Optic Group Room E006. a.j.l.adam@ back of using LED is that the light illumination is coming from tudelft.nl almost point source. So far, the way to diffuse it is to use rather absorbing scattering materials. The idea here is to use diffraction THz properties of Thin Film gratings to perform the same trick, with more directional The Microelectronics group in TUD is fabricating lager membrane behaviour. The simulation will be done using conventional of designed thin films of SiC and other materials for antennas optical software and in house ones. The fabrication can be done improvement. Good calibration and properties at THz frequencies with one of our partner in Finland. are needed. Our current set-up has to be tuned in order to This work is a collaboration with Philips lighting. perform accuratly these measurements. Post processing of the data acquired is also needed in order to compare the simulated Contact: Dr. Aurèle Adam, Optic Group Room E006. a.j.l.adam@ or planed results and the measurements. tudelft.nl This work is in collaboration with the group of Microelectronics (TUD) Contact: Dr. Aurèle Adam, Optic Group Room E006. a.j.l.adam@ tudelft.nl Direct application of Terahertz technology In collaboration with a multinational company, we would like to investigate the possible use of THz radiation to solve a very concrete problem in an industrial environment. The project

22 RESEARCH GROUP GUIDE 2016 Imaging Physics Quantitative Imaging Medical Imaging in phase contrast imaging holds the promise of improved contrast of soft tissues. Advancing this technique requires table-top sized CT Colonography: automatic assessment high brightness sources, and innovations in image acquisition of image quality and processing. We explore different methods for source evaluation, tomographic reconstruction and disentanglement of The objective of this project is to develop attenuation and phase. Contact: Sjoerd Stallinga, S.Stallinga@ automatic quality masurements on CT tudelft.nl /Lucas van Vliet, [email protected] colonography data and relate this to the quality assessments done by radiologists. Contact: Frans Vos, [email protected]/ Lucas van Vliet, [email protected] Computational Microscopy CT colonography: An integrated system for automated cleansing and polyp detection Nanometer resolution in cryo-Electron Tomography TU Delft is developing sophisticated methods for electronic The study of viruses and small sub-cellular components requires cleansing, i.e. image processing algorithms to automatically an increase in the resolution of 3D cryo-electron tomography. We segment the colon surface from the CT data, prior to visualization. use forward modeling of the image formation process based on The objective of this project is to develop a polyp detection parameters that are estimated from the sample itself to achieve algorithm that is integrated into our methods for electronic the resolution goals. Contact: Bernd Rieger, [email protected] cleansing. Contact: Frans Vos, [email protected]/ Lucas van Super-resolution microscopy: precise to the nanometer Vliet, [email protected] The position of stochastically blinking fluorescent molecules can Diffusion Tensor MRI: Automatic detection of be measured with nanometer precision from a movie acquired characteristic points with a conventional widefield microscope. A super-resolution This project aims to automatically indentify salient points in image can be reconstructed from the localization data, thereby which the registration is optimal, after which the differences circumventing the classical diffraction barrier to resolution. We between Alzheimer patients and controls are to be studied. develop new imaging modalities in this area (measuring emission Contact: Frans Vos, [email protected]/ Lucas van Vliet, colour and molecular orientation along with emitter position) [email protected] and work on image analysis methods for image quantitation, for establishing performance limits, and for optimizing image Diffusion Tensor MRI: 4D analysis of Alzheimer’s disease acquisition and reconstruction protocols. Contact: Bernd Rieger, This project aims to study the evolution over time of DTI [email protected] / Sjoerd Stallinga, [email protected] parameters along relevant white matter tracts, e.g. by means of Pathology going digital: how automated slide scanning a 4D Principal Component Analysis. Contact: Frans Vos, F.M.Vos@ helps tudelft.nl/ Lucas van Vliet, [email protected] Digital pathology is an emerging clinical practice in which a Automatic classification of Dynamic Contrast Enhanced pathologist makes a diagnosis by examining a digital high- (DCE) MRI resolution image of a tissue slide. These images are acquired Dynamic Contrast Enhanced MRI visualizes the dynamic response with a high-throughput automated microscope (“whole slide of tissue to the inflow of blood. This project aims to automatically scanner”). We develop efficient optical quality testing methods identify inflammatory tissue in patients suffering from Crohn’s for inspection of manufacturing quality and for monitoring disease in order to quantify disease activity. Contact: Frans Vos, systems during their operational lifetime, we work on new [email protected]/ Lucas van Vliet, [email protected] ways for scanning multiple focal slices simultaneously, and we investigate image analysis algorithms for diagnostic assistance. Bending X-rays on a table-top: phase contrast imaging Contact: Sjoerd Stallinga. [email protected] of soft tissues Shining light: illumination patterns for efficient hi-res 3D Conventional X-ray imaging relies on local variations in microscopy absorption. The slight deviation in refractive index from unity gives rise to refraction and diffraction of X-rays, using this effect An intriguing way to make a 3D fluorescence image is to record a set of (2D) images on a camera for a set of specifically designed illumination patterns. As a bonus the in-plane resolution can be doubled as well. The design of illumination patterns in combination with various ways of scanning these patterns and image analysis methods can improve light efficiency and robustness. Contact: Sjoerd Stallinga, S. [email protected]/ Bernd Rieger, [email protected] 3D from 2D: light field imaging A light field imager can make a 3D-image of an object using only a single image obtained with a 2D image sensor. This remarkable feat is achieved by introducing a lenslet array

RESEARCH GROUP GUIDE 2016 23 Imaging Physics Quantitative Imaging MSc project ‘Optical trapping and Raman spectroscopie van bacteria en vesicles’ Lab-on-a-chip technieken trekken de aandacht voor allerlei sensing toepassingen, i.h.b. technieken gebaseerd op optische spectroscopie. In het project zal een lab-on-a-chip voor optische trapping en Raman spectroscopie verder ontwikkeld en toegepast worden. Met Raman spectroscopie, een optische techniek, kan een moleculaire vingerafdruk bepaald worden van het gemeten object. Werking van de chip is gebaseerd op het gebruik van optische waveguides en microfluidica. De chip zal in (“plenoptic imaging”) or a semi-random checkerboard mask het onderzoek ingezet worden voor identificatie van bacteriën, (“coded aperture”) into the optical system. We investigate the bloedcellen en celblaasjes (vesicles), waarvan bepaling van applicability of these principles to microscopy, in particular the de eigenschappen van belang zijn voor veilig drinkwater en trade-off between the depth sectioning capability and lateral diagnose van ziektes bij de mens. resolution. Contact: Sjoerd Stallinga, [email protected] Contact: Jaap Caro, [email protected] The research activities of DCSC cover the development and Biophotonic imaging & spectroscopy application of methods and tools for modelling, measurement BSc/MSc project ‘Flow quantification in parallel optical and control to practical challenges in various fields of physics. coherence tomography’ The target application domain of physical imaging systems is performed in the section N4CI led by Michel Verhaegen. The In a collaboration between Academic Medical Center, Amsterdam, section is very diverse and made up of people from different and the TU Delft we aim to investigate flow quantification in backgrounds, like systems and control, physics, mathematics, parallel OCT. Using a novel OCT sample arm, designed in this computer science, aerospace engineering, electrical engineering project, you determine low flow velocities from the temporal and mechanical engineering. Because of this unique crossroads correlation of the depth resolved OCT signal. You are a highly positioning of the group, imphys students can make a valuable motivated student with an interest in optics, experimental contribution. design, hands on work, fluid dynamics, and signal processing. Contact: Jeroen Kalkman, [email protected] Michel Verhaegen BSc project ‘Sampling strategies in video rate volumetric Michel Verhaegen is principal investigator of the group Control for Scientific Imaging & Instrumentation (CSI2) , focusing OCT’ on smart optics, especially ground-based telescopes (the Optical Coherence Tomography (OCT) is a high resolution 3D European Extremely Large Telescope or EELT) and microscopy. imaging technique that can image up to a few millimeters in A combination of numerics, systems and control, and optics tissue. A three-dimensional OCT image is made by sequential research performed in a dedicated smart optics laboratory scanning the beam over the sample. In this project you perform makes the research group unique in the Netherlands and a a theoretical study of a novel sampling strategy to acquire key player in the field. The recently expanded smart optics OCT data from a line in parallel using a 2D detector. This work laboratory will be officially opened on the 4th of March during is closely linked to the work on optical coherence computed the symposium ‘Open Window on the Future of Smart Optics’ tomography. You are a highly motivated student with an interest (see DCSC website). in optics, experimental design, and signal processing. Contact: Jeroen Kalkman, [email protected] Gleb Vdovin Gleb Vdovin received his MSc in Laser Optics from The Leningrad Technical University of Fine Mechanics and Optics, USSR, and his Phd from TU Delft, with thesis “Adaptive Mirror Micromachined

24 RESEARCH GROUP GUIDE 2016 Imaging Physics Systems and Control (DCSC) in Silicon”. He founded Flexible Optical B.V, a company that Experience of a student (Carlas Smith) develops, produces and delivers a wide range of adaptive optical (2012 excerpt) In 2005 I started my TU-Delft bachelor degree in systems and components for adaptive wave-front correction Applied Physics and after finishing my graduation project in New and generation. Professor Vdovin is working alongside of Michel Mexico I bought a car and travelled through the USA for half a Verhaegen in the Smart Optics Laboratory as part time professor, year. When I came back to The Netherlands in the beginning of intensifying the already fruitful collaboration. 2009 after an exciting adventure I was accepted to the Aerospace master degree Simulation & Control of Aerospace Vehicles and the Applied Physics master degree Research & Development. After a year I took a break because I got the amazing opportunity to travel overland to Malaysia by train. When I returned from this half year trip I continued with both my master degrees which I have completed on the 26th of March. After finishing, Michel gave me the opportunity to define my own research, which will be related to the realization of Adaptive deep tissue super resolution microscopy for biomedical imaging.

Sander Wahls Sander Wahls received his doctorate in electrical engineering (summa cum laude) from TU Berlin, and holds a Diplom degree in mathematics from the same university. He spent two years as a Postdoc Fellow at Princeton University. His research is focused on computational methods in signal processing and control, currently in the areas of fiber-optic communication and optical imaging. For his work on fast nonlinear Fourier transforms he received the prestigious Johann-Philipp-Reis Award named after the scientist-inventor. Raf van de Plas Raf van de Plas works on the computational analysis of molecular imaging modalities such as imaging mass spectrometry and microscopy. His research interests are focused on the interface between three areas: (i) mathematical engineering and machine learning; (ii) analytical chemistry and instrumentation; and (iii) life sciences and medicine. He recently published an article in Nature Methods on a successful method for image fusion between various molecular imaging techniques. Bachelor and Master Projects Our research is divided in 5 technological focus areas: EUV and Optical Lithograph, Microscopy, Astronomy, Broadband Smart Optical Antennas, Optical Coherence Tomography (OCT), and Imaging Mass Spectrometry. For a bachelor or master project, you may contact one of the group leaders. There are plenty of opportunities to contribute to research that leads to journal publications.

RESEARCH GROUP GUIDE 2016 25 Imaging Physics Systems and Control (DCSC) Some relevant subjects Statistics • Introduction to Waves • Professors: 2 • Systems and Signals • Assistant Professors: 2 • Stochastic Signal analysis • PhD students: 8 • Imaging Systems • Postdocs: 5 • Control for High Resolution Imaging • Machine Learning Contact information Section chair: Prof.dr.ir. Michel Verhaegen [email protected] www.dcsc.tudelft.nl

• Pattern Recognition • Matlab for Advanced Users Supervision Each student is assigned a mentor, typically a graduate student or a postdoc, who has daily contact with the student. The work is supervised by a member of the scientific staff. Weekly progress meetings are held to assist you in making your thesis project a success. Collaborations Collaborations include TNO, Philips, ASML, Leica, Zeiss, Dimes, Flexible Optical, AMC, Vanderbilt University, Erasmus MC, and Universiteit Twente. Future career Students graduating from our section choose for very different careers, from moving to industry, consultancy to pursuing a PhD and continuing into a scientific career. Quite a number have already become assistant professors.

26 RESEARCH GROUP GUIDE 2016 Quantum Nanoscience High Resolution Electron Microscopy Description Possible Bachelor projects Materials Research is aimed at the understanding of the relation Research of the group is aimed at the relation between crystal between structure and properties of materials. The HREM group structure, electronic structure (via quantum mechanical is doing that by studying the atomic and electronic structure of calculations in relation with crystal structure) and materials materials and devices, in relation to their physical properties. properties, given the need of this type of research by society. For this purpose, new electron microscopy techniques are To realize this research very advanced and expensive equipment developed by the group. Also, structures and devices on a is used. The choice of materials follows mainly from the strong nanometer scale are being made and measured using focussed relation existing with the many research groups and companies. ion and electron beams. Possible research topics for students are: The group also serves as a National Centre for high-resolution Materials / properties electron microscopy, resulting in collaborations with some • Nano-structuring and electrical characterization of graphene 20 (inter)national research groups. Examples are: groups specialised in theory of diffraction (Dirk van Dyck in Antwerp), • Surface oxidation Al alloys groups specialised in solid state physics/chemistry (Bob Cava in • NanoBatteries Princeton,) or nano sized devices (Herre van der Zant and others in Delft). • Electromigration to make nano-electrodes, and to place therein nano-particles to be measured Relevant courses • Catalysts (heterogeneous catalysts, zeolites) • Introduction to charged particle optics AP3401 Method Development • Geometrical optics AP3391 • Quantitative analysis of high-resolution images • Advanced Solid State Physics AP3211 D • In-situ and operando experiments with gases and liquids • Nano- en biomaterials for Nanotechnology Applications AP 3251 Guidance Experimental research (electron microscopes, specimen holder design) as well as theoretical research (simulations of images, EELS spectra, etc.) can be done. Students will join running research topics of a PhD student or post doc. Every 3 or 4 weeks a project discussion will be held with all people involved in the project. Student are encouraged to give a presentation of their work on a (inter)national conference. The possibility exists to perform experiments in laboratories abroad (for example: Princeton, Brookhaven, Antwerp, Cambridge, Oxford). Collaborations Strong collaborations exist with companies like FEI (manufacturer of electron microscopes), Corus (steels and Al alloys), and with DENSsolutions (a spinoff of TUDelft). Contact Group leader: Prof.dr. H.W. Zandbergen [email protected] Tel.: +31 15 278 2266 Homepage: http://www.nchrem.nl/

RESEARCH GROUP GUIDE 2016 27 Quantum Nanoscience Kavli Nanolab Relevant courses The Kavli Nanolab group teaches the Applied Physics Departmental Master course Nanotechnology AP3222, which includes lectures, student literature studies, and (clean room) lab work. Possible Bachelor projects The projects are linked to the goup’s newest development and research activities at the frontier of nanofabrication. Description of the Kavli Nanolab group Thus, they are related to high-resolution e-beam lithography, The Kavli Nanolab is the central research laboratory of the imprint technology, focused ion beam technologies, atomic Kavli Institute of Nanoscience (Quantum Nanoscience and layer deposition, plasma processing, and relatively simple Bionanoscience) for the fabrication of nanostructures and nanofabrication problems. In general, a project will include devices. Its main clean room is housed in the Van Leeuwenhoek device fabrication and its characterization. Laboratory, one of the largest clean room labs in Europe. Technology development is mainly situated in and around the In this lab, researchers –students to senior– make their devices Van Leeuwenhoek Laboratory. in which they e.g. study the electronic, optical, (quantum-) Possible Master projects mechanical, or magnetic properties or use them as artificial environments of biological cells. The topic of the projects is similar, but more extended than that of bachelor projects. A few examples are described below. Engineering on the nano-scale is based on techniques like nanolithography, thin film deposition, plasma processing, and You cut small ribbons in graphene by ion beam bombardment. inspection. The field combines physics, materials science, First you will study the damage that the ion bombardment chemistry, biology, and instrumentation. The multidisciplinary might cause in the ribbon. Next you will make contacts and do field is highly experimental and is continuously growing. electrical measurements. In another project you will study the physical and chemical reactions that take place in resist material during focused The Kavli Nanolab group participates in technology development helium or gallium ion beam bombardment. We trying to optimize with many internal and external partners. In the newest resists to get the best spatial resolution. developments, there is ample room for MSc and BSc student research projects. Currently our focus is on ultrahigh resolution In the third project you will grow tiny structures with a nanometer- nanofabrication with electron and focused ion beams. We have a wide ion beam to decompose adsorbing molecules. An example large program on nanofabrication with sub-nanometer focused structure to be made is a needle with a “hammerhead”, that helium ion beam. one can use to image surfaces in a 3-dimensional atomic force microscope. Student’s experience Guidance By doing your bachelors (or masters) project in the Kavli Nanolab Group you get to understand and develop (new) nanofabrication The Kavli Nanolab is a strongly interacting group of highly- techniques. You’ll really work at the edge of what is currently educated nanotechnologists. All permanent and temporary known and do a project that will give new insights into the group members, including students, are part of a ‘family’. physical workings of these techniques. You’ll also get to work Because the lines to the experts of the various nanotechniques with the staff that maintains and supervises the use of the are short, students can work on a high level with advanced clean-room facility. These people are very experienced with the instruments. specific processes and the equipment they maintain and are Daily guidance is usually by the permanent scientific staff (mainly willing to assist and help you to get to know that as well. You’ll Paul Alkemade) plus one of the PhD students or postdocs. also be able to independently work on your project; if you have questions or need help the scientific staff, the PhD student(s), or Left: nano-imprint tool, that presses a nanostructure into a thin some one else of the staff is always more than willing to answer them or point you in the right direction to find the solutions. Most times the group eats lunch together, which is a great time to get to know them better and have some great conversations.

film. Right: deposition system, films are grown atomic layer by atomic layer.

28 RESEARCH GROUP GUIDE 2016 Quantum Nanoscience Kavli Nanolab Collaborations Statistics Because of its main function, the Kavli Nanolab collaborates • Managing director: 1 with many research groups at the TU Delft. The most intensive • UHD: 1 collaborations are with the groups within Quantum Nanoscience and Bio Nanoscience. Kavli Nanolab participates in a national • Technologists: 7 consortium for infrastructure for nanotechnology (NanoLab • Technicians: 1 NL). Many contacts exist for research collaborations and traineeships. Typically, the list includes companies like Mapper, • PhD: 1 Philips, ASML, FEI, Zeiss, Shell, Vistec, and national research • Postdoc: 1 institutes like AMOLF and TNO. In addition, the Kavli Nanolab has many contacts with various national and international research • Students: 4 groups. Contact information Future career Group Leader: Frank Dirne, [email protected] The work in the clean room of the Van Leeuwenhoek Laboratory Education and research projects: Paul Alkemade, will give you skills, relevant in high tech research at technical [email protected] universities and in related industries. Lab tours are organized by Frank Dirne Secretary: Erika van Versseveld , [email protected] (015-2782898) Website: http://www.tnw.tudelft.nl/en/about-faculty/ departments/quantum-nanoscience/kavli-nanolab-delft/

left: example of a fabricated device. Right: student loading a sample in the electron beam pattern generator.

RESEARCH GROUP GUIDE 2016 29 Quantum Nanoscience Molecular Electronics & Devices Traditionally, industry has used the electronic properties of As an extension to our core activities, MED hosts a number of semiconductors to make functional devices, such as transistors. guest staff members who share interest in device technology In our group, we go beyond this by exploring the physical and valorization. For example, Akira Endo and Jian Rong Gao properties of nanostructures based on a variety of novel are developing and operating superconducting sensors for materials, ranging from two-dimensional layered materials, such astronomical research, taking nanoscience out to the deserts as graphene, to individual molecules, and even down to single of Chile (Endo) and Antarctica (Gao) to study our world on its atoms. In these new types of devices, the electrical currents largest scale. can be strongly influenced by mechanical, optical or magnetic excitations. This coupling adds new functionalities to the device, Experience of a student Why do your Master’s project at MED? Because you can work on fundamental research at a high level. You will be working in the field of Molecular Electronics, which is a relatively new research direction. Consequently, knowledge and understanding change rapidly in time. It is a fascinating aspect of the work in which your contribution is appreciated from the first day. The projects show a large variety and range from sample fabrication to measurements and interpretation including theoretical analyses. In the course of the work, enthusiastic PhD students and Postdocs will help you with all these aspects. For sure, you won’t be bored. Relevant courses • Inleiding Technische natuurkunde (casus), TN1002 • Moderne Natuurkunde,TN1312 • BSc Honours Track, 3x2h lectures, TN2110-HT • Kwantummechanica I, TN2304 • Klassieke Mechanica, TN2321

which can be of use in future applications. • Vaste Stof Fysica, TN2844 As a few concrete examples, we study the coupling of electrical currents to the nano-mechanical motion of sheets of graphene • Advanced Solid State Physics, AP3211 and single carbon nanotubes, which have exceptional mechanical • Nanotechnology, AP3221D properties due to the carbon honeycomb lattice they are made from (research led by Gary Steele). In another approach we make • Mesoscopic Physics, AP3261 D atomic-scale electrical contacts and bridge them with a single • Molecular Electronics, AP3271 molecule (research led by Herre van der Zant). Here, electrical transport is used to probe intrinsic properties of the engineered • Submm and Terahertz Physics and Applications, AP3701 molecules, such as magnetic ordering in so-called “molecular magnets”. In yet another approach, we fabricate nanoscale devices in artificial crystals formed by stacking individual atomic layers of quantum materials (research led by Andrea Caviglia). At even smaller length scales, we use a Scanning Tunneling Microscope (STM) to probe the magnetic properties of single atoms and of “artificial molecules” that are built by placing atoms one - by- one on a surface (research led by Sander Otte). A new research direction in the group (led by Simon Groeblacher) is the study of quantum physics on a meso- and microscopic level using mechanical oscillators coupled to an optical cavity field through radiation pressure. This will ultimately allow to obtain full control over macroscopic mechanical quantum systems. Finally, in the lab led by Peter Steeneken, the integration of two- dimensional nanomaterials with semiconductors technologies is studied, in order to create novel electromechanical sensors. Since materials like graphene can be suspended as atomically thin membranes, they provide ultimate flexibility. This opens up the possibility to create sensors with unprecedented sensitivity.

30 RESEARCH GROUP GUIDE 2016 Quantum Nanoscience Molecular Electronics & Devices Possible bachelor projects Statistics BEPs are integrated into the research program of the group. BEP • BSc students 18 students work together with a graduate student or a postdoc and • MSc students 17 contribute to research that will be published in an international scientific journal. The successful completion of a BEP requires • PhD 25 a good background in physics, perseverance, imagination, and • PD 19 initiative. It gives you an inside look at the world of research, which is at the frontiers of our understanding. Examples of • Assistant professors 3 (incl. Akira Endo) possible BEP projects can be found on the MED website, but • Associate professors 3 (incl. Gao) other projects are possible. For details, contact Andrea Caviglia: [email protected]. • Professors 4 Possible master projects • Technicians 2 • Publications per year ong. 65 A master’s project in MED typically involves working in a cleanroom or at a chemical bench to prepare the sample Contact and then making careful electrical measurements. Often the Department Leader: Professor Herre van der Zant, electrical conductivity is studied as a function of temperature [email protected] and magnetic field. The results of the experiment are compared to a theoretical model where sometimes computer simulations Professor Peter Steeneken, [email protected] are used to apply the theory. Examples of MEP projects can be Professor Teun Klapwijk, [email protected] found on the MED webpage. Because we are doing research and our understanding of these systems is continuously evolving, Associate Professor Gary Steele, [email protected] projects change accordingly. For further information, it is Associate Professor Sander Otte, [email protected] therefore useful to contact the PhD students directly or one of the staff members. J.R. Gao, [email protected] Guidance Assistant Professor Andrea Caviglia, [email protected] Research is done in a team of students, graduate students, Assistant Professor Simon Groeblacher, s.groeblacher@tudelft. postdocs, and research staff members. Everyone has their own nl project but the projects are interrelated in such a way that it is Assistant Professor Akira Endo, [email protected] useful to attack many problems as a team. New results that Guided Tour: Maria Roodenburg-van Dijk m.roodenburg- appear in scientific journals are regularly discussed. At the [email protected] (of jouw naam) beginning you learn from the experiences of the rest of the team Student: Floris Kalff, [email protected] but as time goes on you will become an expert in the work that your project is focused on. From that point on you can play an Website: http://qn-med.tudelft.nl important role in determining the direction the research should take. Often the results that you produce will be published in an international scientific journal. Collaborations Research projects in MED are often monitored by industrial ‘users committees’ to see how the results of the research can be applied. Of these partners, MED has the most intensive interaction with Philips, NXP, Holst Center PolymerVision, and SRON Netherlands Institute of Space Research. We also maintain contact with research groups around the world. Internships at industrial partners or foreign research groups can be arranged.

RESEARCH GROUP GUIDE 2016 31 Quantum Nanoscience Quantum Transport

The activities in the Quantum Transport section now form part scalable architecture for quantum computation using Si. We are of the newly founded QuTech Institute. We study fundamental currently aiming at taking qubit control to a new level, where quantum behaviour of nanoscale systems. The central multiple qubits can be integrated and interact. The student will theme is exploring and controlling quantum properties at be mainly involved in the design and measurement of quantum the single- particle level, and investigating the interactions dot devices fabricated on undoped Si-SiGe heterostructures and entanglement of multiple particles. Our research covers grown by our collaborators at Intel or the University of a range of nanodevices: semiconductor quantum dots (in Wisconsin. He/she will learn to use the clean room facilities and/ several materials),, superconducting circuits, nanowires and or perform sophisticated electrical measurements at cryogenic colorcenters in diamond, and also a range of degrees of temperatures to demonstrate multi-qubit control. freedom: single spins, single photons, even the quantum state of electrical (superconducting) circuits. Our experiments exploit Guidance state-of-art setups, many of which operate at low temperatures Doing a Bachelor’s or Master’s project within QT/QuTech is a down to 10 milliKelvin. Recent breakthrough experiments include unique experience at the frontier of research. You work with the observation of Majorana Fermions and a demonstration of a PhD-student or a postdoc on a running research program entanglement between spins in two diamonds, separated by within which you will have your own project. By performing 1.3 km. One of the long-term goals is to develop the essential measurements you develop your experimental skills, such as components of a quantum computer and implement ideas for working with advanced optical setups (lasers, single-photon a quantum internet. To make this happen, we collaborate with detectors), highly sensitive electronics (low-noise amplifiers, major industry partners (Microsoft and Intel) as well as with microwave generators) and/or low temperature setups (dilution technologists from TNO. refrigerators and 3He- and 4He-cryostats). In the end your data will have to be understood, often by supporting it with Experience of a student (Fokko de Vries) calculations or simulations. This demands good insight into For my master project at QT I am working in the group of prof. quantum theory and often mesoscopic physics. In several cases Kouwenhoven and fabricating and measuring nanowire devices. the project ends with a publication in a highly ranked journal. So far I really enjoy my team in this motivated and enthousiastic In weekly team meetings data is presented and problems are group. In the last two months I learned everything from fabricating discussed. The Master students also have a separate bimonthly a device in the cleanroom to measuring it at 100 mK. The people group meeting with the supervising staff member. As a Master in the group are glad to help you with anything, but there is also enough freedom to work on your project independently. Apart from being an excellent research group with a great international reputation, QT also offers a great social environment. During a weekly game of soccer, a paper discussion group, the weekly werkbespreking, one of the many “cakes at the coffee table” or the group-trip (last year to Terschelling) you will meet nice and interesting people from all over the world, assuring that you will never have to have lunch alone. Relevant courses • Advanced Quantum Mechanics AP3051 G • Mesoscopic Physics NS3521-TU • Quantum Information Processing NS3621 Possible Bachelor project The Josephson short – In Delft we have recently achieved control over the quantum state of very small superconducting structures that we use as quantum bits. As is known from quantum mechanics, to measure the state of a quantum system, you have to perturb it. This means that our qubits gradually lose their state because they are connected to the rest of the universe via the wires that we attach to its detector. The goal of the project is to characterize a new type of filter, consisting of a Josephson junction shorting the noise to ground, by measuring its electric response at low temperatures and determine how well it isolates from different sources of noise and signals. Possible Master project Building qubits from silicon. – The existing silicon (Si) microfabrication infrastructure makes it attractive to develop a

32 RESEARCH GROUP GUIDE 2016 Quantum Nanoscience Quantum Transport Statistics: • BSc students 4 • MSc students 10 • PhD students 30 • Post-docs 20 • U(H)D’s 2 • Professors 3 • Technicians 6 • Publications per year 30 Website: http://qutech.nl QuTech QuTech welcomes students who are driven to work on problems at the very frontier of quantum technologies. Students are given the opportunity to develop the exeprtise that will enable the mto undertake projects in the most advanced fiels of research. As an example, students helped perform the first loophole free Bell test at QuTech. You can work with QuTech Scientists who are experienced in guiding students and passing on the knowledge and expertise that prepare them for their future careers. QuTech currently has three research & technology roadmaps and one partnering roadmap:

• Fault - tolerant Quantum Computing student you write a small report, and give a presentation after 3 Leo DiCarlo and Lieven Vandersypen months. After that, you will be given feedback by your supervisor, • Quantum Internet and a plan for the rest of the project is developed. Both as a Bachelor and Master student you will grow in your skills and Ronald Hanson along with that become independent. At the end of your period • QuTech Shared Development you should be a specialist on the subject you have chosen! Rogier Verberk Collaborations • Topological Quantum Computing We have strong collaborations with other universities, including the University of Copenhagen, the University of Wisconsin, Leo Kouwenhoven the University of Tokyo, the University of Chicago, Harvard At QuTech, BEPs (Bachelor thesis projects) and MEPs (Master University, and with industry partners, in particular Intel and thesis projects) are available year round for motivated students Microsoft, which has resulted in many of our students doing from the fields of Computer Engineering, Electrical Engineering, their internship at one of these institutes. Applied Maths, Computer Science, and Physics. Join us and take Future career up the challenge to contribute to the scientific success of one of the world’s leading institutes in the field of quantum computing. This can be really anything. The skills you acquire in QT are valuable for doing a PhD as well as for working in a consultancy firm! Contact The section leader is Lieven Vandersypen. If you have questions about Bachelor or Master projects you can contact Ronald Hanson (r.hanson@ tudelft.nl).

RESEARCH GROUP GUIDE 2016 33 Quantum Nanoscience Quantum Transport Stephanie Wehner Group

Project Experimental/Theory Master/Bachelor Simulating routing in a quantum network Theory Master Quantum protocols in space Theory Master Testing quantum thermodynamics Theory Master Studying thermal operations Theory Master

Lieven Vandersypen Lab

Project Experimental/Theory Master/Bachelor Measuring correlated spin systems Experimental Master Silicon MOS Quantum Dots Experimental Master Quantum simulations using quantum dot arrays Experimental Master

Leo Kouwenhoven Lab

Project Experimental/Theory Master/Bachelor Topological Quantum Computation Experimental Master Correlations of Majorana Fermions Experimental Master Flux-Tunable Majorana Coupling Experimental Master Quantum noise of Majorana particles Experimental Master

Leonardo DiCarlo Lab

Project Experimental/Theory Master/Bachelor Improving the coherence time of superconducting qubits by design Experimental Bachelor Building Transmon Qubits with Semiconducting Nanowire Experimental Master Chip to Chip entanglement with Superconducting Qubits Experimental Master Experimentally simulating ultra strong atom-light interactions beyond Experimental Master Jaynes-Cummings in circuit QED

34 RESEARCH GROUP GUIDE 2016 Quantum Nanoscience Theoretical Physics In the Theoretical Physics section we investigate quantum- Relevant Courses mechanical properties of condensed matter systems. Typically, • Advanced Quantum Mechanics AP3051 these are many-particle systems that are often also disordered and/or chaotic, and we are especially interested in tiny, • Advanced Solid State Physics AP3211 often phase-coherent, conducting structures consisting of • Advanced Statistical Physics AP3021 semiconductors, carbon nanotubes, single molecules, or metals in which phenomena such as • Quantum Transport AP3281 superconductivity and magnetism occur. We develop both • Mathematics courses analytical and numerical models. Although the ‘tools’ that we Master thesis Examples use for our research are thus purely theoretical, the research topics are nearly always inspired by experiments. We often Titles of recent Master theses are: work together with the experimentalists of the Kavli Institute • Scattering theory of the spin transistor; of NanoScience in Delft as well as many Dutch and international groups. • A proposal for deterministic teleportation of an electron in a quantum dot nanostructure; Student Experience • Skyrmions in disordered heterostructures; When hearing “Theoretical Physics” you probably immediately think of things like quantum gravity, black holes and string theory. • Detection of Quantum Noise; Given this, a more accurate name for the theorectical physics • Persistent current and magnetic susceptibility in toroidal section here in Delft might actually be “Theory of Nanodevices” carbon nanotubes; – for Delft is a technical university and the prospect of (future) • Photon-assisted transport through double quantum dots; applications of the research that is done here, experimental ànd theoretical, is essential. • Dynamical circuit theory of ferromagnetic nanostructures; This means, in practice, that your research project is often • A density functional non-equilibrium Green function approach related to experimental research, and that during your theory to ab-initio molecular electronics; project you may also be in contact with experimentalists, who • Current and noise in nanoelectromechanical systems with typically ask questions such as: “Why do we find this dip in strong mechanical feedback. our I-V curve?” or “What kind of characteristic behavior can we expect when measuring this device?” or “Which parameters do Bachelor Thesis Examples we need to control with high precision to make this experiment The subjects for students doing their final (BEP or Double work?” These questions can be a guideline during your project. Bachelor) project are not different from those of the Master Examples of recent projects are research on physical theses but, of course, shorter and doable with the knowledge of implementations of quantum information processing, on devices a third-year Bachelor student. in which both quantum mechanical and classical behavior plays Recent BEP thesis titles are: a role and simulating conductance through complex molecules. • The behavior of a Lambda atom in a cavity; While doing theory in Delft you explore interesting and fascinating theoretical ideas about how nature works in the • Quantum teleportation of electrons in a double quantum dot; context of developing novel, often cutting edge, nanodevices. • Dynamics of a single-spin in a quantum dot: the If you like quantum mechanics, solid-state physics and/or statistical mechanics and are not afraid of a little mathematics, • effect of spin-orbit coupling; this might well be the right section for you. • Conduction through a single molecule; Nanomechanics of a Wouter Hordijk, master student (2014) cantilever; • Transport in nanostructures with spin-orbit • scattering; • Realizing simple quantum models using • Josephson junction arrays.

RESEARCH GROUP GUIDE 2016 35 Quantum Nanoscience Theoretical Physics Guidance Students have a choice of a large diversity of research topics and supervisors. The topic of your research is always original and your work often, certainly for master projects, leads to a publication. If you are interested, inquire about current possibilities. Collaboration We have an extended national, European, and international network of collaborators. Among the institutes we collaborate with are the ScuolaNormaleSuperiore in Pisa, the CNRS in Grenoble, the Weizmann Institute of Science, in Israel, the Norwegian University of Science and Technology in Trondheim, Harvard, the University of Copenhagen and Northwestern University in the US. Future Career Graduates from our group move on to all kinds of jobs (in industry, governmental organisations, academic institutions elsewhere, etc.) – this is no different than when you’ve done experimental research. Theoretical physicists often have excellent analytical skills, which are also much valued in jobs outside academia.

Statistics • Professors: 3 • U(H)D’s: 3 • PhD students: 10 • Postdocs: 4 • Supporting staff: 1 • Students: 4

Contact Information Group Leader: Yuli Nazarov (Y.V.Nazarov@tudelft. nl); Professors: Gerrit Bauer ([email protected]) Yaroslav Blanter ([email protected]) U(H)D’s: Miriam Blaauboer ([email protected]) Jos Thijssen ([email protected] ) Anton Akhmerov ([email protected]) Secretary: Erika van Verseveld (f.g.vanverseveld@ tudelft.nl) Website: www.ns.tudelft.nl/en/ – Theoretical Physics

36 RESEARCH GROUP GUIDE 2016 Radiation Science and Technology How to make our energy supply fully sustainable and how to Reactor Institute Delft (RID) diagnose, treat and prevent cancers and other diseases? To Close collaboration with both the Reactor Institute Delft (RID) contribute to these two big questions of society, the Radiation and international institutions guarantees access to first-class Science and Technology department focuses on radiation reactor and radiation facilities. RID and the RST department research in the areas of energy and health. Energy research bring together the national expertise in neutron- and positron includes reactor systems of the fourth generation and beyond, radiation and reactor physics and forms the basis for its unique and material studies on tailored materials for energy production, role as national knowledge center for academic radiation saving, storage and conversion. Health research comprises associated research and teaching. functional materials for imaging (scintillators), imaging detectors and complete imaging systems (SPECT and PET), the use of Bachelor and Master thesis projects radiation and radionuclides for microscopic structural studies, The Bachelor and Master thesis projects within the department diagnostics and therapy, and innovative production routes of of Radiation Science & Technology contribute directly to the real relevant radionuclides. ongoing research projects. There is a broad diversity of Bachelor Five research priority areas and Master thesis projects. For each section an example of such a thesis project is given below to give an idea of the type of Nuclear reactions and radiation are the main themes in the projects. For a complete overview of thesis projects, please have education and research programmes of the department, which a look at the website http://www.rst.tudelft.nl, the websites of focus on five research priority areas. These priority areas are the sections, of contact one of the contact-persons. rooted within five sections, as shown in Table 1. Experimental investigation & numerical modeling The research within the department comprises physical, chemical, biological and engineering viewpoints, experimental work and extensive first principle or numerical modeling for investigating functional materials and the relation between structure, dynamics and function. The programme embodies long-term expertise on materials for energy, the production of radionuclides, analytical techniques and cellular biology methods, luminescence materials, SPECT and PET imaging.

Tabel 1. Research priority areas of the department of Radiation Science & Technology rooted within its five sections.

RESEARCH PRIORITY AREA SECTION Improving the coherence time of superconducting qubits by design RIH | Radiation and Isotopes for Health Building Transmon Qubits with Semiconducting Nanowire RD&M | Radiation Detection and Medical Imaging Chip to Chip entanglement with Superconducting Qubits NERA | Nuclear Energy and Radiation Applications

Experimentally simulating ultra strong atom-light interactions beyond NPM2 | Neutron & Positron Methods in Materials Jaynes-Cummings in circuit QED Functional materials and materials for energy storage and conversion, FAME | Fundamental Aspects of Materials and Energy with focus on the relationship between structure, dynamics and function at the atomic and nano-scale levels.

RESEARCH GROUP GUIDE 2016 37 Radiation Science and Technology Radation and Isotopes for Health (RIH) Radiation Detection and Medical Imaging (RD&M) Faculty Faculty Antonia Denkova | Elisabeth Oehlke | Freek Beekman | Marlies Goorden Dennis Schaart | Pablo Serra-Crespo | Facts & Figures Albert van de Wiel | Bert Wolterbeek Professors: 1 Facts & Figures Assistant & Associate Professors: 1 Professors: 2 PhD Students: 2 Assistant & Associate Professors: 4 Post-docs: 3 PhD Students: 11 Support Staff: 4 Post-docs: 4 Example of thesis project Support Staff: 5 Biomedical imaging with ultra-high resolution SPECT and PET Example of thesis project The RD&M group develops basic technologies and complete imaging systems that are able to track molecules and cells in Using microfluidics to optimise the synthesis of therapeutic living beings. The group has been highly successful in developing radiopharmaceutica Single Photon Emission Computed Tomography (SPECT), Positron 177Lu-DOTATATE is a radiopharmaceutical that is used to Emission Tomography (PET) and Computed Tomography (CT) treat metastatic gastrointestinal or pancreatic tumors. It kills systems for small animals that provide images of molecular these tumors by selectively targeting receptors that are over- processes in organs and tumors and of the animal’s anatomy expressed on the tumor cells. To synthesize this pharmaceutical with a world record spatial and temporal resolution. This gives large set-ups are used that require space and shielding which is many unique opportunities to develop new pharmaceuticals often scarce in a hospital setting. Also, the chemicals needed and biomarkers for treatment and diagnosis of e.g. cancer, for the synthesis are quite expensive, and lowering the amounts brain and cardiac disease. We are currently also working on of chemicals needed would lower the cost of treatment. This human scanners. Thesis projects can have strong experimental project looks into doing the synthesis of 177Lu-DOTATATE in components or be more computer-programming oriented. An micron-sized channels (dimensions of 10 - 300 μm). The transfer example is the development of improved CT image reconstruction of the synthesis of diagnostic radiopharmaceuticals onto in which Compton scatter of X-ray photons is corrected for. The microfluidic chips has shown that the unique physical behavior idea is that you would use an initial reconstructed image to of fluids in microchannels can enhance reaction control and estimate the amount of scattered photons on the detector by makes it possible to do reactions faster, at lower temperatures, doing photon transport simulations. This scatter estimate can and with lower amounts of chemicals. Additionally, the width be used to correct the measured detector images and from for instance of such a reactor is reduced from over 100 cm to these corrected detector images a new -more accurate image- about 2 cm. The project will not only look into if the same kind of of the object that you are scanning can then be reconstructed. synthesis improvement can be seen for 177Lu-DOTATATE, but will This process can be repeated in an iterative correction method also involve the production and automation of the microfluidic resulting in more and more accurate images. chips and theoretical calculations of the processes observed. Contact Contact Marlies Goorden Elisabeth Oehlke [email protected] [email protected] +31 15 27 86007 +31 15 27 82640 Website Website http://www.rst.tudelft.nl/rdm http://www.rst.tudelft.nl/rih Health Physics level 5B All students at RIH will be trained to work safely with radiation and are expected to complete a short radiation safety course, for which they will receive the nationally recognized certificate Health Physics level 5B. This radiation safety course is included in the curriculum for RIH students and must be completed before or at the start of the student project.

38 RESEARCH GROUP GUIDE 2016 Radiation Science and Technology Nuclear Energy and Radiation Applications (NERA) Neutron & Positron Methods in Materials (NPM2) Faculty Faculty Jan Leen Kloosterman | Rudy Konings | Wim Bouwman | Lambert van Eijck | Danny Lathouwers | Martin Rohde | Anna Smith Harry van der Graaf | Katia Pappas | Henk Schut | Facts & Figures Ad van Well Professors: 2 Facts & Figures Assistant & Associate Professors: 3 Professors: 2 PhD Students: 14 Assistant & Associate Professors: 3 Post-docs: 2 PhD Students: 5 Support Staff: 3 Post-docs: 4 Example of thesis project Support Staff: 5 The supercritical-water Small, Modular Reactor Example of thesis project SMR’s (Small Modular Reactors) are interesting for remote areas Structure determination of oil/water emulsions by small-angle and/or offers a more controlled way to invest in nuclear power. neutron scattering One may start with one small reactor (e.g. 200 MWe) and build The section NPM2 focuses on the innovative and complementary additional ones if required. Another feature is that small reactors use of neutrons and positrons in a broad area of fields relevant to are easier to cool in the case of a station blackout (no power to health and energy. Neutron scattering accesses the microscopic extract decay heat from the core), as the coolant inventory is and mesoscopic length. The development of new experimental smaller. methods for neutrons and positrons is one of the traditional The design of this reactor is based on the NUSCALE reactor. The fields of excellence of NPM2. The section has a long-standing difference is that this reactor is cooled by supercritical water, experience in Larmor labelling, which led to the development which enhances efficiency and is better for natural circulation of SESANS. of the coolant through the primary circuit. The vessel is entirely Oil in water emulsions are crucial in many industrial processes, submerged into a large pool of water, which is used to cool the as in oil and food industry. In this project relevant samples are reactor if a station-blackout occurs. made, and process conditions will be simulated to measure The project is two-fold: 1) the neutronics need to be investigated the effect of surfactants, salt, temperature or shear on the (i.e. the inventory of the nuclear core such that the reactor microstructure. operates safely, has a high burnup etc.) and 2) the thermal- hydraulics need to studied, i.e. the cooling process of this Contact reactor. Especially the heat transfer and flow inside the pool Wim Bouwman requires attention. [email protected] Tools that are being used are CFD and Matlab. +31 15 27 85687 Contact Website Martin Rohde http://www.rst.tudelft.nl/npm2 [email protected] +31 15 27 86962 Website http://www.nera.rst.tudelft.nl

RESEARCH GROUP GUIDE 2016 39 Radiation Science and Technology Fundamental Aspects of Materials and Energy (FAME) why they lose capacity over time and what needs to be done to improve them. The practical part includes making electrode Faculty coatings, assembling batteries and testing them with the Ekkes Brück | Niels van Dijk | Pieter Dorenbos | Stephan Eijt | Erik MACCOR battery tester. X-ray diffraction of the Li-ion battery Kelder | Erik van der Kolk | Marnix Wagemaker material. Ex situ & In situ NDP measurements (the measurement also requires the SRIM software - modelling the interaction Facts & Figures of the charged particles produced by NDP with the battery Professors: 2 electrode to determine the thickness of your electrodes). In preparation of the in-situ experiments one has to adapt the cell Assistant & Associate Professors: 5 design to make it suitable for NDP, and test if these cells still PhD Students: 18 work electrochemically. Post-docs: 8 Overall the project provides knowledge on how electrochemical storage works, and how we can observe and understand it Support Staff: 8 through direct measurements utilizing neutron beams. Example of thesis project Contact Neutron Depth Profiling in Li-ion batteries Stephan Eijt This project is based on the neutron depth profiling technique, [email protected] a direct way of detecting Li-ions inside host materials. The exothermal neutron capture reaction between 6Li and a neutron +31 15 27 89053 enable the interpretation of a Li amount vs. electrode depth Website profile giving us insight on how good a material performs in terms of kinetics. This principle forms the main aim of this project http://www.rst.tudelft.nl/fame as the students will have to characterize Li-ion distributions in battery materials and determine the influence of the conductive additives that are known to make Li-ion batteries to work much better. This will be done by both ex-situ and in-situ Neutron Depth Profiling (NDP), and will require the design and testing of a battery suitable for the NDP measurements. In this project, students will also learn how Li-ion batteries work, how to make and test them, and of course the basic principles of NDP as well as modelling the transport of the charged NDP particles through your electrodes.

More specifically, the project addresses how batteries work,

40 RESEARCH GROUP GUIDE 2016

Vereniging voor Technische Physica (015)2789725 [email protected]