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 studies 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: Curli 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