Available Projects

We are constantly hiring postdocs and graduate students. Various backgrounds from EE, ME, BE and Physics are welcome to apply. The projects listed below are NOT necessarily our current focus. There is a never ending evolution of ideas and directions in the group. Simply send your CV to Prof. Ozcan if you would like to apply.

Some projects that might be available for both graduate and undergraduate students are listed below.

      Research Projects for Graduate Students

      1. Near-field Optical Microscopy Modalities with Nanometer Resolution

      Optical imaging modalities that can achieve nanometer level resolution are of high importance for closing the gap between electron microscopy and conventional light microscopy. In my research group, I plan to develop new super-resolution optical microscopy techniques to achieve nanometer level resolution required to study especially biology related problems, such as DNA mapping, optical monitoring of single cell growth and intercellular activities in engineered tissue samples. Specifically I plan to pursue the following projects:

      A. Differential Near-field Scanning Optical Microscopy

      In my research group, I will continue working on my invention “Differential Near-field Scanning Optical Microscopy” (DNSOM) to significantly improve the conventional Near-field Scanning Optical Microscopes (NSOM). Initially, this project will involve showing the superior performance of DNSOM by achieving <10 nm optical resolution with at least two orders of magnitude improvement in signal-to-noise ratio of the acquired images. The current NSOM systems are qualitatively equivalent to time-domain optical coherence tomography (OCT) systems, and DNSOM concept will revolutionize the near-field imaging performance by providing an alternative detection scheme. Such an ultra-high optical resolution (e.g., ~5 nm), with an unprecedented signal-to-noise ratio will yield a new avenue for many important applications such as real time DNA mapping and single molecule spectroscopy at room temperatures. Required Skills [Some of these requirements will be looser for graduate students]: Prior experience on AFM, NSOM, FIB, and E-beam lithography is a big plus. The project will involve extensive use of the concepts of Fourier Optics; and Matlab will be frequently used to make simulations and/or to analyze data. Therefore, the candidate should be good at both experimental and mathematical concepts.

      B. Scanning-free Wide-field Near-field Optical Microscopy

      One drawback of NSOM is that it involves mechanical scanning during image acquisition. This brings certain challenges for application of conventional NSOM based techniques to image biological specimens. In my research group, I will demonstrate a fundamentally different near-field optical imaging modality that does not involve any mechanical scanning and still achieves nanometer level resolution. My initial demonstration of this technique will be in the mid-infrared (MIR, i.e., ~2-15 um) region of the optical spectrum by utilizing a focal-plane-array based FTIR microscope. Today, a state-of-the-art conventional FTIR microscope can yield spectroscopic images of any biological or chemical specimen with a spatial resolution of ~5-10 um. However for many biological problems, such as cellular imaging, this resolution is not sufficient. With the proposed scanning-free wide-field near-field imaging modality, I will build a powerful microscope with a spatial resolution of ~100-200 nm in MIR, which is almost two orders of magnitude better in resolution than any commercially available FTIR microscope. Required Skills [Some of these requirements will be looser for graduate students]: Prior experience on FIB, E-beam lithography, and other basic nanofabrication equipment is a requirement for a postdoc candidate. The project will involve extensive use of finite-difference time-domain (FDTD) modeling, and will also require nano-fabrication and experimental testing of the designed system to be compared with the FDTD modeling results. Matlab will also be frequently used to make simulations and/or to analyze data. Therefore, the candidate should be good at both experimental and mathematical concepts.

      2. Label-free, Ultra-wide field and Massively Parallel Optical Cell Counting Technologies for HIV and Related Global Health Problems

      Counting of cells, especially in resource limited settings (such as in a small village in Africa) has a huge impact especially for the diagnostics of HIV and other related global health problems. For instance, accurate counting of CD4 T lymphocytes in blood is vital for evaluating HIV-infected patients and has important prognostic and therapeutic implications. In my research group I will be developing a novel, label-free (i.e., no fluorescent labeling of cells is necessary) optical cell counting platform that will enable two orders of magnitude wider field-of-view than any conventional microscope could achieve. This ultra-wide field-of-view (e.g., 36 mm x 25 mm) of this cell-counting platform will enable massively parallel and rapid counting of cells, where e.g., over 1 million cells can be counted in less than a second. A very important application of this technology will be counting of CD4 cells per 1 um of blood taken from HIV patients in resource limited settings. This technology has the potential to be integrated with a digital cell-phone, which will permit transmission of cell count information of HIV patients in the deserts of Africa. In this respect, this project will have a huge impact on HIV and other related global health problems. Required Skills [Some of these requirements will be looser for graduate students]: Prior experience on micro-fluidic channel fabrication and cell culturing is required for a postdoc candidate. The project will involve setting up a relatively simple optical system, and will involve using Matlab extensively to process the acquired images.

      3. Optical Coherence Tomography based Label-free Sensor Networks for High-throughput Screening Applications

      Potential applications of microarrays in biology include cell proteome screening and high-throughput screening of arrayed small molecules, antibodies and peptides. For protein microarray technologies to become powerful there are several important research steps that need to be taken. Analysis of many complex binding events requires multiplexed detection systems that can analyze tens of thousands of binding reactions simultaneously. Therefore, high speed and high precision detection of large volumes is a must in proteomics. In my research group, I will provide a powerful solution utilizing optical coherence tomography (OCT) based techniques to achieve high speed and high precision detection of molecular interactions for a dense microarray platform. The ultimate aim in this project is real time simultaneous monitoring of ~1 Million spots in an area of 1 cm x 1 cm, roughly the same area as the Biacore’s FLEXChip technology. Currently, there exists no alternative technology that can analyze this many spots all in parallel in a microarray platform! The closest technology of Biacore’s FLEXChip can only achieve ~400 spots in parallel. Required Skills [Some of these requirements will be looser for graduate students]: Prior experience on optical coherence tomography is a must for a postdoc candidate. Other requirements are having experience on integrated photonics circuit fabrication and silane based surface chemistry.

      4. Optical Monitoring of Cell Viability and Growth in Engineered 3D Tissues

      Tissue engineering offers a great potential to create 3D tissues that can be used to treat various diseases or to develop in vitro tissue models applicable to drug discovery and biomedical studies. In engineered 3D tissue models, a key question that needs to be addressed is the cell viability and growth especially in the deeper parts of the 3D tissue structure. In order to effectively image the deeper parts of an engineered 3D tissue with high resolution I plan to utilize biodegradable porous optical fibers that will serve not only as microfluidic channels but also act as waveguides that carry optical signals with a significantly reduced loss, enabling deep tissue imaging using a rapid volumetric imaging modality such as OCT or optical frequency domain imaging (OFDI). Required Skills [Some of these requirements will be looser for graduate students]: Prior experience on optical coherence tomography is a must for a postdoc candidate. Another requirement is having experience on cell culturing.

      Research Projects for Undergraduate Students

      For undergraduate students who want to join my lab, I have a few smaller scale projects that can easily result in a journal publication within half a year. These projects will be given to determined undergraduate students (preferably seniors) who are seriously considering graduate school. These projects require good mathematical skills together with Matlab programming experience. In some cases, the project can also involve doing relatively simple photonics experiments to verify our theoretical predictions. Some of the topics of these “half-cooked” projects involve: (1) nonlinear optics; (2) photonic bandgap fibers; or (3) optical coherence tomography.

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