PhD Research Rotation
First year Department of Physics PhD students may use this form to select their research rotation preferences.
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Research Rotations
| Faculty Name | Type | Research Area | Research Title | Research/Project Short Description |
|---|---|---|---|---|
| Robert Ros | Experimental | Biological and Soft Matter Physics | Exploring Biomolecular Dielectrophoresis with Nanoprobes | Dielectrophoresis (DEP) refers to the migration of polarizable particles in an electric field gradient. DEP has been successfully applied to bioanalytical applications for bioparticles such as bacteria and organelles, whereas established theoretical frameworks exist for such settings. However, the foundations of biomolecular DEP are still not fully revealed. An experimental challenge still remains for assessing the forces biomolecules are subjected to in dielectrophoretic studies, which would on the other hand allow to uncover the fundamental biomolecular properties leading to their frequency dependent polarization and the underlying theoretical framework. This project will address this challenge by subjecting selected proteins, DNA, and RNA to dielectrophoresis using an atomic force microscope probe as nanoscale electrode in combination with fluorescence microscopy and spectroscopy. The student will develop the adequate experimental setup to characterize dielectrophoretic trapping forces of biomolecules in a range of conditions. Beside the determination of fundamental biomolecular properties, this work will be relevant for biomedical studies with the aim to gather important parameters to eventually develop diagnostic applications through biomolecular dielectrophoresis. The project will be carried out jointly in the biophysics laboratories of Dr. Robert Ros and the Biodesign Institute in Dr. Alexandra Ros’ laboratory. |
| Rogier Windhorst | Experimental | Cosmology, Particle, and Astrophysics | Cosmology and Astrophysics Research with the Hubble and James Webb Space Telescopes | The student will study current hot topics in cosmology, the epoch of cosmic reionization, star-formation in a cosmological context, galaxy formation and evolution, gravitational lensing via galaxy clusters and cluster caustic transits, and the growth of super-massive black holes in the centers of galaxies. The student will will get hands-on experience and learn how to reduce and analyze Hubble and JWST data. We meet with the whole research group once a week (currently Fr. 1:30-3:30 pm in GWC-505) to assign projects, train students, monitor progress, and discuss specific research aspects, skills, and progress on papers. |
| Sabine Botha | Experimental | Biological and Soft Matter Physics | Exploring the Impact of Sample Injection on Diffraction Quality in Protein Serial Crystallography Experiments | During serial crystallography experiments, protein microcrystals are streamed across an X-ray beam at a Synchroton or Free Electron Laser via a viscous or liquid jet in random orientations. Due to the technical restraints of the ultra-fast experiments, the crystals are not optimally positioned in the beam during exposure, and it is unclear how much this influences the diffraction quality, or exacerbates absorption effects during phasing attempts. This project aims to reconstruct the crystal orientation and position in the X-ray beam towards a better understanding of these underlying effects. |
| Samuel Teitelbaum | Experimental | Nanoscience and Materials Physics | Laser Physics at the ASU CXFEL Project | The ASU CXFEL Project (https://biodesign.asu.edu/cxfel/) is focused on constructing novel x-ray sources based on inverse Compton scattering (ICS), where a strong laser field scatters off of a laser beam to produce x-rays. Currently, we are commissioning the compact x-ray source (CXLS), an incoherent hard x-ray source that can produce an average x-ray flux similar to that of a synchrotron bend magnet beamline, but with femtosecond pulse duration. A research rotation student would be expected to attend weekly all-hands stand-up meetings, laser team meetings, and act as part of a team constructing and commissioning the source. Day to day work on this involves hands-on work constructing optical setups, characterizing laser diagnostic tools such as beam profilers, cross-correlators, and novel instrumentation, controls programming, analysis of optical characterization data, and working with a large interdisciplinary collaboration to construct a complex mid-scale instrument. The expected overall time commitment to the project is 10-20 hours/week. Prior experience with optics is desired but not required, and some experience with scientific programming and data analysis (e.g. Python, MATLAB, Igor Pro, etc.) is highly encouraged. |
| Sanchayeeta Borthakur | Experimental | Cosmology, Particle, and Astrophysics | Gas distribution and properties in the circumgalactic and intergalactic medium | We will investigate data from cosmological hydrodynamical simulations such as Illustris-TNG and Simba to compared to data from the "real" Universe to investigate the nature and state of the gas in the media surrounding galaxies. |
| Seth Tongay | Experimental | Nanoscience and Materials Physics | The synthesis, manufacturing and device applications of next-generation oxychalcogenide semiconductors | Bi2O2Se is an emerging high mobility, 2D layered semiconductor (Eg 1.1 eV) with a naturally occurring oxide, Bi2SeO5. Its layered structure allows for controlled oxidation, resulting in an atomically sharp interface with Bi2SeO5, a high-k dielectric. This feature enables thin, effective oxide layers with an EOT ~0.9 nm and a low gate leakage, crucial for creating high-performance field-effect transistors (FETs) with excellent mobilities, on/off current ratios, and low subthreshold swings. This demonstrates its potential for significant microelectronics advancements using 2D materials for high-speed and low-power electronic applications. The PhD rotation will explore large-area deposition of Bi2O2Se thin films and its family of materials (Bi2O2Te and Bi2O2S) using Chemical Vapour Deposition (CVD), and Pulsed Laser Deposition (PLD) for full wafer coverage, targeting IR and MID IR photodetectors and transistors. The project entails experimenting with ultra-high vacuum deposition techniques, extensive thin film characterisation through XPS, XRD and HR-STEM, and device fabrication to establish electronic and optical properties through Physical Property Measurement Systems. This research aims to capitalise on Bi2O2Se's family materials and unique properties to innovate in IR imaging. |
| Simon Foreman | Theoretical | Cosmology, Particle, and Astrophysics | 21cm Cosmology and Large-Scale Structure | The clustering patterns of matter, galaxies, and hydrogen gas contain a huge amount of information about astrophysics, cosmology, and fundamental physics, but extracting this information is challenging: theoretical predictions are subtle, analysis techniques must be robust to known and unknown systematics, and sometimes it is not even clear how to make measurements that are optimal for a given science goal. Several rotation projects are available, ranging from more data-oriented to more theory-oriented, and each one addressing a different aspect of the issues listed above. Possible projects include: - Data analysis and infrastructure development for the CHIME telescope. CHIME was custom-built to map the universe by measuring 21cm emission from neutral hydrogen, and relating the fluctuations in this emission to the underlying distribution of matter. Analysis of 5 years of CHIME data is currently underway, with the ultimate goal of measuring large-scale structure over redshifts 0.8 to 2.5 to learn about dark energy and other topics in cosmology. There are rotation opportunities to work on development of analysis methods to mitigate systematics and maximize the amount of useful information we can get from the data. These projects involve a mix of analytical and computational work. - Making predictions for joint analyses between 21cm intensity maps and other cosmological probes. The mapping between pure-theory predictions and predictions for what the telescope actually measures involves several steps, and some of these steps have not been worked out at the level of precision that is needed for current data. These projects involve a mix of analytical and computational work. - Other topics related to 21cm cosmology and/or large-scale structure and the cosmic microwave background. Some of these lean more to the side of analytical calculations, while others are more computational. Please contact Prof. Foreman if you would like further information. |
| Steve Pressé | Experimental | Biological and Soft Matter Physics | From bacterial hydrodynamics to bacterial predator-prey dynamics |
We have previously shown that bacterial predators, Bdellovibrio bacteriovorus, hunt their prey, E. coli, by leveraging passive hydrodynamic forces rather than actively seeking out their prey through, say, chemical signaling. In particular, hydrodynamic forces can become manifest when predators move near surfaces forcing them to co-localize with prey. Here we propose to take this idea a step further and investigate the predator's hunting efficiency when it is part of a population of predator and prey within the microbiome of a living organism (in this case, the worm c. elegans). In living organisms, questions as to how predators hunt abound. For example we hope to address these questions: 1) how do we go about quantifying the kinetics of predation when all of the action takes place within the gut of an organism?; 2) how does the effect of physical confinement within the gut of c. elegans impact the predator's predation efficiency?; 3) what kind of (statistical mechanical) theories are required in order to describe predation dynamics when large fluctuations in levels of predator and prey are present within a living organism's gut?; 4) can we ever use this knowledge to engineer the predator as a living antibiotic? |
| Steve Pressé | Theoretical | Biological and Soft Matter Physics, Nanoscience and Materials Physics | Statistical mechanics meets AI/ML | We live in an age where data abound and there is an explosion of new tools (AI/ML) inspiring us to think quantitatively about these data. Yet these tools, often inspired by developments in Mathematics and CS, are often black boxes and not suitable for applications within the Natural Sciences. Our goal is to advance computational tool, appropriate for the Natural Sciences, critical in gathering insights on life's processes observed through advanced microscopy techniques or astronomical events observed using modern telescopes. In particular, we develop tools of AI and machine learning, many grounded in computational statistics, to glean insights about our physical universe otherwise unavailable using traditional analysis techniques. For example, of particular interest, is unraveling the collective dynamics of molecular machines (i.e., transcription factors) operating cohesively at gene loci to read DNA's instructions. Unraveling these dynamics is especially complex as most events of interest occur on length scales far smaller than the light we use to observe them. Thus from a smattering of photons in space, of wavelength hundreds of times larger than the objects we care to characterize, must be derived insight on life's fundamental processes. Students working on this project will quickly become experts in state-of-the-art tools of AI and machine learning. |
| Steve Pressé | Theoretical | Biological and Soft Matter Physics, Nanoscience and Materials Physics | Statistical mechanics meets AI/ML | We live in an age where data abound and there is an explosion of new tools (AI/ML) inspiring us to think quantitatively about these data. Yet these tools, often inspired by developments in Mathematics and CS, are often black boxes and not suitable for applications within the Natural Sciences. Our goal is to advance computational tool, appropriate for the Natural Sciences, critical in gathering insights on life's processes observed through advanced microscopy techniques or astronomical events observed using modern telescopes. In particular, we develop tools of AI and machine learning, many grounded in computational statistics, to glean insights about our physical universe otherwise unavailable using traditional analysis techniques. For example, of particular interest, is unraveling the collective dynamics of molecular machines (i.e., transcription factors) operating cohesively at gene loci to read DNA's instructions. Unraveling these dynamics is especially complex as most events of interest occur on length scales far smaller than the light we use to observe them. Thus from a smattering of photons in space, of wavelength hundreds of times larger than the objects we care to characterize, must be derived insight on life's fundamental processes. Students working on this project will quickly become experts in state-of-the-art tools of AI and machine learning. |
| Wenwei Zheng | Theoretical | Biological and Soft Matter Physics | Elucidating the mechanism of interactions involving intrinsically disordered proteins | Intrinsically disordered proteins (IDPs), characterized by the absence of a well-defined folded structure, assume pivotal roles in diverse intracellular activities. Their functional significance often arises from a disorder-to-order transition during interactions with other biomolecules. However, there is a growing body of evidence emphasizing the indispensable contribution of conformational flexibility and dynamics in the regulation of biological activities. Resolving this structural complexity solely through experimental techniques is challenging, given the diverse conformations explored within the limited experimental time resolution. We aim at developing computational methods tailored to unravel the roles of structural flexibility when IDPs interact with a broad spectrum of biomolecules. This project is supported by an NIH R35 grant. |
| Wenwei Zheng | Theoretical | Biological and Soft Matter Physics | Advancing biodegradation of emerging contaminants | An increasing amount of synthetic chemicals released into the environment deteriorate the water quality. Bacteria living in nature deploy enzymes capable of breaking down certain pollutants and utilizing them as carbon sources. However, the inherent pace of the natural biodegradation process often proves insufficient in eliminating these contaminants. This project aims to enhance the efficiency of bacterial enzymes by systematically modifying and optimizing them using a combination of experimental and computational methods, thereby accelerating their degradation rates. Our approach involves harnessing collaborative experimental findings to inform the development of a computational model. This model will simulate the intricate interactions between these engineered enzymes and the targeted contaminants. Through this synergy of experimentation and computation, we aim to unravel the underlying physical mechanisms governing the enzyme-contaminant interplay, identifying key parameters for optimizing enzyme activities. The development of this integrative framework is supported by an NSF collaborative grant. |
| William Terrano | Experimental | Cosmology, Particle, and Astrophysics | Quantum control with nuclear spins. | We are developing new techniques to more precisely control the quantum state of nuclear spins. These developments can be used in sensors of beyond the standard model physics, and quantum sensors of magnetic fields and rotations. |
| Xihong Peng | Theoretical | Nanoscience and Materials Physics | Quantum mechanical computations of material properties | Prof. Peng’s group performs first-principles electronic structure calculations to explore novel materials and seek their application in nanoelectronics and renewable energies, as well as to gain a fundamental understanding of the materials’ properties at the atomic level. Her key research interests are first-principle calculations of mechanical, electronic properties of group IV, III-V, II-VI nanostructures including one- and two-dimension for potential application in nanoelectronic devices, and investigation of novel materials for photocatalysts and high capacity Li-ion battery electrodes. Dr. Peng has close collaboration with experimental groups and students will have an opportunity to work or closely interaction with researchers in experimental labs. Funding for hiring students as summer research assistant is possible. |
| Xihong Peng | Theoretical | Nanoscience and Materials Physics | Clathrates as Anodes for Li-ion Batteries | Types I and II Si/Ge clathrate materials recently have been studied for their electrochemical properties as potential anodes for lithium-ion batteries due to their unique cage structures and ability to incorporate extrinsic guest atoms. This project is to investigate the electrochemical and structural properties of clathrates through a concerted theoretical and experimental approach to understand the electrochemically obtained structures. Prof. Xihong Peng’s group performs First-principles density functional theory (DFT) calculations and Prof. Candace Chan’s lab synthetizes and characterizes the electrochemical properties of the materials. Students participated in this project will have an opportunity to work and closely interaction with researchers in both theoretical and experimental labs. This project is funded by NSF. Funding for hiring students as research assistant is possible. |