PhD Research Rotation
First year Department of Physics PhD students may use this form to select their research rotation preferences.
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|Faculty Name||Type||Research Area||Research Title||Research/Project Short Description|
|Andrei Belitsky||Theoretical||Cosmology, Particle, and Astrophysics||Scattering amplitudes in gauge theories and Feynman integrals||The sector of the Standard Model of Particle Physics dealing with strong interactions is described by Quantum Chromodynamics. The strong force between elementary constituents of matter is responsible for its very existence. However, to date, analytical treatment of the strong interaction is beyond the grasp of analytic field-theoretical methods. Thus, the bulk of applications is based on factorization theorems which separate the physics of short and long distances. The short-distance portion is calculable in terms of scattering of elementary constituents of matter (quarks and gluons). Quantum effect are of paramount importance for achieving theoretical accuracy on par with experimental uncertainties. This requires calculation of multiloop Feynman integrals. The latter are amenable to a number of field-theoretical techniques. The current project is intended to introduce a graduate student to this subject.|
|Arunima Singh||Theoretical||Nanoscience and Materials Physics||Ab-Initio Theory and Simulations of 2D Materials||This project will involve the study of 2D materials' heterostructures for nanoelectronics and solar-energy conversion applications. You will be using density-functional theory simulations, excited state theory simulations, and machine learning methods to study the fundamental interface structure, charge transfer at the interface, band offsets, and molecular affinity of the heterostructures. The work done in this rotation will be extendable to your thesis.|
|Arunima Singh||Theoretical||Nanoscience and Materials Physics||Excited State Theory Simulations of Ultra Materials||In this project, you will be studying the charged defects in ultra-wideband gap (UWBG) materials via excited state theory simulations. The simulations will be performed under the GW approximation and will involve studying the charge-transition levels in UWBG material AlN, which is widely used for power electronics. The work done in this rotation will be extendable to your thesis. For more information about our research group see https://cmd.lab.asu.edu/|
|Banu Ozkan||Theoretical||Biological and Soft Matter Physics||The thermodynamic paradox of dorman state in bacteria||Bacterial spores represent the most dormant and resilient state of any known viable cell. Spores are found everywhere on our planet, from the oceans to the desert, from the tropics to the arctic and even in the stratosphere. However, wild-type isolates of bacterial spores remain stable over many years, even when stored in water, and do not exhibit spontaneous germination (i.e. going back to the active/live state). The absence of spontaneous germination indicates that spores must reside in a deep free energy minimum near equilibrium. Such a minimum energy state can account for the absence of spontaneous germination, but poses yet another conundrum: How can spores germinate within minutes? The spore is not known to produce metabolic energy that would help it overcome a high free energy barrier and force its way towards a return to life. Furthermore, even if the spore can escape its deep dormant state, it is unclear how the spore can resume full physiological activity and start to grow and replicate so quickly. Specifically, how can a spore with no measurable physiological activity initiate all the various processes necessary for vegetative growth and replication in just a few minutes?
Our objective is to resolve this paradox by developing a theoretical and mathematical framework based on nonequilibrium statistical mechanics and test its predictions directly through quantitative experiments. Successful outcome will provide a new and deep understanding of how a living cell can reside in an extremely dormant and stable state and yet retain the ability to rapidly return to life. This mission will lay the groundwork to develop novel methods to exert unprecedented control over spores and even take advantage of their unique biology.
|Banu Ozkan||Theoretical||Biological and Soft Matter Physics||Developing a novel framework to understanding long-range regulations conducted by ionic interactions in cell||The goal is to develop here a new mathematical framework based on a new hypothesis and biological concept, which we refer to as IonicAllostery. The effect of ligand binding at one site regulates the activity of a functional site at a distance. Monod considered his contribution to allostery even more significant than his Nobel Prize, claiming that he had discovered “the second secret of life”. We postulate that the concept of allostery goes beyond remote modulation within a protein and can couple distant processes within the cell. By pursuing our postulate of IonicAllostery, we aim to unravel life’s third secret: How allosteric regulation can propagate through ionic interactions among distant biological macromolecules to modulate cell physiology and function. Specifically, we will integrate coarse grained molecular models with cellular-level models to determine whether competition for a limited and dynamic pool of inorganic metal ions can give rise to unexpected long-range interaction between charged macromolecules, such as DNA, RNA and proteins. This work can thus reveal whether the “central dogma of biology” is subject to an unknown layer of control that couples fundamental processes such as transcription and translation through ionic interactions.|
|Damien Easson||Theoretical||Cosmology, Particle, and Astrophysics||Exploration of non-canonical field theories in cosmological and gravitational systems.||Student will examine cosmological and black hole solutions in theories with non-standard kinetic terms. The goal is to discover novel applications of such theories to inflation, dark energy, bouncing cosmologies and/or compact objects such as black holes and wormholes.|
|Damien Easson||Theoretical||Cosmology, Particle, and Astrophysics||Selected topics in high energy theoretical physics and gravity.||TBA|
|dmitry matyushov||Theoretical||Biological and Soft Matter Physics||Calculation of diffusion coefficients of ions in water
||The project aims to calculate the effect of charge asymmetry on ionic mobility. Most proteins have charge distributed over their surfaces such that the center of mass and the center of charge do not coincide. Simulations of diffusion of proteins are computationally expensive and this project aims at a model study to understand the principles behind diffusion of particles with asymmetric charge distribution.
A spherical solute will be placed in MD-Pol model of water and molecular dynamics simulation trajectories will be produced using LAMMPS. Those will be analyzed to calculate the diffusion coefficient by different algorithms to test the consistency. The simulations will be repeated with the center of charge shifted relative to the center of mass and the dependence of the diffusion coefficient on the shift magnitude will be produced. Basic knowledge of programming with Python or Mathematica will be required to analyze the data.
|Doug Shepherd||Experimental||Biological and Soft Matter Physics, Nanoscience and Materials Physics||New approaches to high-speed optical microscopy||One area of research of the Quantitative Imaging and Inference lab (QI2lab) is to push the boundaries of speed and resolution in optical microscopy. We recently demonstrated the first quantitative imaging of the microscale correlated Brownian motion for helices using light-sheet fluorescence microscopy and are now working towards perform optical diffraction tomography, as type of optical quantitative phase imaging, at 3D rates faster than 1,000 times per second. The goal of these microscopy and associated computational approaches are provide new insights into how biological systems interact with the laws of physics, such as the motion of individual viruses in the nucleus of a cell or how bacteria swimming different in bulk fluid versus near a solid surface. These methods can also be used for nanoscience, such as mapping charge transfer between adjacent semiconductor nanocrystals or density changes in atomic gases.
The student will help prototype new optical microscopy approaches, work on the theory of light interacting with matter to improve tomography reconstruction, and perform experiments along other lab members. Skills learned can include laser alignment, calibration, instrument control electronics and programming, inverse modeling of optical microscopes, and quantitative modeling of soft matter or condensed matter systems. This project can be continued towards a PhD dissertation in Physics.
|Doug Shepherd||Experimental||Biological and Soft Matter Physics||Scalable, multiplexed 3D RNA imaging in human tissue||One area of research in the Quantitative Imaging and Inference Lab (QI2lab) is to unravel the mysterious of when and how gene regulation occurs during tissue development. To this end, we are developing a new approach to imaging-based 3D spatial transcriptomics. Using high resolution single-objective light-sheet fluorescence microscopy, biochemical fluorescent labeling of RNA, single-molecule imaging, and computational approaches - we are working to build the first nanoscale 3D maps of how genes are expressed in the human olfactory bulb. The olfactory bulb is the first part of the human responsible for processing the input from your olfactory neurons, as known as your sense of smell. Using our newly developed 3D RNA imaging approaches, we aim to map the location and number of 100s to 1000s of genes, leading to the first molecular map of the human olfactory bulb. Our unique approaches provide nanometer precision in centimeter size samples at high speed.
The student will help prototype new optical microscopy approaches, perform single-molecule labeling and imaging, learn data analysis tools, and perform experiments along other lab members. Skills learned can include laser alignment, instrument calibration, biochemical sample preparation, basic genetics, and large dataset analysis. This project can be continued towards a PhD dissertation in Physics.
|Douglas Shepherd||Experimental||Biological and Soft Matter Physics, Nanoscience and Materials Physics||Stimulated emission imaging||Stimulated emission from a single molecule or a collection of molecules is thought of as indistinguishable from the stimulating beam. Recent theoretical work has suggested it may be possible to performing "stimulated emission imaging" using careful spatial and temporal patterning of the stimulating beam combined with sensitive detectors. Such stimulated emission imaging would allow for a new approach to quantify spatial location and concentrations of molecules with high sensitivity.
This project aims to determine the best class of molecule(s) to use for prototype stimulated emission imaging with the custom optical microscopy and interferometers available in the Shepherd lab. The student will be responsible for understanding the theory of stimulated emission, research available molecules to use for the experiment, preparing samples, preforming proof-of-concept experiments, and analyzing the resulting data.
|Igor Shovkovy||Theoretical||Cosmology, Particle, and Astrophysics||Professor||Relativistic plasma under extreme conditions (strong magnetic fields, high temperatures), physics of heavy-ion collisions, neutron stars|
|Igor Shovkovy||Theoretical||Cosmology, Particle, and Astrophysics||Chiral anomalous processes in magnetospheres of magnetars||Quantum field theoretical studies of chiral anomalous processes and their consequences in the gap regions of the magnetospheres of magnetars.|
|Jingyue Liu||Experimental||Nanoscience and Materials Physics||Electrochemical Conversion of Molecules for Sustainable Energy||Design and develop nanoscale architectures for electrochemical conversion of molecules with a focus on producing clean energy; understand the fundamental processes of fabricating functional structures at the single-atom limit; and correlate synthesis-structure-performance relationships.|
|Jose Menendez||Experimental||Nanoscience and Materials Physics||Spectroscopic ellipsometry and Raman scattering of semiconductors||The student will learn to perform spectroscopic ellipsometry measurements in the infrared and visible/UV as well as Raman scattering measurements. Ellipsometry is an optical technique that yields the complex dielectric function of the material. It is used to study the electronic structure and the effect of extrinsic perturbations such as doping. While ellipsometry looks at elastically reflected light, Raman spectroscopy investigates inelastically scattered light associated with elementary excitations in the sample, such as phonons. These are low-probability events that require laser excitation for their observation.
Samples of current interest include GeSn alloys with very narrow band gaps that may have applications in the mid-IR.
The analysis of Raman data provides important information on sample composition and strain, while the study of ellipsometry data provides critical clues on the electronic structure of the materials. In both cases, computer simulations are needed to extract the desired physical information, and the student will be trained in performing this analysis.
This is a project for a student who is seriously considering a career in experimental physics. A significant advantage is that the skills the student will acquire are highly sought by potential employers in industry, so that the project will make a positive impact on the student’s CV even if he/she decides to complete a dissertation in some other field.
|Jose Menendez||Theoretical||Nanoscience and Materials Physics||Trap-assisted tunneling in semiconductor diodes||Trap-assisted tunneling is an important process that leads to electron-hole recombination in semiconductor diodes. While the area is very broad and requires a very strong background in semiconductor and device physics, this project focuses on a narrow (but important) technical point that can be handled during a research rotation.
In semiconductors, traps act as intermediate states in the transfer of electrons from the conduction band to the valence band. Under the large electric fields that usually prevails in the depletion layers of devices, carriers can tunnel off the traps by emitting phonons or other elementary excitations. The process is quite complex and requires very elaborate quantum-mechanical calculations which are not suitable for device simulators. For this reason, researchers have developed approximate models that provide analytical expressions for the tunneling process. One of the most popular ones in a model by Hurkx, which reduces the problem to the calculation of a one-dimensional integral. This integral is itself approximated by an analytical expression, but under certain experimental conditions this approximation is rather poor. The purpose of this rotation is to test a new approximation of the Hurkx integral and to explore possible further improvements.
This project will give the student the opportunity to familiarize themselves with the basic aspects of semiconductor device physics while making a contribution to the field that might be publishable.
|Kevin Schmidt||Theoretical||Cosmology, Particle, and Astrophysics, Nanoscience and Materials Physics||Quantum Monte Carlo Studies||I have several projects using quantum Monte Carlo methods to study quantum many-particle systems. These include novel superfluidity, cold atomic gases, and effective field theories of nucleons and mesons. These calculations generally require translation of theory into numerical computer programs, so programming ability or a willingness to learn to write computer programs is necessary.|
|Michael Treacy||Experimental||Nanoscience and Materials Physics||Euler's disk||This project is appropriate for students who have taken graduate mechanics, PHY 521. In that class, I demonstrated a disk spinning and wobbling on a table – the so-called "Euler's disk". There was a homework question deriving a theory predicting components of the angular velocity as a function of disk tilt angle.
This project will use a student's smartphone as the experimental detector, along with the free app, PHYPHOX, to record the acoustic and visual frequencies – rate of rotation of the contact point on the table, and the rate of rotation of the disk itself – to explore how well the theory predicts these frequencies as a function of tilt angle. The work will consist of:
(1) establishing a successful experimental protocol (ie how to measure frequencies),
(2) acquiring good data,
(3) analyzing the data and comparing with theory,
(4) analyzing the effect of damping (if all goes well),
(5) writing up the report.
|Navish Wadhwa||Experimental||Biological and Soft Matter Physics||Single-molecule imaging of bacterial flagellar stator||Can we "see" single proteins in action? In this project, you will develop fluorescently labeled versions of a protein that is directly responsible for allowing bacteria to swim around. You will image this protein in living cells using total internal reflection microscopy. From these images, you will quantify the behavior of this protein, such as diffusion and binding rates, to understand how various stimuli from the environment affect its activity. You will them perform theoretical calculations and computational analyses to identify and enumerate its behavioral states. Findings from this work will assist in improving the understanding of how cells and molecular machines adapt to their environment and how bacteria might use this to perform intracellular signaling.
This project combines state-of-the-art biophysics experiments with theoretical modeling and will be suitable for any physics graduate students who are curious about the working of the living world. This project can be continued towards a PhD dissertation in Physics. The work is funded by National Institutes of Health under the grant GM134124.
|Navish Wadhwa||Experimental||Biological and Soft Matter Physics||Going with the flow: how bacteria deal with fluid flows||In nature as well as in disease, pathogens such as bacteria experience significant flow rates from the environment. For instance, during urinary tract infections, bacteria often move against urinary flow to reach the upper urinary tract including kidneys, which leads to a more severe infection. Despite its medical and scientific importance, the interaction between swimming bacteria and flows remains poorly understood. In this project, you will combine microfluidics, quantitative microscopy, low Reynolds number hydrodynamics, and theoretical biophysics to ask a simple question: What happens when we subject bacteria to flows? There will be a significant opportunity to develop this project into a competitive grant application and to continue this work as part of a PhD dissertation.|
|Navish Wadhwa||Experimental||Biological and Soft Matter Physics||Dealing with stress: how cells respond to mechanical stimuli||A major goal of the Wadhwa lab (www.wadhwalab.com) is to understand how living matter responds to mechanical stimuli from their environment. Projects in our lab use bacteria as a model to experimentally investigate the interactions with cells and their physical environment. This includes how cells move within their environment (Thrust 1: Motility) and how they sense mechanical signals from their environment (Thrust 2: Mechanosensing). We have several projects within the lab that fall under one of both of these thrusts. Main experimental approaches in the lab include quantitative microscopy, microfluidics, electrorotation, and other forms of electric, magnetic, or fluidic perturbations. Theoretical work typically involve approaches related to stochastic processes and statistical physics.
We welcome inquiries from new graduate students who are interested in exploring biological physics. We are happy to give you a lab tour and an opportunity to look at swimming bacteria under the microscope. Email Dr. Wadhwa (firstname.lastname@example.org) for further information or to schedule an informal chat.
|Navish Wadhwa||Experimental||Biological and Soft Matter Physics||Dynamics of mechano-adaptation in bacterial flagella||Bacterial flagella are one of the most intricate molecular machines found in nature. These helical propellers power bacterial motility by generating hydrodynamic thrust that pushes bacteria through aquatic environments. Flagella are driven from the base, by a rotary biological motor known as the bacterial flagellar motor. Made up of over 20 different kinds of proteins, the bacterial flagellar motor is a canonical example of a biological nanomachine.
In nature, bacteria inevitably experience dramatically different mechanical environments, such as water, mucus, soil, and tissues. How does the flagellar motor cope with large variations in mechanical load? To study this question experimentally, we have adopted the technique of electrorotation, in which a high-frequency rotating electric field applies an external torque on individual motors in single bacterial cells. Electrorotation allows us to apply step changes in mechanical load on the motor and to precisely quantify its response. Previous results show that the motor adapts to changes in load by dynamically adjusting the number of torque-generating subunits in its assembly. In other words, it continuously rebuilds itself to always keep its output (torque) matched to the demand (load). Bacterial flagella have an automatic gearshift, just like our cars. This rotation project will pursue the cutting edge of the question of flagellar mechano-adaptation. You will be involved in building electrorotation apparatus, conducting experiments with bacteria, analyzing data, and writing the results.
Other projects in the general area of bacterial biomechanics are also available. Contact Dr. Wadhwa for more details.
|Navish Wadhwa||Experimental||Biological and Soft Matter Physics||Osmosensing and osmoregulation in bacteria||In order to survive in their natural environments, bacteria must rapidly adapt and respond to a variety of chemical and physical stresses. While bacterial sensing and adaptation to chemicals is well-studied, how bacteria deal with mechanical stresses remains poorly explored. Osmotic stress is a common physical stress that bacterial routinely experience and it can lead to large deformations of the cell body even leading to cell death. Therefore, bacteria have evolved clever mechanisms to respond to osmotic perturbations quickly and efficiently.
In this project, we will investigate how bacterial response to osmotic stress at high temporal resolution. We will apply osmotic perturbations to single bacteria in microfluidic cells and quantify their response using high-speed imaging. Combining these results with previously collected data, we aim to discover a previously unknown link between bacterial mechanics and cellular energetics.
Other projects in the general area of bacterial biomechanics are also available. Contact Dr. Wadhwa for more details.
|Oliver Beckstein||Theoretical||Biological and Soft Matter Physics||Dimensionality reduction to reveal fundamental motions of biomolecules||Living cells contain "molecular machines" (proteins named transporters) in their cell membranes that use a source of free energy to transport other substances into and out of the cell. These transporters move through a cycle of well-defined molecular states. Although molecular dynamics (MD) computer simulations have provided an atomically detailed view of key parts of the cycle, it has been extremely challenging to characterize the collective atomic motions (the equivalent of excitations such as phonons in solid materials) that are ultimately driving the function of these biomolecules. Although a protein system has on the order of 100,000 degrees of freedom, it has been hypothesized that the effective dimensionality of the manifold (surface in high dimensional space) that describes the collective motion has many fewer degrees of freedom, perhaps less than ten, and perhaps even three or less might be sufficient. In this project you will investigate the application of dimensionality reduction techniques to MD simulations with the goal to reveal the functional modes in the transport cycle of a medically important membrane protein.
|Oliver Beckstein||Theoretical||Biological and Soft Matter Physics||Efficient predictions of membrane protein conformational dynamics||(Collaboration with Prof. Matthias Heyden in the School of Molecular Sciences. The student will be working both with Dr. Beckstein and Dr. Heyden and members of both labs.)
Biological cells contain "molecular machines" in their membranes to actively move small ions and molecules into and out of the cell . These transporters undergo an intricate work cycle, similar to a man-made engine, although this engine self-assembles and exists at the molecular scale. To understand how transporters function we must observe the molecular motions in these cycles, which remains a major challenge for experiments. Atomistic computer simulations provide an alternative approach and in a few cases we have been able to directly simulate conformational transitions in membrane proteins. However, this is typically associated with an enormous computational cost. Recent work from the Heyden lab shows that small anharmonic motions can encode the information necessary to rapidly simulate conformational transitions in proteins.
In this project you will investigate if anharmonicity analysis can predict the functionally important conformational changes in a transporter protein. You will learn to run and analyze molecular dynamics (MD) simulations of biomolecules on high performance computing platforms. Knowledge of programming (in particular in Python) or a keen interest in learning programming is necessary. The longer term goal is to develop an efficient computational method to study essential large scale motions in membrane transporter proteins.
 Oliver Beckstein and Fiona Naughton. General principles of secondary active transporter function. Biophysics Reviews, 3(1):011307, 2022. doi: 10.1063/5.0047967. URL https://doi.org/10.1063/5.0047967.
 Michael A. Sauer and Matthias Heyden. Frequency-Selective Anharmonic Mode Analysis of Thermally Excited Vibrations in Proteins. Journal of Chemical Theory and Computation, in press URL: https://doi.org/10.1021/acs.jctc.2c01309 (available soon).
|Philip Mauskopf||Experimental||Nanoscience and Materials Physics||Superconducting quantum devices||Work on a variety of superconducting devices including high frequency qubits, single photon detectors, microwave resonators and kinetic inductance detectors.|
|Quan Qing||Experimental||Biological and Soft Matter Physics, Nanoscience and Materials Physics||Integration of Raman spectrometer with quantum conductance measurement for multi-parameter single-molecule identification||How do charges transport through a single molecule sandwiched between two metal electrodes? It has long been shown that the conductance strongly depends on the molecule’s structure, and the interface between the molecule and the metal surface. But such measurements have proved to be very delicate and conflicting results have been all over the map. For example, DNA molecules have been shown to be insulators, conductors as well as superconductors in different experiments. Indeed, with the rapidly expanding studies of conductivity of biomolecules, where hydrogen bonds, pi-pi stacking, hydrophobic interactions, and allosteric structures are actively involved, more and more results have been shown to fall outside the realm of conventional quantum tunneling theories. New developments at the intersect of physics and biology reveal a wide open field for exploration, promising new paradigms of how charges can transport in a 3D complex molecular systems, as well as label-free biosensors based on the dynamic conductance measurements.
However, all studies have been significantly limited by the techniques for constructing the metal-molecule-metal structure, mostly based on scanning tunneling microscope, mechanical break junctions, or brute-force top-down lithography. All measurements so far rely on the random diffusion and binding of molecules, and statistical analysis of hundreds to thousands of repetitive operations. It is extremely challenging to control the position and states of the molecule bridge between electrodes, and the operation typically require strict environment control and with high technical skills. Is it possible to construct a platform for highly reproducible measurements that brings together single molecule delivery, conductivity measurements and molecule structure characterization, such that a broad range of biomolecules can be easily investigated under physiological conditions? The goal of this project is to develop a microchip-based universal platform that integrates nanopore, tunneling junction and Raman spectroscopy for multi-parameter investigation of different biomolecules in physiological conditions during enzymatic activities.
The student will help the development of a customized Raman spectrometer and integrate with a nanoelectropore system to perform preliminary experiments on correlated Raman and quantum conductivity measurements on model molecules ranging from simple small molecules such as 4-mercaptobenzoic acid, to double-strand DNA molecules, and even larger proteins that can form molecule bridge through antibody-antigen interactions.
|Ricardo Alarcon||Experimental||Cosmology, Particle, and Astrophysics||Fundamental Physics Experiments with Cold and Ultra-cold Neutrons.||Work on different aspects connected with ongoing fundamental physics experiments: a precise measurement of the neutron beta decay and a search for the electric dipole moment of the neutron.|
|Ricardo Alarcon||Experimental||Physics and Society||Proton Computed Tomography for Cancer and Cardiac Arrhythmia Treatment||Proton CT (pCT) is widely recognized as a beneficial alternative to conventional X-ray CT for treatment planning in proton beam radiotherapy. In partnership with a small company, Proton Calibration Technologies (PCT) (www.protonct.com), and the Mayo Clinic Proton Center (https://www.mayoclinic.org/departments-centers/proton-beam-therapy-program/sections/overview/ovc-20185491) in Phoenix, AZ, we are embarking on a new project to develop pCT based on a novel algorithm developed by PCT. The development of a pCT system will follow the same general path that X-Ray CT used. We are looking for a new graduate student who would like to help us track this path to develop a pCT system. This will entail the design of instrumentation and data acquisition combined with sensitivity analysis via computer simulation. The Mayo Clinic Proton Center has agreed to provide beam time for these studies If you are interested, please get in touch with Professor Ricardo Alarcon (email@example.com).|
|Richard Kirian||Experimental||Biological and Soft Matter Physics||Femtosecond x-ray biomolecular imaging technologies (various projects)||X-ray Free-Electron Lasers (XFELs) such as the Linac Coherent Light Source at SLAC National Lab produce extremely intense femtosecond pulses of x-rays. These pulses are sufficiently short in duration to detect motion on molecular timescales, and the wavelengths are sufficiently short to resolve molecular features at atomic resolution. Even though a single XFEL pulse can vaporize anything at its focus, the diffraction wavefront can "outrun" the destruction process and therefore allow for ultrafast, stroboscopic molecular imaging. In addition to the large (mile-long) XFEL facilities around the world (USA, Germany, Japan, Switzerland, South Korea), ASU is constructing the first compact femtosecond x-ray source that will have instruments dedicated to biomolecular imaging, which can provide a great opportunity for PhD student projects. There are numerous technologies under development in the Kirian lab for the purpose of imaging biomolecules with XFELs. These include algorithm and software development for the reconstruction of electron density maps from large diffraction datasets, and various types of "sample injection" hardware such as aerodynamically focused protein beams, electrodynamic traps, triggered liquid microdrops, high-speed nanojets, ultrathin sheet jets, 3D nanoprinted microfluidics, and so on.|
|Rizal Hariadi||Experimental||Biological and Soft Matter Physics, Nanoscience and Materials Physics||Chiral Metamaterials for Information Storage||Big data has increased the demand for technological innovations in data storage while traditional electronics are reaching their physical limit. DNA is an emerging data storage material as a viable alternative to silicon-based technology due to its high capacity and low operational energy. However, current DNA storage technologies lack the structural access and allocated organization of data encoded in DNA, and the core operations require complex and slow writing and readout processes such as sequencing, which leads to practical barriers in speed, sustainability, and scalability. To address these challenges, this project aims to develop the first DNA-encoded metamaterial data storage system, which could lead to a rewritable and high-speed integrated random access. Uniquely integrating DNA nanotechnology with an optical metamaterial platform, information bits will be designed and encoded by the helicity or handedness with DNA origami-enabled chiral meta-atoms. Biomolecular-based computation coupled with metamaterial modeling will inform all the design aspects of the system from molecular, and meta-atom to systems level scales. Random access in such systems will be achieved dynamically via deep subwavelength electromagnetic modulation, providing high capacity, light speed readout capability that breaks the limits in transient electronics.
This project is supported by a $1.5M NSF SemiSynBio III grant.
|Rizal Hariadi||Experimental||Biological and Soft Matter Physics, Nanoscience and Materials Physics||Structures and functions of molecular machines under mechanical tension||We aim to investigate the cell membrane force receptor of single-molecule integrin signaling pathways, dynamics, ligand-binding kinetics, and structure in the presence of realistic applied multiaxial tension enabled by DNA origami multiaxial tension device that we propose combined with single-molecule fluorescence resonance energy transfer (FRET), fluorescence correlation spectroscopy (FCS) and Cryo-Electron Microscopy (CryoEM). We will study two different types of integrins, Alpha1-Beta1, and Alpha5-Beta1, strongly related to the cardiovascular system and diseases, especially in cardiac fibrosis, as well as during healing and remodeling after a heart attack. If successful, the study will contribute to a better understanding of Alpha1-Beta1 and Alpha5-Beta1 integrins signaling pathways and structure under tension, leading to a more complete view of cardiac fibrosis and a therapeutic strategy for cardiovascular diseases targeting integrins.|
|Robert Kaindl||Experimental||Nanoscience and Materials Physics||Broadband Ultrafast Probes of Quantum Materials||Our research explores fundamental and applied physical phenomena in correlated and nanoscale quantum materials using advanced ultrafast tools. Femtosecond light pulses provide unique opportunities to perturbatively resolve fast dynamics and interactions in these materials, and they can drive materials into new transient or metastable regimes via intense excitation. We are developing a new laboratory for tailored driving and detection of quantum and collective excitations using broadband terahertz, mid-IR, and visible light pulses as well as probing of electronic structure dynamics via time- and angle-resolved photoelectron spectroscopy (trARPES).
This effort provides many project opportunities, spanning initially the range from literature research and simulations, fabrication and characterization of 2D and correlated samples, to the design and development of nonlinear optical setups in the terahertz, mid-IR, and extreme-UV regimes. Moreover, our research is closely aligned with the ASU CXFEL program making possible laser-science projects connected to the femtosecond X-ray source and pump-probe setup that is currently under commissioning. At a later stage, the student can also get involved with the first time-resolved THz/mid-IR and ARPES experiments in our group to investigate the dynamics of quasi-particles and order parameters as well the properties of light-induced phases in two-dimensional, topological, and superconducting materials.
|Robert Nemanich||Experimental||Nanoscience and Materials Physics||Interfaces of Ultra Wide Bandgap Semiconductors and Dielectrics||Ultra wide bandgap semiconductors are now projected to be crucial for the future electricity grid, which will combine renewable energy sources, battery storage, bidirectional power distribution and DC and AC networks and transmission. High voltage electronics based on ultra wide bandgap materials such as diamond, boron nitride and aluminum nitride are central to achieving this goal. This research rotation project will employ photoemission spectroscopy to measure interface properties of wide bandgap oxide layers on doped diamond. The results will be important for design and fabrication of a new generation of power transistors.
|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.
|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.|
|Siddharth Karkare||Experimental||Cosmology, Particle, and Astrophysics, Nanoscience and Materials Physics||Novel quantum effects in photoemission at the milli-eV scale: A route to brighter electron beams||Photoemission is used as a source of electron for ultrafast electron microscopes and for large particle accelerators used for x-ray production or studying particle physics. Our lab has developed a 3D energy-momentum analyzer to measure the energy and momentum distributions of such photoemitted electrons with record-breaking precision of sub-milli-eV energy scale. This project involves upgrading the electron energy analyzer, measuring energy-momentum distributions of electrons emitted from such photoemisison sources to identify new quantum scale effects in photoemisison that occur only at the milli-eV scale and can dilute the beam brightness. The eventual goal is to design photoemitters that overcome these effects resulting in increased brightness of electron beams in electron microscopy and particle accelerator applications revolutionizing their performance.
This project can be continued as your PhD topic.
|Siddharth Karkare||Experimental||Cosmology, Particle, and Astrophysics, Nanoscience and Materials Physics||Nanoscale photoemission electron sources||Nanopatterning of electron beams from the source can lead to novel regimes in electron beam dynamics in electron microscope and particle accelerators resulting in brighter electron beams for electron microscopy and particle accelerator applications. This project involves nanofabricating cathodes that use plasmonic and photonic technologies on the emission surface along with novel materials to generate patterned electron beams in the position-momentum phase space to obtain brighter electron beams. The student will work on spatial and momentum distributions of electrons photoemitted from various nanofabricated cathode surfaces using the photoemission electron microscope in conjunction with an ultrafast laser. For more information about our lab please visit https://pbbl.lab.asu.edu/
This project can be continued to contribute towards the PhD thesis.
|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 identifying and mitigating systematics in CHIME data, and developing analysis infrastructure (often borrowing techniques from other areas of cosmology) to measure power spectra, remove astrophysical foregrounds, and more.
- Making predictions for joint analyses between 21cm intensity maps and other cosmological probes. Foreground filtering in 21cm observations will have a nontrivial impact on ways in which these observations can be combined with other datasets, and a possible rotation project would focus on developing mathematical techniques for taking this into account, such that detection sensitivities can be accurately quantified for a variety of current and proposed observations.
- Other topics related to 21cm cosmology and/or large-scale structure and the cosmic microwave background.
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.|
|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.