Research Rotations

  1. Faculty Name: Chao Wang
    Experimental
    Research Area: Biological and Soft Matter Physics, Nanoscience and Materials Physics
    Research Title: Sapphire-supported Nanopores for fast readout of DNA molecules and protein markers
    Research/Project Short Description: This research is to fill the knowledge gap in nanopore sensing research by creating a significantly improved nanopore sensor platform that integrates low-optical background membranes (titanium oxide and 2D materials) on low-capacitance and hence low-electrical-noise sapphire. The research team will fabricate small membranes on sapphire, establish high-throughput manufacturing methods for both membrane formation and nanopore drilling, perform single-molecule DNA and protein translocation, study the DNA-protein binding , and analyze the data for biomarker detection. The proposed sensor platform has a number of key features to support the development of a wide variety of emerging biomolecular diagnostic technologies. First, the creation of ultrasmall (<10 μm) dielectric membranes on insulating sapphire eliminates substrate conductance, and drastically minimizes the chip capacitance to a few picoFarads even for high-dielectric-constant and ultrathin (<5 nm) membranes , thus significantly reducing the background high-frequency electrical noise and markedly improving high-bandwidth sensing. Further, both membrane formation and nanopore drilling will be achieved by high-throughput manufacturing methods, i.e. wafer-scale and batch-processing compatible sapphire etching and direct laser drilling, thus enabling low-cost and repeatable production. The scalably manufactured, low-noise, high-sensitivity nanopores will facilitate high-resolution gene identification and quantitation of their methylation status in a single measurement and at a greatly reduced cost.

    This project is currently by NSF grants 2020464 and 2027215.

    The students are expected to participate in device fabrication, DNA molecular design, nanopore signal collection, and data analysis.
  2. Faculty Name: Chao Wang
    Experimental
    Research Area: Biological and Soft Matter Physics, Nanoscience and Materials Physics
    Research Title: Photochemically Induced, Polymer-Assisted Deposition for 3D Printing of Nanophotonic Devices and Biosensors
    Research/Project Short Description: Prevalent additive metal manufacturing mainly relies on thermal or laser assisted metal fusion or ink-jet printing of metal powders and nanoparticles, and has serious limitations, including large feature sizes, rough surfaces, high optical/electrical loss, and incompatibility with soft materials. This research will fill this knowledge gap by exploring a new solution-based photochemically-induced polymer-assisted deposition process to allow scalable production of metal microstructures. The research team will introduce a three-dimensional molecular precursor, consisting of an interlaid network of polymers, metal salt, and reductants, that can turn into continuous metal films and structures upon ultraviolet illumination. The research team will build a model to study the fundamental chemical and physical aspects of the growth mechanism, design a series of experiments to verify the model, explore the fundamental limits of the critical dimensions of the printed structures, combine theoretical and experimental studies, and characterize the structural, optical, and electrical performance of the printed films.

    The project is currently supported by NSF 1947753.

    In this project, we will explore the technology to create nanophotonic structures for color printing and biosensing.
  3. Faculty Name: Tanmay Vachaspati
    Theoretical
    Research Area: Cosmology, Particle, and Astrophysics
    Research Title: To be determined.
    Research/Project Short Description: To be determined.
  4. Faculty Name: Arunima Singh
    Theoretical
    Research Area: Nanoscience and Materials Physics
    Research Title: Excited State Theory Simulations of Ultra Materials Heterostructures
    Research/Project Short Description: This project will involve the study of ultra-wide bandgap (UWBG) materials (diamond, AlN, BN, and AlxB1-xN) heterostructure using excited state theory simulations. You will use ab-initio simulations, such as density-functional theory and excited state theory simulations, to study the interface structure, intrinsic dipole, band offsets, and defect levels of the heterostructures of the UWBG materials. The work done in the rotation will be extendable to your thesis.



    The project will be a part of the ULTRA materials Department of Energy EFRC center (https://ultracenter.asu.edu/). The Ultra EFRC

    center’s mission is to achieve extreme electrical properties and phenomena through a fundamental understanding of UWBG materials which will enable a resilient, smart electricity grid. It is funded at $12.4 million/4 years and is a multi-university collaborative initiative.
  5. Faculty Name: Ying-Cheng Lai
    Theoretical
    Research Area: Physics and Society
    Research Title: Physics enhanced machine learning
    Research/Project Short Description: Physical principles or constraints have recently been exploited to design neural networks with highly efficient learning capabilities to solve specific physics problems. Through the rotation project in Prof. Lai's lab in the School of Electrical, Computer and Energy Engineering, graduate students will be exposed to and possibly develop an interest in this modern and rapidly evolving sub-field of machine learning with broad applications.
  6. Faculty Name: Philip Mauskopf
    Experimental
    Research Area: Cosmology, Particle, and Astrophysics
    Research Title: Design study for an Axion Detector
    Research/Project Short Description: Axions are particles (proposed to exist by Frank Wilczek) that explain a symmetry in strong interactions and are a candidate for dark matter in the universe. We are working with an international collaboration to design a next generation detector that will be capable of exploring much more of the possible discovery space for axions than has been attempted so far. The design involves simulations of electromagnetic structures with 3D tools like Ansoft HFSS, calculations of properties of superconducting wires under different conditions and design of quantum limited RF amplifiers and single photon detectors.
  7. Faculty Name: Andrei Belitsky
    Theoretical
    Research Area: Cosmology, Particle, and Astrophysics
    Research Title: Conformal operator product expansion for correlation functions
    Research/Project Short Description: The project is designed for a student who wants to learn basics of partial wave expansion in conformal field theories as a tool to study observables. Prior knowledge of quantum field theory is required.
  8. Faculty Name: Siddharth Karkare
    Experimental
    Research Area: Cosmology, Particle, and Astrophysics, Nanoscience and Materials Physics
    Research Title: Development of the 200 kV cryogenically cooled DC electron gun
    Research/Project Short Description: The Photoemission and Bright Beams lab headed by Prof. Karkare is building a 200 kV, cryogenically cooled DC electron gun. The student will assist with various aspects of developing this gun which will be used for fundamental studies of future electron sources and developing ultra-bright electron beams for particle accelerator and electron microscopy applications. This project will give you hands-on experience with various technologies related to high voltage, cryogenic cooling, ultrahigh vacuum and electron beams. This project can be continued towards your the PhD dissertation.
  9. Faculty Name: Samuel Teitelbaum
    Experimental
    Research Area: Nanoscience and Materials Physics
    Research Title: Coherent X-ray scattering of Emergent Order
    Research/Project Short Description: How does an ordered state like a crystal “choose” its orientation (e.g. crystal axes) out of an isotropic system like a liquid or glass? This is one of the key questions in condensed matter physics, and yet is tricky to address directly, because the spontaneous fluctuations that give rise to these ordering events are not usually reproducible. We are trying to experimentally access these events, or understand them if they are not obviously visible in real-time.



    One system were this might be possible is where the “atoms” are not atoms at all, but nanoparticles of heavy elements like gold and lead sulfide. We are interested in forming “strongly coupled superlattices” of these materials. Much in the same way that atoms arrange themselves in a crystal, nanocryatals can arrange themselves in a lattice (thus a crystal of crystals, or “superlattice”. The “strong coupling” comes about if the material connecting the nanocrystals is conductive enough that the nanocrystals can exchange electrons, forming delocalized orbitals and enabling conductivity. These superlattices are promising for next-generation electronics, energy harvesting, and more, because the properties of the “crystal” can be tuned by the size, shape, and coupling strength of the nanocrystals in ways not possible with traditional crystals. However, forming these materials remains a challenge, and we need to understand more about how these superlattices form, and how the interaction between individual nanoparticles (i.e. the effective potential) gives rise to an ordered state in order to unleash the potential of these materials.



    To get more insight into the mechanism of superlattice formation, we use a variety of x-ray techniques, such as small angle scattering and x-ray correlation spectroscopy to investigate how the crystals grow, what defects are present in fully formed crystals (and how they anneal away), and where we lie on the phase diagram to extend this process to more diverse systems. This project will involve analysis of beamline data from beamlines like LCLS, NSLS-II, and SSRL, as well as preparation and proposal writing for upcoming experiments.
  10. Faculty Name: Alexandra Ros
    Experimental
    Research Area: Biological and Soft Matter Physics, Nanoscience and Materials Physics
    Research Title: Exploiting novel bioanalyte migration mechanisms as the microscale
    Research/Project Short Description: The Ros lab is interested in exploiting the microenvironment to develop novel migration mechanisms for bioanalytes (https://biodesign.asu.edu/alexandra-ros). We employ tailored mirofluidic devices to induce migration mechanisms that can otherwise not be accomplished in the macro world. In most cases, we combine a suitable geometry of the micro devices with electrical potentials and analyte flows to induce selectivity between bioanalytes such as differently sized DNA strands or differently sized organelles. In this project, students will design microfluidic devices for separation applications and study the response of selected bioanalytes to applied forces. The novel separation approaches will help to improve disease diagnostics and fundamental studies of disease origin. This is an interdisciplinary project ideally suited for students with a broad interest including biophysics, engineering and chemistry.
  11. Faculty Name: Sara M. Vaiana
    Experimental
    Research Area: Biological and Soft Matter Physics
    Research Title: Dynamics of internal contact formation in the intrinsically disordered protein NTAIL from the Measles virus

    Research/Project Short Description: RNA viruses such as SARS-CoV-2 or the Measles virus, pack their genetic information in the form of an RNA strand, which is wrapped around the nucleoprotein (N), which in turn assembles into a helical structure known as nucleocapsid. In order for such viruses to replicate, the genetic code of the RNA needs to be accessed and read by a specific protein complex. In the Measles virus, an intrinsically disordered portion of protein N, called NTAIL, which protrudes from the nucleocapsid, is responsible for setting of such process, by binding to its binding partner, the phosphoprotein (P). Very little is understood about the highly dynamic process of folding upon binding, between an intrinsically disordered protein (IDP) and its folded binding partner.

    In this project the student will use a nanosecond laser-pump spectroscopy technique developed in our lab, based on photo-induced electron transfer (PET), to quantify internal contact formation times of NTAIL free in solution, and bound to its binding partner. Direct comparison between experiments, theoretical polymer models, and molecular simulations will be used to identify key protein interactions, and key dynamical properties, which regulate the folding upon binding of NTAIL to protein P.



    The long term goal of this project is to identify, through novel experiments and theoretical methods, the underlying physics principles that govern intrinsically disordered protein (IDP) dynamics, and how this regulates biological function. In this project, students will have the opportunity to collaborate with leading groups in theoretical modeling and molecular simulations based in the US and in Europe (University of Marseille and Max Plank Institute, Goettingen).

  12. Faculty Name: Sara M. Vaiana
    Experimental
    Research Area: Biological and Soft Matter Physics
    Research Title: Intrinsically Disordered Proteins: combining polymer physics theory and nanosecond laser pump spectroscopy to study this new class of proteins.
    Research/Project Short Description: Intrinsically Disordered Proteins (IDPs) are a recently discovered class of proteins which lack a well defined three dimensional structure in solution. Unlike natively folded proteins which often function as enzymes, IDPs play a crucial role in cell signaling, regulation and control. Because IDPs sample many conformations on short spatio-temporal scales, new approaches and novel high resolution experimental techniques are needed to study their properties.



    In this project the student will learn about this newly emerging field of research and the challenges it poses both theoretically and experimentally. Polymer physics theory and light scattering techniques will be used, in combination with a newly built nanosecond laser pump spectrometer, to characterize the disordered states of biologically relevant IDPs in solution. The student will be trained in both theoretical and experimental aspects of the project while working in the newly renovated Laser Spectroscopy and Biophysics Laboratory (LSBL) in a closely mentored group setting.



    The project involves:

    -Operating home-built laser-pump instrumentation (optics, lasers, oscilloscopes, LabView interface).

    -Preparing IDP samples for measurements (no biology required, but “good hands” in the lab and attention to sample prep. details)

    -Data analysis using MatLab, Python, or Mathematica

    Skills acquired will be useful for a career in either industry or academia.



    References:

    -S.M. Vaiana, R.B. Best, W-M Yau, W.A. Eaton and J. Hofrichter. Evidence for partially structured state of the amylin monomer. Biophys. J. 97, 2009.

    -S.M. Sizemore, S. M. Cope, A. Roy, G. Ghirlanda and S.M. Vaiana. Slow internal dynamics and charge expansion in the disordered protein CGRP: a comparison with amylin. Biophys. J. 109, 2015.



  13. Faculty Name: Sara M. Vaiana
    Experimental
    Research Area: Biological and Soft Matter Physics
    Research Title: Liquid-Liquid Phase Separation: a mechanism of spontaneous order formation in highly disordered systems
    Research/Project Short Description: Liquid-liquid phase separation (LLPS) is a well known phase transition that can occur in binary mixtures and depends on the interactions between the elements in the system. The physics description of such a phase transition is surprisingly independent from the details of the system, and displays universal properties. In fact, it applies to systems as different as ferromagnets, polymer mixtures and gels, and (as recently discovered) proteins in living cells.

    In the past, we have been studying the physics of LLPS in protein solutions. This leads to the formation of liquid droplets, within the main liquid, containing higher than average protein concentration. We argued that this mechanism of spontaneous symmetry breaking must be exploited by nature in living systems to create compartments where specialized functions can take place. This may very well be at the origins of life itself. This hypothesis was recently confirmed by the direct observations of liquid-like organelles inside the cell, which do not have a surrounding membrane, but behave like spontaneously forming liquid-droplets.



    In this project, the student will apply scattering and other techniques developed in our lab, to study the physics of LLPS in proteins of high biomedical importance. By combining experiments and theory, we will measure molecular interaction parameters in solution. Our goal is to directly measure how disease mutations in proteins alter protein-protein, protein-water, and water-water interactions, leading to protein aggregation diseases such as ALS, and other neurodegenerative diseases. Along the way, we will learn some new exciting physics, on how LLPS and anomalous fluctuations near a phase transition, affect nucleation processes. Students will have the opportunity to collaborate with leading groups in theoretical modeling and molecular simulations based in the US and in Europe.



    This project involves:

    -Using advanced scattering methods to structural and dynamical properties of liquids, their concentration fluctuations, correlation length, and critical behavior.

    -Preparing protein samples for measurements (no biology required, but “good hands” in the lab and attention to sample preparation details)

    -Data analysis using MatLab, Python, or Mathematica

    Skills acquired will be useful for a career in either industry or academia.



    References:

    -Spinodal lines and Flory-Huggins free energies for solutions of human hemoglobins HbS and HbA. Biophys. J. 60, 1991.

    -S.M. Vaiana, M.B. Palma-Vittorelli and M.U. Palma. Time scale of protein aggregation dictated by liquid-liquid demixing. Proteins, 51, 2003.

    -S.M. Vaiana, M.A. Rotter, A. Emanuele, F.A. Ferrone, and M.B. Palma-Vittorelli. Effect of T-R conformational change on sickle-cell hemoglobin interactions and aggregation. Proteins, 58 2005.

  14. Faculty Name: Jeff Yarger
    Experimental
    Research Area: Biological and Soft Matter Physics, Nanoscience and Materials Physics
    Research Title: Polyamorphism and Related Amorphous-Amorphous Phase Transitions.
    Research/Project Short Description: Fluid polyamorphism, the existence of two distinct amorphous structures in a single-component condensed fluid, is a surprisingly ubiquitous, yet poorly understood, phenomenon. It is either found or predicted for helium, sulfur, carbon, phosphorous, silicon, cerium, tin tetraiodide, tellurium, and hydrogen. This phenomenon is also hypothesized for deeply supercooled water, presumably located a few degrees below the empirical limit of homogeneous ice formation. Prof. Yarger’s research group along with collaborators (Princeton University and University of Maryland) are developing and verifying a generic phenomenological approach to describe polyamorphism in a single-component fluid, either in the presence (supercooled water, silicon, silica, etc.) or absence (helium, sulfur, phosphorous) of fluid-fluid phase separation. The concept underlying polyamorphism phenomenology is equilibrium interconversion between alternative molecular or supramolecular structures. The phenomenology will be verified by simulations of molecular models of various systems exhibiting fluid polyamorphism and by experiments (calorimetry, optical microscopy, DLS, IR and Raman spectroscopy, transmission electron microscopy.)
  15. Faculty Name: Wenwei Zheng
    Theoretical
    Research Area: Biological and Soft Matter Physics
    Research Title: Computational biophysics of intrinsically disordered proteins
    Research/Project Short Description: Dr. Zheng's lab has multiple RA openings for motivated graduate students in computational biophysics research. There are currently three research directions that are well supported and in close collaboration with experimental labs:

    1. membraneless organelles and pathological aggregates

    2. role of transient interactions in intrinsically disordered proteins

    3. machine learning aided enzyme designing for biodegradation

    Please see the group webpage http://www.public.asu.edu/~wzheng38/index.html for more information. Feel free to contact wenweizheng@asu.edu if you are interested.
  16. Faculty Name: Philip Mauskopf
    Experimental
    Research Area: Nanoscience and Materials Physics
    Research Title: Superconducting single photon detectors
    Research/Project Short Description: Superconducting nanowires detect optical and near infrared photons with timing resolution of a few picoseconds and maximum count rates up to 10s of MHz. The next generation space-based and ground-based telecommunications systems (i.e. the quantum internet) will need single photon detectors with timing resolution ~ 1 ps and count rates up to 10s of GHz. This project is to design a new superconducting single photon detector that has an increase in count rate and timing resolution of over an order of magnitude compared to current devices using kinetic inductance pulses and read out with a superconducting quantum limited parametric amplifier.
  17. Faculty Name: Philip Mauskopf
    Experimental
    Research Area: Nanoscience and Materials Physics
    Research Title: Superconducting qubits for high frequency quantum computing
    Research/Project Short Description: Quantum computers based on superconducting devices (qubits) are rapidly being developed into systems with 10s-100s of qubits. These qubits are coupled superconducting microwave resonators operating at frequencies up to about 10 GHz. This project is to design and test a qubit that works at 100 GHz. This would enable operation at higher temperatures than existing quantum computers and enable larger scale integration. Some design, fabrication and testing would be part of the project.
  18. Faculty Name: Maxim Sukharev
    Theoretical
    Research Area: Nanoscience and Materials Physics
    Research Title: Quantum optics at nanoscale interfaces
    Research/Project Short Description: Several graduate level projects pertaining to DOD sponsored program on nonlinear quantum optics are available. See our recent review talk: https://www.youtube.com/watch?v=2WZo7ujUfjQ



    More on the subject and ongoing collaborations can be found at: http://sukharev.faculty.asu.edu



    Please, send your inquires at maxim.sukharev@asu.edu
  19. Faculty Name: Kevin Schmidt
    Theoretical
    Research Area: Nanoscience and Materials Physics
    Research Title: Quantum Monte Carlo
    Research/Project Short Description: This research area uses numerical methods to solve a class of quantum many-body problems. One possible problem would be to study calculations for accurately describing p-f wave superfluid pairing contributions in neutron star matter.
  20. Faculty Name: Robert Kaindl
    Experimental
    Research Area: Nanoscience and Materials Physics
    Research Title: Broadband Ultrafast Probes of Quantum Materials
    Research/Project Short Description: 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. At present 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.

  21. Faculty Name: Samuel Teitelbaum
    Experimental
    Research Area: Nanoscience and Materials Physics
    Research Title: Visualizing complex structural motion in layered materials
    Research/Project Short Description: Two layered transition metal dichalgogenides such as TaS2, TiSe2 and TaSe2, possess fascinating properties arising from a combination of their two-dimensional nature and strong electron-phonon coupling (meaning structure and function are closely related). Similarly, the rare-earth tritellurides ReTe3 (Re = La, Nb, Er, etc.) possess a zoo complex charge density wave states. How can we control the ordered states (e.g. charge density waves and superconductivity) in these materials, and manipulate them? We are particularly interested in the photo-sensitivity of the charge density waves states in these materials, and how their manipulation with light will teach us more about the underlying physics that controls their phase diagrams.



    Our main tool for study of light-driven modification of the CDW states is optical pump, x-ray probe experiments at x-ray free electron lasers. This rotation project will involve preparation for an upcoming experiment at LCLS in the fall, as well as reviewing and analyzing data from previous optical pump, x-ray probe experiments at x-ray lasers around the world. You will (1) review the literature and previous experiments on these materials to identify incisive experiments we can perform, (2) use Python and MATLAB code to analyze data from previous experiments and begin building physical models for these systems (3) prepare for upcoming experiments using the codebase you’ve built from data analysis. If the rotation continues through the spring, we expect attendance and participation in future experiments and optical ultrafast spectroscopy on these systems. This project could be extended into a full PhD project related to photoinduced modification of interatomic forces of charge density waves.
  22. Faculty Name: Robert Ros
    Experimental
    Research Area: Biological and Soft Matter Physics
    Research Title: Properties of Chromatin of Cancerous and Non-cancerous Cells
    Research/Project Short Description: While cancer is mostly viewed as a genetic disease and characterized by genetic markers and expression of mutant proteins, there is considerable evidence that there is more to cancer than somatic mutations. For example, the first signature looked for by a pathologist is a grossly aberrant cell nucleus. Chromatin compaction and structure play a major role in the overall nuclear structure. We compare chromatin compaction, structure and gene expression for non-cancerous and cancerous cells by using a combination of salt fractionation, DNA quantification by spectroscopy, atomic force microscopy, and sequencing.
  23. Faculty Name: William Terrano
    Experimental
    Research Area: Cosmology, Particle, and Astrophysics
    Research Title: Testing Fundamental Physics with Nuclear Spins
    Research/Project Short Description: Our research involves studying fundamental physics using precision measurements of nuclear spin states. We are currently building a new laboratory and experimental apparatus on campus, with the design goal of a thousand-fold improvement in energy sensitivity. Doing so will open a new regime in measuring the standard model of particle physics, including searches for new forces, dark matter and testing the symmetries of the standard model.

    This effort requires combining several cutting-edge technologies, from cryogenic SQUID (superconducting quantum interference devices) to nuclear spin optical pumping and quantum control. This provides many project opportunities, with initial projects in literature research, simulations and design of the experimental apparatus. Down the road, the student would develop and implement the first use of quantum control and decoupling in such an experiment, and finally use the apparatus in a world-leading fundamental physics measurement, whether of Dark Matter properties, electric-dipole-moments, or a new force.

  24. Faculty Name: Banu Ozkan
    Experimental
    Research Area: Biological and Soft Matter Physics
    Research Title: Unravelling physical principles of the second secret of life
    Research/Project Short Description: Allostery is a process of remote regulation of functional activity by which biological macromolecules (mostly proteins) transmit the effect of binding at one site to a distal functional site through protein dynamics. Allostery has even been referred to as the ‘second secret of life’, and has remained as central focus in biophysics. A quantitative description of allostery is fundamental to understand most processes beyond the molecular level, such as cellular signaling and information propagation in cell.. Thus, it is the critical phenomenon to bridge different length scales in biology. In this rotation project, the goal is to explore the physical principle of allostery through computational and information theory based method. The goal is to elucidate how allostery shapes information progation in cell. The student will closely work with PI and the lab members on a on going project and will learn new computational tools.



  25. Faculty Name: Quan Qing
    Experimental
    Research Area: Biological and Soft Matter Physics, Nanoscience and Materials Physics
    Research Title: DNA manipulation and sequencing with nanopore devices
    Research/Project Short Description: DNA molecules carry the key information of cells. Nanopore sequencing represents the most promising direction for rapid single-molecule level sequencing techniques, which drives the advancements in accurate and affordable gene analysis to bring paradigm shifts in biology and health care, including, for example, genomic studies, cancer research and personalized medicine. Nanopore sensing requires no complex labeling or DNA amplification, which makes it possible to work with low copy numbers of molecules, and the long read length could substantially help the alignment and assembly of highly repetitive DNAs, which have been a persistent challenge for existing high-throughput sequencing techniques. In this project, we are going to explore a new strategy to construct nanopore device integrated with a pair of quantum tunneling electrodes such that for every DNA molecule that moves through the nanopore, a tunneling signal can be detected for high resolution sequencing. We are going to use 3D printing, CNC machining, and customized electronics to construct a nanofluidic platform that can be used to deliver different biological samples to a nanopore chip for single-molecule detection and sequencing.
  26. Faculty Name: Quan Qing
    Experimental
    Research Area: Biological and Soft Matter Physics
    Research Title: Modulating cell behaviors using electric field and nano-topographical features
    Research/Project Short Description: Many receptors at the cell membrane can trigger the extracellular-signal-regulated kinase, which activates a variety of downstream proteins, including other protein kinases and transcription regulators in the nucleus that are important to the cell cycle. The ERK signaling pathway regulates many stimulated cellular processes and plays an important role in cell survival, motility, differentiation and proliferation. Recent studies have shown that external electric field (EF) stimulation can also activate ERK. This provides a powerful way to modulate cell development and behaviors, and has demonstrated great potential in assisting wound healing, cancer therapies, as well as stem cell therapies.In addition, nanoscale topographical features on the substrate can also trigger cell response that involves a network of signaling pathways and change the behaviors of cells such as migration and proliferation. In this project, we are going to construct a hybrid system that can integrate programmable EF and nano-topographical perturbations on a cell culture and imaging platform. We are going to evaluate how global and local EF, and nano-topographical features can be used to change the behaviors of cells, for a better understanding of the coupling between the electric, biological and mechanical signaling networks in living cells.
  27. Faculty Name: Petr Sulc
    Theoretical
    Research Area: Biological and Soft Matter Physics, Nanoscience and Materials Physics
    Research Title: Principles of self-assembly
    Research/Project Short Description: Self-assembly is a process ubiquitous in all living systems. In biomimetic nanotechnology, we design interactions between nanoscale particles to assemble complex mutlicomponent structures, creating nanostructures and self-assembled materials with applications to photonics, molecular factories, diagnostics and therapeutics. This research project will explore the solutions to the inverse problem: "Given a target structure, how do we design individual componets that self-assemble into that target object and avoid undesired alternative assemblies?" The project will harness methods of statistical physics, computer science and molecular simulation to address these questions. Even though we will use abstract models to answer these questions, the theoretical work will be done in close interactions with experimental DNA nanotechnology groups, and successful designs can be then experimentally realized and verified.
  28. Faculty Name: Steve Presse
    Theoretical
    Research Area: Biological and Soft Matter Physics
    Research Title: Inference on stochastic processes from complex cellular environments one photon at a time using Data Science
    Research/Project Short Description: Life unfolds within the cellular nucleus one molecule at a time as these molecular actors interact to undertake their vital tasks (e.g., gene transcription). Yet resolving the many body physics and stochastic dynamics of these interacting components from imaging and spectroscopic data is fundamentally limited by intrinsic sources of noise be they of thermal, quantum mechanical and other origins. Here we develop new mathematical algorithms, inspired by state-of-the-art Data Science, to unravel the relevant many-body physics one photon detection at a time.
  29. Faculty Name: Steve Presse
    Experimental
    Research Area: Biological and Soft Matter Physics
    Research Title: Bacterial hydrodynamics
    Research/Project Short Description: Bacterial predators present an interesting conceptual challenge. They locate their bacterial prey by propelling themselves through viscous fluid in search for prey. Our own experiments reveal that unique dynamical features, such as being trapped in geometric orbit around large surface defects, are driven by hydrodynamics. This search strategy raises questions as to how bacteria adapt their energetically demanding propulsion strategy in the absence of cues from prey. Here we explore the interplay between bacterial hydrodynamic energy expenditure and velocity adaptation strategies relevant to bacterial predation in extreme environments.
  30. Faculty Name: Robert Nemanich
    Experimental
    Research Area: Nanoscience and Materials Physics
    Research Title: Interfaces of Ultra Wide Bandgap Semiconductors and Dielectrics
    Research/Project Short Description: 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.



  31. Faculty Name: Ricardo Alarcon
    Experimental
    Research Area: Cosmology, Particle, and Astrophysics
    Research Title: Fundamental Physics Experiments with Cold and Ultra-cold Neutrons.
    Research/Project Short Description: 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.
  32. Faculty Name: Siddharth Karkare
    Experimental
    Research Area: Cosmology, Particle, and Astrophysics, Nanoscience and Materials Physics
    Research Title: Development of the 200-kV cryogenic DC electron gun for ultra-bright electron beam production
    Research/Project Short Description: The brightness of electron beams limits the performance of a variety of scientific instruments and facilities, ranging from small meter-scale electron microscopes to large km-scale particle colliders and electron-beam-based light sources. We are developing a novel electron source that can generate electron beams of unprecedented brightness for all of the above applications. This project will involve hands-on work in developing and commissioning the 200kV cryogenically cooled DC electron gun and related electron beam diagnostics which will be used to generate and characterize such bright beams.
  33. Faculty Name: Philip Mauskopf
    Experimental
    Research Area: Nanoscience and Materials Physics
    Research Title: Superconducting quantum devices
    Research/Project Short Description: Work on a variety of superconducting devices including high frequency qubits, single photon detectors, microwave resonators and kinetic inductance detectors.
  34. Faculty Name: Igor Shovkovy
    Theoretical
    Research Area: Cosmology, Particle, and Astrophysics
    Research Title: Professor
    Research/Project Short Description: Relativistic plasma under extreme conditions (strong magnetic fields, high temperatures), physics of heavy-ion collisions, neutron stars
  35. Faculty Name: Kenan Song
    Experimental
    Research Area: Biological and Soft Matter Physics, Nanoscience and Materials Physics
    Research Title: Polymer Physics and Nanoparticle Engineering
    Research/Project Short Description: Our target is to explore polymer-based composite and polymer-nanoparticle hybrid materials through advanced manufacturing regarding their design, fabrication, characterization, and, simulation. We are interested in fundamental science and practical applications to establishing the manufacturing-structure-property-performance relationships in structural and functional systems when soft matter and nanoparticles interactions become issues.
  36. Faculty Name: Xihong Peng
    Theoretical
    Research Area: Nanoscience and Materials Physics
    Research Title: Quantum mechanical computations of material properties
    Research/Project Short Description: 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.
  37. Faculty Name: Xihong Peng
    Theoretical
    Research Area: Nanoscience and Materials Physics
    Research Title: Clathrates as Anodes for Li-ion Batteries
    Research/Project Short Description: 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.
  38. Faculty Name: William Terrano
    Experimental
    Research Area: Cosmology, Particle, and Astrophysics
    Research Title: Quantum Control of Nuclear Spin States
    Research/Project Short Description: A key challenge in studying fundamental physics using quantum states is how well the state of interest can be prepared. The project is to improve our experimental control of nuclear spins, by building a new system where self-interactions can be turned on and off. In this way we can amplify non-linearities and develop quantum control techniques to control them as desired.



  39. Faculty Name: Douglas Shepherd
    Experimental
    Research Area: Biological and Soft Matter Physics, Nanoscience and Materials Physics
    Research Title: Stimulated emission imaging
    Research/Project Short Description: 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.
  40. Faculty Name: Rizal Hariadi
    Experimental
    Research Area: Biological and Soft Matter Physics, Nanoscience and Materials Physics
    Research Title: Chiral Metamaterials for Information Storage
    Research/Project Short Description: 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.
  41. Faculty Name: Damien Easson
    Theoretical
    Research Area: Cosmology, Particle, and Astrophysics
    Research Title: Exploration of non-canonical field theories in cosmological and gravitational systems.
    Research/Project Short Description: 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.
  42. Faculty Name: Igor Shovkovy
    Theoretical
    Research Area: Cosmology, Particle, and Astrophysics
    Research Title: Chiral anomalous processes in magnetospheres of magnetars
    Research/Project Short Description: Quantum field theoretical studies of chiral anomalous processes and their consequences in the gap regions of the magnetospheres of magnetars.
  43. Faculty Name: Oliver Beckstein
    Theoretical
    Research Area: Biological and Soft Matter Physics
    Research Title: Inverse problems in molecular biophysics
    Research/Project Short Description: When solving an "inverse problem" we are trying to determine the causes from an observation. This is the case when we are experimentally measuring a macroscopic quantity and want to deduce the microscopic interactions that gave rise to the observation. One approach to solve inverse problems is to first construct a mathematical model containing the essential physics of the problem. We then use approaches from Bayesian statistics to find that set of parameters of the model that best represent the measured data. In this project you will develop a computational approach to solve the inverse problem for the interaction of molecules with ions and small molecules. The underlying model will be formulated as a graph in such a way that the laws of thermodynamics are fullfilled and thus correct statistical mechanics are ensured.

  44. Faculty Name: Oliver Beckstein
    Theoretical
    Research Area: Biological and Soft Matter Physics
    Research Title: Dimensionality reduction to reveal fundamental motions of biomolecules
    Research/Project Short Description: 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.

  45. Faculty Name: Siddharth Karkare
    Experimental
    Research Area: Cosmology, Particle, and Astrophysics, Nanoscience and Materials Physics
    Research Title: Milli-eV Energy Scale Electron Spectroscopy for Photoemission Electron Sources
    Research/Project Short Description: The aim of this project is to measure electron energy and momentum distributions of photoemitted milli-eV energy scale electrons from photocathode samples to be used as sources of bright electron beams for particle accelerator (colliders and X-ray Free Electron Lasers) and electron microscopy applications. The project will involve hands-on experience with unique instrumentation for performing electron energy and momentum distribution measurements with record high resolution, ultrafast lasers, ultra-high-vacuum techniques, atomic scale surface preparation, and characterization techniques like Auger-Electron Spectroscopy and Low Energy Electron Diffraction. The eventual goal is to investigate the low-energy-photoemission process and develop novel materials that can increase the brightness of electron beams for various particle accelerator and electron microscopy applications. The student can continue this project towards their PhD thesis.
  46. Faculty Name: Siddharth Karkare
    Experimental
    Research Area: Cosmology, Particle, and Astrophysics, Nanoscience and Materials Physics
    Research Title: Development of Electron Beam Characterization Techniques
    Research/Project Short Description: The aim of the project is to develop instrumentation to measure the brightness and bunch duration of ultrafast electron beams obtained from the ASU 200kV cryocooled DC gun. The student will gain hands-on experience in High Voltage Technology, Ultrafast Lasers, ultrafast timing synchronization techniques, ultra-high-vacuum techniques, cryogenic technologies and beam physics. The gun is developed to be a test bed for novel photoemission-based electron sources for particle accelerator and electron microscopy applications and will be developed into a state-of-the-art Ultrafast Electron Diffraction facility in the future. If interested, the student can continue this project towards their Ph.D thesis.
  47. Faculty Name: Sanchayeeta Borthakur
    Experimental
    Research Area: Cosmology, Particle, and Astrophysics
    Research Title: Exploring the nature of gas in the intergalactic medium
    Research/Project Short Description: The project involves using techniques from machine learning and probabilistic programming to identify the origin of absorption features in spectra of Quasi-Stellar Objects (QSOs). Absorbers represent gas clouds between the QSO and ourselves, and their distribution is a critical probe of structure in the Universe. Some of the QSOs of interest are - how is gas distribution in the Universe, especially outside the galaxies? what does the nature of these gas clouds tell us about the physical processes shaping most of the ordinary matter in the Universe?

    The data comes from Hubble Space Telescope, which has already been cataloged. This project is in collaboration with colleagues from the computer-science department.
  48. Faculty Name: Cecilia Lunardini
    Theoretical
    Research Area: Cosmology, Particle, and Astrophysics
    Research Title: Cosmology and astrophysics with neutrinos
    Research/Project Short Description: Neutrinos have a unique role in the physics of the universe, from its birth to the present time. The Earth constantly receives a large flux of neutrinos from as close as the Sun to as far as the epoch when the Universe was only a second old. These neutrinos can give us very important information that would be inaccessible otherwise, and that span different disciplines like cosmology, particle physics, nuclear physics, planetary science, and others. Depending on interest and level of ability, the student will work on modeling the production and propagation of neutrinos in astrophysical or cosmological environments, with the ultimate goal to understand what physics can be learned from them. The effect of possible exotic particle physics (Beyond the Standard Model) in this context may be studied.  The only background required is a good physics foundation at the undergraduate level. Basic skills of numerical computation a plus. This project might be especially suited to students with broad, interdisciplinary interests.
  49. Faculty Name: Arunima Singh
    Theoretical
    Research Area: Nanoscience and Materials Physics
    Research Title: Ab-Initio Theory and Simulations of 2D Materials
    Research/Project Short Description: 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.
  50. Faculty Name: Sabine Botha
    Experimental
    Research Area: Biological and Soft Matter Physics
    Research Title: Exploring the Impact of Sample Injection on Diffraction Quality in Protein Serial Crystallography Experiments
    Research/Project Short Description: 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.