# Research Experience for Undergraduates

## Projects and Mentors

Many projects are available for students to choose from, covering a wide variety of research in physics, astronomy and optics. The details of each project may vary from what is described below, as projects are continually evolving. The below descriptions for each project include a research overview for the mentor, a description of the REU project, and details of what the student will do and how the student will be supervised.

### Biophysics – Keith Lidke

**Research Overview**. Prof. Lidke's primary area of research is single molecule fluorescence microscopy for biological imaging. This includes techniques such as single particle tracking, super-resolution and hyperspectral imaging. The lab is currently funded by an NSF CAREER award to Lidke as well as several NIH grants. In addition, Lidke is one of the leaders for the ‘The New Mexico Center for the Spatiotemporal Modeling of Cell Signaling (STMC),' an NIH center for systems biology, and he directs its ‘Super-Resolution Microscopy Core'. The biological focus for many of these projects is observing and measuring kinetic parameters of interacting of proteins in live cells as well as their spatial distributions. The Lidke lab is a very active environment that typically employs a staff scientist, two post-docs, two to three graduate students and one or two undergraduate students. Since arriving at UNM in 2007, Lidke has given research opportunities to seven undergraduates whose majors include physics, biology, chemistry, and biochemistry. Two undergraduates have been included in published work. A third is currently preparing a first-author manuscript.

**Project for REU student.** An REU student will be integrated into ongoing research projects and will be allowed to develop a research area that could help to advance the aims of these projects. Projects include: exploring the precision limits of 3D single molecule localization; using imaging data to build or fit physical models of biological structures such as microtubules or membranes; developing and constructing a microscopy or spectroscopy setup.

**What the Student Will Do.** In addition to topic-specific aspects of his/her chosen research project, the student will learn to use the fluorescent microscope and become competent if not proficient in programming using MATLAB.

**Supervision.** The student will be guided by daily meetings with Lidke and will be directly supervised by a graduate student or post-doc involved in the project. The student will attend regular lab meetings.

### Biophysics – James Thomas

**Research Overview**. This project is a combination of experiment and computer simulation to improve methods for measuring the interactions of membrane receptors. Experimental work is based on fluorescence fluctuation analysis, using a two-channel fluorescence correlation microscope. Two physics majors have recently done undergraduate honors research in the lab, and both have gone on to graduate study.

**REU Project**. Receptor Dynamics on Cell Membranes. A substantial library of MATLAB subroutines has been written to simulate diffusion and reaction of membrane proteins, including the effects of photobleaching.

**What The Student Will Do**. The student will use these routines on the supercomputer cluster at the Center for Advanced Research Computing (CARC) at UNM to simulate different measurement protocols to determine which are most effective at determining protein subunit dimerization with least systematic error from photobleaching. Different measurement protocols include:

- Modifying the shape and motion of the illuminated region on the cell surface
- Analyzing fluorescence “hops” between successive timepoints, rather than using signal auto- and cross-correlation.

The student will gain an understanding of random walks and how diffusion and reaction can be modeled in both lattice and lattice-free simulations.

**Supervision**. The student will work under the direct supervision of Prof. Thomas for the entire 10-week period.

### Computational Physics– Susan Atlas

**Research Overview**. Prof. Atlas' research is focused on theoretical and computational modeling of problems in chemical physics, including the development of charge-transfer force fields for atomistic simulation; molecular genomics and biophysics; polymer physics modeling; the electron correlation problem and entanglement in density functional and quantum information theory; and non-equilibrium materials physics. Techniques used include functional analysis, electronic structure calculations; statistical machine learning and optimization, molecular dynamics and Monte Carlo simulation, and parallel programming. Her research group currently consists of two PhD students and one post-PhD master's student (co-supervised with Computer Science). Prof. Atlas has mentored over 40 students in her lab, ranging from high school through postdoctoral, and has previously served as a lecturer in the Los Alamos/UNM Summer School and REU Program. Two high-school teams mentored by Prof. Atlas won first place and the Cray Award in the statewide New Mexico Supercomputing Challenge, for projects on neural network modeling in genomics, and computational biophysics.

**Project for REU student**. The student will join an ongoing polymer physics modeling project aimed at studying liquid-liquid phase separation of designed elastin-like polypeptides (ELPs), using molecular dynamics and lattice Monte Carlo simulations. Machine-learning techniques will be utilized for optimization of parameters in statistical mechanical models of the simulated ELPs, using experimental data. ELPs serve as important model systems for understanding how the molecular structure and composition of intrinsically disordered proteins (IDPs) influence the emergent properties of membraneless organelles in the cell, and for the practical development of new functional biomaterials.

**What the Student Will Do**. The student will assist in ongoing code development (Fortran and C) in a high-performance computing (Linux) computing environment, using the resources of the GPU supercomputing cluster at the UNM Center for Advanced Research Computing. They will perform Monte Carlo and molecular dynamics simulations for downstream data analysis and gain experience in technical writing for the presentation of research results. Training in Linux, Matlab visualization, supercomputing job submission, scripting, and high-level language syntax will be provided.

**Supervision**. The student will work under the direct supervision of Prof. Atlas. The student will participate in project group meetings with Prof. Bruna Jacobson (Computer Science; modeling) and Prof. Nick Carroll (Chemical and Biological Engineering; experimental).

### Cosmology Microwave Background Instrumentation -- Darcy Barron

**Research overview**: The cosmic microwave background (CMB) is the remnant radiation from the Big Bang. It has helped us understand the origins and composition of our Universe since its accidental discovery by Penzias and Wilson in 1964. The latest challenge is precisely characterizing the polarization of the CMB, which will give further insight into inflation and the large scale structure of the universe. Measuring these faint signals requires large arrays of superconducting detectors, cooled to 0.1 Kelvin.

Our group is involved in both analyzing data from current measurements from the POLARBEAR project, as well as testing devices and technologies for future telescopes with improved sensitivity.

**Project for REU student**: Potential summer research projects would be related to the characterization and testing of superconducting devices and technologies for CMB telescopes, using a dilution refrigerator cryostat.

What the student will do: The student will first gain a background in basic cryogenic principals and techniques, necessary to successfully cool samples to sub-Kelvin temperatures. They will learn about our custom electronics and specialized read out systems, including SQUID amplifiers and superconducting transition-edge bolometers. All of our control and analysis code is written collaboratively in Python, with many opportunities to learn and develop new programs. After learning the basic skills, the student should be able to independently take measurements and perform basic data analysis. Depending on the student’s skills and interests, they can further develop skills in electronics, machining, programming, and data analysis.

**Supervision**: The student will work in the lab with Dr. Barron and her students, and will attend weekly group meetings. They will also have the opportunity to collaborate and communicate with students at other institutions.

### Geophysics – Mousumi Roy

**Research Overview**. Prof. Roy's research focuses on modeling deformation in the crust and upper mantle. Continuum mechanics is used to understand the inflation/deflation of magma bodies, in addition to percolative transport of magma. The flow of a low-viscosity magma within a matrix of solid rock is relevant to the extraction of melt at volcanic systems on Earth and other terrestrial bodies. Roy is currently supported on a CSES grant from the LANL for this work and has a strong record of undergraduate research supervision. Two undergraduate majors have done Honors theses with Roy, and a third is currently working toward an Honors thesis. These theses are the basis of a publication with three undergraduate co-authors. Additionally, Roy has supervised undergraduate summer research through the NSF-funded IRIS internship program for seismology.

**Project for REU student.** The REU student will investigate the interaction of surface faults with inflation and deflation events within a magma body. Using a viscoelastic model for crustal deformation, the student will study how localized uplift above a magma body could cause stress-changes on upper crustal fault systems, potentially bringing them closer to failure.

**What the Student Will Do.** The student will first read relevant background papers. The work will be conducted using the open-source software package Pylith for modeling the deformation of viscoelastic media. The student will test the effect of periodic pressure variations in a buried magma-body on loading/unloading of stresses on a system of near-surface faults above and near the magma chamber. Model results will be compared to previously-acquired GPS data for deformation near the Socorro Magma Body in New Mexico – a classic example of a mid-crustal magma chamber. This work will likely lead to a student presentation at the annual AGU meeting and potentially a refereed publication. The student will gain skills in Python programming, working with GPS observations, and continuum mechanics.

**Supervision.** The student will meet twice a week with Prof. Roy and more often with other members of her group.

### Ion Source Research - Paul Schwoebel

**Research Overview**. Ion source research involves a wide range of studies in both fundamental and applied physics. Fundamental studies focus on surface physics, materials science, plasma physics, and thin film phenomena. Applied studies are in the areas of ion sources for lithography, microscopy, neutron generators, and medical proton therapy treatment systems. In the past decade, six undergraduates have been mentored with one staying on to complete a graduate degree.

**Project for REU student.** The student would work on an ongoing DARPA-funded effort to develop deuteron sources for electronic neutron generators.

**What the Student Will Do.** The student will assist Prof. Schwoebel in upgrading a time-of-flight mass analysis system to higher resolution. The student will be exposed to ultra-high vacuum technology, mass spectrometry, and nuclear instrumentation while participating in testing of the upgraded system. Direct practical laboratory experience will be gained in electronics and machine shop practices, including circuit breadboarding, electronics assembly and soldering, drawing of schematic diagrams and use of basic machine tools.

**Supervision.** The student will work under the direct supervision of Prof. Schwoebel.

### Nanophotonics – Alejandro Manjavacas

**Research Overview**. The research of the group is focused on the theoretical description of the interaction between light and matter at the nanoscale, with the aim of discovering new physical phenomena and developing new applications in the field of nanophotonics. Currently there are one graduate and two undergraduate students involve in three different research projects.

**Project for REU student.** Heat dissipation in nanostructures is a technological problem of paramount importance for the development of smaller and faster computers. Among the different cooling mechanisms that can take place in such systems, radiative heat transfer plays a key role when the size of the structures involved or the distance between them becomes smaller than the thermal wavelength, which, for reasonable temperatures, is on the order of microns. In that limit, radiative transfer, which occurs in absence of physical contact and is enhanced by the photonic modes of the nanostructures, can dominate the overall heat exchange. Therefore, a deep understanding of the physics behind radiative transfer is of vital importance to develop novel cooling schemes for nanoscale systems.

**What the Student Will Do.** The student will read the relevant literature and acquire the necessary background in the topic of research. After that, the student will assist in the development of computational tools, primarily using C++ and Matlab, for the description of the radiative heat transfer between ensembles of nanostructures. Using the developed computational tools and the resources provided by the Center for Advanced Research Computing (CARC) of UNM, the student will investigate the effect of the geometrical arrangement and the topology of the nanostructures in the efficiency of the radiative heat exchange. In particular, the student will search for unconventional geometries that could lead to extraordinary radiative transfers.

**Supervision.** The student will work under the direct supervision of Prof. Manjavacas and will interact strongly with other students working in the group.

### Optical Sciences – Arash Mafi

**Research Overview**. Prof. Mafi heads the Photonics Research Group, whose primary focus is the application of theoretical, computational, and experimental methods for cutting-edge research in photonics, especially on nonlinear and quantum aspects of guided-wave optics. His work is currently funded by an NSF Career award, and recently by grants from AFOSR. Over ten undergraduates have participated in research in his lab in the past six years - the most recent student co-authored four journal papers.

**Project for REU student.** The main objective of the proposed project is to develop an endoscopic optical fiber imaging system that unequivocally outperforms commercial imaging fibers on key metrics of image quality, while maintaining their robustness for real-world applications. Conventional multimode optical fibers, as well as Anderson-localized disordered fibers will be used in this research.

**What the Student Will Do.** The student will be involved in developing computer codes (MATLAB or Python) to extract the transported image in the case of the multimode fibers or enhance the quality of the transported image in the case of the disordered fibers. The student will also assist in the fabrication and assembly of the imaging components, experimental characterization, and system integration of the fiber-optic imaging system. While the student will participate in both theory/computation and experiment, the percentage will depend on the skills and interests of the student. In the first 3 weeks of the 10-week period, the student will participate in various optics laboratory activities to become familiar with the equipment. At the same time, the student will read several papers to establish the theoretical background needed for the work. After the initial training period, the mentor and the student will agree on a set of goals and the required tasks to achieve them. The student will work with the graduate students on the project to contribute to the computer code development and data analysis. At the same time, the student will participate in the experimental and system development efforts. In the final 2 weeks, the student will spend 50% of the time to prepare a final report of the research activities.

**Supervision.** The student will work under the direct supervision of Prof. Mafi.

### Optical Sciences - Mansoor Sheik-Bahae

**Research Overview**. Laser cooling of solids (also known as optical refrigeration) is the processes of removing vibrational quanta by way of anti-Stokes florescence. UNM's team is the only group in the world that has performed laser cooling of solids to cryogenic temperatures. This project has been funded by NSF, and currently by AFOSR and DARPA. A major 5-year MURI project (led by UNM) for investigating “athermal lasers” will commence in the fall of 2016. We closely collaborate on this project with all three New Mexico national labs, namely LANL, SNL, and AFRL. The laboratories in Professor Sheik-Bahae's group have established a tradition of mentoring undergraduate students. Notable is his group's active participation in the department's previous REU, and UNM's NASA PURSUE Program in the late ‘90's to 2002. Also, as a Co-PI in an NSF-funded IGERT program, his group made undergraduate mentoring a key requirement for the trainees during their fellowship. Altogether, Sheik-Bahae has supervised more than 15 undergraduate researchers over the last 19 years.

**Project for REU student.** The REU student will engage in experiments involving laser cooling, optics, and thermal management.

**What the Student Will Do.** The student will be involved with laser cooling of thulium and holmium doped crystals. That includes working with a homemade tunable optical parametric oscillator (OPO) to conduct spectroscopy on the samples in the mid-IR regime. Subsequently she/he will perform laser cooling experiments that involve optical cavity design and high vacuum and thermal management techniques.

**Supervision**: The REU student's overall experience will be guided via frequent interaction with Prof. Sheik-Bahae, while the day-to-day activities will be mentored and supervised in the laboratory by graduate students working on this project. The student will also participate in regular group meetings.

### Particle Astrophysics - Francis-Yan Cyr-Racine

**Research Overview**: Prof. Cyr-Racine’s research mixes astrophysics, cosmology, and particle physics to search for new physics in astronomical data. In particular, a significant part of his research aims at unveiling the nature of dark matter, a mysterious substance forming the vast majority of the matter density in our Universe. Dark matter governs the growth of structure we observe throughout the Universe over a broad range of length scales. Recently, the mainstream paradigm for what dark matter could be has come under great scrutiny as several observations appear in tension with its predictions. Resolving this mystery is one of the largest questions in astronomy nowadays.

**Project for REU student**: Important clues about what dark matter is made of can be found by looking at the inner structure and abundance of the smallest dwarf galaxies orbiting our own Milky Way. Indeed, these faint galaxies are some of the most dark matter-dominated objects in our Universe and are thus ideal laboratories to study the particle nature of dark matter. The number of known dwarf galaxies orbiting the Milky Way has grown dramatically in the last few years and many more are expected to be discovered once the Large Synoptic Survey Telescope (LSST) comes online. Extracting information about dark matter from these faint galaxies requires detailed modeling of how the dark matter particle properties influence their key characteristics such as their stellar dispersions, luminosities, half-light radii, and radial distribution. The project consists of building a simple yet accurate numerical model that can generate realistic populations of Milky Way satellite galaxies that can then be compared to observations. The goal here is to determine and forecast which dark matter properties will be best constrained by observations of local dwarf galaxies.

**What the Student Will Do**: Building on the previous work of the PI in modeling the properties of the Milky Way dwarf galaxy population, the student will develop and numerically implement an improved model for how the dark matter density profile of each galaxy depends on how strongly dark matter is self-interacting. This work will be done in Python. The student will then use this improved model to compute the current constraint on the dark matter self-interaction from known Milky Way satellites, and perform forecasts for the reach of LSST in the near future.

**Supervision**:
The student will work under the direct supervision of Prof. Cyr-Racine.

### Quantum Information - Elohim Becerra

**Research Overview**. Prof. Becerra studies quantum properties of light and matter and their interaction, and methodologies for the determination of the quantum states of these physical systems via quantum tomography.

**Project for REU student.** Detection schemes to efficiently characterize photonic and atomic quantum states with high precision are being investigated. A compact optical coherent-detection setup for real-time data acquisition is being developed to study the statistical properties of light, which is necessary for homodyne tomography. This setup is essential for fundamental studies of entanglement transfer between single photons and complex collective atomic quantum states. The goal is to develop a homodyne optical setup to test the viability of implementing tomographic schemes in real time, and to identify the critical experimental parameters for homodyne tomographic reconstructions.

**What the Student Will Do**. The student will read literature about homodyne tomography and coherent detection. The student will characterize the efficiency and the noise properties of a low-noise differential detector, and create the optical setup for coherent homodyne detection. The student will also test the setup with coherent laser light and record data with fast acquisition systems (such as a digital-storage oscilloscope) for data processing. The student will learn about the basics of optics and electronics, homodyne detection, and characterization of states of light.

**Supervision.** The student will work under the direct supervision of Prof. Becerra and will interact with graduate students working in the laboratory.

### Quantum Information Theory - Akimasa Miyake

**Research Overview**. Theory of quantum information and computation, with a focus on quantum many-body systems and their relevance to quantum computation and thermodynamics. Partially funded by NSF. The mentor taught upper-division quantum mechanics twice successfully through the academic years 2013-2014, and is keen to bridge a gap between undergraduate materials and research frontiers.

**Project for REU student**. The research of quantum computation keeps expanding and has recently cross-fertilized with other fields like quantum many-body physics and condensed matter physics. For instance, it is recently recognized that dynamics of quantum entanglement in many-body systems is deeply connected to thermalization of the systems, and experimental observations of such behaviors offer an interesting opportunity to revisit fundamental assumptions of thermodynamics.

**What the Student Will Do**. The student will first learn basic knowledge about entanglement and numerical simulation of 1D quantum systems by reading a couple of introductory papers. After the student learns how to use an open-source computer code to calculate time evolution of entanglement in terms of so-called matrix product states, the goal will be to explore connections to thermodynamics and many-body localization using the code. The project will enable the student to develop scientific skills needed to read articles analytically and use computer programs for numerical calculations, as well as providing a glimpse into a rapidly expanding frontier in contemporary physics.

**Supervision**. The student will be supervised by Prof. Miyake and graduate students from the department's Center for Quantum Information and Control.

### Quantum Sensing – Victor Acosta

**Research Overview**. Acosta's research lies at the intersection of condensed-matter physics, quantum optics, and biomedical imaging. His group specializes in using color centers in diamond as quantum sensors to study nanoscale magnetic phenomena in physical, chemical, and biological systems. Their model qubit system is the Nitrogen Vacancy (NV) center in diamond which offers a unique combination of high-fidelity optical detection and long spin coherence times at room temperature. The group currently consists of 7 graduate students and two postdocs.

**REU Project**. The student will work on an ongoing quantum sensing project aimed at using NV centers to detect the magnetic fields produced by superparamagnetic iron oxide nanoparticles attached to cancer cells. These experiments present a number of impressive spectroscopy, imaging, and biochemistry challenges, which make for an exciting learning opportunity for an undergraduate student working within a broader team.

**What the Student Will Do.** The student will develop methods for using NV centers to image the time-dependent magnetic fields produced by superparamagnetic iron oxide nanoparticles. Together with two graduate students, they will use these methods to optimize the performance of a diamond magnetic microscope and work towards detecting nanoparticle-labeled cancer cells flowing in microfluidic chips. The student will gain experience in quantum sensing and spin physics theory, optical breadboarding, experimental control (LabVIEW), data analysis (Mathematica, MatLab, and/or Python), and communicating results (presentations at group meetings). The student will present their work at an external conference and may be involved as a co-author in a subsequent journal publication.

**Supervision**. The student will be supervised through weekly 1:1 meetings as well as daily interactions in the lab with Acosta. They will also work closely with two graduate students working on the project.

### Long Wavelength Radio Astronomy - Greg Taylor

**Research Overview**. The Long Wavelength Array project is managed by the Physics and Astronomy Dept. at UNM and is currently supported by National Science Foundation grants and the Air Force Research Lab. The major goals of the project are

- To provide observing capability in the frequency range 5-88 MHz
- Develop engineering talent required for future instruments
- Provide opportunities for student engagement

Undergraduates currently take care of much of the operations: they learn how the array works, and they are responsible for scheduling observations and monitoring the array in a linux-based environment. They also work with one of the LWA staff (comprised of two regular faculty, one research faculty, two postdocs, and several graduate students) on an LWA project so that they have a chance to work with real data, learn analysis techniques and learn how to present their results. Interaction with collaborators at LANL, Caltech, JPL, NRL and Harvard broadens the cross-disciplinary experience of the students. Six of Prof. Taylor's past undergraduates have first-authored a paper, and two others have co-authored papers.

**REU Projects**. Available research projects concern new pulsar, transient, and AGN science opened up by the LWA.

**What the Student Will Do**. The student will learn to operate the array and participate in a project, with the goal of contributing to a publication. The student will gain all the aforementioned skills and will interact with other undergraduates and the LWA staff.

**Supervision**. A dedicated staff member will directly supervise the student, who will also interact frequently with Prof. Taylor.

### Transiting Exoplanet Survey Satellite TESS – Diana Dragomir

**Research Overview**. The Transiting Exoplanet Survey Satellite (TESS) is well into the second year of its primary mission. With all data released publicly within a month of download, and an extended 2.2-year mission recently approved by NASA, TESS will continue to generate many exciting discoveries for the foreseeable future.

The most conspicuous legacy that TESS promises to leave is the discovery of individual systems suitable for detailed atmospheric characterization. However, the survey will also prompt a revolution in exoplanet research simply by considerably increasing the number of small planets transiting bright stars. These planets will be accessible to a wide swath of follow-up observations, including measurements of their mass, dynamical properties and system architecture, as well as the precise characterization of their host stars. One of the research programs in Dr. Dragomir’s group is to leverage this enhanced ensemble to uncover new statistical trends and gain deeper insights into the composition, dynamical evolution, and demographics of small exoplanets.

**REU Project**. Two of the areas of exoplanet demographics research that TESS will shed new light upon are:

- The occurrence rate (and formation) of small ultra-short period exoplanets (USPs) around M dwarfs, which TESS will observe many more of than the Kepler transit survey did.
- The radius distribution (and ultimately the formation and evolution history) of planets in multi-planet systems, for which we can measure the masses and search for additional non-transiting planets using radial velocities (RVs).

**What the Student Will Do**. The student will have a choice of one of the two projects described above.

- For the first project, the student will carry out a search for USPs in the first two years of TESS data, and determine an occurrence rate (frequency) of USPs around M dwarf stars. A careful completeness analysis will be a necesary part of the project.
- The second project involves investigating the properties of planets in multi-planet systems with radii on either side of the “radius gap”. This “radius gap” in the small planet radius distribution was recently found to be at around 1.5 - 2 Earth radii. In other words, planets below and above this range are more frequent than planets in this “gap”. Generally, planets below the gap (many of which are suspected to be rocky) orbit closer to their stars, while planets above the gap (suspected to host a substantial gaseous atmosphere) tend to orbit furher away. This makes sense if the radius distribution is sculpted by photoevaporation, such that closer-in, hotter planets would lose their atmospheres due the high stellar irradiation, while more distant planets do not. However, not every multi-planet system follows this pattern. For this project, the student will investigate the properties of multi-planet systems (including orbital properties such as eccentricity, and the system architecture) to study what determines the small planet radius distribution in a given system.

With either project, the student will also learn how to distinguish likely planet from false positives in the TESS data (and by making use of existing ground-based follow-up data). Either IDL or Python can be used to write the code for this work.

**Supervision**. The student will work under the direct supervision of Dr. Dragomir, and will also interact with grad students in the group.