Summer Research Projects, Department of Physics and Astronomy

Check back occasionally, as the list of projects might change. If you are interested in research opportunities, please click on the links below. We also encourage you to contact the individual department members associated with the projects for further information about the research.

Program Dates

May 31, 2022 - August 5, 2022

Click on the project name for a more detailed description of the project

Theoretical and computational modeling of bacteria colony growth (JD-1) JiaJia Dong
Microscale mechanics of actomyosin networks (BJG-1) Bekele Gurmessa
Development of Cesium Atomic Magnetometer (IS-1) Ibrahim Sulai
Spectroscopy of Palladium Atoms and Ions (IS-2) Ibrahim Sulai
Chaotic Mixing, Swimming Microbes, and Propagating Reaction Fronts (THS-1) Tom Solomon
Computer Simulation of a Jammed Granular System (KVL-1) Katharina Vollmayr-Lee
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Project Name: Theoretical and computational modeling of bacteria colony growth
Project Mentor: JiaJia Dong
Project Code: (JD-1)

In the forefront of population dynamics, the pioneering work by Lotka and Volterra in the 1920s sparked the interest in the class of predator-and-prey model in which the survival of each population depends directly on its interactions with the other. Motivated by the rich morphologic patterns found in bacteria colonies, we study a parasite-host type model by using a combination of theoretical and computational tools.

Through this project, you will have the opportunity to:

  • study paradigmatic models in population dynamics;
  • learn computer programming using Python, a general-purpose programming language widely used in research and industry;
  • interact with research scientists and students;
  • develop your own project;
  • and many more challenging and exciting experiences as a physicist.

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Project Name: Microscale mechanics of actomyosin networks
Project Mentor: Bekele Gurmessa
Project Code: (BJG-1)

Eukaryotic cells dynamically change their viscoelastic properties by restructuring networks of actin filaments in the cytoskeleton to enable key cellular processes, including cell motility and mitosis. The network's restructuring is modulated by various actin-binding proteins, motor proteins, and counterions. For example, when used with the motor protein myosin-II, high concentrations of $\mathrm{Mg^{2+}}$ induce bundling and cross-linking of actin filaments while high concentrations of $\mathrm{K^{+}}$ destabilize the minifilaments of myosin II, a motor protein necessary to cross-link actin filaments transiently. In this project, we use active microrheology to explore how the mechanics and structure of actomyosin networks evolve under competing effects of varying $\mathrm{Mg^{2+}}$ and $\mathrm{K^{+}}$ concentrations. We vary the chemical environment through a microfluidics platform while simultaneously measuring time-varying linear viscoelastic moduli of myosin-II cross-linked actin networks as we cycle between low and high salt concentrations. The interested student would work on all aspects of this project ranging from developing a microfluidics setup and experimental protocols to creating \emph{in vitro} actin networks and characterizing. Developing skills includes getting experience in cutting-edge biophysical research, which is transferable to any future career path. Previous experiences in wet-lab and imaging experiments and programming in Matlab or Labview are desirable but not required.

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Project Name: Development of Cesium Atomic Magnetometer
Project Mentor: Ibrahim Sulai
Project Code: (IS-1)

The interaction of atoms and magnetic fields enables us to make magnetic field sensors of sensitivity at the femto-Tesla level (i.e. $10^{-15}$ Tesla). For scale, the earth's magnetic field is on the micro $10^{-6}$ Tesla level. The choice of which atom to use is dictated by the details of its atomic structure, as well as available light sources for preparing and reading out the atom. This project involves developing a cesium atomic magnetometer. Cesium is attractive to us because of its low vapor pressure, and we have recently acquired light sources to probe its levels. The goals of this project are to investigate ways of amplifying the signal using optical cavities, as well as to assess the feasibility of operating the sensor outside a magnetic shield. The work involves electronics, hardware design, 3d printing, and optics.

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Project Name: Spectroscopy of Palladium Atoms and Ions
Project Mentor: Ibrahim Sulai
Project Code: (IS-2)

Palladium has six stable isotopes -- five of which have nuclear spin of zero. A consequence of this is that there is no nuclear magnetic interaction between the electrons and the nucleus and so the atomic structure of five of the six isotopes is significantly simplified. We are interested in determining the energy levels of some narrow transitions in the neutral and singly ionized palladium. The narrowness of the transition is related to the Heisenberg principle, as the excited states are long lived, and hence we call them metastable. We are able to determine the energy levels with high precision and this precision will allow us to search for (or constrain) subtle signatures of physics beyond the standard model that arise in interactions between neutrons and electrons. As a first step in performing this experiment, we will be developing a metastable atom source and observe the light that is emitted by the atoms using a spectrometer. A next step is to excite the atoms with an external light source -- looking at the absorption spectra. The work involves electronics, hardware design and optics.

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Project Name: Chaotic mixing, swimming microbes, and propagating reaction fronts
Project Mentor: Tom Solomon
Project Code: (THS-1)

In a forest fire, the dividing line between burned and unburned trees is called a front. The motion of this front determines how the fire spreads through the forest. Similar front dynamics characterize the spreading of a disease in society, as well as numerous chemical processing applications, biological processes in cells and developing embryos, and plasmas in fusion reactors. We are currently conducting experiments that explore how the motion of fronts is affected by fluid mixing, e.g., forced flows in a chemical processor, winds in a forest fire, or the motion of people in society while a disease spreads. Table-top experiments using a simple chemical reaction (the well-known Belousov-Zhabotinsky reaction) focus on how fronts are affected by simple flow patterns -- vortices (whirlpools) and jets.

We are testing theories of "burning invariant manifolds" that predict barriers that stop the motion of reaction fronts in laminar (smooth) fluid flows. We have already done several experiments that have verified these predictions in two-dimensional flows, and we are currently extending these experiments to three-dimensional fluid flows.

We have also initiated studies of the motion of swimming bacteria in fluid flows. It turns out that the same theories that predict barriers for the motion of chemical fronts also predicts barriers in the motion of mutated "smooth-swimming" bacteria. We are doing experiments that study these barriers for bacteria swimming in microfluidic channel flows.

There is a lot of "hands-on" work involved in these projects, including the designing, building and testing of the experimental apparatus, mixing chemicals for the reaction, culturing of bacteria, and doing numerous experimental data runs. The experimental work also involves a substantial amount of computer-aided image analysis, almost exclusively on Linux workstations running a program called IDL. We also frequently conduct numerical simulations of the phenomena, also with IDL. Although experience in computer analysis is useful, it is not required as long as the student involved is willing and eager to learn IDL.

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Computer Simulation of a Jammed Granular System
Project Mentor: Katharina Vollmayr-Lee
Project Code: (KVL-1)

Examples for granular materials are soap bubbles, rice grains, sand, and snow. They all have in common that the entities (e.g. bubbles) interact and energy is dissipated. At high density granular systems display fascinating phenomena such as avalanches and the jamming transition. In this project we study a system of disks which are packed in between to plates and sheared. In addition to the moving disks are not moving small disks, pins, representing obstacles. We study how these pins influence the jamming transition, the structure (spatial arrangement) and the dynamics of the moving disks. This project is part of a collaboration with the research group of Brian Utter at UC Merced, as well as the research groups of Amy Graves, and Cacey Bester at Swarthmore.

The student would work on implementing and running computer simulations using the public software package LAMMPS, as well as working on the analysis of the resulting simulations. No prior computer programming skills are required.

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