Bacterial antibiotic resistance is a rapidly growing concern for global health care. Typically, clinical antibiotics work by targeting essential pathways involved in bacterial metabolism or growth while leaving host cells unaffected. There are three basic mechanisms of bacterial resistance: (1) bacteria can chemically modify the antibiotic to a non- toxic form, (2) pump the antibiotic out of the cell, or (3) modify the enzyme or pathway targeted by the antibiotic. The second two mechanisms can be thought of as being selfish, as the mechanism doesn't directly help the community on a macroscale. However, the first mechanism helps the whole community, thus it can be thought of as cooperative. We hypothesize that the class of resistance mechanism, i.e. cooperative or selfish, is the primary factor that determines the geometry of colony morphology surrounding an antibiotic source. To test this hypothesis, we computationally simulated the diffusion of antibiotic on a plate inoculated with bacteria that express a cooperative resistance mechanism. Using insights gained from these simulations, we also experimentally explored this phenomena by imaging the growth of resistant E. coli cells in the presence of various antibiotics. In my talk I will discuss the results from the simulation and the experimental stage, as well as the current state of the analysis.

With any particle physics experiment, precision is paramount. In experiments with electromagnetic shields, the inherent magnetic field noise from the shield itself can impede the accuracy of high precision experiments. For this research project I designed a model of an electromagnetic shield to find the magnetic field noise of the shield; the results of which can be used to increase the precision of a particle physics experiment being conducted at the University of Washington, searching for a potential source of time reversal symmetry by looking for a permanent electric dipole moment of a specific isotope of mercury (the existence of which would suggest a source of CP-violation). The cylindrical electromagnetic shield was modeled in the finite element analysis application, COMSOL Mulitphysics. The model is initially configured with a single magnetic dipole arranged on the axis of symmetry of the magnetic shield. The accuracy of the model is then compared to an analytic solution found by S.-K. Lee and M. V. Romalis at Princeton University. After refining the model to reflect the analytic solution, the number and orientation of magnetic dipoles is changed, producing the first, second and third derivatives of the magnetic field noise of the shield being used. Accounting for the magnetic field noise will increase the sensitivity of the experiment being conducted.

The field of Brain Computer Interface (BCI) systems is concerned with the study of how thoughts alone can be used to interface with and control the actions of external systems. Such BCI systems have been actively studied since 1969 when the seminal work of Fitz, et. al. at the University of Washington showed that monkeys could voluntarily control the deflection of an external meter with their thoughts alone. To date, there has been extensive research in this area as concerns thought-control of external devices in focused-activity environments, such as video gaming, but research into the effectiveness of BCI methods in more-realistic, distracted-environments is somewhat sparse, with notable exceptions including the work of Lalor, et. al., who performed a non-controlled and non-randomized study of the effects of Steady-State Visual Evoked Potentials (SSVEP) on real-time video-gaming control and Friedricha, et. al. who performed a study on the effects of auditory distractions on the accuracy of BCIs. Our present study represents a refinement of the Lalor approach in a broader scope than video-game control through the addition of more carefully defined controls, and we further extend this research through the study of the effects of simultaneous auditory and visual environmental conditioning. Based on the study of Friedricha, et. al. involving auditory distractions, we expect a constant auditory tone to have no impact on BCI performance.

β-Ga2O3 is a transparent conducting oxide that is well suited to ultraviolet (UV) photovoltaics. One application possibility is as a UV energy harvesting device in space, where UV light is much more abundant than solar. Because of the anisotropy of β-Ga2O3, spectroscopic measurements for a full range of polarization with respect to angles of orientation were taken to obtain optical constants. These measurements were made for both single crystal and thin film samples. As expected, the optical constants vary depending on both the sample type and the orientation of the sample. From these data a model was built that is able to identify the orientation of the single crystal samples. The next step is to build a model that will be used to determine thin film thickness of β-Ga2O3 deposited by our group on different known substrates.

The purpose of the double slit experiment is to observe the wave-particle duality of light. When a steady stream of photons hits a double slit, the resulting interference pattern is a clear indicator of the wave nature of light. However, if at a given time only a few photons hit the double slit and the signal is recorded over time, one can observe both the particle and wave nature of light: individual particles (particle nature) are recorded over time while their sum will eventually produce the familiar interference pattern (wave nature). The experimental setup uses light filters to reduce the intensity of a laser beam to just a trickle of photons. These photons, after passing through a double slit, slowly produce an interference pattern on a detector. The detector is a digital video recorder set up to record photon hits. The video frames are superimposed to show the production of an interference pattern over time. The double slit experiment has been done numerous times and in different forms. The experiment conducted here does not produce, but confirm previous results using a new experimental setup. The challenge will be to successfully show the wave-particle duality of light with readily available equipment to allow for a straightforward demonstration to future students. The enormous historical importance of the double slit experiment lies in the fact that it is at the heart of quantum mechanics, a field of physics viewed as challenging yet vitally important to the future of human technological advancements.

Acoustic levitation is a method of levitating matter against the influence of gravity using sound waves.  Small droplets of fluid can, for example, be suspended in standing wave fields produced by high-power ultrasonic transducers at locations where the gradients of the sound field potentials counterbalance the gravitational forces acting on the droplets, creating a simulated microgravity environment.  These environments could be useful in simulating and studying how chemical and biochemical reactions might take place in space.  Our research builds on earlier work by J.Santa Cruz and J. Griffith who successfully achieved acoustic levitation at EdCC in 2011.  Santa Cruz and Griffith were able to experimentally demonstrate rough preliminary agreement with Bjerknes theory for levitation stability points in a planar field approximation, but they also observed stable particle orbits completely beyond explanation by the planar theory.  Here, we compare our experimental findings to the more general Gor’kov theory of levitation to explain both one- and two-dimensional levitation stability subspaces.

The goal of the New Muon (g-2) Experiment at Fermilab is a fourfold precision increase of the measurement of the anomalous magnetic dipole moment of the muon, with the hope of achieving a 5σ deviation from theory. Such a discovery would provide a basis for the exploration of new physics beyond the Standard Model. Many candidates exist for explaining this discrepancy, such as supersymmetry, dark photons, or lepton substructure. My work involves the characterization and analysis of Silicon Photomultipliers (SiPM’s) in support of the development of the (g-2) calorimeters — the central detector systems required to make the measurement. These avalanche photodiode arrays are a significant change from the previously used vacuum photomultiplier tubes (PMT’s). SiPM’s are extremely compact and can be mounted directly inside the magnetic field of the muon storage ring; characteristics such as these them a distinct advantage over PMT’s. A thorough study of pulse resolution, temperature dependence, gain, rate, and other properties is necessary to understand how SiPM’s may be most effectively utilized in the (g-2) experiment. Analyzing pulse resolution and gain involves exciting the SiPM with two laser pulses spaced 2 to 100 nanoseconds apart and determining how closely the pulses can overlap before a significant amount of information contained in the output of the SiPM is lost. Variations in the size and strength of each pulse have also been introduced in the study, such as saturating the SiPM circuit with a blast of laser light and studying how long it takes the device to recover.

The discovery of a new particle, which we suspect is the long-sought-after Higgs boson, has opened a wide range of opportunities to explore new physics at the Large Hadron Collider (LHC). One particularly promising direction is the search for "flavor violation" in Higgs decays, where a Higgs decays to a non-matching pair of particles. We focus particularly on decays into a tau and a mu lepton (both of which are heavier relatives of the electron). At present, indirect data from low-energy experiments allows these Higgs-to-tau-mu decays to make up up to 10% of all Higgs decays, while the current Standard Model of particle physics does not expect them to happen at all. The goal of my research is to develop a method for separating these decays out of the other billions of collisions that happen every second in the ATLAS detector, and analyzing them in such a way to make flavor violating decays stand out against background events (which look similar but have different origins). This will allow us to put much stricter limits on the rate at which these decays occur, and if any do occur we will have made a big step into previously-unexplored physics territory.

Neutral donor-bound electrons and excitons in bulk semiconductors provide a system that may have interesting prospects for quantum information processing (QIP). In GaAs, the donor-bound exciton system exhibits extremely high optical homegeneity with spin relaxation times similar to that of negatively charged quantum dots. The complex excited state structure, however, makes full coherent optical control of the spin state challenging. Exhibiting a simpler excited-state structure and a higher exciton binding energy than GaAs, coherent optical control of donor-bound electron spin states in InP may be more accessible. In this work we investigate the spin relaxation properties of donor-bound electrons in InP using continous wave polarized laser spectroscopy at liquid helium temperature. Current progress towards measuring the spin relaxation time via polarization-induced optical pumping will be presented. 

Next generation DNA sequencing, with high throughput and low costs, has already greatly benefitted life sciences and personalized medicine. Nanopore sequencing is a new single molecule technique with potential to further revolutionize DNA sequencing. In this technique DNA is electrophoretically drawn through the nanopore, an integrated membrane channel protein, while an ionic current is recorded. We use the nanopore Mycobacterium smegmatis porin A, MspA, a porin engineered to provide a robust nanopore with the necessary features for nanopore sequencing. To control DNA translocation, we use a phi29 DNA polymerase to pull single stranded DNA through MspA in single nucleotide steps. For each step, the recorded current can be mapped the four standard bases, A, C, G, and T, present in the pore’s narrow constriction. Additionally, the modified nucleobases associated with suppressed gene expression and a number of diseases, 5-methylcytosine and 5-hydroxymethylcytosine, may be directly detected with MspA. We compare two mutants of MspA and examine how different amino groups within MspA’s constriction affect the nucleotide-specific current. We find that additional modifications to MspA may be used to tailor the pore for specific sequencing applications, such as increased accuracy in detecting and, other modified DNA detection.

The study of defects (nitrogen-vacancy centers) in diamond may be instrumental in developing better biological sensors that optically detect tagged biological molecules without interfering with natural processes. Using nitrogen-vacancy (NV) centers, our goal is to develop highly sensitive microscopes that detect magnetic fields produced by magnetic nanotags. Since the NV center photoluminescence intensity depends on its spin state, a decrease in photoluminescence will occur when a magnetic field is applied to the NV center. We employ this property in the detection of nanotags. The applications of this research include the study of biological systems, and faster, cheaper and earlier detection of diseases. While performing optically-detected magnetic resonance in NV centers results in high-sensitivity detection of magnetic fields, a reduction in signal occurs when the NV center symmetry axis is misaligned from the instrument’s externally applied magnetic field. Helmholtz coils, which produce near uniform magnetic fields, may be used to align the magnetic field to the proper orientation. Two Helmholtz coils, placed on the horizontal plane of our sample, will allow for clearer detection of photoluminescence dips as the magnetic field will be aligned to one of the NV center axis. In this work, we integrate and test Helmholtz coils in our NV based magneto-optical microscopes. This includes the development of electrostatic simulations and a search algorithm for the alignment of the magnetic field, as well as the fabrication of the coils.

 The overall project that I work in is to see how quantum states can be used to process information. To realize this, we utilize crystal defects in diamond that exhibit quantum properties. We then network the defects using GaP as a photonic waveguide. GaP is used because at the wavelength of the defect, it is transparent and its index of refraction is higher than diamond. My contribution to this project is to investigate the feasibility of using polydimethylsiloxane (PDMS), a material similar to rubber, as a way to transfer gallium phosphide (GaP) on to the diamond. Using PDMS allows the amount of GaP transferred to be easily scaled due to the surface area of PDMS. I will first use more widely available silicon on insulator substrates to develop a general process flow. The silicon will be patterned as 50 by 50 micrometer squares using photo-lithography and plasma etching. The squares are then transferred to a secondary substrate using a PDMS stamp. We expect then to be able to apply the processing scheme developed for silicon to the transfer of GaP onto diamond.

The nitrogen-vacancy (NV) in color center is regarded as a leading qubit candidate in quantum information processing (QIP) since its spin state can be controlled and measured by optical methods. Efficient collection of photons emitted from NV centers is desirable for scalable QIP schemes. In order to achieve this, we design an integrated waveguide-cavity system in the GaP-diamond hybrid material system. GaP ring waveguides and cavities guide light on the surface of diamond and the guided evanescent mode interacts with NV center located 10 nm from the diamond surface. When a transition from the excited state to the ground state occurs in the NV center, light with a particular wavelength corresponding to the difference in the energy levels (637nm for NV centers) will be emitted. This emission is efficiently emitted into the cavity mode when the cavity is on resonance with the NV transition. We present the optical design of a grating-waveguide-cavity system optimized for efficient collection of photons, which is based on computationally intensive numerical simulation of the optical components. For this, we use a finite-difference time-domain simulation of Maxwell’s equations (open-source software MEEP). In order to make the simulation process faster, we utilize parallel computing on the Amazon cloud. We expect to show that theoretical coupling efficiency greater than 50% is possible in the hybrid GaP/diamond material system.