Alumni
Corey Adams Bonnie Fleming 
First Detection of Low Energy Electron Neutrinos in Liquid Argon Time Projection ChambersElectron neutrino appearance is the signature channel to address the most pressing questions in neutrino oscillations physics, at both long and short baselines. This includes the search for CP violation in the neutrino sector, which the U.S. flagship neutrino experiment DUNE will address. In addition, the Short Baseline Neutrino Program at Fermilab (MicroBooNE, SBND, ICARUST600) searches for new physics, such as sterile neutrinos, through electron neutrino appearance. Liquid argon time projection chambers are the forefront of neutrino detection technology, and the detector of choice for both short and long baseline neutrino oscillation experiments. This work presents the first experimental observation and study of electron neutrinos in the 110 GeV range, the essential oscillation energy regime for the above experiments. The systematic uncertainties for an electron neutrino appearance search for the Fermilab Short Baseline Neutrino Program are carefully quantified, and the characterization of separation between electrons and high energy photons is examined. 

Marco BonettMatiz Yoram Alhassid 
Statistical and Spectroscopic Properties of Nuclei in the Shell Model Monte Carlo MethodThe predictive power of the interacting shell model in describing properties of nuclei is restricted by the limitations of conventional diagonalization techniques. The shell model Monte Carlo (SMMC) method allows the calculation of thermal properties in very large model spaces, much beyond what is possible with exact diagonalization. In particular, the SMMC has become the stateoftheart method for the calculation of statistical properties of nuclei. The total state density that is calculated in SMMC includes the magnetic degeneracy of nuclear levels. On the other hand, the quantity that is usually measured experimentally is the level density, in which each level is counted once irrespective of its spin. We present a method to calculate level densities in SMMC and apply it to midmass and heavy nuclei. In particular, we present the first calculation of densities for oddmass nuclei, circumventing a sign problem that originates in the projection on odd number of particles. We find good agreement with various experimental results. We also introduce and validate a method to calculate lowlying excitation energies, for the first systematic calculation of spectroscopic properties within SMMC. The method is based on the imaginary timedependent correlation matrix (ITCM) of the onebody densities. We successfully reproduce the first few lowlying excitation energies for each spin and parity in a light nucleus, for which exact diagonalization is possible. 

Brendon O'Leary David DeMille 
In search of the electron's electric dipole moment in thorium monoxide: an improved upper limit, systematic error models, and apparatus upgradesSearches for violations of discrete symmetries can be sensitive probes of physics beyond the Standard Model. Many models, such as supersymmetric theories, introduce new particles at higher masses that include new CPviolating phases which are thought to be of order unity. Such phases could generate measurable permanant electric dipole moments (EDMs) of particles. The ACME collaboration has measured the electron’s EDM to be consistent with zero with an order of magnitude improvement in precision compared to the previous best precision (J. Baron et al., ACME collaboration, Science 343 (2014), 269272) with a spin precession measurement performed in the $H$ state of a beam of thorium monoxide (ThO). This limit constrains timereversal violating physics for particles with masses well into the TeV scale. In this thesis I discuss the details of this measurement with an emphasis on the data analysis, search for systematic errors, and systematic error models that contributed to this result. I also discuss implemented and planned upgrades to the experimental apparatus intended to both improve the statistical sensitivity and reduce its susceptibility to systematic errors. At this time, the upgraded apparatus has been demonstrated to have a statistical sensitivity to the electron EDM that is more than a factor of 10X better than that our previous measurement. 

Andrei Petrenko Robert Schoelkopf 
Enhancing the Lifetime of Quantum Information with Cat States in Superconducting CavitiesThe field of quantum computation faces a central challenge that has thus far impeded the fullscale realization of quantum computing machines: decoherence. Remarkably, however, protocols in Quantum Error Correction (QEC) exist to correct qubit errors and thus extend the lifetime of quantum information. Reaching the "breakeven" point of QEC, at which a qubit's lifetime exceeds the lifetime of the system's constituents, has thus far remained an outstanding goal. In this work, we implement a QEC code within a superconducting cavity Quantum Electrodynamics (cQED) architecture that exploits the advantages of encoding quantum information in superpositions of coherent states, or cat states, in highly coherent superconducting cavities. This hardwareefficient approach, termed the cat code, simplifies the encoding scheme and requires the extraction of just one error syndrome via singleshot photon number parity measurements. By implementing the cat code within a full QEC system, we demonstrate for the first time quantum computing that reaches the breakeven point. Beyond applications to error correction, logical qubit encodings based on the cat code paradigm can be used to probe more fundamental questions of quantum entanglement between physical qubits and coherent states. We demonstrate the violation of a Bell inequality in such a setup, which not only exhibits our ability to efficiently extract information from continuous variables encodings, but moreover illustrates a striking example of a system straddling the quantumtoclassical interface. These results highlight the power of novel, hardwareefficient qubit encodings over traditional QEC schemes. Furthermore, they advance the field of experimental error correction from confirming the basic concepts to exploring the metrics that drive system performance and the challenges in implementing a faulttolerant system. 

Toshihiko Shimasaki David DeMille 
Continuous Production of 85Rb133Cs Molecules in the Rovibronic Ground State via ShortRange PhotoassociationWe present our results on continuous production of ultracold ^{85}Rb^{133}Cs molecules in the rovibronic ground state via shortrange photoassociation (PA). Starting with ultracold Rb and Cs atoms trapped in dualspecies darkSPOT MOT, we photoassociate a pair of Rb and Cs atoms into an excited molecular state, which decays into the electronic ground state by spontaneous emission. We apply depletion spectroscopy to the RbCs system and establish a rotationallyresolved, stateselective detection method for molecules in the vibronic ground state X^1S+(v = 0). With this technique, we verified molecule production in the rovibronic ground state X^1S+(v = J = 0). We explored a variety of shortrange PA pathways, namely, via excitation to the 2^3P_0+ and 2^3P_0 states, the 2^1P_12^3P_13^3S^+_1 complex, and the b^3P_1^c^3S^+_1B^1P_1 complex. One of the b^3P_1^c^3S^+_1B^1P_1 complex of states, with PA frequency 10151.24 cm^1, was found to be the most efficient pathway so far. Using PA through this state, we achieved a molecule production rate of up to 8000 molecules /s in X1^S+(v = J = 0). This opens up the possibility of utilizing shortrange PA for preparing a large sample of ultracold, rovibronic ground state molecules via continuous accumulation. 
Filip Kos David Poland 
Bootstrapping 3D CFTsWe use the method of conformal bootstrap to systematically study the space of allowed conformal field theories (CFT) in three spacetime dimensions. We consider the crossing symmetry equations coming from the correlators of several lowest dimension operators in a given CFT and show how to setup the semidefinite program to explore the constraints implied by the equations. Constraints lead to general bounds on dimensions and 3point functions of the operators in CFT. Three classes of CFTs considered in this work are theories containing scalars with Z_2 symmetry, theories containing scalars with O(N) symmetry and theories containing fermions with parity symmetry. While studying the general constraints on such theories, we rediscover several previously known CFTs – Ising model, O(N) vector models and GrossNeveuYukawa models. We determine the properties of the spectrum of lowlying operators in all of these cases. We show that conformal bootstrap can be a very powerful method for precise computation of CFT spectrum. In particular, our result for the dimensions of two lowest lying operators in the Ising model leads to the most precise determination of critical exponents in the model while our results for the 3point functions in O(N) models lead to most precise determination of the highfrequency conductance in O(N) vector models. 

Tomomi Sunayama Nikhil Padamanabhan 
Using galaxy surveys as a precision tool to measure dark energyFuture surveys will provide a deeper understanding of dark energy, dark matter, and early universe physics through the measurements of large scale structure. In particular, the baryon acoustic oscillation (BAO) method and the redshiftspace distortion (RSD) method aim to achieve subpercent precision on cosmological parameters. Understanding and reducing the systematics caused by the nonlinear evolution of gravitational structures and galaxy formation and evolution is crucial for future galaxy spectroscopic surveys. Over the course of this thesis, I develop the tools necessary to understand and quantify these systematic effects, and present a series of applications relevant to future surveys. I first constructed mock catalogs using the Nbody simulations with a reduced number of time steps for future galaxy surveys. Then, I investigated the effects of galaxy bias on the BAO peak and the robustness of the reconstruction method, which is a standard technique used in the BAO measurements to reduce the error. We tested whether the reconstruction method could be applicable to the RSD method to test gravity models. In addition to these studies on large scales, I also explored how assembly history of dark matter halos affects its internal structure and clustering on small scales, including a first measurement of the scale dependence of this effect. These effects of the assembly history on small scales can be a potential source of systematics for future galaxy surveys. 

Mitchell Underwood Jack Harris 
Cryogenic Optomechanics with a Silicon Nitride MembraneThe field of optomechanics involves the study of the interaction between light and matter via the radiation pressure force. Though the radiation pressure force is quite weak compared with forces we normally experience in the macroscopic world, modern optical and microwave resonators are able to enhance the radiation pressure force so that it can be used to both measure and control the motion of macroscopic mechanical oscillators. Recently, optomechanical systems have reached a regime where the sensitivity to mechanical motion is limited only by quantum effects. Together with optical cooling techniques such as sideband cooling, this sensitivity has allowed experiments to probe the quantum behaviors of macroscopic objects, and also the quantum limits of measurement itself. In this dissertation I describe the physics underlying the modern field of optomechanics and provide an overview of experimental accomplishments of the field such as ground state cooling of mechanical oscillators, detection of radiation pressure shot noise, and preparation, storage, and transfer of quantum states between macroscopic objects and the electromagnetic field. I then describe the specific experimental work done in pursuit of my degree involving the ground state cooling of a silicon nitride membrane in a high finesse FabryPerot cavity, and a systematic characterization of the dynamics that occur when the membrane is coupled to two nearly degenerate cavity modes at an avoided crossing in the cavity spectrum. In the section on ground state cooling, particular attention is given to the influence of classical laser noise on the measurement of the membrane’s motion at low phonon occupancies, and techniques for laser noise measurement and reduction are discussed. 
Rostislav Boltyanskiy Eric Dufresne 
Mechanical Response of Single Cells to StretchA living cell is a complex soft matter system far from equilibrium. While it consists of components with definite mechanical properties such as stiffness, viscosity, and surface tension, the mechanics of a cell as a whole are more elusive. We explore cell mechanics by stretching single fibroblast cells and simultaneously measuring their traction stresses. Upon stretch there is a sudden, drastic increase in traction stresses, often followed by a relaxation over a time scale of ~1min. Upon release of stretch, traction stresses initially drop and often recover on a similar time scale of ~1min. We propose a minimally active linear viscoelastic model that captures the main features of cell response to stretch. The response we observe is also consistent with a biological model of tensional buffering. We propose that cell behavior in response to a mechanical perturbation, such as stretch, consists of crosstalk between these two models. 

Diego Caballero Orduna Corey O'Hern 
Computational Studies of Protein StructureDespite the abundance of crystallographic and structural data and many recent advances in computational methods for protein design, we still lack a quantitative and predictive understanding of the driving forces that control protein folding and stability. For example, we do not know the relative magnitudes of the sidechain entropy, van der Waals contact interactions, and other enthalpic contributions to the free energy of folded proteins. The inadequacy of current computational approaches to the analysis and design of protein structures has hampered the development of many novel therapeutic and diagnostic agents, and is arguably one of the biggest open challenges in biophysics and biochemistry. My work will build on the pioneering work of Ponder and Richards in the 1980s, who while at Yale demonstrated that steric constraints and packing criteria in protein interiors were the most stringent criteria in determining protein conformations. I will present my work developing and using a sterically centered molecular dynamics force field to study amino acid conformations. I specifically use this force field to model hydrophobic amino acids and study the fundamental driving forces that determine amino acid side chain conformations. In my research, I have employed a hardsphere plus stereochemical constraint molecular dynamics model. I have complemented this approach with other numerical and computational techniques such as approximate Markov state models to predict and rank amino acid conformations in different environments. This dissertation presents three separate but related computational studies. In the first one, I present an analysis of the equilibrium backbone conformations that the amino acid Alanine can take. I also study the interconversion mechanisms between these equilibrium states and compare my predictions with crystallographic data. I then generalize the... 

Jane Cummings Sarah Demers 
Tau Polarization at a Hadron Collider: W to tau,nu and Z to tau,tau decays at ATLASIn this thesis, the first measurement of tau polarization at a hadron collider, and the first measurement of tau polarization in W boson decays to a tau and neutrino altogether, is presented. The measurement of tau polarization is a test of the structure of the vector (V) and axial vector (A) couplings of the W boson to the third generation leptons. Such a test is not possible with first and second generation leptons for which the helicity state is not accessible in a collider experiment. The VA structure of the charged current weak interaction at small W virtuality (Q^2) is well established from the kinematics of tau decays while the structure at Q^2 = m_W^2 had not been measured explicitly. In addition, an advanced analysis of the tau polarization in Z boson decays to tau pairs is presented. 

Arvin Kakekhani Sohrab IsmailBeigi 
Ferroelectrics to Tackle Fundamental Challenges in CatalysisSurface catalysis based on transition metals and their alloys has been one of the most important research fields in theoretical and experimental catalysis and chemistry. Recently, the development of a microscopic theoretical framework combined with the computational capability and accuracy of first principles calculations has changed the nature of this field from a largely trial and error approach to a predictive and controlled design process. In addition to deepening our knowledge of catalysis at the microscopic scale and helping design improved catalysts for important chemical reactions, this framework for heterogeneous catalysis has helped us understand some of the fundamental limitations of the catalytic activities of current materials and processes. In this thesis, we briefly introduce these limitations and their root causes in terms of electronic and structural properties. Next, we describe how using ferroelectric surfaces and exploiting their polarization dependent switchable surface chemistry can tackle some of these fundamental challenges. We then design processes and materials that can catalyze reactions that are considered challenging (if not near impossible) using current catalytic materials and processes. As specific examples, we discuss the possibility of using ferroelectricbased materials to catalyze industrially and environmentally important reactions including water splitting, direct NO$_{x}$ decomposition, and partial oxidation of methane to methanol. 

Nicole Larsen Daniel McKinsey 
An Effective Field Theory Analysis of The First LUX Dark Matter SearchA wealth of astrophysical research supports the existence of dark matter in the universe, yet the exact nature of this unknown particle remains elusive. The Large Underground Xenon (LUX) experiment is a 370kg dualphase xenonbased time projection chamber (TPC) that seeks to detect dark matter candidates such as Weakly Interacting Massive Particles (WIMPs) through the light and ionization signals generated by their collisions with xenon nuclei. The first part of this talk details the design of the LUX experiment and describes several novel hardware developments that enable LUX to search for these rare events with extremely high precision. In 2013, with the release of the world's first subzeptobarn spinindependent WIMPnucleon crosssection limit, the LUX (Large Underground Xenon) experiment emerged as a frontrunner in the field of dark matter direct detection. However, tension between experiments and the absence of a definitive positive detection suggest a search for answers outside the standard spinindependent/spindependent analyses. In particular, the standard analyses neglect momentum and velocitydependent interactions on the grounds that WIMPnucleus collisions are nonrelativistic. At the parton level, this is not always the case, and moreover, models exist in which the standard spinindependent and spindependent interactions are subdominant to momentum and velocitydependent interactions. Recent theoretical work has identified a complete set of 14 possible independent WIMPnucleon interactions using basic symmetries and an effective field theory formulation. In the second part of this talk we report on the extension of the LUX analysis to search for all 14 of these new interactions, we comment on the possible suppression of event rates due to operator interference, and we show that under this new framework LUX again exhibits worldleading sensitivity. 

Manuel Mai Corey O'Hern 
Outcome Prediction and Reconstruction for Systems of Ordinary Differential EquationsI will present two related analyses of systems of ordinary differential equations (ODEs). The first one investigates outcome prediction in several systems of ODEs for the immune response to infection. We show that patienttopatient variability sets a fundamental limit on the outcome prediction accuracy. However, accuracy can be increased at the expense of delayed prognosis. In the second study, I develop a method to build, general nonlinear ODE models from time series data using machine learning techniques related to sparse coding. I employ sparse basis learning to identify a basis set of functions that accurately represents the system of ODEs. We then employ L1regularized regression, which finds sparse solutions to underdetermined systems of equations. We use this method to recover a full function (i.e. the righthand side of an ODE) from a small number of measurements. Results are presented for one, two and three dimensional nonlinear ODEs. 

Eric Norrgard David DeMille 
Magnetooptical trapping of diatomic moleculesLaser cooling in a magnetooptical trap (MOT) is the workhorse technique for atomic physics in the ultracold regime, serving as the starting point in applications from optical clocks to quantumdegenerate gases. It was recently shown that optical cycling, and thus laser cooling, should be possible for a class of at least 40 molecular species, using just three (or fewer) lasers. In this work, we demonstrate the first laser slowing and first magnetooptical trapping of a molecule, strontium monofluoride (SrF). In our experiments, a laserslowed molecular beam is used to load a MOT. The rotational structure in molecules prevents cycling on a twolevel system (as is typical with atoms) and leads to populating states which are dark to the confining laser. In the first molecular MOT demonstration, the confining forces were very weak compared to typical atomic MOTs. In a second iteration, with the aid of recent theoretical insights into the origin of the restoring force in a MOT, we optimized the confining force for static fields in the MOT in lieu of the dark states. We then demonstrated a trap which eliminates dark states by trapping in timevarying fields. This method allows for capture of a large sample of molecules at ultracold temperatures and high phase space densities with long trap lifetimes. The trapped population is sufficiently cold to proceed with many proposed experiments posed to expand the frontiers of knowledge, such as operation of molecular fountains and study of ultracold moleculeatom collisions. 