Biophysics techniques and models for mapping protein function: from fluorescence imaging to molecular dynamics modeling with Yasmene Wang Elhady
An Experimental History of CP Violation with Heather Harrington
Phase transitions in neutron stars with Mia Kumamoto
Planning and Learning for Quantum Control with Andy Goldschmidt
Simulation of SU(3) hadrons on a quantum computer using the 1-D lattice Schwinger model with Ivan Chernyshev
Biophysics techniques and models for mapping protein function: from fluorescence imaging to molecular dynamics modeling with Yasmene Wang Elhady
Proteins perform a broad range of functions in our cells. They are involved in cellular signaling, immune responses, motor functions, they facilitate DNA replication and expression, etc. Protein misfolding is believed to be a primary cause of a host of diseases. A quick Google search will list Alzheimer's disease, type 2 diabetes, cancer, Parkinson's disease, cystic fibrosis, Huntington's disease, cataracts, and many others. Biophysicists have contributed to the field of structural proteomics by developing and adopting a broad range of techniques and models to observe and predict how proteins structure themselves and perform their functions. I'd like to do a survey of these techniques and models and get a sense of some of the different angles people are approaching structural proteomics with. If you find a certain angle particularly interesting, we can go deeper and maybe play with some of the math.
Reading:
The reading list will depend on our discussion. As starting off points, we can look at
Molecular Dynamics Simulation for All by Hollingsworth and Dror
An Overview of Current Methods to Confirm Protein-Protein Interactions by Kenji Miura
Advancing Biophysics Using DNA Origami by Engelen and Dietz
If particular topics stand out we can look deeper.
Requirements: none
An Experimental History of CP Violation with Heather Harrington
One of the most unexpected results in the mid 20th century in Physics was the discovery of the pure left-handedness of the Weak Interaction. This was followed by the discovery of CP violation in neutral Kaons leading to the prediction of a before-unobserved generation of quarks and the formulation of the CKM matrix and it's CP-violating phase. So far, CP violation has only been observed in these small effects in the Weak Interaction, however we know that there must be more. This is because CP violation is necessary to explain the baryon asymmetry between matter and antimatter in our universe. In this DRIP course we will read the experimental (and some theoretical) papers that tell this story, from the Wu experiment and Lee and Yang, to B-meson factories and Electric Dipole searches. I hope to also get to Standard Model predictions for Charged Lepton Flavor Violation (CLFV), status and prospects for CPT Tests with the ALPHA experiment, search for Lorentz violation using high-energy atmospheric neutrinos in IceCube, and CPT- and Lorentz-violation tests with Muon g-2.
Reading:
A.K. Wroblewski, THE DOWNFALL OF PARITY — THE REVOLUTION THAT HAPPENED FIFTY YEARS AGO, 2008
T.D. Lee, C.N. Yang, Question of Parity Conservation in Weak Interactions, 1956
C.S. Wu, Experimental Test of Parity Conservation in Beta Decay, 1957
R.L. Garwin, L.M. Lederman, and M. Weinrich, Observations of the Failure of Conservation of Parity and Charge Conjugation in Meson Decays: the Magnetic Moment of the Free Muon, 1957
J.H. Christenson, J.W. Cronin, V.L. Fitch, and R.Turlay, Evidence for the 2π Decay of the K02 Meson, 1964
H. Georgi, g H. R. Quinn, and S. Weinberg, Hierarchy of Interactions in Unified Gauge Theories, 1974
M. Kobayashi, T. Maskawa, CP. Violation in the Renormalizahle Theory of Weak Interaction, 1972
KTeV Collaboration, Observation of Direct CP Violation in K-> ππ Decays, 1999
NA48 Collaboration. A new measurement of direct CP violation
in two pion decays of the neutral kaon, 1999
BaBar Collaboration, Measurement of CP-Violating Asymmetries in B0 Decays to CP Eigenstates, 2001
Belle Collaboration, Observation of Large CP Violation in the Neutral B Meson System, 2001
A.E. Nelson and Huangyu Xiao, Baryogenesis from B meson oscillations, 2019
T2K Collaboration, Constraint on the matter–antimatter symmetry-violating phase in neutrino oscillations, 2020
Requirements: PHYS 440, PHYS 441
Phase transitions in neutron stars with Mia Kumamoto
Neutron stars feature some of the most extreme conditions found anywhere in the universe. At such high densities, it is possible that nuclear matter will undergo a phase transition to matter with deconfined quarks, meson condensates, or other exotica. This can have significant effects on the equation of state and other observables. Such phase transitions can feature mixed phases and other rich structure. Possible applications based on student interest include finite size effects, superfluidity and cooling, and pulsar glitches.
Reading:
Compact Stars by Glendenning
https://arxiv.org/abs/nucl-th/0010075
https://arxiv.org/pdf/astro-ph/0411619
Requirements: Phys 325, Phys 328
Planning and Learning for Quantum Control with Andy Goldschmidt
Many people are excited by the near possibility of real world applications for quantum computers. The justification is that special algorithms programmed on a quantum computer can perform specific but useful tasks faster than the equivalent algorithms running on our best supercomputers. If a programmer wants to write a quantum algorithm, she uses the quantum programming language of gates: these are specific operations that act on 1 or 2 qubits at a time. Gates are used to do computer things like flipping a 0 to a 1 or quantum things like entangling a pair of qubits. By combining gates, the programmer can design any quantum algorithm on any number of qubits. Under the hood, gates are implemented by electric pulses that tell the physical system what to do to make the computation happen. In this DRiP, we will think about control at the levels of gates and pulses. We will read about different ways to think about control design. We will look at how engineers design classical controllers and explore how quantum engineers design quantum controllers.
Reading:
Selected readings will come from:
Reinforcement learning, R. Sutton and A. Barto
Data-Driven Science and Engineering, S. Brunton and N. Kutz
Quantum Computation and Quantum Information, M. Nielson and I. Chuang
Also, here are a few relevant papers we might discuss depending on what direction we pursue:
Qiskit pulse: programming quantum computers through the cloud with pulses, T. Alexander et al.
Model-based Reinforcement Learning: A Survey, T. Moerland et al.
Reinforcement Learning in Different Phases of Quantum Control, M. Bukov et al.
Quantum Architecture Search via Deep Reinforcement Learning, E. Kuo et al.
Optimization Landscape of Quantum Control Systems, X. Ge et al.
Second order gradient ascent pulse engineering, P.de Fouquieres et al.
Requirements: Quantum mechanics (Phys 324), Linear algebra (Math 208 or similar)
Simulation of SU(3) hadrons on a quantum computer using the 1-D lattice Schwinger model with Ivan Chernyshev
Quantum chromodynamics (QCD) is the theory that governs the strong nuclear force which binds together and governs the mechanics of nuclear matter. Due to it being strongly coupled, it often cannot be solved analytically using perturbation theory, so instead it is simulated numerically. Current simulations have several limiting factors, among them the fact that resources required to simulate a quantum system using a classical computer rise exponentially with system size, that can potentially be addressed by quantum computing. In the past several years, companies such as IBM have been creating quantum chips with 1-100 qubits, though they currently have substantial noise. This project will help provide a framework for quantum simulations of QCD by attempting to find the meson and baryon ground states on a 1-dimensional lattice governed by SU(3), QCD's symmetry group, and simulating the dynamics of nuclei on said lattice.
Reading:
David Tong’s notes on Quantum Field Theory (Specifically Ch.1 and 4)
Quantum computing: https://qiskit.org/learn/ for everything from brief introductions to a full online textbook
Quantum Computation and Quantum Information by Michael Nielsen and Isaac Chuang
Papers:
Hamiltonian formulation of Wilson's lattice gauge theories
SU(2) hadrons on a quantum computer via a variational approach
Requirements: PHYS 226, PHYS 324, PHYS 325
Recommended: PHYS 329
Helpful: PHYS 419