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Circuit quantization is an extraordinarily successful theory that describes the behavior of quantum circuits with high precision. The most widely used approach of circuit quantization relies on introducing a classical Lagrangian whose degrees of freedom are either magnetic fluxes or electric charges in the circuit. By combining nonlinear circuit elements (such as Josephson junctions or quantum phase slips), it is possible to build circuits where a standard Lagrangian description (and thus the standard quantization method) does not exist. Inspired by the mathematics of symplectic geometry and graph theory, we address this challenge, and present a Hamiltonian formulation of non-dissipative electrodynamic circuits. The resulting procedure for circuit quantization is independent of whether circuit elements are linear or nonlinear, or if the circuit is driven by external biases. We explain how to re-derive known results from our formalism, and provide an efficient algorithm for quantizing circuits, including those that cannot be quantized using existing methods., Comment: 30 pages, 8 figures

We examine the hydrodynamics of systems with spontaneously broken multipolar symmetries using a systematic effective field theory. We focus on the simplest non-trivial setting: a system with charge and dipole symmetry, but without momentum conservation. When no symmetries are broken, our formalism reproduces the quartic subdiffusion ($\omega \sim -i k^4$) characteristic of `fracton hydrodynamics' with conserved dipole moment. Our formalism also captures spontaneous breaking of charge and/or dipole symmetry. When charge symmetry is spontaneously broken, the hydrodynamic modes are quadratically propagating and quartically relaxing ($\omega \sim \pm k^2 - ik^4$). When the dipole symmetry is spontaneously broken but the charge symmetry is preserved, then we find quadratically relaxing (diffusive) transverse modes, plus another mode which depending on parameters may be either purely diffusive ($\omega \sim -i k^2$) or quadratically propagating and quadratically relaxing ($\omega \sim \pm k^2 -i k^2$). Our work provides concrete predictions that may be tested in near-term cold atom experiments, and also lays out a general framework that may be applied to study systems with spontaneously broken multipolar symmetries., Comment: 4+2+epsilon pages, 3 figures

Using holographic duality, we present an analytically controlled theory of quantum critical points without quasiparticles, at finite disorder and finite charge density. These fixed points are obtained by perturbing a disorder-free quantum critical point with weakly Harris-relevant disorder. We analyze these fixed points both using field theoretic arguments, and by solving the bulk equations of motion in holography. We calculate the critical exponents of the IR theory, together with thermoelectric transport coefficients. Our predictions for the critical exponents of the disordered fixed point are consistent with previous work, both in holographic and non-holograpic models., Comment: 5+11 pages

We describe a simple quantum error correcting code built out of a time-dependent transverse field Ising model. The code is similar to a repetition code, but has two advantages: an $N$-qubit code can be implemented with a finite-depth spatially local unitary circuit, and it can subsequently protect against both $X$ and $Z$ errors if $N\ge 10$ is even. We propose an implementation of this code with 10 ultracold Rydberg atoms in optical tweezers, along with further generalizations of the code., Comment: 15 pages, 7 figures

We present the hydrodynamics of fluids in three spatial dimensions with helical symmetry, wherein only a linear combination of a rotation and translation is conserved in one of the three directions. The hydrodynamic degrees of freedom consist of scalar densities (e.g. energy or charge) along with two velocity fields transverse to the helical axis when the corresponding momenta are conserved. Nondissipative hydrodynamic coefficients reminiscent of chiral vortical coefficients arise. We write down microscopic Hamiltonian dynamical systems exhibiting helical symmetry, and we demonstrate using kinetic theory that these systems will generically exhibit the new helical phenomena that we predicted within hydrodynamics. We also confirm our findings using modern effective field theory techniques for hydrodynamics. We postulate regimes where pinned cholesteric liquid crystals may possess transport coefficients of a helical fluid, which appear to have been overlooked in previous literature., Comment: 24 pages, 1 figure

We prove that prethermalization is a generic property of gapped local many-body quantum systems, subjected to small perturbations, in any spatial dimension. More precisely, let $H_0$ be a Hamiltonian, spatially local in $d$ spatial dimensions, with a gap $\Delta$ in the many-body spectrum; let $V$ be a spatially local Hamiltonian consisting of a sum of local terms, each of which is bounded by $\epsilon \ll \Delta$. Then, the approximation that quantum dynamics is restricted to the low-energy subspace of $H_0$ is accurate, in the correlation functions of local operators, for stretched exponential time scale $\tau \sim \exp[(\Delta/\epsilon)^a]$ for any $a, Comment: 5+35 pages; 1+4 figures, 1+0 tables. v2: added some results, improved presentation

We extend recent work on hydrodynamics with global multipolar symmetries -- known as "fracton hydrodynamics" -- to systems in which the multipolar symmetries are gauged. We refer to the latter as "fracton magnetohydrodynamics", in analogy to conventional magnetohydrodynamics (MHD), which governs systems with gauged charge conservation. We show that fracton MHD arises naturally from higher-rank Maxwell's equations and in systems with one-form symmetries obeying certain constraints; while we focus on "minimal" higher-rank generalizations of MHD that realize diffusion, our methods may also be used to identify other, more exotic hydrodynamic theories (e.g., with magnetic subdiffusion). In contrast to semi-microscopic derivations of MHD, our approach elucidates the origin of the hydrodynamic modes by identifying the corresponding higher-form symmetries. Being rooted in symmetries, the hydrodynamic modes may persist even when the semi-microscopic equations no longer provide an accurate description of the system., Comment: 44 pages, 2 figures; "Microscopic Hamiltonians" section added in v2

During the last two decades many new insights into the dynamics of strongly coupled quantum many-body systems have been obtained using gauge/gravity duality, with black holes often playing a universal role. In this white paper we summarize the results obtained and offer some outlook for future developments, including the ongoing mutually beneficial feedback loop with the study of more general, not necessarily holographic, quantum many-body systems., Comment: 18+24 pages

Supplemental Material for The patient acceptability of a remotely delivered pain management programme for people with persistent musculoskeletal pain: A qualitative evaluation by Gregory Booth, Sonia Zala, Chloe Mitchell, Roxaneh Zarnegar, Andrew Lucas and Anthony W Gilbert in British Journal of Pain

We present a review of theories of states of quantum matter without quasiparticle excitations. Solvable examples of such states are provided through a holographic duality with gravitational theories in an emergent spatial dimension. We review the duality between gravitational backgrounds and the various states of quantum matter which live on the boundary. We then describe quantum matter at a fixed commensurate density (often described by conformal field theories), and also compressible quantum matter with variable density, providing an extensive discussion of transport in both cases. We present a unified discussion of the holographic theory of transport with memory matrix and hydrodynamic methods, allowing a direct connection to experimentally realized quantum matter. We also explore other important challenges in non-quasiparticle physics, including symmetry broken phases such as superconductors and non-equilibrium dynamics., Comment: 178 pages, 43 figures; Draft of a review article for hep-th and cond-mat readers, comments welcome; (v2) added clarifications and references; expanded version, with exercises, published as a book by MIT Press: https://mitpress.mit.edu/books/holographic-quantum-matter

*† ‡ § Summary The preprophase band (PPB) marks the site on the plant cell cortex where the cell plate will fuse during the final stage of cytokinesis. Recent studies have shown that several cytoskeletal proteins are depleted at the PPB site, but the processes that bring about these changes are still unknown. We have investigated the membrane systems associated with the PPB regions of epidermal cells of onion cotyledons by means of serial thin sections and electron tomograms. In contrast with specimens preserved by chemical fixatives, our highpressure frozen cells demonstrated the presence of large numbers of clathrin-coated pits and vesicles in the PPB regions. The vesicles were of two types: clathrin-coated and structurally related, non-coated vesicles. Quantitative analysis of the data revealed that the number of clathrin-coated pits and vesicles is higher in the PPB regions than outside of these regions. Immunofluorescent microscopy using anti-plant clathrin-antibody confirmed this result. In contrast, no differences in secretory activities were observed. We postulate that the removal of membrane proteins by endocytosis plays a role in the formation of PPB ‘memory’ structures.

Presentation at the 5th International Barcode of Life Conference, Kunming, China, 27-31 October 2013

Plenary presentation at the Third European Conference for the Barcode of Life, 17-20 September 2012, Brussels, Belgium

Doxorubicin, a widely used anticancer agent, exhibits antitumor activity against a wide variety of malignancies. The drug exerts its cytotoxic effects by binding to and intercalating within the DNA of tumor and tissue cells. However, current assays are unable to accurately determine the concentration of intracellular active form of doxorubicin. Thus, we have developed a high performance liquid chromatography (HPLC) methodology in order to quantify the concentrations of doxorubicin that are bound to DNA in tumors and tissues as an intracellular cytotoxic measure of doxorubicin exposure after administration of small molecule and nanoparticle formulations of doxorubicin. The assay uses daunorubicin as an internal standard; liquid-liquid phase extraction to isolate bound drug; a Shimadzu HPLC with fluorescence detection equipped with a Phenomenex Luna C18 (2 um, 2.0 x 100 mm) analytical column; and a gradient mobile phase of 0.1% formic acid in water and acetonitrile. The assay has a lower limit of quantification (LLOQ) of 10 ng/mL and is shown to be linear up to 3,000 ng/mL. We demonstrated the suitability of this assay for doxorubicin bound to DNA in vivo by using it to quantify the doxorubicin concentration within tumor samples from SKOV3 and HEC1A mice obtained 72 hours after administering PEGylated liposomal doxorubicin (Doxil®; PLD) IV at 6 mg/kg. This HPLC assay allows for a sensitive and simple intracellular quantification of doxorubicin as compared to other methods and will be an important tool for future studies evaluating intracellular pharmacokinetics of doxorubicin and various nanoparticle carriers.

Plenary presentation at the Third European Conference for the Barcode of Life, 17-20 September 2012, Brussels, Belgium

In recent decades, optical LOS communications such as flag semaphore or flashing light have atrophied to the point where, if they are required, U.S. Naval forces are at a distinct disadvantage. RF communications have become critical to nearly all operations, but this capability comes at the cost of disclosing the location of operations. Depending on the platform, these RF communications can become a critical vulnerability. EMCON attempts to minimize this vulnerability through the elimination of any RF emissions from a ship, but communication requirements in recent years have essentially prevented a complete suppression of RF emissions. This work proposes mitigating emissions vulnerability by utilizing a new method of optical communications at LOS visual ranges reminiscent of flag semaphore. Tactical QR code communications streaming digital data through optical signaling has the potential to provide tactical communications at a moderate range, allowing critical communications to be relayed to and from off-ship platforms. Additional technological advances can be used to overcome current range, security, reliability, and throughput barriers. This project demonstrates how a combination of essential technical capabilities can be used to establish a QR code communications system as a potentially useful approach for tactical operations. http://archive.org/details/digitalsemaphore1094534699 Outstanding Thesis Lieutenant Commander, United States Navy Approved for public release; distribution is unlimited.

The Wide-field Infrared Survey Explorer (WISE) observed 52 Centaurs and Scattered Disk Objects in the thermal infrared, including the 15 discoveries that were new. We present analyses of these observations to estimate sizes and mean optical albedos. We find mean albedos of 0.08 +/- 0.04 for the entire data set. Thermal fits yield average beaming parameters of 0.9 +/- 0.2 that are similar for both SDO and Centaur sub-classes. Biased cumulative size distributions yield size-frequency distribution power law indices ~ -1.7 +/- 0.3. The data also reveal a relation between albedo and color at the 3-sigma level. No significant relation between diameter and albedos is found., Comment: Accepted by ApJ, not proofed. 4 Tables, 8 Figures

We show that the mean field equations for the SIR epidemic can be exactly solved for a network with arbitrary degree distribution. Our exact solution consists of reducing the dynamics to a lone first order differential equation, which has a solution in terms of an integral over functions dependent on the degree distribution of the network, and reconstructing all mean field functions of interest from this integral. Irreversibility of the SIR epidemic is crucial for the solution. We also find exact solutions to the sexually transmitted disease SI epidemic on bipartite graphs, to a simplified rumor spreading model, and to a new model for recommendation spreading, via similar techniques. Numerical simulations of these processes on scale free networks demonstrate the qualitative validity of mean field theory in most regimes., Comment: 20 pages, 8 figures

Evidence gathered three decades ago showed persistently elevated total and new primary production over the continental shelf of the Southern California Bight. This dissertation examines the mechanisms that drive the flux of nitrate necessary to support the phytoplankton productivity over the shelf. Using results gathered from an intensive field experiment, I show that strong, persistent cross-shelf gradients in phytoplankton standing stock, primary productivity and community composition result from nitrate flux due to internal waves of tidal and higher frequency. I report the first estimates of the horizontal flux of nitrate due to the internal tide, and demonstrate that it is quantitatively similar to the nitrate demand of the inner shelf phytoplankton population. The local winds, contrary to expectations based on previous research, support a biologically- relevant tilt of the nitracline. Variability in the magnitude of the cross-shore shoaling of the nitracline in turn impacts the magnitude of the internal tide mediated nitrate flux. Remotely-forced large scale variability in the offshore depth of the nitracline controls the continental shelf ǹitrate climate.' During episodes of anomalously warm ocean temperatures, a correspondingly deep nitracline can shut off nitrate supply to the continental shelf, resulting in low phytoplankton biomass. During more typical conditions, the phytoplankton community over the inner shelf is dominated by taxa capable of rapid nitrate assimilation, while offshore waters have a proportionally greater amount of oligotrophic species. The results of this dissertation indicate that relatively small changes in the offshore depth of the nitracline could account for the long-term increase primary productivity and phytoplankton biomass noted by recent studies, even in the absence of increased local wind-forced upwelling. Finally, I examine the baroclinic semidiurnal variability in currents and water column structure in the shallow water of the inner shelf. The results of this analysis demonstrate that the behavior of the semidiurnal variability is not consistent with a propagating or standing low mode internal wave. Analyses of linearized momentum balances suggest that the semidiurnal variability may result from the interaction of barotropic tidal flow, friction in the bottom boundary layer, and rotation

The Arabian Sea circulation is forced by strong monsoonal winds and is characterized by vigorous seasonally reversing currents, extreme differences in sea surface salinity, localized substantial upwelling, and widespread submesoscale thermohaline structures. Its complicated sea surface temperature patterns are important for the onset and evolution of the Asian monsoon. This article describes a program that aims to elucidate the role of upper-ocean processes and atmospheric feedbacks in setting the sea surface temperature properties of the region. The wide range of spatial and temporal scales and the difficulty of accessing much of the region with ships due to piracy motivated a novel approach based on state-of-the-art autonomous ocean sensors and platforms. The extensive data set that is being collected, combined with numerical models and remote sensing data, confirms the role of planetary waves in the reversal of the Somali Current system. These data also document the fast response of the upper equatorial ocean to monsoon winds through changes in temperature and salinity and the connectivity of the surface currents across the northern Indian Ocean. New observations of thermohaline interleaving structures and mixing in setting the surface temperature properties of the northern Arabian Sea are also discussed.

Immune mediated adverse drug reactions (IM-ADRs) remain a significant source of patient morbidity that have more recently been shown to be associated with specific class I and/or II human leukocyte antigen (HLA) alleles. Abacavir- induced hypersensitivity syndrome is a CD8+ T cell dependent IM-ADR that is exclusively mediated by HLA-B*57:01. We and others have previously shown that abacavir can occupy the floor of the peptide binding groove of HLA-B*57:01 molecules, increasing the affinity of certain self peptides resulting in an altered peptide-binding repertoire. Here, we have identified another drug, acyclovir, which appears to act in a similar fashion. As with abacavir, acyclovir showed a dose dependent increase in affinity for peptides with valine and isoleucine at their C-terminus. In agreement with the binding studies, HLA-B*57:01 peptide-elution studies performed in the presence of acyclovir revealed an increased number of endogenously bound peptides with a C-terminal isoleucine. Accordingly, we have hypothesized that acyclovir acts by the same mechanism as abacavir, although our data also suggest the overall effect is much smaller: the largest changes of peptide affinity for acyclovir were 2-5 fold, whereas for abacavir this effect was as much as 1000-fold. Unlike abacavir, acyclovir is not known to cause IM-ADRs. We conclude that the modest effect of acyclovir on HLA binding affinity in contrast to the large effect of abacavir is insufficient to trigger a hypersensitivity syndrome. We further support this by functional in vitro studies where acyclovir, unlike abacavir, was unable to produce an increase in IFN-γ upon expansion of HLA-B*57:01+ PBMCs from healthy donors. Using abacavir and acyclovir as examples we therefore propose an in vitro pre-clinical screening strategy, whereby thresholds can be applied to MHC-peptide binding assays to determine the likelihood that a drug could cause a clinically relevant IM-ADR.