Linear response theory of Josephson junction arrays in a microwave cavity

Recent experiments on Josephson junction arrays (JJAs) in microwave cavities have opened up a new avenue for investigating the properties of these devices while minimising the amount of external noise coming from the measurement apparatus itself. These experiments have already shown promise for probing many-body quantum effects in JJAs. In this work, we develop a general theoretical description of such experiments by deriving a quantum phase model for planar JJAs containing quantized vortices. The dynamical susceptibility of this model is calculated for some simple circuits, and signatures of the injection of additional vortices are identified. The effects of decoherence are considered via a Lindblad master equation.Comment: 15 pages, 10 figure

B\"uttiker probes and the Recursive Green's Function; an efficient approach to include dissipation in general configurations

An efficient and compact approach to the inclusion of dissipative effects in Non-Equilibrium Green's Function (NEGF) simulations of electronic systems is introduced. The algorithm is based on two well known methods in the literature, firstly that of the so-called Recursive Green's Function (RGF) and secondly that of B\"uttiker probes. Numerical methods for exact evaluation of the Jacobian are presented by a direct extension to RGF which can be modularly included in any codebase that uses it presently. Then using both physical observations and numerical methods, the computation time of the B\"uttiker probe Jacobian is improved significantly. An improvement to existing phonon models within B\"uttiker probes is then demonstrated in the simulation of fully atomistic graphene nanoribbon based field effect transistors in n-i-n and p-i-n operation.Comment: 13 pages, 7 figure

Catalysts on Demand: Selective Oxidations by Laboratory-Evolved Cytochrome P450 BM3

Efficient catalysts for selective oxidation of C-H bonds using atmospheric oxygen are highly desirable to decrease the economic and environmental costs associated with conventional oxidation processes. We have used methods of directed evolution to generate variants of bacterial cytochrome P450 BM3 that catalyze hydroxylation and epoxidation of a wide range of nonnative substrates. This fatty acid hydroxylase was converted to a propane monooxygenase (PMO) capable of hydroxylating propane at rates comparable to that of BM3 on its natural substrates. Variants along the PMO evolutionary lineage showed broadened substrate scope; these became the starting points for evolution of a wide array of enzymes that can hydroxylate and derivatize organic scaffolds. This work demonstrates how a single member of enzyme family is readily converted by evolution into a whole family of catalysts for organic synthesis

Correlated transport through junction arrays in the small Josephson energy limit: incoherent Cooper-pairs and hot electrons

We study correlated transport in a Josephson junction array for small Josephson energies. In this regime transport is dominated by Cooper-pair hopping, although we observe that quasiparticles can not be neglected. We assume that the energy dissipated by a Cooper-pair is absorbed by the intrinsic impedance of the array. This allows us to formulate explicit Cooper-pair hopping rates without adding any parameters to the system. We show that the current is correlated and crucially, these correlations rely fundamentally on the interplay between the Cooper-pairs and equilibrium quasiparticles.Comment: 11 pages, 9 figures - Published Versio

Depinning of disordered bosonic chains

We consider one-dimensional bosonic chains with a repulsive boson-boson interaction that decays exponentially on large length-scales. This model describes transport of Cooper-pairs in a Josepshon junction array, or transport of magnetic flux quanta in quantum-phase-slip ladders, i.e. arrays of superconducting wires in a ladder-configuration that allow for the coherent tunnelling of flux quanta. In the low-frequency, long wave-length regime these chains can be mapped to an effective model of a one-dimensional elastic field in a disordered potential. The onset of transport in these systems, when biased by external voltage, is described by the standard depinning theory of elastic media in disordered pinning potentials. We numerically study the regimes that are of relevance for quantum-phase-slip ladders. These are (i) very short chains and (ii) the regime of weak disorder. For chains shorter than the typical pinning length, i.e., the Larkin length, the chains reach a saturation regime where the depinning voltage does not depend on the decay length of the repulsive interaction. In the regime of weak disorder we find an emergent correlation length-scale that depends on the disorder strength. For arrays shorter than this length the onset of transport is similar to the clean arrays, i.e., is due to the penetration of solitons into the array. We discuss the depinning scenarios for longer arrays in this regime.Comment: 11 pages, 6 figure

Black holes, compact objects and solar system tests in non-relativistic general covariant theory of gravity

We study spherically symmetric static spacetimes generally filled with an anisotropic fluid in the nonrelativistic general covariant theory of gravity. In particular, we find that the vacuum solutions are not unique, and can be expressed in terms of the $U(1)$ gauge field $A$. When solar system tests are considered, severe constraints on $A$ are obtained, which seemingly pick up the Schwarzschild solution uniquely. In contrast to other versions of the Horava-Lifshitz theory, non-singular static stars made of a perfect fluid without heat flow can be constructed, due to the coupling of the fluid with the gauge field. These include the solutions with a constant pressure. We also study the general junction conditions across the surface of a star. In general, the conditions allow the existence of a thin matter shell on the surface. When applying these conditions to the perfect fluid solutions with the vacuum ones as describing their external spacetimes, we find explicitly the matching conditions in terms of the parameters appearing in the solutions. Such matching is possible even without the presence of a thin matter shell.Comment: Singular behavior of the fluid at the center is clarified. New references are added. Version to appear in JCA

Towards understanding two-level-systems in amorphous solids -- Insights from quantum circuits

Amorphous solids show surprisingly universal behaviour at low temperatures. The prevailing wisdom is that this can be explained by the existence of two-state defects within the material. The so-called standard tunneling model has become the established framework to explain these results, yet it still leaves the central question essentially unanswered -- what are these two-level defects? This question has recently taken on a new urgency with the rise of superconducting circuits in quantum computing, circuit quantum electrodynamics, magnetometry, electrometry and metrology. Superconducting circuits made from aluminium or niobium are fundamentally limited by losses due to two-level defects within the amorphous oxide layers encasing them. On the other hand, these circuits also provide a novel and effective method for studying the very defects which limit their operation. We can now go beyond ensemble measurements and probe individual defects -- observing the quantum nature of their dynamics and studying their formation, their behaviour as a function of applied field, strain, temperature and other properties. This article reviews the plethora of recent experimental results in this area and discusses the various theoretical models which have been used to describe the observations. In doing so, it summarises the current approaches to solving this fundamentally important problem in solid-state physics.Comment: 34 pages, 7 figures, 1 tabl

Enzymatic functionalization of carbon-hydrogen bonds

The development of new catalytic methods to functionalize carbon–hydrogen (C–H) bonds continues to progress at a rapid pace due to the significant economic and environmental benefits of these transformations over traditional synthetic methods. In nature, enzymes catalyze regio- and stereoselective C–H bond functionalization using transformations ranging from hydroxylation to hydroalkylation under ambient reaction conditions. The efficiency of these enzymes relative to analogous chemical processes has led to their increased use as biocatalysts in preparative and industrial applications. Furthermore, unlike small molecule catalysts, enzymes can be systematically optimized via directed evolution for a particular application and can be expressed in vivo to augment the biosynthetic capability of living organisms. While a variety of technical challenges must still be overcome for practical application of many enzymes for C–H bond functionalization, continued research on natural enzymes and on novel artificial metalloenzymes will lead to improved synthetic processes for efficient synthesis of complex molecules. In this critical review, we discuss the most prevalent mechanistic strategies used by enzymes to functionalize non-acidic C–H bonds, the application and evolution of these enzymes for chemical synthesis, and a number of potential biosynthetic capabilities uniquely enabled by these powerful catalysts (110 references)