Junction Chains Research Articles

SQANTI-reads: a tool for the quality assessment of long read data in multi-sample lrRNA-seq experiments.

SQANTI-reads leverages SQANTI3, a tool for the analysis of the quality of transcript models, to develop a read-level quality control framework for replicated long-read RNA-seq experiments. The number and distribution of reads, as well as the number and distribution of unique junction chains (transcript splicing patterns), in SQANTI3 structural categories are informative of raw data quality. Multi-sample visualizations of QC metrics are presented by experimental design factors to identify outliers. We introduce new metrics for 1) the identification of potentially under-annotated genes and putative novel transcripts and for 2) quantifying variation in junction donors and acceptors. We applied SQANTI-reads to two different datasets, a Drosophila developmental experiment and a multi-platform dataset from the LRGASP project and demonstrate that the tool effectively reveals the impact of read coverage on data quality, and readily identifies strong and weak splicing sites. SQANTI-reads is open source and available for download at GitHub.

Nonequilibrium Transport in a Superfluid Josephson Junction Chain: Is There Negative Differential Conductivity?

We consider the far-from-equilibrium quantum transport dynamics in a 1D Josephson junction chain of multimode Bose-Einstein condensates. We develop a theoretical model to examine the experiment of Labouvie etal. [Phys. Rev. Lett. 115, 050601 (2015)PRLTAO0031-900710.1103/PhysRevLett.115.050601], wherein the phenomenon of negative differential conductivity (NDC) was reported in the refilling dynamics of an initially depleted site within the chain. We demonstrate that a unitary c-field description can quantitatively reproduce the experimental results over the full range of tunnel couplings, and requires no fitted parameters. With a view toward atomtronic implementations, we further demonstrate that the filling is strongly dependent on spatial phase variations stemming from quantum fluctuations. Our findings suggest that the interpretation of the device in terms of NDC is invalid outside of the weak coupling regime. Within this restricted regime, the device exhibits a hybrid behavior of NDC and the ac Josephson effect. A simplified circuit model of the device will require an approach tailored to atomtronics that incorporates quantum fluctuations.

Magnetic Eigenmodes in Chains of Coupled φ0-Josephson Junctions with Ferromagnetic Weak Links

A coupled chain of superconductor/ferromagnet/superconductor (S/F/S) with anomalous ground phase shift \\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$${{\\varphi }_{0}}$$\\end{document} represents a system realizing long-range interaction between magnetic moments of the weak links. The interaction is of magnetoelectric origin and is mediated by the condensate phase of superconductors. The system is a paradigmic platform for investigation of collective magnetic states governed by the superconducting phase. Here we study the magnetic eigenmodes of such a system and demonstrate that the eigenfrequencies are determined by the magnetic configuration of the whole system and are controlled by the superconducting phase. Depending on the orientation of the magnetic easy axis the eigenmodes can be very different ranging from individual oscillations of different magnets to highly-cooperative behavior.

Bistability and nonequilibrium condensation in a driven-dissipative Josephson array: A c-field model

Developing theoretical models for nonequilibrium quantum systems poses significant challenges. Here we develop and study a multimode model of a driven-dissipative Josephson junction chain of atomic Bose-Einstein condensates, as realised in the experiment of Labouvie et al. [Phys. Rev. Lett. 116, 235302 (2016)]. The model is based on c-field theory, a beyond-mean-field approach to Bose-Einstein condensates that incorporates fluctuations due to finite temperature and dissipation. We find the c-field model is capable of capturing all key features of the nonequilibrium phase diagram, including bistability and a critical slowing down in the lower branch of the bistable region. Our model is closely related to the so-called Lugiato-Lefever equation, and thus establishes new connections between nonequilibrium dynamics of ultracold atoms with nonlinear optics, exciton-polariton superfluids, and driven damped sine-Gordon systems.

Noise and generation effects in parallel Josephson junction chains

We consider mutual effects of soliton dynamics and noise in a chain of Josephson junctions in the framework of the Frenkel-Kontorova model. The investigations are performed by the analysis of experimentally relevant quantities such as oscillation power and spectral linewidth, which both can be derived from the power spectral density of the system as, respectively, its integral and its width. Taking into account both ohmic and surface losses together with bias inhomogeneity, and considering dense soliton chain under the effect of external magnetic field, it is demonstrated that increase of the system discreteness (decrease of coupling between neighboring elements) leads to the oscillation power reduction and spectral linewidth increase, which signals about increase of the total noise in the system. Drastic increase of the linewidth is observed when the distance between elements becomes comparable with the soliton size, which is explained by an increase of stochasticity due to reflections of solitons from the system edges and noise.

High On/Off Ratio Spintronic Multi‐Level Memory Unit for Deep Neural Network (Adv. Sci. 13/2022)

Spintronic Multi-Level Memory Unit In article number 2103357 by Kun Zhang, Yue Zhang, and co-workers, a spintronic multi-level memory unit (MLMU) with high on/off ratio is constructed by integrating a magnetic tunnel junction chain and a diode in parallel. This MLMU can enable high-accuracy artificial intelligence applications, such as a deep neural network accelerator for image classification. Just as described in the cover design, the MLMUs are regarded as building blocks to assemble the artificial-intelligence brain.

Noise and Generation Effects in Parallel Josephson Junction Chains

Noise and Generation Effects in Parallel Josephson Junction Chains

Fragile many-body ergodicity from action diffusion.

Weakly nonintegrable many-body systems can restore ergodicity in distinctive ways depending on the range of the interaction network in action space. Action resonances seed chaotic dynamics into the networks. Long-range networks provide well connected resonances with ergodization controlled by the individual resonance chaos time scales. Short-range networks instead yield a dramatic slowing down of ergodization in action space, and lead to rare resonance diffusion. We use Josephson junction chains as a paradigmatic study case. We exploit finite time average distributions to characterize the thermalizing dynamics of actions. We identify an action resonance diffusion regime responsible for the slowing down. We extract the diffusion coefficient of that slow process and measure its dependence on the proximity to the integrable limit. Independent measures of correlation functions confirm our findings. The observed fragile diffusion is relying on weakly chaotic dynamics in spatially isolated action resonances. It can be suppressed, and ergodization delayed, by adding weak action noise, as a proof of concept.

Complexes of Parallel Grain Boundaries in YBa2Cu3O7 Film for Josephson Junction Chains and Arrays

Substrates consisting of five parallel planar grain boundaries (GBs), oriented perpendicular to the surface and spaced by several micrometers, have been grown by solid-phase bonding of fianite crystals in order to obtain large complexes of closely spaced bicrystal Josephson junctions based on high-temperature superconductor (HTSC) films. The substrates had a crystallographic orientation (100) and dimensions of 1.0 × 10.0 × 10.0 mm3. All GBs were of symmetrical type, and their lattices were rotated by 12° in opposite directions around the axis perpendicular to the surface. The distance between GBs in a packet complex was 15 µm, and this value was maintained with an error of no more than 1 µm along their entire length of 10 mm. The deviation of the shape of all five GBs from an ideal geometric plane was within 1 µm along their entire length. Films of HTSC YBa2Cu3O7 with inheritance of GBs were grown on these substrates. Structures of two types were formed on the films using lithography. It is shown that the use of these fianite substrates in HTSC-based devices of cryogenic electronics increases significantly the density of bicrystal Josephson junctions; reduces several times the total length of superconducting lines connecting these junctions; and, correspondingly, decreases significantly the inductive resistance of these circuits and improves their electrical characteristics in comparison with the structures having similar functions but based on one or two parallel GBs.

Superconductor-insulator transition in Josephson junction chains by quantum Monte Carlo calculations

We study the zero-temperature phase diagram of a dissipationless and disorder-free Josephson junction chain. Namely, we determine the critical Josephson energy below which the chain becomes insulating, as a function of the ratio of two capacitances: the capacitance of each Josephson junction and the capacitance between each superconducting island and the ground. We develop an imaginary-time path integral Quantum Monte-Carlo algorithm in the charge representation, which enables us to efficiently handle the electrostatic part of the chain Hamiltonian. We find that a large part of the phase diagram is determined by anharmonic corrections which are not captured by the standard Kosterlitz-Thouless renormalization group description of the transition.

Спектральный отклик матриц полуволновых и электрически малых антенн с СИНИС-болометрами

Two types arrays of ring half – wave and electrically small antennas (the typical sizes of the elements correspond to 1/10 of the wavelength) of SubTHz band with integrated Superconductor – Insulator – Normal metal – Insulator-Superconductor (SINIS) bolometers have been developed, fabricated and investigated. It is necessary to make numerical modeling of the full structure and to use additional reference channels in experimental studies for improving the accuracy of the spectral response estimations of receiving arrays. In this work, three reference channels were used for normalization: a pyroelectric receiver outside the cryostat and two cold channels – a RuO2 bolometer and chain of NIS junctions as a thermometer.

Theory of coherent phase modes in insulating Josephson junction chains

Recent microwave reflection measurements of Josephson junction chains have suggested the presence of nearly coherent collective charge oscillations deep in the insulating phase. Here we develop a qualitative understanding of such coherent charge modes by studying the local dynamical polarizability of the insulating phase of a finite length sine-Gordon model. By considering parameters near the noninteracting fermion limit where the charge operator dominantly couples to soliton-antisoliton pairs of the sine-Gordon model, we find that the local dynamical polarizability shows an array of sharp peaks in frequency representing coherent phase oscillations on top of an incoherent background. The strength of the coherent peaks relative to the incoherent background increases as a power law in frequency as well as exponentially as the Luttinger parameter approaches a critical value. The dynamical polarizability also clearly shows the insulating gap. We then compare the results in the high frequency limit to a perturbative estimate of phase-slip-induced decay of plasmons in the Josephson junction chain.

Towards quantum phase slip based standard of electric current

An accurate standard of electric current is a long-standing challenge of modern metrology. It has been predicted that a superconducting nanowire in the regime of quantum fluctuations can be considered as the dynamic equivalent of a chain of conventional Josephson junctions. In full analogy with the quantum standard of electric voltage based on the Josephson effect, the quantum phase slip phenomenon in ultrathin superconducting nanowires could be used for building the quantum standard of electric current. This work presents advances toward this ultimate goal.

Microwave Spectroscopy of a Weakly Pinned Charge Density Wave in a Superinductor.

A chain of small Josephson junctions (a.k.a. superinductor) emerged recently as a high-inductance, low-loss element of superconducting quantum devices. We notice that the intrinsic parameters of a typical superinductor in fact place it into the Bose glass universality class for which the propagation of waves in a sufficiently long chain is hindered by pinning. Its weakness provides for a broad crossover from the spectrum of well-resolved plasmon standing waves at high frequencies to the low-frequency excitation spectrum of a pinned charge density wave. We relate the scattering amplitude of microwave photons reflected off a superinductor to the dynamics of a Bose glass. The dynamics at long and short scales compared to the Larkin pinning length determines the low- and high-frequency asymptotes of the reflection amplitude.

A non-Gaussian model for the chemo-mechanical coupling behavior of largely deformed hydrogels

ABSTRACTA non-Gaussian model is developed to precisely describe the chemo-mechanical coupled large deformation of responsive hydrogels. In this model, the free-energy density is composed of two parts, including the elastic energy due to stretching of cross-linked polymer networks described by Gent hyperelastic model, and the mixture energy of polymer network and described by Flory–Huggins theory. The effects of junction functionality and chain entanglements are investigated by analyzing free swelling of a cubic hydrogel and constrained swelling of a blanket layer of the gel. The present model is found to exhibit obvious hardening characteristic during large deformation of the hydrogel, and the considerations of functionality of junctions and chain entanglements are essential in the coupled chemo-mechanical deformation analysis of hydrogels.

Dynamical Glass and Ergodization Times in Classical Josephson Junction Chains.

Models of classical Josephson junction chains turn integrable in the limit of large energy densities or small Josephson energies. Close to these limits the Josephson coupling between the superconducting grains induces a short-range nonintegrable network. We compute distributions of finite-time averages of grain charges and extract the ergodization time T_{E} which controls their convergence to ergodic δ distributions. We relate T_{E} to the statistics of fluctuation times of the charges, which are dominated by fat tails. T_{E} is growing anomalously fast upon approaching the integrable limit, as compared to the Lyapunov time T_{Λ}-the inverse of the largest Lyapunov exponent-reaching astonishing ratios T_{E}/T_{Λ}≥10^{8}. The microscopic reason for the observed dynamical glass is rooted in a growing number of grains evolving over long times in a regular almost integrable fashion due to the low probability of resonant interactions with the nearest neighbors. We conjecture that the observed dynamical glass is a generic property of Josephson junction networks irrespective of their space dimensionality.

Decay of plasmonic waves in Josephson junction chains

We study the damping of plasma waves in linear Josephson junction chains as well as in two capacitively coupled chains. In the parameter regime where the ground capacitance can be neglected, the theory of the antisymmetric mode in the double chain can be mapped onto the theory of a single chain. We consider two sources of relaxation: the scattering from quantum phase slips (QPS) and the interaction among plasmons related to the nonlinearity of the Josephson potential. The contribution to the relaxation rate $1/\tau$ from the nonlinearity scales with the fourth power of frequency $\omega$, while the phase-slip contribution behaves as a power law with a non-universal exponent. In the parameter regime where the charging energy related to the junction capacitance is much smaller than the Josephson energy, the amplitude of QPS is strongly suppressed. This makes the relaxation mechanism related to QPS efficient only at very low frequencies. As a result, for chains that are in the infrared limit on the insulating side of the superconductor-insulator transition, the quality factor $\omega\tau$ shows a strongly non-monotonic dependence on frequency, as was observed in a recent experiment.

Chain of magnetic tunnel junctions as a spintronic memristor

In the context of neuromorphic computation, spintronic memristors are investigated for their use as synaptic weights. In this paper, we propose and experimentally demonstrate a resistive synaptic device based on ten magnetic tunnel junctions (MTJs) connected in a serial configuration. Our device exhibits multiple resistance levels that support its use as a synaptic element. It allows for two operating knobs: external magnetic field and voltage pulses (Spin-Transfer Torque). Moreover, it can be operated in different ways. When varying continuously the amplitude of the voltage pulse and/or the magnetic field, eleven resistance states can be reached. In contrast, if the initial state of the chain is reset between every step, a very large number of levels are reached. Ideally, a total of 2N resistance levels could be accessible. This coincides well with the desired analog-like behavior in ideal memristors. Since this device consists of a scalable number of N MTJs, and MTJ technology is continuously optimized and improved, the proposed memristor shows promise as a scalable synapse solution for neuromorphic hardware implementations.

Kerr nonlinearity in a superconducting Josephson metamaterial

We present a detailed experimental and theoretical analysis of the dispersion and non-linear Kerr frequency shifts of plasma modes in a one-dimensional Josephson junction chain containing 500 SQUIDs in the regime of weak nonlinearity. The measured low-power dispersion curve agrees perfectly with the theoretical model if we take into account the Kerr renormalisation of the bare frequencies and the long-range nature of the island charge screening by a remote ground plane. We measured the self- and cross-Kerr shifts for the frequencies of the eight lowest modes in the chain. We compare the measured Kerr coefficients with theory and find good agreement.

Effect of disorder on coherent quantum phase slips in Josephson junction chains

We study coherent quantum phase-slips in a Josephson junction chain, including two types of quenched disorder: random spatial modulation of the junction areas and random induced background charges. Usually, the quantum phase-slip amplitude is sensitive to the normal mode structure of superconducting phase oscillations in the ring (Mooij-Sch\"on modes, which are all localized by the area disorder). However, we show that the modes' contribution to the disorder-induced phase-slip action fluctuations is small, and the fluctuations of the action on different junctions are mainly determined by the local junction parameters. We study the statistics of the total QPS amplitude on the chain and show that it can be non-Gaussian for not sufficiently long chains.