Direct Observation of Vortex Dynamics in Superconducting Films with Regular Arrays of Defects

Transcriptional and methylation outcomes of didehydro-cortistatin A use in HIV-1-infected CD4+ T cells

Ongoing viral transcription from the reservoir of HIV-1 infected long-lived memory CD4+ T cells presents a barrier to cure and associates with poorer health outcomes for people living with HIV, including chronic immune activation and inflammation. We previously reported that didehydro-cortistatin A (dCA), an HIV-1 Tat inhibitor, blocks HIV-1 transcription. Here, we examine the impact of dCA on host immune CD4+ T-cell transcriptional and epigenetic states. We performed a comprehensive analysis of genome-wide transcriptomic and DNA methylation profiles upon long-term dCA treatment of primary human memory CD4+ T cells. dCA prompted specific transcriptional and DNA methylation changes in cell cycle, histone, interferon-response, and T-cell lineage transcription factor genes, through inhibition of both HIV-1 and Mediator kinases. These alterations establish a tolerogenic Treg/Th2 phenotype, reducing viral gene expression and mitigating inflammation in primary CD4+ T cells during HIV-1 infection. In addition, dCA suppresses the expression of lineage-defining transcription factors for Th17 and Th1 cells, critical HIV-1 targets, and reservoirs. dCA's benefits thus extend beyond viral transcription inhibition, modulating the immune cell landscape to limit HIV-1 acquisition and inflammatory environment linked to HIV infection.

Anti-matching effect in a two dimensional driven vortex lattice in the presence of periodic pinning

The dynamics of a driven superconducting vortex lattice in a two-dimensional (2D) periodic potential of square symmetry is studied using Brownian dynamics simulations. The range and strength of the vortex-substrate interaction are taken to be of the same order as that of the vortex-vortex interaction. The matching effect in a driven vortex lattice in the presence of a periodic array of pinning centers refers to the enhanced resistance to the vortex lattice motion when the ratio of the number of vortices to the number of pinning centers (called the filling fraction) takes simple fractional values. In particular, one expects a pronounced matching effect when the filling fraction is one. Contrary to this expectation, a drop in the vortex lattice mobility is observed as the filling fraction is increased from value one. This anti-matching effect can be understood in terms of the structural change in the vortex lattice as the filling fraction is varied. The dip observed in vortex mobility as a function of temperature when the filling fraction equals one (Joseph T 2020PhysicaA556124737), is studied for other values of filling above and below one. The behavior is found to persist for other fillings as well and is associated with the melting of the vortex lattice. The temperature at which the lattice melts is found to increase with drive and explains the shift in the temperature at which mobility is a minimum, locally.

Peak effect and dynamics of stripe- and pattern-forming systems on a periodic one-dimensional substrate

We examine the ordering, pinning, and dynamics of two-dimensional pattern-forming systems interacting with a periodic one-dimensional substrate. In the absence of the substrate, particles with competing long-range repulsion and short-range attraction form anisotropic crystal, stripe, and bubble states. When the system is tuned across the stripe transition in the presence of a substrate, we find that there is a peak effect in the critical depinning force when the stripes align and become commensurate with the substrate. Under an applied drive, the anisotropic crystal and stripe states can exhibit soliton depinning and plastic flow. When the stripes depin plastically, they dynamically reorder into a moving stripe state that is perpendicular to the substrate trough direction. We also find that when the substrate spacing is smaller than the widths of the bubbles or stripes, the system forms pinned stripe states that are perpendicular to the substrate trough direction. The system exhibits multiple reentrant pinning effects as a function of increasing attraction, with the anisotropic crystal and large bubble states experiencing weak pinning but the stripe and smaller bubble states showing stronger pinning. We map out the different dynamic phases as a function of filling, the strength of the attractive interaction term, the substrate strength, and the drive, and demonstrate that the different phases produce identifiable features in the transport curves and particle orderings.

Noise reduction of electron holography observations for a thin-foiled Nd-Fe-B specimen using the wavelet hidden Markov model

In this study, we investigate the effectiveness of noise reduction in electron holography, based on the wavelet hidden Markov model (WHMM), which allows the reasonable separation of weak signals from noise. Electron holography observations from a Nd2Fe14B thin foil showed that the noise reduction method suppressed artificial phase discontinuities generated by phase retrieval. From the peak signal-to-noise ratio, it was seen that the impact of denoising was significant for observations with a narrow spacing of interference fringes, which is a key parameter for the spatial resolution of electron holography. These results provide essential information for improving the precision of electron holography studies.

Vortex Lattices in Active Nematics with Periodic Obstacle Arrays

We numerically model a two-dimensional active nematic confined by a periodic array of fixed obstacles. Even in the passive nematic, the appearance of topological defects is unavoidable due to planar anchoring by the obstacle surfaces. We show that a vortex lattice state emerges as activity is increased, and that this lattice may be tuned from "ferromagnetic" to "antiferromagnetic" by varying the gap size between obstacles. We map the rich variety of states exhibited by the system as a function of distance between obstacles and activity, including a pinned defect state, motile defects, the vortex lattice, and active turbulence. We demonstrate that the flows in the active turbulent phase can be tuned by the presence of obstacles, and explore the effects of a frustrated lattice geometry on the vortex lattice phase.

A Superconducting Micro-Magnetometer for Quantum Vortex in Superconducting Nanoflakes

Superconducting quantum interferometer device (SQUID) plays a key role in understanding electromagnetic properties and emergent phenomena in quantum materials. The technological appeal of SQUID is that its detection accuracy for the electromagnetic signal can precisely reach the quantum level of a single magnetic flux. However, conventional SQUID techniques normally can only be applied to a bulky sample and do not have the capability to probe the magnetic properties of micro-scale samples with small magnetic signals. Herein, it is demonstrated that, based on a specially designed superconducting nano-hole array, the contactless detection of magnetic properties and quantized vortices in micro-sized superconducting nanoflakes is realized. An anomalous hysteresis loop and a suppression of Little-Parks oscillation are observed in the detected magnetoresistance signal, which originates from the disordered distribution of the pinned vortices in Bi₂ Sr₂ CaCu₂ O_8+δ . Therefore, the density of pinning centers of the quantized vortices on such micro-sized superconducting samples can be quantitatively evaluated, which is technically inaccessible for conventional SQUID detection. The superconducting micro-magnetometer provides a new approach to exploring mesoscopic electromagnetic phenomena of quantum materials.

HIV-1 infection of genetically engineered iPSC-derived central nervous system-engrafted microglia in a humanized mouse model

The central nervous system (CNS) is a major human immunodeficiency virus type 1 reservoir. Microglia are the primary target cell of HIV-1 infection in the CNS. Current models have not allowed the precise molecular pathways of acute and chronic CNS microglial infection to be tested with in vivo genetic methods. Here, we describe a novel humanized mouse model utilizing human-induced pluripotent stem cell-derived microglia to xenograft into murine hosts. These mice are additionally engrafted with human peripheral blood mononuclear cells that served as a medium to establish a peripheral infection that then spread to the CNS microglia xenograft, modeling a trans-blood-brain barrier route of acute CNS HIV-1 infection with human target cells. The approach is compatible with iPSC genetic engineering, including inserting targeted transgenic reporter cassettes to track the xenografted human cells, enabling the testing of novel treatment and viral tracking strategies in a comparatively simple and cost-effective way vivo model for neuroHIV.

Superlubric-pinned transition of a two-dimensional solid dusty plasma under a periodic triangular substrate

The superlubric-pinned transition in the depinning dynamics of a two-dimensional (2D) solid dusty plasma modulated by 2D triangular periodic substrates is investigated using Langevin dynamical simulations. When the lattice structure of the 2D solid dusty plasma perfectly matches the triangular substrate, two distinctive pinned and moving ordered states are observed as the external uniform driving force gradually increases from zero. When there is a mismatch between the lattice structure and the triangular substrate, however, on shallow substrates, it is discovered that all of the particles can slide freely on the substrate even when the applied driving force is tiny. This is a typical example of superlubricity, which is caused by the competition between the substrate-particle and particle-particle interactions. If the substrate depth increases further, as the driving force increases from zero, there are three dynamical states consisting of the pinned state, the disordered plastic flow state, and the moving ordered state. In an underdense system, where there are fewer particles than potential well minima, it is found that the occurrence of the three different dynamical states is controlled by the depth of the substrate, which is quantitatively characterized using the average mobility.

Directional locking in a two-dimensional Yukawa solid modulated by a two-dimensional periodic substrate

Directional depinning dynamics of a two-dimensional (2D) dusty plasma solid modulated by a 2D square periodic substrate are investigated using Langevin dynamical simulations. We observe prominent directional locking effects when the direction of the external driving force is varied relative to the underlying square substrate. These locking steps appear when the direction of the driving force is close to the symmetry direction of the substrate, corresponding to the different dynamical flow patterns and the structures. In the conditions between the adjacent locking steps, moving ordered states are observed. Although the discontinuous transitions often occur between the locking steps and the nonlocking portion, the continuous transitions are also found around the locking step associated with the disordered plastic flow close to its termini. Our results show that directional locking also occurs for underdamped systems, which could be tested experimentally in dusty plasmas modulated by 2D substrates.

Reversible to Irreversible Transitions for Cyclically Driven Particles on Periodic Obstacle Arrays

We examine the collective dynamics of disks moving through a square array of obstacles under cyclic square wave driving. Below a critical density we find that system organizes into a reversible state in which the disks return to the same positions at the end of every drive cycle. Above this density, the dynamics are irreversible and the disks do not return to the same positions after each cycle. The critical density depends strongly on the angle θ between the driving direction and a symmetry axis of the obstacle array, with the highest critical densities appearing at commensurate angles such as θ=0{degree sign} and θ=45{degree sign} and the lowest critical densities falling at θ=arctan(0.618), the inverse of the golden ratio, where the flow is the most frustrated. As the density increases, the number of cycles required to reach a reversible state grows as a power law with an exponent near ν=1.36, similar to what is found in periodically driven colloidal and superconducting vortex systems.

Phonon spectra of a two-dimensional solid dusty plasma modified by two-dimensional periodic substrates

Phonon spectra of a two-dimensional (2D) solid dusty plasma modulated by 2D square and triangular periodic substrates are investigated using Langevin dynamical simulations. The commensurability ratio, i.e., the ratio of the number of particles to the number of potential well minima, is set to 1 or 2. The resulting phonon spectra show that propagation of waves is always suppressed due to the confinement of particles by the applied 2D periodic substrates. For a commensurability ratio of 1, the spectra indicate that all particles mainly oscillate at one specific frequency, corresponding to the harmonic oscillation frequency of one single particle inside one potential well. At a commensurability ratio of 2, the substrate allows two particles to sit inside the bottom of each potential well, and the resulting longitudinal and transverse spectra exhibit four branches in total. We find that the two moderate branches come from the harmonic oscillations of one single particle and two combined particles in the potential well. The other two branches correspond to the relative motion of the two-body structure in each potential well in the radial and azimuthal directions. The difference in the spectra between the square and triangular substrates is attributed to the anisotropy of the substrates and the resulting alignment directions of the two-body structure in each potential well.

Superconducting Properties and Electron Scattering Mechanisms in a Nb Film with a Single Weak-Link Excavated by Focused Ion Beam

Granularity is one of the main features restricting the maximum current which a superconductor can carry without losses, persisting as an important research topic when applications are concerned. To directly observe its effects on a typical thin superconducting specimen, we have modeled the simplest possible granular system by fabricating a single artificial weak-link in the center of a high-quality Nb film using the focused ion beam technique. Then, its microstructural, magnetic, and electric properties in both normal and superconducting states were studied. AC susceptibility, DC magnetization, and magneto-transport measurements reveal well-known granularity signatures and how they negatively affect superconductivity. Moreover, we also investigate the normal state electron scattering mechanisms in the Boltzmann theory framework. The results clearly demonstrate the effect of the milling technique, giving rise to an additional quadratic-in-temperature contribution to the usual cubic-in-temperature sd band scattering for the Nb film. Finally, by analyzing samples with varying density of incorporated defects, the emergence of the additional contribution is correlated to a decrease in their critical temperature, in agreement with recent theoretical results.

Skyrmion-(Anti)Vortex Coupling in a Chiral Magnet-Superconductor Heterostructure

We report experimental coupling of chiral magnetism and superconductivity in [IrFeCoPt]/Nb heterostructures. The stray field of skyrmions with radius ≈50  nm is sufficient to nucleate antivortices in a 25 nm Nb film, with unique signatures in the magnetization, critical current, and flux dynamics, corroborated via simulations. We also detect a thermally tunable Rashba-Edelstein exchange coupling in the isolated skyrmion phase. This realization of a strongly interacting skyrmion-(anti)vortex system opens a path toward controllable topological hybrid materials, unattainable to date.

Active matter commensuration and frustration effects on periodic substrates

We show that self-driven particles coupled to a periodic obstacle array exhibit active matter commensuration effects that are absent in the Brownian limit. As the obstacle size is varied for sufficiently large activity, a series of commensuration effects appear in which the motility induced phase separation produces commensurate crystalline states, while for other obstacle sizes we find frustrated or amorphous states. The commensuration effects are associated with peaks in the amount of sixfold ordering and the maximum cluster size. When a drift force is added to the system, the mobility contains peaks and dips similar to those found in transport studies for commensuration effects in superconducting vortices and colloidal particles.

Continuous and discontinuous transitions in the depinning of two-dimensional dusty plasmas on a one-dimensional periodic substrate

Langevin dynamical simulations are performed to study the depinning dynamics of two-dimensional dusty plasmas on a one-dimensional periodic substrate. From the diagnostics of the sixfold coordinated particles P_{6} and the collective drift velocity V_{x}, three different states appear, which are the pinning, disordered plastic flow, and moving ordered states. It is found that the depth of the substrate is able to modulate the properties of the depinning phase transition, based on the results of P_{6} and V_{x}, as well as the observation of hysteresis of V_{x} while increasing and decreasing the driving force monotonically. When the depth of the substrate is shallow, there are two continuous phase transitions. When the potential well depth slightly increases, the phase transition from the pinned to the disordered plastic flow states is continuous; however, the phase transition from the disordered plastic flow to the moving ordered states is discontinuous. When the substrate is even deeper, the phase transition from the pinned to the disordered plastic flow states changes to discontinuous. When the depth of the substrate further increases, as the driving force increases, the pinned state changes to the moving ordered state directly, so that the disordered plastic flow state disappears completely.

Reconfigurable Pinwheel Artificial-Spin-Ice and Superconductor Hybrid Device

The ability to control the potential landscape in a medium of interacting particles could lead to intriguing collective behavior and innovative functionalities. Here, we utilize spatially reconfigurable magnetic potentials of a pinwheel artificial-spin-ice (ASI) structure to tailor the motion of superconducting vortices. The reconstituted chain structures of the magnetic charges in the pinwheel ASI and the strong interaction between magnetic charges and superconducting vortices allow significant modification of the transport properties of the underlying superconducting thin film, resulting in a reprogrammable resistance state that enables a reversible and switchable vortex Hall effect. Our results highlight an effective and simple method of using ASI as an in situ reconfigurable nanoscale energy landscape to design reprogrammable superconducting electronics, which could also be applied to the in situ control of properties and functionalities in other magnetic particle systems, such as magnetic skyrmions.

Non-Gaussian tail in the force distribution: a hallmark of correlated disorder in the host media of elastic objects

Inferring the nature of disorder in the media where elastic objects are nucleated is of crucial importance for many applications but remains a challenging basic-science problem. Here we propose a method to discern whether weak-point or strong-correlated disorder dominates based on characterizing the distribution of the interaction forces between objects mapped in large fields-of-view. We illustrate our proposal with the case-study system of vortex structures nucleated in type-II superconductors with different pinning landscapes. Interaction force distributions are computed from individual vortex positions imaged in thousands-vortices fields-of-view in a two-orders-of-magnitude-wide vortex-density range. Vortex structures nucleated in point-disordered media present Gaussian distributions of the interaction force components. In contrast, if the media have dilute and randomly-distributed correlated disorder, these distributions present non-Gaussian algebraically-decaying tails for large force magnitudes. We propose that detecting this deviation from the Gaussian behavior is a fingerprint of strong disorder, in our case originated from a dilute distribution of correlated pinning centers.

Commensurate states and pattern switching via liquid crystal skyrmions trapped in a square lattice

Using continuum based simulations we show that a rich variety of skyrmion liquid crystal states can be realized in the presence of a periodic obstacle array. As a function of the number of skyrmions per obstacle we find hexagonal, square, dimer, trimer and quadrimer ordering, where the n-mer structures are a realization of a molecular crystal state of skyrmions. As a function of external field and obstacle radius we show that there are transitions between the different crystalline states as well as mixed and disordered structures. We discuss how these states are related to commensurate effects seen in other systems, such as vortices in type-II superconductors and colloids interacting with two dimensional substrates.

Collective Directional Locking of Colloidal Monolayers on a Periodic Substrate

We investigate the directional locking effects that arise when a monolayer of paramagnetic colloidal particles is driven across a triangular lattice of magnetic bubbles. We use an external rotating magnetic field to generate a two-dimensional traveling wave ratchet forcing the transport of particles along a direction that intersects two crystallographic axes of the lattice. We find that, while single particles show no preferred direction, collective effects induce transversal current and directional locking at high density via a spontaneous symmetry breaking. The colloidal current may be polarized via an additional bias field that makes one transport direction energetically preferred.

Electric readout of magnetic stripes in insulators

In superconductors, a topological configuration of the superconducting order parameter called a superconducting vortex carries magnetization. Such a magnetic topological object behaves like a minute particle generating a magnetic flux. Since the flux is localized with a nanometer scale, the vortex provides a nano-scale probe for local magnetic fields. Here we show that information of magnetic stripes in insulators can be read out by using vortices in an adjacent superconductor film as a probe. The orientation and width of magnetic micro stripes are both transcribed into resistance change of the superconductor through the modulation of vortex mobility affected by local magnetization. By changing the direction of external magnetic fields, zero-field resistance changes continuously according to the stripe orientation, and its modulation magnitude reaches up to 100%. The width of the stripes can also be estimated from the oscillatory magnetoresistance. Our results demonstrate a new possibility for non-volatile analog memory devices based on topological objects.

Use of thermal gradients for control of vortex matter in mesoscopic superconductors

Usually, the measurements of electronic and magnetic properties of superconducting samples are carried out under a constant temperature bath. On the other hand, thermal gradients induce local variation of the superconducting order parameter, and the vortex dynamics can present interesting behaviors. In this work, we solved the time-dependent Ginzburg-Landau equations simulating samples under two different thermal gradients, and considering two values of the Ginzburg-Landau parameter, [Formula: see text]. We find that both parameters, i.e. [Formula: see text] and thermal gradients, play an important role on the vortex dynamics and on the magnetization behavior of the samples.

Manipulation of a stable dark soliton train in polariton condensate

With a potential trap to mimic the finite-size effect, we predict the generation of dark soliton train in a nonresonant polariton condensate excited with the spatially homogeneous continuous wave (cw) field by exploiting the quantum interference in spatial domain. The number of solitons in the train is demonstrated to be controllable on demand in the domain of material parameters. We show that, similar to dark solitons in conservative systems, these nonlinear excitations have infinite lifetime and remain spatially localized even for the periodically oscillating and colliding state of dark soliton train, which do not depend on the parameters of the condensate. Especially, a final state of anti-dark soliton is observed for all kinds of dark soliton trains with the increase of pump power.

Microfluidic manipulation of magnetic flux domains in type-I superconductors: droplet formation, fusion and fission

The magnetic flux domains in the intermediate state of type-I superconductors are known to resemble fluid droplets, and their dynamics in applied electric current is often cartooned as a "dripping faucet". Here we show, using the time-depended Ginzburg-Landau simulations, that microfluidic principles hold also for the determination of the size of the magnetic flux-droplet as a function of the applied current, as well as for the merger or splitting of those droplets in the presence of the nanoengineered obstacles for droplet motion. Differently from fluids, the flux-droplets in superconductors are quantized and dissipative objects, and their pinning/depinning, nucleation, and splitting occur in a discretized form, all traceable in the voltage measured across the sample. At larger applied currents, we demonstrate how obstacles can cause branching of laminar flux streams or their transformation into mobile droplets, as readily observed in experiments.

Dynamic Control of the Vortex Pinning Potential in a Superconductor Using Current Injection through Nanoscale Patterns

Control over the vortex potential at the nanoscale in a superconductor is a subject of great interest for both fundamental and technological reasons. Many methods for achieving artificial pinning centers have been demonstrated, for example, with magnetic nanostructures or engineered imperfections, yielding many intriguing effects. However, these pinning mechanisms do not offer dynamic control over the strength of the patterned vortex potential because they involve static nanostructures created in or near the superconductor. Dynamic control has been achieved with scanning probe methods on the single vortex level but these are difficult so scale up. Here, we show that by applying controllable nanopatterned current injection, the superconductor can be locally driven out of equilibrium, creating an artificial vortex potential that can be tuned by the magnitude of the injected current, yielding a unique vortex channeling effect.

Creation and Manipulation of Stable Dark Solitons and Vortices in Microcavity Polariton Condensates

Solitons and vortices obtain widespread attention in different physical systems as they offer potential use in information storage, processing, and communication. In exciton-polariton condensates in semiconductor microcavities, solitons and vortices can be created optically. However, dark solitons are unstable and vortices cannot be spatially controlled. In the present work we demonstrate the existence of stable dark solitons and vortices under nonresonant incoherent excitation of a polariton condensate with a simple spatially periodic pump. In one dimension, we show that an additional coherent light pulse can be used to create or destroy a dark soliton in a controlled manner. In two dimensions we demonstrate that a coherent light beam can be used to move a vortex to a specific position on the lattice or be set into motion by simply switching the periodic pump structure from two-dimensional (lattice) to one-dimensional (stripes). Our theoretical results open up exciting possibilities for optical on-demand generation and control of dark solitons and vortices in polariton condensates.

Dynamic phases, clustering, and chain formation for driven disk systems in the presence of quenched disorder

We numerically examine the dynamic phases and pattern formation of two-dimensional monodisperse repulsive disks driven over random quenched disorder. We show that there is a series of distinct dynamic regimes as a function of increasing drive, including a clogged or pile-up phase near depinning, a homogeneous disordered flow state, and a dynamically phase separated regime consisting of high-density crystalline regions surrounded by a low density of disordered disks. At the highest drives the disks arrange into one-dimensional moving chains. The phase separated regime has parallels with the phase separation observed in active matter systems, but arises from a distinct mechanism consisting of the combination of nonequilibrium fluctuations with density-dependent mobility. We discuss the pronounced differences between this system and previous studies of driven particles with longer-range repulsive interactions moving over random substrates, such as superconducting vortices or electron crystals, where dynamical phase separation and distinct one-dimensional moving chains are not observed. Our results should be generic to a broad class of systems in which the particle-particle interactions are short ranged, such as sterically interacting colloids or Yukawa particles with strong screening driven over random pinning arrays, superconducting vortices in the limit of small penetration depths, or quasi-two-dimensional granular matter flowing over rough landscapes.

Depinning and nonequilibrium dynamic phases of particle assemblies driven over random and ordered substrates: a review

We review the depinning and nonequilibrium phases of collectively interacting particle systems driven over random or periodic substrates. This type of system is relevant to vortices in type-II superconductors, sliding charge density waves, electron crystals, colloids, stripe and pattern forming systems, and skyrmions, and could also have connections to jamming, glassy behaviors, and active matter. These systems are also ideal for exploring the broader issues of characterizing transient and steady state nonequilibrium flow phases as well as nonequilibrium phase transitions between distinct dynamical phases, analogous to phase transitions between different equilibrium states. We discuss the differences between elastic and plastic depinning on random substrates and the different types of nonequilibrium phases which are associated with specific features in the velocity-force curves, fluctuation spectra, scaling relations, and local or global particle ordering. We describe how these quantities can change depending on the dimension, anisotropy, disorder strength, and the presence of hysteresis. Within the moving phase we discuss how there can be a transition from a liquid-like state to dynamically ordered moving crystal, smectic, or nematic states. Systems with periodic or quasiperiodic substrates can have multiple nonequilibrium second or first order transitions in the moving state between chaotic and coherent phases, and can exhibit hysteresis. We also discuss systems with competing repulsive and attractive interactions, which undergo dynamical transitions into stripes and other complex morphologies when driven over random substrates. Throughout this work we highlight open issues and future directions such as absorbing phase transitions, nonequilibrium work relations, inertia, the role of non-dissipative dynamics such as Magnus effects, and how these results could be extended to the broader issues of plasticity in crystals, amorphous solids, and jamming phenomena.

Lower Viral Loads and Slower CD4+ T-Cell Count Decline in MRKAd5 HIV-1 Vaccinees Expressing Disease-Susceptible HLA-B*58:02

Background. HLA strongly influences human immunodeficiency virus type 1 (HIV-1) disease progression. A major contributory mechanism is via the particular HLA-presented HIV-1 epitopes that are recognized by CD8⁺ T-cells. Different populations vary considerably in the HLA alleles expressed. We investigated the HLA-specific impact of the MRKAd5 HIV-1 Gag/Pol/Nef vaccine in a subset of the infected Phambili cohort in whom the disease-susceptible HLA-B*58:02 is highly prevalent.

Methods. Viral loads, CD4⁺ T-cell counts, and enzyme-linked immunospot assay–determined anti-HIV-1 CD8⁺ T-cell responses for a subset of infected antiretroviral-naive Phambili participants, selected according to sample availability, were analyzed.

Results. Among those expressing disease-susceptible HLA-B*58:02, vaccinees had a lower chronic viral set point than placebo recipients (median, 7240 vs 122 500 copies/mL; P = .01), a 0.76 log₁₀ lower longitudinal viremia level (P = .01), and slower progression to a CD4⁺ T-cell count of <350 cells/mm³ (P = .02). These differences were accompanied by a higher Gag-specific breadth (4.5 vs 1 responses; P = .04) and magnitude (2300 vs 70 spot-forming cells/10⁶ peripheral blood mononuclear cells; P = .06) in vaccinees versus placebo recipients.

Conclusions. In addition to the known enhancement of HIV-1 acquisition resulting from the MRKAd5 HIV-1 vaccine, these findings in a nonrandomized subset of enrollees show an HLA-specific vaccine effect on the time to CD4⁺ T-cell count decline and viremia level after infection and the potential for vaccines to differentially alter disease outcome according to population HLA composition.

Clinical Trials Registration. NCT00413725, DOH-27-0207-1539.

Block copolymer self-assembly-directed synthesis of mesoporous gyroidal superconductors

Superconductors with periodically ordered mesoporous structures are expected to have properties very different from those of their bulk counterparts. Systematic studies of such phenomena to date are sparse, however, because of a lack of versatile synthetic approaches to such materials. We demonstrate the formation of three-dimensionally continuous gyroidal mesoporous niobium nitride (NbN) superconductors from chiral ABC triblock terpolymer self-assembly-directed sol-gel-derived niobium oxide with subsequent thermal processing in air and ammonia gas. Superconducting materials exhibit a critical temperature (T c) of about 7 to 8 K, a flux exclusion of about 5% compared to a dense NbN solid, and an estimated critical current density (J c) of 440 A cm(-2) at 100 Oe and 2.5 K. We expect block copolymer self-assembly-directed mesoporous superconductors to provide interesting subjects for mesostructure-superconductivity correlation studies.

Proximity Driven Commensurate Pinning in YBa2Cu3O7 through All-Oxide Magnetic Nanostructures

The design of artificial vortex pinning landscapes is a major goal toward large scale applications of cuprate superconductors. Although disordered nanometric inclusions have shown to modify their vortex phase diagram and to produce enhancements of the critical current ( MacManus-Driscoll , J. L. ; Foltyn , S. R. ; Jia , Q. X. ; Wang , H. ; Serquis , A. ; Civale , L. ; Maiorov , B. ; Hawley , M. E. ; Maley , M. P. ; Peterson , D. E. Nat. Mater. 2004 , 3 , 439 - 443 and Yamada , Y. ; Takahashi , K. ; Kobayashi , H. ; Konishi , M. ; Watanabe , T. ; Ibi , A. ; Muroga , T. ; Miyata , S. ; Kato , T. ; Hirayama , T. ; Shiohara , Y. Appl. Phys. Lett. 2005 , 87 , 1 - 3 ), the effect of ordered oxide nanostructures remains essentially unexplored. This is due to the very small nanostructure size imposed by the short coherence length, and to the technological difficulties in the nanofabrication process. Yet, the novel phenomena occurring at oxide interfaces open a wide spectrum of technological opportunities to interplay with the superconductivity in cuprates. Here, we show that the unusual long-range suppression of the superconductivity occurring at the interface between manganites and cuprates affects vortex nucleation and provides a novel vortex pinning mechanism. In particular, we show evidence of commensurate pinning in YBCO films with ordered arrays of LCMO ferromagnetic nanodots. Vortex pinning results from the proximity induced reduction of the condensation energy at the vicinity of the magnetic nanodots, and yields an enhanced friction between the nanodot array and the moving vortex lattice in the liquid phase. This result shows that all-oxide ordered nanostructures constitute a powerful, new route for the artificial manipulation of vortex matter in cuprates.

Critical behavior at a dynamic vortex insulator-to-metal transition

An array of superconducting islands placed on a normal metal film offers a tunable realization of nanopatterned superconductivity. This system enables investigation of the nature of competing vortex states and phase transitions between them. A square array creates the eggcrate potential in which magnetic field-induced vortices are frozen into a vortex insulator. We observed a vortex insulator-vortex metal transition driven by the applied electric current and determined critical exponents that coincided with those for thermodynamic liquid-gas transition. Our findings offer a comprehensive description of dynamic critical behavior and establish a deep connection between equilibrium and nonequilibrium phase transitions.

A radio-frequency coil for the microwave characterization of vortex dynamics in thin film superconductors

A radio-frequency coil for the experimental investigation of the magnetic properties of thin superconducting films under microwave fields at different values of temperature and dc magnetic field has been developed. The system has been used for low-temperature microwave frequency-dependent magnetization measurements in a Pb thin film with an engineered periodical antidot array. The characteristic frequencies and the electric and magnetic fields of the resonant system formed by a multi-turn coil with a sample loaded in its core are estimated using the helical approach. A good agreement of the calculated values with those recorded in swept-frequency spectra is obtained. The relation between the characteristics of the resonant structure and the frequency-driven magnetic response of the sample at different nominal microwave powers documents the capability and sensitivity of the layout.

Universal, strong and long-ranged trapping by optical conveyors

Optical conveyors are active tractor beams that selectively transport illuminated objects either upstream or downstream along their axes. Formed by the coherent superposition of coaxial Bessel beams, an optical conveyor features an axial array of equally spaced intensity maxima that act as optical traps for small objects. We demonstrate through measurements on colloidal spheres and numerical calculations based on the generalized Lorenz-Mie theory that optical conveyors' interferometric structure endows them with trapping characteristics far superior to those of conventional optical tweezers. Optical conveyors form substantially stiffer traps and can transport a wider variety of materials over a much longer axial range.

Freezing and thawing of artificial ice by thermal switching of geometric frustration in magnetic flux lattices

The problem of an ensemble of repulsive particles on a potential-energy landscape is common to many physical systems and has been studied in multiple artificial playgrounds. However, the latter usually involve fixed energy landscapes, thereby impeding in situ investigations of the particles' collective response to controlled changes in the landscape geometry. Here, we experimentally realize a system in which the geometry of the potential-energy landscape can be switched using temperature as the control knob. This realization is based on a high-temperature superconductor in which we engineer a nanoscale spatial modulation of the superconducting condensate. Depending on the temperature, the flux quanta induced by an applied magnetic field see either a geometrically frustrated energy landscape that favours an ice-like flux ordering, or an unfrustrated landscape that yields a periodic flux distribution. This effect is reflected in a dramatic change in the superconductor's magneto-transport. The thermal switching of the energy landscape geometry opens new opportunities for the study of ordering and reorganization in repulsive particle manifolds.

Aspects of jamming in two-dimensional athermal frictionless systems

In this work we provide an overview of jamming transitions in two dimensional systems focusing on the limit of frictionless particle interactions in the absence of thermal fluctuations. We first discuss jamming in systems with short range repulsive interactions, where the onset of jamming occurs at a critical packing density and where certain quantities show a divergence indicative of critical behavior. We describe how aspects of the dynamics change as the jamming density is approached and how these dynamics can be explored using externally driven probes. Different particle shapes can produce jamming densities much lower than those observed for disk-shaped particles, and we show how jamming exhibits fragility for some shapes while for other shapes this is absent. Next we describe the effects of long range interactions and jamming behavior in systems such as charged colloids, vortices in type-II superconductors, and dislocations. We consider the effect of adding obstacles to frictionless jamming systems and discuss connections between this type of jamming and systems that exhibit depinning transitions. Finally, we discuss open questions such as whether the jamming transition in all these different systems can be described by the same or a small subset of universal behaviors, as well as future directions for studies of jamming transitions in two dimensional systems, such as jamming in self-driven or active matter systems.

Microscopy image segmentation tool: robust image data analysis

We present a software package called Microscopy Image Segmentation Tool (MIST). MIST is designed for analysis of microscopy images which contain large collections of small regions of interest (ROIs). Originally developed for analysis of porous anodic alumina scanning electron images, MIST capabilities have been expanded to allow use in a large variety of problems including analysis of biological tissue, inorganic and organic film grain structure, as well as nano- and meso-scopic structures. MIST provides a robust segmentation algorithm for the ROIs, includes many useful analysis capabilities, and is highly flexible allowing incorporation of specialized user developed analysis. We describe the unique advantages MIST has over existing analysis software. In addition, we present a number of diverse applications to scanning electron microscopy, atomic force microscopy, magnetic force microscopy, scanning tunneling microscopy, and fluorescent confocal laser scanning microscopy.

Dynamic regimes for driven colloidal particles on a periodic substrate at commensurate and incommensurate fillings

We numerically examine colloidal particles driven over a muffin tin substrate. Previous studies of this model identified a variety of commensurate and incommensurate static phases in which topological defects can form domain walls, ordered stripes, superlattices, or disordered patchy regimes as a function of the filling fraction. Here, we show that the addition of an external drive to these static phases can produce distinct dynamical responses. At incommensurate fillings the flow occurs in the form of localized pulses or solitons correlated with topological defect structures. Transitions between different modes of motion can occur as a function of increasing drive. We measure the average particle velocity for specific ranges of external drive and show that changes in the velocity response correlate with changes in the topological defect arrangements. We also demonstrate that in the different dynamic phases, the particles have distinct trajectories and velocity distributions. Dynamic transitions between ordered and disordered flows exhibit hysteresis, while in strongly disordered regimes there is no hysteresis and the velocity-force curves are smooth. When stripe patterns are present, transport can occur at an angle to the driving direction.

CCR5 expression is reduced in lymph nodes of HIV type 1-infected women, compared with men, but does not mediate sex-based differences in viral loads

BACKGROUND

Human immunodeficiency virus type 1 (HIV-1)-infected women have lower viral loads than men but similar rates of disease progression. We hypothesized that sex-based differences in CCR5 expression mediate viral load differences.

METHODS

CCR5 was analyzed by flow cytometry in disaggregated lymph node cells from untreated HIV-1-infected women (n = 28) and men (n = 27). The frequencies of HIV-1 RNA-producing cells in the lymph node were determined by in situ hybridization. Linear and generalized linear regression models were used.

RESULTS

The percentage of CCR5(+)CD3(+)CD4(+) cells was lower in women (mean, 12%) than men (mean, 16%; P = .034). Neither the percentage of CCR5(+)CD3(+)CD4(+) cells nor the CCR5 density predicted viral load or HIV-1 RNA-producing lymph node cells (P ≥ .24), after adjusting for CD4(+) T-cell count, race, and age. Women had marginally fewer HIV-1 RNA-producing cells (mean, 0.21 cells/mm(2)) than men (mean, 0.44 cells/mm(2); P = .046). After adjusting for the frequency of HIV-1 RNA-producing cells and potential confounders, the viral load in women were 0.46 log10 copies/mL lower than that in men (P = .018).

CONCLUSIONS

Reduced lymph node CCR5 expression in women did not account for the viral load difference between sexes. CCR5 expression did not predict viral load or frequencies of HIV-1 RNA-producing cells, indicating that physiologic levels of CCR5 do not limit HIV-1 replication in lymph node. Less plasma virus was associated with each HIV-1 RNA-producing cell in women as compared to men, suggesting that women may either produce fewer virions per productively infected cell or more effectively clear extracellular virus.

Strongly enhanced pinning of magnetic vortices in type-II superconductors by conformal crystal arrays

Conformal crystals are nonuniform structures created by a conformal transformation of regular two-dimensional lattices. We show that gradient-driven vortices interacting with a conformal pinning array exhibit substantially stronger pinning effects over a much larger range of field than found for random or periodic pinning arrangements. The pinning enhancement is partially due to matching of the critical flux gradient with the pinning gradient, but the preservation of local ordering in the conformally transformed hexagonal lattice and the arching arrangement of the pinning also play crucial roles. Our results can be generalized to a wide class of gradient-driven interacting particle systems such as colloids on optical trap arrays.

Vortex kinks in superconducting films with periodically modulated thickness

We report magnetoresistance measurements in Nb films having a periodic thickness modulation. The cylinder shaped thicker regions of the sample, which form a square lattice, act as repulsive centers for the superconducting vortices. For low driving currents along one of the axes of the square lattice, the resistivity ρ increases monotonously with increasing magnetic field B and the ρ-B characteristics are approximately piecewise linear. The linear ρ versus B segments change their slope at matching fields where the number of vortices is an integer or a half integer times the number of protruding cylinders in the sample. Numerical simulations allow us to associate the different segments of linear magnetoresistance to different vortex-flow regimes, some of which are dominated by the propagation of discommensurations (kinks).

Host factor transcriptional regulation contributes to preferential expression of HIV type 1 in IL-4-producing CD4 T cells

HIV type 1 (HIV-1) replicates preferentially in IL-4-producing CD4 T cells for unclear reasons. We show increased HIV-1 expression is irrespective of viral tropism for chemokine receptors as previously suggested, but rather transcription of the HIV-1 long terminal repeat (LTR) is increased in IL-4-producing CD4 T cells. Increased expression of HIV-1 message is also confirmed in IL-4-producing CD4 T cells from HIV-1-infected individuals ex vivo. In exploring a transcriptional mechanism, we identify a novel c-maf (required for IL-4 expression) transcription factor binding site just upstream of the dual NF-κB/NFAT binding sites in the proximal HIV-1 LTR. We demonstrate that c-maf binds this site in vivo and synergistically augments HIV-1 transcription in cooperation with NFAT2 and NF-κB p65, but not NFAT1 or NF-κB p50. Conversely, small interfering RNA inhibition of c-maf reduces HIV-1 transcription in IL-4-producing T cells. Thus, c-maf increases HIV-1 expression in IL-4-producing CD4 T cells by binding the proximal HIV-1 LTR and augmenting HIV-1 transcription in partnership with NFAT2 and NF-κB p65 specifically. This has important implications for selective targeting of transcription factors during HIV-1 infection because, over the course of HIV-1 progression/AIDS, IL-4-producing T cells frequently predominate and substantially contribute to disease pathology.

Transcriptional network predicts viral set point during acute HIV-1 infection

BACKGROUND

HIV-1-infected individuals with higher viral set points progress to AIDS more rapidly than those with lower set points. Predicting viral set point early following infection can contribute to our understanding of early control of HIV-1 replication, to predicting long-term clinical outcomes, and to the choice of optimal therapeutic regimens.

METHODS

In a longitudinal study of 10 untreated HIV-1-infected patients, we used gene expression profiling of peripheral blood mononuclear cells to identify transcriptional networks for viral set point prediction. At each sampling time, a statistical analysis inferred the optimal transcriptional network that best predicted viral set point. We then assessed the accuracy of this transcriptional model by predicting viral set point in an independent cohort of 10 untreated HIV-1-infected patients from Malawi.

RESULTS

The gene network inferred at time of enrollment predicted viral set point 24 weeks later in the independent Malawian cohort with an accuracy of 87.5%. As expected, the predictive accuracy of the networks inferred at later time points was even greater, exceeding 90% after week 4. The composition of the inferred networks was largely conserved between time points. The 12 genes comprising this dynamic signature of viral set point implicated the involvement of two major canonical pathways: interferon signaling (p<0.0003) and membrane fraction (p<0.02). A silico knockout study showed that HLA-DRB1 and C4BPA may contribute to restricting HIV-1 replication.

CONCLUSIONS

Longitudinal gene expression profiling of peripheral blood mononuclear cells from patients with acute HIV-1 infection can be used to create transcriptional network models to early predict viral set point with a high degree of accuracy.

Structural transitions and dynamical regimes for directional locking of vortices and colloids driven over periodic substrates

We examine collective dynamical locking effects for superconducting vortices and colloids interacting with square and triangular substrate arrays under a slowly rotated dc drive. A rich variety of lattice configurations associated with a series of steps in the velocity-force curves occur during the locking transitions. These include triangular, square, smectic, and disordered particle arrangements that can be identified using the structure factor. We show that the step widths vary with the ratio of the number of particles to the number of pinning sites. Unlike a static system, where matching effects occur at simple integer commensuration ratios, we find dynamical commensuration effects that arise when an integer number of particle chains flow between rows of pins. We identify two distinct types of locking as a function of substrate strength, distinguished by whether the particles flow along or between the pinning rows.

Wire network behavior in superconducting Nb films with diluted triangular arrays of holes

We present results of transport measurements on superconducting Nb films with diluted triangular arrays (honeycomb and kagomé) of holes. The patterned films have large disk-shaped interstitial regions even when the edge-to-edge separations between nearest neighboring holes are comparable to the coherence length. Changes in the field interval of two consecutive minima in the field dependent resistance R(H) curves are observed. In the low field region, fine structures in the R(H) and T(c)(H) curves are identified in both arrays. Comparison of experimental data with calculation results reveals that these structures observed in honeycomb and kagomé hole arrays resemble those in wire networks with triangular and T(3) symmetries, respectively. The findings suggest that even in these specified periodic hole arrays with very large interstitial regions, the low field fine structures are determined by the connectivity of the nanostructures.

Mortality trends in the US Perinatal AIDS Collaborative Transmission Study (1986-2004)

BACKGROUND

Highly active antiretroviral therapy (HAART) has improved human immunodeficiency virus (HIV)-associated morbidity and mortality. The bimodal mortality distribution in HIV-infected children makes it important to evaluate temporal effects of HAART among a birth cohort with long-term, prospective follow-up.

METHODS

Perinatal AIDS Collaborative Transmission Study (PACTS)/PACTS-HIV Follow-up of Perinatally Exposed Children (HOPE) study was a Centers for Disease Control and Prevention-sponsored multicenter, prospective birth cohort study of HIV-exposed uninfected and infected infants from 1985 until 2004. Mortality was evaluated for the no/monotherapy, mono-/dual-therapy, and HAART eras, that is, 1 January 1986 through 31 December 1990, from 1 January 1991 through 31 December 1996, and 1 January 1997 through 31 December 2004.

RESULTS

Among 364 HIV-infected children, 56% were female and 69% black non-Hispanic. Of 98 deaths, 79 (81%) and 61 (62%) occurred in children ≤3 and ≤2 years old, respectively. The median age at death increased significantly across the eras (P < .0001). The average annual mortality rates were 18 (95% confidence interval [CI], 11.6-26.8), 6.9 (95% CI, 5.4-8.8), and 0.8 (95% CI, 0.4-1.5) events per 100 person-years for the no/monotherapy, mono-/dual-therapy and HAART eras, respectively. The corresponding 6-year survival rates for children born in these eras were 57%, 76%, and 91%, respectively (P < .0001). Among children who received HAART in the first 6 months of age, the probability of 6-year survival was 94%. Ten-year survival rates for HAART and non-HAART recipients were 94% and 45% (P < .05). HAART-associated reductions in mortality remained significant after adjustment for confounders (hazard ratio, 0.3; 95% CI, .08-.76). Opportunistic infections (OIs) caused 31.8%, 16.9%, and 9.1% of deaths across the respective eras (P = .051).

CONCLUSIONS

A significant decrease in annual mortality and a prolongation in survival were seen in this US perinatal cohort of HIV-infected children. Temporal decreases in OI-associated mortality resulted in relative proportional increases of non-OI-associated deaths.

Viremia copy-years predicts mortality among treatment-naive HIV-infected patients initiating antiretroviral therapy

BACKGROUND

Cross-sectional plasma human immunodeficiency virus (HIV) viral load (VL) measures have proven invaluable for clinical and research purposes. However, cross-sectional VL measures fail to capture cumulative plasma HIV burden longitudinally. We evaluated the cumulative effect of exposure to HIV replication on mortality following initiation of combination antiretroviral therapy (ART).

METHODS

We included treatment-naive HIV-infected patients starting ART from 2000 to 2008 at 8 Center for AIDS Research Network of Integrated Clinical Systems sites. Viremia copy-years, a time-varying measure of cumulative plasma HIV exposure, were determined for each patient using the area under the VL curve. Multivariable Cox models were used to evaluate the independent association of viremia copy-years for all-cause mortality.

RESULTS

Among 2027 patients contributing 6579 person-years of follow-up, the median viremia copy-years was 5.3 log₁₀ copy × y/mL (interquartile range: 4.9-6.3 log₁₀ copy × y/mL), and 85 patients (4.2%) died. When evaluated separately, viremia copy-years (hazard ratio [HR] = 1.81 per log₁₀ copy × y/mL; 95% confidence interval [CI], 1.51-2.18 per log(10) copy × y/mL), 24-week VL (1.74 per log₁₀ copies/mL; 95% CI, 1.48-2.04 per log₁₀ copies/mL), and most recent VL (HR = 1.89 per log₁₀ copies/mL; 95% CI: 1.63-2.20 per log₁₀ copies/mL) were associated with increased mortality. When simultaneously evaluating VL measures and controlling for other covariates, viremia copy-years increased mortality risk (HR = 1.44 per log₁₀ copy × y/mL; 95% CI, 1.07-1.94 per log₁₀ copy × y/mL), whereas no cross-sectional VL measure was independently associated with mortality.

CONCLUSIONS

Viremia copy-years predicted all-cause mortality independent of traditional, cross-sectional VL measures and time-updated CD4+ T-lymphocyte count in ART-treated patients, suggesting cumulative HIV replication causes harm independent of its effect on the degree of immunodeficiency.

Effect of half-quantum vortices on magnetoresistance of perforated superconducting films

Recent cantilever magnetometry measurements of annular micron-size samples of Sr2RuO4 have revealed evidence for the existence of half-quantum vortices (HQVs) in this material [J. Jang et al., Science 331, 186 (2011)]. We propose to look for HQVs in transport measurements and calculate magnetoresistance of a perforated superconducting film close to the transition temperature in the presence of HQVs. We analyze the dependence of magnetoresistance on the thermodynamic stability of HQVs which, according to Jang et al., can be varied by the application of an in-plane magnetic field and point out features which may help to identify them.

Dynamical ordering and directional locking for particles moving over quasicrystalline substrates

We use molecular dynamics simulations to study the driven phases of particles such as vortices or colloids moving over a decagonal quasiperiodic substrate. In the regime where the pinned states have quasicrystalline ordering, the driven phases can order into moving square or smectic states, or into states with aligned rows of both square and triangular tiling which we term dynamically induced Archimedean-like tiling. We show that when the angle of the drive is varied with respect to the substrate, directional locking effects occur where the particle motion locks to certain angles. It is at these locking angles that the dynamically induced Archimedean tiling appears. We also demonstrate that the different dynamical orderings and locking phases show pronounced changes as a function of filling fraction.

Impact of CCR5delta32 host genetic background and disease progression on HIV-1 intrahost evolutionary processes: efficient hypothesis testing through hierarchical phylogenetic models

The interplay between C-C chemokine receptor type 5 (CCR5) host genetic background, disease progression, and intrahost HIV-1 evolutionary dynamics remains unclear because differences in viral evolution between hosts limit the ability to draw conclusions across hosts stratified into clinically relevant populations. Similar inference problems are proliferating across many measurably evolving pathogens for which intrahost sequence samples are readily available. To this end, we propose novel hierarchical phylogenetic models (HPMs) that incorporate fixed effects to test for differences in dynamics across host populations in a formal statistical framework employing stochastic search variable selection and model averaging. To clarify the role of CCR5 host genetic background and disease progression on viral evolutionary patterns, we obtain gp120 envelope sequences from clonal HIV-1 variants isolated at multiple time points in the course of infection from populations of HIV-1-infected individuals who only harbored CCR5-using HIV-1 variants at all time points. Presence or absence of a CCR5 wt/Δ32 genotype and progressive or long-term nonprogressive course of infection stratify the clinical populations in a two-way design. As compared with the standard approach of analyzing sequences from each patient independently, the HPM provides more efficient estimation of evolutionary parameters such as nucleotide substitution rates and d(N)/d(S) rate ratios, as shown by significant shrinkage of the estimator variance. The fixed effects also correct for nonindependence of data between populations and results in even further shrinkage of individual patient estimates. Model selection suggests an association between nucleotide substitution rate and disease progression, but a role for CCR5 genotype remains elusive. Given the absence of clear d(N)/d(S) differences between patient groups, delayed onset of AIDS symptoms appears to be solely associated with lower viral replication rates rather than with differences in selection on amino acid fixation.