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At least 1,135 records · Page 63

Design and applications of a clamp for Green Fluorescent Protein with picomolar affinity

Green fluorescent protein (GFP) fusions are pervasively used to study structures and processes. Specific GFP-binders are thus of great utility for detection, immobilization or manipulation of GFP-fused molecules. We determined structures of two designed ankyrin repeat proteins (DARPins), complexed with GFP, which revealed different but overlapping epitopes. Here in this paper we show a structure-guided design strategy that, by truncation and computational reengineering, led to a stable construct where both can bind simultaneously: by linkage of the two binders, fusion constructs were obtained that “wrap around” GFP, have very high affinities of about 10–30 pM, and extremely slow off-rates. They can be natively produced in E. coli in very large amounts, and show excellent biophysical properties. Their very high stability and affinity, facile site-directed functionalization at introduced unique lysines or cysteines facilitate many applications. As examples, we present them as tight yet reversible immobilization reagents for surface plasmon resonance, as fluorescently labelled monomeric detection reagents in flow cytometry, as pull-down ligands to selectively enrich GFP fusion proteins from cell extracts, and as affinity column ligands for inexpensive large-scale protein purification. We have thus described a general design strategy to create a “clamp” from two different high-affinity repeat proteins, even if their epitopes overlap.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Controlling Metastable Native Point-Defect Populations in Cu(In,Ga)Se 2 and Cu 2 ZnSnSe 4 Materials and Solar Cells through Voltage-Bias Annealing

Our contribution describes the influence of low-temperature annealing with and without applied voltage bias on thin-film Cu 2 ZnSnSe 4 (CZTSe), Cu(In,Ga)Se 2 (CIGS), and CdS material properties and solar cell performance. In order to quantify the effects of cation disorder on CZTSe device performance, completed devices were annealed under open-circuit conditions at various temperatures from 110 degrees C to 215 degrees C and subsequently quenched. Measurements on these devices document systematic, reversible changes in solar-cell performance consistent with a reduction in CZTSe band tails at lower annealing temperatures. CIGS and CZTSe solar cells were also annealed at various temperatures (200 degrees C for CIGS and 110 degrees C-215 degrees C for CZTSe) and subsequently quenched with continuously applied voltage bias to explore the effects of non-equilibrium annealing conditions. For both absorbers, large reversible changes in device characteristics correlated with the magnitude and sign of the applied voltage bias were observed. For CZTSe devices, the voltage-bias annealing (VBA) produced reversible changes in open-circuit voltage (VOC) from 289 meV to 446 meV. For CIGS solar cells, even larger changes were observed in device performance: photovoltaic (PV) conversion efficiency of the CIGS device varied from below 3% to above 15%, with corresponding changes in CIGS hole density of about three orders of magnitude. Findings from these VBA experiments are interpreted in terms of changes to the metastable point-defect populations that control key properties in the absorber layers, and in the CdS buffer layer. Computational device modeling was performed to assess the impacts of cation disorder on the CZTSe VOC deficit, and to elucidate the effects of VBA treatments on metastable point defect populations in CZTSe, CIGS, and CdS. Our results indicate that band tails impose important limitations on CZTSe device performance. Device modeling results also indicate that non-equilibrium processing conditions including the effects of voltage bias can dramatically alter point-defect-mediated opto-electronic properties of semiconductors. Implications for optimization of PV materials and connections to long-term stability of PV devices are discussed.

14 SOLAR ENERGY↗

Intrinsic dynamics of the electric-field-induced phase switching in antiferroelectric PbZrO 3 ultrathin films

Antiferroelectric ultrathin PbZrO3 films can exhibit both ferroelectric and antiferroelectric behavior depending on the thickness. We use first-principles-based nanoscopic simulations to investigate the intrinsic high-frequency dynamics of the electric-field-induced phase switching in such films which so far remains unknown. Here in this comprehensive study we report (i) the size and frequency evolution of the polarization response to the electric field;(ii)the intrinsic time for the phase switching; (iii) detailed comparison between the polarization reversal in the films with ferroelectric and antiferroelectric behavior; (iv) dynamics of the antiferroelectric and antiferrodistortive order parameters; (v) nanoscopic mechanism responsible for the phase switching. The nanoscopic insight leads to the prediction of the existence of two possible scenarios for the antipolar-polar phase switching depending on the mutual orientation of the antiferroelectric order parameter and the electric field. The two scenarios have different dynamical fingerprints. The polar-antipolar phase switching is found to be assisted by the formation of a nonpolar phase. Computational data indicate that the phase switching time is only fractions of nanoseconds for the polar-polar phase switching in ferroelectric films and polar-antipolar phase switching in antiferroelectric films. The antipolar-polar phase switching in antiferroelectric films is just a bit slower and takes the order of nanosecond. Under nonequilibrium conditions we find formation of antiferroelectric and antiferrodistortive nanodomains and coexistence of polar and antipolar order parameters.

25 ENERGY STORAGE↗

Mesospheric Non-Migrating Tides Generated With Planetary Waves: II Influence of Gravity Waves

We demonstrated that, in our model, non-linear interactions between planetary waves (PW) and migrating tides could generate in the upper mesosphere non-migrating tides with amplitudes comparable to those observed. The Numerical Spectral Model (NSM) we employ incorporates Hines Doppler Spread Parameterization for small-scale gravity waves (GW), which affect in numerous ways the dynamics of the mesosphere. The latitudinal (seasonal) reversals in the temperature and zonal circulation, which are largely caused by GWs (Lindzen, 198l), filter the PWs and contribute to the instabilities that generate the PWs. The PWs in turn are amplified by the momentum deposition of upward propagating GWs, as are the migrating tides. The GWs thus affect significantly the migrating tides and PWs, the building blocks of non-migrating tides. In the present paper, we demonstrate that GW filtering also contributes to the non-linear coupling between PWs and tides. Two computer experiments are presented to make this point. In one, we simply turn off the GW source to show the effect. In the second case, we demonstrate the effect by selectively suppressing the momentum source for the m = 0 non-migrating tides.

Mayr, H. G.↗

ALESEP. Part 2: A computer program for the analysis of leading edge separation bubbles on infinite swept wings

A program called ALESEP is presented for the analysis of the inviscid-viscous interaction which occurs due to the presence of a closed laminar-transitional separation bubble on an airfoil or infinite swept wing. The ALESEP code provides an iterative solution of the boundary layer equations expressed in an inverse formulation coupled to a Cauchy integral representation of the inviscid flow. This interaction analysis is treated as a local perturbation to a known solution obtained from a global airfoil analysis; hence, part of the required input to the ALESEP code are the reference displacement thickness and tangential velocity distributions. Special windward differencing may be used in the reversed flow regions of the separation bubble to accurately account for the flow direction in the discretization of the streamwise convection of momentum. The ALESEP code contains a forced transition model based on a streamwise intermittency function, a natural transition model based on a solution of the integral form of the turbulent kinetic energy equation, and an empirical natural transition model.

Davis, R. L.↗

EMAPS: An Efficient Multiscale Approach to Plasma Systems with Non-MHD Scale Effects

Global interactions of energetic ions with magnetoplasmas and neutral gases lie at the core of many space and laboratory plasma phenomena ranging from solar wind entry into and transport within planetary magnetospheres and exospheres to fast-ion driven instabilities in fusion devices to astrophysics-in-lab experiments. The ability of computational models to properly account for physical effects that underlie such interactions, namely ion kinetic, ion cyclotron, Hall, collisional and ionization processes is important for the success and planning of experimental research in plasma physics. Understanding the physics of energetic ions, in particular their nonlinear resonance interactions with Alfvén waves, is central to improving the heating performance of magnetically confined plasmas for future energy generation. Fluid models are not adequate for high-beta plasmas as they cannot fully capture ion kinetic and cyclotron physics (e.g., ion behavior in the presence of magnetic nulls, shock structures, plasma interpenetration, etc.). Recent results from global reconnection simulations show that even in a MHD-like regime there may be significant differences between kinetic and MHD simulations. Therefore, kinetic modeling becomes essential for meeting modern day challenges in plasma physics. The hybrid approximation is an intermediate approximation between the fluid and fully kinetic approximations. It eliminates light waves, removes the electron inertial temporal and spatial scales from the problem and enables full-orbit ion kinetics. As a result, hybrid codes have become effective tools for exploring ion-scale driven phenomena associated with ion beams, shocks, reconnection and turbulence that control the large-scale behavior of laboratory and space magnetoplasmas. A number of numerical issues, however, make three-dimensional (3D) large-scale hybrid simulations of inhomogeneous magnetized plasmas prohibitively expensive or even impossible. To resolve these difficulties we have developed a novel Event-driven Multiscale Asynchronous Parallel Simulation (EMAPS) technology that replaces time stepping with self-adaptive update events. Local calculations are carried out only on an “as needed basis”. EMAPS (i) guarantees accurate and stable processing of physical variables in time accurate simulations, and (ii) eliminates unnecessary computation. Applying EMAPS to the hybrid model has resulted in the development of a unique parallel code, dimension-independent (compile-time-configurable) HYPERS (Hybrid Parallel Event-Resolved Simulator) that scales to hundreds of thousands of parallel processors. HYPERS advances electromagnetic fields and particles asynchronously on time scales determined by local physical laws and mesh properties. To achieve high computational accuracy in complex device geometries, HYPERS employs high-fidelity Cartesian grids with masked conductive cells. The HYPERS model includes multiple ion species, energy and momentum conserving ion-ion collisions, and provides a number of approximations for plasma resistivity and vacuum regions. Both local and periodic boundary conditions are allowed. The HYPERS solver preserves zero divergence of magnetic field. The project has demonstrated HYPERS capabilities on a number of applications of interest to fusion and astrophysical plasma physics applications listed below. 1. Theta-pinch formation of FRCs The formation, spontaneous spin-up, and stability of theta-pinch formed field-reversed configurations have been studied self-consistently in 3D. The end-to-end hybrid simulations reveal poloidal profiles of implosion-driven fast toroidal plasma rotation and demonstrate three discharge regimes as a function of experimental parameters: the decaying stable configuration, the tilt unstable configuration, and the nonlinear evolution of a fast growing tearing mode. 2. FRC collisions with magnetic mirrors Interactions of fast plasma streams and objects with magnetic obstacles (dipoles, mirrors, etc) lie at the core of many space and laboratory plasma phenomena ranging from magnetoshells and solar wind interactions with planetary magnetospheres to compact fusion plasmas. HYPERS simulations are compared with data from the MSX experiment (LANL) that focuses on the physics of magnetized collisionless shocks through the acceleration and subsequent stagnation of FRC plasmoids against a strong magnetic mirrors and flux-conserving boundaries. 3. Exploding magnetoplasmas Results from hybrid simulations of two experiments at the LAPD and Nevada Terawatt Facility are discussed where short-pulse lasers are used to ablate solid targets to produce plasmas that expand across external magnetic fields. The first simulation recreates flutelike density striations observed at the leading edge of a carbon plasma and predicts an early destruction of the magnetic cavity in agreement with experimental evidence. In the second simulation a polyethylene target is ablated into a mixture of protons and carbon ions. A mechanism is demonstrated that allows protons to penetrate the magnetic field in the form of a collimated flow. The results are compared to experimental data and single-fluid MHD simulations. The EMAPS framework has the potential for wide application in many other engineering and scientific fields, such as climate models, biological systems, electronic devices, seismic events, oil reservation simulators that all involve advancing solutions of partial differential equations in time where the rate of activity can be adapted widely over the spatial domain depending on locally space/time phenomena (“events”).

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Discovery of Calcium-Metal Alloy Anodes for Reversible Ca-Ion Batteries

Ca-ion batteries (CIBs) show promise to achieve the high energy density required by emerging applications like electric vehicles because of their potentially improved capacities and high operating voltages. The development of CIBs is hindered by the failure of traditional graphite and calcium metal anodes due to the intercalation difficulty and the lack of efficient electrolytes. Recently, a high voltage (4.45 V) CIB cell using Sn as the anode has been reported to achieve a remarkable cyclability (>300 cycles). The calciation of Sn is observed to end at Ca 7 Sn 6 , which is surprising, since higher Ca-content compounds are known (e.g., Ca 2 Sn). In our paper, the Sn electrochemical calciation reaction process is investigated computationally and the reaction driving force as a function of Ca content is explored using density functional theory (DFT) calculations. This exploration allows the identification of threshold voltages which govern the limits of the calciation process. This information is then used to design a four-step screening strategy and high-throughput DFT is utilized to search for anode materials with higher properties. Finally, many metalloids (Si, Sb, Ge), (post-)transition metals (Al, Pb, Cu, Cd, CdCu 2 ) are predicted to be promising inexpensive anode candidates and warrant further experimental investigations.

25 ENERGY STORAGE↗

Preparation of blue-emitting CaMgSi{sub 2}O{sub 6}:Eu{sup 2+} phosphors in reverse micellar system and their application to transparent emissive display devices

Blue-emitting Eu{sup 2+}-doped CaMgSi{sub 2}O{sub 6} phosphors were prepared by the reverse micelle method. The resultant particles were nanocrystalline with a grain size of about <300 nm and exhibited a characteristic blue emission spectrum centered at 445 nm induced by the oxygen coordinated Eu{sup 2+} ions. By using the corresponding nanophosphors followed by the formation of a uniform phosphor layer, we have demonstrated the mini-sized transparent plasma-discharge panels and investigated their luminance characteristics. Phosphor coated panel is properly transparent, {>=}65%, at the visible wavelength region and illuminates a characteristic blue emission under Ne/Xe plasma discharge conditions. Thus, we can obtain a fast decaying, robust blue-emitting silicate phosphor layer under excited plasma radiation for upcoming emissive display devices like as transparent and three-dimensional plasma display panels. - Graphical abstract: Blue-emitting CaMgSi{sub 2}O{sub 6}:Eu{sup 2+} nanophosphors coated transparent luminescent layers can be obtained. It illuminates the characteristic blue emission, spectrum centered at 425 nm wavelength, under the Ne-Xe mixed gas plasma discharge condition. Highlights: > Blue-emitting CaMgSi{sub 2}O{sub 6}:Eu{sup 2+} nanophosphors via reverse micelle method. > Transparent blue-emitting layer was prepared by using corresponding phosphors. > Fast decaying with degradation-free luminescent layer under plasma radiation. > Promising luminescent layer for the upcoming plasma discharged transparent displays.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Mixed quantum/classical theory for rotational energy exchange in symmetric-top-rotor + linear-rotor collisions and a case study of the ND 3 + D 2 system

The extension of mixed quantum/classical theory (MQCT) to describe collisional energy transfer is developed for a symmetric-top-rotor + linear-rotor system and is applied to ND 3 + D 2 . State-to-state transition cross sections are computed in a broad energy range for all possible processes: when both ND 3 and D 2 molecules are excited or both are quenched, when one is excited while the other is quenched and vice versa, when the ND 3 state changes its parity while D 2 is excited or quenched, and when ND 3 is excited or quenched while D 2 remains in the same state, ground or excited. In all these processes the results of MQCT are found to approximately satisfy the principle of microscopic reversibility. For a set of sixteen state-to-state transitions available from the literature for a collision energy of 800 cm –1 the values of cross sections predicted by MQCT are within 8% of accurate full-quantum results. A useful time-dependent insight is obtained by monitoring the evolution of state populations along MQCT trajectories. It is shown that, if before the collision, D 2 is in its ground state, the excitation of ND 3 rotational states proceeds through a two-step mechanism in which the kinetic energy of molecule–molecule collision is first used to excite D 2 and only then is transferred to the excited rotational states of ND 3 . Finally, it is found that both potential coupling and Coriolis coupling play important roles in ND 3 + D 2 collisions.

inelastic cross-sections↗

Three-terminal resistive switching memory in a transparent vertical-configuration device

The resistive switching phenomenon has attracted much attention recently for memory applications. It describes the reversible change in the resistance of a dielectric between two non-volatile states by the application of electrical pulses. Typical resistive switching memories are two-terminal devices formed by an oxide layer placed between two metal electrodes. Here, we report on the fabrication and operation of a three-terminal resistive switching memory that works as a reconfigurable logic component and offers an increased logic density on chip. The three-terminal memory device we present is transparent and could be further incorporated in transparent computing electronic technologies.

36 MATERIALS SCIENCE↗

Novel superposed kinklike and pulselike solutions for several nonlocal nonlinear equations

In this work, we show that a number of nonlocal nonlinear equations, including the Ablowitz–Musslimani and Yang variant of the nonlocal nonlinear Schrödinger (NLS) equation, the nonlocal modified Korteweg de Vries (mKdV) equation, and the nonlocal Hirota equation, admit novel kinklike and pulselike superposed periodic solutions. Furthermore, we show that the nonlocal mKdV equation also admits the superposed (hyperbolic) kink–antikink solution. In addition, we show that while the nonlocal Ablowitz–Musslimani variant of the NLS admits complex parity-time reversal-invariant kink and pulse solutions, neither the local NLS nor the Yang variant of the nonlocal NLS admits such solutions. Finally, except for the Yang variant of the nonlocal NLS, we show that the other three nonlocal equations admit both the kink and pulse solutions in the same model.

97 MATHEMATICS AND COMPUTING↗

Accelerated kinetic model for global macro stability studies of high-beta fusion reactors

The field reversed configuration (FRC), such as studied in the C-2W experiment at TAE Technologies, is an attractive candidate for realizing a nuclear fusion reactor. In an FRC, kinetic ion effects play the majority role in macroscopic stability, which allows global stability studies to make use of fluid-kinetic hybrid (also referred to as Ohm's law) models wherein ions are treated kinetically while electrons are treated as a fluid. The development and validation of such a hybrid particle-in-cell algorithm in the Exascale Computing Project code WarpX are reported here. Implementation of this model in the WarpX framework benefits from the numerical efficiency of WarpX as well as its scalability on large HPC systems and portability to different architectures. Performance benchmarks of the new algorithm for large, 3-dimensional, full device simulations from the Perlmutter supercomputer are presented. Results of a series of FRC simulations are discussed in which the impact of two-fluid effects on the tilt-mode growth rate was studied. It was observed that, in agreement with previous Hall-MHD studies, two-fluid effects have a stabilizing impact on the tilt mode.

Physics↗

On the large-eddy simulation of transitional wall-bounded flows

The structure of the subgrid scale fields in plane channel flow has been studied at various stages of the transition process to turbulence. The residual stress and subgrid scale dissipation calculated using velocity fields generated by direct numerical simulations of the Navier-Stokes equations are significantly different from their counterparts in turbulent flows. The subgrid scale dissipation changes sign over extended areas of the channel, indicating energy flow from the small scales to the large scales. This reversed energy cascade becomes less pronounced at the later stages of transition. Standard residual stress models of the Smagorinsky type are excessively dissipative. Rescaling the model constant improves the prediction of the total (integrated) subgrid scale dissipation, but not that of the local one. Despite the somewhat excessive dissipation of the rescaled Smagorinsky model, the results of a large eddy simulation of transition on a flat-plate boundary layer compare quite well with those of a direct simulation, and require only a small fraction of the computational effort. The inclusion of non-dissipative models, which could lead to further improvements, is proposed.

Piomelli, Ugo↗

On the large-eddy simulation of transitional wall-bounded flows

The structure of the subgrid scale fields in plane channel flow has been studied at various stages of the transition process to turbulence. The residual stress and subgrid scale dissipation calculated using velocity fields generated by direct numerical simulations of the Navier-Stokes equations are significantly different from their counterparts in turbulent flows. The subgrid scale dissipation changes sign over extended areas of the channel, indicating energy flow from the small scales to the large scales. This reversed energy cascade becomes less pronounced at the later stages of transition. Standard residual stress models of the Smagorinsky type are excessively dissipative. Rescaling the model constant improves the prediction of the total (integrated) subgrid scale dissipation, but not that of the local one. Despite the somewhat excessive dissipation of the rescaled Smagorinsky model, the results of a large eddy simulation of transition on a flat-plate boundary layer compare quite well with those of a direct simulation, and require only a small fraction of the computational effort. The inclusion of non-dissipative models, which could lead to further improvements, is proposed.

Piomelli, Ugo↗

Effect of patch borders on coercivity in amorphous rare earth-transition metal thin films

The coercivity at the micron scale is a very important property of magneto-optical media. It is a key factor that determines the magnetic domain wall movement and domain reversal. How the coercivity is influenced by a special type of patch borders is discussed. Patch formation is a general phenomenon in growth processes of amorphous rare earth transition metal thin films. Different patches may stem from different seeds and the patch borders are formed when they merge. Though little is known about the exact properties of the borders, we may expect that the exchange interaction at the patch border is weaker than that within a patch, since there is usually a spatial gap between two patches. Computer simulations were performed on a 2-D hexagonal lattice consisting of 37 complete patches with random shape and size. From the series of simulations we may conclude that the domain in the patch with borders of 30 percent exchange strength can expand most easily to the whole lattice, because the exchange strength can expand most easily to the whole lattice, because the exchange strength of the border is not too high to prevent the domain from growing within the patch and it is not too low to prevent the domain from expanding beyond the patch.

Patterson, G.↗

LYAPUNOV-Based Sensor Failure Detection and Recovery for the Reverse Water Gas Shift Process

Livingstone, a model-based AI software system, is planned for use in the autonomous fault diagnosis, reconfiguration, and control of the oxygen-producing reverse water gas shift (RWGS) process test-bed located in the Applied Chemistry Laboratory at KSC. In this report the RWGS process is first briefly described and an overview of Livingstone is given. Next, a Lyapunov-based approach for detecting and recovering from sensor failures, differing significantly from that used by Livingstone, is presented. In this new method, models used are in t e m of the defining differential equations of system components, thus differing from the qualitative, static models used by Livingstone. An easily computed scalar inequality constraint, expressed in terms of sensed system variables, is used to determine the existence of sensor failures. In the event of sensor failure, an observer/estimator is used for determining which sensors have failed. The theory underlying the new approach is developed. Finally, a recommendation is made to use the Lyapunov-based approach to complement the capability of Livingstone and to use this combination in the RWGS process.

Haralambous, Michael G.↗

CFD and Experimental Data Comparisons for Conventional and AFC-Enabled CRM High-Lift Configurations

Numerical simulations have been performed for a simplified high-lift (SHL) version of the Common Research Model (CRM) configuration, where the Fowler flaps of a representative conventional high-lift (CRM-HL) configuration are replaced by a set of simple hinged flaps. These hinged flaps are equipped with integrated modular active flow control (AFC) cartridges on the suction surface of the flap shoulder, and the resulting geometry is known as the CRM-SHL-AFC configuration. The main objective is to make use of AFC devices on the CRM-SHL-Configuration to produce the aerodynamic performance (lift) comparable to that of the CRM-HL configuration over a large angle of attack range encompassing maximum lift conditions. For comparison purposes, computations are also per-formed for the CRM-HL configuration. In the current paper, PowerFLOWR©, a CFD code based on the Lattice Boltzmann method (LBM), is used to simulate the entire flow field associated with the CRM-SHL-AFC configuration equipped with a combination of two different types of AFC actuators. The transonic version of the PowerFLOWR© code that has been validated for high-speed flows is used to simulate the flow field generated by the high-momentum actuators required to mitigate reversed flow regions on the suction surfaces of the main wing and the flap. This study is focused on the AFC systems and actuator arrangements that had emerged based on the parametric studies conducted previously at the nominal landing condition. Comparisons of the numerical solutions for lift and surface pressures are presented here with the experimental data, demonstrating the usefulness of CFD for predicting the flow field and lift characteristics of AFC-enabled high-lift configurations over a broad angle of attack range. The numerical solutions predict the expected trends in aerodynamic forces with angle of attack variation.

Veer N Vatsa↗

Quantum information processing with majorana bound states in superconducting circuits

In a weak link of two s-wave superconductors (SCs) coupled via a time-reversal-invariant (TRI) topological superconducting (TSC) island, a Josephson current can flow due to Cooper pairs tunneling in and out of spatially separated Majorana Kramers pairs (MKPs), which are doublets of Majorana bound states (MBSs). The sign of the resulting Josephson current is fixed by the joint parity of the four Majorana bound states that make up the MKPs on the TSC island. This parity-controlled Josephson effect can be used as a read-out mechanism for the joint parity in Majorana-based quantum computing. For a TSC island with four terminals, the SC leads can address a Majorana superconducting qubit (MSQ) formed by the charge ground states of the TSC island's terminals. Cooper pair splitting enables single-qubit operations, qubit read-out, as well as two-qubit entangling gates. Hence, TSC islands between SC leads may provide an alternative approach to superconducting quantum computation.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗