BioWorkbench: A High-Performance Framework for Managing and Analyzing Bioinformatics Experiments

Advances in sequencing techniques have led to exponential growth in biological data, demanding the development of large-scale bioinformatics experiments. Because these experiments are computation- and data-intensive, they require high-performance computing (HPC) techniques and can benefit from specialized technologies such as Scientific Workflow Management Systems (SWfMS) and databases. In this work, we present BioWorkbench, a framework for managing and analyzing bioinformatics experiments. This framework automatically collects provenance data, including both performance data from workflow execution and data from the scientific domain of the workflow application. Provenance data can be analyzed through a web application that abstracts a set of queries to the provenance database, simplifying access to provenance information. We evaluate BioWorkbench using three case studies: SwiftPhylo, a phylogenetic tree assembly workflow; SwiftGECKO, a comparative genomics workflow; and RASflow, a RASopathy analysis workflow. We analyze each workflow from both computational and scientific domain perspectives, by using queries to a provenance and annotation database. Some of these queries are available as a pre-built feature of the BioWorkbench web application. Through the provenance data, we show that the framework is scalable and achieves high-performance, reducing up to 98% of the case studies execution time. We also show how the application of machine learning techniques can enrich the analysis process

Quantum Computing in Molecular Magnets

Shor and Grover demonstrated that a quantum computer can outperform any classical computer in factoring numbers and in searching a database by exploiting the parallelism of quantum mechanics. Whereas Shor's algorithm requires both superposition and entanglement of a many-particle system, the superposition of single-particle quantum states is sufficient for Grover's algorithm. Recently, the latter has been successfully implemented using Rydberg atoms. Here we propose an implementation of Grover's algorithm that uses molecular magnets, which are solid-state systems with a large spin; their spin eigenstates make them natural candidates for single-particle systems. We show theoretically that molecular magnets can be used to build dense and efficient memory devices based on the Grover algorithm. In particular, one single crystal can serve as a storage unit of a dynamic random access memory device. Fast electron spin resonance pulses can be used to decode and read out stored numbers of up to 10^5, with access times as short as 10^{-10} seconds. We show that our proposal should be feasible using the molecular magnets Fe8 and Mn12.Comment: 13 pages, 2 figures, PDF, version published in Nature, typos correcte

Spin qubits with electrically gated polyoxometalate molecules

Spin qubits offer one of the most promising routes to the implementation of quantum computers. Very recent results in semiconductor quantum dots show that electrically-controlled gating schemes are particularly well-suited for the realization of a universal set of quantum logical gates. Scalability to a larger number of qubits, however, remains an issue for such semiconductor quantum dots. In contrast, a chemical bottom-up approach allows one to produce identical units in which localized spins represent the qubits. Molecular magnetism has produced a wide range of systems with tailored properties, but molecules permitting electrical gating have been lacking. Here we propose to use the polyoxometalate [PMo12O40(VO)2]q-, where two localized spins-1/2 can be coupled through the electrons of the central core. Via electrical manipulation of the molecular redox potential, the charge of the core can be changed. With this setup, two-qubit gates and qubit readout can be implemented.Comment: 9 pages, 6 figures, to appear in Nature Nanotechnolog

Quiet SDS Josephson Junctions for Quantum Computing

Unconventional superconductors exhibit an order parameter symmetry lower than the symmetry of the underlying crystal lattice. Recent phase sensitive experiments on YBCO single crystals have established the d-wave nature of the cuprate materials, thus identifying unambiguously the first unconventional superconductor. The sign change in the order parameter can be exploited to construct a new type of s-wave - d-wave - s-wave Josephson junction exhibiting a degenerate ground state and a double-periodic current-phase characteristic. Here we discuss how to make use of these special junction characteristics in the construction of a quantum computer. Combining such junctions together with a usual s-wave link into a SQUID loop we obtain what we call a `quiet' qubit --- a solid state implementation of a quantum bit which remains optimally isolated from its environment.Comment: 4 pages, 2 ps-figure

Quantum Nucleation in a Ferromagnetic Film Placed in a Magnetic Field at an Arbitrary Angle

We study the quantum nucleation in a thin ferromagnetic film placed in a magnetic field at an arbitrary angle. The dependence of the quantum nucleation and the temperature of the crossover from thermal to quantum regime on the direction and the strength of the applied field are presented. It is found that the maximal value of the rate and that of the crossover temperature are obtained at a some angle with the magnetic field, not in the direction of the applied field opposite to the initial easy axis.Comment: 15 pages, RevTex, 3 PostScript figures. To appear in Phys. Rev.

Topologically protected quantum bits from Josephson junction arrays

All physical implementations of quantum bits (qubits), carrying the information and computation in a putative quantum computer, have to meet the conflicting requirements of environmental decoupling while remaining manipulable through designed external signals. Proposals based on quantum optics naturally emphasize the aspect of optimal isolation, while those following the solid state route exploit the variability and scalability of modern nanoscale fabrication techniques. Recently, various designs using superconducting structures have been successfully tested for quantum coherent operation, however, the ultimate goal of reaching coherent evolution over thousands of elementary operations remains a formidable task. Protecting qubits from decoherence by exploiting topological stability, a qualitatively new proposal due to Kitaev, holds the promise for long decoherence times, but its practical physical implementation has remained unclear so far. Here, we show how strongly correlated systems developing an isolated two-fold degenerate quantum dimer liquid groundstate can be used in the construction of topologically stable qubits and discuss their implementation using Josephson junction arrays.Comment: 6 pages, 4 figure

Bloch oscillations of magnetic solitons in anisotropic spin-1/2 chains

We study the quantum dynamics of soliton-like domain walls in anisotropic spin-1/2 chains in the presence of magnetic fields. In the absence of fields, domain walls form a Bloch band of delocalized quantum states while a static field applied along the easy axis localizes them into Wannier wave packets and causes them to execute Bloch oscillations, i.e. the domain walls oscillate along the chain with a finite Bloch frequency and amplitude. In the presence of the field, the Bloch band, with a continuum of extended states, breaks up into the Wannier-Zeeman ladder -- a discrete set of equally spaced energy levels. We calculate the dynamical structure factor in the one-soliton sector at finite frequency, wave vector, and temperature, and find sharp peaks at frequencies which are integer multiples of the Bloch frequency. We further calculate the uniform magnetic susceptibility and find that it too exhibits peaks at the Bloch frequency. We identify several candidate materials where these Bloch oscillations should be observable, for example, via neutron scattering measurements. For the particular compound CoCl_2.2H_2O we estimate the Bloch amplitude to be on the order of a few lattice constants, and the Bloch frequency on the order of 100 GHz for magnetic fields in the Tesla range and at temperatures of about 18 Kelvin.Comment: 31 single-spaced REVTeX pages, including 7 figures embedded with eps

Semiclassical mechanics of a non-integrable spin cluster

We study detailed classical-quantum correspondence for a cluster system of three spins with single-axis anisotropic exchange coupling. With autoregressive spectral estimation, we find oscillating terms in the quantum density of states caused by classical periodic orbits: in the slowly varying part of the density of states we see signs of nontrivial topology changes happening to the energy surface as the energy is varied. Also, we can explain the hierarchy of quantum energy levels near the ferromagnetic and antiferromagnetic states with EKB quantization to explain large structures and tunneling to explain small structures.Comment: 9 pages. For related works see "http://www.msc.cornell.edu/~clh/clh.html

Evaluation of adrenal tumors by magnetic resonance imaging with histological correlation

A ressonância magnética é ferramenta importante para a detecção e caracterização dos tumores adrenais. O conhecimento das diferentes apresentações dos tumores primários e secundários à ressonância magnética e sua correlação com dados da histologia são essenciais para o correto raciocínio diagnóstico. Este artigo revisa os aspectos que podem estreitar o diagnóstico diferencial dos tumores adrenais, dando ênfase à correlação histológica daqueles mais comuns.Magnetic resonance imaging is an important tool for the detection and characterization of adrenal tumors. The knowledge about the different presentations of primary and secondary adrenal tumors at magnetic resonance imaging and their correlation with histological data are essential for the establishment of a correct diagnosis. The present study reviews magnetic resonance imaging aspects which may narrow the differential diagnosis of adrenal tumors, emphasizing the histological correlation of the most frequent ones

Tunable few-electron double quantum dots and Klein tunnelling in ultra-clean carbon nanotubes

Quantum dots defined in carbon nanotubes are a platform for both basic scientific studies and research into new device applications. In particular, they have unique properties that make them attractive for studying the coherent properties of single electron spins. To perform such experiments it is necessary to confine a single electron in a quantum dot with highly tunable barriers, but disorder has until now prevented tunable nanotube-based quantum-dot devices from reaching the single-electron regime. Here, we use local gate voltages applied to an ultra-clean suspended nanotube to confine a single electron in both a single quantum dot and, for the first time, in a tunable double quantum dot. This tunability is limited by a novel type of tunnelling that is analogous to that in the Klein paradox of relativistic quantum mechanics.Comment: 21 pages including supplementary informatio