Cerulean: A hybrid assembly using high throughput short and long reads

Genome assembly using high throughput data with short reads, arguably, remains an unresolvable task in repetitive genomes, since when the length of a repeat exceeds the read length, it becomes difficult to unambiguously connect the flanking regions. The emergence of third generation sequencing (Pacific Biosciences) with long reads enables the opportunity to resolve complicated repeats that could not be resolved by the short read data. However, these long reads have high error rate and it is an uphill task to assemble the genome without using additional high quality short reads. Recently, Koren et al. 2012 proposed an approach to use high quality short reads data to correct these long reads and, thus, make the assembly from long reads possible. However, due to the large size of both dataset (short and long reads), error-correction of these long reads requires excessively high computational resources, even on small bacterial genomes. In this work, instead of error correction of long reads, we first assemble the short reads and later map these long reads on the assembly graph to resolve repeats. Contribution: We present a hybrid assembly approach that is both computationally effective and produces high quality assemblies. Our algorithm first operates with a simplified version of the assembly graph consisting only of long contigs and gradually improves the assembly by adding smaller contigs in each iteration. In contrast to the state-of-the-art long reads error correction technique, which requires high computational resources and long running time on a supercomputer even for bacterial genome datasets, our software can produce comparable assembly using only a standard desktop in a short running time.Comment: Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013

The Solution Space of the Unitary Matrix Model String Equation and the Sato Grassmannian

The space of all solutions to the string equation of the symmetric unitary one-matrix model is determined. It is shown that the string equation is equivalent to simple conditions on points $V_1$ and $V_2$ in the big cell \Gr of the Sato Grassmannian $Gr$. This is a consequence of a well-defined continuum limit in which the string equation has the simple form \lb \cp ,\cq_- \rb =\hbox{\rm 1}, with \cp and \cq_- $2\times 2$ matrices of differential operators. These conditions on $V_1$ and $V_2$ yield a simple system of first order differential equations whose analysis determines the space of all solutions to the string equation. This geometric formulation leads directly to the Virasoro constraints \L_n\,(n\geq 0), where \L_n annihilate the two modified-KdV \t-functions whose product gives the partition function of the Unitary Matrix Model.Comment: 21 page

Current-Driven Magnetization Dynamics in Magnetic Multilayers

We develop a quantum analog of the classical spin-torque model for current-driven magnetic dynamics. The current-driven magnetic excitation at finite field becomes significantly incoherent. This excitation is described by an effective magnetic temperature rather than a coherent precession as in the spin-torque model. However, both the spin-torque and effective temperature approximations give qualitatively similar switching diagrams in the current-field coordinates, showing the need for detailed experiments to establish the proper physical model for current-driven dynamics.Comment: 5 pages, 2 figure

Analytical solution of generalized Burton--Cabrera--Frank equations for growth and post--growth equilibration on vicinal surfaces

We investigate growth on vicinal surfaces by molecular beam epitaxy making use of a generalized Burton--Cabrera--Frank model. Our primary aim is to propose and implement a novel analytical program based on a perturbative solution of the non--linear equations describing the coupled adatom and dimer kinetics. These equations are considered as originating from a fully microscopic description that allows the step boundary conditions to be directly formulated in terms of the sticking coefficients at each step. As an example, we study the importance of diffusion barriers for adatoms hopping down descending steps (Schwoebel effect) during growth and post-growth equilibration of the surface.Comment: 16 pages, REVTeX 3.0, IC-DDV-94-00

Current induced switching of magnetic domains to a perpendicular configuration

In a ferromagnet--normal-metal--ferromagnet trilayer, a current flowing perpendicularly to the layers creates a torque on the magnetic moments of the ferromagnets. When one of the contacts is superconducting, the torque not only favors parallel or antiparallel alignment of the magnetic moments, as is the case for two normal contacts, but can also favor a configuration where the two moments are perpendicular. In addition, whereas the conductance for parallel and antiparallel magnetic moments is the same, signalling the absence of giant magnetoresistance in the usual sense, the conductance is greater in the perpendicular configuration. Thus, a negative magnetoconductance is predicted, in contrast with the usual giant magnetoresistance.Comment: 4 pages, 3 figures, major rewriting of the technical par

New Kadampa Buddhists and Jungian psychological type

Building on previous studies on Canadian Anglicans and Catholics, this study examines and discusses the psychological type profile of 31 adherents to New Kadampa Buddhism. Like Anglicans and Catholics, Buddhists preferred introversion (I). Like Anglicans who preferred intuition (N) and unlike Catholics who preferred sensing (S), Buddhists displayed a preference for intuition (N). Unlike Anglicans and Catholics who both preferred feeling (F), Buddhists displayed a balance between feeling (F) and thinking (T). Like Anglicans and unlike Catholics, Buddhists preferred the Apollonian temperament (NF) over the Epimethean temperament (SJ). These data are discussed to interpret the psychological appeal of New Kadampa Buddhism

Magnetization dynamics with a spin-transfer torque

The magnetization reversal and dynamics of a spin valve pillar, whose lateral size is 64$\times$64 nm$^2$, are studied by using micromagnetic simulation in the presence of spin transfer torque. Spin torques display both characteristics of magnetic damping (or anti-damping) and of an effective magnetic field. For a steady-state current, both M-I and M-H hysteresis loops show unique features, including multiple jumps, unusual plateaus and precessional states. These states originate from the competition between the energy dissipation due to Gilbert damping and the energy accumulation due to the spin torque supplied by the spin current. The magnetic energy oscillates as a function of time even for a steady-state current. For a pulsed current, the minimum width and amplitude of the spin torque for achieving current-driven magnetization reversal are quantitatively determined. The spin torque also shows very interesting thermal activation that is fundamentally different from an ordinary damping effect.Comment: 15 figure

Stationary Einstein-Maxwell fields in arbitrary dimensions

The Einstein-Maxwell equations in D-dimensions admitting (D-3) commuting Killing vector fields have been investigated. The existence of the electric, magnetic and twist potentials have been proved. The system is formulated as the harmonic map coupled to gravity on three-dimensional base space generalizing the Ernst system in the four-dimensional stationary Einstein-Maxwell theory. Some classes of the new exact solutions have been provided, which include the electro-magnetic generalization of the Myers-Perry solution, which describes the rotating black hole immersed in a magnetic universe, and the static charged black ring solution.Comment: 26 page

Magnetic exchange interaction induced by a Josephson current

We show that a Josephson current flowing through a ferromagnet-normal-metal-ferromagnet trilayer connected to two superconducting electrodes induces an equilibrium exchange interaction between the magnetic moments of the ferromagnetic layers. The sign and magnitude of the interaction can be controlled by the phase difference between the order parameters of the two superconductors. We present a general framework to calculate the Josephson current induced magnetic exchange interaction in terms of the scattering matrices of the different layers. The effect should be observable as the periodic switching of the relative orientation of the magnetic moments of the ferromagnetic layers in the ac Josephson effect.Comment: 12 pages, 7 figure

Spin pumping and magnetization dynamics in metallic multilayers

We study the magnetization dynamics in thin ferromagnetic films and small ferromagnetic particles in contact with paramagnetic conductors. A moving magnetization vector causes \textquotedblleft pumping\textquotedblright of spins into adjacent nonmagnetic layers. This spin transfer affects the magnetization dynamics similar to the Landau-Lifshitz-Gilbert phenomenology. The additional Gilbert damping is significant for small ferromagnets, when the nonmagnetic layers efficiently relax the injected spins, but the effect is reduced when a spin accumulation build-up in the normal metal opposes the spin pumping. The damping enhancement is governed by (and, in turn, can be used to measure) the mixing conductance or spin-torque parameter of the ferromagnet--normal-metal interface. Our theoretical findings are confirmed by agreement with recent experiments in a variety of multilayer systems.Comment: 10 pages, 6 figure