Topological Quantum Computing with p-Wave Superfluid Vortices

It is shown that Majorana fermions trapped in three vortices in a p-wave superfluid form a qubit in a topological quantum computing (TQC). Several similar ideas have already been proposed: Ivanov [Phys. Rev. Lett. {\bf 86}, 268 (2001)] and Zhang {\it et al.} [Phys. Rev. Lett. {\bf 99}, 220502 (2007)] have proposed schemes in which a qubit is implemented with two and four Majorana fermions, respectively, where a qubit operation is performed by exchanging the positions of Majorana fermions. The set of gates thus obtained is a discrete subset of the relevant unitary group. We propose, in this paper, a new scheme, where three Majorana fermions form a qubit. We show that continuous 1-qubit gate operations are possible by exchanging the positions of Majorana fermions complemented with dynamical phase change. 2-qubit gates are realized through the use of the coupling between Majorana fermions of different qubits.Comment: 5 pages, 2 figures. Two-qubit gate implementation is added

Vortex structures and zero energy states in the BCS-to-BEC evolution of p-wave resonant Fermi gases

Multiply quantized vortices in the BCS-to-BEC evolution of p-wave resonant Fermi gases are investigated theoretically. The vortex structure and the low-energy quasiparticle states are discussed, based on the self-consistent calculations of the Bogoliubov-de Gennes and gap equations. We reveal the direct relation between the macroscopic structure of vortices, such as particle densities, and the low-lying quasiparticle state. In addition, the net angular momentum for multiply quantized vortices with a vorticity $\kappa$ is found to be expressed by a simple equation, which reflects the chirality of the Cooper pairing. Hence, the observation of the particle density depletion and the measurement of the angular momentum will provide the information on the core-bound state and $p$-wave superfluidity. Moreover, the details on the zero energy Majorana state are discussed in the vicinity of the BCS-to-BEC evolution. It is demonstrated numerically that the zero energy Majorana state appears in the weak coupling BCS limit only when the vortex winding number is odd. There exist the $\kappa$ branches of the core bound states for a vortex state with vorticity $\kappa$, whereas only one of them can be the zero energy. This zero energy state vanishes at the BCS-BEC topological phase transition, because of interference between the core-bound and edge-bound states.Comment: 15 pages, 9 figures, published versio

Majorana bound state in rotating superfluid 3He-A between parallel plates

A concrete and experimentally feasible example for testing the putative Majorana zero energy state bound in a vortex is theoretically proposed for a parallel plate geometry of superfluid $^3$He-A phase. We examine the experimental setup in connection with ongoing rotating cryostat experiments. The theoretical analysis is based on the well-established Ginzburg--Landau functional, supplemented by microscopic calculations of the Bogoliubov--de Gennes equation, both of which allow the precise location of the parameter regions of the Majorana state to be found in realistic situations.Comment: 5 pages, 4 figure

A Minimum-Labeling Approach for Reconstructing Protein Networks across Multiple Conditions

The sheer amounts of biological data that are generated in recent years have driven the development of network analysis tools to facilitate the interpretation and representation of these data. A fundamental challenge in this domain is the reconstruction of a protein-protein subnetwork that underlies a process of interest from a genome-wide screen of associated genes. Despite intense work in this area, current algorithmic approaches are largely limited to analyzing a single screen and are, thus, unable to account for information on condition-specific genes, or reveal the dynamics (over time or condition) of the process in question. Here we propose a novel formulation for network reconstruction from multiple-condition data and devise an efficient integer program solution for it. We apply our algorithm to analyze the response to influenza infection in humans over time as well as to analyze a pair of ER export related screens in humans. By comparing to an extant, single-condition tool we demonstrate the power of our new approach in integrating data from multiple conditions in a compact and coherent manner, capturing the dynamics of the underlying processes.Comment: Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013

Collective Oscillations of Vortex Lattices in Rotating Bose-Einstein Condensates

The complete low-energy collective-excitation spectrum of vortex lattices is discussed for rotating Bose-Einstein condensates (BEC) by solving the Bogoliubov-de Gennes (BdG) equation, yielding, e.g., the Tkachenko mode recently observed at JILA. The totally symmetric subset of these modes includes the transverse shear, common longitudinal, and differential longitudinal modes. We also solve the time-dependent Gross-Pitaevskii (TDGP) equation to simulate the actual JILA experiment, obtaining the Tkachenko mode and identifying a pair of breathing modes. Combining both the BdG and TDGP approaches allows one to unambiguously identify every observed mode.Comment: 5 pages, 4 figure

Effect of Quadratic Zeeman Energy on the Vortex of Spinor Bose-Einstein Condensates

The spinor Bose-Einstein condensate of atomic gases has been experimentally realized by a number of groups. Further, theoretical proposals of the possible vortex states have been sugessted. This paper studies the effects of the quadratic Zeeman energy on the vortex states. This energy was ignored in previous theoretical studies, although it exists in experimental systems. We present phase diagrams of various vortex states taking into account the quadratic Zeeman energy. The vortex states are calculated by the Gross-Pitaevskii equations. Several new kinds of vortex states are found. It is also found that the quadratic Zeeman energy affects the direction of total magnetization and causes a significant change in the phase diagrams.Comment: 6 pages, 5 figures. Published in J. Phys. Soc. Jp

Asymmetric Fermi superfluid with different atomic species in a harmonic trap

We study the dilute fermion gas with pairing between two species and unequal concentrations in a harmonic trap using the mean field theory and the local density approximation. We found that the system can exhibit a superfluid shell structure sandwiched by the normal fermions. This superfluid shell structure occurs if the mass ratio is larger then certain critical value which increases from the weak-coupling BCS region to the strong-coupling BEC side. In the strong coupling BEC regime, the radii of superfluid phase are less sensitive to the mass ratios and are similar to the case of pairing with equal masses. However, the lighter leftover fermions are easier to mix with the superfluid core than the heavier ones. A partially polarized superfluid can be found if the majority fermions are lighter, whereas phase separation is still found if they are heavier.Comment: 12 pages, 7 figure

Larkin-Ovchinnikov-Fulde-Ferrell phase in the superconductor (TMTSF)2ClO4: Theory versus experiment

We consider a formation of the Larkin-Ovchinnikov-Fulde-Ferrell (LOFF) phase in a quasi-one-dimensional (Q1D) conductor in a magnetic field, parallel to its conducting chains, where we take into account both the paramagnetic spin-splitting and orbital destructive effects against superconductivity. We show that, due to a relative weakness of the orbital effects in a Q1D case, the LOFF phase appears in (TMTSF)$_2$ClO$_4$ superconductor for real values of its Q1D band parameters. We compare our theoretical calculations with the recent experimental data by Y. Maeno's group [S. Yonezawa et al., Phys. Rev. Lett. \textbf{100}, 117002 (2008)] and show that there is a good qualitative and quantitative agreement between the theory and experimental data.Comment: 4 pages, 1 figur

Impaired Autophagy of an Intracellular Pathogen Induced by a Crohn's Disease Associated ATG16L1 Variant

The genetic risk factors predisposing individuals to the development of inflammatory bowel disease are beginning to be deciphered by genome-wide association studies. Surprisingly, these new data point towards a critical role of autophagy in the pathogenesis of Crohn's disease. A single common coding variant in the autophagy protein ATG16L1 predisposes individuals to the development of Crohn's disease: while ATG16L1 encoding threonine at amino acid position 300 (ATG16L1*300T) confers protection, ATG16L1 encoding for alanine instead of threonine (ATG16L1*300A, also known as T300A) mediates risk towards the development of Crohn's disease. Here we report that, in human epithelial cells, the Crohn's disease-associated ATG16L1 coding variant shows impairment in the capture of internalized Salmonella within autophagosomes. Thus, we propose that the association of ATG16L1*300A with increased risk of Crohn's disease is due to impaired bacterial handling and lowered rates of bacterial capture by autophagy

Majorana edge modes of superfluid 3He A-phase in a slab

Motivated by a recent experiment on the superfluid 3He A-phase with a chiral p-wave pairing confined in a thin slab, we propose designing a concrete experimental setup for observing the Majorana edge modes that appear around the circumference edge region. We solve the quasi-classical Eilenberger equation, which is quantitatively reliable, to evaluate several observables. To derive the property inherent to the Majorana edge state, the full quantum mechanical Bogoliubov-de Gennes equation is solved in this setting. On the basis of the results obtained, we perform decisive experiments to check the Majorana nature.Comment: 5 pages, 5 figure