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

E1-Like Activating Enzyme Atg7 Is Preferentially Sequestered into p62 Aggregates via Its Interaction with LC3-I

p62 is constitutively degraded by autophagy via its interaction with LC3. However, the interaction of p62 with LC3 species in the context of the LC3 lipidation process is not specified. Further, the p62-mediated protein aggregation's effect on autophagy is unclear. We systemically analyzed the interactions of p62 with all known Atg proteins involved in LC3 lipidation. We find that p62 does not interact with LC3 at the stages when it is being processed by Atg4B or when it is complexed or conjugated with Atg3. p62 does interact with LC3-I and LC3-I:Atg7 complex and is preferentially recruited by LC3-II species under autophagic stimulation. Given that Atg4B, Atg3 and LC3-Atg3 are indispensable for LC3-II conversion, our study reveals a protective mechanism for Atg4B, Atg3 and LC3-Atg3 conjugate from being inappropriately sequestered into p62 aggregates. Our findings imply that p62 could potentially impair autophagy by negatively affecting LC3 lipidation and contribute to the development of protein aggregate diseases. © 2013 Gao et al

Simultaneously optimizing the interdependent thermoelectric parameters in Ce(Ni1−x_{1-x}Cux_x)2_2Al3_3

Substitution of Cu for Ni in the Kondo lattice system CeNi$_2$Al$_3$ results in a simultaneous optimization of the three interdependent thermoelectric parameters: thermoelectric power, electrical and thermal conductivities, where the electronic change in conduction band induced by the extra electron of Cu is shown to be crucial. The obtained thermoelectric figure of merit $zT$ amounts to 0.125 at around 100 K, comparable to the best values known for Kondo compounds. The realization of ideal thermoelectric optimization in Ce(Ni$_{1-x}$Cu$_x$)$_2$Al$_3$ indicates that proper electronic tuning of Kondo compounds is a promising approach to efficient thermoelectric materials for cryogenic application.Comment: 4 pages, 4 figures. Accepted for publication in Physical Review

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

Semiflexible Filamentous Composites

Inspired by the ubiquity of composite filamentous networks in nature we investigate models of biopolymer networks that consist of interconnected floppy and stiff filaments. Numerical simulations carried out in three dimensions allow us to explore the microscopic partitioning of stresses and strains between the stiff and floppy fractions c_s and c_f, and reveal a non-trivial relationship between the mechanical behavior and the relative fraction of stiff polymer: when there are few stiff polymers, non-percolated stiff ``inclusions`` are protected from large deformations by an encompassing floppy matrix, while at higher fractions of stiff material the stiff network is independently percolated and dominates the mechanical response.Comment: Phys. Rev. Lett, to appear (4 pages, 2 figures

Functions of sensor 1 and sensor 2 regions of Saccharomyces cerevisiae Cdc6p in vivo and in vitro

Cdc6p is a key regulator of the cell cycle in eukaryotes and is a member of the AAA(+) (ATPases associated with a variety of cellular activities) family of proteins. In this family of proteins, the sensor 1 and sensor 2 regions are important for their function and ATPase activity. Here, site-directed mutagenesis has been used to examine the role of these regions of Saccharomyces cerevisiae Cdc6p in controlling the cell cycle progression and initiation of DNA replication. Two important amino acid residues (Asn(263) in sensor 1 and Arg(332) in sensor 2) were identified as key residues for Cdc6p function in vivo. Cells expressing mutant Cdc6p (N263A or R332E) grew slowly and accumulated in the S phase. In cells expressing mutant Cdc6p, loading of the minichromosome maintenance (MCM) complex of proteins was decreased, suggesting that the slow progression of S phase in these cells was due to inefficient MCM loading on chromatin. Purified wild type Cdc6p but not mutant Cdc6p (N263A and R332E) caused the structural modification of origin recognition complex proteins. These results are consistent with the idea that Cdc6p uses its ATPase activity to change the conformation of origin recognition complex, and then together they recruit the MCM complex

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

Following autophagy step by step

Autophagy is an evolutionarily conserved lysosomal degradation route for soluble components of the cytosol and organelles. There is great interest in identifying compounds that modulate autophagy because they may have applications in the treatment of major diseases including cancer and neurodegenerative disease. Hundeshagen and colleagues describe this month in BMC Biology a screening assay based on flow cytometry that makes it possible to track distinct steps in the autophagic process and thereby identify novel modulators of 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

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