Chirality-2 fermion induced anti-Klein tunneling in 2D checkerboard lattice

The quantum tunneling effect in the two-dimensional (2D) checkerboard lattice is investigated. By analyzing the pseudospin texture of the states in a 2D checkerboard lattice based on the low-energy effective Hamiltonian, we find that this system has a chiral symmetry with chirality equal to 2. Although compared to regular chiral fermions, its pseudospin orientation does not vary uniformly. This suggests that the perfect reflection chiral tunneling, also known as the anti-Klein tunneling, is expected to appear in checkerboard lattice as well. In order to verify the conjecture, we calculate the transmission probability and find that normally incident electron states can be perfectly reflected by the barrier with hole states inside, and vice versa. Furthermore, we also numerically calculate the tunneling conductance of the checkerboard nanotube using the recursive Green's function method. The results show that a perfect on-off ratio can be achieved by confining the energy of the incident states within a certain range. It also suggests that, by tuning the barrier, the checkerboard nanotube is able to work as a perfect ``band filter" or ``tunneling field effect transistor", which transmits electrons selectively with respect to the pseudospin of the incident electrons.Comment: 13 pages, 6 figure

The Long-term Radiative Evolution of Anomalous X-ray Pulsar 1E 2259+586 after its 2002 Outburst

We present an analysis of five X-ray Multi-Mirror Mission (XMM) observations of the anomalous X-ray pulsar (AXP) 1E 2259+586 taken in 2004 and 2005 during its relaxation following its 2002 outburst. We compare these data with those of five previous XMM observations taken in 2002 and 2003, and find the observed flux decay is well described by a power-law of index -0.69+/-0.03. As of mid-2005, the source may still have been brighter than preoutburst, and was certainly hotter. We find a strong correlation between hardness and flux, as seen in other AXP outbursts. We discuss the implications of these results for the magnetar model.Comment: 23 Pages, 4 figures, 3 tables, published on Ap

Progress in strategies for sequence diversity library creation for directed evolution

Protein engineering has been the most attractive strategy for biologists to redesign enzymes. As the simplest technique of protein engineering, directed evolution has been applied to many fields, such as industry, agriculture and medicine. An experiment of directed evolution comprises mutant libraries creation and screening or selection for enzyme variants with desired properties. Therefore, a successful application of directed evolution depends on whether or not one can generate a quality library and perform effective screening to find the desired properties. Directed evolution is already increasingly used in many laboratories to improve protein stability and activity, alter enzyme substrate specificity, or design new activities. Meanwhile, many more effective novel strategies of mutant library generation and screening or selection have emerged in recent years, and will continue to be developed. Combining computational/rational design with directed evolution has been developed as more available means to redesign enzymes.Keywords: Protein engineering, directed evolution, sequence diversity creation, novel strategy, computational design, rational desig

Origin of Improved Photoelectrochemical Water Splitting in Mixed Perovskite Oxides

Owing to the versatility in their chemical and physical properties, transition metal perovskite oxides have emerged as a new category of highly efficient photocatalysts for photoelectrochemical water splitting. Here, to understand the underlying mechanism for the enhanced photoelectrochemical water splitting in mixed perovskites, we explore ideal epitaxial thin films of the BiFeO3-SrTiO3 system. The electronic struture and carrier dynamics are determined from both experiment and density-functional theory calculations. The intrinsic phenomena are measured in this ideal sytem, contrasting to commonly studied polycrstalline solid solutions where extrinsic structural features obscure the intrinsic phenomena. We determined that when SrTiO3 is added to BiFeO3 the conduction band minimum position is raised and an exponential tail of trap states from hybridized Ti 3d and Fe 3d orbitals emerges near the conduction band edge. The presence of these trap states strongly suppresses the fast electron-hole recombination and improves the photocurrent density in the visible-light region, up to 16 times at 0 VRHE compared to the pure end member compositions. Our work provides a new design approach for optimising the photoelectrochemical performance in mixed perovksite oxides.Comment: 7 pages and 5 figure

SSAGES : Software Suite for Advanced General Ensemble Simulations

Molecular simulation has emerged as an essential tool for modern-day research, but obtaining proper results and making reliable conclusions from simulations requires adequate sampling of the system under consideration. To this end, a variety of methods exist in the literature that can enhance sampling considerably, and increasingly sophisticated, effective algorithms continue to be developed at a rapid pace. Implementation of these techniques, however, can be challenging for experts and non-experts alike. There is a clear need for software that provides rapid, reliable, and easy access to a wide range of advanced sampling methods and that facilitates implementation of new techniques as they emerge. Here we present SSAGES, a publicly available Software Suite for Advanced General Ensemble Simulations designed to interface with multiple widely used molecular dynamics simulations packages. SSAGES allows facile application of a variety of enhanced sampling techniques—including adaptive biasing force, string methods, and forward flux sampling—that extract meaningful free energy and transition path data from all-atom and coarse-grained simulations. A noteworthy feature of SSAGES is a user-friendly framework that facilitates further development and implementation of new methods and collective variables. In this work, the use of SSAGES is illustrated in the context of simple representative applications involving distinct methods and different collective variables that are available in the current release of the suite. The code may be found at: https://github.com/MICCoM/SSAGES-public

A comprehensive functional analysis of tissue specificity of human gene expression

<p>Abstract</p> <p>Background</p> <p>In recent years, the maturation of microarray technology has allowed the genome-wide analysis of gene expression patterns to identify tissue-specific and ubiquitously expressed ('housekeeping') genes. We have performed a functional and topological analysis of housekeeping and tissue-specific networks to identify universally necessary biological processes, and those unique to or characteristic of particular tissues.</p> <p>Results</p> <p>We measured whole genome expression in 31 human tissues, identifying 2374 housekeeping genes expressed in all tissues, and genes uniquely expressed in each tissue. Comprehensive functional analysis showed that the housekeeping set is substantially larger than previously thought, and is enriched with vital processes such as oxidative phosphorylation, ubiquitin-dependent proteolysis, translation and energy metabolism. Network topology of the housekeeping network was characterized by higher connectivity and shorter paths between the proteins than the global network. Ontology enrichment scoring and network topology of tissue-specific genes were consistent with each tissue's function and expression patterns clustered together in accordance with tissue origin. Tissue-specific genes were twice as likely as housekeeping genes to be drug targets, allowing the identification of tissue 'signature networks' that will facilitate the discovery of new therapeutic targets and biomarkers of tissue-targeted diseases.</p> <p>Conclusion</p> <p>A comprehensive functional analysis of housekeeping and tissue-specific genes showed that the biological function of housekeeping and tissue-specific genes was consistent with tissue origin. Network analysis revealed that tissue-specific networks have distinct network properties related to each tissue's function. Tissue 'signature networks' promise to be a rich source of targets and biomarkers for disease treatment and diagnosis.</p

Plasmin Plays an Essential Role in Amplification of Psoriasiform Skin Inflammation in Mice

BACKGROUND: Although increased levels of plasminogen activators have been found in psoriatic lesions, the role of plasmin converted from plasminogen by plasminogen activators in pathogenesis of psoriasis has not been investigated. METHODOLOGY/PRINCIPAL FINDINGS: Here we examined the contribution of plasmin to amplification of inflammation in patients with psoriasis. We found that plasminogen was diminished, but that the amount and activity of its converted product plasmin were markedly increased in psoriasis. Moreover, annexin II, a receptor for plasmin was dramatically increased in both dermis and epidermis in psoriasis. Plasmin at sites of inflammation was pro-inflammatory, eliciting production of inflammatory factors, including CC chemokine ligand 20 (CCL20) and interleukin-23 (IL-23), that was mediated by the nuclear factor-kappaB (NF-κB) signaling pathway and that had an essential role in the recruitment and activation of pathogenic C-C chemokine receptor type 6 (CCR6)+ T cells. Moreover, intradermal injection of plasmin or plasmin together with recombinant monocyte/macrophage chemotactic protein-1 (MCP-1) resulted in induction of psoriasiform skin inflammation around the injection sites with several aspects of human psoriasis in mice. CONCLUSIONS/SIGNIFICANCE: Plasmin converted from plasminogen by plasminogen activators plays an essential role in amplification of psoriasiform skin inflammation in mice, and targeting plasmin receptor--annexin II--may harbor therapeutic potential for the treatment of human psoriasis