Spontaneous edge-defect formation and defect-induced conductance suppression in graphene nanoribbons

We present a first-principles study of the migration and recombination of edge defects (carbon adatom and/or vacancy) and their influence on electrical conductance in zigzag graphene nanoribbons (ZGNRs). It is found that at room temperature, the adatom is quite mobile while the vacancy is almost immobile along the edge of ZGNRs. The recombination of an adatom-vacancy pair leads to a pentagon-heptagon ring defect structure having a lower energy than the perfect edge, implying that such an edge-defect can be formed spontaneously. This edge defect can suppresses the conductance of ZGNRs drastically, which provides some useful hints for understanding the observed semiconducting behavior of the fabricated narrow GNRs.Comment: 6 pages, 4 figures, to appear in PR

Two Affine Scaling Methods for Solving Optimization Problems Regularized with an L1-norm

In finance, the implied volatility surface is plotted against strike price and time to maturity. The shape of this volatility surface can be identified by fitting the model to what is actually observed in the market. The metric that is used to measure the discrepancy between the model and the market is usually defined by a mean squares of error of the model prices to the market prices. A regularization term can be added to this error metric to make the solution possess some desired properties. The discrepancy that we want to minimize is usually a highly nonlinear function of a set of model parameters with the regularization term. Typically monotonic decreasing algorithm is adopted to solve this minimization problem. Steepest descent or Newton type algorithms are two iterative methods but they are local, i.e., they use derivative information around the current iterate to find the next iterate. In order to ensure convergence, line search and trust region methods are two widely used globalization techniques. Motivated by the simplicity of Barzilai-Borwein method and the convergence properties brought by globalization techniques, we propose a new Scaled Gradient (SG) method for minimizing a differentiable function plus an L1-norm. This non-monotone iterative method only requires gradient information and safeguarded Barzilai-Borwein steplength is used in each iteration. An adaptive line search with the Armijo-type condition check is performed in each iteration to ensure convergence. Coleman, Li and Wang proposed another trust region approach in solving the same problem. We give a theoretical proof of the convergence of their algorithm. The objective of this thesis is to numerically investigate the performance of the SG method and establish global and local convergence properties of Coleman, Li and Wang’s trust region method proposed in [26]. Some future research directions are also given at the end of this thesis

Structural analysis and insight into novel MMP-13 inhibitors from natural chemiome as disease-modifying osteoarthritis drugs

Purpose: To identify natural chemiome that inhibits matrix-metalloproteinases (MMPs) with a view to discovering novel disease-modifying osteoarthritis drugs (DMOADs).Methods: Computer-aided drug design (CADD) with virtual screening, ADME/Tox, molecular docking, molecular dynamics simulation, and MM-PBSA calculations were used in search of novel natural compounds that inhibit MMPs.Results: From more than fifty thousand compounds, a single lead compound (IBS ID: 77312) was shortlisted using bias based on binding energy and drug-likeness. This lead compound synergistically bound to the S1 domain of MMP-13 protein through five hydrogen bonds. The interactions became stable within 100-nanosecond molecular dynamics simulation run. The in vitro data for the lead compound showed that its minimal non-lethal dose increased collagen content but decreased aggrecan level in chondrocytes.Conclusion: This study has identified a natural lead compound that may pave the way for a novel DMOAD of natural origin against OA.Keywords: Osteoarthritis, MMP-13, Natural chemiome, Disease-modifying osteoarthritis drug, Molecular dockin

Molecular evolution of Cide family proteins: Novel domain formation in early vertebrates and the subsequent divergence

<p>Abstract</p> <p>Background</p> <p>Cide family proteins including Cidea, Cideb and Cidec/Fsp27, contain an N-terminal CIDE-N domain that shares sequence similarity to the N-terminal CAD domain (NCD) of DNA fragmentation factors Dffa/Dff45/ICAD and Dffb/Dff40/CAD, and a unique C-terminal CIDE-C domain. We have previously shown that Cide proteins are newly emerged regulators closely associated with the development of metabolic diseases such as obesity, diabetes and liver steatosis. They modulate many metabolic processes such as lipolysis, thermogenesis and TAG storage in brown adipose tissue (BAT) and white adipose tissue (WAT), as well as fatty acid oxidation and lipogenesis in the liver.</p> <p>Results</p> <p>To understand the evolutionary process of Cide proteins and provide insight into the role of Cide proteins as potential metabolic regulators in various species, we searched various databases and performed comparative genomic analysis to study the sequence conservation, genomic structure, and phylogenetic tree of the CIDE-N and CIDE-C domains of Cide proteins. As a result, we identified signature sequences for the N-terminal region of Dffa, Dffb and Cide proteins and CIDE-C domain of Cide proteins, and observed that sequences homologous to CIDE-N domain displays a wide phylogenetic distribution in species ranging from lower organisms such as hydra (<it>Hydra vulgaris</it>) and sea anemone (<it>Nematostella vectensis</it>) to mammals, whereas the CIDE-C domain exists only in vertebrates. Further analysis of their genomic structures showed that although evolution of the ancestral CIDE-N domain had undergone different intron insertions to various positions in the domain among invertebrates, the genomic structure of <it>Cide </it>family in vertebrates is stable with conserved intron phase.</p> <p>Conclusion</p> <p>Based on our analysis, we speculate that in early vertebrates CIDE-N domain was evolved from the duplication of NCD of Dffa. The CIDE-N domain somehow acquired the CIDE-C domain that was formed around the same time, subsequently generating the Cide protein. Subsequent duplication and evolution have led to the formation of different Cide family proteins that play unique roles in the control of metabolic pathways in different tissues.</p

Bethe states of the trigonometric SU(3) spin chain with generic open boundaries

By combining the algebraic Bethe ansatz and the off-diagonal Bethe ansatz, we investigate the trigonometric SU(3) model with generic open boundaries. The eigenvalues of the transfer matrix are given in terms of an inhomogeneous T-Q relation, and the corresponding eigenstates are expressed in terms of nested Bethe-type eigenstates which have well-defined homogeneous limit. This exact solution provides a basis for further analyzing the thermodynamic properties and correlation functions of the anisotropic models associated with higher rank algebras.Comment: 17 pages, 3 tables. arXiv admin note: text overlap with arXiv:1705.0947