Sequence‐based prediction of protein–peptide binding sites using support vector machine

Protein–peptide interactions are essential for all cellular processes including DNA repair, replication, gene‐expression, and metabolism. As most protein – peptide interactions are uncharacterized, it is cost effective to investigate them computationally as the first step. All existing approaches for predicting protein – peptide binding sites, however, are based on protein structures despite the fact that the structures for most proteins are not yet solved. This article proposes the first machine‐learning method called SPRINT to make Sequence‐based prediction of Protein – peptide Residue‐level Interactions. SPRINT yields a robust and consistent performance for 10‐fold cross validations and independent test. The most important feature is evolution‐generated sequence profiles. For the test set (1056 binding and non‐binding residues), it yields a Matthews’ Correlation Coefficient of 0.326 with a sensitivity of 64% and a specificity of 68%. This sequence‐based technique shows comparable or more accurate than structure‐based methods for peptide‐binding site prediction. SPRINT is available as an online server at: http://sparks-lab.org/ . © 2016 Wiley Periodicals, Inc.     

Synthesis and characterization of a new ternary imide-Li2Ca(NH)2

The ternary imide Li(2)Ca(NH)2 was successfully synthesized by dehydrogenating a mixture of LiNH(2) and CaH(2) at a molar ratio of 2:1 in a stream of purified argon at 300 degrees C. A powder X-ray diffraction measurement revealed that Li(2)Ca(NH)2 was of the trigonal anti-La(2)O(3) structure (space group Pm1) with lattice constants of a = 3.5664(3)A and c = 5.9540(8) A. Ca occupied the 1b site (0, 0, 1/2), Li occupied the 2d site (1/3, 2/3, 0.8841(22)), and N occupied the 2d site (1/3, 2/3, 0.2565(15)). Nuclear magnetic resonance and X-ray absorption fine structure analyses demonstrated that each Li ion was coordinated with four imide ions and each Ca ion was coordinated with six imide ions.     

Rheological behavior and prediction for blending conditions of a thermotropic liquid crystalline polyester with nylon

The dynamic rheological behavior of a liquid crystalline polymer (LCP), Vectra™ A, and nylons was investigated. The viscosities of nylon 66 and nylon 6 decrease slowly with an increase in temperature, while the viscosity of Vectra A drops dramatically at 280 °C, but remains slightly changed above 300 °C. At constant frequency and above 300 °C, the mean value of the activation energy of Vectra A is about 87.0 kJ/mole, but jumps to a much higher value of about 407.0 kJ/mole if the melt temperature is below 300 °C. The activation energy of Vectra A above 300 °C is lower than nylon 66, which shows that the viscosity of nylon 66 has a greater temperature dependence than Vectra A. The viscosity ratio of Vectra A to Nylon 66 is less than 1 at temperatures higher than 290 °C, which indicates that Vectra A can form the fibrils in the nylon 66 matrix and reinforce nylon 66 when blending them above this temperature. Experimental data confirm our prediction. Copyright © 2000 John Wiley & Sons, Ltd.     

Growth of well-aligned Bi nanowire on Ag(1 1 1)

We report the fabrication of one-dimensional (1D) Bi nanowires grown on Ag(1 1 1) with average lateral width from 9 to 20 nm by physical vapor deposition in ultra high vacuum conditions. In situ low-temperature scanning tunneling microscopy analyses reveal that the preferred growth of 1D Bi nanostructures is driven by the highly anisotropic bonding in the crystallographic structure of the Bi(1 1 0) plane. The Bi nanowires grow along direction and align with the directions on Ag(1 1 1). The growth of the Bi nanowires proceeds in a bilayer growth mode resulting from the layer pairing in Bi(1 1 0) which saturates the dangling bonds and lowers the total energy.     

Low-temperature scanning tunneling microscopy and near-edge X-ray absorption fine structure investigation of epitaxial growth of F<Subscript>16</Subscript>CuPc thin films on graphite

Low-temperature scanning tunneling microscopy (LT-STM) and near-edge X-ray absorption fine structure (NEXAFS) measurements are used to study the epitaxial growth and molecular orientation of organic thin films of copper hexadecafluorophthalocyanine (F₁₆CuPc) on highly oriented pyrolytic graphite (HOPG). Our results show that F₁₆CuPc molecules lie flat on HOPG up to 5 nm thickness, stabilized by interfacial and interlayer π–π interactions. LT-STM experiments reveal the coexistence of two different in-plane orientations of the F₁₆CuPc monolayer on HOPG. On the second layer of F₁₆CuPc on HOPG, however, all F₁₆CuPc molecules possess the same in-plane orientation.     

Surface transfer doping of semiconductors

Surface transfer doping relies on charge separation at interfaces, and represents a valuable tool for the controlled and nondestructive doping of nanostructured materials or organic semiconductors at the nanometer-scale. It cannot be easily achieved by the conventional implantation process with energetic ions. Surface transfer doping can effectively dope semiconductors and nanostructures at relatively low cost, thereby facilitating the development of organic and nanoelectronics. The aim of this review is to highlight recent advances of surface transfer doping of semiconductors. Special focus is given to the effective doping of diamond, epitaxial graphene thermally grown on SiC, and organic semiconductors. The doping mechanism of various semiconductors and their possible applications in nanoelectronic devices will be discussed, including the interfacial charge transfer and the energy level alignment mechanisms.     

Rational Design of an Organometallic Glutathione Transferase Inhibitor

Double trouble : A hybrid organic–inorganic (organometallic) inhibitor was designed to target glutathione transferases. The metal center is used to direct protein binding, while the organic moiety acts as the active‐site inhibitor (see picture). The mechanism of inhibition was studied using a range of biophysical and biochemical methods.

     

Optimal warranty policies for systems with imperfect repair

We investigate a system whose basic warranty coverage is minimal repair up to a specified warranty length. An additional service is offered whereby first failure is restored up to the consumers’ chosen level of repair. The problem is studied under two system replacement strategies: periodic maintenance before and after warranty. It turns out that our model generalizes the model of Rinsaka and Sandoh [K. Rinsaka, H. Sandoh, A stochastic model with an additional warranty contract, Computers and Mathematics with Applications 51 (2006) 179–188] and the model of Yeh et al. [R.H. Yeh, M.Y. Chen, C.Y. Lin, Optimal periodic replacement policy for repairable products under free-repair warranty, European Journal of Operational Research 176 (2007) 1678–1686]. We derive the optimal maintenance period and optimal level of repair based on the structures of the cost function and failure rate function. We show that under certain assumptions, the optimal repair level for additional service is an increasing function of the replacement time. We provide numerical studies to verify some of our results.     

Cap representations of G2 and the spin L-function of PGSp6

We give a construction of a family of CAP representations of the exceptional group G ₂, whose existence is predicted by Arthur’s conjecture. These are constructed by lifting certain cuspidal representations of PGS _p6. To show that the lifting is non-zero, we establish a Rankin-Selberg integral for the degree 8 Spin L-function of these cuspidal representations of PGS _p6.     

Configuration-dependent interface charge transfer at a molecule-metal junction

The role of the molecule-metal interface is a key issue in molecular electronics. Interface charge transfer processes for 4-fluorobenzenethiol monolayers with different molecular orientations on Au(111) were studied by resonant photoemission spectroscopy. The electrons excited into the LUMO or LUMO+1 are strongly localized for the molecules standing up on Au(111). In contrast, an ultrafast charge transfer process was observed for the molecules lying down on Au(111). This configuration-dependent ultrafast electron transfer is dominated by an adiabatic mechanism and directly reflects the delocalization of the molecular orbitals for molecules lying down on Au(111). Theoretical calculations confirm that the molecular orbitals indeed experience a localization-delocalization transition resulting from hybridization between the molecular orbitals and metal surface. Such an orientation-dependent transition could be harnessed in molecular devices that switch via charge transfer when the molecular orientation is made to change.