Mono-allelic retrotransposon insertion addresses epigenetic transcriptional repression in human genome

Background: Retrotransposons have been extensively studied in plants and animals and have been shown to have an impact on human genome dynamics and evolution. Their ability to move within genomes gives retrotransposons to affect genome instability. Methods: we examined the polymorphic inserted AluYa5, evolutionary young Alu, in the progesterone receptor gene to determine the effects of Alu insertion on molecular environment. We used mono-allelic inserted cell lines which carry both Alu-present and Alu-absent alleles. To determine the epigenetic change and gene expression, we performed restriction enzyme digestion, Pyrosequencing, and Chromatin Immunoprecipitation. Results: We observed that the polymorphic insertion of evolutionally young Alu causes increasing levels of DNA methylation in the surrounding genomic area and generates inactive histone tail modifications. Consequently the Alu insertion deleteriously inactivates the neighboring gene expression. Conclusion: The mono-allelic Alu insertion cell line clearly showed that polymorphic inserted repetitive elements cause the inactivation of neighboring gene expression, bringing aberrant epigenetic changes

Hydrated copper and gold monovalent cations: Ab initio study

To understand the hydration phenomena of noble transition metals, we investigated the structures, hydration energies, electronic properties, and spectra of the Cu+(H3O)(1-6) and Au+ (H2O)(1-6) clusters using ab initio calculations. The coordination numbers of these clusters are found to be only two, which is highly contrasted to those of Ag+ (H2O)(n) (which have the coordination numbers of 3-4) as well as the hydrated alkali metal ions (which have the coordination numbers of similar to6). For the possible identification of their interesting hydration structures, we predict their IR spectra for the OH stretch modes. (C) 2005 American Institute of Physics.open384

Efficient electron dynamics with the planewave-based real-time time-dependent density functional theory: Absorption spectra, vibronic electronic spectra, and coupled electron-nucleus dynamics

The electron dynamics with complex third-order Suzuki-Trotter propagator (ST(3)) has been implemented into a planewave (PW) based density functional theory program, and several applications including linear absorption spectra and coupled electron-nucleus dynamics have been calculated. Since the ST(3) reduces the number of Fourier transforms to less than half compared to the fourth-order Suzuki-Trotter propagator (ST(4)), more than twice faster calculations are possible by exploiting the ST(3). We analyzed numerical errors of both the ST(3) and the ST(4) in the presence/absence of an external field for several molecules such as Al(2), N(2), and C(2)H(4). We obtained that the ST(3) gives the same order of numerical errors (10(-5) Ry after 100 fs) as the ST(4). Also, the time evolution of dipole moments, hence the absorption spectrum, is equivalent for both ST(3) and ST(4). As applications, the linear absorption spectrum for an ethylene molecule was studied. From the density difference analysis, we showed that the absorption peaks at 6.10 eV and 7.65 eV correspond to the pi -> 4a(g) and pi -> pi* excitation bands, respectively. We also investigated the molecular vibrational effect to the absorption spectra of an ethylene molecule and the dynamics of a hydrogen molecule after the sigma -> sigma* transition by formulating coupled electron-nucleus dynamics within the Ehrenfest regime. The trajectory of nuclei follows the excited state potential energy curve exactly. (C) 2011 American Institute of Physics. [doi: 10.1063/1.3671952close

Structure and spectral features of H+(H2O)(7): Eigen versus Zundel forms

The two dimensional (2D) to three dimensional (3D) transition for the protonated water cluster has been controversial, in particular, for H+(H2O)(7). For H+(H2O)(7) the 3D structure is predicted to be lower in energy than the 2D structure at most levels of theory without zero-point energy (ZPE) correction. On the other hand, with ZPE correction it is predicted to be either 2D or 3D depending on the calculational levels. Although the ZPE correction favors the 3D structure at the level of coupled cluster theory with singles, doubles, and perturbative triples excitations [CCSD(T)] using the aug-cc-pVDZ basis set, the result based on the anharmonic zero-point vibrational energy correction favors the 2D structure. Therefore, the authors investigated the energies based on the complete basis set limit scheme (which we devised in an unbiased way) at the resolution of the identity approximation Moller-Plesset second order perturbation theory and CCSD(T) levels, and found that the 2D structure has the lowest energy for H+(H2O)(7) [though nearly isoenergetic to the 3D structure for D+(D2O)(7)]. This structure has the Zundel-type configuration, but it shows the quantum probabilistic distribution including some of the Eigen-type configuration. The vibrational spectra of MP2/aug-cc-pVDZ calculations and Car-Parrinello molecular dynamics simulations, taking into account the thermal and dynamic effects, show that the 2D Zundel-type form is in good agreement with experiments. (c) 2006 American Institute of Physics.open353

Is the Molecular Berry Phase an Artifact of the Born-Oppenheimer Approximation?

We demonstrate that the molecular Berry phase and the corresponding nonanalyticity in the electronic Born-Oppenheimer wave function is, in general, not a true topological feature of the exact solution of the full electron-nuclear Schrodinger equation. For a numerically exactly solvable model we show that a nonanalyticity, and the associated geometric phase, only appear in the limit of infinite nuclear mass, while a perfectly smooth behavior is found for any finite nuclear mass.open

Structural Transformations in self-assembled Semiconductor Quantum Dots as inferred by Transmission Electron Microscopy

Transmission electron microscopy studies in both the scanning and parallel illumination mode on samples of two generic types of self-assembled semiconductor quantum dots are reported. III-V and II-VI quantum dots as grown in the Stranski-Krastanow mode are typically alloyed and compressively strained to a few %, possess a more or less random distribution of the cations and/or anions over their respective sublattices, and have a spatially non-uniform chemical composition distribution. Sn quantum dots in Si as grown by temperature and growth rate modulated molecular beam epitaxy by means of two mechanisms possess the diamond structure and are compressively strained to the order of magnitude 10 %. These lattice mismatch strains are believed to trigger atomic rearrangements inside quantum dots of both generic types when they are stored at room temperature over time periods of a few years. The atomic rearrangements seem to result in long-range atomic order, phase separation, or phase transformations. While the results suggest that some semiconductor quantum dots may be structurally unstable and that devices based on them may fail over time, triggering and controlling structural transformations in self-assembled semiconductor quantum dots may also offer an opportunity of creating atomic arrangements that nature does not otherwise provide

Correlated multiplexity and connectivity of multiplex random networks

Nodes in a complex networked system often engage in more than one type of interactions among them; they form a multiplex network with multiple types of links. In real-world complex systems, a node's degree for one type of links and that for the other are not randomly distributed but correlated, which we term correlated multiplexity. In this paper we study a simple model of multiplex random networks and demonstrate that the correlated multiplexity can drastically affect the properties of giant component in the network. Specifically, when the degrees of a node for different interactions in a duplex Erdos-Renyi network are maximally correlated, the network contains the giant component for any nonzero link densities. In contrast, when the degrees of a node are maximally anti-correlated, the emergence of giant component is significantly delayed, yet the entire network becomes connected into a single component at a finite link density. We also discuss the mixing patterns and the cases with imperfect correlated multiplexity.Comment: Revised version, 12 pages, 6 figure

Magic structures and quantum conductance of [110] silver nanowires

We investigate the pathway of thinning process for transient [110] nanowires (NWs) of Ag. The result is in good agreement with experimental observations. An unambiguous identification of the structure of a NW requires at least two views along different directions. In the cases where two views of different NW structures are practically the same for very thin NWs which pose experimental difficulty due to small signal-to-noise ratio, our theoretical analysis helps distinguish these structures. On the basis of conductance (G) calculations vis-a-vis the structure of transient NWs, the puzzling experimental observation of fractionally quantized G values is explained by considering the existence of mixed structures for thin wires.open353

A small-specimen investigation of the fracture toughness of Ti 5 Si 3

The fracture toughness of the refractory hardmetal Ti 5 Si 3 , with a grain size between 5 and 6 μm, was measured using the controlled-flaw method in conjunction with the miniaturized disc-bend test. The specimens used in these experiments were 3 mm diameter and varied in thickness from 150–450 μm. They were indented using a Vickers pyramid indentor to indention loads varying from 2.9–79.2 N. Indentation cracking was experienced at all indentation loads, and R -curve behaviour was exhibited. The fracture toughness was determined to be 2.69 ± 0.21 MPam 1/2 using a straightforward graphical procedure involving an empirical R -curve equation. This value is almost 30% higher than that of similar material (2.1 MPam 1/2 ) with a larger grain size, suggesting that the fracture toughness of this material, which fractures intergranularly, might be grain-size dependent.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/44735/1/10853_2004_Article_BF00351561.pd