Spatial dynamics of the light emission from a microplasma array

The spatial dynamics of the optical emission from an array of 50x50 individual microplasma devices is reported. The array is operated in noble gas at atmospheric pressure with an ac voltage. The optical emission is analyzed with phase and space resolution. It has been found that the emission is not continuous over the entire ac period, it occurs only twice in each cycle. Each of the observed emission phases shows a self-pulsing of the discharge, with several bursts of emission of a fixed width and repetition rate. Cross-talk between the individual devices can be observed through spatially resolved measurements. (C) 2008 American Institute of Physics.

Modelling non-adiabatic processes using correlated electron-ion dynamics

Here we survey the theory and applications of a family of methods (correlated electron-ion dynamics, or CEID) that can be applied to a diverse range of problems involving the non-adiabatic exchange of energy between electrons and nuclei. The simplest method, which is a paradigm for the others, is Ehrenfest Dynamics. This is applied to radiation damage in metals and the evolution of excited states in conjugated polymers. It is unable to reproduce the correct heating of nuclei by current carrying electrons, so we introduce a moment expansion that allows us to restore the spontaneous emission of phonons. Because of the widespread use of Non-Equilibrium Green's Functions for computing electric currents in nanoscale systems, we present a comparison of this formalism with that of CEID with open boundaries. When there is strong coupling between electrons and nuclei, the moment expansion does not converge. We thus conclude with a reworking of the CEID formalism that converges systematically and in a stable manner.

Vortex line and ring dynamics in trapped Bose-Einstein condensates

Vortex dynamics in inhomogeneous Bose-Einstein condensates are studied numerically in two and three dimensions. We simulate the precession of a single vortex around the center of a trapped condensate, and use the Magnus force to estimate the precession frequency. Vortex ring dynamics in a spherical trap are also simulated, and we discover that a ring undergoes oscillatory motion around a circle of maximum energy. The position of this locus is calculated as a function of the number of condensed atoms. In the presence of dissipation, the amplitude of the oscillation will increase, eventually resulting in self-annihilation of the ring.

Infinite Dimensional Banach spaces of functions with nonlinear properties

The aim of this paper is to show that there exist infinite dimensional Banach spaces of functions that, except for 0, satisfy properties that apparently should be destroyed by the linear combination of two of them. Three of these spaces are: a Banach space of differentiable functions on Rn failing the Denjoy-Clarkson property; a Banach space of non Riemann integrable bounded functions, but with antiderivative at each point of an interval; a Banach space of infinitely differentiable functions that vanish at infinity and are not the Fourier transform of any Lebesgue integrable function.

The Carboxy-Terminal Modulator Protein (CTMP) Regulates Mitochondrial Dynamics

Background: Mitochondria are central to the metabolism of cells and participate in many regulatory and signaling events. They are looked upon as dynamic tubular networks. We showed recently that the Carboxy-Terminal Modulator Protein (CTMP) is a mitochondrial protein that may be released into the cytosol under apoptotic conditions.

Molecular Modeling on Inhibitor Complexes and Active-Site Dynamics of Cytochrome P450 C17, a Target for Prostate Cancer Therapy

A molecular model for the P450 enzyme cytochrome P450 C17 (CYP17) is presented based on sequence alignments of multiple template structures and homology modeling. This enzyme plays a central role in the biosynthesis of testosterone and is emerging as a major target in prostate cancer, with the recently developed inhibitor abiraterone currently in advanced clinical trials. The model is described in detail, together with its validation, by providing structural explanations to available site-directed mutagenesis data. The CYP17 molecule in this model is in the form of a triangular prism, with an edge of similar to 55 angstrom and a thickness of similar to 37 angstrom. It is predominantly helical, comprising 13 alpha helices interspersed by six 3(10) helices and 11 beta-sheets. Multinanosecond molecular dynamics simulations in explicit solvent have been carried out, and principal components analysis has been used to reveal the details of dynamics around the active site. Coarse-grained methods have also been used to verify low-frequency motions, which have been correlated with active-site gating. The work also describes the results of docking synthetic inhibitors, including the drug abiraterone and the natural substrate pregnenolone, in the CYP17 active site together with molecular dynamics simulations on the complexes. (C) 2010 Elsevier Ltd. All rights reserved.

Molecular dynamics and principal components analysis of human telomeric quadruplex multimers.

Guanine-rich DNA repeat sequences located at the terminal ends of chromosomal DNA can fold in a sequence-dependent manner into G-quadruplex structures, notably the terminal 150–200 nucleotides at the 3' end, which occur as a single-stranded DNA overhang. The crystal structures of quadruplexes with two and four human telomeric repeats show an all-parallel-stranded topology that is readily capable of forming extended stacks of such quadruplex structures, with external TTA loops positioned to potentially interact with other macromolecules. This study reports on possible arrangements for these quadruplex dimers and tetramers, which can be formed from 8 or 16 telomeric DNA repeats, and on a methodology for modeling their interactions with small molecules. A series of computational methods including molecular dynamics, free energy calculations, and principal components analysis have been used to characterize the properties of these higher-order G-quadruplex dimers and tetramers with parallel-stranded topology. The results confirm the stability of the central G-tetrads, the individual quadruplexes, and the resulting multimers. Principal components analysis has been carried out to highlight the dominant motions in these G-quadruplex dimer and multimer structures. The TTA loop is the most flexible part of the model and the overall multimer quadruplex becoming more stable with the addition of further G-tetrads. The addition of a ligand to the model confirms the hypothesis that flat planar chromophores stabilize G-quadruplex structures by making them less flexible.

Framework for Establishing Limits of Tabular Aerodynamic Models for Flight Dynamics Analysis

This paper describes the use of the Euler equations for the generation and testing of tabular aerodynamic models for flight dynamics analysis. Maneuvers for the AGARD Standard Dynamics Model sharp leading-edge wind-tunnel geometry are considered as a test case. Wind-tunnel data is first used to validate the prediction of static and dynamic coefficients at both low and high angles, featuring complex vortical flow, with good agreement obtained at low to moderate angles of attack. Then the generation of aerodynamic tables is described based on a data fusion approach. Time-optimal maneuvers are generated based on these tables, including level flight trim, pull-ups at constant and varying incidence, and level and 90 degrees turns. The maneuver definition includes the aircraft states and also the control deflections to achieve the motion. The main point of the paper is then to assess the validity of the aerodynamic tables which were used to define the maneuvers. This is done by replaying them, including the control surface motions, through the time accurate computational fluid dynamics code. The resulting forces and moments are compared with the tabular values to assess the presence of inadequately modeled dynamic or unsteady effects. The agreement between the tables and the replay is demonstrated for slow maneuvers. Increasing rate maneuvers show discrepancies which are ascribed to vortical flow hysteresis at the higher rate motions. The framework is suitable for application to more complex viscous flow models, and is powerful for the assessment of the validity of aerodynamics models of the type currently used for studies of flight dynamics.