Design, implementation, and testing of advanced virtual coordinate-measuring machines

Copyright @ 2011 IEEE. This article has been made available through the Brunel Open Access Publishing Fund.Advanced virtual coordinate-measuring machines (CMMs) (AVCMMs) have recently been developed at Brunel University, which provide vivid graphical representation and powerful simulation of CMM operations, together with Monte-Carlo-based uncertainty evaluation. In an integrated virtual environment, the user can plan an inspection strategy for a given task, carry out virtual measurements, and evaluate the uncertainty associated with the measurement results, all without the need of using a physical machine. The obtained estimate of uncertainty can serve as a rapid feedback for the user to optimize the inspection plan in the AVCMM before actual measurements or as an evaluation of the measurement results performed. This paper details the methodology, design, and implementation of the AVCMM system, including CMM modeling, probe contact and collision detection, error modeling and simulation, and uncertainty evaluation. This paper further reports experimental results for the testing of the AVCMM

Flexible protein folding by ant colony optimization

Protein structure prediction is one of the most challenging topics in bioinformatics. As the protein structure is found to be closely related to its functions, predicting the folding structure of a protein to judge its functions is meaningful to the humanity. This chapter proposes a flexible ant colony (FAC) algorithm for solving protein folding problems (PFPs) based on the hydrophobic-polar (HP) square lattice model. Different from the previous ant algorithms for PFPs, the pheromones in the proposed algorithm are placed on the arcs connecting adjacent squares in the lattice. Such pheromone placement model is similar to the one used in the traveling salesmen problems (TSPs), where pheromones are released on the arcs connecting the cities. Moreover, the collaboration of effective heuristic and pheromone strategies greatly enhances the performance of the algorithm so that the algorithm can achieve good results without local search methods. By testing some benchmark two-dimensional hydrophobic-polar (2D-HP) protein sequences, the performance shows that the proposed algorithm is quite competitive compared with some other well-known methods for solving the same protein folding problems

Dynamics of multiply charged ions in intense laser fields

We numerically investigate the dynamics of multiply charged hydrogenic ions in near-optical linearly polarized laser fields with intensities of order 10^16 to 10^17 W/cm^2. Depending on the charge state Z of the ion the relation of strength between laser field and ionic core changes. We find around Z=12 typical multiphoton dynamics and for Z=3 tunneling behaviour, however with clear relativistic signatures. In first order in v/c the magnetic field component of the laser field induces a Z-dependent drift in the laser propagation direction and a substantial Z-dependent angular momentum with repect to the ionic core. While spin oscillations occur already in first order in v/c as described by the Pauli equation, spin induced forces via spin orbit coupling only appear in the parameter regime where (v/c)^2 corrections are significant. In this regime for Z=12 ions we show strong splittings of resonant spectral lines due to spin-orbit coupling and substantial corrections to the conventional Stark shift due to the relativistic mass shift while those to the Darwin term are shown to be small. For smaller charges or higher laser intensities, parts of the electronic wavepacket may tunnel through the potential barrier of the ionic core, and when recombining are shown to give rise to keV harmonics in the radiation spectrum. Some parts of the wavepacket do not recombine after ionisation and we find very energetic electrons in the weakly relativistic regime of above threshold ionization.Comment: submitte

Tipstreaming of a drop in simple shear flow in the presence of surfactant

We have developed a multi-phase SPH method to simulate arbitrary interfaces containing surface active agents (surfactants) that locally change the properties of the interface, such the surface tension coefficient. Our method incorporates the effects of surface diffusion, transport of surfactant from/to the bulk phase to/from the interface and diffusion in the bulk phase. Neglecting transport mechanisms, we use this method to study the impact of insoluble surfactants on drop deformation and breakup in simple shear flow and present the results in a fluid dynamics video.Comment: Two videos are included for the Gallery of Fluid Motion of the APS DFD Meeting 201

Nonequilibrium Phase Transitions of Vortex Matter in Three-Dimensional Layered Superconductors

Large-scale simulations on three-dimensional (3D) frustrated anisotropic XY model have been performed to study the nonequilibrium phase transitions of vortex matter in weak random pinning potential in layered superconductors. The first-order phase transition from the moving Bragg glass to the moving smectic is clarified, based on thermodynamic quantities. A washboard noise is observed in the moving Bragg glass in 3D simulations for the first time. It is found that the activation of the vortex loops play the dominant role in the dynamical melting at high drive.Comment: 3 pages,5 figure

Coherent population trapping in a dressed two-level atom via a bichromatic field

We show theoretically that by applying a bichromatic electromagnetic field, the dressed states of a monochromatically driven two-level atom can be pumped into a coherent superposition termed as dressed-state coherent population trapping. Such effect can be viewed as a new doorknob to manipulate a two-level system via its control over dressed-state populations. Application of this effect in the precision measurement of Rabi frequency, the unexpected population inversion and lasing without inversion are discussed to demonstrate such controllability.Comment: 14 pages, 6 figure