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

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

Spin relaxation and decoherence of two-level systems

We revisit the concepts of spin relaxation and spin decoherence of two level (spin-1/2) systems. From two toy-models, we clarify two issues related to the spin relaxation and decoherence: 1) For an ensemble of two-level particles each subjected to a different environmental field, there exists an ensemble relaxation time $T_1^*$ which is fundamentally different from $T_1$. When the off-diagonal coupling of each particle is in a single mode with the same frequency but a random coupling strength, we show that $T_1^*$ is finite while the spin relaxation time of a single spin $T_1$ and the usual ensemble decoherence time $T_2^*$ are infinite. 2) For a two-level particle under only a random diagonal coupling, its relaxation time $T_1$ shall be infinite but its decoherence time $T_2$ is finite.Comment: 5 pages, 2 figure

An Efficient Method for GPS Multipath Mitigation Using the Teager-Kaiser-Operator-based MEDLL

An efficient method for GPS multipath mitigation is proposed. The motivation for this proposed method is to integrate the Teager-Kaiser Operator (TKO) with the Multipath Estimating Delay Lock Loop (MEDLL) module to mitigate the GPS multipath efficiently. The general implementation process of the proposed method is that we first utilize the TKO to operate on the received signal’s Auto-Correlation Function (ACF) to get an initial estimate of the multipaths. Then we transfer the initial estimated results to the MEDLL module for a further estimation. Finally, with a few iterations which are less than those of the original MEDLL algorithm, we can get a more accurate estimate of the Line-Of-Sight (LOS) signal, and thus the goal of the GPS multipath mitigation is achieved. The simulation results show that compared to the original MEDLL algorithm, the proposed method can reduce the computation load and the hardware and/or software consumption of the MEDLL module, meanwhile, without decreasing the algorithm accuracy

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

Secure thermal infrared communications using engineered blackbody radiation

The thermal (emitted) infrared frequency bands, from 20–40 THz and 60–100 THz, are best known for applications in thermography. This underused and unregulated part of the spectral range offers opportunities for the development of secure communications. The ‘THz Torch' concept was recently presented by the authors. This technology fundamentally exploits engineered blackbody radiation, by partitioning thermally-generated spectral noise power into pre-defined frequency channels; the energy in each channel is then independently pulsed modulated and multiplexing schemes are introduced to create a robust form of short-range secure communications in the far/mid infrared. To date, octave bandwidth (25–50 THz) single-channel links have been demonstrated with 380 bps speeds. Multi-channel ‘THz Torch' frequency division multiplexing (FDM) and frequency-hopping spread-spectrum (FHSS) schemes have been proposed, but only a slow 40 bps FDM scheme has been demonstrated experimentally. Here, we report a much faster 1,280 bps FDM implementation. In addition, an experimental proof-of-concept FHSS scheme is demonstrated for the first time, having a 320 bps data rate. With both 4-channel multiplexing schemes, measured bit error rates (BERs) of < 10(−6) are achieved over a distance of 2.5 cm. Our approach represents a new paradigm in the way niche secure communications can be established over short links