Potential function of simplified protein models for discriminating native proteins from decoys: Combining contact interaction and local sequence-dependent geometry

An effective potential function is critical for protein structure prediction and folding simulation. For simplified models of proteins where coordinates of only $C_\alpha$ atoms need to be specified, an accurate potential function is important. Such a simplified model is essential for efficient search of conformational space. In this work, we present a formulation of potential function for simplified representations of protein structures. It is based on the combination of descriptors derived from residue-residue contact and sequence-dependent local geometry. The optimal weight coefficients for contact and local geometry is obtained through optimization by maximizing margins among native and decoy structures. The latter are generated by chain growth and by gapless threading. The performance of the potential function in blind test of discriminating native protein structures from decoys is evaluated using several benchmark decoy sets. This potential function have comparable or better performance than several residue-based potential functions that require in addition coordinates of side chain centers or coordinates of all side chain atoms.Comment: 4 pages, 2 figures, Accepted by 26th IEEE-EMBS Conference, San Francisc

Effects of practical impairments on cooperative distributed antennas combined with fractional frequency reuse

Cooperative Multiple Point (CoMP) transmission aided Distributed Antenna Systems (DAS) are proposed for increasing the received Signal-to-Interference-plus-Noise-Ratio (SINR) in the cell-edge area of a cellular system employing Fractional Frequency Reuse (FFR) in the presence of realistic imperfect Channel State Information (CSI) as well as synchronisation errors between the transmitters and the receivers. Our simulation results demonstrate that the CoMP aided DAS scenario is capable of increasing the attainable SINR by up to 3dB in the presence of a wide range of realistic imperfections

Statistical Geometry of Packing Defects of Lattice Chain Polymer from Enumeration and Sequential Monte Carlo Method

Voids exist in proteins as packing defects and are often associated with protein functions. We study the statistical geometry of voids in two-dimensional lattice chain polymers. We define voids as topological features and develop a simple algorithm for their detection. For short chains, void geometry is examined by enumerating all conformations. For long chains, the space of void geometry is explored using sequential Monte Carlo importance sampling and resampling techniques. We characterize the relationship of geometric properties of voids with chain length, including probability of void formation, expected number of voids, void size, and wall size of voids. We formalize the concept of packing density for lattice polymers, and further study the relationship between packing density and compactness, two parameters frequently used to describe protein packing. We find that both fully extended and maximally compact polymers have the highest packing density, but polymers with intermediate compactness have low packing density. To study the conformational entropic effects of void formation, we characterize the conformation reduction factor of void formation and found that there are strong end-effect. Voids are more likely to form at the chain end. The critical exponent of end-effect is twice as large as that of self-contacting loop formation when existence of voids is not required. We also briefly discuss the sequential Monte Carlo sampling and resampling techniques used in this study.Comment: 29 pages, including 12 figure

Enhanced entanglement of two optical modes in optomechanical systems via an optical parametric amplifier

We investigate the effect of a degenerate optical parametric amplifier (OPA) placed inside an optomechanical cavity on the steady-state entanglement of two cavity modes, which jointly interact with a mechanical resonator. Two cavity modes are respectively driven at the red and blue sideband associated with the mechanical resonator, which generates entanglement between them in the limit of resolved sideband. The OPA gives rise to single-mode squeezing of the cavity fields, which results in significant improvement of the two-mode entanglement. It is found that an optimal nonlinear gain of the OPA exists, depending on the system temperatures, which yields the maximum entanglement. The improvement is particularly remarkable for the system at cryogenic temperatures.Comment: 14 pages, 5 figures, to appear in J. Phys.

Word Embedding based Correlation Model for Question/Answer Matching

With the development of community based question answering (Q&A) services, a large scale of Q&A archives have been accumulated and are an important information and knowledge resource on the web. Question and answer matching has been attached much importance to for its ability to reuse knowledge stored in these systems: it can be useful in enhancing user experience with recurrent questions. In this paper, we try to improve the matching accuracy by overcoming the lexical gap between question and answer pairs. A Word Embedding based Correlation (WEC) model is proposed by integrating advantages of both the translation model and word embedding, given a random pair of words, WEC can score their co-occurrence probability in Q&A pairs and it can also leverage the continuity and smoothness of continuous space word representation to deal with new pairs of words that are rare in the training parallel text. An experimental study on Yahoo! Answers dataset and Baidu Zhidao dataset shows this new method's promising potential.Comment: 8 pages, 2 figure