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

The Research on Development of the Teaching Choral Music in Non-Professional Music Colleges in China

This thesis explores the cultivation of emotional quality in the teaching of choral music in non- professional music colleges in China With the increasing popularity of choral music in China it is important to understand the effectiveness of teaching methods and how students connect emotionally with the genre The research examines the current state of choral music education including the strengths and weaknesses inherent in pedagogical approache