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

Fluctuations and Correlations of Conserved Charges near the QCD Critical Point

We study the fluctuations and correlations of conserved charges, i.e. the baryon number, electric charge and the strangeness at finite temperature and nonzero baryon chemical potential with an effective model. The fluctuations are calculated up to the fourth-order and the correlations to the third-order. We find that the second-order fluctuations and correlations have a peak or valley structure when the chiral phase transition takes place with the increase of the baryon chemical potential; the third-order fluctuations and correlations change their signs during the chiral phase transition and the fourth-order fluctuations have two maximum and one minimum. we also depict contour plots of various fluctuations and correlations of conserved charges in the plane of temperature and baryon chemical potential. We find that higher order fluctuations and correlations of conserved charges are superior to the second-order ones to be used to search for the critical point in heavy ion collision experiments.Comment: 22 pages, 12 figures, version accepted by Phys. Rev.