Giant Magnons and Spiky Strings on S^3 with B-field

We study solutions for a rotating string on S^3 with a background NS-NS B-field and show the existence of spiky string and giant magnon as two limiting solutions. We make a connection to the sine-Gordon model via the Polyakov worldsheet action and study the effect of B-field. In particular, we find the magnon solution can be mapped to the excitation of a fractional spin chain. We conjecture a B-deformed SYM to be the gauge theory dual to this background.Comment: 22 pages, 3 figures, more references adde

Domain-Based Predictive Models for Protein-Protein Interaction Prediction

Protein interactions are of biological interest because they orchestrate a number of cellular processes such as metabolic pathways and immunological recognition. Recently, methods for predicting protein interactions using domain information are proposed and preliminary results have demonstrated their feasibility. In this paper, we develop two domain-based statistical models (neural networks and decision trees) for protein interaction predictions. Unlike most of the existing methods which consider only domain pairs (one domain from one protein) and assume that domain-domain interactions are independent of each other, the proposed methods are capable of exploring all possible interactions between domains and make predictions based on all the domains. Compared to maximum-likelihood estimation methods, our experimental results show that the proposed schemes can predict protein-protein interactions with higher specificity and sensitivity, while requiring less computation time. Furthermore, the decision tree-based model can be used to infer the interactions not only between two domains, but among multiple domains as well

Domain-Based Predictive Models for Protein-Protein Interaction Prediction

Protein interactions are of biological interest because they orchestrate a number of cellular processes such as metabolic pathways and immunological recognition. Recently, methods for predicting protein interactions using domain information are proposed and preliminary results have demonstrated their feasibility. In this paper, we develop two domain-based statistical models (neural networks and decision trees) for protein interaction predictions. Unlike most of the existing methods which consider only domain pairs (one domain from one protein) and assume that domain-domain interactions are independent of each other, the proposed methods are capable of exploring all possible interactions between domains and make predictions based on all the domains. Compared to maximum-likelihood estimation methods, our experimental results show that the proposed schemes can predict protein-protein interactions with higher specificity and sensitivity, while requiring less computation time. Furthermore, the decision tree-based model can be used to infer the interactions not only between two domains, but among multiple domains as well

Gapped spin liquid with Z2\mathbb{Z}_2-topological order for kagome Heisenberg model

We apply symmetric tensor network state (TNS) to study the nearest neighbor spin-1/2 antiferromagnetic Heisenberg model on Kagome lattice. Our method keeps track of the global and gauge symmetries in TNS update procedure and in tensor renormalization group (TRG) calculation. We also introduce a very sensitive probe for the gap of the ground state -- the modular matrices, which can also determine the topological order if the ground state is gapped. We find that the ground state of Heisenberg model on Kagome lattice is a gapped spin liquid with the $\mathbb{Z}_2$-topological order (or toric code type), which has a long correlation length $\xi\sim 10$ unit cell length. We justify that the TRG method can handle very large systems with over thousands of spins. Such a long $\xi$ explains the gapless behaviors observed in simulations on smaller systems with less than 300 spins or shorter than 10 unit cell length. We also discuss experimental implications of the topological excitations encoded in our symmetric tensors.Comment: 10 pages, 7 figure

Knowledge-guided inference of domain–domain interactions from incomplete protein–protein interaction networks

Motivation: Protein-protein interactions (PPIs), though extremely valuable towards a better understanding of protein functions and cellular processes, do not provide any direct information about the regions/domains within the proteins that mediate the interaction. Most often, it is only a fraction of a protein that directly interacts with its biological partners. Thus, understanding interaction at the domain level is a critical step towards (i) thorough understanding of PPI networks; (ii) precise identification of binding sites; (iii) acquisition of insights into the causes of deleterious mutations at interaction sites; and (iv) most importantly, development of drugs to inhibit pathological protein interactions. In addition, knowledge derived from known domain–domain interactions (DDIs) can be used to understand binding interfaces, which in turn can help discover unknown PPIs

Assessing reliability of protein-protein interactions by integrative analysis of data in model organisms

Background: Protein-protein interactions play vital roles in nearly all cellular processes and are involved in the construction of biological pathways such as metabolic and signal transduction pathways. Although large-scale experiments have enabled the discovery of thousands of previously unknown linkages among proteins in many organisms, the high-throughput interaction data is often associated with high error rates. Since protein interaction networks have been utilized in numerous biological inferences, the inclusive experimental errors inevitably affect the quality of such prediction. Thus, it is essential to assess the quality of the protein interaction data. Results: In this paper, a novel Bayesian network-based integrative framework is proposed to assess the reliability of protein-protein interactions. We develop a cross-species in silico model that assigns likelihood scores to individual protein pairs based on the information entirely extracted from model organisms. Our proposed approach integrates multiple microarray datasets and novel features derived from gene ontology. Furthermore, the confidence scores for cross-species protein mappings are explicitly incorporated into our model. Applying our model to predict protein interactions in the human genome, we are able to achieve 80% in sensitivity and 70% in specificity. Finally, we assess the overall quality of the experimentally determined yeast protein-protein interaction dataset. We observe that the more high-throughput experiments confirming an interaction, the higher the likelihood score, which confirms the effectiveness of our approach. Conclusion: This study demonstrates that model organisms certainly provide important information for protein-protein interaction inference and assessment. The proposed method is able to assess not only the overall quality of an interaction dataset, but also the quality of individual protein-protein interactions. We expect the method to continually improve as more high quality interaction data from more model organisms becomes available and is readily scalable to a genome-wide application