Protein folding in hydrophobic-polar lattice model: a flexible ant colony optimization approach

This paper proposes a flexible ant colony (FAC) algorithm for solving protein folding problems based on the hydrophobic-polar square lattice model. Collaborations of novel pheromone and heuristic strategies in the proposed algorithm make it more effective in predicting structures of proteins compared with other state-of-the-art algorithms

Consecutive retrieval with redundancy: an optimal linear and an optimal cyclic arrangement and their storage space requirements

Information retrieval, file organization, consecutive retrieval property, consecutive retrieval with redundancy, storage space requirements 1

Pinwheel Scheduling for Fault-tolerant Broadcast Disks in Real-time Database Systems

The design of programs for broadcast disks which incorporate real-time and fault-tolerance requirements is considered. A generalized model for real-time fault-tolerant broadcast disks is defined. It is shown that designing programs for broadcast disks specified in this model is closely related to the scheduling of pinwheel task systems. Some new results in pinwheel scheduling theory are derived, which facilitate the efficient generation of real-time fault-tolerant broadcast disk programs.National Science Foundation (CCR-9308344, CCR-9596282

Discrete radar ambiguity problems

In this paper, we pursue the study of the radar ambiguity problem started in \cite{Ja,GJP}. More precisely, for a given function $u$ we ask for all functions $v$ (called \emph{ambiguity partners}) such that the ambiguity functions of $u$ and $v$ have same modulus. In some cases, $v$ may be given by some elementary transformation of $u$ and is then called a \emph{trivial partner} of $u$ otherwise we call it a \emph{strange partner}. Our focus here is on two discrete versions of the problem. For the first one, we restrict the problem to functions $u$ of the Hermite class, $u=P(x)e^{-x^2/2}$, thus reducing it to an algebraic problem on polynomials. Up to some mild restriction satisfied by quasi-all and almost-all polynomials, we show that such a function has only trivial partners. The second discretization, restricting the problem to pulse type signals, reduces to a combinatorial problem on matrices of a special form. We then exploit this to obtain new examples of functions that have only trivial partners. In particular, we show that most pulse type signals have only trivial partners. Finally, we clarify the notion of \emph{trivial partner}, showing that most previous counterexamples are still trivial in some restricted sense

Storing cycles in Hopfield-type networks with pseudoinverse learning rule: admissibility and network topology

Cyclic patterns of neuronal activity are ubiquitous in animal nervous systems, and partially responsible for generating and controlling rhythmic movements such as locomotion, respiration, swallowing and so on. Clarifying the role of the network connectivities for generating cyclic patterns is fundamental for understanding the generation of rhythmic movements. In this paper, the storage of binary cycles in neural networks is investigated. We call a cycle $\Sigma$ admissible if a connectivity matrix satisfying the cycle's transition conditions exists, and construct it using the pseudoinverse learning rule. Our main focus is on the structural features of admissible cycles and corresponding network topology. We show that $\Sigma$ is admissible if and only if its discrete Fourier transform contains exactly $r={rank}(\Sigma)$ nonzero columns. Based on the decomposition of the rows of $\Sigma$ into loops, where a loop is the set of all cyclic permutations of a row, cycles are classified as simple cycles, separable or inseparable composite cycles. Simple cycles contain rows from one loop only, and the network topology is a feedforward chain with feedback to one neuron if the loop-vectors in $\Sigma$ are cyclic permutations of each other. Composite cycles contain rows from at least two disjoint loops, and the neurons corresponding to the rows in $\Sigma$ from the same loop are identified with a cluster. Networks constructed from separable composite cycles decompose into completely isolated clusters. For inseparable composite cycles at least two clusters are connected, and the cluster-connectivity is related to the intersections of the spaces spanned by the loop-vectors of the clusters. Simulations showing successfully retrieved cycles in continuous-time Hopfield-type networks and in networks of spiking neurons are presented.Comment: 48 pages, 3 figure

Some Applications of Coding Theory in Computational Complexity

Error-correcting codes and related combinatorial constructs play an important role in several recent (and old) results in computational complexity theory. In this paper we survey results on locally-testable and locally-decodable error-correcting codes, and their applications to complexity theory and to cryptography. Locally decodable codes are error-correcting codes with sub-linear time error-correcting algorithms. They are related to private information retrieval (a type of cryptographic protocol), and they are used in average-case complexity and to construct ``hard-core predicates'' for one-way permutations. Locally testable codes are error-correcting codes with sub-linear time error-detection algorithms, and they are the combinatorial core of probabilistically checkable proofs

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