In this paper, we introduce a path embedding problem inspired by the well-known hydrophobic-polar (HP) model of protein folding. A graph is said bicolored if each vertex is assigned a label in the set {red, blue}. For a given bicolored path P and a given bicolored graph G, our problem asks whether we can embed P into G in such a way as to match the colors of the vertices. In our model, G represents a protein's “blueprint,” and P is an amino acid sequence that has to be folded to form (part of) G. We first show that the bicolored path embedding problem is NP-complete even if G is a rectangular grid (a typical scenario in protein folding models) and P and G have the same number of vertices. By contrast, we prove that the problem becomes tractable if the height of the rectangular grid G is constant, even if the length of P is independent of G. Our proof is constructive: we give a polynomial-time algorithm that computes an embedding (or reports that no embedding exists), which implies that the problem is in XP when parameterized according to the height of G. Additionally, we show that the problem of embedding P into a rectangular grid G in such a way as to maximize the number of red-red contacts is NP-hard. (This problem is directly inspired by the HP model of protein folding; it was previously known to be NP-hard if G is not given, and P can be embedded in any way on a grid.) Finally, we show that, given a bicolored graph G, the problem of constructing a path P that embeds in G maximizing red-red contacts is Poly-APX-hard.

Photo Diode Array (PDA) is the key semiconductor component expected to produce specified output voltage in photo couplers and photo sensors when the light is on. PDA partitioning problem, which is to design PDA, is: Given die area, anode and cathode points, divide the area into N cells, with identical areas, connected in series from anode to cathode. In this paper, we first make restrictions for the problem and reveal the underlying properties of necessary and sufficient conditions for the existence of solutions when the restrictions are satisfied. Then, we propose a method to solve the problem using recursive algorithm, which can be guaranteed to obtain a solution in polynomial time.

There is increasing interest in quantum computing, because of its enormous computing potential. A small number of powerful quantum algorithms have been proposed to date; however, the development of new quantum algorithms for practical use remains essential. Parallel computing with a neural network has successfully realized certain unique functions such as learning and recognition; therefore, the introduction of certain neural computing techniques into quantum computing to enlarge the quantum computing application field is worthwhile. In this paper, a novel quantum associative memory (QuAM) is proposed, which is achieved with a quantum neural network by employing adiabatic Hamiltonian evolution. The memorization and retrieval procedures are inspired by the concept of associative memory realized with an artificial neural network. To study the detailed dynamics of our QuAM, we examine two types of Hamiltonians for pattern memorization. The first is a Hamiltonian having diagonal elements, which is known as an Ising Hamiltonian and which is similar to the cost function of a Hopfield network. The second is a Hamiltonian having non-diagonal elements, which is known as a neuro-inspired Hamiltonian and which is based on interactions between qubits. Numerical simulations indicate that the proposed methods for pattern memorization and retrieval work well with both types of Hamiltonians. Further, both Hamiltonians yield almost identical performance, although their retrieval properties differ. The QuAM exhibits new and unique features, such as a large memory capacity, which differs from a conventional neural associative memory.

In this paper, we investigate the fault-tolerant Hamiltonian problems of crossed cubes with a faulty path. More precisely, let P denote any path in an n-dimensional crossed cube CQn for n ≥ 5, and let V(P) be the vertex set of P. We show that CQn-V(P) is Hamiltonian if |V(P)|≤n and is Hamiltonian connected if |V(P)| ≤ n-1. Compared with the previous results showing that the crossed cube is (n-2)-fault-tolerant Hamiltonian and (n-3)-fault-tolerant Hamiltonian connected for arbitrary faults, the contribution of this paper indicates that the crossed cube can tolerate more faulty vertices if these vertices happen to form some specific types of structures.

In the present paper, we consider fully asynchronous parallelism in membrane computing, and propose two asynchronous P systems for the satisfiability (SAT) and Hamiltonian cycle problem. We first propose an asynchronous P system that solves SAT with n variables and m clauses, and show that the proposed P system computes SAT in O(mn2n) sequential steps or O(mn) parallel steps using O(mn) kinds of objects. We next propose an asynchronous P system that solves the Hamiltonian cycle problem with n nodes, and show that the proposed P system computes the problem in O(n!) sequential steps or O(n2) parallel steps using O(n2) kinds of objects.

Let G=(V,E) be a graph of order n. A Hamiltonian cycle of G is a cycle that contains every vertex in G. Two Hamiltonian cycles C1= and C2= of G are independent if u1=v1 and ui ≠ vi for 2 ≤ i ≤ n. A set of Hamiltonian cycles {C1, C2, , Ck} of G is mutually independent if its elements are pairwise independent. The mutually independent hamiltonicity IHC(G) of a graph G is the maximum integer k such that for any vertex u of G there are k mutually independent Hamiltonian cycles of G starting at u. For the n-dimensional burnt pancake graph Bn, this paper proved that IHC(B2)=1 and IHC(Bn)=n for n ≥ 3.

Let u and v be any two distinct vertices of an undirected graph G, which is k-connected. For 1 w k, a w-container C(u, v) of a k-connected graph G is a set of w-disjoint paths joining u and v. A w-container C(u, v) of G is a w *-container if it contains all the vertices of G. A graph G is w *-connected if there exists a w *-container between any two distinct vertices. Let κ(G) be the connectivity of G. A graph G is super spanning connected if G is i *-connected for 1 i κ(G). In this paper, we prove that the n-dimensional burnt pancake graph Bn is super spanning connected if and only if n ≠ 2.

Longest path problem is a problem for finding a longest path in a given graph. While the graph classes in which the Hamiltonian path problem can be solved efficiently are widely investigated, there are few known graph classes such that the longest path problem can be solved efficiently. Polynomial time algorithms for finding a longest cycle and a longest path in a Ptolemaic graph are proposed. Ptolemaic graphs are the graphs that satisfy the Ptolemy inequality, and they are the intersection of chordal graphs and distance-hereditary graphs. The algorithms use the dynamic programming technique on a laminar structure of cliques, which is a recent characterization of Ptolemaic graphs.

The Mobius cube MQn proposed by Cull et al. is an alternative to the popular hypercube network. Recently, MQn was shown to be pancyclic, i.e., cycles of any lengths at least four can be embedded into it. Due to the importance of the fault tolerance in the parallel processing area, in this paper, we study an injured MQn with mixed node and link faults. We show that it is (n - 2)-fault-tolerant pancyclic for n 3, that is, an injured n-dimensional MQn is still pancyclic with up to (n - 2) faults. Furthermore, our result is optimal.

In this paper, the previous definition of the Reverse Jacket matrix (RJM) is revised and generalized. In particular, it is shown that the inverse of the RJM can be obtained easily by a constructive approach similar to that used for the RJM itself. As new results, some useful properties of RJMs, such as commutativity and the Hamiltonian symmetry appearing in half the blocks of a RJM, are shown, and also 1-D fast Reverse Jacket transform (FRJT) is presented. The algorithm of the FRJT is remarkably efficient than that of the center-weighted Hadamard transform (CWHT). The FRJT is extended in terms of the Kronecker products of the Hadamard matrix. The 1-D FRJT is applied to the discrete Fourier transform (DFT) with order 4, and the N-point DFT can be expressed in terms of matrix decomposition by using 4 4 FRJT.

This paper presents a new interconnection network called bi-rotator graph. It is originated from the rotator graph. The rotator graph has many unidirectional edges and the bi-rotator graph is constructed by making edges of the rotator graph bidirectional. The bidirectional edges can help to reduce the average routing distance and increase the flexibility of applications. Therefore, we propose the bi-rotator graph as an alternative to the rotator graph. In this paper, we will first illustrate how to construct the bi-rotator graph and present the node-to-node routing algorithm. Next, we will propose the algorithm for building Hamiltonian cycle, which demonstrates that the bi-rotator graph is Hamiltonian. Finally, we provide a dilation-one algorithm for embedding arbitrary size of cycle into the bi-rotator graph and show that the bi-rotator graph is Hamiltonian-connected.

An n-dimensional crossed cube, CQn, is a variation of the hypercube. In this paper, we prove that CQn is (n-2)-Hamiltonian and (n-3)-Hamiltonian connected. That is, a ring of length 2n-fv can be embedded in a faulty CQn with fv faulty nodes and fe faulty edges, where fv+fen-2 and n3. In other words, we show that the faulty CQn is still Hamiltonian with n-2 faults. In addition, we also prove that there exists a Hamiltonian path between any pair of vertices in a faulty CQn with n-3 faults. The above results are optimum in the sense that the fault-tolerant Hamiltonicity (fault-tolerant Hamiltonian connectivity respectively) of CQn is at most n-2 (n-3 respectively). A recent result has shown that a ring of length 2n-2fv can be embedded in a faulty hypercube, if fv+fen-1 and n4, with a few additional constraints. Our results, in comparison to the hypercube, show that longer rings can be embedded in CQn without additional constraints.

In this paper, a new family of interconnection networks which we call the Incrementally Extensible Twisted Cube (IETQ) is proposed. The topology of this network is a novel generalization of the twisted cube. It inherits all the merits but without the limitations owned by a twisted cube. First, this proposed IETQ is incrementally extensible and can be adapted for use in any number of nodes; therefore, this network is particularly well suited for the design of a distributed communication network with an arbitrary number of nodes. Second, the vertex connectivity of IETQ is n. Measured by this vertex connectivity, we demonstrate that this network is optimally fault-tolerant . And it is almost regular, because the difference between the maximum and minimum degree of any node in an IETQ is at most one. A shortestpath routing algorithm for IETQ is proposed to generate path for any given pair of vertices in the network. Third, comparing with most of the other competitors, the diameter of this IETQ network is only half in size. This low diameter helps to reduce the internode communication delay. Moreover, IETQ also possesses the property of a pancyclic network. This attractive property would enable us to map rings of any length into the proposed network.

We present calculations of the linear-response conductance of a SiGe based single-electron transistor (SET). The conductance and the discrete charging of the quantum dot are calculated by free-energy minimization. The free-energy calculation takes the discrete level-spectrum as well as complex many-body interactions into account. The tunneling rates for tunneling through the source and lead barrier are calculated using Bardeen's transfer Hamiltonian formalism. The tunneling matrix elements are calculated for transitions between the zero-dimensional states in the quantum dot and the lowest subband in the one-dimensional constriction. We compare the results for the conductance peaks with those from calculations with a constant tunneling rate where the shape of the peaks is only due to energetic arguments.

As a super class of tournament digraphs, Bang-Jensen, Huang and Prisner defined an in-tournament digraph (in-tournament for short) and investigated a number of its nice properties. The in-tournament is a directed graph in which the set of in-neighbors of every vertex induces a tournament digraph. In other words, the presence of arcs (x,z) and (y,z) implies that exactly one of (x,y) or (y,x) exists. In this paper, we propose, for in-tournaments, parallel algorithms for examining the existence of a Hamiltonian path and a Hamiltonian cycle and for constructing them, if they exist.

Efficient parallel algorithms for several problems on proper circular arc graphs are presented in this paper. These problems include finding a maximum matching, partitioning into a minimum number of induced subgraphs each of which has a Hamiltonian cycle (path), partitioning into induced subgraphs each of which has a Hamiltonian cycle (path) with at least k vertices for a given k, and adding a minimum number of edges to make the graph contain a Hamiltonian cycle (path). It is shown here that the above problems can all be solved in logarithmic time with a linear number of EREW PRAM processors, or in constant time with a linear number of BSR processors. A more important part of this work is perhaps the extension of basic BSR to allow simultaneous multiple BROADCAST instructions.