Biomolecular autonomous solution of the Hamiltonian path problem via hairpin formation

Molecular computing has proved its possibility to solve weighted graph problem such as Hamiltonian Path Problem (HPP), Traveling Salesman Problem (TSP) and the Shortest Path Problem (SPP). Normally, in molecular computation, the DNA sequences used for the computation should be critically designed in order to reduce error that could occur during computation. In the previous paper, we have proposed a readout method tailored specifically to HPP in DNA Computing using real-time PCR for output visualization. Six nodes of HPP was considered. Based on the example instance, the method requires 11 oligonucleotides, where 6 oligonucleotides are for the nodes and 5 oligonucleotides are for the edges. Three TaqMan probes and five primers are required as well. In this study, a procedure for DNA sequence design is presented in order to obtain good sequences for those nodes, primers, and probes. The experiment is done based on the generated DNA sequences and the Hamiltonian Path can be determined successfully.

This dissertation is to illustrate the current state of the art of DNA computing achievements, especially of new approaches to solve theoretical 3-SAT problems and the hitting-set problem. Beginning with Adleman’s breakthrough which is an molecular algorithm for the solution of a NP-complete, combinatorial problem, the directed Hamiltonian path problem (HPP). Today, many researchers all over the world concentrate on proposing new methods to solve engineering or application problems with a DNA computing approach. Satisfiability problem is given a Boolean formula, and decide if a satisfying truth assignment exists. ( ) ( ) … ( ) ( ) is an example of Boolean formula. k-SAT problem means that each clause has exactly k literals. Not-All-Equal (NAE) 3-SAT problem and One-In-Three (1IN3) 3-SAT problem are both NP-complete problems. In this dissertation, we present molecular solutions to find all true assignments (3-SAT problem) and furthermore find Not-All-Equal (NAE) solutions and One-In-Three (1IN3) solutions in DNA-based Supercomputing. Hitting-set problem assume that there exists a collection C of subsets of a finite set S, and a positive integer K  |S|, and we need to know if there is a subset  S with | |  K such that contains at least one element of each subset in C. In other words, is the subset that intersects every subset in C and is called the hitting-set. In this dissertation, a DNA-based algorithm is proposed to solve the small hitting-set problem. A small hitting-set is a hitting-set with the smallest K value, i.e., the hitting-set with the smallest number of elements. Furthermore, an algorithm is introduced to find the number of ones from 2n combinations and minimum numbers of ones represents the small hitting-set since K is expected to be as small as possible. The complexity of all the presented DNA-based algorithms is also discussed. We describe time complexity and volume complexity of three Algorithms, numbers of test tube used and the longest library strand in solution space of all three Algorithms. Finally, the simulated experiment is applied to verify correctness of the proposed DNA-based algorithm for solving the One-In-Three (1IN3) 3-SAT problem, and simulation of Not-All-Equal (NAE) 3-SAT problem is similar. Also, another simulated experiment is applied to our proposed DNA-based algorithm 6-2, in order to solve the well-known hitting-set problem. This research has been motivated by the benefit and the application of DNA computing and gives new methods to solve two 3-SAT problems and the hitting-set problem which are NP-complete.

In this article we consider the Directed Steiner Path Cover problem on directed co-graphs. Given a directed graph G=(V,E) and a set T subseteq V of so-called terminal vertices, the problem is to find a minimum number of vertex-disjoint simple directed paths, which contain all terminal vertices and a minimum number of non-terminal vertices (Steiner vertices). The primary minimization criteria is the number of paths. We show how to compute in linear time a minimum Steiner path cover for directed co-graphs. This leads to a linear time computation of an optimal directed Steiner path on directed co-graphs, if it exists. Since the Steiner path problem generalizes the Hamiltonian path problem, our results imply the first linear time algorithm for the directed Hamiltonian path problem on directed co-graphs. We also give binary integer programs for the (directed) Hamiltonian path problem, for the (directed) Steiner path problem, and for the (directed) Steiner path cover problem. These integer programs can be used to minimize change-over times in pick-and-place machines used by companies in electronic industry.

In the past few years since Adleman’s pioneering work on solving the HPP(Hamiltonian Path Problem) with a DNA-based computer [1], many algorithms have been designed on solving NP problems. Most of them are in the solution bases and need some error correction or tolerance technique in order to get good and correct results [3] [7] [9] [11] [21] [22]. The advantage of surface-based DNA computing technique, with very low error rate, has been shown many times [12] [18] [17] [20] over the solution based DNA computing, but this technique has not been widely used in the DNA computer algorithms design. This is mainly due to the restriction of the surface-based technique comparing with those methods using the DNA strands in solutions. In this paper, we introduce a surface-based DNA computing algorithm for solving a hard computation problem: expansion of symbolic determinants given their patterns of zero entries. This problem is well-known for its exponential difficulty. It is even more difficult than evaluating determinants whose entries are merely numerical [15]. We will show how this problem can be solved with the low error rate surface-based DNA computer using our naive algorithm.

Let G V , E be a simple undirected complete graph with vertex and edge sets V and E , respectively. In this paper, we consider the degree-constrained k -minimum spanning tree (DC k MST) problem which consists of finding a minimum cost subtree of G formed with at least k vertices of V where the degree of each vertex is less than or equal to an integer value d ≤ k − 2 . In particular, in this paper, we consider degree values of d ∈ 2,3 . Notice that DC k MST generalizes both the classical degree-constrained and k -minimum spanning tree problems simultaneously. In particular, when d = 2 , it reduces to a k -Hamiltonian path problem. Application domains where DC k MST can be adapted or directly utilized include backbone network structures in telecommunications, facility location, and transportation networks, to name a few. It is easy to see from the literature that the DC k MST problem has not been studied in depth so far. Thus, our main contributions in this paper can be highlighted as follows. We propose three mixed-integer linear programming (MILP) models for the DC k MST problem and derive for each one an equivalent counterpart by using the handshaking lemma. Then, we further propose ant colony optimization (ACO) and variable neighborhood search (VNS) algorithms. Each proposed ACO and VNS method is also compared with another variant of it which is obtained while embedding a Q-learning strategy. We also propose a pure Q-learning algorithm that is competitive with the ACO ones. Finally, we conduct substantial numerical experiments using benchmark input graph instances from TSPLIB and randomly generated ones with uniform and Euclidean distance costs with up to 400 nodes. Our numerical results indicate that the proposed models and algorithms allow obtaining optimal and near-optimal solutions, respectively. Moreover, we report better solutions than CPLEX for the large-size instances. Ultimately, the empirical evidence shows that the proposed Q-learning strategies can bring considerable improvements.

The Hamiltonian Cycle problem is the problem of deciding whether an n-vertex graph G has a cycle passing through all vertices of G. This problem is a classic NP-complete problem. Finding an exact algorithm that solves it in \({\mathcal {O}}^{*}(\alpha^{n})\) time for some constant α<2 was a notorious open problem until very recently, when Björklund presented a randomized algorithm that uses \({\mathcal {O}}^{*}(1.657^{n})\) time and polynomial space. The Longest Cycle problem, in which the task is to find a cycle of maximum length, is a natural generalization of the Hamiltonian Cycle problem. For a claw-free graph G, finding a longest cycle is equivalent to finding a closed trail (i.e., a connected even subgraph, possibly consisting of a single vertex) that dominates the largest number of edges of some associated graph H. Using this translation we obtain two deterministic algorithms that solve the Longest Cycle problem, and consequently the Hamiltonian Cycle problem, for claw-free graphs: one algorithm that uses \({\mathcal {O}}^{*}(1.6818^{n})\) time and exponential space, and one algorithm that uses \({\mathcal {O}}^{*}(1.8878^{n})\) time and polynomial space.

The Hamiltonian cycle problem is a well-known NP-complete problem in graph theory. This problem relates to lots of practical problems such as designing very large scale integration (VLSI) and travel-ling salesman problem (TSP). Since it is NP-complete, there is no efficient algorithm to solve the Hamiltonian cycle problem, and hence, its solution is valuable. In this paper, we propose new physical zero-knowledge proof protocols for the Hamiltonian cycle problem, whereby an entity can prove its knowledge of a solution to another entity without leaking any information about the valuable solution. Our protocols are more efficient than the previous protocols. We also propose a physical zero-knowledge proof protocol for TSP, one of whose building blocks is a new representation of an integer commitment with a secure addition protocol.

The Hamiltonian cycle and path problems are fundamental in graph theory and useful in modelling real-life problems. Research in this area is directed toward designing better and better algorithms for general problems, but also toward defining new special cases for which exact polynomial-time algorithms exist. In the paper, such new classes of digraphs are proposed. The classes include, among others, quasi-adjoint graphs, which are a superclass of adjoints, directed line graphs, and graphs modelling a DNA sequencing problem.

In this paper, we describe the simulation of Ising minimization on a classical machine by executing variational quantum algorithms on our density-matrix simulator. We outline the Ising formulation of the Graph Partitioning problem and the Hamiltonian Cycle problem, and solve the Max-Cut variant of graph partitioning for a weighted square graph S <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">q2</sub> using the Quantum Approximate Optimization Algorithm. We finally study the effect of errors present in Noisy Intermediate-Scale Quantum processors on the obtained solutions. This paper illustrates the approach to approximately solving hard combinatorial optimization problems using a hybrid quantum-classical scheme and describes the issues in hardware implementation of such schemes. The simulations of NISQ noise models will be useful in understanding the performance and capabilities of such approaches.

A digraph is semicomplete if it has no pair of non-adjacent vertices. It is complete if every pair of distinct vertices induces a 2-cycle. A digraph is semicomplete multipartite if it can be obtained from a semicomplete digraph D by choosing a collection of vertex-disjoint subsets X₁,…,X_c of V(D) and then deleting all arcs both of whose end-vertices lie inside some X_i. We can also think of a semicomplete digraph as being obtained from a semicomplete multipartite digraph on the same vertex set and partite sets V₁,…,V_c by adding the arcs of a semicomplete digraph D_i on V_i for each partite set V_i. It is well known that both the hamiltonian path and the hamiltonian cycle problem can be solved in polynomial time for semicomplete multipartite digraphs. In this paper we study the complexity of finding a hamiltonian path or cycle in a semicomplete digraph S which is obtained as above from a semicomplete multipartite digraph D and semicomplete digraphs D_i=(V_i,A_i), i∈[c] such that the path or cycle uses as few arcs of A₁∪…A_c as possible. We obtain a number of results for the case when each D_i is a complete digraph. Already this case is highly nontrivial in the cycle case and the complexity is still open. We show how to find a Hamiltonian path which uses as few arcs from the D_i’s as possible in polynomial time and obtain a number of results, both structural and algorithmic on hamiltonian cycles that use the minimum or close to the minimum number of arcs from the D_i’s. Our results imply the polynomial solvability of some special cases of the NP-complete {0,1}-TSP problem. Finally we show that two natural questions about properties of quasi-hamiltonian cycles, that is, cycles meeting all partite sets in semicomplete multipartite digraphs are NP-complete.

Not being (super)thin or solid is hard: A study of grid Hamiltonicity

Kombinatorische entscheidungsprobleme: Methoden und anwendungen; fortbildungskurs des instituts für operations research der ETH Zürich: Thomas M. Liebling, Max Rössler (Eds.) Springer, Berlin, 1978, 206 pages, Dfl. 32.75 Soft cover

We consider the complexity of the Hamilton cycle decision problem when restricted to k-uniform hypergraphs H of high minimum codegree delta(H). We show that for tight Hamilton cycles this problem is NP-hard even when restricted to k-uniform hypergraphs H with delta(H) >= n/2 - C, where n is the order of H and C is a constant which depends only on k. This answers a question raised by Karpinski, Rucinski and Szymanska. Additionally we give a polynomial-time algorithm which, for a sufficiently small constant epsilon > 0, determines whether or not a 4-uniform hypergraph H on n vertices with delta(H) >= n/2 - epsilon * n contains a Hamilton 2-cycle. This demonstrates that some looser Hamilton cycles exhibit interestingly different behaviour compared to tight Hamilton cycles. A key part of the proof is a precise characterisation of all 4-uniform hypergraphs H on n vertices with delta(H) >= n/2 - epsilon * n which do not contain a Hamilton 2-cycle; this may be of independent interest. As an additional corollary of this characterisation, we obtain an exact Dirac-type bound for the existence of a Hamilton 2-cycle in a large 4-uniform hypergraph.

We consider the Hamiltonian cycle problem on a given graph $G$. With such a graph we can associate a family $\mathcal{F}$ of probability transition matrices of Markov chains whose entries represent the probabilities of traversing corresponding arcs of the graph. When the underlying graph is Hamiltonian, we show the transition probability matrix induced by a Hamiltonian cycle maximizes—over $\mathcal{F}$—the determinant of a matrix that is a rank-one correction of the generator matrix of a Markov chain. In the case when the graph does not possess a Hamiltonian cycle, the above maximization yields a transition matrix of a chain with a longest simple cycle (in $G$) comprising that chain's unique ergodic class. These problems also have analogous eigenvalue interpretations.

Hamiltonian problems in directed graphs with simple row patterns