Fundamenta Informaticae - Volume 164, issue 2-3

Authors: Pan, Linqiang | Pérez-Jiménez, Mario J. | Zhang, Gexiang

Article Type: Other

DOI: 10.3233/FI-2019-1758

Citation: Fundamenta Informaticae, vol. 164, no. 2-3, pp. i-ii, 2019

Authors: Carandang, Jym Paul | Cabarle, Francis George C. | Adorna, Henry Natividad | Hernandez, Nestine Hope S. | Martínez-del-Amor, Miguel Ángel

Article Type: Research Article

Abstract: Spiking Neural P system is a computing model inspired on how the neurons in a living being are interconnected and exchange information. As a model in embrane computing, it is a non-deterministic and massively-parallel system. The latter makes GPU a good candidate for accelerating the simulation of these models. A matrix representation for systems with and without delay have been previously designed, and algorithms for simulating them with deterministic systems was also developed. So far, non-determinism has been problematic for the design of parallel simulators. In this work, an algorithm for simulating non-deterministic spiking neural P system with delays is …presented. In order to study how the simulations get accelerated on a GPU, this algorithm was implemented in CUDA and used to simulate non-uniform and uniform solutions to the Subset Sum problem as a case study. The analysis is completed with a comparison of time and space resources in the GPU of such simulations. Show more

Keywords: Membrane Computing, Spiking Neural P systems, Matrix Representation, CUDA, GPU, Subset Sum

DOI: 10.3233/FI-2019-1759

Citation: Fundamenta Informaticae, vol. 164, no. 2-3, pp. 139-155, 2019

Authors: Cooper, James | Nicolescu, Radu

Article Type: Research Article

Abstract: The Hamiltonian Cycle Problem (HCP) and Travelling Salesman Problem (TSP) are long-standing and well-known NP-hard problems. The HCP is concerned with finding paths through a given graph such that those paths visit each node exactly once after the start, and end where they began (i.e., Hamiltonian cycles). The TSP builds on the HCP and is concerned with computing the lowest cost Hamiltonian cycle on a weighted (di)graph. Many solutions to these problems exist, including some from the perspective of P systems. For the TSP however, almost all these papers have combined membrane computing with other approaches for approximate solution algorithms, …which is surprising given the plethora of P systems solutions to the HCP. A recent paper presented a brute-force style P systems solution to the TSP with a time complexity of O (n 2 ), exploiting the ability of P systems to reduce time complexity in exchange for space complexity, but the resultant system had a fairly high number of rules, around 50. Inspired by this paper, and seeking a more concise representation of an exact brute-force TSP algorithm, we have devised a P systems algorithm based on cP systems (P systems with Complex Objects) which requires five rules and takes n + 3 steps. We first provide some background on cP systems and demonstrate a fast new cP systems method to find the minimum of a multiset, then describe our solution to the HCP, and build on that for our TSP algorithm. This paper describes said algorithms, and provides an example application of our TSP algorithm to a given graph and a digraph variant. Show more

Keywords: cP systems, P systems, Prolog terms and unification, Travelling Salesman Problem, Hamiltonian Cycle Problem

DOI: 10.3233/FI-2019-1760

Citation: Fundamenta Informaticae, vol. 164, no. 2-3, pp. 157-180, 2019

Authors: Cui, Guangzhao | Jiao, Yangyang | Liu, Jianxia | Li, Jixiang | Zhang, Xuncai | Sun, Zhonghua

Article Type: Research Article

Abstract: In recent years, DNA strand displacement technology has become an integral part of DNA computing, which is proved that the complement circuit played an important role in computer circuits. In this paper, a four-bit complement logic circuit based on DNA strand displacement is designed and simulated. The simulation results show that the designed circuit is reliable and the four-bit complement logic circuit based on DNA strand displacement also indicates that the DNA strand displacement has bright future in the construction of large-scale logic circuits.

Keywords: DNA strand displacement, Four-bit complement, Complement circuit, Visual DSD

DOI: 10.3233/FI-2019-1761

Citation: Fundamenta Informaticae, vol. 164, no. 2-3, pp. 181-194, 2019

Authors: Guo, Bingjie | Wang, Luhui | Wu, Tao | Dong, Yafei

Article Type: Research Article

Abstract: Here, two two-way ion detector (TWID) and one DNA cascade logic circuit and signal amplifier model had been created. Firstly, we have constructed two bidirectional mercury and silver ion detectors, both of which can be used to detect mercury and silver ions at the same time, that means a single molecule can detect two kinds of heavy metal ions at the same time. The unique design of the switches offers significant advantages over existing methods. In addition, the two bidirectional ion detectors enable the design of the logic gates (OR, AND) using Ag+ and Hg2+ as inputs. Secondly, …we constructed a two-level “AND” logic gate by combining the above two logic gates. This logic model takes the output of “OR” logic gate as the input of the next logic gate, which not only realizes the logic operation, but also achieves the function of signal amplification. We are able to recognize the logic output signals effortlessly by observing the amount of fluorescence. It’s a simple, economic and safe approach for the design of a complex multiple-input DNA logic circulation amplification model. Finally, we proved the feasibility of our model by PAGE and fluorescence alteration. Show more

Keywords: logic gate, detect, ions-medicated, DNA computing

DOI: 10.3233/FI-2019-1762

Citation: Fundamenta Informaticae, vol. 164, no. 2-3, pp. 195-205, 2019

Authors: Jiang, Suxia | Wang, Yanfeng | Xu, Jinbang | Xu, Fei

Article Type: Research Article

Abstract: Cell-like P systems with symport/antiport rules (CSA P systems, for short) are a class of computational models in membrane computing, inspired by the way of transmembrane transport of substances through membrane channels between neighboring regions in a cell. In this work, we propose a variant of CSA P systems, called cell-like P systems with symport/antiport rules and promoters (CSAp P systems, for short), where symport/antiport rules are regulated by multisets of promoters. The computational power of CSAp P systems is investigated. Specifically, it is proved that CSAp P systems working in the maximally parallel mode, having arbitrary large number of …membranes and promoters and using only symport rules of length 1 or antiport rules of length 2, are able to compute only finite sets of non-negative integers. Furthermore, we show that CSAp P systems with two membranes working in a sequential mode when having at most two promoters and using only symport rules of length 2, or having at most one promoter and using symport rules of length 1 and antiport rules of length 2, are Turing universal. Show more

Keywords: Bio-inspired computing, Membrane computing, Cell-like P system, Symport/antiport rule, Promoter, Universality

DOI: 10.3233/FI-2019-1763

Citation: Fundamenta Informaticae, vol. 164, no. 2-3, pp. 207-225, 2019

Authors: Choi, Tae Jong | Lee, Jong-Hyun | Youn, Hee Yong | Ahn, Chang Wook

Article Type: Research Article

Abstract: Differential Evolution (DE) algorithm is one of the popular evolutionary algorithms that is designed to find a global optimum on multi-dimensional continuous problems. In this paper, we propose a new variant of DE algorithm by combining a self-adaptive DE algorithm called dynNP-DE with Elite Opposition-Based Learning (EOBL) scheme. Since dynNP-DE algorithm uses a small number of population size in the later of the search process, the population diversity becomes low, and therefore premature convergence may occur. We have therefore extended an OBL scheme to dynNP-DE algorithm to overcome this shortcoming and improve the optimization performance. By combining EOBL scheme to …dynNP-DE algorithm, the population diversity can be supplemented because not only the information of individuals but also their opposition information can be utilized. We measured the optimization performance of the proposed algorithm on CEC 2005 benchmark problems and breast cancer detection, which is a research field that has recently attracted a lot of attention. It was verified that the proposed algorithm could find better solutions than five state-of-the-art DE algorithms. Show more

Keywords: Artificial Neural Networks, Differential Evolution Algorithm, Opposition-Based Learning, Feed-Forward Neural Network, Neural Network Training

DOI: 10.3233/FI-2019-1764

Citation: Fundamenta Informaticae, vol. 164, no. 2-3, pp. 227-242, 2019

Authors: Niu, Ying | Han, Feng | Zhang, Xuncai | Zhou, Zheng

Article Type: Research Article

Abstract: DNA strand displacement technology has been widely used in the field of molecular computing. In the traditional strand displacement circuits, the DNA strands of the toehold domain and the branch migration domain are connected by covalent bonds, while the toehold domain and the branch migration domain of the combinatorial strand displacement are located in different single-stranded DNA (ssDNA), and the flexible combinations of the two domains are realized by the hybridization of the linking domains. It has obvious advantages in the design of multi-input circuits. In this paper, the AND gate, OR gate and XOR gate are constructed by the …combinatorial strand displacement mechanism. On this basis, the half-adder and encoder circuit are constructed. The Visual DSD simulation results show that when the DNA molecular signal strands are input, the desired DNA molecular signal strands are output by the specific intermolecular hybridization reaction and the intermolecular strand displacement reaction, which proves the validity and feasibility of the logic circuit. Show more

Keywords: Combinatorial strand displacement, Logic circuit, Visual DSD, Encoder circuit, DNA reaction network

DOI: 10.3233/FI-2019-1765

Citation: Fundamenta Informaticae, vol. 164, no. 2-3, pp. 243-257, 2019

Authors: Sun, Junwei | Li, Nan | Wang, Yanfeng | Wang, Wei

Article Type: Research Article

Abstract: In this paper, a new chaotic system is proposed, whose dynamical behaviors are discussed with the change of the parameters in detail. The specific effects of different parameters on the system are also discussed. By adjusting these parameters of the proposed circuit, this nonlinear circuit can produce the different dynamical behaviors, such as, hyper chaotic behavior, periodic behavior, transient behavior, etc. Furthermore, a novel kind of modified compound synchronization has been investigated, where the multiple chaotic systems have been considered for different combination modes: the compound system of four scaling drive systems and one response system. The corresponding controllers are …designed to realize the modified compound synchronization. The theoretical proofs and numerical simulations are given to demonstrate the validity and applicability of the proposed chaotic system and the modified compound synchronization. Show more

Keywords: Chaotic system, Dynamical analysis, Lyapunov exponent, Bifurcation diagrams, Modified compound synchronization

DOI: 10.3233/FI-2019-1766

Citation: Fundamenta Informaticae, vol. 164, no. 2-3, pp. 259-275, 2019

Authors: Xie, Wendan | Zhou, Changjun | Lv, Hui | Zhang, Qiang

Article Type: Research Article

Abstract: DNA strand replacement technology has the advantages of simple operation which makes it becomes a common method of DNA computing. A four bit binary number Complementer based on two-domain DNA strand displacement is proposed in this paper. It implements the function of converting binary code into complement code. Simulation experiment based on Visual DSD software is carried out. The simulation results show the correctness and feasibility of the logic model of the Complementer, and it makes useful exploration for further expanding the application of molecular logic circuit.

Keywords: Two-Domain, DNA Strand Displacement, Complementer, Logic Circuit

DOI: 10.3233/FI-2019-1767

Citation: Fundamenta Informaticae, vol. 164, no. 2-3, pp. 277-288, 2019

Authors: Yang, Jing | Yin, Zhi-xiang | Cui, Jian-zhong | Huang, Kai-feng

Article Type: Research Article

Abstract: Detecting the quality of drinking water is very important in researching the current status and predicting trends of variation, as well as fundamentally solving the water pollution problem. Recently, the application and development of biosensor provide a powerful analytical tool for detecting pollutants of drinking water, but high selectivity, specificity, short response time, and low cost are particularly desired in the detection process. In this paper, RNA molecules in combination with nano-gold and magnetic nano-particles were proposed as design strategies of the biosensor. The proposed designs have distinct advantages over conventional biosensor in the following aspects: the high affinity capacity, …sensitivity, and practicability. Our work provided an alternative method to monitor the environment of drinking water, and may find applications in various monitoring fields. Show more

Keywords: RNA biosensor, magnetic nano-particle, gold nano-particle, environmental monitoring

DOI: 10.3233/FI-2019-1768

Citation: Fundamenta Informaticae, vol. 164, no. 2-3, pp. 289-298, 2019