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- Zuwairie Ibrahim, Yusei Tsuboi, Osamu Ono, Marzuki Khalid
- IJCSA
- 2004

Deoxyribonucleic Acid or DNA computing has emerged as an interdisciplinary field that draws together chemistry, molecular biology, computer science, and mathematics. From the DNA computing point of view, it has been proven that it is possible to solve weighted graph problems by exploiting some characteristics of DNA such as length, concentration, and… (More)

A new readout approach for the Hamiltonian Path Problem (HPP) in DNA computing based on the real-time polymerase chain reaction (PCR) is investigated. Several types of fluorescent probes and detection mechanisms are currently employed in real-time PCR, including SYBR Green, molecular beacons, and hybridization probes. In this study, real-time amplification… (More)

- Yusei Tsuboi, Zuwairie Ibrahim, Osamu Ono
- Int. J. Hybrid Intell. Syst.
- 2005

- Zuwairie Ibrahim, Yusei Tsuboi, Osamu Ono
- IEEE transactions on nanobioscience
- 2006

Previously, direct-proportional length-based DNA computing (DPLB-DNAC) for solving weighted graph problems has been reported. The proposed DPLB-DNAC has been successfully applied to solve the shortest path problem, which is an instance of weighted graph problems. The design and development of DPLB-DNAC is important in order to extend the capability of DNA… (More)

In this work, a new DNA-based semantic model is proposed and described theoretically for implementing DNA-based semantic memories. This model, referred to as 'semantic model based on molecular computing' (SMC) has the structure of a graph formed by the set of all (attribute, attribute values) pairs contained in the set of represented objects, plus a tag… (More)

- Zuwairie Ibrahim, Yusei Tsuboi, Mohd Saufee Muhammad, Osamu Ono, Marzuki Khalid
- Congress on Evolutionary Computation
- 2005

In this paper, a demonstration of DNA computing for k-shortest paths of a weighted graph is realized by biochemical experiments in such a way that every path is encoded by oligonucleotides and the length of the path is directly proportional to the length of oligonucleotides. For initial pool generation, parallel overlap assembly is employed for efficient… (More)

In this paper, an in vitro implementation of DNA computing for solving k-shortest paths problem of a weighted graph is reported. The encoding is designed in such a way that every path is encoded by oligonucleotides and the length of the path is directly proportional to the length of oligonucleotides. For initial pool generation, parallel overlap assembly is… (More)

- Zuwairie Ibrahim, Yusei Tsuboi, Osamu Ono, Marzuki Khalid
- BioADIT
- 2006

DNA computing often makes use of hybridization, whether for vastly generating the initial candidate answers or amplification by using polymerase chain reaction (PCR). The main idea behind DNA computing approaches for solving weighted graph problems is that if the degree of hybridization can be controlled, then it is able to generate more double stranded… (More)

- Zuwairie Ibrahim, Yusei Tsuboi, Osamu Ono, Marzuki Khalid
- IJUC
- 2007

Bio-molecular or DNA computing has emerged as an interdiscipli-nary field that draws together chemistry, molecular biology, computer science, engineering, and mathematics. From DNA computing point of view, it has been proven that it is possible to solve weighted graph problems such as Traveling Salesman Problem (TSP) and the shortest path problem by… (More)

- Yusei Tsuboi, Zuwairie Ibrahim, Nobuyuki Kasai, Osamu Ono
- ICNC
- 2005

In this paper, after a new DNA-based semantic model is theoretically proposed, the preliminary experiment on construction of the small test model is successfully done. This model, referred to as 'semantic model based on molecular computing' (SMC) has the structure of a graph formed by the set of all (attribute, attribute values) pairs contained in the set… (More)