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Application of lengthbased DNA computing for complex scheduling problem
 International Journal of Information Technology
, 2006
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All intext references underlined in blue are linked to publications on ResearchGate, letting you access and read them immediately.
DNA Algorithm Employing Temperature Gradient for Multiple Traveling Salesperson Problem
"... The biological Deoxyribo Nucleic Acid (DNA) strand is found to be a promising computing unit. An attempt has been made to solve symmetric Multiple Travelling Salesperson Problem (MTSP) with single depot using DNA. In this paper, the thermodynamic properties of DNA have been utilized along with other ..."
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The biological Deoxyribo Nucleic Acid (DNA) strand is found to be a promising computing unit. An attempt has been made to solve symmetric Multiple Travelling Salesperson Problem (MTSP) with single depot using DNA. In this paper, the thermodynamic properties of DNA have been utilized along with other biochemical operations to obtain the optimal solution. Actual distance values are possible to be represented using the thermodynamic properties of DNA. Moreover, the proposed approach can be adopted in solving more reallife applications like Vehicle Routing problems and Scheduling problems, with necessary modifications. In this work, an instance with seven cities and three salespersons is solved using DNA computing. This method exhibits the ability to solve NPcomplete problems using molecular computing.
A Design and Implementation Method for Elevator Scheduling Problem Using DNA Computing Approach
"... We present a design and implementation method to solve an elevator scheduling problem using DNA computing in this research. DNA sequences of length directly proportional to the elevator’s traveling time are encoded to represent all possible travel path combinations based on certain initial condition ..."
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We present a design and implementation method to solve an elevator scheduling problem using DNA computing in this research. DNA sequences of length directly proportional to the elevator’s traveling time are encoded to represent all possible travel path combinations based on certain initial conditions such as present and destination floors, and hall calls from a floor. Parallel overlap assembly is employed for initial pool generation and polymerase chain reaction for amplification. Gel electrophoresis is then performed to separate the sequences according to its length and its image is captured to visualize the optimal path. Experimental result obtained verifies that this approach can be wellsuited to solve such realworld problem of this nature. Key words: Elevator scheduling problem, DNA computing, gel electrophoresis, optimal path.
Design and Implementation Method for a Scheduling Problem Using DNA Computing Approach
"... Abstract — A design and implementation method to solve a scheduling problem using DNA computing approach is presented. Here, an elevator scheduling problem is chosen as the input problem where DNA sequences of length directly proportional to the elevator’s traveling time are encoded to represent all ..."
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Abstract — A design and implementation method to solve a scheduling problem using DNA computing approach is presented. Here, an elevator scheduling problem is chosen as the input problem where DNA sequences of length directly proportional to the elevator’s traveling time are encoded to represent all possible travel path combinations based on certain initial conditions such as present and destination floors, and hall calls from a floor. Parallel overlap assembly is employed for initial pool generation and polymerase chain reaction for amplification. Gel electrophoresis is then performed to separate the sequences according to its length and its image is captured to visualize the optimal path. Experimental result obtained verifies that this approach can be wellsuited to solve such realworld problem of this nature. T I.
Hybrid ConcentrationControlled DirectProportional LengthBased DNA Computing for Numerical Optimization of the Shortest Path Problem
"... Abstract. 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 ca ..."
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Abstract. 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 DNAs (dsDNAs), which represent the answer of the problem during in vitro computation. Previously, length, concentration, and melting temperature, have been exploited for encoding of weights of a weighted graph problem. In this paper, we present a hybrid approach, which is called concentrationcontrolled directproportional lengthbased DNA computing (CCDPLBDNAC), that combines two characteristics: length and concentration, for encoding and at the same time, effectively control the degree of hybridization of DNA. The encoding by length is realized whereby the cost of each path is encoded by the length of the oligonucleotides (oligos) in a proportional way. On the other hand, the hybridization control by concentration is done by varying the amount of oligos, as the input of computation,
Application of LengthBased DNA Computing for an Elevator Scheduling Problem Application of LengthBased DNA Computing for an Elevator Scheduling Problem
"... This paper discussed the implementation ideas and experimental procedures to solve an engineering related combinatorial problem using DNA computing approach. An elevator scheduling problem is chosen as a benchmark where all the elevator travel paths are represented by DNA sequences of specific lengt ..."
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This paper discussed the implementation ideas and experimental procedures to solve an engineering related combinatorial problem using DNA computing approach. An elevator scheduling problem is chosen as a benchmark where all the elevator travel paths are represented by DNA sequences of specific lengths that represent the elevators traveling time in a proportional way based on certain initial conditions such as elevator’s present and destination floors, and hall calls for an elevator from a floor. Parallel overlap assembly method is employed for initial pool generation for a more efficient generation of all possible elevator travel paths. The initial pool generation solution is then subjected to polymerase chain reaction and gel electrophoresis to extract the required optimal path. Experimental result obtained shows that DNA computing approach can be wellsuited for solving such realworld application in the near future.
Tehran, Iran.
"... Two new models for implementing finite state machines with DNA computing are presented. The operations used in both models are simple and easy to implement. Operations include immobilization of DNA strands onto paramagnetic beads, DNA hybridization, DNA ligation and restriction enzyme cleavage. Use ..."
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Two new models for implementing finite state machines with DNA computing are presented. The operations used in both models are simple and easy to implement. Operations include immobilization of DNA strands onto paramagnetic beads, DNA hybridization, DNA ligation and restriction enzyme cleavage. Use of paramagnetic beads greatly reduces performance time and demonstrates DNA chip compatibility of the models. In one of the models, the length of DNA strands created during the intermediate operations are independent of the length of the input string. Optical extraction in both models detects the final state.
In Vitro Implementation of kshortest Paths Computation with Graduated PCR
"... Abstract: In this paper, an in vitro implementation of DNA computing for solving kshortest 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 oligon ..."
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Abstract: In this paper, an in vitro implementation of DNA computing for solving kshortest 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 employed for efficient generation of all candidate answers. After the initial solution is subjected to amplification by polymerase chain reaction (PCR), kshortest paths could be visualized by polyacrylamide gel electrophoresis (PAGE) and the selection can be done. The visualization of the output, in fact, relies on the appearance of DNA bands on a gel image. Further, it is shown that a method called graduated PCR is a good subsequent biomolecular reaction for obtaining molecular information hidden in the output DNA. Graduated PCR is also crucial to prove the correctness of the in vitro computation. The experimental results show the effectiveness of the proposed DNAbased computation and prove that the kshortest paths problem has been successfully solved on a DNA computer. Keywords: DNA computing, kshortest paths, graduated PCR, hybridizationligation, parallel overlap assembly. I.
EXPERIMENTAL IMPLEMENTATION OF DIRECT PROPORTIONAL LENGTHBASED DNA COMPUTING FOR ELEVATOR SCHEDULING PROBLEM
"... Abstract: Previously, ideas and implementation methods for solving elevator scheduling problem using DNA computing method had been proposed. In this paper, results of biochemical experiments that have been carried out to realize the computing approach are presented. Every possible elevators travel p ..."
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Abstract: Previously, ideas and implementation methods for solving elevator scheduling problem using DNA computing method had been proposed. In this paper, results of biochemical experiments that have been carried out to realize the computing approach are presented. Every possible elevators travel path combinations are encoded by DNA sequences of length directly proportional to the elevator’s traveling time based on certain initial conditions such as elevators present and destination floors, and hall calls from a floor. Parallel overlap assembly is employed for an efficient initial pool generation of all possible travel path combinations and polymerase chain reaction for sequence amplification. Finally, gel electrophoresis is performed to separate the DNA sequence according to its length, and the shortest DNA sequence representing the elevator’s optimal path can thus be visualized from the gel electrophoresis image. The experimental result shows that the DNA computing approach can be wellsuited for solving such realworld problem of this type of nature.
DNA COMPUTING AND ITS APPLICATIONS: SURVEY
, 2007
"... Abstract. The aim of the paper is to make a review of DNA computing achievements on current stage, especially on new approaches or methods contributing to solve either theoretical or application problems. Starting with the NPproblem that Adleman solved by means of wet DNA experiment in 1994, DNA be ..."
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Abstract. The aim of the paper is to make a review of DNA computing achievements on current stage, especially on new approaches or methods contributing to solve either theoretical or application problems. Starting with the NPproblem that Adleman solved by means of wet DNA experiment in 1994, DNA becomes one of the most appropriate alternatives to overcome the silicon computer limitations. Today, many researchers concentrate on this research subject either to improve available methods used in DNA computing itself or to suggest a new way to solve engineering or application problems with a DNA computing approach. This paper gives an overview of research achievements in DNA computing and touches on the achievements of improving methods employed in DNA computing as well as in solving application problems. At the end of discussion we address several challenges that DNA computing are facing in the society.