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Solving Knapsack Problems in a Sticker Based Model [chapter]

Mario J. Pérez-Jiménez, Fernando Sancho-Caparrini
2002 Lecture Notes in Computer Science  
Our main goal in this paper is to give molecular solutions for two NP-complete problems, namely Subset-sum and Knapsack, in a sticker based model for DNA computations.  ...  In order to achieve this, we have used a finite set sorting subroutine together with the description of a procedure to formally verify the designed programs through the labeling of test tubes using inductive  ...  to solve the Subset-Sum problem and the Knapsack problem in the following sections.  ... 
doi:10.1007/3-540-48017-x_15 fatcat:ekhb5tmlxrgrpedodxdzix5gmq

Solving the 0/1 Knapsack Problem by a Biomolecular DNA Computer

Hassan Taghipour, Mahdi Rezaei, Heydar Ali Esmaili
2013 Advances in Bioinformatics  
Sticker-based DNA computing is one of the methods of DNA computing. In this paper, the sticker based DNA computing was used for solving the 0/1 knapsack problem.  ...  Then, by the application of a sticker-based parallel algorithm using biological operations, knapsack problem was resolved in polynomial time.  ...  Solving the 0/1 Knapsack Problem in Sticker-Based DNA Computers Definition of the Knapsack Problem.  ... 
doi:10.1155/2013/341419 pmid:23509451 pmcid:PMC3588402 fatcat:kk34t2wf2zbnjfbshu2jrv7cie

Solving the independent set problem by sticker based DNA computers

Hassan Taghipour, Ahad Taghipour, Mahdi Rezaei, Heydar Ali Esmaili
2012 American Journal of Molecular Biology  
Then, by application of a sticker based parallel algorithm using biological operations, independent set problem was resolved in polynomial time.  ...  In this paper, the sticker based DNA computing was used for solving the independent set problem. At first, solution space was constructed by using appropriate DNA memory complexes.  ...  Section 3 introduces a DNA based algorithm for solving the independent set problem in sticker model. A" from one strand bond to "T" from opposite strand, and "C" bond to "G".  ... 
doi:10.4236/ajmb.2012.22017 fatcat:essc466rvzgtlmwdnixtorqqea

Molecular Sticker Model Stimulation on Silicon for a Maximum Clique Problem

Jianguo Ning, Yanmei Li, Wen Yu
2015 International Journal of Molecular Sciences  
The stickers model, as a typical DNA-based computer, is computationally complete and universal, and can be viewed as a bit-vertically operating machine.  ...  Owing to the limited computing sources on SOPC architecture, the DEM could solve moderate-size problems in polynomial time.  ...  performed theoretically to solve Boolean satisfiability problems, the 0-1 Knapsack problem.  ... 
doi:10.3390/ijms160613474 pmid:26075867 pmcid:PMC4490504 fatcat:xoxysshlincejjblwxgcsneqem

Towards solution of the set-splitting problem on gel-based DNA computing

Weng-Long Chang, Minyi Guo, Michael Ho
2004 Future generations computer systems  
In this paper, it proves how to apply sticker in the sticker-based model to construct solution space of DNA in the set-splitting problem and how to apply DNA operations in the Adleman-Lipton model to solve  ...  that problem from the solution space of sticker.  ...  In this paper, we use sticker in the sticker-based model to construct solution spaces of DNA strands for the set-splitting problem.  ... 
doi:10.1016/j.future.2003.10.010 fatcat:auhdsdlsyrf45nmji5s3dw3xxy

Applying Surface-Based DNA Computing for Solving the Dominating Set Problem

Hassan Taghipour, Mahdi Rezaei, Heydar Ali Esmaili
2012 American Journal of Molecular Biology  
In this paper, we applied surface-based DNA computing for solving the dominating set problem. At first step, surface-based DNA solution space was constructed by using appropriate DNA strands.  ...  Then, by application of a DNA parallel algorithm, dominating set problem was resolved in polynomial time.  ...  [9] introduced the Sticker based DNA computing model and applied it in solving the Minimal Set Cover problem.  ... 
doi:10.4236/ajmb.2012.23030 fatcat:nbvwoxbblzg6jmrbvqq2hpoguq

Disruption-Tolerant Spatial Dissemination

Bo Xing, Sharad Mehrotra, Nalini Venkatasubramanian
2010 2010 7th Annual IEEE Communications Society Conference on Sensor, Mesh and Ad Hoc Communications and Networks (SECON)  
Sticker employs the store-carry-and-forward model, and strives to optimize dissemination performance by addressing three subproblems -replication, forwarding and purging.  ...  In this paper, we develop a distributed solution to spatial dissemination, that can work without the need for such an infrastructure.  ...  Sticker employs a greedy approximation algorithm to efficiently solve the knapsack problem -the general idea being to sort the items in decreasing order of value per unit of weight, and to pack them in  ... 
doi:10.1109/secon.2010.5508274 dblp:conf/secon/XingMV10 fatcat:qha7dndaw5ambf4qlmin4ysi3y

Fast parallel bio-molecular solutions: the set-basis problem

Weng Long Chang, Michael Ho, Minyi Guo, Chengfei Liu
2006 International Journal of Computational Science and Engineering (IJCSE)  
In the paper, it is demonstrated how to apply sticker in the sticker-based model for constructing solution space of DNA for the setbasis problem and how to apply DNA operations in the Adleman-Lipton model  ...  to solve that problem from solution space of sticker.  ...  ., 1999) proposed sticker for enhancing the Adleman-Lipton model. In this paper, we use a sticker in the sticker based model for constructing a solution space of DNA for the setbasis problem.  ... 
doi:10.1504/ijcse.2006.009937 fatcat:ysqez4f4hba4lfnmvnxcnwk72i

Fast parallel molecular solution to the dominating-set problem on massively parallel bio-computing

Minyi Guo, Michael (Shan-Hui) Ho, Weng-Long Chang
2004 Parallel Computing  
In order to achieve this, we have proposed some DNA based parallel algorithms using the operations in Adleman-Lipton model, together with the analysis of the computational complexity for DNA parallel algorithms  ...  This paper shows how to use DNA strands to construct solution space of molecules for the dominating-set problem and how to apply biological operations to solve the problem from the solution space of molecules  ...  [15] employed sticker-based model [14] to resolve knapsack problems. Fu [21] proposed new algorithms to resolve 3-SAT, 3-Coloring and the independent set. In our previous work, Chang et al.  ... 
doi:10.1016/j.parco.2004.07.014 fatcat:2pc4lqsje5b3lhebdriul44xc4

Is optimal solution of every NP-complete or NP-hard problem determined from its characteristic for DNA-based computing

Minyi Guo, Weng-Long Chang, Machael Ho, Jian Lu, Jiannong Cao
2005 Biosystems (Amsterdam. Print)  
Cook's Theorem has been demonstrated to be correct in a general digital electronic computer. In this paper, we first propose a DNA algorithm for solving the vertex-cover problem.  ...  Adleman and co-workers proposed sticker for enhancing the Adleman-Lipton model (Roweis et al., 1999) .  ...  Perez-Jimenez and Sancho-Caparrini (2001) employed sticker-based model (Roweis et al., 1999) to solve knapsack problems.  ... 
doi:10.1016/j.biosystems.2004.10.003 pmid:15740836 fatcat:ucosdlfnbrakdgoctrnvtwumk4

Solving the Rubik's Cube Without Human Knowledge [article]

Stephen McAleer, Forest Agostinelli, Alexander Shmakov, Pierre Baldi
2018 arXiv   pre-print
A generally intelligent agent must be able to teach itself how to solve problems in complex domains with minimal human supervision.  ...  Our algorithm is able to solve 100% of randomly scrambled cubes while achieving a median solve length of 30 moves -- less than or equal to solvers that employ human domain knowledge.  ...  Bello et. al. train an RNN through policy gradients to solve simple traveling salesman and knapsack problems [4] .  ... 
arXiv:1805.07470v1 fatcat:gr4einiiefffzg3gnykgaofxfa

Using sticker to solve the 3-dimensional matching problem in molecular supercomputers

Minyi Guo, Weng-Long Chang, Jiannong Cao
2004 International Journal of High Performance Computing and Networking  
Then, in the Adleman-Lipton model, we propose an algorithm to remove illegal solution and find legal solution for the 3-dimensional matching problem from solution space of sticker.  ...  In this paper, we first use sticker to construct solution space of DNA library sequences for the 3-dimensional matching problem.  ...  Perez-Jimenez and Sancho-Caparrini (2001) employed sticker-based model (Roweis et al., 1999) to resolve knapsack problems.  ... 
doi:10.1504/ijhpcn.2004.007572 fatcat:f7aei6j5ovcmbocpv6y5axxpqm

Development of a method to linearize the quadratic assignment problem

Elias Munapo
2021 Eastern-European Journal of Enterprise Technologies  
The quadratic assignment problem (QAP) is a well-known problem whereby a set of facilities are allocated to a set of locations in such a way that the cost is a function of the distance and flow between  ...  In this problem, the costs are associated with a facility being placed at a certain location. The objective is to minimize the assignment of each facility to a location.  ...  The paper [4] addresses the problem of how to solve QAP under the Adleman-Lipton-sticker model. There are five main classes of heuristics for the quadratic assignment problem and these are: 1.  ... 
doi:10.15587/1729-4061.2021.225311 fatcat:d7gaswymcfgadajiuzgvfuvqtq

Model Checking Temporal Logic Formulas Using Sticker Automata

Weijun Zhu, Changwei Feng, Huanmei Wu
2017 BioMed Research International  
To address this challenge, a model checking method is proposed for checking the basic formulas in the above three temporal logic types with DNA molecules.  ...  First, one-type single-stranded DNA molecules are employed to encode the Finite State Automaton (FSA) model of the given basic formula so that a sticker automaton is obtained.  ...  published an article in ⟨Science⟩ that presented a DNA-computing-based model for solving the maximal clique problem [3] . Benenson et al.  ... 
doi:10.1155/2017/7941845 pmid:29119114 pmcid:PMC5651143 fatcat:qmkxsujjnzc3dayatmpcgfg3re

Parallelizing Assignment Problem with DNA Strands

Babak Khorsand, Abdorreza Savadi, Mahmoud Naghibzadeh
2020 Iranian Journal of Biotechnology  
Applying bio molecular operations of Adelman Lipton model, a novel parallel DNA algorithm have been proposed for solving the assignment problem.  ...  In this article, using DNA computing, we proposed a parallel DNA algorithm to solve the assignment problem in linear time.  ...  Ouyang (6) solved Maximal clique problem in 1997 by designing Restriction enzyme model. Roweis designed sticker model (7) in 1998. The Self-assembly model was designed by Winfree in 1998 (8) .  ... 
doi:10.30498/ijb.2020.195413.2547 pmid:32884959 pmcid:PMC7461708 fatcat:rvjzf6qglvhzfpprnwr2aprv34
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