A DNA length reducing computing model for maximum independent set problem  

作　　者：Zhang Cheng Yang Jing Xu Jin Zhao DongMing 

机构地区：[1]Peking Univ, Key Lab High Confidence Software Technol, Sch Elect Engn & Comp Sci, Inst Software,Minist Educ, Beijing 100871, Peoples R China

出　　处：《Chinese Science Bulletin》2010年第9期892-898,共7页

基　　金：The authors sincerely acknowledge the anonymous referee’s suggestions to this paper. This work was supported by the National Natural Science Foundation of China (Grant Nos. 60533010, 30670540, 60874036 and 60503002);National High-Tech Research and Development Program of China (Grant No. 2006AA01Z104);Ph.D. Programs Foundation of the Ministry of Education of China (Grant No. 20070001020);the Postdoctoral Science Foundation of China (Grant No. 20060400344)

摘　　要：In this paper, a new molecular computing model is developed to solve the maximum independent set problem, based on the method of DNA length reducing. To solve the maximum independent set problem with n-vertices and m-edges, the time complexity is O(n+m). With the enlargement of the problem scale, the numbers of the required tubes will increase linearly. Two important methods in this experiment are single strand DNA (ssDNA) circularization and DNA length reducing. In addition, using reverse polymerase chain reaction (PCR) and circligase, the structure of DNA molecules is changed in each computing step, transforming from linear double strand DNA (dsDNA) to linear ssDNA and circular ssDNA. Using the circular DNA structure, the recombina-tion among DNA molecules is avoided. To verify this computing model, a small maximum independent set problem was solved.In this paper, a new molecular computing model is developed to solve the maximum independent set problem, based on the method of DNA length reducing. To solve the maximum independent set problem with n-vertices and m-edges, the time complexity is O(n+m). With the enlargement of the problem scale, the numbers of the required tubes will increase linearly. Two important methods in this experiment are single strand DNA (ssDNA) circularization and DNA length reducing. In addition, using reverse polymerase chain reaction (PCR) and circligase, the structure of DNA molecules is changed in each computing step, transforming from linear double strand DNA (dsDNA) to linear ssDNA and circular ssDNA. Using the circular DNA structure, the recombina-tion among DNA molecules is avoided. To verify this computing model, a small maximum independent set problem was solved.

关 键 词：NP-COMPLETE PROBLEM reverse PCR linear ssDNA CIRCULARIZATION DNA LENGTH REDUCING 

分 类 号：N[自然科学总论]