Two personification strategies are presented, which yield a highly efficient and practical algorithm for solving one of the NP hard problems——circles packing problem on the basis of the quasi-physical algorithm. A v...Two personification strategies are presented, which yield a highly efficient and practical algorithm for solving one of the NP hard problems——circles packing problem on the basis of the quasi-physical algorithm. A very clever polynomial time complexity degree approximate algorithm for solving this problem has been reported by Dorit S.Hochbaum and Wolfgang Maass in J. ACM. Their algorithm is extremely thorough-going and of great theoretical significance. But, just as they pointed out, their algorithm is feasible only in conception and even for examples frequently encountered in everyday life and of small scale, it is the case more often than not that up to a million years would be needed to perform calculations with this algorithm. It is suggested toward the end of their paper that a heuristic algorithm of higher practical effectiveness should be sought out. A direct response to their suggestion is intented to provide.展开更多
In this paper, we study an off-lattice protein AB model with two species of monomers, hydrophobic and hydrophilic, and present a heuristic quasi-physical algorithm. First, by elaborately simulating the movement of the...In this paper, we study an off-lattice protein AB model with two species of monomers, hydrophobic and hydrophilic, and present a heuristic quasi-physical algorithm. First, by elaborately simulating the movement of the smooth solids in the physical world, we find low-energy conformations for a given monomer chain. A subsequent off-trap strategy is then proposed to trigger a jump for a stuck situation in order to get out of the local minima. The algorithm has been tested in the three-dimensional AB model for all sequences with lengths of 13-55 monomers. In several cases, we renew the putative ground state energy values. The numerical results show that the proposed methods are very promising for finding the ground states of proteins.展开更多
A quasi physical algorithm was proposed for solving the linear separation problem of point set in n dimensional space.The original idea of the quasi physical algorithm is to find an equivalent physical world for the p...A quasi physical algorithm was proposed for solving the linear separation problem of point set in n dimensional space.The original idea of the quasi physical algorithm is to find an equivalent physical world for the primitive mathematical problem and to observe the vivid images of the motion of matter in it so as to be inspired to obtain an algorithm for solving the mathematical problem. In this work, the electrostatics with two kinds of matter is found to be the equivalent physical world. As a result,the proposed algorithm is evidently more efficient and robust than the famous LMS algorithm and ETL algorithm. The efficiency of the quasi physical algorithm is about 10-50 times of the LMS algorithm’s for representative instances. A typical Boolean valued instance shows that it is hard for ETL algorithm but very easy for the quasi physical algorithm.In this instance, point set A and B is {000, 010, 011, 111} and {001,100}, respectively.展开更多
Protein folding problem is one of the most prominent problems of bioinformatics. In this paper, we study a three-dimensional off-lattice protein AB model with two species of monomers, hydrophobic and hydrophilic, and ...Protein folding problem is one of the most prominent problems of bioinformatics. In this paper, we study a three-dimensional off-lattice protein AB model with two species of monomers, hydrophobic and hydrophilic, and present a heuristic quasi-physical algorithm. By elaborately simulating the movement of the smooth elastic balls in the physical world, the algorithm finds low-energy configurations for a given monomer chain. A subsequent ＂off-trap＂ strategy is proposed to trigger a jump for a stuck situation in order to get out of local minima. The methods have been tested in the off-lattice AB model. The computational results show promising performance. For all sequences with 13 to 55 monomers, the algorithm finds states with lower energy than previously proposed putative ground states. Furthermore, for the sequences with 21, 34 and 55 monomers, new putative ground states are found, which are different from those given in present literature.展开更多
The basic problem of a radar group monitoring an object group that has all along been a problem of concern in the international circles of military science has been solved for the first time.A mathematical model for s...The basic problem of a radar group monitoring an object group that has all along been a problem of concern in the international circles of military science has been solved for the first time.A mathematical model for solving the 3-D monitoring problem has been developed based on the quasi-physical concept and a practical fast algorithm has been found.A high-efficiency tracking and monitoring system can be designed for use by radar troops and the administrative and commercial departments concerned using this algorithm.展开更多
A three-dimensional off-lattice protein model with two species of monomers, hydrophobic and hydrophilic, is studied. Enligh- tened by the law of reciprocity among things in the physical world, a heuristic quasi-physic...A three-dimensional off-lattice protein model with two species of monomers, hydrophobic and hydrophilic, is studied. Enligh- tened by the law of reciprocity among things in the physical world, a heuristic quasi-physical algorithm for protein structure prediction problem is put forward. First, by elaborately simulating the movement of the smooth elastic balls in the physical world, the algorithm finds low energy configurations for a given monomer chain. An ＂off-trap＂ strategy is then proposed to get out of local minima. Experimental results show promising performance. For all chains with lengths 13≤n ≤55, the proposed algorithm finds states with lower energy than the putative ground states reported in literatures. Furthermore, for chain lengths n = 21, 34, and 55, the algorithm finds new low energy configurations different from those given in literatures.展开更多
We study a three-dimensional off-lattice protein folding model, which involves two species of residues interacting through Lennard-Jones potentials. By incorporating an extra energy contribution into the original pote...We study a three-dimensional off-lattice protein folding model, which involves two species of residues interacting through Lennard-Jones potentials. By incorporating an extra energy contribution into the original potential function, we replace the original constrained problem with an unconstrained minimization of a mixed potential function. As such an efficient quasi-physical algorithm for solving the protein folding problem is presented. We apply the proposed algorithm to sequences with up to 55 residues and compare the computational results with the putative lowest energy found by several of the most famous algorithms, showing the advantages of our method. The dynamic behavior of the quasi-physlcal algorithm is also discussed.展开更多
基金Project supported by the 973 National Focus Program of China on Development of Fundamental Research, 863 National HighTech Programme of China, National Natural Science Foundation of China, and Chinese Science Foundation for National Doctoral Training.
文摘Two personification strategies are presented, which yield a highly efficient and practical algorithm for solving one of the NP hard problems——circles packing problem on the basis of the quasi-physical algorithm. A very clever polynomial time complexity degree approximate algorithm for solving this problem has been reported by Dorit S.Hochbaum and Wolfgang Maass in J. ACM. Their algorithm is extremely thorough-going and of great theoretical significance. But, just as they pointed out, their algorithm is feasible only in conception and even for examples frequently encountered in everyday life and of small scale, it is the case more often than not that up to a million years would be needed to perform calculations with this algorithm. It is suggested toward the end of their paper that a heuristic algorithm of higher practical effectiveness should be sought out. A direct response to their suggestion is intented to provide.
文摘In this paper, we study an off-lattice protein AB model with two species of monomers, hydrophobic and hydrophilic, and present a heuristic quasi-physical algorithm. First, by elaborately simulating the movement of the smooth solids in the physical world, we find low-energy conformations for a given monomer chain. A subsequent off-trap strategy is then proposed to trigger a jump for a stuck situation in order to get out of the local minima. The algorithm has been tested in the three-dimensional AB model for all sequences with lengths of 13-55 monomers. In several cases, we renew the putative ground state energy values. The numerical results show that the proposed methods are very promising for finding the ground states of proteins.
基金TheNationalKeyBasicResearchProgram (973) (No .G 19980 30 6 0 0 )
文摘A quasi physical algorithm was proposed for solving the linear separation problem of point set in n dimensional space.The original idea of the quasi physical algorithm is to find an equivalent physical world for the primitive mathematical problem and to observe the vivid images of the motion of matter in it so as to be inspired to obtain an algorithm for solving the mathematical problem. In this work, the electrostatics with two kinds of matter is found to be the equivalent physical world. As a result,the proposed algorithm is evidently more efficient and robust than the famous LMS algorithm and ETL algorithm. The efficiency of the quasi physical algorithm is about 10-50 times of the LMS algorithm’s for representative instances. A typical Boolean valued instance shows that it is hard for ETL algorithm but very easy for the quasi physical algorithm.In this instance, point set A and B is {000, 010, 011, 111} and {001,100}, respectively.
基金This work was supported by the National Grand Fundamental Research 973 Program of China(Grant No.2004CB318000)the National Natural Science Foundation of China nnder Grant No.10471051.
文摘Protein folding problem is one of the most prominent problems of bioinformatics. In this paper, we study a three-dimensional off-lattice protein AB model with two species of monomers, hydrophobic and hydrophilic, and present a heuristic quasi-physical algorithm. By elaborately simulating the movement of the smooth elastic balls in the physical world, the algorithm finds low-energy configurations for a given monomer chain. A subsequent ＂off-trap＂ strategy is proposed to trigger a jump for a stuck situation in order to get out of local minima. The methods have been tested in the off-lattice AB model. The computational results show promising performance. For all sequences with 13 to 55 monomers, the algorithm finds states with lower energy than previously proposed putative ground states. Furthermore, for the sequences with 21, 34 and 55 monomers, new putative ground states are found, which are different from those given in present literature.
文摘The basic problem of a radar group monitoring an object group that has all along been a problem of concern in the international circles of military science has been solved for the first time.A mathematical model for solving the 3-D monitoring problem has been developed based on the quasi-physical concept and a practical fast algorithm has been found.A high-efficiency tracking and monitoring system can be designed for use by radar troops and the administrative and commercial departments concerned using this algorithm.
基金The National Natural Science Founda-tion of China (No.10471051) and the National Basic Research Program (973) of China (No.2004CB318000)
文摘A three-dimensional off-lattice protein model with two species of monomers, hydrophobic and hydrophilic, is studied. Enligh- tened by the law of reciprocity among things in the physical world, a heuristic quasi-physical algorithm for protein structure prediction problem is put forward. First, by elaborately simulating the movement of the smooth elastic balls in the physical world, the algorithm finds low energy configurations for a given monomer chain. An ＂off-trap＂ strategy is then proposed to get out of local minima. Experimental results show promising performance. For all chains with lengths 13≤n ≤55, the proposed algorithm finds states with lower energy than the putative ground states reported in literatures. Furthermore, for chain lengths n = 21, 34, and 55, the algorithm finds new low energy configurations different from those given in literatures.
基金The project partially supported by National Key Basic Research Project of China under Grant No. 2004GB318000 and National Natural Science Foundation of China under Grant No. 10471051
文摘We study a three-dimensional off-lattice protein folding model, which involves two species of residues interacting through Lennard-Jones potentials. By incorporating an extra energy contribution into the original potential function, we replace the original constrained problem with an unconstrained minimization of a mixed potential function. As such an efficient quasi-physical algorithm for solving the protein folding problem is presented. We apply the proposed algorithm to sequences with up to 55 residues and compare the computational results with the putative lowest energy found by several of the most famous algorithms, showing the advantages of our method. The dynamic behavior of the quasi-physlcal algorithm is also discussed.
