A surface-based DNA algorithm for the minimal vertex cover problem

Abstract DNA computing was proposed for solving a class of intractable computational problems, of which the computing timewill grow exponentially with the problem size. Up to now, many achievements have been made to improve its performance and increase itsreliability. It has been shown many times that the surface-based DNA computing technique has very low error rate, but the technique hasnot been widely used in the DNA computing algorithms design. In this paper, a surface-based DNA computing algorithm for minimal ver-tex cover problem, a problem well-known for its exponential difficulty, is introduced. This work provides further evidence for the abilityof surface-based DNA computing in solving NP-complete problems.     

Multi-objective carrier chaotic evolutionary algorithm for DNA sequences design

DNA computing is a new vista of computation, which is of biochemical type. Since each piece of information is encoded in biological sequences, their design is crucial for successful DNA computation. DNA sequence design is involved with a number of design criteria, which is difficult to be solved by the traditional optimization methods. In this paper, the multi-objective carrier chaotic evolution algorithm (MCCEA) is introduced to solve the DNA sequence design problem. By merging the chaotic search base on power function carrier, a set of good DNA sequences are generated. Furthermore, the simulation results show the efficiency of our method.     

Hybrid ant colony algorithm for traveling salesman problem

A hybrid approach based on ant colony algorithm for the traveling salesman problem is proposed, which is an improved algorithm characterized by adding a local search mechanism, a cross-removing strategy and candidate lists. Experimental results show that it is competitive in terms of solution quality and computation time.     

Personification algorithm for protein folding problem：Improvements in PERM

PERM is the most efficient approach for solving protein folding problem based on simple lattice model. In this article a personification explanation of PERM is proposed. A new version of PERM, population control algorithm with two main improvements is presented: one is that it is able to redefine the weight and its predicted value in PERM,and the other is that it is able to unify the calculation of weight when choosing possible branches. The improved PERM is more efficient than the previous version; specifically it can find the known lowest energy states for the four well-known difficult instances and is generally several to hundreds times faster than PERM. It is noteworthy that with the improved PERM we found new lowest energy configurations of three of the four difficult problems missed in previous papers.     

An effective absorbing boundary algorithm for acoustical wave propagator

In this paper,Berenger's perfectly matched layer(PML)absorbing boundary condition for electromagnetic waves is introduced as the truncation area of the computational domain to absorb one-dimensional acoustic wave for the scheme of acoustical wave propagator(AWP).To guarantee the efficiency of the AWP algorithm,a regulated propagator matrix is derived in the PML medium.Numerical simulations of a Gaussian wave packet propagating in one-dimensional duct are carried out to illustrate the efficiency of the combination of PML and AWP.Compared with the traditional smoothing truncation windows technique of AWP,this scheme shows high computational accuracy in absorbing acoustic wave when the acoustical wave arrives at the computational edges.Optimal coefficients of the PML configurations are also discussed.     

Genetic algorithm in DNA computing： A solution to the maximal clique problem

Genetic algorithm is one of the possible ways tobreak the limit of brute-force method in DNA computing.Using the idea of Darwinian evolution, we introduce a geneticDNA computing algorithm to solve the maximal clique prob-lem. All the operations in the algorithm are accessible withtoday‘s molecular biotechnoiogy. Our computer simulationsshow that with this new computing algorithm, it is possible toget a solution from a very small initial data pool, avoidingenumerating all candidate solutions. For randomly generatedproblems, genetic algorithm can give correct solution withina few cycles at high probability. Although the current speedof a DNA computer is slow compared with silicon computers,our simulation indicates that the number of cycles needed inthis genetic algorithm is approximately a linear function ofthe number of vertices in the network. This may make DNAcomputers more powerfully attacking some hard computa-tional problems.     

Fast algorithm for inverting structure parameters of the horizontal multi-layer soil

A fast algorithm is presented to invert the structure parameter of the horizontal multi-layer soil. The procedure is divided into two independent stages. First, Fredholm equation of the first kind with respect to the apparent resistivity is solved by the technology of decay spectrum to reduce computation time greatly. Second, the structure parameter of soil is determined by the generalized Newton-Kantorovich method, which is more robust and less noise sensitive because of using the generalized inverse algorithm to solve the nonlinear equation group. The numerical results show the validities and main features of the proposed approach.     

On the boundary value problem for harmonic maps of the Poincaré disc

The boundary value problem for harmonic maps of the Poincare disc is discussed. The emphasis is on the non-smoothness of the given boundary values in the problem. Let T . be a subspace of the universal Teichmüller space, defined as a set of normalized quasisymmetric homeomorphisms h of the unit circle S onto itself where h admits a quasiconformal extension to the unit disc D with a complex dilatation μ satisfying where ρ(z)|dz|2 is the Poincare metric of D. Let B . be a Banach space consisting of holomorphic quadratic differentials φ in D with norms It is shown that for any given quasisymmetric homeomorphism h : S1→S1∈ T . , there is a unique quasiconformal harmonic map of D with respect to the Poincare metric whose boundary corresponding is h and the Hopf differential of such a harmonic map belongs to B .     

Node ordinal encoded genetic algorithm for the optimal allocation of water resources

The shortage of water supply and the increasingdemand for water resources is a severe problem, andthe optimal allocation is the key to solving this prob lem in management of water resources. It is very dif ficult to solve the large scale discrete problem of waterresources programming because of the intricate rela tion between resources and environment. Combina tion exploding exists in traditional programmingmethods, such as enumerative and dynamic program ming methods. People are …     

Node ordinal encoded genetic algorithm for the optimal allocation of water resources

A new method, node ordinal encoded genetic algorithm (NOEGA), is proposed for solving water resources optimal allocation problems, in which the capacity of water resources is split into a number of smaller parts so that successive operations can be overlapped. Our objective is to maximize the whole benefit function. To overcome the “dimensionality and algorithm complexity curse” while searching for solutions and looking for an optimal solution, the operations of one-point crossover operator, gene exchange operator, gene random operator, gene shift operator and node ordinal strings are established. It is proved to be an effective optimal method in searching for global solutions. The NOEGA does not need a diversity of initial population, and it does not have the problem of immature convergence. The results of two cases show that using NOEGA to solve the optimal allocation model is very efficient and robust. In addition, the algorithm complexity of NOEGA is discussed.     

He-H2 mixture and Er3NiHx packing for the refrigeration enhancement of pulse tube refrigerator

The computation with the theory of modified Brayton Cycle indicates that higher cooling power and coefficient of performance for a pulse tube refrigerator can be achieved with He-H2 mixture as working gas than those with pure He in the temperature region of 30 K. In addition, it is found that Er3Ni, a regenerative material, is able to absorb H2 and produces Er3NiHx. The computation presents that the regenerative performance of Er3NiHx is better than that of Er3Ni due to its higher volume specific heat. Experimental results show that the pulse tube refrigeration performance in 30 K temperature region is enhanced greatly with He-H2 mixture and Er3NiHx packing.     

He-H_2 mixture and Er_3NiH_χ packing for the refrigeration enhancement of pulse tube refrigerator

The computation with the theory of modified Brayton Cycle indicates that higher cooling power and coefficient of performance for a pulse tube refrigerator can be achieved with He-H_2 mixture as working gas than those with pure He in the temperature region of 30 K. In addition, it is found that Er_3Ni, a regenerative material, is able to absorb H_2 and produces Er_3NiH_x. The computation presents that the regenerative performance of Er_3NiH_x is better than that of Er_3Ni due to its higher volume specific heat. Experimental results show that the pulse tube refrigeration performance in 30 K temperature region is enhanced greatly with He-H_2 mixture and Er_3NiH_x packing.     

Grain-size evidence for multiple origins of the reticulate red clay in southern China

The loess-paleosol sequences in Chinese Loess Plateau record the multi-cyclic paleo-climatic changes in the Quaternary period[1]. Presently, what interests people most is that at what degrees and scales the climates in southern China had corresponded to the alternating changes be-tween the glacial and interglacial climates in northern China in the Quaternary period. Many researchers[2―10] hope to find some potential Quaternary sediment materials in southern China, just as the loess-paleoso…     

An ECN—based Optimal Flow Control Algroithm for the Internet

According to the Wide Area Network model,we formulate Internet flow control as a constrained convex programming problem,where the objective is to maximize the total utility of all sources over their transmission rates,Based on this formulation,flow control can be converted to a normal unconstrained optimization problem through the barrier function method.so that it can be solved by means of a gradient projection algorithm with properly rate iterations.We prove that the algorithm converges to the global optimal point,which is also a stable proportional fair rate allocation point,provided that the step size is properly chosen.The main difficulty facing the realization of iteration algorithm is the distributed computation of congestion measure.Fortunately,Explicit Congestion Notification (ECN) is likely to be used to improve the performance of TCP in the near future.By using ECN,it is possible to realize the iteration algorithm in IP networks.Our algorithm is divided into two parts,algorithms in the router and in the source.The router marks the ECN bit with a probability that varies as its buffer occupancy varies,so that the congestion measure of links can be communicated to the source when the marked ECN bits are reflected back from its destination.Source rates are then updated by all sessions according to the received congestion measure.The main advantage of our scheme is its fast convergence ability and robustness;it can also provide the network with zero packet loss by properly choosing the queue threshold and provide differentiated service to users by applying different utility functions.     

Wavelet domain adaptive filtering algorithm for removing the seamless pipe noise contained in the magnetic flux leakage data

With the widespread application and fast development of gas and oil pipeline network in China, the pipeline inspection technology has been used more extensively. The magnetic flux leakage （MFL） method has established itself as the most widely used in-line inspection technique for the evaluation of gas and oil pipelines. The MFL data obtained from seamless pipeline inspection is usually contaminated by the seamless pipe noise （SPN）. SPN can in some cases completely mask MFL signals from certain type of defects, and therefore considerably reduces the detectability of the defect signals. In this paper, a new de-noising algorithm called wavelet domain adaptive filtering is proposed for removing the SPN contained in the MFL data. The new algorithm results from combining the wavelet transform with the adaptive filtering technique. Results from application of the proposed algorithm to the MFL data from field tests show that the proposed algorithm has good performance and considerably improves the detectability of the defect signals in the MFL data.     

Regularization strategy for the Cauchy problem of Laplace’s equation from the viewpoint of regularization theory

Within the framework of the regularization theory, a spectral regularization method is introduced and analyzed. The convergence estimate under an appropriate choice of regularization parameter is obtained. A numerical implementation is described. Numerical examples show that the proposed method is effective and stable.     

A new algorithm for EEG source reconstruction based on LORETA by contracting the source region

A new method is presented for EEG source reconstruction based on multichannel surface EEG recordings. From the low-resolution tomography obtained by the low resolution electromagnetic tomography algorithm (LORETA), this method acquires the source tomography, which has high-resolution by contracting the source region. In contrast to focal underdetermined system solver (FOCUSS), this method can gain more accurate result under certain circumstances.