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Evolutionary algorithms have been used to solve a variety of many-objective optimization problems, where these problems contain more than three conflicting objectives. Most existing evolutionary algorithms have shown to perform well on many-objective optimization problems with regular Pareto optimal fronts, their performance, however, will often considerably deteriorate on those whose Pareto optimal fronts are irregular, e.g., discontinuous, degenerated and convex. To address this issue, in this paper, we propose a region division based many-objective optimization evolutionary algorithm, termed RdEA, where a region division approach is suggested to maintain diversity of population for many-objective optimization (especially for problems with irregular Pareto fronts). In the proposed region division based diversity maintaining approach, the geometric information of Pareto optimal fronts is taken into account by using the non-dominated solutions found at each generation, which helps to solve the problems with irregular Pareto optimal fronts better. The proposed RdEA is compared with five state-of-the-art many-objective evolutionary algorithms on 16 test problems from two test suites DTLZ and WFG and a real-world optimization problem. Experimental results on these problems demonstrate that the competitiveness of the proposed algorithm in solving many-objective optimization problems, especially for those with irregular Pareto optimal fronts. [ABSTRACT FROM AUTHOR]

Tissue P systems are a class of distributed parallel computing devices inspired by biochemical interactions between cells in a tissue-like arrangement, where objects can be exchanged by means of communication channels. In this work, inspired by the biological facts that the movement of most objects through communication channels is controlled by proteins and proteins can move through lipid bilayers between cells (if these cells are fused), we present a new class of variant tissue P systems, called tissue P systems with protein on cells, where multisets of objects (maybe empty), together with proteins between cells are exchanged. The computational power of such P systems is studied. Specifically, an efficient (uniform) solution to the SAT problem by using such P systems with cell division is presented. We also prove that any Turing computable set of numbers can be generated by a tissue P system with protein on cells. Both of these two results are obtained by such P systems with communication rules of length at most 4 (the length of a communication rule is the total number of objects and proteins involved in that rule). [ABSTRACT FROM AUTHOR]

P systems are a class of computational models inspired by the structure and the functioning of a living cell. In the semantics of P systems, there exists a global clock, which marks the time for the system, and the execution time of each rule takes exactly one time unit. However, in living cells, the execution time of different biochemical reactions is dependent on many uncontrollable factors, and it is hard to know precisely the specific execution time of a reaction. In this work, with this biological inspiration, we consider the class of P systems with active membranes that are "robust" against the execution time of rules. Specifically, we give a time-free uniform solution to the SAT problem using P systems with active membranes, where the constructed P system can solve a family of instances with an arbitrarily given size, and the execution time of the involved rules has no influence on the correctness of the solution. We also prove that any Turing computable set of numbers can be generated by a time-free P system with active membranes in the sense that the set of numbers generated by the given P system with active membranes does not depend on the execution time of rules. [ABSTRACT FROM AUTHOR]

Background Abnormal states in human liver metabolism are major causes of human liver diseases ranging from hepatitis to hepatic tumor. The accumulation in relevant data makes it feasible to derive a large-scale human liver metabolic network (HLMN) and to discover important biological principles or drugtargets based on network analysis. Some studies have shown that interesting biological phenomenon and drug-targets could be discovered by applying structural controllability analysis (which is a newly prevailed concept in networks) to biological networks. The exploration on the connections between structural controllability theory and the HLMN could be used to uncover valuable information on the human liver metabolism from a fresh perspective. Results We applied structural controllability analysis to the HLMN and detected driver metabolites. The driver metabolites tend to have strong ability to influence the states of other metabolites and weak susceptibility to be influenced by the states of others. In addition, the metabolites were classified into three classes: critical, high-frequency and low-frequency driver metabolites. Among the identified 36 critical driver metabolites, 27 metabolites were found to be essential; the high-frequency driver metabolites tend to participate in different metabolic pathways, which are important in regulating the whole metabolic systems. Moreover, we explored some other possible connections between the structural controllability theory and the HLMN, and find that transport reactions and the environment play important roles in the human liver metabolism. Conclusion There are interesting connections between the structural controllability theory and the human liver metabolism: driver metabolites have essential biological functions; the crucial role of extracellular metabolites and transport reactions in controlling the HLMN highlights the importance of the environment in the health of human liver metabolism. [ABSTRACT FROM AUTHOR]

In a biological nervous system, astrocytes play an important role in the functioning and interaction of neurons, and astrocytes have excitatory and inhibitory influence on synapses. In this work, with this biological inspiration, a class of computation devices that consist of neurons and astrocytes is introduced, called spiking neural P systems with astrocytes (SNPA systems). The computation power of SNPA systems is investigated. It is proved that SNPA systems with simple neurons (all neurons have the same rule, one per neuron, of a very simple form) are Turing universal in both generative and accepting modes. If a bound is given on the number of spikes present in any neuron along a computation, then the computation power of SNPA systems is diminished. In this case, a characterization of semilinear sets of numbers is obtained. [ABSTRACT FROM AUTHOR]

In a biological nervous system, astrocytes play an important role in the functioning and interaction of neurons, and astrocytes have excitatory and inhibitory influence on synapses. In this work, with this biological inspiration, a class of computation devices that consist of neurons and astrocytes is introduced, called spiking neural P systems with astrocytes (SNPA systems). The computation power of SNPA systems is investigated. It is proved that SNPA systems with simple neurons (all neurons have the same rule, one per neuron, of a very simple form) are Turing universal in both generative and acceptingmodes. If a bound is given on the number of spikes present in any neuron along a computation, then the computation power of SNPA systems is diminished. In this case, a characterization of semilinear sets of numbers is obtained. [ABSTRACT FROM AUTHOR]

The P systems (or membrane systems) are a class of distributed parallel computing devices of a biochemical type, where membrane division is the frequently investigated way for obtaining an exponential working space in a linear time, and on this basis solving hard problems, typically NP-complete problems, in polynomial (often, linear) time. In this paper, using another way to obtain exponential working space – membrane separation, it was shown that Satisfiability Problem and Hamiltonian Path Problem can be deterministically solved in linear or polynomial time by a uniform family of P systems with separation rules, where separation rules are not changing labels, but polarizations are used. Some related open problems are mentioned. [ABSTRACT FROM AUTHOR]

DNA computing has the potential to tackle computationally difficult problems that have real-world implications. The parallel search capabilities of DNA make it a valuable tool for approaching intractable computational problems, for which conventional computers have limited potentials. Up to now, many accomplishments have been achieved to improve its performance and increase its reliability. In this paper, the coloring problem has been solved by means of molecular biology techniques. The coloring problem is a well-known NP-complete problem. This work represents further evidence for the ability of DNA computing to solve NP-complete problems. [ABSTRACT FROM AUTHOR]

P systems are parallel molecular computing models based on processing multisets of objects in cell-like membrane structures. Recently, Petr Sosík has shown that a semi-uniform family of P systems with active membranes and 2-division is able to solve the PSPACE-complete problem QBF-SAT in linear time; he has also conjectured that the membrane dissolving rules of the (d) type may be omitted, but probably not the (f) type rules for non-elementary membrane division. In this paper, we partially confirm the conjecture proving that dissolving rules are not necessary. Moreover, the construction is now uniform. It still remains open whether or not non-elementary membrane division is needed. [ABSTRACT FROM AUTHOR]

Presents mathematical solutions to hypertournaments. Theorems proved on hypertournaments; Hamiltonian cycle; Theorem and lemma.

DNA computing was proposed for solving a class of intractable computational problems, of which the computing time will grow exponentially with the problem size. Up to now, many achievements have been made to improve its performance and increase its reliability. It has been shown many times that the surface-based DNA computing technique has very low error rate, but the technique has not been widely used in the DNA computing algorithms design. In this paper, a surface-based DNA computing algorithm for minimal vertex cover problem, a problem well-known for its exponential difficulty, is introduced. This work provides further evidence for the ability of surface-based DNA computing in solving NP-complete problems. [ABSTRACT FROM AUTHOR]

The robustness in real-world complex systems with dependency connectivities differs from that in isolated networks. Although most complex network research has focused on interdependent undirected systems, many real-world networks--such as gene regulatory networks and traffic networks--are directed. We thus develop an analytical framework for examining the robustness of networks made up of directed networks of differing topologies. We use it to predict the phase transitions that occur during node failures and to generate the phase diagrams of a number of different systems, including treelike and random regular (RR) networks of directed Erdős-Rényi (ER) networks and scale-free networks. We find that the the phase transition and phase diagram of networks of directed networks differ from those of networks of undirected networks. For example, the RR networks of directed ER networks show a hybrid phase transition that does not occur in networks of undirected ER networks. In addition, system robustness is affected by network topology in networks of directed networks. As coupling strength q increases, treelike networks of directed ER networks change from a second-order phase transition to a first-order phase transition, and RR networks of directed ER networks change from a second-order phase transition to a hybrid phase transition, then to a first-order phase transition, and finally to a region of collapse. We also find that heterogenous network systems are more robust than homogeneous network systems. We note that there are multiple phase transitions and triple points in the phase diagram of RR networks of directed networks and this helps us understand how to increase network robustness when designing interdependent infrastructure systems. [ABSTRACT FROM AUTHOR]

When controlling a complex networked system it is not feasible to control the full network because many networks, including biological, technological, and social systems, are massive in size and complexity. But neither is it necessary to control the full network. In complex networks, the giant connected components provide the essential information about the entire system. How to control these giant connected components of a network remains an open question. We derive the mathematical expression of the degree distributions for four types of giant connected components and develop an analytic tool for studying the controllability of these giant connected components. We find that for both Erdős-Rényi (ER) networks and scale-free (SF) networks with p fraction of remaining nodes, the minimum driver node density to control the giant component first increases and then decreases as p increases from zero to one, showing a peak at a critical point p=pm. We find that, for ER networks, the peak value of the driver node density remains the same regardless of its average degree ⟨k⟩ and that it is determined by pm ⟨k⟩. In addition, we find that for SF networks the minimum driver node densities needed to control the giant components of networks decrease as the degree distribution exponents increase. Comparing the controllability of the giant components of ER networks and SF networks, we find that when the fraction of remaining nodes p is low, the giant in-connected, out-connected, and strong-connected components in ER networks have lower controllability than those in SF networks. [ABSTRACT FROM AUTHOR]

A preface for this issue, based on the conference Bio-Inspired Computing--Theory and Applications," is presented.

A preface for the April 2007 issue of "Progress in Natural Science," Volume 17, Number 4, is presented.

Numerical P systems are a class of P systems inspired both from the structure of living cells and from economics. In this work, we further investigate the generative capacity of numerical P systems as language generators. The families of languages generated by non-enzymatic, by enzymatic, and by purely enzymatic (all programs are enzymatic) numerical P systems working in the sequential mode are compared with the language families in the Chomsky hierarchy. Especially, a characterization of recursively enumerable languages is obtained by using purely enzymatic numerical P systems working in the sequential mode. [ABSTRACT FROM AUTHOR]

Spiking neural P systems (SN P systems) are a class of distributed parallel computing devices inspired by spiking neurons, where the spiking rules are usually used in a sequential way (an applicable rule is applied one time at a step) or an exhaustive way (an applicable rule is applied as many times as possible at a step). In this letter, we consider a generalized way of using spiking rules by "combining" the sequential way and the exhaustive way: if a rule is used at some step, then at that step, it can be applied any possible number of times, nondeterministically chosen. The computational power of SN P systems with a generalized use of rules is investigated. Specifically, we prove that SN P systems with a generalized use of rules consisting of one neuron can characterize finite sets of numbers. If the systems consist of two neurons, then the computational power of such systems can be greatly improved, but not beyond generating semilinear sets of numbers. SN P systems with a generalized use of rules consisting of three neurons are proved to generate at least a nonsemilinear set of numbers. In the case of allowing enough neurons, SN P systems with a generalized use of rules are computationally complete. These results show that the number of neurons is crucial forSNP systems with a generalized use of rules to achieve a desired computational power. [ABSTRACT FROM AUTHOR]

A variant of spiking neural P systems with positive or negative weights on synapses is introduced, where the rules of a neuron fire when the potential of that neuron equals a given value. The involved values-weights, firing thresholds, potential consumed by each rule-can be real (computable) numbers, rational numbers, integers, and natural numbers. The power of the obtained systems is investigated. For instance, it is proved that integers (very restricted: 1,-1 for weights, 1 and 2 for firing thresholds, and as parameters in the rules) suffice for computing all Turing computable sets of numbers in both the generative and the accepting modes. When only natural numbers are used, a characterization of the family of semilinear sets of numbers is obtained. It is shown that spiking neural P systemswith weights can efficiently solve computationally hard problems in a nondeterministic way. Some open problems and suggestions for further research are formulated. [ABSTRACT FROM AUTHOR]

Spiking neural P systems are a class of distributed parallel computing models inspired from the way the neurons communicate with each other by means of electrical impulses (called "spikes"). In this paper, we consider a restricted variant of spiking neural P systems, called homogeneous spiking neural P systems, where each neuron has the same set of rules. The universality of homogeneous spiking neural P systems is investigated. One of universality results is that it is sufficient for homogeneous spiking neural P system to have only one neuron that behaves nondeterministically in order to achieve Turing completeness. [ABSTRACT FROM AUTHOR]

The problem of finding small universal spiking neural P systems was recently investigated by Andrei Păun and Gheorghe Păun, for spiking neural P systems used as devices computing functions and as devices generating sets of numbers. For the first case, a universal spiking neural P system was produced by using 84 neurons for standard rules and using 49 neurons for extended rules. For spiking neural P systems used as generators of sets of numbers, a universal system with standard rules having 76 neurons, and one with extended rules having 50 neurons were obtained. In this paper, we continue the study of small universal spiking neural P systems and we improve in the number of neurons as follows. The small universal spiking neural P systems use 67 neurons for standard rules and 41 neurons for extended rules in the case of computing functions, and 63 neurons for standard rules and 41 neurons for extended rules in the case of generating sets of numbers. [ABSTRACT FROM AUTHOR]

Abstract  We continue the study of (extended) spiking neural P systems with exhaustive use of rules by considering these computing devices as language generators. Specifically, a step is associated with a symbol according to the number of spikes emitted by the output neuron and the sequence of these symbols associated with a halting computation constitutes a string. Two cases are considered: one of them interprets a step when no spike is emitted as a specified symbol, the other interprets such a step as the empty string. In both cases, it is proved that finite and recursively enumerable languages are characterized by extended spiking neural P systems working in the exhaustive mode. The relationships with regular languages are also investigated. [ABSTRACT FROM AUTHOR]

A control strategy on the computations in a one-catalyst P system is provided: the rules are assumed "colored" and in each step only rules of the same "color" are used. Such control leads to Turing universality for one-catalyst P systems with one membrane. Turing universality is also reached for purely catalytic P systems with two catalysts, and for purely catalytic P systems with only one catalyst and cooperating rules working in the so-called terminal mode. [ABSTRACT FROM AUTHOR]

Inspired by mitosis process and membrane fission processes, cell-like P systems with symport/antiport rules and membrane division rules or membrane separation rules have been introduced, respectively. These computation systems have two key features: the ability to have infinite copies of some objects (within an active environment) and to generate an exponential workspace in polynomial time. In this work, we extend the P-Lingua framework for simulating that kind of P systems taking into account these two features. Consequently, a new simulator has been developed and included in pLinguaCore library. The functioning of the simulator has been checked by simulating efficient solutions to SAT problem using a family of cell-like P systems with symport/antiport rules and membrane division rules or membrane separation rules. The corresponding MeCoSim based application is also provided. [ABSTRACT FROM AUTHOR]

Spiking neural P systems with weights are a new class of distributed and parallel computingmodels inspired by spiking neurons. In such models, a neuron fireswhen its potential equals a given value (called a threshold). In this work, spiking neural P systems with thresholds (SNPT systems) are introduced, where a neuron fires not only when its potential equals the threshold but also when its potential is higher than the threshold. Two types of SNPT systems are investigated. In the first one, we consider that the firing of a neuron consumes part of the potential (the amount of potential consumed depends on the rule to be applied). In the second one, once a neuron fires, its potential vanishes (i.e., it is reset to zero). The computation power of the two types of SNPT systems is investigated. We prove that the systems of the former type can compute all Turing computable sets of numbers and the systems of the latter type characterize the family of semilinear sets of numbers. The results show that the firing mechanism of neurons has a crucial influence on the computation power of the SNPT systems, which also answers an open problem formulated in Wang, Hoogeboom, Pan, P?aun, and P'erez-Jim'enez (2010). [ABSTRACT FROM AUTHOR]

Spiking neural P systems (SN P systems) are a class of distributed parallel computing devices inspired by the way neurons communicate by means of spikes; neurons work in parallel in the sense that each neuron that can fire should fire, but the work in each neuron is sequential in the sense that at most one rule can be applied at each computation step. In this work, with biological inspiration, we consider SN P systems with the restriction that at each step, one of the neurons (i.e., sequential mode) or all neurons (i.e., pseudo-sequential mode) with the maximum (or minimum) number of spikes among the neurons that are active (can spike) will fire. If an active neuron has more than one enabled rule, it nondeterministically chooses one of the enabled rules to be applied, and the chosen rule is applied in an exhaustive manner (a kind of local parallelism): the rule is used as many times as possible. This strategy makes the system sequential or pseudo-sequential from the global view of the whole network and locally parallel at the level of neurons. We obtain four types of SN P systems: maximum/minimum spike number induced sequential/pseudo-sequential SNP systemswith exhaustive use of rules. We prove that SN P systems of these four types are all Turing universal as number-generating computation devices. These results illustrate that the restriction of sequentiality may have little effect on the computation power of SN P systems. [ABSTRACT FROM AUTHOR]

Single-stranded tile (SST) strategy offers precise control over the circumferences of nanotubes while the kinetic trap in the process of the self-assembly prevents the formation of wider tubes. Here, we report a simple and efficient method to build DNA nanotubes using only 2 SSTs via one-pot annealing. The diameters of the 2-SST nanotubes were much larger than what the kinetic trap theory would predict, indicating a new mechanism was at play in the formation of these nanotubes. Further investigation suggested that the 2-SST nanotubes were assembled through a hierarchical pathway that involved an intermediate formation of 2-SST nano-lines. [ABSTRACT FROM AUTHOR]