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Gene insertion and deletion are the operations that occur commonly in DNA processing and RNA editing. Based on these evolutionary transformations, a computing model has been formulated in formal language theory known as insertion-deletion systems. In this paper, we study about the ambiguity issues of insertion systems. First, we define six levels of ambiguity for insertion systems based on the components used in the derivation such as axiom, contexts and strings. Next, we show that there are inherently i-ambiguous insertion languages which are j-unambiguous for the combinations (i, j) ∈ {(5,0), (5,4), (4,3), (4,2), (3,1),(2,1), (1,0), (0,1)}. Finally, we prove an important result that the ambiguity problem of insertion systems is undecidable. [ABSTRACT FROM AUTHOR]

Abstract: Petri Nets are promising methods for modelling and simulating biological systems. Spiking Neural P system with anti-spikes (SN PA systems) is a biologically inspired computing model that incorporates two types of objects called spikes and anti-spikes thus representing binary information in a natural way. In this paper, we propose a methodology to simulate SN PA systems using a Petri net tool called Pnet Lab. It provides a promising way for SN PA systems because of its parallel execution semantics and appropriateness to represent typical working processes of these systems. This enables us to verify system properties, system soundness and to simulate the dynamic behaviour. [Copyright &y& Elsevier]

Abstract: Gene insertion and deletion are the operations that occur commonly in DNA processing and RNA editing. Based on these operations, a computing model has been formulated in formal language theory known as insertion–deletion systems. In this paper we study about ambiguity issues of these systems. First, we define six levels of ambiguity for insertion–deletion systems that are based on the components used in the derivation such as axiom, contexts and strings. Next, we show that there are inherently -ambiguous insertion–deletion languages which are -unambiguous for the combinations . As an application, we discuss with an example that how some of these ambiguity levels can be interpreted in gene sequences. Further, we prove an important result that the ambiguity problem of insertion–deletion systems is undecidable. Then, we define six new measures for insertion–deletion systems based on used contexts and strings. Finally, we analyze the trade-off between ambiguity levels and measures. We note that there are languages which are inherently -ambiguous (for ) when a measure is minimal for the languages but they are -unambiguous otherwise. [Copyright &y& Elsevier]

The article proposes a class of P automata in which each membrane has a state, like in tissue P systems. The computation starts at some initial state and ends in a final state. In the discussion a variant is considered to apply the rules in a variant mode. The characterization of P automata in recursively enumerable sets and vectors of natural numbers is shown.