Capacity Bounded Grammars and Petri Nets

A capacity bounded grammar is a grammar whose derivations are restricted by assigning a bound to the number of every nonterminal symbol in the sentential forms. In the paper the generative power and closure properties of capacity bounded grammars and their Petri net controlled counterparts are investigated

On Languages Accepted by P/T Systems Composed of joins

Recently, some studies linked the computational power of abstract computing systems based on multiset rewriting to models of Petri nets and the computation power of these nets to their topology. In turn, the computational power of these abstract computing devices can be understood by just looking at their topology, that is, information flow. Here we continue this line of research introducing J languages and proving that they can be accepted by place/transition systems whose underlying net is composed only of joins. Moreover, we investigate how J languages relate to other families of formal languages. In particular, we show that every J language can be accepted by a log n space-bounded non-deterministic Turing machine with a one-way read-only input. We also show that every J language has a semilinear Parikh map and that J languages and context-free languages (CFLs) are incomparable

Translation from Classical Two-Way Automata to Pebble Two-Way Automata

We study the relation between the standard two-way automata and more powerful devices, namely, two-way finite automata with an additional "pebble" movable along the input tape. Similarly as in the case of the classical two-way machines, it is not known whether there exists a polynomial trade-off, in the number of states, between the nondeterministic and deterministic pebble two-way automata. However, we show that these two machine models are not independent: if there exists a polynomial trade-off for the classical two-way automata, then there must also exist a polynomial trade-off for the pebble two-way automata. Thus, we have an upward collapse (or a downward separation) from the classical two-way automata to more powerful pebble automata, still staying within the class of regular languages. The same upward collapse holds for complementation of nondeterministic two-way machines. These results are obtained by showing that each pebble machine can be, by using suitable inputs, simulated by a classical two-way automaton with a linear number of states (and vice versa), despite the existing exponential blow-up between the classical and pebble two-way machines

The Nondeterministic Waiting Time Algorithm: A Review

We present briefly the Nondeterministic Waiting Time algorithm. Our technique for the simulation of biochemical reaction networks has the ability to mimic the Gillespie Algorithm for some networks and solutions to ordinary differential equations for other networks, depending on the rules of the system, the kinetic rates and numbers of molecules. We provide a full description of the algorithm as well as specifics on its implementation. Some results for two well-known models are reported. We have used the algorithm to explore Fas-mediated apoptosis models in cancerous and HIV-1 infected T cells