Tree transducers, L systems, and two-way machines

A relationship between parallel rewriting systems and two-way machines is investigated. Restrictions on the “copying power” of these devices endow them with rich structuring and give insight into the issues of determinism, parallelism, and copying. Among the parallel rewriting systems considered are the top-down tree transducer; the generalized syntax-directed translation scheme and the ETOL system, and among the two-way machines are the tree-walking automaton, the two-way finite-state transducer, and (generalizations of) the one-way checking stack automaton. The. relationship of these devices to macro grammars is also considered. An effort is made .to provide a systematic survey of a number of existing results

Hierarchies of hyper-AFLs

For a full semi-AFL K, B(K) is defined as the family of languages generated by all K-extended basic macro grammars, while H(K) B(K) is the smallest full hyper-AFL containing K; a full basic-AFL is a full AFL K such that B(K) = K (hence every full basic-AFL is a full hyper-AFL). For any full semi-AFL K, K is a full basic-AFL if and only if B(K) is substitution closed if and only if H(K) is a full basic-AFL. If K is not a full basic-AFL, then the smallest full basic-AFL containing K is the union of an infinite hierarchy of full hyper-AFLs. If K is a full principal basic-AFL (such as INDEX, the family of indexed languages), then the largest full AFL properly contained in K is a full basic-AFL. There is a full basic-AFL lying properly in between the smallest full basic-AFL and the largest full basic-AFL in INDEX

Active Self-Assembly of Algorithmic Shapes and Patterns in Polylogarithmic Time

We describe a computational model for studying the complexity of self-assembled structures with active molecular components. Our model captures notions of growth and movement ubiquitous in biological systems. The model is inspired by biology's fantastic ability to assemble biomolecules that form systems with complicated structure and dynamics, from molecular motors that walk on rigid tracks and proteins that dynamically alter the structure of the cell during mitosis, to embryonic development where large-scale complicated organisms efficiently grow from a single cell. Using this active self-assembly model, we show how to efficiently self-assemble shapes and patterns from simple monomers. For example, we show how to grow a line of monomers in time and number of monomer states that is merely logarithmic in the length of the line. Our main results show how to grow arbitrary connected two-dimensional geometric shapes and patterns in expected time that is polylogarithmic in the size of the shape, plus roughly the time required to run a Turing machine deciding whether or not a given pixel is in the shape. We do this while keeping the number of monomer types logarithmic in shape size, plus those monomers required by the Kolmogorov complexity of the shape or pattern. This work thus highlights the efficiency advantages of active self-assembly over passive self-assembly and motivates experimental effort to construct general-purpose active molecular self-assembly systems

Extended macro grammars and stack controlled machines

K-extended basic macro grammars are introduced, where K is any class of languages. The class B(K) of languages generated by such grammars is investigated, together with the class LB(K) of languages generated by the corresponding linear basic grammars. For any full semi-AFL K, B(K) is a full AFL closed under iterated LB(K)-substitution, but not necessarily under substitution. For any machine type D, the stack controlled machine type corresponding to D is introduced, denoted S(D), and the checking-stack controlled machine type CS(D). The data structure of this machine is a stack which controls a pushdown of data structures from D. If D accepts K, then S(D) accepts B(K) and CS(D) accepts LB(K). Thus the classes B(K) are characterized by stack controlled machines and the classes LB(K), i.e., the full hyper-AFLs, by checking-stack controlled machines. A full basic-AFL is a full AFL K such that B(K)C K. Every full basic-AFL is a full hyper-AFL, but not vice versa. The class of OI macro languages (i.e., indexed languages, i.e., nested stack automaton languages) is a full basic-AFL, properly containing the smallest full basic-AFL. The latter is generated by the ultrabasic macro grammars and accepted by the nested stack automata with bounded depth of nesting (and properly contains the stack languages, the ETOL languages, i.e., the smallest full hyper-AFL, and the basic macro languages). The full basic-AFLs are characterized by bounded nested stack controlled machines

Hypertrees: a study in language specification

A hierarchy of data structures, called the hypertree hierarchy, is presented which has strings and trees as its smallest two elements. A generalized frontiering operation is presented. Grammars, automata and regular expressions are extended to this hierarchy. These are shown to be equivalent and the resulting languages are called regular. This leads to a hierarchy of regular languages on the hypertree hierarchy. These are projected onto the set of strings by the frontier operation resulting in a true hierarchy of string languages. This hierarchy is called the (IO) algebraic language hierarchy. It has regular languages, context free languages and macro languages as its first three levels. It is contained in the set of context sensitive languages but is not equal to it. Other characterizations are presented