Allosteric RNA devices are increasingly being viewed as important tools capable of monitoring enzyme evolution, optimizing engineered metabolic pathways, facilitating gene discovery and regulators of nucleic acid-based therapeutics. A key bottleneck in the development of these platforms is the availability of small-molecule-binding RNA aptamers that robustly function in the cellular environment...

We develop a practical approach to querying temporal data stored in temporal SQL:2011 databases through the semantic layer of OWL 2 QL ontologies. An interval-based temporal query language (TQL), which we propose for this task, is defined via naturally characterizable combinations of temporal logic with conjunctive queries. This foundation warrants well-defined semantics and formal properties o...

We consider the Rosenfeld-Gröbner algorithm for computing a regular decomposition of a radical differential ideal generated by a set of ordinary differential polynomials in n indeterminates. For a set of ordinary differential polynomials F , let M(F ) be the sum of maximal orders of differential indeterminates occurring in F . We propose a modification of the Rosenfeld-Gröbner algorithm, in whi...

In this paper we extend the work by Michaelis (1999) which shows how to encode an arbitrary Minimalist Grammar in the sense of Stabler (1997) into a weakly equivalent multiple contextfree grammar (MCFG). By viewing MCFG rules as terms in a free Lawvere theory we can translate a given MCFG into a regular tree grammar. The latter is characterizable by both a tree automaton and a corresponding for...

In this paper we extend the work by Michaelis (1999) which shows how to encode an arbitrary Minimalist Grammar in the sense of Stabler (1997) into a weakly equivalent multiple contextfree grammar (MCFG). By viewing MCFG rules as terms in a free Lawvere theory we can translate a given MCFG into a regular tree grammar. The latter is characterizable by both a tree automaton and a corresponding for...

Hertrampf’s locally definable acceptance types showed that many complexity classes can be defined in terms of polynomially time bounded NTM’s with simple local conditions on the nodes of its computation tree, rather than global concepts like number of accepting paths etc. We introduce extended locally definable acceptance types as a generalization of Hertrampf’s concept in order to formally cap...

In this paper we show that non-context-free phenomena can be captured using only limited logical means. In particular, we show how to encode a Tree Adjoining Grammar [16] into a weakly equivalent monadic context-free tree grammar (MCFTG). By viewing MCFTG-rules as terms in a free Lawvere theory, we can translate a given MCFTG into a regular tree grammar. The latter is characterizable by both a ...

In this paper we extend the work by Michaelis (1999) which shows how to encode an arbitrary Minimalist Grammar in the sense of Stabler (1997) into a weakly equivalent multiple contextfree grammar (MCFG). By viewing MCFG-rules as terms in a free Lawvere theory we can translate a given MCFG into a regular tree grammar. The latter is characterizable by both a tree automaton and a corresponding for...

Bacteria are easily characterizable model organisms with an impressively complicated set of abilities. Among them is quorum sensing, a cell-cell signaling system that may have a common evolutionary origin with eukaryotic cell-cell signaling. The two systems are behaviorally similar, but quorum sensing in bacteria is more easily studied in depth than cell-cell signaling in eukaryotes. Because of...

We consider the Rosenfeld-Gröbner algorithm for computing a regular decomposition of a radical differential ideal generated by a set of ordinary differential polynomials in n indeterminates. For a set of ordinary differential polynomials F , let M(F ) be the sum of maximal orders of differential indeterminates occurring in F . We propose a modification of the Rosenfeld-Gröbner algorithm, in whi...