Automata theory in nominal sets

We study languages over infinite alphabets equipped with some structure that can be tested by recognizing automata. We develop a framework for studying such alphabets and the ensuing automata theory, where the key role is played by an automorphism group of the alphabet. In the process, we generalize nominal sets due to Gabbay and Pitts

Local cloning of entangled states

We investigate the conditions under which a set \SC of pure bipartite quantum states on a $D\times D$ system can be locally cloned deterministically by separable operations, when at least one of the states is full Schmidt rank. We allow for the possibility of cloning using a resource state that is less than maximally entangled. Our results include that: (i) all states in \SC must be full Schmidt rank and equally entangled under the $G$-concurrence measure, and (ii) the set \SC can be extended to a larger clonable set generated by a finite group $G$ of order $|G|=N$, the number of states in the larger set. It is then shown that any local cloning apparatus is capable of cloning a number of states that divides $D$ exactly. We provide a complete solution for two central problems in local cloning, giving necessary and sufficient conditions for (i) when a set of maximally entangled states can be locally cloned, valid for all $D$; and (ii) local cloning of entangled qubit states with non-vanishing entanglement. In both of these cases, a maximally entangled resource is necessary and sufficient, and the states must be related to each other by local unitary "shift" operations. These shifts are determined by the group structure, so need not be simple cyclic permutations. Assuming this shifted form and partially entangled states, then in D=3 we show that a maximally entangled resource is again necessary and sufficient, while for higher dimensional systems, we find that the resource state must be strictly more entangled than the states in \SC. All of our necessary conditions for separable operations are also necessary conditions for LOCC, since the latter is a proper subset of the former. In fact, all our results hold for LOCC, as our sufficient conditions are demonstrated for LOCC, directly.Comment: REVTEX 15 pages, 1 figure, minor modifications. Same as the published version. Any comments are welcome

Gr\"obner methods for representations of combinatorial categories

Given a category C of a combinatorial nature, we study the following fundamental question: how does the combinatorial behavior of C affect the algebraic behavior of representations of C? We prove two general results. The first gives a combinatorial criterion for representations of C to admit a theory of Gr\"obner bases. From this, we obtain a criterion for noetherianity of representations. The second gives a combinatorial criterion for a general "rationality" result for Hilbert series of representations of C. This criterion connects to the theory of formal languages, and makes essential use of results on the generating functions of languages, such as the transfer-matrix method and the Chomsky-Sch\"utzenberger theorem. Our work is motivated by recent work in the literature on representations of various specific categories. Our general criteria recover many of the results on these categories that had been proved by ad hoc means, and often yield cleaner proofs and stronger statements. For example: we give a new, more robust, proof that FI-modules (originally introduced by Church-Ellenberg-Farb), and a family of natural generalizations, are noetherian; we give an easy proof of a generalization of the Lannes-Schwartz artinian conjecture from the study of generic representation theory of finite fields; we significantly improve the theory of $\Delta$-modules, introduced by Snowden in connection to syzygies of Segre embeddings; and we establish fundamental properties of twisted commutative algebras in positive characteristic.Comment: 41 pages; v2: Moved old Sections 3.4, 10, 11, 13.2 and connected text to arxiv:1410.6054v1, Section 13.1 removed and will appear elsewhere; v3: substantial revision and reorganization of section

AND-NOT logic framework for steady state analysis of Boolean network models

Finite dynamical systems (e.g. Boolean networks and logical models) have been used in modeling biological systems to focus attention on the qualitative features of the system, such as the wiring diagram. Since the analysis of such systems is hard, it is necessary to focus on subclasses that have the properties of being general enough for modeling and simple enough for theoretical analysis. In this paper we propose the class of AND-NOT networks for modeling biological systems and show that it provides several advantages. Some of the advantages include: Any finite dynamical system can be written as an AND-NOT network with similar dynamical properties. There is a one-to-one correspondence between AND-NOT networks, their wiring diagrams, and their dynamics. Results about AND-NOT networks can be stated at the wiring diagram level without losing any information. Results about AND-NOT networks are applicable to any Boolean network. We apply our results to a Boolean model of Th-cell differentiation