Programmability of Chemical Reaction Networks

Motivated by the intriguing complexity of biochemical circuitry within individual cells we study Stochastic Chemical Reaction Networks (SCRNs), a formal model that considers a set of chemical reactions acting on a finite number of molecules in a well-stirred solution according to standard chemical kinetics equations. SCRNs have been widely used for describing naturally occurring (bio)chemical systems, and with the advent of synthetic biology they become a promising language for the design of artificial biochemical circuits. Our interest here is the computational power of SCRNs and how they relate to more conventional models of computation. We survey known connections and give new connections between SCRNs and Boolean Logic Circuits, Vector Addition Systems, Petri Nets, Gate Implementability, Primitive Recursive Functions, Register Machines, Fractran, and Turing Machines. A theme to these investigations is the thin line between decidable and undecidable questions about SCRN behavior

Exponential Separation of Quantum and Classical Online Space Complexity

Although quantum algorithms realizing an exponential time speed-up over the best known classical algorithms exist, no quantum algorithm is known performing computation using less space resources than classical algorithms. In this paper, we study, for the first time explicitly, space-bounded quantum algorithms for computational problems where the input is given not as a whole, but bit by bit. We show that there exist such problems that a quantum computer can solve using exponentially less work space than a classical computer. More precisely, we introduce a very natural and simple model of a space-bounded quantum online machine and prove an exponential separation of classical and quantum online space complexity, in the bounded-error setting and for a total language. The language we consider is inspired by a communication problem (the set intersection function) that Buhrman, Cleve and Wigderson used to show an almost quadratic separation of quantum and classical bounded-error communication complexity. We prove that, in the framework of online space complexity, the separation becomes exponential.Comment: 13 pages. v3: minor change

Unbounded-error quantum computation with small space bounds

We prove the following facts about the language recognition power of quantum Turing machines (QTMs) in the unbounded error setting: QTMs are strictly more powerful than probabilistic Turing machines for any common space bound $s$ satisfying $s(n)=o(\log \log n)$. For "one-way" Turing machines, where the input tape head is not allowed to move left, the above result holds for $s(n)=o(\log n)$. We also give a characterization for the class of languages recognized with unbounded error by real-time quantum finite automata (QFAs) with restricted measurements. It turns out that these automata are equal in power to their probabilistic counterparts, and this fact does not change when the QFA model is augmented to allow general measurements and mixed states. Unlike the case with classical finite automata, when the QFA tape head is allowed to remain stationary in some steps, more languages become recognizable. We define and use a QTM model that generalizes the other variants introduced earlier in the study of quantum space complexity.Comment: A preliminary version of this paper appeared in the Proceedings of the Fourth International Computer Science Symposium in Russia, pages 356--367, 200

Bounded Counter Languages

We show that deterministic finite automata equipped with $k$ two-way heads are equivalent to deterministic machines with a single two-way input head and $k-1$ linearly bounded counters if the accepted language is strictly bounded, i.e., a subset of $a_1^*a_2^*... a_m^*$ for a fixed sequence of symbols $a_1, a_2,..., a_m$. Then we investigate linear speed-up for counter machines. Lower and upper time bounds for concrete recognition problems are shown, implying that in general linear speed-up does not hold for counter machines. For bounded languages we develop a technique for speeding up computations by any constant factor at the expense of adding a fixed number of counters

(Tissue) P Systems with Vesicles of Multisets

We consider tissue P systems working on vesicles of multisets with the very simple operations of insertion, deletion, and substitution of single objects. With the whole multiset being enclosed in a vesicle, sending it to a target cell can be indicated in those simple rules working on the multiset. As derivation modes we consider the sequential mode, where exactly one rule is applied in a derivation step, and the set maximal mode, where in each derivation step a non-extendable set of rules is applied. With the set maximal mode, computational completeness can already be obtained with tissue P systems having a tree structure, whereas tissue P systems even with an arbitrary communication structure are not computationally complete when working in the sequential mode. Adding polarizations (-1, 0, 1 are sufficient) allows for obtaining computational completeness even for tissue P systems working in the sequential mode.Comment: In Proceedings AFL 2017, arXiv:1708.0622

Quantum computation with devices whose contents are never read

In classical computation, a "write-only memory" (WOM) is little more than an oxymoron, and the addition of WOM to a (deterministic or probabilistic) classical computer brings no advantage. We prove that quantum computers that are augmented with WOM can solve problems that neither a classical computer with WOM nor a quantum computer without WOM can solve, when all other resource bounds are equal. We focus on realtime quantum finite automata, and examine the increase in their power effected by the addition of WOMs with different access modes and capacities. Some problems that are unsolvable by two-way probabilistic Turing machines using sublogarithmic amounts of read/write memory are shown to be solvable by these enhanced automata.Comment: 32 pages, a preliminary version of this work was presented in the 9th International Conference on Unconventional Computation (UC2010

(Tissue) P Systems with Vesicles of Multisets

We consider tissue P systems working on vesicles of multisets with the very simple operations of insertion, deletion, and substitution of single objects. With the whole multiset being enclosed in a vesicle, sending it to a target cell can be indicated in those simple rules working on the multiset. As derivation modes we consider the sequential mode, where exactly one rule is applied in a derivation step, and the set maximal mode, where in each derivation step a non-extendable set of rules is applied. With the set maximal mode, computational completeness can already be obtained with tissue P systems having a tree structure, whereas tissue P systems even with an arbitrary communication structure are not computationally complete when working in the sequential mode. Adding polarizations (-1, 0, 1 are sufficient) allows for obtaining computational completeness even for tissue P systems working in the sequential mode.Comment: In Proceedings AFL 2017, arXiv:1708.0622