Computing with cells: membrane systems - some complexity issues.

Membrane computing is a branch of natural computing which abstracts computing models from the structure and the functioning of the living cell. The main ingredients of membrane systems, called P systems, are (i) the membrane structure, which consists of a hierarchical arrangements of membranes which delimit compartments where (ii) multisets of symbols, called objects, evolve according to (iii) sets of rules which are localised and associated with compartments. By using the rules in a nondeterministic/deterministic maximally parallel manner, transitions between the system configurations can be obtained. A sequence of transitions is a computation of how the system is evolving. Various ways of controlling the transfer of objects from one membrane to another and applying the rules, as well as possibilities to dissolve, divide or create membranes have been studied. Membrane systems have a great potential for implementing massively concurrent systems in an efficient way that would allow us to solve currently intractable problems once future biotechnology gives way to a practical bio-realization. In this paper we survey some interesting and fundamental complexity issues such as universality vs. nonuniversality, determinism vs. nondeterminism, membrane and alphabet size hierarchies, characterizations of context-sensitive languages and other language classes and various notions of parallelism

Reversible simulation of bipartite product Hamiltonians

Consider two quantum systems A and B interacting according to a product Hamiltonian H = H_A x H_B. We show that any two such Hamiltonians can be used to simulate each other reversibly (i.e., without efficiency losses) with the help of local unitary operations and local ancillas. Accordingly, all non-local features of a product Hamiltonian -- including the rate at which it can be used to produce entanglement, transmit classical or quantum information, or simulate other Hamiltonians -- depend only upon a single parameter. We identify this parameter and use it to obtain an explicit expression for the entanglement capacity of all product Hamiltonians. Finally, we show how the notion of simulation leads to a natural formulation of measures of the strength of a nonlocal Hamiltonian.Comment: 10 page

Rapid Water Reduction to H_2 Catalyzed by a Cobalt Bis(iminopyridine) Complex

A cobalt bis(iminopyridine) complex is a highly active electrocatalyst for water reduction, with an estimated apparent second order rate constant k_(app) ≤ 10^7 M^(–1)s^(–1) over a range of buffer/salt concentrations. Scan rate dependence data are consistent with freely diffusing electroactive species over pH 4–9 at room temperature for each of two catalytic reduction events, one of which is believed to be ligand based. Faradaic H_2 yields up to 87 ± 10% measured in constant potential electrolyses (−1.4 V vs SCE) confirm high reactivity and high fidelity in a catalyst supported by the noninnocent bis(iminopyridine) ligand. A mechanism involving initial reduction of Co^(2+) and subsequent protonation is proposed

Macrocyclic cyanocobalamin (vitamin B12) as a homogeneous electrocatalyst for water oxidation under neutral conditions

Highly water-soluble cyanocobalamin (also known as vitamin B-12) is the most structurally macrocyclic complex comprising cobalt in the center of a corrin ring. Interestingly, it acts as a robust electrocatalyst in water oxidation at similar to 0.58 V overpotential with a faradaic efficiency of 97.50% under neutral buffered conditions. The catalyst is impressively stable even after long-term bulk electrolysis, and homogeneous in nature, as established by a series of experiments and characterization techniques

Catalysis in non--local quantum operations

We show how entanglement can be used, without being consumed, to accomplish unitary operations that could not be performed with out it. When applied to infinitesimal transformations our method makes equivalent, in the sense of Hamiltonian simulation, a whole class of otherwise inequivalent two-qubit interactions. The new catalysis effect also implies the asymptotic equivalence of all such interactions.Comment: 4 pages, revte

Modeling and evolving biochemical networks: insights into communication and computation from the biological domain

This paper is concerned with the modeling and evolving of Cell Signaling Networks (CSNs) in silico. CSNs are complex biochemical networks responsible for the coordination of cellular activities. We examine the possibility to computationally evolve and simulate Artificial Cell Signaling Networks (ACSNs) by means of Evolutionary Computation techniques. From a practical point of view, realizing and evolving ACSNs may provide novel computational paradigms for a variety of application areas. For example, understanding some inherent properties of CSNs such as crosstalk may be of interest: A potential benefit of engineering crosstalking systems is that it allows the modification of a specific process according to the state of other processes in the system. This is clearly necessary in order to achieve complex control tasks. This work may also contribute to the biological understanding of the origins and evolution of real CSNs. An introduction to CSNs is first provided, in which we describe the potential applications of modeling and evolving these biochemical networks in silico. We then review the different classes of techniques to model CSNs, this is followed by a presentation of two alternative approaches employed to evolve CSNs within the ESIGNET project. Results obtained with these methods are summarized and discussed

Influence of surface diffusion on catalytic reactivity of spatially inhomogeneous surfaces mean field modeling

Kinetics of model catalytic processes proceeding on inhomogeneous surfaces is studied. We employ an extended mean-field model that takes into account surface inhomogeneities. The influence of surface diffusion of adsorbent on the kinetics of the catalytic process is investigated. It is shown that diffusion is responsible for differences in the reaction rate of systems with different arrangements of active sites. The presence of cooperative effects between inactive and active sites is demonstrated and the conditions when these effects are important are discussed. We show that basic catalytic phenomena on nonuniform surfaces can be studied with mean-field modeling methods.Comment: Submitted to Chemical Physics Letters. Includes supporting material in Appendice

BCR-ABL residues interacting with ponatinib are critical to preserve the tumorigenic potential of the oncoprotein

Patients with chronic myeloid leukemia in whom tyrosine kinase inhibitors (TKIs) fail often present mutations in the BCR-ABL catalytic domain. We noticed a lack of substitutions involving 4 amino acids (E286, M318, I360, and D381) that form hydrogen bonds with ponatinib. We therefore introduced mutations in each of these residues, either preserving or altering their physicochemical properties. We found that E286, M318, I360, and D381 are dispensable for ABL and BCR-ABL protein stability but are critical for preserving catalytic activity. Indeed, only a "conservative" I360T substitution retained kinase proficiency and transforming potential. Molecular dynamics simulations of BCR-ABLI360T revealed differences in both helix αC dynamics and protein-correlated motions, consistent with a modified ATP-binding pocket. Nevertheless, this mutant remained sensitive to ponatinib, imatinib, and dasatinib. These results suggest that changes in the 4 BCR-ABL residues described here would be selected against by a lack of kinase activity or by maintained responsiveness to TKIs. Notably, amino acids equivalent to those identified in BCR-ABL are conserved in 51% of human tyrosine kinases. Hence, these residues may represent an appealing target for the design of pharmacological compounds that would inhibit additional oncogenic tyrosine kinases while avoiding the emergence of resistance due to point mutations.This work was supported by an investigator grant to P.V. from Associazione Italiana per la Ricerca sul Cancro (AIRC) and by funding from the Biotechnology and Biological Sciences Research Council (BB/I023291/1 and BB/H018409/1 to AP and FF). P.B. is the recipient of an AIRC - Marie Curie fellowship

ModuLand plug-in for Cytoscape: determination of hierarchical layers of overlapping network modules and community centrality

Summary: The ModuLand plug-in provides Cytoscape users an algorithm for determining extensively overlapping network modules. Moreover, it identifies several hierarchical layers of modules, where meta-nodes of the higher hierarchical layer represent modules of the lower layer. The tool assigns module cores, which predict the function of the whole module, and determines key nodes bridging two or multiple modules. The plug-in has a detailed JAVA-based graphical interface with various colouring options. The ModuLand tool can run on Windows, Linux, or Mac OS. We demonstrate its use on protein structure and metabolic networks. Availability: The plug-in and its user guide can be downloaded freely from: http://www.linkgroup.hu/modules.php. Contact: [email protected] Supplementary information: Supplementary information is available at Bioinformatics online.Comment: 39 pages, 1 figure and a Supplement with 9 figures and 10 table