Conditions for duality between fluxes and concentrations in biochemical networks

Mathematical and computational modelling of biochemical networks is often done in terms of either the concentrations of molecular species or the fluxes of biochemical reactions. When is mathematical modelling from either perspective equivalent to the other? Mathematical duality translates concepts, theorems or mathematical structures into other concepts, theorems or structures, in a one-to-one manner. We present a novel stoichiometric condition that is necessary and sufficient for duality between unidirectional fluxes and concentrations. Our numerical experiments, with computational models derived from a range of genome-scale biochemical networks, suggest that this flux-concentration duality is a pervasive property of biochemical networks. We also provide a combinatorial characterisation that is sufficient to ensure flux-concentration duality. That is, for every two disjoint sets of molecular species, there is at least one reaction complex that involves species from only one of the two sets. When unidirectional fluxes and molecular species concentrations are dual vectors, this implies that the behaviour of the corresponding biochemical network can be described entirely in terms of either concentrations or unidirectional fluxes

Centralized versus market-based approaches to mobile task allocation problem: State-of-the-art

Centralized approach has been adopted for finding solutions to resource allocation problems (RAPs) in many real-life applications. On the other hand, market-based approach has been proposed as an alternative to solve the problem due to recent advancement in ICT technologies. In spite of the existence of some efforts to review the pros and cons of each approach in RAPs, the studies cannot be directly applied to specific problem domains like mobile task allocation problem which is characterised with high level of uncertainty on the availability of resources (workers). This paper aims to review existing studies on task allocation problems(TAPs) focusing on those two approaches and their comparison and identify major issues that need to be resolved for comparing the two approaches in mobile task allocation problems. Mobile Task Allocation Problem (MTAP) is defined and its problematic structures are explained in relation with task allocation to mobile workers. Solutions produced by each approach to some applications and variations of MTAP are also discussed and compared. Finally, some future research directions are identified in order to compare both approaches in function of uncertainty emerging from the mobile nature of the MTAP

Groupoid Semantics for Thermal Computing

A groupoid semantics is presented for systems with both logical and thermal degrees of freedom. We apply this to a syntactic model for encryption, and obtain an algebraic characterization of the heat produced by the encryption function, as predicted by Landauer's principle. Our model has a linear representation theory that reveals an underlying quantum semantics, giving for the first time a functorial classical model for quantum teleportation and other quantum phenomena.Comment: We describe a groupoid model for thermodynamic computation, and a quantization procedure that turns encrypted communication into quantum teleportation. Everything is done using higher category theor

Finite Computational Structures and Implementations

What is computable with limited resources? How can we verify the correctness of computations? How to measure computational power with precision? Despite the immense scientific and engineering progress in computing, we still have only partial answers to these questions. In order to make these problems more precise, we describe an abstract algebraic definition of classical computation, generalizing traditional models to semigroups. The mathematical abstraction also allows the investigation of different computing paradigms (e.g. cellular automata, reversible computing) in the same framework. Here we summarize the main questions and recent results of the research of finite computation.Comment: 12 pages, 3 figures, will be presented at CANDAR'16 and final version published by IEEE Computer Societ