Polynomial time algorithms to determine weakly reversible realizations of chemical reaction networks

Weak reversibility is a crucial structural property of chemical reaction networks (CRNs) with mass action kinetics, because it has major implications related to the existence, uniqueness and stability of equilibrium points and to the boundedness of solutions. In this paper, we present two new algorithms to find dynamically equivalent weakly reversible realizations of a given CRN. They are based on linear programming and thus have polynomial time-complexity. Hence, these algorithms can deal with large-scale biochemical reaction networks, too. Furthermore, one of the methods is able to deal with linearly conjugate networks, too. © 2014 Springer International Publishing Switzerland

An RND-Type Efflux System in Borrelia burgdorferi Is Involved in Virulence and Resistance to Antimicrobial Compounds

Borrelia burgdorferi is remarkable for its ability to thrive in widely different environments due to its ability to infect various organisms. In comparison to enteric Gram-negative bacteria, these spirochetes have only a few transmembrane proteins some of which are thought to play a role in solute and nutrient uptake and excretion of toxic substances. Here, we have identified an outer membrane protein, BesC, which is part of a putative export system comprising the components BesA, BesB and BesC. We show that BesC, a TolC homolog, forms channels in planar lipid bilayers and is involved in antibiotic resistance. A besC knockout was unable to establish infection in mice, signifying the importance of this outer membrane channel in the mammalian host. The biophysical properties of BesC could be explained by a model based on the channel-tunnel structure. We have also generated a structural model of the efflux apparatus showing the putative spatial orientation of BesC with respect to the AcrAB homologs BesAB. We believe that our findings will be helpful in unraveling the pathogenic mechanisms of borreliae as well as in developing novel therapeutic agents aiming to block the function of this secretion apparatus

Generating Correct-by-Construction Distributed Implementations from Formal Maude Designs

Developing a reliable distributed system meeting desired performance requirements is a hard and very labor-intensive task. Formal specification of a system design and formal analysis can yield provably correct designs as well as reliable performance predictions. But there is still a formality gap between verified designs and distributed implementations. We present a correct-by-construction automatic transformation mapping a formal specification of a system design M in Maude to a distributed implementation D(M) with the same safety and liveness properties as M. Two case studies applying this transformation to state-of-the art distributed transaction systems show that high-quality implementations with acceptable performance and meeting performance predictions can be obtained in this way. To the best of our knowledge, this is the first time that formal models of distributed systems analyzed within the same formal framework for both logical and performance properties are automatically transformed into correct-by-construction implementations for which similar performance trends can be shown.Ope

Complex Methods and Class Allocation in Distributed OODBSs

In a distributed object-oriented database system (DODBS), queries which invoke methods executing at different sites and access different classes need to be executed very efficiently. Therefore, the methods invoked and classes accessed by the queries need to be allocated to sites so as to reduce the data transfer cost in processing a given set of queries. The methods and class allocation(MCA) problem needs to take into consideration complex interdependencies among queries, methods and classes. In this paper, we develop a comprehensive cost model for total data transfer incurred in processing a given set of queries by incorporating the dependencies among the queries, methods and classes. Further, we develop an iterative approach to generate near-optimal solution for the combined MCA problems by using the above cost model. In this approach, we start with an initial class allocation(CA) which is used for method allocation (MA), which in turn is used for CA, and so on. We stop this iterativ..