SNAP: Stateful Network-Wide Abstractions for Packet Processing

Early programming languages for software-defined networking (SDN) were built on top of the simple match-action paradigm offered by OpenFlow 1.0. However, emerging hardware and software switches offer much more sophisticated support for persistent state in the data plane, without involving a central controller. Nevertheless, managing stateful, distributed systems efficiently and correctly is known to be one of the most challenging programming problems. To simplify this new SDN problem, we introduce SNAP. SNAP offers a simpler "centralized" stateful programming model, by allowing programmers to develop programs on top of one big switch rather than many. These programs may contain reads and writes to global, persistent arrays, and as a result, programmers can implement a broad range of applications, from stateful firewalls to fine-grained traffic monitoring. The SNAP compiler relieves programmers of having to worry about how to distribute, place, and optimize access to these stateful arrays by doing it all for them. More specifically, the compiler discovers read/write dependencies between arrays and translates one-big-switch programs into an efficient internal representation based on a novel variant of binary decision diagrams. This internal representation is used to construct a mixed-integer linear program, which jointly optimizes the placement of state and the routing of traffic across the underlying physical topology. We have implemented a prototype compiler and applied it to about 20 SNAP programs over various topologies to demonstrate our techniques' scalability

Protein engineering of Pseudomonas fluorescens peroxidase Dyp1B for oxidation of phenolic and polymeric lignin substrates

Directed evolution was applied to dye-decolourizing peroxidase Dyp1B from Pseudomonas fluorescens Pf-5, in order to enhance the activity for oxidation of phenolic and lignin substrates. Saturation mutagenesis was used to generate focused libraries at 7 active site residues in the vicinity of the heme cofactor, and the libraries were screened for activity towards 2,6-dichlorophenol. Mutants N193 L and H169 L were found to show 7–8 fold enhanced kcat/KM towards DCP, and replacements at Val205 and Ala209 also showed enhanced activity towards alkali Kraft lignin. Residues near the predicted Mn(II) binding site were also investigated by site-directed mutagenesis, and mutants S223 N and H127R showed 4-7-fold increased kcat/KM for Mn(II) oxidation. Mutant F128R also showed enhanced thermostability, compared to wild-type Dyp1B. Testing of mutants for low molecular weight product release from Protobind alkali lignin revealed that mutant H169 L showed enhanced product release, compared with WT enzyme, and the formation of three low molecular weight metabolites by this mutant was detected by reverse phase HPLC analysis

Computing by Temporal Order: Asynchronous Cellular Automata

Our concern is the behaviour of the elementary cellular automata with state set 0,1 over the cell set Z/nZ (one-dimensional finite wrap-around case), under all possible update rules (asynchronicity). Over the torus Z/nZ (n<= 11),we will see that the ECA with Wolfram rule 57 maps any v in F_2^n to any w in F_2^n, varying the update rule. We furthermore show that all even (element of the alternating group) bijective functions on the set F_2^n = 0,...,2^n-1, can be computed by ECA57, by iterating it a sufficient number of times with varying update rules, at least for n <= 10. We characterize the non-bijective functions computable by asynchronous rules.Comment: In Proceedings AUTOMATA&JAC 2012, arXiv:1208.249

Three-dimensional Structure of L-2-Haloacid Dehalogenase from Xanthobacter autotrophicus GJ10 Complexed with the Substrate-analogue Formate

The L-2-haloacid dehalogenase from the 1,2-dichloroethane degrading bacterium Xanthobacter autotrophicus GJ10 catalyzes the hydrolytic dehalogenation of small L-2-haloalkanoic acids to yield the corresponding D-2-hydroxyalkanoic acids. Its crystal structure was solved by the method of multiple isomorphous replacement with incorporation of anomalous scattering information and solvent flattening, and was refined at 1.95-Å resolution to an R factor of 21.3%. The three-dimensional structure is similar to that of the homologous L-2-haloacid dehalogenase from Pseudomonas sp. YL (1), but the X. autotrophicus enzyme has an extra dimerization domain, an active site cavity that is completely shielded from the solvent, and a different orientation of several catalytically important amino acid residues. Moreover, under the conditions used, a formate ion is bound in the active site. The position of this substrate-analogue provides valuable information on the reaction mechanism and explains the limited substrate specificity of the Xanthobacter L-2-haloacid dehalogenase.