Heteropolymer Sequence Design and Preferential Solvation of Hydrophilic Monomers: One More Application of Random Energy Model

In this paper, we study the role of surface of the globule and the role of interactions with the solvent for designed sequence heteropolymers using random energy model (REM). We investigate the ground state energy and surface monomer composition distribution. By comparing the freezing transition in random and designed sequence heteropolymers, we discuss the effects of design. Based on our results, we are able to show under which conditions solvation effect improves the quality of sequence design. Finally, we study sequence space entropy and discuss the number of available sequences as a function of imposed requirements for the design quality

Hilbert-Post completeness for the state and the exception effects

In this paper, we present a novel framework for studying the syntactic completeness of computational effects and we apply it to the exception effect. When applied to the states effect, our framework can be seen as a generalization of Pretnar's work on this subject. We first introduce a relative notion of Hilbert-Post completeness, well-suited to the composition of effects. Then we prove that the exception effect is relatively Hilbert-Post complete, as well as the "core" language which may be used for implementing it; these proofs have been formalized and checked with the proof assistant Coq.Comment: Siegfried Rump (Hamburg University of Technology), Chee Yap (Courant Institute, NYU). Sixth International Conference on Mathematical Aspects of Computer and Information Sciences , Nov 2015, Berlin, Germany. 2015, LNC

Focusing in Asynchronous Games

Game semantics provides an interactive point of view on proofs, which enables one to describe precisely their dynamical behavior during cut elimination, by considering formulas as games on which proofs induce strategies. We are specifically interested here in relating two such semantics of linear logic, of very different flavor, which both take in account concurrent features of the proofs: asynchronous games and concurrent games. Interestingly, we show that associating a concurrent strategy to an asynchronous strategy can be seen as a semantical counterpart of the focusing property of linear logic

Protein folding rates correlate with heterogeneity of folding mechanism

By observing trends in the folding kinetics of experimental 2-state proteins at their transition midpoints, and by observing trends in the barrier heights of numerous simulations of coarse grained, C-alpha model, Go proteins, we show that folding rates correlate with the degree of heterogeneity in the formation of native contacts. Statistically significant correlations are observed between folding rates and measures of heterogeneity inherent in the native topology, as well as between rates and the variance in the distribution of either experimentally measured or simulated phi-values.Comment: 11 pages, 3 figures, 1 tabl

Leveraging Semantic Web Service Descriptions for Validation by Automated Functional Testing

Recent years have seen the utilisation of Semantic Web Service descriptions for automating a wide range of service-related activities, with a primary focus on service discovery, composition, execution and mediation. An important area which so far has received less attention is service validation, whereby advertised services are proven to conform to required behavioural specifications. This paper proposes a method for validation of service-oriented systems through automated functional testing. The method leverages ontology-based and rule-based descriptions of service inputs, outputs, preconditions and effects (IOPE) for constructing a stateful EFSM specification. The specification is subsequently utilised for functional testing and validation using the proven Stream X-machine (SXM) testing methodology. Complete functional test sets are generated automatically at an abstract level and are then applied to concrete Web services, using test drivers created from the Web service descriptions. The testing method comes with completeness guarantees and provides a strong method for validating the behaviour of Web services

Non-Markovian Configurational Diffusion and Reaction Coordinates for Protein Folding

The non-Markovian nature of polymer motions is accounted for in folding kinetics, using frequency-dependent friction. Folding, like many other problems in the physics of disordered systems, involves barrier crossing on a correlated energy landscape. A variational transition state theory (VTST) that reduces to the usual Bryngelson-Wolynes Kramers approach when the non-Markovian aspects are neglected is used to obtain the rate, without making any assumptions regarding the size of the barrier, or the memory time of the friction. The transformation to collective variables dependent on the dynamics of the system allows the theory to address the controversial issue of what are ``good'' reaction coordinates for folding.Comment: 9 pages RevTeX, 3 eps-figures included, submitted to PR

Genetic embedded matching approach to ground states in continuous-spin systems

Due to an extremely rugged structure of the free energy landscape, the determination of spin-glass ground states is among the hardest known optimization problems, found to be NP-hard in the most general case. Owing to the specific structure of local (free) energy minima, general-purpose optimization strategies perform relatively poorly on these problems, and a number of specially tailored optimization techniques have been developed in particular for the Ising spin glass and similar discrete systems. Here, an efficient optimization heuristic for the much less discussed case of continuous spins is introduced, based on the combination of an embedding of Ising spins into the continuous rotators and an appropriate variant of a genetic algorithm. Statistical techniques for insuring high reliability in finding (numerically) exact ground states are discussed, and the method is benchmarked against the simulated annealing approach.Comment: 17 pages, 12 figures, 1 tabl