Verification of Hierarchical Artifact Systems

Data-driven workflows, of which IBM's Business Artifacts are a prime exponent, have been successfully deployed in practice, adopted in industrial standards, and have spawned a rich body of research in academia, focused primarily on static analysis. The present work represents a significant advance on the problem of artifact verification, by considering a much richer and more realistic model than in previous work, incorporating core elements of IBM's successful Guard-Stage-Milestone model. In particular, the model features task hierarchy, concurrency, and richer artifact data. It also allows database key and foreign key dependencies, as well as arithmetic constraints. The results show decidability of verification and establish its complexity, making use of novel techniques including a hierarchy of Vector Addition Systems and a variant of quantifier elimination tailored to our context.Comment: Full version of the accepted PODS pape

Analysis of the convergence of the 1/t and Wang-Landau algorithms in the calculation of multidimensional integrals

In this communication, the convergence of the 1/t and Wang - Landau algorithms in the calculation of multidimensional numerical integrals is analyzed. Both simulation methods are applied to a wide variety of integrals without restrictions in one, two and higher dimensions. The errors between the exact and the calculated values of the integral are obtained and the efficiency and accuracy of the methods are determined by their dynamical behavior. The comparison between both methods and the simple sampling Monte Carlo method is also reported. It is observed that the time dependence of the errors calculated with 1/t algorithm goes as N^{-1/2} (with N the MC trials) in quantitative agreement with the simple sampling Monte Carlo method. It is also showed that the error for the Wang - Landau algorithm saturates in time evidencing the non-convergence of the methods. The sources for the error are also determined.Comment: 8 pages, 5 figure

Active role of elongation factor G in maintaining the mRNA reading frame during translation.

During translation, the ribosome moves along the mRNA one codon at a time with the help of elongation factor G (EF-G). Spontaneous changes in the translational reading frame are extremely rare, yet how the precise triplet-wise step is maintained is not clear. Here, we show that the ribosome is prone to spontaneous frameshifting on mRNA slippery sequences, whereas EF-G restricts frameshifting. EF-G helps to maintain the mRNA reading frame by guiding the A-site transfer RNA during translocation due to specific interactions with the tip of EF-G domain 4. Furthermore, EF-G accelerates ribosome rearrangements that restore the ribosome's control over the codon-anticodon interaction at the end of the movement. Our data explain how the mRNA reading frame is maintained during translation

Wang-Landau Algorithm: a Theoretical Analysis of the Saturation of the Error

In this work we present a theoretical analysis of the convergence of the Wang-Landau algorithm [Phys. Rev. Lett. 86, 2050 (2001)] which was introduced years ago to calculate the density of states in statistical models. We study the dynamical behavior of the error in the calculation of the density of states.We conclude that the source of the saturation of the error is due to the decreasing variations of the refinement parameter. To overcome this limitation, we present an analytical treatment in which the refinement parameter is scaled down as a power law instead of exponentially. An extension of the analysis to the N-fold way variation of the method is also discussed.Comment: 7 pages, 5 figure

Non-canonical binding site for bacterial initiation factor 3 on the large ribosomal subunit.

Canonical translation initiation in bacteria entails the assembly of the 30S initiation complex (IC), which binds the 50S subunit to form a 70S IC. IF3, a key initiation factor, is recruited to the 30S subunit at an early stage and is displaced from its primary binding site upon subunit joining. We employed four different FRET pairs to monitor IF3 relocation after 50S joining. IF3 moves away from the 30S subunit, IF1 and IF2, but can remain bound to the mature 70S IC. The secondary binding site is located on the 50S subunit in the vicinity of ribosomal protein L33. The interaction between IF3 and the 50S subunit is largely electrostatic with very high rates of IF3 binding and dissociation. The existence of the non-canonical binding site may help explain how IF3 participates in alternative initiation modes performed directly by the 70S ribosomes, such as initiation on leaderless mRNAs or re-initiation

Programmed –1 frameshifting by kinetic partitioning during impeded translocation.

Programmed –1 ribosomal frameshifting (−1PRF) is an mRNA recoding event utilized by cells to enhance the information content of the genome and to regulate gene expression. The mechanism of –1PRF and its timing during translation elongation are unclear. Here, we identified the steps that govern –1PRF by following the stepwise movement of the ribosome through the frameshifting site of a model mRNA derived from the IBV 1a/1b gene in a reconstituted in vitro translation system from Escherichia coli. Frameshifting occurs at a late stage of translocation when the two tRNAs are bound to adjacent slippery sequence codons of the mRNA. The downstream pseudoknot in the mRNA impairs the closing movement of the 30S subunit head, the dissociation of EF-G, and the release of tRNA from the ribosome. The slippage of the ribosome into the –1 frame accelerates the completion of translocation, thereby further favoring translation in the new reading frame

Critical behavior of hard-core lattice gases: Wang-Landau sampling with adaptive windows

Critical properties of lattice gases with nearest-neighbor exclusion are investigated via the adaptive-window Wang-Landau algorithm on the square and simple cubic lattices, for which the model is known to exhibit an Ising-like phase transition. We study the particle density, order parameter, compressibility, Binder cumulant and susceptibility. Our results show that it is possible to estimate critical exponents using Wang-Landau sampling with adaptive windows. Finite-size-scaling analysis leads to results in fair agreement with exact values (in two dimensions) and numerical estimates (in three dimensions).Comment: 20 pages, 11 figure

Thermal fluctuations of an interface near a contact line

The effect of thermal fluctuations near a contact line of a liquid interface partially wetting an impenetrable substrate is studied analytically and numerically. Promoting both the interface profile and the contact line position to random variables, we explore the equilibrium properties of the corresponding fluctuating contact line problem based on an interfacial Hamiltonian involving a "contact" binding potential. To facilitate an analytical treatment we consider the case of a one-dimensional interface. The effective boundary condition at the contact line is determined by a dimensionless parameter that encodes the relative importance of thermal energy and substrate energy at the microscopic scale. We find that this parameter controls the transition from a partially wetting to a pseudo-partial wetting state, the latter being characterized by a thin prewetting film of fixed thickness. In the partial wetting regime, instead, the profile typically approaches the substrate via an exponentially thinning prewetting film. We show that, independently of the physics at the microscopic scale, Young's angle is recovered sufficiently far from the substrate. The fluctuations of the interface and of the contact line give rise to an effective disjoining pressure, exponentially decreasing with height. Fluctuations therefore provide a regularization of the singular contact forces occurring in the corresponding deterministic problem.Comment: 40 Pages, 12 Figure