Interaction Pressure Tensor for a class of Multicomponent Lattice Boltzmann models

We present a theory to obtain the pressure tensor for a class of non-ideal multicomponent lattice Boltzmann models, thus extending the theory presented by Shan (X. Shan, Phys. Rev. E 77, 066702 (2008)) for single component fluids. We obtain the correct form of the pressure tensor directly on the lattice and the resulting equilibrium properties are shown to agree very well with those measured from numerical simulations. Results are compared with those of alternative theories.Comment: 7 Pages, 5 figure

Lattice Boltzmann Simulations of Droplet formation in confined Channels with Thermocapillary flows

Based on mesoscale lattice Boltzmann simulations with the "Shan-Chen" model, we explore the influence of thermocapillarity on the break-up properties of fluid threads in a microfluidic T-junction, where a dispersed phase is injected perpendicularly into a main channel containing a continuous phase, and the latter induces periodic break-up of droplets due to the cross-flowing. Temperature effects are investigated by switching on/off both positive/negative temperature gradients along the main channel direction, thus promoting a different thread dynamics with anticipated/delayed break-up. Numerical simulations are performed at changing the flow-rates of both the continuous and dispersed phases, as well as the relative importance of viscous forces, surface tension forces and thermocapillary stresses. The range of parameters is broad enough to characterize the effects of thermocapillarity on different mechanisms of break-up in the confined T-junction, including the so-called "squeezing" and "dripping" regimes, previously identified in the literature. Some simple scaling arguments are proposed to rationalize the observed behaviour, and to provide quantitative guidelines on how to predict the droplet size after break-up.Comment: 18 pages, 9 figure

Fluctuating Multicomponent Lattice Boltzmann Model

Current implementations of fluctuating lattice Boltzmann equations (FLBE) describe single component fluids. In this paper, a model based on the continuum kinetic Boltzmann equation for describing multicomponent fluids is extended to incorporate the effects of thermal fluctuations. The thus obtained fluctuating Boltzmann equation is first linearized to apply the theory of linear fluctuations, and expressions for the noise covariances are determined by invoking the fluctuation-dissipation theorem (FDT) directly at the kinetic level. Crucial for our analysis is the projection of the Boltzmann equation onto the ortho-normal Hermite basis. By integrating in space and time the fluctuating Boltzmann equation with a discrete number of velocities, the FLBE is obtained for both ideal and non-ideal multicomponent fluids. Numerical simulations are specialized to the case where mean-field interactions are introduced on the lattice, indicating a proper thermalization of the system.Comment: 30 pages, 6 figure

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

Extended sources of the main events of the Umbria-Marche (1997) seismic sequence inverted from geophysical data

The three largest events of the 1997 Umbria-Marche (Italy) sequence occurred on September 26, 1997 at 00:33 GMT (Event 1, MW=5.7) and 09:40 GMT (Event 2, MW=6.0) in the Colfiorito area and on the October 14, 1997 at 15:23 (Event 3, MW=5.6) in the Sellano area. The availability of different sets of geodetic and seismological data allowed several studies to characterize the extended sources of events 1-3. In this work, I review some of the studies that obtain the properties of the seismic sources by inversion of available data. Generally these studies assume the seismic sources as dislocations or distributions of equivalent point sources in elastic half-spaces. Following their chronological order, they model increasing complexities of the sources by using an increasing number of data. Some of the differences between results obtained, such as the top edge depth estimates, are shown to be due to the different approaches used. Commonly a 1-D crustal model is used in inverting strongmotion data. Instead homogeneous elastic half-spaces are mainly assumed in inverting geodetic data to obtain the three main sources of the 1997 Umbria-Marche sequence. Assuming the same crustal structure is important to make comparable results obtained analyzing seismological data or geodetic data separately, as it has been done till now for this sequence

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

The quasi-static approximation of the spring-slider motion

International audienceThe spring-slider is a simple dynamical system consisting in a massive block sliding with friction and pulled through a spring at a given velocity. Understanding the block motion is fundamental for studying more complex phenomena of frictional sliding, such as the seismogenic fault motion. We analyze the dynamical properties of the system, subject to rate- and state-dependent friction laws and forced at a constant load velocity. In particular we study the limits within which the quasi-static model can be used. The latter model approximates the complete model of the system without taking into account the inertia effects. The system parameters are here found to be grouped into three characteristic times of the three dynamics present in the complete model. A necessary condition for the quasi-static approximation to hold is that the characteristic time of the inertial equation is much smaller than the other two characteristic times. We have studied a modification of one of the classical forms of the rate- and state-dependent friction laws. Subsequently we have developed a linear analysis in the neighbourhood of the equilibrium point of the system. For the quasi-static model we rigorously found, by means of a nonlinear analysis, a supercritical Hopf bifurcation, a dynamical property of the complete model. The classical form of the friction laws can be obtained as a particular case of the one we considered, but fails to preserve the Hopf bifurcation in the quasi-static approximation. We conclude that to have a good quasi-static approximation of the system, even in nonlinear conditions, the form of the friction laws considered is a critical factor

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

Modeling instantaneous dynamic triggering in a 3–D fault system: application to the June 2000 South Iceland seismic sequence

We present a model of seismogenesis on an extended 3–D fault subjected to the external perturbations of coseismic stress changes due to an earthquake occurred on another fault (the causative fault). As an application, we consider the spatio–temporal stress distribution produced by the MS = 6.6 June 17, 2000 mainshock in the South Iceland Seismic Zone (SISZ) on the Hvalhnúkur fault. The latter is located nearly 64 km from the causative fault and failed 26 s after the mainshock with an estimated magnitude Mw  [5, 5.5], providing an example of instantaneous dynamic triggering. The stress perturbations are computed by means of a discrete wavenumber and reflectivity code. The response of the perturbed fault is then analyzed solving the truly 3–D, fully dynamic (or spontaneous) problem, accounting for crustal stratification. In a previous study, the response of the Hvalhnúkur fault was analyzed by using a spring–slider fault model, comparing the estimated perturbed failure time with the observed origin time. In addition to the perturbed failure time, the present model can provide numerical estimates of many other dynamical features of the triggered event that can be compared with available observations: the rupture history of the whole fault plane and its final extension and the seismic moment of the 26 s event. We show the key differences existing between a mass–spring model and the present extended fault model, in particular we show the essential role of the load exerted by the other slipping points of the fault. By considering both rate– and state–dependent laws and non–linear slip–dependent law, we show how the dynamics of the 26 s fault strongly depends on the assumed constitutive law and initial stress conditions. In the case of rate– and state– dependent governing laws, assuming an initial effective normal stress distribution which is suitable for the SISZ and consistent with previously stated conditions of instantaneous dynamic triggering of the Hvalhnúkur fault, we obtain results in general agreement with observations