Solution structure of the N-terminal transactivation domain of ERM modified by SUMO-1.

ERM is a member of the PEA3 group of the Ets transcription factor family that plays important roles in development and tumorigenesis. The PEA3s share an N-terminal transactivation domain (TADn) whose activity is inhibited by small ubiquitin-like modifier (SUMO). However, the consequences of sumoylation and its underlying molecular mechanism remain unclear. The domain structure of ERM TADn alone or modified by SUMO-1 was analyzed using small-angle X-ray scattering (SAXS). Low resolution shapes determined ab initio from the scattering data indicated an elongated shape and an unstructured conformation of TADn in solution. Covalent attachment of SUMO-1 does not perturb the structure of TADn as indicated by the linear arrangement of the SUMO moiety with respect to TADn. Thus, ERM belongs to the growing family of proteins that contain intrinsically unstructured regions. The flexible nature of TADn may be instrumental for ERM recognition and binding to diverse molecular partners.

Antibody deficiency due to a missense mutation in CD19 demonstrates the importance of the conserved tryptophan 41 in immunoglobulin superfamily domain formation.

Immunoglobulin superfamily (IgSF) domains are conserved structures present in many proteins in eukaryotes and prokaryotes. These domains are well-capable of facilitating sequence variation, which is most clearly illustrated by the variable regions in immunoglobulins (Igs) and T cell receptors (TRs). We studied an antibody-deficient patient suffering from recurrent respiratory infections and with impaired antibody responses to vaccinations. Patient's B cells showed impaired Ca(2+) influx upon stimulation with anti-IgM and lacked detectable CD19 membrane expression. CD19 sequence analysis revealed a homozygous missense mutation resulting in a tryptophan to cystein (W52C) amino acid change. The affected tryptophan is CONSERVED-TRP 41 located on the C-strand of the first extracellular IgSF domain of CD19 and was found to be highly conserved, not only in mammalian CD19 proteins, but in nearly all characterized IgSF domains. Furthermore, the tryptophan is present in all variable domains in Ig and TR and was not mutated in 117 Ig class-switched transcripts of B cells from controls, despite an overall 10% amino acid change frequency. In vitro complementation studies and CD19 western blotting of patient's B cells demonstrated that the mutated protein remained immaturely glycosylated. This first missense mutation resulting in a CD19 deficiency demonstrates the crucial role of a highly conserved tryptophan in proper folding or stability of IgSF domains.

VegeDog: Formalism, vegetarian dogs, and partonomies in transition

The pragmatics of 'vegetarian' and 'carnivorous' exhibits an asymmetry that we put in evidence by analyzing a newspaper report about vegetarian dog-owners imposing a vegetarian diet on their pets. More fundamental is the problem of partonomy versus containment, for which we attempt a naive but formal analysis applied to ingestion and the food chain, an issue we derive from the same text analyzed. Our formal tools belong in commonsense modelling, a domain of artificial intelligence related to extra-linguistic knowledge and pragmatics. We first provide an interpretation of events analyzed, and express it graphically in a semantic-network related representation, and propose an alternative that we express in terms of a modal logic, avoiding the full representational power of Hayes's "ontology for liquids".

A domain decomposition algorithm for viscous/inviscid coupling

In fluid mechanics, it is well accepted that the Euler equation is one of the reduced forms of the Navier-Stokes equation by truncating the viscous effect. There are other truncation techniques currently being used in order to truncate the Navier-Stokes equation to a reduced form. This paper describes one such technique, suitable for adaptive domain decomposition methods for the solution of viscous flow problems. The physical domain of a viscous flow problem is partitioned into viscous and inviscid subdomains without overlapping regions, and the technique is embedded into a finite volume method. Some numerical results are provided for a flat plate and the NACA0012 aerofoil. Issues related to distributed computing are discussed.

A defect equation approach for the coupling of subdomains in domain decomposition methods

A defect equation for the coupling of nonlinear subproblems defined in nonoverlapped subdomains arise in domain decomposition methods is presented. Numerical solutions of defect equations by means of quasi-Newton methods are considered.

Multilevel mesh partitioning for optimizing domain shape

Multilevel algorithms are a successful class of optimization techniques that address the mesh partitioning problem for mapping meshes onto parallel computers. They usually combine a graph contraction algorithm together with a local optimization method that refines the partition at each graph level. To date, these algorithms have been used almost exclusively to minimize the cut-edge weight in the graph with the aim of minimizing the parallel communication overhead. However, it has been shown that for certain classes of problems, the convergence of the underlying solution algorithm is strongly influenced by the shape or aspect ratio of the subdomains. Therefore, in this paper, the authors modify the multilevel algorithms to optimize a cost function based on the aspect ratio. Several variants of the algorithms are tested and shown to provide excellent results.

Guest Editorial. Special Issue: Temporal logic in engineering

Logic-based models are thriving within artificial intelligence. A great number of new logics have been defined, and their theory investigated. Epistemic logics introduce modal operators for knowledge or belief; deontic logics are about norms, and introduce operators of deontic necessity and possibility (i.e., obligation or prohibition). And then we have a much investigated class—temporal logics—to whose application to engineering this special issue is devoted. This kind of formalism deserves increased widespread recognition and application in engineering, a domain where other kinds of temporal models (e.g., Petri nets) are by now a fairly standard part of the modelling toolbox.

Micromagnetic simulation of domain walls in iron films

The micromagnetic structure and energy of 180° domain walls spanning laminar crystals of iron having (100) or (110) surfaces and ranging in thickness from 145 to 580 nm have been investigated by numerical integration of the Landau-Lifshitz-Gilbert equation. Stable equilibrium structures with two flux symmetries were obtained for both crystal orientations at all thicknesses studied.

Coupled 3-D finite difference time domain and finite volume methods for solving microwave heating in porous media

Computational results for the microwave heating of a porous material are presented in this paper. Combined finite difference time domain and finite volume methods were used to solve equations that describe the electromagnetic field and heat and mass transfer in porous media. The coupling between the two schemes is through a change in dielectric properties which were assumed to be dependent both on temperature and moisture content. The model was able to reflect the evolution of temperature and moisture fields as the moisture in the porous medium evaporates. Moisture movement results from internal pressure gradients produced by the internal heating and phase change.

Domain decomposition using a 2-level correction scheme

The PHYSICA software was developed to enable multiphysics modelling allowing for interaction between Computational Fluid Dynamics (CFD) and Computational Solid Mechanics (CSM) and Computational Aeroacoustics (CAA). PHYSICA uses the finite volume method with 3-D unstructured meshes to enable the modelling of complex geometries. Many engineering applications involve significant computational time which needs to be reduced by means of a faster solution method or parallel and high performance algorithms. It is well known that multigrid methods serve as a fast iterative scheme for linear and nonlinear diffusion problems. This papers attempts to address two major issues of this iterative solver, including parallelisation of multigrid methods and their applications to time dependent multiscale problems.

A domain decomposition algorithm for inverse welding problems

A mathematical model and a numerical scheme for the inverse determination of heat sources generated by means of a welding process is presented in this paper. The accuracy of the heat source retrieval is discussed.

Domain decomposition methods for welding problems

This paper, a 2-D non-linear electric arc-welding problem is considered. It is assumed that the moving arc generates an unknown quantity of energy which makes the problem an inverse problem with an unknown source. Robust algorithms to solve such problems e#ciently, and in certain circumstances in real-time, are of great technological and industrial interest. There are other types of inverse problems which involve inverse determination of heat conductivity or material properties [CDJ63][TE98], inverse problems in material cutting [ILPP98], and retrieval of parameters containing discontinuities [IK90]. As in the metal cutting problem, the temperature of a very hot surface is required and it relies on the use of thermocouples. Here, the solution scheme requires temperature measurements lied in the neighbourhood of the weld line in order to retrieve the unknown heat source. The size of this neighbourhood is not considered in this paper, but rather a domain decomposition concept is presented and an examination of the accuracy of the retrieved source are presented. This paper is organised as follows. The inverse problem is formulated and a method for the source retrieval is presented in the second section. The source retrieval method is based on an extension of the 1-D source retrieval method as proposed in [ILP].

Electronic packaging and reduction in modelling time using domain decomposition

The domain decomposition method is directed to electronic packaging simulation in this article. The objective is to address the entire simulation process chain, to alleviate user interactions where they are heavy to mechanization by component approach to streamline the model simulation process.

On a parallel time-domain method for the nonlinear Black-Scholes equation

A parallel time-domain algorithm is described for the time-dependent nonlinear Black-Scholes equation, which may be used to build financial analysis tools to help traders making rapid and systematic evaluation of buy/sell contracts. The algorithm is particularly suitable for problems that do not require fine details at each intermediate time step, and hence the method applies well for the present problem.

The completeness and soundness of temporal theories

Generally speaking, the term temporal logic refers to any system of rules and symbolism for representing and reasoning about propositions qualified in terms of time. In computer science, particularly in the domain of Artificial Intelligence, there are mainly two known approaches to the representation of temporal information: modal logic approaches including tense logic and hybrid temporal logic, and predicate logic approaches including temporal arguement method and reified temporal logic. On one hand, while tense logic, hybrid temporal logic and temporal argument method enjoy formal theoretical foundations, their expressiveness has been criticised as not power enough for representing general temporal knowledge; on the other hand, although reified temporal logic provides greater expressive power, most of the current systems following the temporal reification lack of complete and sound axiomatic theories. With there observations in mind, a new reified temporal logic with clear syntax and semantics in terms of a sound and complete axiomatic formalism is introduced in this paper, which retains all the expressive power of temporal reification.