A recent Monte Carlo simulation determined the potential of mean force between two lysozyme molecules in various aqueous solutions [M. Lund, Phys. Rev. Lett. 100, 258105 (2008)]. The study involved a combination of explicit solvent and continuum model simulations and showed that there are significant ion-specific protein-protein interactions due to hydrophobic patches on the protein surfaces. I...

Programming object interactions is at the heart of object-oriented programming. To improve reusability of the interactions, it is important to program object interactions generically. We present two tools that facilitate programming of object interactions. StructureBuilder, a commercial tool, achieves genericity with respect to data structure implementations for collections, following ideas fro...

A crucial aspect of the architecture of a software system is its decomposition into components and the specification of component interactions. In this paper we use an enhanced variant of Extended Event Traces [SHB96] as a graphical technique for the description of such component interactions. It allows us to define interaction patterns that occur frequently within an architecture, in the form ...

UML (OMG, 2011) is considered as a contemporary standard in information systems development. Being a graphical modeling language it offers a family of diagrams that may be used for specification and designing of information systems. Sequence diagrams, being a part of the family, are very often used to specify functional requirements of the developed systems and are typically associated with the...

This work is conducted to obtain mechanical properties of microtubule. For this aim, interaction energy in alpha-beta, beta-alpha, alpha-alpha, and beta-beta dimers was calculated using the molecular dynamic simulation. Force-distance diagrams for these dimers were obtained using the relation between potential energy and force. Afterwards, instead of each tubulin, one sphere with 55 KDa weight ...

It is difficult to construct correct models for distributed large-scale service-oriented applications. Typically, the behavior of such an application emerges from the interaction and collaboration of multiple components/services. On the other hand, each component, in general, takes part in multiple scenarios. Consequently, not only components, but also their interaction protocols are important ...

Two tools are described that help designers visualize the structure of a system in the requirements phase of a project. First, a matrix is constructed that represents the tendency of components to interact. The matrix is derived from sequence diagrams, which in turn are based on textual scenarios. This interaction matrix is transformed into a structure plot of the system, showing a graph of the...

The UML suggests the employment of use cases for capturing the requirements and for specifying the interaction between the users and the system being modeled. Use cases are easily understood by users since they are essentially textual descriptions, but lack the precision and the conciseness accomplished by the other diagrammatic tools of UML. Besides, there is no systematic method that helps th...

Sequence diagrams depict the interaction between entities as a sequence of messages arranged in a temporal order. However, they lack a formal execution semantics: the Unified Modeling Language (UML) specification opts to use natural language to describe fundamental concepts such as interaction operators that alter the behaviour of a fragment. Communicating Sequential Processes (CSP) is a proces...