Visualising and controlling the flow in biomolecular systems at and between multiple scales:from atoms to hydrodynamics at different locations in time and space

A novel framework for modelling biomolecular systems at multiple scales in space and time simultaneously is described. The atomistic molecular dynamics representation is smoothly connected with a statistical continuum hydrodynamics description. The system behaves correctly at the limits of pure molecular dynamics (hydrodynamics) and at the intermediate regimes when the atoms move partly as atomistic particles, and at the same time follow the hydrodynamic flows. The corresponding contributions are controlled by a parameter, which is defined as an arbitrary function of space and time, thus, allowing an effective separation of the atomistic 'core' and continuum 'environment'. To fill the scale gap between the atomistic and the continuum representations our special purpose computer for molecular dynamics, MDGRAPE-4, as well as GPU-based computing were used for developing the framework. These hardware developments also include interactive molecular dynamics simulations that allow intervention of the modelling through force-feedback devices.

Intelligent System for Computer Aided Assembly Process Planning

This paper presents the concepts of the intelligent system for aiding of the module assembly technology. The first part of this paper presents a project of intelligent support system for computer aided assembly process planning. The second part includes a coincidence description of the chosen aspects of implementation of this intelligent system using technologies of artificial intelligence (artificial neural networks, fuzzy logic, expert systems and genetic algorithms).

Hardware Implementations of Video Watermarking

Various digital watermarking (WM) techniques for still imaging have been studied in the last several years. Recently, many new WM schemes have been proposed for other types of digital multimedia data, such as text, audio and video. This paper presents a brief overview of existing digital video WM. We classify WM techniques and discuss the properties of video WM. Since each WM application has its own specific requirements, WM design must take the intended application into consideration. Video WM applications are also discussed in the paper. The features of video WM implementations in software and hardware and their differences are presented through the description of four examples of existing work.

Ontology-Based Model of Representation of Knowledge about Language Mappings

The paper presents a short review of some systems for program transformations performed on the basis of the internal intermediate representations of these programs. Many systems try to support several languages of representation of the source texts of programs and solve the task of their translation into the internal representation. This task is still a challenge as it is effort-consuming. To reduce the effort, different systems of translator construction, ready compilers with ready grammars of outside designers are used. Though this approach saves the effort, it has its drawbacks and constraints. The paper presents the general idea of using the mapping approach to solve the task within the framework of program transformations and overcome the disadvantages of the existing systems. The paper demonstrates a fragment of the ontology model of high-level languages mappings onto the single representation and gives the example of how the description of (a fragment) a particular mapping is represented in accordance with the ontology model.

Computer Support of Semantic Text Analysis of a Technical Specification on Designing Software

The given work is devoted to development of the computer-aided system of semantic text analysis of a technical specification. The purpose of this work is to increase efficiency of software engineering based on automation of semantic text analysis of a technical specification. In work it is offered and investigated a technique of the text analysis of a technical specification is submitted, the expanded fuzzy attribute grammar of a technical specification, intended for formalization of limited Russian language is constructed with the purpose of analysis of offers of text of a technical specification, style features of the technical specification as class of documents are considered, recommendations on preparation of text of a technical specification for the automated processing are formulated. The computer-aided system of semantic text analysis of a technical specification is considered. This system consist of the following subsystems: preliminary text processing, the syntactic and semantic analysis and construction of software models, storage of documents and interface.

Tempura Reengineering

Interval Temporal Logic provides time-dependant formal description of hardware and software. Such formalism is needed for description of behaviors of the middleware of AOmLE project, depending on different scenarios of operation. In order to use ITL, we need an interpreter. Tempura provides executable ITL framework, written in C language. We cannot use Tempura as is, because AOmLE is developed entirely in Java. For this reason we need Java version of Tempura. This paper describes our plan for reengineering of CTempura and creating Java version if the ITL interpreter.

Two-Language, Two-Paradigm Introductory Computing Curriculum Model and its Implementation

This paper analyzes difficulties with the introduction of object-oriented concepts in introductory computing education and then proposes a two-language, two-paradigm curriculum model that alleviates such difficulties. Our two-language, two-paradigm curriculum model begins with teaching imperative programming using Python programming language, continues with teaching object-oriented computing using Java, and concludes with teaching object-oriented data structures with Java.

A Language for Compositional Programming: A Rationale and Design

Бойко Бл. Банчев - Представена е обосновка и описание на език за програмиране в композиционен стил за опитни и учебни цели. Под “композиционен” имаме предвид функционален стил на програмиране, при който пресмятането е йерархия от композиции и прилагания на функции. Един от данновите типове на езика е този на геометричните фигури, които могат да бъдат получавани чрез прости правила за съотнасяне и така също образуват йерархични композиции. Езикът е силно повлиян от GeomLab, но по редица свойства се различава от него значително. Статията разглежда основните черти на езика; подробното му описание и фигурноконструктивните му възможности ще бъдат представени в съпътстваща публикация.

CloudMPL:a domain specific language for describing management policies for an autonomic cloud infrastructure

To benefit from the advantages that Cloud Computing brings to the IT industry, management policies must be implemented as a part of the operation of the Cloud. Among others, for example, the specification of policies can be used for the management of energy to reduce the cost of running the IT system or also for security policies while handling privacy issues of users. As cloud platforms are large, manual enforcement of policies is not scalable. Hence, autonomic approaches for management policies have recently received a considerable attention. These approaches allow specification of rules that are executed via rule-engines. The process of rules creation starts by the interpretation of the policies drafted by high-rank managers. Then, technical IT staff translate such policies to operational activities to implement them. Such process can start from a textual declarative description and after numerous steps terminates in a set of rules to be executed on a rule engine. To simplify the steps and to bridge the considerable gap between the declarative policies and executable rules, we propose a domain-specific language called CloudMPL. We also design a method of automated transformation of the rules captured in CloudMPL to the popular rule-engine Drools. As the policies are changed over time, code generation will reduce the time required for the implementation of the policies. In addition, using a declarative language for writing the specifications is expected to make the authoring of rules easier. We demonstrate the use of the CloudMPL language into a running example extracted from a management energy consumption case study.

ASIC microcontroller design of a radiation monitoring system using VHDL modeling and FPGA implementation

Three new technologies have been brought together to develop a miniaturized radiation monitoring system. The research involved (1) Investigation a new HgI$\sb2$ detector. (2) VHDL modeling. (3) FPGA implementation. (4) In-circuit Verification. The packages used included an EG&G's crystal(HgI$\sb2$) manufactured at zero gravity, the Viewlogic's VHDL and Synthesis, Xilinx's technology library, its FPGA implementation tool, and a high density device (XC4003A). The results show: (1) Reduced cycle-time between Design and Hardware implementation; (2) Unlimited Re-design and implementation using the static RAM technology; (3) Customer based design, verification, and system construction; (4) Well suited for intelligent systems. These advantages excelled conventional chip design technologies and methods in easiness, short cycle time, and price in medium sized VLSI applications. It is also expected that the density of these devices will improve radically in the near future. ^

Multipurpose portable system for environmental, industrial, and medical applications

This dissertation is about the research carried on developing an MPS (Multipurpose Portable System) which consists of an instrument and many accessories. The instrument is portable, hand-held, and rechargeable battery operated, and it measures temperature, absorbance, and concentration of samples by using optical principles. The system also performs auxiliary functions like incubation and mixing. This system can be used in environmental, industrial, and medical applications. ^ Research emphasis is on system modularity, easy configuration, accuracy of measurements, power management schemes, reliability, low cost, computer interface, and networking. The instrument can send the data to a computer for data analysis and presentation, or to a printer. ^ This dissertation includes the presentation of a full working system. This involved integration of hardware and firmware for the micro-controller in assembly language, software in C and other application modules. ^ The instrument contains the Optics, Transimpedance Amplifiers, Voltage-to-Frequency Converters, LCD display, Lamp Driver, Battery Charger, Battery Manager, Timer, Interface Port, and Micro-controller. ^ The accessories are a Printer, Data Acquisition Adapter (to transfer the measurements to a computer via the Printer Port and expand the Analog/Digital conversion capability), Car Plug Adapter, and AC Transformer. This system has been fully evaluated for fault tolerance and the schemes will also be presented. ^

Refinement methods for software architecture design using the software architecture model

Modern software systems are often large and complicated. To better understand, develop, and manage large software systems, researchers have studied software architectures that provide the top level overall structural design of software systems for the last decade. One major research focus on software architectures is formal architecture description languages, but most existing research focuses primarily on the descriptive capability and puts less emphasis on software architecture design methods and formal analysis techniques, which are necessary to develop correct software architecture design. ^ Refinement is a general approach of adding details to a software design. A formal refinement method can further ensure certain design properties. This dissertation proposes refinement methods, including a set of formal refinement patterns and complementary verification techniques, for software architecture design using Software Architecture Model (SAM), which was developed at Florida International University. First, a general guideline for software architecture design in SAM is proposed. Second, specification construction through property-preserving refinement patterns is discussed. The refinement patterns are categorized into connector refinement, component refinement and high-level Petri nets refinement. These three levels of refinement patterns are applicable to overall system interaction, architectural components, and underlying formal language, respectively. Third, verification after modeling as a complementary technique to specification refinement is discussed. Two formal verification tools, the Stanford Temporal Prover (STeP) and the Simple Promela Interpreter (SPIN), are adopted into SAM to develop the initial models. Fourth, formalization and refinement of security issues are studied. A method for security enforcement in SAM is proposed. The Role-Based Access Control model is formalized using predicate transition nets and Z notation. The patterns of enforcing access control and auditing are proposed. Finally, modeling and refining a life insurance system is used to demonstrate how to apply the refinement patterns for software architecture design using SAM and how to integrate the access control model. ^ The results of this dissertation demonstrate that a refinement method is an effective way to develop a high assurance system. The method developed in this dissertation extends existing work on modeling software architectures using SAM and makes SAM a more usable and valuable formal tool for software architecture design. ^

A framework for transforming, analyzing, and realizing software designs in unified modeling language

Unified Modeling Language (UML) is the most comprehensive and widely accepted object-oriented modeling language due to its multi-paradigm modeling capabilities and easy to use graphical notations, with strong international organizational support and industrial production quality tool support. However, there is a lack of precise definition of the semantics of individual UML notations as well as the relationships among multiple UML models, which often introduces incomplete and inconsistent problems for software designs in UML, especially for complex systems. Furthermore, there is a lack of methodologies to ensure a correct implementation from a given UML design. The purpose of this investigation is to verify and validate software designs in UML, and to provide dependability assurance for the realization of a UML design.^ In my research, an approach is proposed to transform UML diagrams into a semantic domain, which is a formal component-based framework. The framework I proposed consists of components and interactions through message passing, which are modeled by two-layer algebraic high-level nets and transformation rules respectively. In the transformation approach, class diagrams, state machine diagrams and activity diagrams are transformed into component models, and transformation rules are extracted from interaction diagrams. By applying transformation rules to component models, a (sub)system model of one or more scenarios can be constructed. Various techniques such as model checking, Petri net analysis techniques can be adopted to check if UML designs are complete or consistent. A new component called property parser was developed and merged into the tool SAM Parser, which realize (sub)system models automatically. The property parser generates and weaves runtime monitoring code into system implementations automatically for dependability assurance. The framework in the investigation is creative and flexible since it not only can be explored to verify and validate UML designs, but also provides an approach to build models for various scenarios. As a result of my research, several kinds of previous ignored behavioral inconsistencies can be detected.^

Signal processing of physiological signals for automated assessment of stress in computer users

The need to provide computers with the ability to distinguish the affective state of their users is a major requirement for the practical implementation of affective computing concepts. This dissertation proposes the application of signal processing methods on physiological signals to extract from them features that can be processed by learning pattern recognition systems to provide cues about a person's affective state. In particular, combining physiological information sensed from a user's left hand in a non-invasive way with the pupil diameter information from an eye-tracking system may provide a computer with an awareness of its user's affective responses in the course of human-computer interactions. In this study an integrated hardware-software setup was developed to achieve automatic assessment of the affective status of a computer user. A computer-based "Paced Stroop Test" was designed as a stimulus to elicit emotional stress in the subject during the experiment. Four signals: the Galvanic Skin Response (GSR), the Blood Volume Pulse (BVP), the Skin Temperature (ST) and the Pupil Diameter (PD), were monitored and analyzed to differentiate affective states in the user. Several signal processing techniques were applied on the collected signals to extract their most relevant features. These features were analyzed with learning classification systems, to accomplish the affective state identification. Three learning algorithms: Naïve Bayes, Decision Tree and Support Vector Machine were applied to this identification process and their levels of classification accuracy were compared. The results achieved indicate that the physiological signals monitored do, in fact, have a strong correlation with the changes in the emotional states of the experimental subjects. These results also revealed that the inclusion of pupil diameter information significantly improved the performance of the emotion recognition system. ^

Design and implementation of a multisite data repository for pediatric epilepsy

This dissertation established a software-hardware integrated design for a multisite data repository in pediatric epilepsy. A total of 16 institutions formed a consortium for this web-based application. This innovative fully operational web application allows users to upload and retrieve information through a unique human-computer graphical interface that is remotely accessible to all users of the consortium. A solution based on a Linux platform with My-SQL and Personal Home Page scripts (PHP) has been selected. Research was conducted to evaluate mechanisms to electronically transfer diverse datasets from different hospitals and collect the clinical data in concert with their related functional magnetic resonance imaging (fMRI). What was unique in the approach considered is that all pertinent clinical information about patients is synthesized with input from clinical experts into 4 different forms, which were: Clinical, fMRI scoring, Image information, and Neuropsychological data entry forms. A first contribution of this dissertation was in proposing an integrated processing platform that was site and scanner independent in order to uniformly process the varied fMRI datasets and to generate comparative brain activation patterns. The data collection from the consortium complied with the IRB requirements and provides all the safeguards for security and confidentiality requirements. An 1-MR1-based software library was used to perform data processing and statistical analysis to obtain the brain activation maps. Lateralization Index (LI) of healthy control (HC) subjects in contrast to localization-related epilepsy (LRE) subjects were evaluated. Over 110 activation maps were generated, and their respective LIs were computed yielding the following groups: (a) strong right lateralization: (HC=0%, LRE=18%), (b) right lateralization: (HC=2%, LRE=10%), (c) bilateral: (HC=20%, LRE=15%), (d) left lateralization: (HC=42%, LRE=26%), e) strong left lateralization: (HC=36%, LRE=31%). Moreover, nonlinear-multidimensional decision functions were used to seek an optimal separation between typical and atypical brain activations on the basis of the demographics as well as the extent and intensity of these brain activations. The intent was not to seek the highest output measures given the inherent overlap of the data, but rather to assess which of the many dimensions were critical in the overall assessment of typical and atypical language activations with the freedom to select any number of dimensions and impose any degree of complexity in the nonlinearity of the decision space.