Branko Jeren

PSAIA – Protein Structure and Interaction Analyzer

BackgroundPSAIA (Protein Structure and Interaction Analyzer) was developed to compute geometric parameters for large sets of protein structures in order to predict and investigate protein-protein interaction sites.ResultsIn addition to most relevant established algorithms, PSAIA offers a new method PIADA (Protein Interaction Atom Distance Algorithm) for the determination of residue interaction pairs. We found that PIADA produced more satisfactory results than comparable algorithms implemented in PSAIA.Particular advantages of PSAIA include its capacity to combine different methods to detect the locations and types of interactions between residues and its ability, without any further automation steps, to handle large numbers of protein structures and complexes. Generally, the integration of a variety of methods enables PSAIA to offer easier automation of analysis and greater reliability of results.PSAIA can be used either via a graphical user interface or from the command-line. Results are generated in either tabular or XML format.ConclusionIn a straightforward fashion and for large sets of protein structures, PSAIA enables the calculation of protein geometric parameters and the determination of location and type for protein-protein interaction sites. XML formatted output enables easy conversion of results to various formats suitable for statistic analysis.Results from smaller data sets demonstrated the influence of geometry on protein interaction sites. Comprehensive analysis of properties of large data sets lead to new information useful in the prediction of protein-protein interaction sites.

Multiprocessor implementation of digital filtering algorithms using a parallel block processing method

An efficient real-time implementation of digital filtering algorithms using a multiprocessor system in a ring network is investigated. This method is based on a parallel block processing approach, where a continuously supplied input data is divided into blocks, and the blocks are processed concurrently by being assigned to each processor in the system. This approach requires only a simple interconnection network and reduces significantly the number of communications among the processors, making the system easily expandable and highly efficient. In addition, various digital signal processing algorithms can be implemented on the same multiprocessor system. The data dependency of the blocks to be processed concurrently brings on dependency problems between the processors. A systematic scheduling method has been developed by using a precedence graph for the analysis of the dependency relation. Methods for solving the dependency problems between the processors are also investigated. Implementation procedures and results for FIR, recursive, and adaptive filtering algorithms are illustrated. >

Clock frequency synchronisation in OFDM system for power line communications

Orthogonal frequency division multiplexing (OFDM) divides the available spectrum into several narrowband subchannels. To obtain a high spectral efficiency, the frequency responses of the subchannels are overlapping and orthogonal. An OFDM system can suffer from two types of frequency errors-a carrier frequency offset and a master clock frequency offset. Both types of frequency error degrade the performance of the OFDM receiver by loosing orthogonality between the subcarriers and introducing interchannel interference. Since the power line communications are performed in the baseband, only the second type of frequency error can occur. This paper analyses the effect of master clock frequency offset and suggests a method for its estimation based on the pilot signal. Furthermore, a method for frequency error correction is presented.

Development of Pyramidia: An Integrative E-Learning Multimedia Tool

The software package described in this paper, Pyramidia, combines two strong elements into one lecturing system. The first is the simple addition of content and interactivity to existing PowerPoint presentations, and the second is video capture of a lecture. These features provide obvious benefits for both sides of the lecturing process: the lecturers and the students. Students can re-experience lectures at anytime, anywhere and at their own pace. Lecturers can add interactivity to their lectures without worrying about learning complex new software. Pyramidia is a descendant of previous software developments and research on ICT usage in education, and has been used and tested throughout a few semesters of lectures for several courses. Although there are many solutions, both commercial and academic, available to potential users, Pyramidia is unique for its. NET framework programming base.

The Structure of the Pyramidia E-learning Tool - the Programmer's Point of View

Pyramidia is a straightforward and easy-to-use software tool developed to record lectures. It records the video and audio of the lecturer and his activities, everything that happens on the screen of the lecturers computer and all audio output from the computer. In addition to standard notes, the tool allows the author to add structured content to the PowerPoint presentation: examples, external links and quizzes. Pyramidia enables the lecturer to rapidly record the lecture, package PowerPoint presentations and the additional information they contains and distribute the recording to students with ease. This paper describes the developing process of Pyramidia, its subsystems and their interrelation.

Practical examples used information and communication technologies in study of "Signals and Systems"

The study of Signals and Systems is one of the basic subjects of study at the Faculty of Electrical Engineering and Computing. For a better understanding of this subject, it is necessary for the students to connect theory with the practical examples. The introduction of new technologies discloses great opportunities for a high-quality organization of the study. The purpose of this paper is to shows in detail two examples where theory is linked to practice in order to achieve a better education. The examples have been chosen according to the criteria of proximity, comprehension and actuality. We assume that the majority of students taking Signals and Systems have a basic knowledge of electronics and an elementary everyday understanding of economics. This paper therefore portrays a simple electronic amplifier as the first example and a game based on a simplified economic interaction as the second example of the application of the theory of signals and systems. This is going to show how to bring the theory closer to the students through practical examples by means of ICT.

EMERGENCE OF POWER-LAW AND TWO-PHASE BEHAVIOR IN FINANCIAL MARKET FLUCTUATIONS

In this paper, we provide an insight into the emergence of power-law and two-phase behavior in the financial market fluctuations by defining an analytical model for time evolution of stock share prices. The defined model can exhibit bimodal behavior in the supply-demand structure of the market. Moreover, it differs from existing Ising-type models. It turns out that the constructed model is a solution of a thermodynamic limit of a Gibbs probability measure when the number of investors and the number of stock shares approaches the infinity. The energy functional of the Gibbs probability measure is derived from the Nash equilibrium of the underlying game.

Model of discrete dynamics of asset price relations based on the minimal arbitrage principle

In this paper we present a deterministic and a probabilistic model of the dynamics of the price relations for a number of assets on the market. The formalism is based on the asset space introduced in a theory by Illinski. We derive, from an action functional for the system of price relations in that space, the corresponding difference equations, which constitute the deterministic description. Furthermore, we obtain the probability density function of the probabilistic model of market dynamics from the same action functional. The deterministic solution corresponds to a geometric sequence for the interest, whereas the derived probability density describes the probability of the next value of the price relations in dependence on their prior value. The formalism is completely developed for systems (markets) with two and three assets, but exactly the same approach is applicable to the systems consisting of an arbitrary number of assets.

SPRINT: a signal processing ring network for high speed applications

The SPRINT system is a high-speed system designed to perform real-time signal processing which cannot be done on a single signal processing-chip. The advantages of using a ring network are given, and the major attributes of the system are highlighted. Attention is given to the system architecture and the basic system operation. The details of the hardware are included in the description of the system architecture. The software development environment shows how both the system software and application software is written. Finally, several digital filter examples demonstrate the usefulness of using such a ring network of signal-processing nodes.<<ETX>>

Question based user authentication in commercial environments

The aim of this paper is to analyze question based user authentication methods with regard to their potential use in commercial environments and the limitations they impose. We provide an overview of current work related to question based authentication and describe the difference between static and dynamic questions in user authentication. Additionally, we give an introduction into some common practices used in user authentication in commercial environments. Based on existing research we suggest that only dynamic questions should be used in commercial environments and propose a set of requirements a data source used for creating authentication challenges should meet. Also, we categorize the types of data that can be leveraged for authenticating users.