Search results for: Ryszard Matysiak

Authors: Ryszard Matysiak, Grzegorz Kamieniarz

Abstract:

The deterministic quantum transfer-matrix (QTM) technique and its mathematical background are presented. This important tool in computational physics can be applied to a class of the real physical low-dimensional magnetic systems described by the Heisenberg hamiltonian which includes the macroscopic molecularbased spin chains, small size magnetic clusters embedded in some supramolecules and other interesting compounds. Using QTM, the spin degrees of freedom are accurately taken into account, yielding the thermodynamical functions at finite temperatures. In order to test the application for the susceptibility calculations to run in the parallel environment, the speed-up and efficiency of parallelization are analyzed on our platform SGI Origin 3800 with p = 128 processor units. Using Message Parallel Interface (MPI) system libraries we find the efficiency of the code of 94% for p = 128 that makes our application highly scalable.

Keywords: Deterministic simulations, low-dimensional magnets, modeling of complex systems, parallelization.

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Authors: Grzegorz Ulacha, Ryszard Stasiński

Abstract:

In the paper an effective context based lossless coding technique is presented. Three principal and few auxiliary contexts are defined. The predictor adaptation technique is an improved CoBALP algorithm, denoted CoBALP+. Cumulated predictor error combining 8 bias estimators is calculated. It is shown experimentally that indeed, the new technique is time-effective while it outperforms the well known methods having reasonable time complexity, and is inferior only to extremely computationally complex ones.

Keywords: Adaptive prediction, context coding, image losslesscoding, prediction error bias correction.

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Authors: Abdellali Kelil, Shengrui Wang, Ryszard Brzezinski

Abstract:

The literature reports a large number of approaches for measuring the similarity between protein sequences. Most of these approaches estimate this similarity using alignment-based techniques that do not necessarily yield biologically plausible results, for two reasons. First, for the case of non-alignable (i.e., not yet definitively aligned and biologically approved) sequences such as multi-domain, circular permutation and tandem repeat protein sequences, alignment-based approaches do not succeed in producing biologically plausible results. This is due to the nature of the alignment, which is based on the matching of subsequences in equivalent positions, while non-alignable proteins often have similar and conserved domains in non-equivalent positions. Second, the alignment-based approaches lead to similarity measures that depend heavily on the parameters set by the user for the alignment (e.g., gap penalties and substitution matrices). For easily alignable protein sequences, it's possible to supply a suitable combination of input parameters that allows such an approach to yield biologically plausible results. However, for difficult-to-align protein sequences, supplying different combinations of input parameters yields different results. Such variable results create ambiguities and complicate the similarity measurement task. To overcome these drawbacks, this paper describes a novel and effective approach for measuring the similarity between protein sequences, called SAF for Substitution and Alignment Free. Without resorting either to the alignment of protein sequences or to substitution relations between amino acids, SAF is able to efficiently detect the significant subsequences that best represent the intrinsic properties of protein sequences, those underlying the chronological dependencies of structural features and biochemical activities of protein sequences. Moreover, by using a new efficient subsequence matching scheme, SAF more efficiently handles protein sequences that contain similar structural features with significant meaning in chronologically non-equivalent positions. To show the effectiveness of SAF, extensive experiments were performed on protein datasets from different databases, and the results were compared with those obtained by several mainstream algorithms.

Keywords: Protein, Similarity, Substitution, Alignment.

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