Wyniki wyszukiwania - BazTech

1

Accelerating molecular dynamics computing using iteration space slicing

Palkowski M.

Journal of Applied Computer Science

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2013

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Vol. 21, nr 2

85--96

EN

Molecular dynamics is an important computational tool to simulate and understand biochemical processes at the atomic level. Accurate modelling of processes such as simulation of the Newtonian equations of motion requires a large number of computation steps for systems with hundreds to millions of particles. In this paper, we present an approach to accelerate molecular dynamics simulations by means of automatic program loop parallelization. To parallelize code of applications, we have used the Iteration Space Slicing framework. The scope of the applicability of the approach is illustrated using the Gromacs package. Results of a performance analysis for parallelized loops executed on a multi-core computer are presented. The future work is discussed.

2

Finite state automata built on DNA

Nowak K., Plucienniczak A.

Biocybernetics and Biomedical Engineering

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2008

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Vol. 28, no. 4

3-19

EN

This paper describes a non-deterministic finite-state automaton based on DNA strands. The automaton uses massive parallel processing offered by molecular approach for computation and exhibits a number of advantages over traditional electronic implementations. This device is used to analyze DNA molecules, whether they are described by specified regular expression. Presented ideas are confirmed by experiment performed in a genetic engineering laboratory.

3

A theoretical model of the Shapiro finite state automaton built on DNA

Krasiński T., Sakowski S.

Theoretical and Applied Informatics

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2006

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Vol. 18, nr 3

161-174

EN

In the paper a theoretical model (in the form of a splicing system) of a DNA computing machine, constructed in Weizmann Institute of Science by Benenson, Adar, Paz-Elizur, Livneh and Shapiro [4] is given. This splicing system exactly reflects the action of the DNA computer. We describe in detail finite state automaton built on DNA and give its scheme of computation.

PL

W obecnie prowadzonych pracach nad nanosystemami informatyki bada się możliwość wykorzystania DNA do kodowania i przetwarzania informacji. W artykule opracowany jest teoretyczny model (w postaci systemu splatania „splicing system") DNA komputera skonstruowanego w Instytucie Weizmanna przez zespół: Benenson, Adar, Paz-Elizur, Livneh i Shapiro. Model ten dokładnie odzwierciedla działanie tego DNA komputera. Omówiono działanie automatu skończonego opartego na DNA oraz podano jego schemat ideowy działania.

4

Searching DNA decision trees using quantum dots detection

Mulawka J.J.

Prace Naukowe Politechniki Warszawskiej. Elektronika

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2006

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z. 156

281-290

EN

Concept of self-assembly of DNA molecules may be utilized to implement different algorithms of computing. In particular, this methodology is useful in artificial intelligence because it operates on symbols. As has been shown by the author [7] DNA computing is suitable for searching the decision tree which is encoded by DNA molecules. Thus, the algorithms of artificial intelligence can be performed by this technique. In the contribution we demonstrate that by proper encoding and manipulating with DNA molecules it is possible to implement reasoning procedure by searching the decision tree. The method uses standard genetic engineering operations like hybridization, ligation, and purification. Quantum dot technique is applied to speed up detection of the final output eliminating the slow operation of electrophoresis. The approach presented is very simple and fast because the technique used allows an enormous number of molecules to be labeled, reduces instrument tie-up and improves analysis throughout the process.

5

Non-deterministic finite state automata built on DNA

Nowak R., Płucienniczak A.

Prace Naukowe Politechniki Warszawskiej. Elektronika

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2006

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z. 156

301-308

EN

This paper describes non-deterministic finite-state automaton based on DNA strands. The automaton uses massive parallel processing offered by molecular approach for computation and exhibits a number of advantages over traditional electronic implementations. This device is used to analyze DNA molecules, whether they are described by specified regular expression. Presented ideas are confirmed by experiment performed in genetic engineering laboratory.

6

Molecular inference network experimental approximation

Wąsiewicz P., Płucienniczak A.

Prace Naukowe Politechniki Warszawskiej. Elektronika

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2006

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z. 156

405-412

EN

Implementation of the inference system based on DNA chains molecular computing is a new paradigm to perform calculations using nanotechnology means. This work presents a new approach to the implementation of inference engines based on DNA. It introduces the subject of inference methods designed to be used with molecular expert systems. The main part of this work includes the concept of the inference engine based on a rule tree specially customized to allow implementation using deoxyribonucleic acid chains. The approach presented allows the drawing of inferences based on a variable number of predicates using the most reliable techniques employed in standard operations of genetic engineering. In this approach cross cells are bases of multidimensional DNA structures. An experiment was conducted to confirm the capabilities of the implementation suggested. In addition, laboratory evaluation results and perspectives for the further use of the proposed architectural approach are discussed.

7

DNA and Membrane Algorithms for SAT

Manca V.

Fundamenta Informaticae

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2002

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Vol. 49, nr 1-3

205-221

EN

Some DNA algorithms proposed in the literature for propositional satisfiability (SAT) are analyzed. In the class of `extract model' the two sub-classes of `literal string' and `clause string' algorithms are compared and a new formulation of these algorithms is given in terms of membrane systems. Then, the duality between literal string and clause string formulation of SAT is expressed by means of `singleton matrices' that introduce another membrane algorithm for SAT. The analysis developed suggests the perspective of membrane systems as problem-solving agents based on molecule localization, transformation, and propagation.