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- A.Herman, Computational Nanotechnology of Silicon Structures. A Challenge for Beyond 2000 - abstract
- P.Arlukowicz, E.Biernat, J.Ciarkowski, C.Czaplewski, M.Groth, R.Kazmierkiewicz, A.Liwo, M.Nowacka, S.Oldziej, S.Rodziewicz, Molecular Simulations with High Performance Computers - abstract
- A.Witkowska, R.J.Barczynski and A.Rybicka, Structural Modelling of Amorphous Vanadium Pentoxide - abstract
- J.Rybicki, G.Mancini, Numerical Studies in non-Ohmic Hopping Conduction in Random Systems - abstract
- L.Kulak and P.Bojarski, Forward and Reverse Exctation Energy Transport Monitored by Monte-Carlo Simulations - abstract
- W. Alda, W. Dzwinel, J. Kitowski, J. Moscinski, New Model of Convection Based on Particle Approach - abstract
- G.Mancini, A Redundance Aware Algorithm for the Ring Perception Problem - abstract
- R.Laskowski, J.Rybicki and M.Chybicki, Application of Tesselation Techniques in the Structural Analysis of MD-Simulated Materials - abstract
- M. Rewienski, Implementation of the Parallel Arnoldi Method in the IBM SP2 Distributed Memory System - abstract
- A.Herman, Computational Nanotechnology of Silicon
Structures. A Challenge for Beyond 2000
- Devices enormously smaller than before will remodel engineering, chemistry, medicine and computer technology. How can we understand machines that are so small? In general it is expected that computational nanotechnology should give the link between today nanometer scale science and technology and future molecular nanotechnology. I feel that the accurate modelling of nanosystems is one of the big challenges for our times. I discuss briefly some of the subject under investigation in the Technical University of Gdansk and proposals for future research. I mention also some of difficulties that nanotechnology has faced to accomplish the research projects and to consolidate in Gdansk.
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P.Arlukowicz, E.Biernat, J.Ciarkowski, C.Czaplewski,
M.Groth, R.Kazmierkiewicz, A.Liwo, M.Nowacka, S.Oldziej, S.Rodziewicz,
Molecular Simulations with High Performance Computers
- In this article we present the work carried out in our group on various fields of theoretical biochemistry. Our main fields of research are as follows: i) design of an algorithm for de novo prediction of protein structure from amino-acid sequence using energetic criteria, ii) theoretical modeling of the structure and dynamics of neurohypophyseal-hormone receptors, iii) quantum-mechanical investigation of reactions in organic chemistry and biochemistry, iv) theoretical conformational analysis of small peptides using experimental information.
- The performance of different machines, depending on the kind of calculations with special focus on the exploitation of parallelism as well as the applicability and performance of various commercial, free, and our home-made software (AMBER, GAUSSIAN, ECEPPAK, GAMESS, SYBYL, Biosym) available at TASK and the importance of graphical processing of the data are discussed.
- A.Witkowska, R.J.Barczynski and A.Rybicka, Structural
Modelling of Amorphous Vanadium Pentoxide
- Amorphous vanadium pentoxide (*-V2O5) is a component of many technically important semiconducting glasses. The transport properties are related directly to the material structure, and so in order to understand the transport mechanism the atom arrangement should be known. Much experimental work has been done to determine the short-range order in *-V2O5, but in view of contradicting conclusions the structure of the glass is still an open question. Thus, computer simulation techniques have been applied to get some insight into the structure of *-V2O5. In particular, the classical molecular dynamics (MD) simulations have been performed, using the original parametrisation of the interatomic interactions. Our effective interaction potential is derived from ab initio calculations of small hydrogen-saturated clusters VOnHn. The results of the MD simulations are discussed and compared to the available experimental data.
- J.Rybicki, G.Mancini, Numerical Studies in non-Ohmic
Hopping Conduction in Random Systems
- Phonon-assisted hopping of carriers between spatially distinct locations is the basic transport mechanisms in low-mobility solids (weakly doped or strongly compensated semiconductors, amorphous solids, glasses, organic solids, transition metal oxides, superionic conductors). In the present paper we consider the electron transport close to the Fermi level. The calculation of the current-field characteristics in random hopping systems for arbitrary strength of the electric field is a rather complicated task. It involves simplified methods such as percolation theory or effective medium approximation (EMA), or requires a purely numerical treatment. A short review of our recent work within the letter approach is presented below. In particular, we discuss the dependence of the current-field, and differential conductivity-field characteristics on: 1) the amount of the off-diagonal disorder; 2) the system dilution; 3) the degree of the macroscopic-scale spatial non-uniformity of the hopping centre density.
- L.Kulak and P.Bojarski, Forward and Reverse Exctation
Energy Transport Monitored by Monte-Carlo Simulations
- A review of the Monte Carlo studies of forward and reverse incoherent transport and trapping of electronic excitations (RNEET) in two-component disordered system is presented. The donor fluorescence decay function, relative quantum yield and emission anisotropy are obtained by computer simulation and compared with theoretical and experimental results.
- W. Alda, W. Dzwinel, J. Kitowski, J. Moscinski, New
Model of Convection Based on Particle Approach
- A new model for thermal convection simulations using molecular dynamics (MD) approach is reported briefly. Preliminary resultsare presented. Development of the method is discussed shortly.
- G.Mancini, A Redundance Aware Algorithm for the
Ring Perception Problem
- Following the guidelines proposed by R.Balducci and R.Pearlman for an efficient exact solution of the Ring Perception Problem, a new approach based on 'pre-filtering' technique is introduced to perceive rings in structures represented by simple graphs in which each node has degree d>=2. The resulting algorithm has proved to reduce both resources allocation and redundant information processing when dealing with chemical cases. Actual computing times have constsntly shown a conspicious reduction with respect to methods using hash-tables to treat redundant informations. Farthermore no user intervention to 'tune' effectivenes is required (e.g. hash-table dimensioning).
- R.Laskowski, J.Rybicki and M.Chybicki, Application
of Tesselation Techniques in the Structural Analysis of MD-Simulated Materials
- A tesselation technique is applied to the structural analysis of MD-simulated materials. The main point of the application is a suitable manipulation of the contracted simplices network. Alghorithms for contraction of the simplices network, as well as for the radical tesselation are presented. The contraction algorithm utilizes the local arrangement recognition technique. Exemplary application of the technique to nickel samples is described.
- M. Rewienski, Implementation of the Parallel
Arnoldi Method in the IBM SP2 Distributed Memory System
- The following article discusses the Implicitly Restarted Arnoldi Method used for solving large sparse eigenvalue problems. It presents the parallel implementation of this algorithm for a distributed memory architecture developed by Maschhoff and Sorensen and included in P\_ARPACK library. The article gives results of performance tests of the P\_ARPACK subroutines in the IBM Scalable POWER2 (SP2) parallel system installation at the Academic Computer Centre TASK in Gdansk and describes some technical problems concerning use of message-passing libraries (particularly the Message Passing Interface (MPI)), as well as communication subsystems available in IBM SP2 with the discussed software package.
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From the History of Science and Technology in Ancient Gdansk