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Search results for: adaptive step of computation
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Application of Multiplexed Replica Exchange Molecular Dynamics to the UNRES Force Field: Tests with α and α+β Proteins
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Implementation of a Serial Replica Exchange Method in a Physics-Based United-Residue (UNRES) Force Field
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Improvement of the Treatment of Loop Structures in the UNRES Force Field by Inclusion of Coupling between Backbone- and Side-Chain-Local Conformational States
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Implementation of Molecular Dynamics and Its Extensions with the Coarse-Grained UNRES Force Field on Massively Parallel Systems: Toward Millisecond-Scale Simulations of Protein Structure, Dynamics, and Thermodynamics
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Simulation of the Opening and Closing of Hsp70 Chaperones by Coarse-Grained Molecular Dynamics
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Replica Exchange and Multicanonical Algorithms with the Coarse-Grained United-Residue (UNRES) Force Field
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Workflow applications in GridLab and PROGRESS projects
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Flexibility and user‐friendliness of Grid portals: the PROGRESS approach
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Plugging grids into computing portals: the PROGRESS grid resource broker plug‐in mechanism
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Anharmonic Infrared Spectroscopy through the Fourier Transform of Time Correlation Function Formalism in ONETEP
PublicationDensity functional theory molecular dynamics (DFT-MD) provides an efficient framework for accurately computing several types of spectra. The major benefit of DFTMD approaches lies in the ability to naturally take into account the effects of temperature and anharmonicity, without having to introduce any ad hoc or a posteriori corrections. Consequently, computational spectroscopy based on DFT-MD approaches plays a pivotal role in...
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Keep It Flexible: Driving Macromolecular Rotary Motions in Atomistic Simulations with GROMACS
PublicationWe describe a versatile method to enforce the rotation of subsets of atoms, e.g., a protein subunit, in molecular dynamics (MD) simulations. In particular, we introduce a “flexible axis” technique that allows realistic flexible adaptions of both the rotary subunit as well as the local rotation axis during the simulation. A variety of useful rotation potentials were implemented for the GROMACS 4.5 MD package. Application to the...
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An Assessment of RASSCF and TDDFT Energies and Gradients on an Organic Donor−Acceptor Dye Assisted by Resonance Raman Spectroscopy
PublicationThe excitation energies and gradients in the ground and the first excited state of a novel donor−(π- bridge)−acceptor 4-methoxy-1,3-thiazole-based chromophore were investigated by means of MS-RASPT2/RASSCF and TDDFT in solution. Within both methods, the excitation energies strongly depend on the employed equilibrium structures, whose differences can be rationalized in terms of bond length alternation indexes. It is shown that functionals with...
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Electronically Excited States in Solution via a Smooth Dielectric Model Combined with Equation-of-Motion Coupled Cluster Theory
PublicationWe present a method for computing excitation energies for molecules in solvent, based on the combination of a minimal parameter implicit solvent model and the equation-of-motion coupled-cluster singles and doubles method (EOM-CCSD). In this method, the solvent medium is represented by a smoothly varying dielectric function, constructed directly from the quantum mechanical electronic density using only two tunable parameters. The...
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Performance of the AMOEBA Water Model in the Vicinity of QM Solutes: A Diagnosis Using Energy Decomposition Analysis
PublicationThe importance of incorporating solvent polarization effects into the modeling of solvation processes has been well-recognized, and therefore a new generation of hybrid quantum mechanics/molecular mechanics (QM/MM) approaches that accounts for this effect is desirable. We present a fully self-consistent, mutually polarizable QM/MM scheme using the AMOEBA force field, in which the total energy of the system is variationally minimized...
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Theoretical Assessment of Excited State Gradients and Resonance Raman Intensities for the Azobenzene Molecule
PublicationThe ground state geometries and vibrational frequencies as well as the excitation energies and excited state gradients of the S 1(nπ*) and S 2(ππ * ) states of trans - and cis -azobenzene are investigated by several DFT methods, namely B3LYP, PBE, M06-2X, CAM-B3LYP, and ω B97X. Excited state properties and in particular gradients are also assessed using the wave function based methods EOM-CCSD and RASPT2/RASSCF. Comparison with...
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A multithreaded CUDA and OpenMP based power‐aware programming framework for multi‐node GPU systems
PublicationIn the paper, we have proposed a framework that allows programming a parallel application for a multi-node system, with one or more GPUs per node, using an OpenMP+extended CUDA API. OpenMP is used for launching threads responsible for management of particular GPUs and extended CUDA calls allow to manage CUDA objects, data and launch kernels. The framework hides inter-node MPI communication from the programmer who can benefit from...
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Dominant Pathways of Adenosyl Radical-Induced DNA Damage Revealed by QM/MM Metadynamics
PublicationBrominated nucleobases sensitize double stranded DNA to hydrated electrons, one of the dominant genotoxic species produced in hypoxic cancer cells during radiotherapy. Such radiosensitizers can therefore be administered locally to enhance treatment efficiency within the solid tumor while protecting the neighboring tissue. When a solvated electron attaches to 8-bromoadenosine, a potential sensitizer, the dissociation of bromide...
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Numerical and experimental investigation of guided ultrasonic wave propagation in non-uniform plates with structural phase variations
PublicationThe article presents the results of numerical and experimental investigations of guided wave propagation in aluminum plates with variable thickness. The shapes of plate surfaces have been specially designed and manufactured using a CNC milling machine. The shapes of the plates were defined by sinusoidal functions varying in phase shift, which forced the changes in thickness variability alongside the propagation path. The main aim...
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Multi-objective design optimization of antenna structures using sequential domain patching with automated patch size deter-mination
PublicationIn this paper, a simple yet efficient and reliable technique for fully automated multi-objective design optimization of antenna structures using sequential domain patching (SDP) is discussed. The optimization procedure according to SDP is a two-step process: (i) obtaining the initial set of Pareto-optimal designs representing the best possible trade-offs between considered conflicting objectives, and (ii) Pareto set refinement...
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Expert systems in quality control of manufacturing processes
PublicationThe paper deals with quality control in conditions of computer integrated manufacturing (CIM). It shows that quality of material stream items have to be analyzed on every stage of manufacturing process. Collecting and analyzing quantity of data with usage of expert systems make it possible to create a system for coordination of cell's work. The system contains error recovery algorithm and adaptive control subsystem based on fuzzy...
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Global Surrogate Modeling by Neural Network-Based Model Uncertainty
PublicationThis work proposes a novel adaptive global surrogate modeling algorithm which uses two neural networks, one for prediction and the other for the model uncertainty. Specifically, the algorithm proceeds in cycles and adaptively enhances the neural network-based surrogate model by selecting the next sampling points guided by an auxiliary neural network approximation of the spatial error. The proposed algorithm is tested numerically...
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Auto adaptation of mobile device characteristics to various acoustic conditions
PublicationThe proposed methodology of auto adaptation of the mobile device characteristics to various acoustic conditions is presented in the paper. The first goal of this study was to determine the parameters of the acoustic path of the mobile device, for both transmitting (speaker) and receiver (microphone). Results of the measurement of characteristics of mobile devices were presented. Information about characteristics of individual parts...
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Complex Root Finding Algorithm Based on Delaunay Triangulation
PublicationA simple and flexible algorithm for finding zeros of a complex function is presented. An arbitrary-shaped search region can be considered and a very wide class of functions can be analyzed, including those containing singular points or even branch cuts. The proposed technique is based on sampling the function at nodes of a regular or a self-adaptive mesh and on the analysis of the function sign changes. As a result, a set of candidate points...
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MRAS-Based Switching Linear Feedback Strategy for Sensorless Speed Control of Induction Motor Drives
PublicationThis paper presents a newly designed switching linear feedback structure of sliding mode control (SLF-SMC) plugged with an model reference adaptive system (MRAS) based sensorless fieldoriented control (SFOC) for induction motor (IM). Indeed, the performance of the MRAS depends mainly on the operating point and the parametric variation of the IM. Hence, the sliding mode control (SMC) could be considered a good control alternative...
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A Convenient Synthesis of Monocationic 1-[(Cyclic amidino)methyl]thymines
Publication1-[(Cyclic amidino)methyl]thymines have been conveniently synthesized from thymine in a three-step procedure via 1-cyanomethyl- and 1-[(thiocarbamoyl) methyl]thymines. The above synthetic intermediates were obtained in good yields by improved methods.
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Photomonitoring of activities carried out as part of prototyping and implementation of the pilot project in the area of the "Polanki" market and its direct neighbourhood, in the Gdańsk-Oliwa district, step1; stage from July 2020 year.
Open Research DataThe data presents photomonitoring (visual documentation report in the form of photographs) of activities carried out as a part of prototyping and implementation of the pilot project in the area of the “Polanki” market and its immediate vicinity in the Gdańsk-Oliwa district documented in July 2020 year, during the 1st step of the monitoring. The monitoring...
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Photomonitoring of activities carried out as part of prototyping and implementation of the pilot project in the area of the "Polanki" market and its direct neighbourhood, in the Gdańsk-Oliwa district, step1; stage from August 2020 year.
Open Research DataThe data presents photomonitoring (visual documentation report in the form of photographs) of activities carried out as a part of prototyping and implementation of the pilot project in the area of the “Polanki” market and its immediate vicinity in the Gdańsk-Oliwa district documented in August 2020 year, during the 1st step of the monitoring. The monitoring...
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Monitoring of activities carried out as part of prototyping and implementation of the pilot project in the area of the "Polanki" market and its and its direct neighbourhood, in the Gdańsk-Oliwa district, step1; stage from October 2020 year.
Open Research DataThe data presents tabular monitoring lists (quantitative and qualitative documentation report in the form of tables) of activities carried out as part of prototyping and implementation of the pilot project in the area of the Polanki market and its immediate vicinity in the Gdańsk-Oliwa district in 2020 year - step 1, stage from July 2020. The monitoring...
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Monitoring of activities carried out as part of prototyping and implementation of the pilot project in the area of the "Polanki" market and its direct neighbourhood, in the Gdańsk-Oliwa district, step1; stage from July 2020 year.
Open Research DataThe data presents tabular monitoring lists (quantitative and qualitative documentation report in the form of tables) of activities carried out as part of prototyping and implementation of the pilot project in the area of the Polanki market and its immediate vicinity in the Gdańsk-Oliwa district in 2020 year - step 1, stage from July 2020. The monitoring...
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Monitoring of activities carried out as part of prototyping and implementation of the pilot project in the area of the "Polanki" market and its and its direct neighbourhood, in the Gdańsk-Oliwa district, step1; stage from September 2020 year.
Open Research DataThe data presents tabular monitoring lists (quantitative and qualitative documentation report in the form of tables) of activities carried out as part of prototyping and implementation of the pilot project in the area of the Polanki market and its immediate vicinity in the Gdańsk-Oliwa district in 2020 year - step 1, stage from September 2020. The monitoring...
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Monitoring of activities carried out as part of prototyping and implementation of the pilot project in the area of the "Polanki" market and its and its direct neighbourhood, in the Gdańsk-Oliwa district, step1; stage from August 2020 year.
Open Research DataThe data presents tabular monitoring lists (quantitative and qualitative documentation report in the form of tables) of activities carried out as part of prototyping and implementation of the pilot project in the area of the Polanki market and its immediate vicinity in the Gdańsk-Oliwa district in 2020 year - step 1, stage from August 2020. The monitoring...
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Photomonitoring of activities carried out as part of prototyping and implementation of the pilot project in the area of the "Polanki" market and its direct neighbourhood, in the Gdańsk-Oliwa district, step1; stage from October 2020 year.
Open Research DataThe data presents photomonitoring (visual documentation report in the form of photographs) of activities carried out as a part of prototyping and implementation of the pilot project in the area of the “Polanki” market and its immediate vicinity in the Gdańsk-Oliwa district documented in October 2020 year, during the 1st step of the monitoring. The monitoring...
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Photomonitoring of activities carried out as part of prototyping and implementation of the pilot project in the area of the "Polanki" market and its direct neighbourhood, in the Gdańsk-Oliwa district, step1; stage from September 2020 year.
Open Research DataThe data presents photomonitoring (visual documentation report in the form of photographs) of activities carried out as a part of prototyping and implementation of the pilot project in the area of the “Polanki” market and its immediate vicinity in the Gdańsk-Oliwa district documented in September 2020 year, during the 1st step of the monitoring. The...
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Ligand-Modified Boron-Doped Diamond Surface: DFT Insights into the Electronic Properties of Biofunctionalization
PublicationWith the increasing power of computation systems, theoretical calculations provide a means for quick determination of material properties, laying out a research plan, and lowering material development costs. One of the most common is Density Functional Theory (DFT), which allows us to simulate the structure of chemical molecules or crystals and their interaction. In developing a new generation of biosensors, understanding the nature...
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Parallelization of Selected Algorithms on Multi-core CPUs, a Cluster and in a Hybrid CPU+Xeon Phi Environment
PublicationIn the paper we present parallel implementations as well as execution times and speed-ups of three different algorithms run in various environments such as on a workstation with multi-core CPUs and a cluster. The parallel codes, implementing the master-slave model in C+MPI, differ in computation to communication ratios. The considered problems include: a genetic algorithm with various ratios of master processing time to communication...
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Construction of glucosamine-6-phosphate synthase with an internal hexahistydyl fragment
PublicationL-Glutamine: D-fructose-6-phosphate aminotransferase (EC 2.6.1.16), known also as glucosamine-6-phosphate (GlcN-6-P) syntase, catalyzes the first committed step in the amino sugar biosynthetic pathway in prokaryotic and eukaryotic organisms. The enzyme carries out a complex reaction involving ammonia transfer and sugar phosphate isomerization. GlcN-6-P syntase is an important point of metabolic control of amino sugar biosynthesis...
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Images of the Seabed of the Gulf of Gdansk Obtained by Means of the Parametric Sonar
PublicationThe main goal of this paper is to present results of the experimental investigation of the seabed by means of parametric echosounder in the form of chosen images. The phenomena of nonlinear interaction between two parallel beams of high intensity gives as a results very narrow beam of low frequency wave, that enables to penetrate the sea bottom. The first step of our investigations was calibration of all the elements of the measuring...
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A compact microstrip rat-race coupler constituted by nonuniform transmission lines
PublicationIn this work, a step-by-step development of a compact microstrip rat-race coupler (RRC) has been presented and discussed. A high degree of miniaturization has been obtained by substituting six quarter-wavelength uniform atomic building blocks of a RRC by their nonuniform counterparts. The miniaturization procedure has been realized in three progressive steps: (i) the first layout solution of a miniaturized RRC has been acquired...
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Measurements and Visualization of Sound Intensity Around the Human Head in Free Field Using Acoustic Vector Sensor
PublicationThis paper presents measurements and visualization of sound intensity around the human head simulator in a free field. A Cartesian robot, applied for precise positioning of the acoustic vector sensor, was used to measure sound intensity. Measurements were performed in a free field using a head and torso simulator and the setup consisting of four different loudspeaker configurations. The acoustic vector sensor was positioned around...
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Systematic approach to binary classification of images in video streams using shifting time windows
Publicationin the paper, after pointing out of realistic recordings and classifications of their frames, we propose a new shifting time window approach for improving binary classifications. We consider image classification in tewo steps. in the first one the well known binary classification algorithms are used for each image separately. In the second step the results of the previous step mare analysed in relatively short sequences of consecutive...
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Thermal degradation kinetics of poly(propylene succinate) prepared with the use of natural origin monomers
PublicationLinear biobased polyester polyols were prepared with the use of succinic acid and 1,3-pro- panediol (both with natural origin). Tetraisopropyl orthotitanate (TPT) was used as a catalyst. In order to determine the effect of various synthesis temperature conditions on the thermal degradation kinet- ics, nine sequences of temperature conditions were used during two-step polycondensation reaction. Thermogravimetric analysis was conducted...
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Footbridges. Dynamic Design – Selected Problems
PublicationModern footbridges create challenge in esthetic and structural design. Breaking the proven canons is a recipe for architectural success. However esthetic form has to be also a functional pedestrian bridge. Therefore a good FEM modeling is a key element in engineering part of design. The paper presents selected problems related to the modeling of the dynamic construction of footbridges. Several basic dynamic problems concerning...
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Manganese–Cobalt Based Spinel Coatings Processed by Electrophoretic Deposition Method: The Influence of Sintering on Degradation Issues of Solid Oxide Cell Oxygen Electrodes at 750 °C
PublicationThis paper seeks to examine how the Mn–Co spinel interconnect coating microstructure can influence Cr contamination in an oxygen electrode of intermediate temperature solid oxide cells, at an operating temperature of 750 °C. A Mn–Co spinel coating is processed on Crofer 22 APU substrates by electrophoretic deposition, and subsequently sintered, following both the one-step and two-step sintering, in order to obtain significantly...
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Regeneration Project of Market Places GOSPOSTRATEG – “Polanki” Market in Gdańsk-Oliwa Pilot Project Monitoring Dataset
PublicationThe dataset entitled Monitoring of activities carried out as part of prototyping and implementation of the pilot project in the area of the “Polanki” market and its direct neighbourhood, in the Gdańsk-Oliwa district, step1; stage from July 2020 year contains tabular monitoring lists (quantitative and qualitative documentation report in the form of tables) of activities carried out as part of the prototyping and implementation of...
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Testing for conformance of parallel programming pattern languages
PublicationThis paper reports on the project being run by TUG and IMAG, aimed at reducing the volume of tests required to exercise parallel programming language compilers and libraries. The idea is to use the ISO STEP standard scheme for conformance testing of software products. A detailed example illustrating the ongoing work is presented.
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On optimal tracking of rapidly varying telecommunication channels
PublicationWhen parameters of mobile telecommunication channels change rapidly, classical adaptive filters, such as exponentially weighted least squares algorithms or gradient algorithms, fail to estimate them with sufficient accuracy. In cases like this, one can use identification methods based on explicit models of parameter changes such as the method of basis functions (BF). When prior knowledge about parameter changes is available the...
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Application of sliding switching functions in backstepping based speed observer of induction machine
PublicationThe paper presents an analysis of the speed observer which is based on the backstepping and sliding mode approach. The speed observer structure is based on the extended mathematical model of an induction machine. The observer structure is based on the measured phase stator currents and transformed to ( αβ ) coordinate system. The stator voltage vector components are treated as known values. Additionally, such an observer structure...
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A Novel Bitrate Adaptation Method for Heterogeneous Wireless Body Area Networks
PublicationIn the article, a novel bitrate adaptation method for data streams allocation in heterogeneous Wireless Body Area Networks (WBANs) is presented. The efficiency of the proposed algorithm was compared with other known algorithms of data stream allocation using computer simulation. A dedicated simulator has been developed using results of measurements in the real environment. The usage of the proposed adaptive data streams allocation...
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A Novel Bitrate Adaptation Method for Heterogeneous Wireless Body Area Networks
PublicationIn the article, a novel bitrate adaptation method for data streams allocation in heterogeneous Wireless Body Area Networks (WBANs) is presented. The efficiency of the proposed algorithm was compared with other known algorithms of data stream allocation using computer simulation. A dedicated simulator has been developed using results of measurements in the real environment. The usage of the proposed adaptive data streams allocation...
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Speed Observer Structure of Induction Machine Based on Sliding Super-Twisting and Backstepping Techniques
PublicationThis paper presents an analysis of the two speed observer structures which are based on the backstepping and sliding super twisting approach. The observer stabilizing functions result from the Lyapunov theorem. To obtain the observer tuning gains the observer structure is linearized near the equilibrium point. The rotor angular speed is obtained from non-adaptive dependence. In the sensorless control system structure the classical...