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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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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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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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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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Advances in computational electrodynamics.
PublicationArtykuł prezentuje wybrane metody, które są rozwijane w Politechnice Gdańskiej, i które mogą być wykorzystane do przyspieszenia komputerowego projektowania układów mikrofalowych i analizy numerycznej układów niskiej i dużej częstotliwości. Przeprowadzono przegląd metod tworzenia układów zastępczych i ich wykorzystanie do automatycznego projektowania filtrów pasmowo-przepustowych. Przedstawiono różne podejścia reprezentacji pola...
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Simulation of parallel similarity measure computations for large data sets
PublicationThe paper presents our approach to implementation of similarity measure for big data analysis in a parallel environment. We describe the algorithm for parallelisation of the computations. We provide results from a real MPI application for computations of similarity measures as well as results achieved with our simulation software. The simulation environment allows us to model parallel systems of various sizes with various components...
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A Bayesian regularization-backpropagation neural network model for peeling computations
PublicationA Bayesian regularization-backpropagation neural network (BRBPNN) model is employed to predict some aspects of the gecko spatula peeling, viz. the variation of the maximum normal and tangential pull-off forces and the resultant force angle at detachment with the peeling angle. K-fold cross validation is used to improve the effectiveness of the model. The input data is taken from finite element (FE) peeling results. The neural network...
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Benchmarking overlapping communication and computations with multiple streams for modern GPUs
PublicationThe paper presents benchmarking a multi-stream application processing a set of input data arrays. Tests have been performed and execution times measured for various numbers of streams and various compute intensities measured as the ratio of kernel compute time and data transfer time. As such, the application and benchmarking is representative of frequently used operations such as vector weighted sum, matrix multiplication etc....
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Parallelization of large vector similarity computations in a hybrid CPU+GPU environment
PublicationThe paper presents design, implementation and tuning of a hybrid parallel OpenMP+CUDA code for computation of similarity between pairs of a large number of multidimensional vectors. The problem has a wide range of applications, and consequently its optimization is of high importance, especially on currently widespread hybrid CPU+GPU systems targeted in the paper. The following are presented and tested for computation of all vector...
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Applying computational intelligence to acoustics.
PublicationW artykule przedstawiono przegląd wybranych zagadnień związanych z zastosowaniem metod inteligencji obliczeniowej w akustyce. Zaprezentowane metody obejmują m.in. sztuczne sieci neuronowe, zbiory przyblizone, logikę rozmytą, algorytmy genetyczne. Problematyka akustyczna dotyczy z kolei klasyfikacji dźwięków muzycznych, inteligentnego przetwarzania muzyki, inteligentnego sterowania trakturą organową oraz obiektywizacji metody oceny...
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Structure and computationally-efficient simulation-driven design of compact UWB monopole antenna
PublicationIn this letter, a structure of a small ultra-wideband (UWB) monopole antenna, its design optimization procedure as well as experimental validation are presented. According to our approach, antenna compactness is achieved by means of a meander line for current path enlargement as well as the two parameterized slits providing additional degrees of freedom that help to ensure good impedance matching. For the sake of reliability, the...
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Generalized Pareto ranking bisection for computationally feasible multi-objective antenna optimization
PublicationMulti-objective optimization (MO) allows for obtaining comprehensive information about possible design trade-offs of a given antenna structure. Yet, executing MO using the most popular class of techniques, population-based metaheuristics, may be computationally prohibitive when full-wave EM analysis is utilized for antenna evaluation. In this work, a low-cost and fully deterministic MO methodology is introduced. The proposed generalized...
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Computationally Efficient Surrogate-Assisted Design of Pyramidal-Shaped 3D Reflectarray Antennas
PublicationReflectarrays (RAs) have been attracting considerable interest in the recent years due to their appealing features, in particular, a possibility of realizing pencil-beam radiation patterns, as in the phased arrays, but without the necessity of incorporating the feeding networks. These characteristics make them attractive solutions, among others, for satellite communications or mobile radar antennas. Notwithstanding, available microstrip...
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Computationally Efficient Multi-Objective Optimization of and Experimental Validation of Yagi-Uda Antenna
PublicationIn this paper, computationally efficient multi-objective optimization of antenna structures is discussed. As a design case, we consider a multi-parameter planar Yagi-Uda antenna structure, featuring a driven element, three directors, and a feeding structure. Direct optimization of the high-fidelity electromagnetic (EM) antenna model is prohibitive in computational terms. Instead, our design methodology exploits response surface...
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A study of rigorous ODE integrators for multi-scale set-oriented computations
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Computations of critical load value of composite shell with random geometric imperfections
PublicationThe work presents the numerical analysis of composite shell with geometric imperfections subjected to compression along its generatrix. The imperfections are described as single indentations and random fields with random parameters of shape and correlation. The fields are generated with the use of the authors made program. Using the authors’ FEM software as well as commercial package Femap with NX Nastran, the critical load values...
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How to render FDTD computations more effective using agraphics accelerator.
PublicationGraphics processing units (GPUs) for years have been dedicated mostly to real time rendering. Recently leading GPU manufactures have extended their research area and decided to support also graphics computing. In this paper, we describe an impact of new GPU features on development process of an efficient finite difference time domain (FDTD) implementation.
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Network-aware Data Prefetching Optimization of Computations in a Heterogeneous HPC Framework
PublicationRapid development of diverse computer architectures and hardware accelerators caused that designing parallel systems faces new problems resulting from their heterogeneity. Our implementation of a parallel system called KernelHive allows to efficiently run applications in a heterogeneous environment consisting of multiple collections of nodes with different types of computing devices. The execution engine of the system is open for...
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A Multi-Fidelity Surrogate-Model-Assisted Evolutionary Algorithm for Computationally Expensive Optimization Problems
PublicationIntegrating data-driven surrogate models and simulation models of different accuracies (or fideli-ties) in a single algorithm to address computationally expensive global optimization problems has recently attracted considerable attention. However, handling discrepancies between simulation models with multiple fidelities in global optimization is a major challenge. To address it, the two major contributions of this paper include:...
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Multi-Fidelity Local Surrogate Model for Computationally Efficient Microwave Component Design Optimization
PublicationIn order to minimize the number of evaluations of high-fidelity (“fine”) model in the optimization process, to increase the optimization speed, and to improve optimal solution accuracy, a robust and computational-efficient multi-fidelity local surrogate-model optimization method is proposed. Based on the principle of response surface approximation, the proposed method exploits the multi-fidelity coarse models and polynomial interpolation...
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Computationally Effcient Solution of a 2D Diffusive Wave Equation Used for Flood Inundation Problems
PublicationThis paper presents a study dealing with increasing the computational efficiency in modeling floodplain inundation using a two-dimensional diffusive wave equation. To this end, the domain decomposition technique was used. The resulting one-dimensional diffusion equations were approximated in space with the modified finite element scheme, whereas time integration was carried out using the implicit two-level scheme. The proposed...
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Computational intelligence-aided character animation
PublicationW pracy przedstawiono pokrótce metody animacji komputerowej, a także podano zasady oceny jakości wyniku animacji postaci. Dodatkowo dokonano przeglądu metod inteligentnych stosowanych w animacji komputerowej i w dziedzinach pokrewnych. W badaniach skupiono się na animacji ruchu w kontekście uzyskiwanej ekspresji. Podano reguły stosowane w animacji tradycyjnej oraz wyznaczono parametry opisujące fazy ruchu w odniesieniu do poszczególnych...
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Computational intelligence methods in production management
PublicationThis chapter presents a survey of selected computational intelligence methods used in production management. This group of methods includes, among others, approaches based on the artificial neural networks, the evolutionary algorithms, the fuzzy logic systems and the particle swarm optimization mechanisms. From the abovementioned methods particularly noteworthy are the evolutionary and the particle swarm algorithms, which are successfully...
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Applications of computational intelligence techqniues to acoustics
PublicationCelem artykułu jest przegląd wybranych zastosowań metod inteligentnych w akustyce, a w szczególności w szeroko rozumianej inżynierii dźwięku. Przedstawione badania i eksperymenty były prowadzone w oparciu o sztuczne sieci neuronowe, metodę zbiorów przybliżonych, logiką rozmytą, grafy przepływowe Pawlaka oraz algorytmy genetyczne. Rozwiązywane problemy dotyczyły klasyfikacji dźwięków muzycznych, rozpoznawania fraz muzycznych, przetwarzania...
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On Computational Aspects of Greedy Partitioning of Graphs
PublicationIn this paper we consider a problem of graph P-coloring consisting in partitioning the vertex set of a graph such that each of the resulting sets induces a graph in a given additive, hereditary class of graphs P. We focus on partitions generated by the greedy algorithm. In particular, we show that given a graph G and an integer k deciding if the greedy algorithm outputs a P-coloring with a least k colors is NP-complete for an infinite...
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Computational aspects of greedy partitioning of graphs
PublicationIn this paper we consider a variant of graph partitioning consisting in partitioning the vertex set of a graph into the minimum number of sets such that each of them induces a graph in hereditary class of graphs P (the problem is also known as P-coloring). We focus on the computational complexity of several problems related to greedy partitioning. In particular, we show that given a graph G and an integer k deciding if the greedy...
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Computational fluid dynamics - lustres and shadows.
PublicationThe paper is devoted to the different aspects of CFD. The advantages of this concept are evident and obvious; powerfuk and effective tools bring this technology closer to the quantifiable world. However, certain weaknesses in this structure are apparent. Sometimes, a simplistic tendency towards simplifications and facilitations may degenerate and lead to negative behaviours and signs. These have not been serious up to date, but...
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Computational modelling of the modification of epoxy resins
PublicationSymulacja komputerowa właściwości fizycznych sieci żywic epoksydowych (DGEBA/DDM) modyfikowanych związkami akrylowymi przy użyciu programu Cheops® MillionZillion Software.
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Computational studies of a hypocycloidal electron monochromator
PublicationPrzeprowadzono badania hipocykolidalnego monochromatora elektronów, wykorzystując komputerowy program optyki elektronowej CPO-3D. Obliczono i przeprowadzono analizę torów elektronów w wiązce o zadanym rozmyciu kątowym przechodzącej przez monochromator. Ustalono, że rozdzielczość energetyczna monochromatora jest wyższa niż odpowiadającego mu monochromatora trochoidalnego.
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Computationally-efficient design optimisation of antennas by accelerated gradient search with sensitivity and design change monitoring
PublicationElectromagnetic (EM) simulation tools are of primary importance in the design of contemporary antennas. The necessity of accurate performance evaluation of complex structures is a reason why the final tuning of antenna dimensions, aimed at improvement of electrical and field characteristics, needs to be based on EM analysis. Design automation is highly desirable and can be achieved by coupling EM solvers with numerical optimisation...
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Computationally efficient two-objective optimization of compact microwave couplers through corrected domain patching
PublicationFinding an acceptable compromise between various objectives is a necessity in the design of contemporary microwave components and circuits. A primary reason is that most objectives are at least partially conflicting. For compact microwave structures, the design trade-offs are normally related to the circuit size and its electrical performance. In order to obtain comprehensive information about the best possible trade-offs, multi-objective...
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Strategies for computationally feasible multi-objective simulation-driven design of compact RF/microwave components
PublicationMulti-objective optimization is indispensable when possible trade-offs between various (and usually conflicting) design objectives are to be found. Identification of such design alternatives becomes very challenging when performance evaluation of the structure/system at hand is computationally expensive. Compact RF and microwave components are representative examples of such a situation: due to highly compressed layouts and considerable...
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Computational Techniques Application in Environmental Exposure Assessment
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Artificial Intelligence and Computational Issues in Engineering Applications
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Computational techniques for efficient conformational sampling of proteins
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Molecular hydrogen solvated in water – A computational study
PublicationThe aqueous hydrogen molecule is studied with molecular dynamics simulations at ambient temperature and pressure conditions, using a newly developed flexible and polarizable H2 molecule model. The design and implementation of this model, compatible with an existing flexible and polarizable force field for water, is presented in detail. The structure of the hydration layer suggests that first-shell water molecules accommodate the...
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Object oriented grid computing for computational electromagnetics
PublicationArtykuł opisuje bibliotekę WiCommGrid napisaną w języku java, która realizuje ideę wymiany informacji pomiędzy węzłami środowiska rozproszonego z zastosowaniem programowania zorientowanego obiektowo. Biblioteka ta przystosowana jest do współdziałania z wieloma systemami operacyjnymi oraz z rożnym środowiskiem sprzętowym. Zbudowaną aplikację zastosowano do zrównoleglonych obliczeń rozkładu pola elektromagnetycznego w oparciu o algorytm...
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Computational collective intelligence for enterprise information systems
PublicationCollective intelligence is most often understood as a kind of intelligence which arises on the basis of a group (collective) of autonomous unites (people, systems) which is taskoriented. There are two important aspects of an intelligent collective: The cooperation aspect and the competition aspect (Levy 1997). The first of them means the possibility for integrating the decisions made by the collective members for creating the decision of...
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Considerations of Computational Efficiency in Volunteer and Cluster Computing
PublicationIn the paper we focus on analysis of performance and power consumption statistics for two modern environments used for computing – volunteer and cluster based systems. The former integrate computational power donated by volunteers from their own locations, often towards social oriented or targeted initiatives, be it of medical, mathematical or space nature. The latter is meant for high performance computing and is typically installed...
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Design-oriented computationally-efficient feature-based surrogate modelling of multi-band antennas with nested kriging
PublicationDesign of modern antenna structures heavily depends on electromagnetic (EM) simulation tools. EM analysis provides reliable evaluation of increasingly complex designs but tends to be CPU intensive. When multiple simulations are needed (e.g., for parameters tuning), the aggregated simulation cost may become a serious bottleneck. As one possible way of mitigating the issue, the recent literature fosters utilization of faster representations,...
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Reliable computationally-efficient behavioral modeling of microwave passives using deep learning surrogates in confined domains
PublicationThe importance of surrogate modeling techniques has been steadily growing over the recent years in high-frequency electronics, including microwave engineering. Fast metamodels are employed to speedup design processes, especially those conducted at the level of full-wave electromagnetic (EM) simulations. The surrogates enable massive system evaluations at nearly EM accuracy and negligible costs, which is invaluable in parameter...
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Local response surface approximations and variable-fidelity electromagnetic simulations for computationally efficient microwave design optimisation
PublicationIn this study, the authors propose a robust and computationally efficient algorithm for simulation-driven design optimisation of microwave structures. Our technique exploits variable-fidelity electromagnetic models of the structure under consideration. The low-fidelity model is optimised using its local response surface approximation surrogates. The high-fidelity model is refined by space mapping with polynomial interpolation of...
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Atomistic Surrogate-Based Optimization for Simulation-Driven Design of Computationally Expensive Microwave Circuits with Compact Footprints
PublicationA robust simulation-driven design methodology for computationally expensive microwave circuits with compact footprints has been presented. The general method introduced in this chapter is suitable for a wide class of N-port un-conventional microwave circuits constructed as a deviation from classic design solutions. Conventional electromagnetic (EM) simulation-driven design routines are generally prohibitive when applied to numerically...
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Variable Data Structures and Customized Deep Learning Surrogates for Computationally Efficient and Reliable Characterization of Buried Objects
PublicationIn this study, in order to characterize the buried object via deep-learning-based surrogate modeling approach, 3-D full-wave electromagnetic simulations of a GPR model has been used. The task is to predict simultaneously and independent of each characteristic parameters of a buried object of several radii at different positions (depth and lateral position) in various dispersive subsurface media. This study has analyzed variable...
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A Computationally Efficient Model for Predicting Successful Memory Encoding Using Machine-Learning-based EEG Channel Selection
PublicationComputational cost is an important consideration for memory encoding prediction models that use data from dozens of implanted electrodes. We propose a method to reduce computational expense by selecting a subset of all the electrodes to build the prediction model. The electrodes were selected based on their likelihood of measuring brain activity useful for predicting memory encoding better than chance (in terms of AUC). A logistic...
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Color prediction from first principle quantum chemistry computations: a case of alizarin dissolved in methanol
PublicationThe electronic spectrum of alizarin (AZ) in methanol solution was measured and used as reference data for color prediction. The visible part of the spectrum was modelled by different DFT functionals within the TD-DFT framework. The results of a broad range of functionals applied for theoretical spectrum prediction were compared against experimental data by a direct color comparison. The tristimulus model of color expressed in terms...
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Dynamic Data Management Among Multiple Databases for Optimization of Parallel Computations in Heterogeneous HPC Systems
PublicationRapid development of diverse computer architectures and hardware accelerators caused that designing parallel systems faces new problems resulting from their heterogeneity. Our implementation of a parallel system called KernelHive allows to efficiently run applications in a heterogeneous environment consisting of multiple collections of nodes with different types of computing devices. The execution engine of the system is open for...
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Predicting bankruptcy with the use of macroeconomic variables
PublicationRegarding the current global financial crisis, the firms can expect the increased uncertainty of their existence. The relevant literature includes extensive studies on bankruptcy prediction. Studies show that the most popular method used for prediction of firms' failures are discriminant analyses (30,3% of all models), then logit and probit models (21,3%), which all three are parametric models. The nature, the structure of the...
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Computational method for determining the static stiffness of the saw blade
PublicationW artykule opisano sposób modelowania i obliczeń odkształceń i naprężeń pił tarczowych o złożonej geometrii korpusu z wykorzystaniem komputerowych programów wspomagających projektowania.