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Search results for: COMPUTATIONAL SYSTEMS
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Iterative Global Sensitivity Analysis Algorithm with Neural Network Surrogate Modeling
PublicationGlobal sensitivity analysis (GSA) is a method to quantify the effect of the input parameters on outputs of physics-based systems. Performing GSA can be challenging due to the combined effect of the high computational cost of each individual physics-based model, a large number of input parameters, and the need to perform repetitive model evaluations. To reduce this cost, neural networks (NNs) are used to replace the expensive physics-based...
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Algorithmic Human Resources Management - Perspectives and Challenges
PublicationTheoretical background: Technology – most notably processes of digitalisation, the use of artificial intelligence, machine learning, big data and prevalence of remote work due to pandemic – changes the way organizations manage human resources. One of the increasing trends is the use of so-called “algorithmic management”. It is notably different than previous e-HRM or HRIS (human resources information systems) applications, as it...
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Accurate Modeling of Antenna Structures by Means of Domain Confinement and Pyramidal Deep Neural Networks
PublicationThe importance of surrogate modeling techniques has been gradually increasing in the design of antenna structures over the recent years. Perhaps the most important reason is a high cost of full-wave electromagnetic (EM) analysis of antenna systems. Although imperative in ensuring evaluation reliability, it entails considerable computational expenses. These are especially pronounced when carrying out EM-driven design tasks such...
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On Accelerated Metaheuristic-Based Electromagnetic-Driven Design Optimization of Antenna Structures Using Response Features
PublicationDevelopment of present-day antenna systems is an intricate and multi-step process requiring, among others, meticulous tuning of designable (mainly geometry) parameters. Concerning the latter, the most reliable approach is rigorous numerical optimization, which tends to be re-source-intensive in terms of computing due to involving full-wave electromagnetic (EM) simu-lations. The cost-related issues are particularly pronounced whenever...
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Study on population dynamics for triple-linked food chain using a simulation-based approach
PublicationThe procedures based on simulation have become a feasible testing method that does not require investing valuable resources to create a concrete prototype, especially with the increasing computational power of computers. Thus, design changes can be adopted and design errors can be fixed before it is too late. Simulation turns to be a cheap, safe and often more acceptable from an ethical perspective. In our work we summarize the...
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Coarse-grained simulation - an efficient approach for studying motions of large proteins
PublicationOne of the most important challenges in performing Molecular Dynamics (MD) simulations of large protein complexes is to accommodate the model accuracy and the simulation timescale. Hitherto, for the most relevant dynamics of protein aggregates in an explicit aqueous environment, the timescale reachable for the all-atoms simulations is of hundreds of nanoseconds. This range is four to six orders of magnitude smaller than processes...
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Mechanics of Micro- and Nano-Size Materials and Structures
PublicationNanotechnology knowledge is always looking to expand its boundaries to achieve the mostsignificant benefit to human life and meet the growing needs of today. In this case, we can refer tomicro- and nanosensors in micro/nano-electromechanical systems (MEMS/NEMS). These electricaldevices can detect minimal physical stimuli up to one nanometer in size. Today, micro/nano-sensordevices are widely used in the...
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4-Node combined shell element with semi-EAS-ANS strain interpolationsin 6-parameter shell theories with drilling degrees of freedom
PublicationW pracy sformułowano 4-węzłowy powłokowy element skończony klasy C0, w ramach nieliniowej 6-parametrowej teorii powłok. W celu uniknięcia zjawiska blokady (locking effect) wykorzystano technikę EAS do niesymetrycznych odkształceń membranowych i ANS do odkształceń poprzecznych.Przedstawiono przykłady potwierdzające poprawność sformułowania.
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Simulations of air and water flow in a model dike during overflow experiments
PublicationFlow in flood dikes, earth dams, and embankments occurs in variably saturated conditions, with pores of the earth material filled partly with water and partly with air. In routine engineering analysis, the influence of pore air is neglected and the air pressure is assumed equal to atmospheric. In some circumstances, for example, during overtopping of the dike by water, the effect of pore air on water flow and stability of the structure...
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An isogeometric finite element formulation for frictionless contact of Cosserat rods with unconstrained directors
PublicationThis paper presents an isogeometric finite element formulation for nonlinear beams with impenetrability constraints, based on the kinematics of Cosserat rods with unconstrained directors. The beam cross-sectional deformation is represented by director vectors of an arbitrary order. For the frictionless lateral beam-to-beam contact, a surface-to-surface contact algorithm combined with an active set strategy and a penalty method...
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Methods of Network Resource Provisioning for the Future Internet IIP Initiative
PublicationIn this paper, we present specification, design and implementation aspects of a network resource provisioning module introduced for the Polish Initiative of Future Internet called System IIP. In particular, we propose a set of novel LP optimization models of network resource provisioning designed to minimize the network resource consumption, either bandwidth or node’s computational power, as well as to maximize the residual capacity....
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The chapter analyses the K-Means algorithm in its parallel setting. We provide detailed description of the algorithm as well as the way we paralellize the computations. We identified complexity of the particular steps of the algorithm that allows us to build the algorithm model in MERPSYS system. The simulations with the MERPSYS have been performed for different size of the data as well as for different number of the processors used for the computations. The results we got using the model have been compared to the results obtained from real computational environment.
PublicationThe chapter analyses the K-Means algorithm in its parallel setting. We provide detailed description of the algorithm as well as the way we paralellize the computations. We identified complexity of the particular steps of the algorithm that allows us to build the algorithm model in MERPSYS system. The simulations with the MERPSYS have been performed for different size of the data as well as for different number of the processors used...
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Global EM-Driven Optimization of Multi-Band Antennas Using Knowledge-Based Inverse Response-Feature Surrogates
PublicationElectromagnetic simulation tools have been playing an increasing role in the design of contemporary antenna structures. The employment of electromagnetic analysis ensures reliability of evaluating antenna characteristics but also incurs considerable computational expenses whenever massive simulations are involved (e.g., parametric optimization, uncertainty quantification). This high cost is the most serious bottleneck of simulation-driven...
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Local Texture Pattern Selection for Efficient Face Recognition and Tracking
PublicationThis paper describes the research aimed at finding the optimal configuration of the face recognition algorithm based on local texture descriptors (binary and ternary patterns). Since the identification module was supposed to be a part of the face tracking system developed for interactive wearable computer, proper feature selection, allowing for real-time operation, became particularly important. Our experiments showed that it is...
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Evolution of physics-based methodology for exploring the conformational energy landscape of proteins
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Ergodicity and model quality in template-restrained canonical and temperature/Hamiltonian replica exchange coarse-grained molecular dynamics simulations of proteins
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Kinetic flux vector splitting scheme for solving non-reactive multi-component flows
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Protein structure prediction with the UNRES force-field using Replica-Exchange Monte Carlo-with-Minimization; Comparison with MCM, CSA, and CFMC
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An efficient molecular docking using conformational space annealing
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Frequency bands selection of the Portevin–LeChatelier effect
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A high-order compact difference algorithm for half-staggered grids for laminar and turbulent incompressible flows
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Quadratic Cohen representations in spectral analysis of serration process in Al-Mg alloys
PublicationIstotny z mechanicznego punktu widzenia efekt Portevina Le-Chateliera charakteryzuje się skomplikowanym profilem widmowym. Jako typowy przykład procesu niestacjonarnego, wymaga specjalnego podejścia umożliwiającego analizę zmian rozkładu energii fluktuacji naprężenia w funkcji odkształcenia. Jako narzędzie umożliwiające realizację powyższego założenia autorzy proponują zastosowanie rodziny przekształceń kwadratowych znanych jako...
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Conformation of six fentanyls revisited
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Theoretical studies of the dependence of nuclear quadrupole coupling constants on intermolecular forces
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CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures
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Evaluation of drawability of tailor-welded blanks made of titanium alloys Grade 2 || Grade 5
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Parallelization Method for a Continuous Property
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Graph Approach to the Computation of the Homology of Continuous Maps
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Computation of cubical homology, cohomology, and (co)homological operations via chain contraction
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Finite Resolution Dynamics
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Generating optimal paths in dynamic environments using RiverFormation Dynamics algorithm
PublicationThe paper presents a comparison of four optimisation algorithms implemented for the purpose of finding the shortest path in static and dynamic environments with obstacles. Two classical graph algorithms –the Dijkstra complete algorithm and A* heuristic algorithm – were compared with metaheuristic River Formation Dynamics swarm algorithm and its newly introduced modified version. Moreover, another swarm algorithm has been compared...
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Personalized prediction of the secondary oocytes number after ovarian stimulation: A machine learning model based on clinical and genetic data
PublicationControlled ovarian stimulation is tailored to the patient based on clinical parameters but estimating the number of retrieved metaphase II (MII) oocytes is a challenge. Here, we have developed a model that takes advantage of the patient’s genetic and clinical characteristics simultaneously for predicting the stimulation outcome. Sequence variants in reproduction-related genes identified by next-generation sequencing were matched...
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Frequency bands selection of the Portevin-LeChatelier
PublicationEfekt Portevina-LeChateliera ujawnia się w postaci skokowych zmian naprężenia w trakcie procesu odkształcenia próbek pewnych stopów. Zjawisko PLC występuje w kilku odmianach charakteryzujących się istotnymi różnicami zarówno w przestrzennym rozkładzie pasm odkształcenia jak też przebiegu krzywej naprężeniowej. Przebiegi odpowiadające różnym odmianom serration charakteryzują się odmiennymi właściwościami rozkładu energetycznego...
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Weighted Ensemble with one-class Classification and Over-sampling and Instance selection (WECOI): An approach for learning from imbalanced data streams
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Ab initio studies of the structure, physicochemical properties and behavior of lead chlorides and chloroplumbate anions in gaseous and aqueous phases
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Optimal shape design of multi-element trawl-doors using local surrogate models
PublicationTrawl-doors have a large influence on the fuel consumption of fishing vessels. Design and optimiza-tion of trawl-doors using computational models are a key factor in minimizing the fuel consump-tion. This paper presents an optimization algorithm for the shape design of trawl-door shapes using computational fluid dynamic (CFD) models. Accurate CFD models are computationally expensive. Therefore, the direct use of traditional optimization...
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Quadratic Cohen representations in spectral analysis of serration process in Al–Mg alloys
PublicationImportant from mechanical point of view the Portevin–Le Chatelier serration phenomenon is being characterized by a complicated spectral profile. As a typical example of nonstationary processes it demands a special treatment allowing to follow the evolution of energy of stress fluctuations as a function of strain. The authors suggest the utilization of a compact system of quadratic transformations, known as Cohen class, as a technique...
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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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Metal salts reduction during parylenes polymerization
PublicationPublikacja o wynikach obliczeń kwantowych o możliwości redukcji niektórych soli metali przy pomocy rodników parylenu w czasie jego polimeryzacji.
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Comparing Phylogenetic Trees by Matching Nodes Using the Transfer Distance Between Partitions
PublicationAbility to quantify dissimilarity of different phylogenetic trees describing the relationship between the same group of taxa is required in various types of phylogenetic studies. For example, such metrics are used to assess the quality of phylogeny construction methods, to define optimization criteria in supertree building algorithms, or to find horizontal gene transfer (HGT) events. Among the set of metrics described so far in...
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Structure and properties of liquid Al–Cu alloys: Empirical potentials compared
PublicationWe report on the structure and mass transport properties of liquid Al–Cu alloys predicted by two recently-developed empirical many-body potentials: MEAM (Jelinek et al., 2012) and EAM-ADP (Apostol and Mishin, 2011), and by the well-known Gupta potential. Total and partial pair correlation functions, angular distribution functions, densities, coordination numbers and self-diffusion coefficients are compared with published experimental...
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Structure-based design and evaluation of novel N-phenyl-1H-indol-2-amine derivatives for fat mass and obesity-associated (FTO) protein inhibition
PublicationFat mass and obesity-associated (FTO) protein contributes to non-syndromic human obesity which refers to excessive fat accumulation in human body and results in health risk. FTO protein has become a promising target for anti-obesity medicines as there is an immense need for the rational design of potent inhibitors to treat obesity. In our study, a new scaffold N-phenyl-1H-indol-2-amine was selected as a base for FTO protein inhibitors...
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Why do G-quadruplexes dimerize through the 5’-ends? Driving forces for G4 DNA dimerization examined in atomic detail
PublicationG-quadruplexes (G4) are secondary structures formed by guanine-rich nucleic acid sequences and shown to exist in living cells where they participate in regulation of gene expression and chromosome maintenance. G-quadruplexes with solvent-exposed guanine tetrads show the tendency to associate together through cofacial stacking, which may be important for packaging of G4-forming sequences and allows for the design of higher-order...
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Generalization of Phylogenetic Matching Metrics with Experimental Tests of Practical Advantages
PublicationThe ability to quantify a dissimilarity of different phylogenetic trees is required in various types of phylogenetic studies, for example, such metrics are used to assess the quality of phylogeny construction methods and to define optimization criteria in supertree building algorithms. In this article, starting from the already described concept of matching metrics, we define three new metrics for rooted phylogenetic trees. One...
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Proximal primal–dual best approximation algorithm with memory
PublicationWe propose a new modified primal–dual proximal best approximation method for solving convex not necessarily differentiable optimization problems. The novelty of the method relies on introducing memory by taking into account iterates computed in previous steps in the formulas defining current iterate. To this end we consider projections onto intersections of halfspaces generated on the basis of the current as well as the previous...
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Two-step mechanism of J-domain action in driving Hsp70 function
PublicationJ-domain proteins (JDPs), obligatory Hsp70 cochaperones, play critical roles in protein homeostasis. They promote key allosteric transitions that stabilize Hsp70 interaction with substrate polypeptides upon hydrolysis of its bound ATP. Although a recent crystal structure revealed the physical mode of interaction between a J-domain and an Hsp70, the structural and dynamic consequences of J-domain action once bound and how Hsp70s...
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Generalized Einstein relation in disordered organic semiconductors: Influence of the acoustic phonons–charge carriers scattering
PublicationIn this work, we analyze the generalized Einstein relation for disordered organic semiconductors with a non-equilibrium Druyvesteyn-type distribution function. The Druyvesteyn behavior of hot electrons in a solid state is associated with the acoustic phonons–charge carriers scattering. Such a case has been experimentally demonstrated in electroluminescent inorganic rare–earth–doped zinc chalcogenides. Therefore, we can assume that,...
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Long‐time scale simulations of virus‐like particles from three human‐norovirus strains
PublicationThe dynamics of the virus like particles (VLPs) corresponding to the GII.4 Houston, GII.2 SMV, and GI.1 Norwalk strains of human noroviruses (HuNoV) that cause gastroenteritis was investigated by means of long-time (about 30 μs in the laboratory timescale) molecular dynamics simulations with the coarse-grained UNRES force field. The main motion of VLP units turned out to be the bending at the junction between the P1 subdomain (that...
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ESCASA : Analytical estimation of atomic coordinates from coarse‐grained geometry for nuclear‐magnetic‐resonance ‐assisted protein structure modeling. I. Backbone and Hβ protons
PublicationA method for the estimation of coordinates of atoms in proteins from coarse-grained geometry by simple analytical formulas (ESCASA), for use in nuclear-magnetic-resonance (NMR) data-assisted coarse-grained simulations of proteins is proposed. In this paper, the formulas for the backbone Hα and amide (HN) protons, and the side-chain Hβ protons, given the Cα-trace, have been derived and parameterized, by using the interproton distances...
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In-depth characterization of icosahedral ordering in liquid copper
PublicationThe presence of icosahedral ordering in liquid copper at temperatures close to the melting point is now well-established both experimentally and through computer simulation. However, a more elaborate analysis of local icosahedral and icosahedron-like structures, together with a system for classifying such structures based on some measure of "icosahedrity", has so far been conspicuously absent in the literature. Similarly, the dynamics...