Search results for: COMPUTATIONAL SCIENCE
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Metal-Organic Framework (MOF)/Epoxy Coatings: A Review
PublicationEpoxy coatings are developing fast in order to meet the requirements of advanced materials and systems. Progress in nanomaterial science and technology has opened a new era of engineering for tailoring the bulk and surface properties of organic coatings, e.g., adhesion to the substrate, anti-corrosion, mechanical, flame-retardant, and self-healing characteristics. Metal-organic frameworks (MOFs), a subclass of coordinative polymers...
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Benefit of the doubt approach to assessing the research performance of Australian universities
PublicationThis paper proposes a benefit of the doubt (BoD) approach to assess the research performance of 37 public Australian universities based on data from 2015. The primary activities of Higher Education institutions are teaching and research, but the prestige of a university depends mainly on the results of its research activities. The BoD method is rooted in the data envelopment analysis methodology, which enables the flexible and...
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The analysis of soil resistance during screw displacement pile installation
PublicationThe analysis of soil resistances during screw displacement pile installation based on model and field tests. The investigations were carried out as a part of research project, financed by the Polish Ministry of Science and Higher Education. A proposal of empirical method for prediction of rotation resistance (torque) during screw auger penetration in non-cohesive subsoil based on CPT result.
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Multi-fidelity aerodynamic design trade-off exploration using point-by-point Pareto set identification
PublicationAerodynamic design is inherently a multi-objective optimization (MOO) problem. Determining the best possible trade-offs between conflicting aerodynamic objectives can be computationally challenging when carried out directly at the level of high-fidelity computational fluid dynamics simulations. This paper presents a computationally cheap methodology for exploration of aerodynamic design trade-offs. In particular, point-by-point...
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Special Issue: Recent Advances in Corrosion Science
PublicationThe dynamic development of the global industry and growing demand for new material technologies generates constantly increasing problems regarding premature material degradation and the requirement to determine corrosion mechanisms and to develop new protection/evaluation approaches. This Special Issue, “Recent Advances in Corrosion Science”, brings together fourteen articles and one review, providing a snapshot of the recent activity...
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Radar and Sonar Imaging and Processing
PublicationThe 21 papers (from 61 submitted) published in the Special Issue “Radar and Sonar Imaging Processing” highlighted a variety of topics related to remote sensing with radar and sonar sensors. The sequence of articles included in the SI dealt with a broad profile of aspects of the use of radar and sonar images in line with the latest scientific trends. The latest developments in science, including artificial intelligence, were used.
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Adaption of Open Science Paradigm at Gdańsk University of Technology
PublicationThe paper describes the basic principles standing behind Open Access and will try to dispel the doubts behind them. Further the solution adapted by the Gdańsk University of Technology is presented. Later on the systems that the University uses and means of their integration into a complex Open Science platform are described. Finally the procedures needed to publish a document in the repository alongside the University's policy...
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Free-surface elevation in open vortex flow controls
PublicationRotational form of fluid motion is complex, but very important in science and technology. The paper is devoted to the hydraulic mechanism of flow in open vortex flow controls, or regulators. The velocity field was described by the kinematic model, and intensity of rotation - by means of the energy balance between the input and dissipation. In consequence some algebraic expresions were obtained, which can be useful in approximated...
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Fast Low-fidelity Wing Aerodynamics Model for Surrogate-Based Shape Optimization
PublicationVariable-fidelity optimization (VFO) can be efficient in terms of the computational cost when compared with traditional approaches, such as gradient-based methods with adjoint sensitivity information. In variable-fidelity methods, the directoptimization of the expensive high-fidelity model is replaced by iterative re-optimization of a physics-based surrogate model, which is constructed from a corrected low-fidelity model. The success...
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Radar and Sonar Imaging and Processing (2nd Edition)
PublicationThe 14 papers (from 29 submitted) published in the Special Issue “Radar and Sonar Imaging Processing (2nd Edition)” highlight a variety of topics related to remote sensing with radar and sonar sensors. The sequence of articles included in the SI deal with a broad profile of aspects of the use of radar and sonar images in line with the latest scientific trends, in which the latest developments in science, including artificial intelligence,...
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Międzynarodowa konferencja IATUL Seminar 2019 „Organizacyjne i prawne aspekty Otwartej Nauki” / International IATUL Seminar 2019 "Organizing the Open Science Framework – Strategies and Legal Aspects”
PublicationIATUL Seminar 2019 was held in Gdańsk/Sopot, Poland (December 10-11th, 2019). The theme of the Seminar was „Organizing the Open Science Framework – Strategies and Legal Aspects”. The event was co-organized by Gdańsk University of Technology Library and International Association of University Libraries (IATUL). IATUL Seminar 2019 event attracted delegates, including directors and senior managers of university and research libraries...
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Jan Daciuk dr hab. inż.
PeopleJan Daciuk received his M.Sc. from the Faculty of Electronics of Gdansk University of Technology in 1986, and his Ph.D. from the Faculty of Electronics, Telecommunications and Informatics of Gdańsk University of Technology in 1999. He has been working at the Faculty from 1988. His research interests include finite state methods in natural language processing and computational linguistics including speech processing. Dr. Daciuk...
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Structural properties of hypothetical CeBa2Cu3O7 compound from LSDA+DMFT calculations
PublicationThe hypothetical stoichiometric CeBa2Cu3O7 (Ce123) compound, which has not been synthesized as a single phase yet, was studied by the density functional theory (DFT). We utilized a method which merges the local spin density approximation (LSDA) with the dynamical mean-field theory (DMFT) to account for the electronic correlations. The LSDA+DMFT calculations were performed in the high-temperature range. The particular emphasis was...
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Alkanethiolates of Group 1,2, and 13-15 Metals
PublicationThis manuscript is an update to the earlier Science of Synthesis contribution describing methods for the synthesis of alkanethiolates of group 1, 2, and 13-15 metals. Alkanethiolates can be converted into S-alkyl thiocarboxylic acid esters, 1-thioglycosides, S-alkyl thiosulfinates, tetrahydro-1,4-thiazine-3-ones, sulfides, disulfides, sulfonium salts, dithioacetals and dithioketals, etc. These transformations are accomplished by...
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Analytical progress on emerging pollutants in the environment: An overview of the topics
PublicationThis overview discusses the ideas behind a collection of articles by invited authors on a diverse range of complex chemical mixtures and analytical methods which represent some of the most relevant and interesting issues on emerging contaminants of environmental health concerns. These chemicals, including those in high volume production, are released on an ongoing basis as a result of various human activities. Moreover, these emerging contaminants...
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Voiceless Stop Consonant Modelling and Synthesis Framework Based on MISO Dynamic System
PublicationA voiceless stop consonant phoneme modelling and synthesis framework based on a phoneme modelling in low-frequency range and high-frequency range separately is proposed. The phoneme signal is decomposed into the sums of simpler basic components and described as the output of a linear multiple-input and single-output (MISO) system. The impulse response of each channel is a third order quasi-polynomial. Using this framework, the...
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Geodesy measurement techniques as an enrichment of archaeological research workflow
PublicationUse of geodesy techniques is widespread in different fields of science. Especially in such an emerging and dynamic branch of science as archaeology. Warsaw Institute of Archaeology, conducts many archaeological expeditions, among the others Polish-Georgian archaeological expedition in Gonio, where ancient Roman Bath has been discovered and excavated. Gonio is located in Adjara, Georgia, placed on the Black Sea coast. Fortress...
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Spatial Modelling in Environmental Analysis and Civil Engineering
PublicationAs can be seen, Spatial Modelling in Environmental Analysis and Civil Engineering applies to a multitude of applications. In an attempt to bring the topic closer to potential readers, the special issue referred to security methods, optimization of calculations, conducting measurements and empirical tests. Each article has made an original contribution to the development of practical science that can be replicated by researchers...
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Tanatoarchitektura [=] Thanatoarchitecture
PublicationApart from medicine and philosophy, deliberations about thanatology - the science of dying and death - are nowadays a subject of interest in psychol-ogy, pedagogy, anthropology, sociology or theology. It seems that there is also space for such deliberations in the field of architecture. This may con-cern the conditions and dignity of death (i.e. in a hospice) but also matters related to the design of the burial and memorial sites....
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Towards an efficient multi-stage Riemann solver for nuclear physics simulations
PublicationRelativistic numerical hydrodynamics is an important tool in high energy nuclear science. However, such simulations are extremely demanding in terms of computing power. This paper focuses on improving the speed of solving the Riemann problem with the MUSTA-FORCE algorithm by employing the CUDA parallel programming model. We also propose a new approach to 3D finite difference algorithms, which employ a GPU that uses surface memory....
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The concept of anti-collision system of autonomous surface vehicle
PublicationThe use of unmanned vehicles in various fields of science and the economy is becoming more common. An extremely important aspect of creating this type of solution is to provide autonomous vehicle navigation, which does not require interference of the human factor or in which it is limited to a minimum. This article discusses the concept of autonomous anti-collision system of unmanned surface vehicle. It proposed a sensor system...
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Tools, Methods and Services Enhancing the Usage of the Kepler-based Scientific Workflow Framework
PublicationScientific workflow systems are designed to compose and execute either a series of computational or data manipulation steps, or workflows in a scientific application. They are usually a part of a larger eScience environment. The usage of workflow systems, however very beneficial, is mostly not irrelevant for scientists. There are many requirements for additional functionalities around scientific workflows systems that need to be...
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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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Conformation of six fentanyls revisited
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A high-order compact difference algorithm for half-staggered grids for laminar and turbulent incompressible flows
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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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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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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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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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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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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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On the joint time-frequency characteristics of chemical oscillations
PublicationZaprezentowano rezultaty analizy czasowo-częstotliwościowej rejestrów potencjałowych oscylacyjnej reakcji Biełousowa-Żabotyńskiego (BŻ). Wybraną reprezentację czasowo-częstotliwościową w postaci algorytmu STFT zastosowano do analizy typowych przebiegów reakcji BŻ, prowadzonej w układzie zamkniętym. Zaprezentowano spektrogramy STFT ukazujące czasowo-częstotliwościową strukturę oscylacji regularnych, mieszanych i chaotycznych. Na...
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A coarse‐grained approach to NMR ‐data‐assisted modeling of protein structures
PublicationThe ESCASA algorithm for analytical estimation of proton positions from coarse-grained geometry developed in our recent work has been implemented in modeling protein structures with the highly coarse-grained UNRES model of polypeptide chains (two sites per residue) and nuclear magnetic resonance (NMR) data. A penalty function with the shape of intersecting gorges was applied to treat ambiguous distance restraints, which automatically...
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Optimization of parallel implementation of UNRES package for coarse‐grained simulations to treat large proteins
PublicationWe report major algorithmic improvements of the UNRES package for physics-based coarse-grained simulations of proteins. These include (i) introduction of interaction lists to optimize computations, (ii) transforming the inertia matrix to a pentadiagonal form to reduce computing and memory requirements, (iii) removing explicit angles and dihedral angles from energy expressions and recoding the most time-consuming energy/force terms...
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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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Explicit solvent repulsive scaling replica exchange molecular dynamics ( RS‐REMD ) in molecular modeling of protein‐glycosaminoglycan complexes
PublicationGlycosaminoglcyans (GAGs), linear anionic periodic polysaccharides, are crucial for many biologically relevant functions in the extracellular matrix. By interacting with proteins GAGs mediate processes such as cancer development, cell proliferation and the onset of neurodegenerative diseases. Despite this eminent importance of GAGs, they still represent a limited focus for the computational community in comparison to other classes...
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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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Molecular mechanism of proton-coupled ligand translocation by the bacterial efflux pump EmrE
PublicationThe current surge in bacterial multi-drug resistance (MDR) is one of the largest challenges to public health, threatening to render ineffective many therapies we rely on for treatment of serious infections. Understanding different factors that contribute to MDR is hence crucial from the global “one health” perspective. In this contribution, we focus on the prototypical broad-selectivity proton-coupled antiporter EmrE, one of the...
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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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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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GPU-Accelerated LOBPCG Method with Inexact Null-Space Filtering for Solving Generalized Eigenvalue Problems in Computational Electromagnetics Analysis with Higher-Order FEM
PublicationThis paper presents a GPU-accelerated implementation of the Locally Optimal Block Preconditioned Conjugate Gradient (LOBPCG) method with an inexact nullspace filtering approach to find eigenvalues in electromagnetics analysis with higherorder FEM. The performance of the proposed approach is verified using the Kepler (Tesla K40c) graphics accelerator, and is compared to the performance of the implementation based on functions from...
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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...