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Wyniki wyszukiwania dla: computational science
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Spatial Modelling in Environmental Analysis and Civil Engineering
PublikacjaAs 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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Metal salts reduction during parylenes polymerization
PublikacjaPublikacja 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
PublikacjaAbility 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
PublikacjaThis 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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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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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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A high-order compact difference algorithm for half-staggered grids for laminar and turbulent incompressible flows
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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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Conformation of six fentanyls revisited
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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
PublikacjaFat 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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Generalization of Phylogenetic Matching Metrics with Experimental Tests of Practical Advantages
PublikacjaThe 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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Two-step mechanism of J-domain action in driving Hsp70 function
PublikacjaJ-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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Why do G-quadruplexes dimerize through the 5’-ends? Driving forces for G4 DNA dimerization examined in atomic detail
PublikacjaG-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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Optimization of parallel implementation of UNRES package for coarse‐grained simulations to treat large proteins
PublikacjaWe 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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Long‐time scale simulations of virus‐like particles from three human‐norovirus strains
PublikacjaThe 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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Molecular mechanism of proton-coupled ligand translocation by the bacterial efflux pump EmrE
PublikacjaThe 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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Explicit solvent repulsive scaling replica exchange molecular dynamics ( RS‐REMD ) in molecular modeling of protein‐glycosaminoglycan complexes
PublikacjaGlycosaminoglcyans (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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A coarse‐grained approach to NMR ‐data‐assisted modeling of protein structures
PublikacjaThe 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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ESCASA : Analytical estimation of atomic coordinates from coarse‐grained geometry for nuclear‐magnetic‐resonance ‐assisted protein structure modeling. I. Backbone and Hβ protons
PublikacjaA 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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Personalized prediction of the secondary oocytes number after ovarian stimulation: A machine learning model based on clinical and genetic data
PublikacjaControlled 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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Insights into the flow characteristics during hydraulic fracturing
PublikacjaThis paper presents a numerical model to study fracture propagation during water-based hydraulic fracturing. To address the computational challenges associated with the numerical model, the proposed approach employs a set of overlapping spheres arranged in a monolayer to construct a porous specimen containing pre-existing cracks. The fluid-filled cracks represent various stages of initiation and propagation of fluid-driven fracture....
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On the joint time-frequency characteristics of chemical oscillations
PublikacjaZaprezentowano 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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Impact of free water on strain rate response of concrete in compression with a fully coupled DEM/CFD approach
PublikacjaW tym artykule zbadano wpływ zawartości wody na dynamiczne zachowanie betonu w stanie jednokierunkowego ściskania w mezoskali. Przeprowadzono obszerne dwuwymiarowe (2D) badania dynamiczne wpływu wolnej wody na dynamiczną wytrzymałość i pękanie betonu o niskiej porowatości. Dogłębnie zbadano wpływ szybkości odkształcania, nasycenia płynem i lepkości płynu. Zachowanie betonu w pełni i częściowo nasyconego płynem symulowano przy użyciu...
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Proximal primal–dual best approximation algorithm with memory
PublikacjaWe 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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How thermal stability of ionic liquids leads to more efficient TiO2-based nanophotocatalysts: Theoretical and experimental studies
PublikacjaIonic liquids (ILs) containing distinct nitrogen-bearing organic cations (pyridinium, pyrrolidinium, imidazolium, ammonium, morpholinium) were first used for the preparation of 23 IL-TiO2 types of composites by ionic liquid assisted solvothermal synthesis. These 23 optimal ILs structures (i.e. compounds exhibiting an optimal combination of specific properties, functionality, and safety) for synthesis and experimental validation...
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Weakly nonlinear dynamics of short acoustic waves in exponentially stratified gas
PublikacjaRozpatruje się dynamika krótkich (w porównywaniu z charakterystyczną skalą zmiany gęstości gazu atmosferycznego) fal akustycznych. Wyprowadzone nowe równanie ewolucyjne, które uwzględnia dyspersję i nieliniowy charakter propagacji tych fal. Porównuje sie liniowa i nieliniowa dynamika. Ilustracje propagacji, numeryczne wyliczione na podstawie nowych wzorów, są przedstawione. Indexed and abstracted (from vol. 32(1) 2007) in Science...
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Multimedia in teaching economics and management in higher education.
PublikacjaNowadays, the use of multimedia teaching materials at universities makes a standard practice. However their saturation is still quite low comparing to the expectations of students - the main consumers of the information contained therein. This article will present the results of research conducted among students of Management and Engineering Management carried at the Technical University of Gdańsk. Some students of Computer Science...
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Use of structural equation modeling in quantitative research in the field of management and economics: A bibliometric analysis in the systematic literature review
PublikacjaPURPOSE: This paper aims to provide a comprehensive review of scholarly research focusing on using quantitative methods and particularly structural equation modeling (SEM) in management and economics studies, as well as provide a bibliometric agenda including the time horizon of individual publications, the highest citation rate, geographic and industry areas, methodological context, and keywords. METHODOLOGY: A systematic literature...
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Application of different modes of nanoscale impedance microscopy in materials research
PublikacjaIn recent years, there is noticeable interest in application of various types of scanning probe microscopy in material science research. One of them is contact atomic force microscopy combined with local impedance measurements, known as nanoscale impedance microscopy. Literature references present its application in investigations of new materials, microelectronics diagnostics, or research of protective coatings performance. In...
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Organic photovoltaics - chosen aspects
PublikacjaThere are many types of organic and organic/inorganic (hybrid) photovoltaic devices that possess many beneficial properties over inorganic solar cells. That makes the former suitable for a broad range of applications and hence so much attention is paid to their development. In spite of intensive research carried on this field of science and technology there are still many crucial problems that need to be solved. Extensive knowledge...
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EFFECT OF WORKING FLUID SELECTION ON THERMAL PERFORMANCE OF HEAT EXCHANGER FILLED BY THE POROUS MATERIAL
PublikacjaThermal management of electronics semiconductor technologies that are located i.e. in a novel marine power plants or computer server rooms become very important issue for designers of such systems. Motivation and need for research in development of novel cooling strategies for modern electronics is of paramount importance. Heat exchangers filled by the porous material are a novel research topic in current heat pipe science. The...
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Research-by-design Best Practices in Architectural Lighting Design: Defragmenting Research Theories for their Effective Use in the Practice of Architectural and Spatial Design After Dark
Publikacja"This paper aims to combine theory and applied science; academia and practice for the creative transformation of spaces after dark taking into account a consistent environmental awareness. It is based on the premise that design research in the realm of architectural lighting design should function as a development of practice, instead of being a distraction to it. Architectural lighting design is a field within architecture and...
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Fotokatalityczna degradacja zanieczyszczeń środowiskowych
PublikacjaFotokataliza uznawana jest za metodę z rosnącym potencjałem do usuwania zanieczyszczeń organicznych i nieorganicznych - zarówno z fazy wodnej, jak i gazowej. Liczba publikacji z ostatnich pięciu lat związana z tematyką fotokatalizy osiąga ponad 4000 rocznie, wg bazy danych Web of Science (2019 r.). Szczególny potencjał fotokatalizy tkwi w możliwości usuwania zanieczyszczeń uporczywie zalegających w środowisku, których źródłem są...
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Deep eutectic solvents – A new platform in membrane fabrication and membrane-assisted technologies
PublikacjaDeep eutectic solvents (DESs) are a new class of solvents that can offset some of the primary drawbacks of typical solvents and ionic liquids (ILs). Since DESs fall into the guidelines of “Twelve Principles of Green Chemistry”, their implementation in several types of applications has exponentially increased over the last years. The usage of DESs has been directed to the designing, manufacture and purification of new materials...
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Analysis of friction ridge evidence for trace amounts of paracetamol in various pharmaceutical industries by Raman spectroscopy
PublikacjaThe detection of potentially harmful substances presents a multifaceted challenge. On one hand, it can directly save lives, on the other, it can significantly aid and enhance police work, thereby increasing the effectiveness of investigations. The research conducted in this study primarily aims to identify paracetamol in fingerprints, considering situations involving direct contact of a person with paracetamol either chronically...
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The influence of selected metal oxides and laser modification on the surfaces of titanium alloys – Bibliometric and systematic review
PublikacjaManufacturing of oxide coatings (ZnO, ZrO2 , CuO) and laser processing are methods for modifying the surface of titanium and its alloys. It is particularly useful in implantology, where these techniques allow for proper connection of the implant to human tissue. The article consists of two complementary parts: a bibliographic review and a literature survey. The results of a bibliographic analysis conducted for a set of 429 publications...
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MobileNet family tailored for Raspberry Pi
PublikacjaWith the advances in systems-on-a-chip technologies, there is a growing demand to deploy intelligent vision systems on low-cost microcomputers. To address this challenge, much of the recent research has focused on reducing the model size and computational complexity of contemporary convolutional neural networks (CNNs). The state-of-the-art lightweight CNN is MobileNetV3. However, it was designed to achieve a good trade-off between...
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Modified DNA polymerases for PCR troubleshooting
PublikacjaPCR has become an essential tool in biological science. However, researchers often encounter problems with difficult targets, inhibitors accompanying the samples, or PCR trouble related to DNA polymerase. Therefore, PCR optimization is necessary to obtain better results. One solution is using modified DNA polymerases with desirable properties for the experiments. In this article, PCR troubleshooting, depending on the DNA polymerase...
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Radio Simulcasting at a Glance: a New Look at Broadcasting and Streaming Services
PublikacjaRadio is by far one of the most popular and accessible medium. With its availability it attracts listeners all around the world. There are numerous ways of delivering content to consumers. The present situation is characterized by the convergence of acoustics, computer science and telecommunications. This paper reviews the current status of radio broadcasting and streaming services. It describes a subjective study concerning different...
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Determinants And Barriers In The Development Of The Entrepreneurial Orientation In The Polish Higher Education Institutions
PublikacjaThe main aim of the paper is to present the results of the research project on the entrepreneurship in the Polish higher education institutions. The project was funded by the Polish National Science Centre and its main aim was to identify the factors that enable, enhance, limit or disable the entrepreneurial potential in higher education institutions. The paper gives an overview of the identified determinants that foster the entrepreneurial...
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How much is Impact Factor worth?
PublikacjaThe purpose of this work is to present an aspect of counting citations, which is correlated to the Impact Factor, very important for journals in scientific communication, and provides information about the position of a scientific journal in a particular research area. Sometimes citations don’t count in a research output, e.g. if an article is published in a predatory journal. Those journals ...