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Search results for: computational science
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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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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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A high-order compact difference algorithm for half-staggered grids for laminar and turbulent incompressible flows
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Conformation of six fentanyls revisited
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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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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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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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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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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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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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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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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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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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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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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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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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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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Weakly nonlinear dynamics of short acoustic waves in exponentially stratified gas
PublicationRozpatruje 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.
PublicationNowadays, 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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How thermal stability of ionic liquids leads to more efficient TiO2-based nanophotocatalysts: Theoretical and experimental studies
PublicationIonic 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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Use of structural equation modeling in quantitative research in the field of management and economics: A bibliometric analysis in the systematic literature review
PublicationPURPOSE: 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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EFFECT OF WORKING FLUID SELECTION ON THERMAL PERFORMANCE OF HEAT EXCHANGER FILLED BY THE POROUS MATERIAL
PublicationThermal 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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Application of different modes of nanoscale impedance microscopy in materials research
PublicationIn 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
PublicationThere 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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Fotokatalityczna degradacja zanieczyszczeń środowiskowych
PublicationFotokataliza 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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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
Publication"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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Deep eutectic solvents – A new platform in membrane fabrication and membrane-assisted technologies
PublicationDeep 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
PublicationThe 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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How much is Impact Factor worth?
PublicationThe 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 ...
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Determinants And Barriers In The Development Of The Entrepreneurial Orientation In The Polish Higher Education Institutions
PublicationThe 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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Modified DNA polymerases for PCR troubleshooting
PublicationPCR 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
PublicationRadio 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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MobileNet family tailored for Raspberry Pi
PublicationWith 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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CONCRETE MIX DESIGN USING ABRAMS AND BOLOMEY METHODS
PublicationOne way to reduce the consumption of cement is to optimize its use. Many known methods of concrete design, based on the Abrams law and the Bolomey method. Therefore, the authors chose those methods for analysis. The concrete composition with the assumed strength class, calculated by any method differs significantly. This applies especially to the cement content, as its content in the composition of concrete varies from 20 to 50%....
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Cops, a fast robber and defensive domination on interval graphs
PublicationThe game of Cops and ∞-fast Robber is played by two players, one controlling c cops, the other one robber. The players alternate in turns: all the cops move at once to distance at most one each, the robber moves along any cop-free path. Cops win by sharing a vertex with the robber, the robber by avoiding capture indefinitely. The game was proposed with bounded robber speed by Fomin et al. in “Pursuing a fast robber on a graph”,...
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Mini-Cave Automatic Virtual Environment Application in Security, Safety, and Defence Studies
PublicationThe aim of the article is to analyse the use of mini-Cave Automatic Virtual Reality Environment (mini-CAVE) in academic studies on security, safety, and defence. The literature review based on Web of Science database and the case study of the War Studies University research activities indicated the mini-CAVE can be used in two areas as a research infrastructure and as a didactic tool. It can be concluded that due to the development...
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Roadmap on dynamics of molecules and clusters in the gas phase
PublicationThis roadmap article highlights recent advances, challenges and future prospects in studies of the dynamics of molecules and clusters in the gas phase. It comprises nineteen contributions by scientists with leading expertise in complementary experimental and theoretical techniques to probe the dynamics on timescales spanning twenty orders of magnitudes, from attoseconds to minutes and beyond, and for systems ranging in complexity...
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An Alternative Proof of a Lower Bound on the 2-Domination Number of a Tree
PublicationA 2-dominating set of a graph G is a set D of vertices of G such that every vertex not in D has a at least two neighbors in D. The 2-domination number of a graph G, denoted by gamma_2(G), is the minimum cardinality of a 2-dominating set of G. Fink and Jacobson [n-domination in graphs, Graph theory with applications to algorithms and computer science, Wiley, New York, 1985, 283-300] established the following lower bound on the 2-domination...
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Important Facts and Observations about Pairwise Comparisons (the special issue edition)
PublicationThis study has been inspired by numerous requests for clarification from researchers who often confuse Saaty’s Analytic Hierarchy Process (AHP) with the pairwise comparisons (PC) method, taking AHP as the only representation of PC. This study should be regarded as an interpretation and clarification of past investigations of PC. In addition, this article is a reflection on general PC research at a higher level of abstraction: the...
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"Problemy Klimatologii Polarnej" w świetle wybranych statystyk
PublicationW pracy przedstawiono analizę cytowań artykułów opublikowanych w 24 tomach rocznika „Problemy Klimatologii Polarnej” w latach 1992-2014 opracowaną na podstawie bazy Web of Science i serwisu naukowo-informacyjnego Google Scholar. Przeprowadzono również kwerendę takich cytowań w polskich publikacjach zwartych z zakresu geografii fizycznej, ekologii i biologii. Analizy ujawniły dużą liczbę cytowań w czasopismach z tzw. Listy Filadelfijskiej...
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The Caustic in the Acoustics of Historic Interiors
PublicationIn the paper, caustics are discussed as ordered forms of focus broadening occurring in concave mirrors. Presented are examples of caustics formed in natural conditions and application of the phenomenon in different fields of science and technology. Against this factual background, the possibility to observe caustics in rooms is pointed out. Special emphasis is put on large rooms of historic character, as such interiors frequently...