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Search results for: cfd computations
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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...
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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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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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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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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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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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Finite Resolution Dynamics
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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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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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Conformation of six fentanyls revisited
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On the decomposition of stochastic cellular automata
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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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Multi-agent large-scale parallel crowd simulation with NVRAM-based distributed cache
PublicationThis paper presents the architecture, main components and performance results for a parallel and modu-lar agent-based environment aimed at crowd simulation. The environment allows to simulate thousandsor more agents on maps of square kilometers or more, features a modular design and incorporates non-volatile RAM (NVRAM) with a fail-safe mode that can be activated to allow to continue computationsfrom a recently analyzed state in...
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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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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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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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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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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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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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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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Applying molecular dynamics simulation to take the fracture fingerprint of polycrystalline SiC nanosheets
PublicationGraphene-like nanosheets are the key elements of advanced materials and systems. The mechanical behavior of the structurally perfect 2D nanostructures is well documented, but that of polycrystalline ones is less understood. Herein, we applied molecular dynamics simulation (MDS) to take the fracture fingerprint of polycrystalline SiC nanosheets (PSiCNS), where monocrystalline SiC nanosheets (MSiCNS) was the reference nanosheet....
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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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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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Negative Poisson’s ratio from pentagons: A new auxetic structure combining three different auxetic mechanisms
PublicationA novel class of two-dimensional auxetic structures based on the pentagon motif is proposed. Their mechanical properties are investigated by combining molecular mechanics simulations with a simple three-parameter mechanical model which assumes perfectly elastic behavior. It is predicted that the proposed structures – termed as double re-entrant honeycomb – may possess unique mechanical characteristics, which include complete and...
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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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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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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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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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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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Influence of synthesis conditions on zinc oxide nanorode layer morphology
PublicationIn recent years one dimensional (1D) nanostructures (nanotubes, nanowires, nanoribbons and nanorods) have been widely studied. Among studied nano-materials, the greatest interest can be seen for zinc oxide (ZnO). However, there is still a need for simple, inexpensive and reproducible fabrication method. In the literature different fabrication methods can be found, most of them requires expensive equipment and involve complex...
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The Quick Measure of a Nurbs Surface Curvature for Accurate Triangular Meshing
PublicationNURBS surfaces are the most widely used surfaces for three-dimensional models in CAD/CAE programs. As a model for FEM calculation is prepared with a CAD program it is inevitable to mesh it finally. There are many algorithms for meshing planar regions. Some of them may be used for meshing surfaces but it is necessary to take the curvature of the surface under consideration to avoid poor quality mesh. The mesh must be denser in the...
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Toward Human Chromosome Knowledge Engine
PublicationHuman chromosomes carry genetic information about our life. Chromosome classification is crucial for karyotype analysis. Existing chromosome classification methods do not take into account reasoning, such as: analyzing the relationship between variables, modeling uncertainty, and performing causal reasoning. In this paper, we introduce a knowledge engine for reasoning-based human chromosome classification that stores knowledge...
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Samooczyszczanie się gruntów z substancji organicznej. W: [CD-ROM] Konfe-rencja Naukowo-Techniczna ''Przyszłość Wrocławskich Pól Irygacyjnych''. Wro- cław 13-14XI 2003. Wrocław: Miejskie Przeds. Wodociągów i Kanalizacji**2003 s. 1-7, 2 rys. bibliog. 7 poz.
PublicationPodstawą rozważań jest teoria procesu samooczyszczania się gruntów w warun-ków aerobowych. W pracy opisano model matematyczny rozkładu zanieczyszczeń organicznych w gruncie oraz dokonano doświadczalnej weryfikacji tego modelu.Wykazano, że dla gruntów nawadnianych ściekami stężenie tlenu w ich fazie gazowej może być wyznaczane doświadczalne i obliczane. Wyniki pomiarów i ob-liczeń okazały się ze sobą zgodne.
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Induction machine model for current diagnostics of bearings. W: [CD-ROM]Proceedings and our Portrait. 48 Internationales Wissenschaftliches Kollo- quium. Ilmenau, 22.-25.09.2003. Ilmenau: Tech. Univ. Ilmenau**2003 s. [1-9] 8 rys. Model maszyny indukcyjnej dla prądowej diagnostyki łożysk.
PublicationPojawienie się określonych typów uszkodzeń w silniku jest źródłem odkształ-cenia tego prądu. Poddając przebieg prądu analizie widmowej obserwuje sięszereg składowych, które związane są z określonymi typami uszkodzeń. Referatprezentuje rezultaty badań modelowych i eksperymentalnych. Badania przepro-wadzono na silniku 1,1 kW czterobiegunowym. Zaprezentowany model pozwala za-równo na wprowadzanie wibracji wirnika jak ekscentryczności...
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Wind resource assessment and energy yield prediction for the small wind turbine on the Szubieniczne Hill
PublicationThe goal of this study is to preliminary assess the wind resources on the Szubieniczne Hill in order to predict the annual energy production for planned small wind turbine. The analyzed site is located close to the Gdańsk University of Technology campus, in complex urban environment additionally surrendered by forested hills. The assessment is based on Computational Fluid Dynamics simulations which allow to evaluate the wind energy potential...
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On the low-cost design of abbreviated multisection planar matching transformer
PublicationA numerically demanding wideband matching transformer composed of three nonuniform transmission lines (NUTLs) has been designed and optimized at a low computational cost. The computational feasibility of the design has been acquired through the exploitation of low-fidelity NUTL models in most steps of the design procedure and an implicit space mapping optimization engine, providing high accuracy results with only a handful of EM...
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Probabilistic Analysis of Structure Models using Target Random Sampling (TRS)
PublicationThe work presents testing methods of sensitivity and reliability of mechanical or structural systems. All computations concerned the case of Zigler column, a simple model of a compressed column involving two random variables only. A conclusion was drawn that the standard Monte Carlo method, its reduction variants and the response surface method allow to assess the sensitivity of structural response to the variation of random structural...
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Experimental verification and comparison of mode shape-based damage detection methods
PublicationThis paper presents experimental verification and comparison of damage detection methods based on changes in mode shapes such as: mode shape curvature (MSC), modal assurance criterion (MAC), strain energy (SE), modified Laplacian operator (MLO), generalized fractal dimension (GFD) and Wavelet Transform (WT).