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Wyniki wyszukiwania dla: computation
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International Symposium on Applied Computational Intelligence and Informatics
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IEEE Workshop on Computational Intelligence in Virtual Environments
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IEEE Symposium on Computational Intelligence in Cyber Security
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IEEE Symposium on Computational Intelligence for Financial Engineering
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IEEE Workshop on Computational Intelligence in Aerospace Applications
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IEEE Symposium on Computational Intelligence and Data Mining
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Australian Conference on Artificial Life and Computational Intelligence
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IEEE Symposium on Computational Intelligence in Control and Automation
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International Conference on Theory and Applications of Computational Science
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IEEE Symposium on Computational intelligence for Image Processing
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IEEE Workshop on Computational Intelligence for Visual Intelligence
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A Review: Applications of the Spectral Finite Element Method
PublikacjaThe Spectral Finite Element Technique (SFEM) has Several Applications in the Sciences, Engineering, and Mathematics, which will be Covered in this Review Article. The Spectral Finite Element Method (SFEM) is a Variant of the Traditional Finite Element Method FEM that Makes use of Higher Order Basis Functions (FEM). One of the most Fundamental Numerical Techniques Employed in the Numerical Simulation is the SFEM, which Outperforms...
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Evolution of physics-based methodology for exploring the conformational energy landscape of proteins
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Ergodicity and model quality in template-restrained canonical and temperature/Hamiltonian replica exchange coarse-grained molecular dynamics simulations of proteins
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Kinetic flux vector splitting scheme for solving non-reactive multi-component flows
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Protein structure prediction with the UNRES force-field using Replica-Exchange Monte Carlo-with-Minimization; Comparison with MCM, CSA, and CFMC
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An efficient molecular docking using conformational space annealing
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Frequency bands selection of the Portevin–LeChatelier effect
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A high-order compact difference algorithm for half-staggered grids for laminar and turbulent incompressible flows
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Quadratic Cohen representations in spectral analysis of serration process in Al-Mg alloys
PublikacjaIstotny z mechanicznego punktu widzenia efekt Portevina Le-Chateliera charakteryzuje się skomplikowanym profilem widmowym. Jako typowy przykład procesu niestacjonarnego, wymaga specjalnego podejścia umożliwiającego analizę zmian rozkładu energii fluktuacji naprężenia w funkcji odkształcenia. Jako narzędzie umożliwiające realizację powyższego założenia autorzy proponują zastosowanie rodziny przekształceń kwadratowych znanych jako...
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Conformation of six fentanyls revisited
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Theoretical studies of the dependence of nuclear quadrupole coupling constants on intermolecular forces
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CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures
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Evaluation of drawability of tailor-welded blanks made of titanium alloys Grade 2 || Grade 5
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Parallelization Method for a Continuous Property
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Finite Resolution Dynamics
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Generating optimal paths in dynamic environments using RiverFormation Dynamics algorithm
PublikacjaThe paper presents a comparison of four optimisation algorithms implemented for the purpose of finding the shortest path in static and dynamic environments with obstacles. Two classical graph algorithms –the Dijkstra complete algorithm and A* heuristic algorithm – were compared with metaheuristic River Formation Dynamics swarm algorithm and its newly introduced modified version. Moreover, another swarm algorithm has been compared...
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Personalized prediction of the secondary oocytes number after ovarian stimulation: A machine learning model based on clinical and genetic data
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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Frequency bands selection of the Portevin-LeChatelier
PublikacjaEfekt Portevina-LeChateliera ujawnia się w postaci skokowych zmian naprężenia w trakcie procesu odkształcenia próbek pewnych stopów. Zjawisko PLC występuje w kilku odmianach charakteryzujących się istotnymi różnicami zarówno w przestrzennym rozkładzie pasm odkształcenia jak też przebiegu krzywej naprężeniowej. Przebiegi odpowiadające różnym odmianom serration charakteryzują się odmiennymi właściwościami rozkładu energetycznego...
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Weighted Ensemble with one-class Classification and Over-sampling and Instance selection (WECOI): An approach for learning from imbalanced data streams
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Ab initio studies of the structure, physicochemical properties and behavior of lead chlorides and chloroplumbate anions in gaseous and aqueous phases
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Optimal shape design of multi-element trawl-doors using local surrogate models
PublikacjaTrawl-doors have a large influence on the fuel consumption of fishing vessels. Design and optimiza-tion of trawl-doors using computational models are a key factor in minimizing the fuel consump-tion. This paper presents an optimization algorithm for the shape design of trawl-door shapes using computational fluid dynamic (CFD) models. Accurate CFD models are computationally expensive. Therefore, the direct use of traditional optimization...
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Quadratic Cohen representations in spectral analysis of serration process in Al–Mg alloys
PublikacjaImportant 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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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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Structure and properties of liquid Al–Cu alloys: Empirical potentials compared
PublikacjaWe report on the structure and mass transport properties of liquid Al–Cu alloys predicted by two recently-developed empirical many-body potentials: MEAM (Jelinek et al., 2012) and EAM-ADP (Apostol and Mishin, 2011), and by the well-known Gupta potential. Total and partial pair correlation functions, angular distribution functions, densities, coordination numbers and self-diffusion coefficients are compared with published experimental...
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Structure-based design and evaluation of novel N-phenyl-1H-indol-2-amine derivatives for fat mass and obesity-associated (FTO) protein inhibition
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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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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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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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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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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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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Generalized Einstein relation in disordered organic semiconductors: Influence of the acoustic phonons–charge carriers scattering
PublikacjaIn 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
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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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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In-depth characterization of icosahedral ordering in liquid copper
PublikacjaThe 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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Multi-agent large-scale parallel crowd simulation with NVRAM-based distributed cache
PublikacjaThis 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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Applying molecular dynamics simulation to take the fracture fingerprint of polycrystalline SiC nanosheets
PublikacjaGraphene-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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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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Negative Poisson’s ratio from pentagons: A new auxetic structure combining three different auxetic mechanisms
PublikacjaA 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...