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Wyniki wyszukiwania dla: computational systems
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Conformation of six fentanyls revisited
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On the decomposition of stochastic cellular automata
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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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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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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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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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A Multi-Fidelity Surrogate-Model-Assisted Evolutionary Algorithm for Computationally Expensive Optimization Problems
PublikacjaIntegrating 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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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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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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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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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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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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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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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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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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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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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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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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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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A new approach to design of weather disruption-tolerant wireless mesh networks
PublikacjaWireless Mesh Networks, offering transmission rates of 1–10 Gb/s per a millimeter-wave link (utilizing the 71–86 GHz band) seem to be a promising alternative to fiber optic backbone metropolitan area networks because of significantly lower costs of deployment and maintenance. However, despite providing high transmission rates in good weather conditions, high-frequency wireless links are very susceptible to weather disruptions....
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Low-Cost and Precise Automated Re-Design of Antenna Structures Using Interleaved Geometry Scaling and Gradient-Based Optimization
PublikacjaDesign of contemporary antennas is an intricate endeavor involving multiple stages, among others, tuning of geometry parameters. In particular, re-designing antennas to different operating frequencies, makes parametric optimization imperative to ensure the best achievable system performance. If the center frequency at the current design is distant from the target one, local tuning methods generally fail, whereas global algorithms...
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Prediction of maximum tensile stress in plain-weave composite laminates with interacting holes via stacked machine learning algorithms: A comparative study
PublikacjaPlain weave composite is a long-lasting type of fabric composite that is stable enough when being handled. Open-hole composites have been widely used in industry, though they have weak structural performance and complex design processes. An extensive number of material/geometry parameters have been utilized for designing these composites, thereby an efficient computational tool is essential for that purpose. Different Machine Learning...
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Comparative Analysis of Text Representation Methods Using Classification
PublikacjaIn our work, we review and empirically evaluate five different raw methods of text representation that allow automatic processing of Wikipedia articles. The main contribution of the article—evaluation of approaches to text representation for machine learning tasks—indicates that the text representation is fundamental for achieving good categorization results. The analysis of the representation methods creates a baseline that cannot...
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NVRAM as Main Storage of Parallel File System
PublikacjaModern cluster environments' main trouble used to be lack of computational power provided by CPUs and GPUs, but recently they suffer more and more from insufficient performance of input and output operations. Apart from better network infrastructure and more sophisticated processing algorithms, a lot of solutions base on emerging memory technologies. This paper presents evaluation of using non-volatile random-access memory as a...
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Information retrieval with semantic memory model
PublikacjaPsycholinguistic theories of semantic memory form the basis of understanding of natural language concepts. These theories are used here as an inspiration for implementing a computational model of semantic memory in the form of semantic network. Combining this network with a vector-based object-relation-feature value representation of concepts that includes also weights for confidence and support, allows for recognition of concepts...
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Mechanism of recognition of parallel G-quadruplexes by DEAH/RHAU helicase DHX36 explored by molecular dynamics simulations
PublikacjaBecause of high stability and slow unfolding rates of G-quadruplexes (G4), cells have evolved specialized helicases that disrupt these non-canonical DNA and RNA structures in an ATP-dependent manner. One example is DHX36, a DEAH-box helicase, which participates in gene expression and replication by recognizing and unwinding parallel G4s. Here, we studied the molecular basis for the high affinity and specificity of DHX36 for parallel-type...
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Applications of water molecules for analysis of macromolecule properties
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Mechanism of recognition of parallel G-quadruplexes by DEAH/RHAU helicase DHX36 explored by molecular dynamics simulations
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Toward a universal Embedded-Atom Method: II. A set of transferable denisty and dimmer referenced embedding energy functions for all elements of the periodic table as tool for removing two gauge degrees of freedom in EAM potentials
PublikacjaZestaw kluczowych właściwości homodwuatomowych cząsteczek o Z ≤ 103 (równowagowa odległość między atomami re, energia dysocjacji DO, Liczba falowa drgań ωe) zostały zestawione na bazie dostępnych danych eksperymantalnych oraz obliczeń za pomocą teorii funkcjonałów gęstości elektronowej B3LYP/SBKJC.
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Construction of highly stable parallel two-step Runge-Kutta methods for delay differential equations
PublikacjaW pracy pokazano, że każda A-stabilna dwukrokowa metoda Rungego-Kutty dla równań różniczkowych zwyczajnych rzędu p1 i rzędu etapowego q=p1 może być uogólniona do P-stabilnej metody dla równań różniczkowych z opóźnieniem zbieżnej jednostajnie z rzędem p=p1.
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CALCULATOR FOR FINDING COMPOSITION OF (Me1)x1(Me2)x2(CcHhNnOo)x3(NO3)x4(H2O)x5(Cl)x6 TYPE COMPLEX FROM ELEMENTAL ANALYSIS DATA
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Toward Mechanosynthesis of Diamondoid Structures: IX Commercial Capped CNT Scanning Probe Microscopy Tip as Nowadays Available Tool for Silylene Molecule and Silicon Atom Transfer
PublikacjaAccording to K. E. Drexler, advanced mechanosynthesis will employ advanced nanomachines, but advanced nanomachines will themselves be product of advanced mechanosynthesis. This circular relationship must be broken in SPM technology development. In the article, the possibility of use easy available commercial CNT tips to assembly silicon-based intermediate generations of nano-devices is considered. Mechanosynthesis of a target class...
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Toward Mechanosynthesis of Diamondoid Structures: X. Commercial Capped CNT SPM Tip as Nowadays Available C2 Dimer Placement Tool for Tip-Based Nanofabrication
PublikacjaAccording to Drexler, advanced mechanosynthesis will employ advanced nano-machines, but advanced nano-machines will themselves be products of advanced mechanosynthesis. This circular relationship must be broken via TBN technology development. In this article, the possibility of using easily available commercial CNT tips to assemble carbon-based intermediate generations of nano-devices is considered. Mechanosynthesis of a target...
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Quasi-solutions for generalized second order differential equations with deviating arguments
PublikacjaThis paper deal with boundary value problems for generalized second order differential equations with deviating arguments. Existence of quasi-solutions and solutions are proved by monotone iterative method. Examples with numerical results are added.
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Toward Mechanosynthesis of diamondoid structures: III. Quantum-chemical study of silylene molecule and silicon atom transfer mechanism from caped SWCNT tip to the reaction center on a hydrogenated Si(111) surface
PublikacjaOpublikowana wcześniej (Modelling Simul. Mater. Sci. Eng., Vol. 7, 1999, pp. 43-58) strategia mechanosyntezy struktur krzemu na uwodornionej płaszczyźnie Si(111) została poszerzona poprzez uwzględnienie ostrza w postaci zamkniętej SWCNT jako urządzenia kontrolującego położenie cząsteczki sililenu oraz atomu krzemu.
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Resolving the role of podoplanin in the motility of papillary thyroid carcinoma-derived cells using RNA sequencing
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Derivation of continuous explicit two-step Runge-Kutta methods oforder three
PublikacjaW pracy podana jest konstrukcja ciągłych rozszerzeń dla nowych reprezentacji dwukrokowych metod Rungego-Kutty rzędu trzeciego. Podane zostały metody oceny błędu lokalnego metody oraz opisany został sposób implementacji tych metod dla zmiennego kroku. Przeprowadzono szereg eksperymentów numerycznych pokazujących ich efektywność i konkurencyjność dla programu dde23 z Matlabu.
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Cooperative mobile guards in grids
PublikacjaPraca dotyczy problemu strzeżenia dwuwymiarowych krat ortogonalnych, przy założeniu, że obszar widoczności strażnika obejmuje jedną ulicę oraz wszystkie ulice ją przecinające. Rozważano wariant straży słabo współpracujących, w którym dodatkowo każdy strażnik musi widzieć przynajmniej jednego innego strażnika. Podano dowód NP-trudności problemu optymalizacyjnego w przypadku ogólnym, algorytm dokładny o złożoności O(n log n) dla...
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Initializing the EM Algorithm for Univariate Gaussian, Multi-Component, Heteroscedastic Mixture Models by Dynamic Programming Partitions
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State-of-the-Art Review on Determining One-Dimensional Consolidation Parameters Based on Compression and Distribution of Pore Water Pressure: Coefficient of Consolidation (cv), End of Primary (EOP) Consolidation
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THE PERFORMANCE OF SELECTED AB INITIO METHODS IN ESTIMATING ELECTRON BINDING ENERGIES OF SUPERHALOGEN ANIONS
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From the Dynamic Lattice Liquid Algorithm to the Dedicated Parallel Computer – mDLL Machine
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Monotone and numerical analytic- methods for differential equations.
PublikacjaPraca dotyczy problemu różniczkowo-całkowego (typu Fredholma) z ogólnym warunkiem początkowo-brzegowo-całkowym. W pierwszej części pracy, stosując metodę iteracji monotonicznych, sformułowano warunki dostateczne które gwarantują, że dyskutowany problem ma rozwiązanie ekstremalne w zbiorze generowanym przez dolne i górne rozwiązania. Rozważania teoretyczne poparto przykładem i dyskusją. W drugiej części pracy zastosowano metodę...
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Existence of solutions of boundary value problems for differential equations with delayed arguments.
PublikacjaPodane zostały warunki dostateczne na istnienie i jednoznaczność rozwiązań problemów brzegowych dla równań różniczkowych z odchylonymi argumentami.Problem istnienia ekstremalnych rozwiązań również był przedmiotem badań. Podano konstrukcję monotonicznych iteracji i pokazano, że iteracje te są zbieżne do szukanego rozwiązania. Praca zawiera przykłady które ilustrują ogólną teorię.
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A Comparison between MD and EXAFS extracted Structural Data for TernaryRbBr(1-x)Ix.
PublikacjaStrukturę trójskładnikowych soli poddano analizie za pomocą metody EXAFS i symulacji M-D. Przedyskutowano przydatność używanego w symulacjach potencjału oddziaływań międzyatomowych.
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Structure of Small Platinum Clusters Revised
PublikacjaW pracy opisano wyniki obliczeń metodą DFT struktury 2-15 atomowych klastrów platyny.