Search results for: COMPUTATIONAL SYSTEMS
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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
PublicationAccording 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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Toward Mechanosynthesis of Diamondoid Structures: IX Commercial Capped CNT Scanning Probe Microscopy Tip as Nowadays Available Tool for Silylene Molecule and Silicon Atom Transfer
PublicationAccording 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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Measurements and Simulations of Engineered Ultrasound Loudspeakers
PublicationSimulation and measurement results of the sound emitted from an ultrasound custom-made system with high spatial directivity are presented. The proposed system is using modulated ultrasound waves which demodulate in nonlinear medium resulting in audible sound. The system is aimed at enhancing the users’ personal audio space, therefore the measurements are performed using the Head and Torso Simulator which provides realistic reproduction...
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Seismic Pounding Between Bridge Segments: A State-of-the-Art Review
PublicationEarthquake-induced structural pounding in bridge structures has been observed in several previous seismic events. Collisions occur at the expansion joints provided between adjacent decks or between the deck and abutment. Pounding between the structural elements may lead to severe damages and even to the unseating of the bridge in certain cases. Several investigations have been performed to study pounding in bridges under uniform...
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Thermal Buckling Analysis of Circular Bilayer Graphene sheets Resting on an Elastic Matrix Based on Nonlocal Continuum Mechanics
PublicationIn this article, the thermal buckling behavior of orthotropic circular bilayer graphene sheets embedded in the Winkler–Pasternak elastic medium is scrutinized. Using the nonlocal elasticity theory, the bilayer graphene sheets are modeled as a nonlocal double–layered plate that contains small scale effects and van der Waals (vdW) interaction forces. The vdW interaction forces between the layers are simulated as a set of linear springs...
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Mechanism of recognition of parallel G-quadruplexes by DEAH/RHAU helicase DHX36 explored by molecular dynamics simulations
PublicationBecause 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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Differential Quadrature Method for Dynamic Buckling of Graphene Sheet Coupled by a Viscoelastic Medium Using Neperian Frequency Based on Nonlocal Elasticity Theory
PublicationIn the present study, the dynamic buckling of the graphene sheet coupled by a viscoelastic matrix was studied. In light of the simplicity of Eringen's non-local continuum theory to considering the nanoscale influences, this theory was employed. Equations of motion and boundary conditions were obtained using Mindlin plate theory by taking nonlinear strains of von Kármán and Hamilton's principle into account. On the other hand, a...
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Analytical predictions for the buckling of a nanoplate subjected to non-uniform compression based on the four-variable plate theory
PublicationIn the present study, the buckling analysis of the rectangular nanoplate under biaxial non-uniform compression using the modified couple stress continuum theory with various boundary conditions has been considered. The simplified first order shear deformation theory (S-FSDT) has been employed and the governing differential equations have been obtained using the Hamilton’s principle. An analytical approach has been applied to obtain...
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Review of Segmentation Methods for Coastline Detection in SAR Images
PublicationSynthetic aperture radar (SAR) images acquired by airborne sensors or remote sensing satellites contain the necessary information that can be used to investigate various objects of interest on the surface of the Earth, including coastlines. The coastal zone is of great economic importance and is also very densely populated. The intensive and increasing use of coasts and changes of coastlines motivate researchers to try to assess...
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Information retrieval with semantic memory model
PublicationPsycholinguistic 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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Modeling energy consumption of parallel applications
PublicationThe paper presents modeling and simulation of energy consumption of two types of parallel applications: geometric Single Program Multiple Data (SPMD) and divide-and-conquer (DAC). Simulation is performed in a new MERPSYS environment. Model of an application uses the Java language with extension representing message exchange between processes working in parallel. Simulation is performed by running threads representing distinct process...
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Computationally efficient two-objective optimization of compact microwave couplers through corrected domain patching
PublicationFinding an acceptable compromise between various objectives is a necessity in the design of contemporary microwave components and circuits. A primary reason is that most objectives are at least partially conflicting. For compact microwave structures, the design trade-offs are normally related to the circuit size and its electrical performance. In order to obtain comprehensive information about the best possible trade-offs, multi-objective...
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Rapid Design Centering of Multi-Band Antennas Using Knowledge-Based Inverse Models and Response Features
PublicationAccounting for manufacturing tolerances as well as uncertainties concerning operating conditions and material parameters is one of the important yet often neglected aspects of antenna development. Appropriate quantification of uncertainties allows for estimating the fabrication yield but also to carry out robust design (e.g., yield maximization). For reliability reasons, statistical analysis should be executed at the accuracy level...
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Parametrization and Correlation Analysis Applied to Music Mood Classification .
PublicationThe paper presents a study on music mood categorization. First, a review of music mood models is presented. Then, the preparation of a set of music excerpts to be used in the experiments and music parametrization is described. Next, some listening tasks performed to obtain mood descriptors are introduced. Finally,the correlation between mood descriptors and features extracted from parameters is discussed. The paper concludes with...
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Model of Rules for IT Organization Evolution
PublicationThe aim of this paper is to introduce the Model of Rules for IT Organization Evolution which shall be in compliance with the Generic IT Organization Evolution Model. Due to its general nature, a set of practical adjustments is proposed in order to adapt the Generic Model to the IT Service Management domain. Further, two sets of rules describing the evolution of the IT Service Management area are defined based on two types of rules...
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Comprehensive Analysis of MILE Gene Expression Data Set Advances Discovery of Leukaemia Type and Subtype Biomarkers
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Region-Specific Methylation Profiling in Acute Myeloid Leukemia
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Computer-Aided Saturation Mutagenesis of Arabidopsis thaliana Ent-Copalyl Diphosphate Synthase
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Hybrid Obfuscation Technique for Reverse Engineering Problems
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Designing Aggregate KPIs as a Method of Implementing Decision-Making Processes in the Management of Smart Cities
PublicationThe aim of the paper is to present a concept of measuring the performance of city management processes by use of a concept of aggregate KPIs. In the management of organizations and, as a consequence of the use of a common design framework also in the management of cities, silo KPIs are commonly used to show the statuses of the processes of organizations/cities. Thus the question arises as to what extent aggregate KPIs, as proposed...
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Vibration of the bridge under moving singular loads - theoretical formulation and numerical solution
PublicationThe paper presents the results of the numerical analysis of a simple vehicle passing over a simply supported bridge span. The bridge is modelled by a Euler-Bernoulli beam. The vehicle is modelled as a linear, visco-elastic oscillator, moving at a constant speed. The system is described by a set of differential equations of motion and solved numerically using the Runge-Kutta algorithm. The results are compared with the solution...
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ON DYNAMICS OF ELASTIC NETWORKS WITH RIGID JUNCTIONS WITHIN NONLINEAR MICRO-POLAR ELASTICITY
PublicationWithin the nonlinear micropolar elasticity we discuss effective dynamic (kinetic) properties of elastic networks with rigid joints. The model of a hyperelastic micropolar continuum is based on two constitutive relations, i.e., static and kinetic ones. They introduce a strain energy density and a kinetic energy density, respectively. Here we consider a three-dimensional elastic network made of three families of elastic fibers connected...
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Fast Antenna Optimization Using Gradient Monitoring and Variable-Fidelity EM Models
PublicationAccelerated simulation-driven design optimization of antenna structures is proposed. Variable-fidelity electromagnetic (EM) analysis is used as well as the trust-region framework with limited sensitivity updates. The latter are controlled by monitoring the changes of the antenna response gradients. Our methodology is verified using three compact wideband antennas. Comprehensive benchmarking demonstrates its superiority over both...
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Low-Cost Surrogate Modeling of Miniaturized Microwave Components Using Nested Kriging
PublicationIn the paper, a recently reported nested kriging methodology is employed for modeling of miniaturized microwave components. The approach is based on identifying the parameter space region that contains high-quality designs, and, subsequently, rendering the surrogate in this subset. The results obtained for a miniaturized unequal-power-split rat-race coupler and a compact three-section impedance transformer demonstrate reliability...
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Nested Kriging Surrogates for Rapid Multi-Objective Optimization of Compact Microwave Components
PublicationA procedure for rapid EM-based multi-objective optimization of compact microwave components is presented. Our methodology employs a recently developed nested kriging modelling to identify the search space region containing the Pareto-optimal designs, and to construct a fast surrogate model. The latter permits determination of the initial Pareto set, further refined using a separate surrogate-assisted process. As an illustration,...
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Spatial aspects of urban air quality management: Estimating the impact of micro-scale urban form on pollution dispersion
PublicationUrban planning and design solutions affect urban ventilation conditions, thus mitigating the effects of atmospheric pollution. However, these findings are not being implemented in the planning practice to a sufficient extent, partly due to the lack of specific guidelines. Moreover, many urban air quality monitoring (AQM) sites have low represnentativeness and thus do not provide comprehensive data for effective urban air pollution control...
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Hydrodynamic reanalysis of currents in the Baltic Sea using the PM3D model
Open Research DataThe dataset contains the results of numerical modeling of currents in the Baltic Sea since 1998. A long-term reanalysis was performed using a three-dimensional hydrodynamic model PM3D (Kowalewski and Kowalewska-Kalkowska, 2017), a new version of the M3D model (Kowalewski, 1997).
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Matching Split Distance for Unrooted Binary Phylogenetic Trees
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Matching Split Distance for Unrooted Binary Phylogenetic Trees
PublicationRekonstrukcja drzew ewolucji jest jednym z głównych celów w bioinformatyce. Drzewa filogenetyczne reprezentuje historię ewolucji i związki pokrewieństwa między różnymi gatunkami. W pracy proponujemy nową ogólną metodę określania odległości między nieukorzenionymi drzewami filogenetycznymi, szczególnie użyteczną dla dużych zbiorów gatunków. Następnie podajemy szczegółowe własności jednej metryki określonej przy użyciu tej metody...
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Molecular modeling and evaluation of novel dibenzopyrrole derivatives as telomerase inhibitors and potential drug for cancer therapy
PublicationDuring previous years, many studies on synthesis, as well as on anti-tumor, anti-inflammatory and anti-bacterial activities of the pyrazole derivatives have been described. Certain pyrazole derivatives exhibit important pharmacological activities and have proved to be useful template in drug research. Considering importance of pyrazole template, in current work the series of novel inhibitors were designed by replacing central...
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3D Computer Model of the Hip Joint Cartilage
PublicationThis paper presents 3D computer model of the hip joint cartilage in the ANSYS program. Model is made on the basis of anatomy and collected data on the material constants of bone and cartilage components. Analysis and comparison of biochemical model, viscoelastic and molecular mixed - aggregation serves to facilitate the creation of the next model of reality, which could be used in the design of joint prostheses. The correctness...
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GaMRed – adaptive filtering of high-throughput biological data
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Adjustment for shape restoration and force control of cable arch stayed bridges
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Pre‐exascale HPC approaches for molecular dynamics simulations. Covid‐19 research: A use case
PublicationExascale computing has been a dream for ages and is close to becoming a reality that will impact how molecular simulations are being performed, as well as the quantity and quality of the information derived for them. We review how the biomolecular simulations field is anticipating these new architectures, making emphasis on recent work from groups in the BioExcel Center of Excellence for High Performance Computing. We exemplified...
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Establishing the allosteric mechanism in CRISPR‐Cas9
PublicationAllostery is a fundamental property of proteins, which regulates biochemical information transfer between spatially distant sites. Here, we report on the critical role of molecular dynamics (MD) simulations in discovering the mechanism of allosteric communication within CRISPR‐Cas9, a leading genome editing machinery with enormous promises for medicine and biotechnology. MD revealed how allostery intervenes during at least three...
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Long-term hindcast simulation of sea ice in the Baltic Sea
Open Research DataThe data set contains the results of numerical modeling of sea ice over a period of 50 years (1958-2007) in the Baltic Sea. A long-term hindcast simulation was performed using a three-dimensional hydrodynamic model PM3D (Kowalewski and Kowalewska-Kalkowska, 2017), a new version of the M3D model (Kowalewski, 1997). A numerical dynamic-thermodynamic model...
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Hydrodynamic reanalysis of ice conditions in the Baltic Sea using the PM3D model
Open Research DataThe dataset contains the results of numerical modeling of sea ice in the Baltic Sea since 1998. A long-term reanalysis was performed using the three-dimensional hydrodynamic model PM3D (Kowalewski and Kowalewska-Kalkowska, 2017), a new version of the M3D model (Kowalewski, 1997). A numerical dynamic-thermodynamic model of sea ice (Herman et al. 2011)...
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Uniform expansion estimates in the quadratic map as a function of the parameter, with a large range of parameters
Open Research DataThis dataset contains selected results of numerical computations described in the paper "Quantitative hyperbolicity estimates in one-dimensional dynamics" by S. Day, H. Kokubu, S. Luzzatto, K. Mischaikow, H. Oka, P. Pilarczyk, published in Nonlinearity, Vol. 21, No. 9 (2008), 1967-1987, doi: 10.1088/0951-7715/21/9/002.
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Uniform expansion estimates in the quadratic map as a function of the parameter, with a very small critical neighborhood
Open Research DataThis dataset contains selected results of numerical computations described in the paper "Quantitative hyperbolicity estimates in one-dimensional dynamics" by S. Day, H. Kokubu, S. Luzzatto, K. Mischaikow, H. Oka, P. Pilarczyk, published in Nonlinearity, Vol. 21, No. 9 (2008), 1967-1987, doi: 10.1088/0951-7715/21/9/002.
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Hydrodynamic reanalysis of sea level in the Baltic Sea using the PM3D model
Open Research DataThe data set contains the results of numerical modelling of sea level fluctuations in the Baltic Sea in the Baltic Sea since 1998. A long-term reanalysis was performed using a three-dimensional hydrodynamic model PM3D (Kowalewski and Kowalewska-Kalkowska, 2017), a new version of the M3D model (Kowalewski, 1997).
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Computer aided materials design of PM duplex stainless steels
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On the importance of volume of eroded material for cavitation erosion
PublicationW pracy przedstawiono model matematyczny opisujący wpływ objętości erodowanego materiału na przebieg krzywych erozji kawitacyjnej
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Modelling of heat and mass transfer through wooden buildings
PublicationThe aim of this review paper is to examine the most recent available studies dealing with theoretical, numerical and experimental aspects related to modelling of heat and mass transfer through wooden buildings. The main thermophysical, mechanical and hygrometric properties of wood are firstly discussed. Then, the basic governing equations of heat and mass transfer phenomena are presented. A detailed description of the physical...
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Uniform expansion estimates in the quadratic map as a function of the partition size, using Johnson’s algorithm
Open Research DataThis dataset contains selected results of numerical computations described in the paper "Quantitative hyperbolicity estimates in one-dimensional dynamics" by S. Day, H. Kokubu, S. Luzzatto, K. Mischaikow, H. Oka, P. Pilarczyk, published in Nonlinearity, Vol. 21, No. 9 (2008), 1967-1987, doi: 10.1088/0951-7715/21/9/002.
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Uniform expansion estimates in the quadratic map with the smallest critical neighborhood for which the expansion exponent λ0 is positive
Open Research DataThis dataset contains selected results of numerical computations described in the paper "Quantitative hyperbolicity estimates in one-dimensional dynamics" by S. Day, H. Kokubu, S. Luzzatto, K. Mischaikow, H. Oka, P. Pilarczyk, published in Nonlinearity, Vol. 21, No. 9 (2008), 1967-1987, doi: 10.1088/0951-7715/21/9/002.
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Uniform expansion estimates in the quadratic map as a function of the partition size, computing λ only
Open Research DataThis dataset contains selected results of numerical computations described in the paper "Quantitative hyperbolicity estimates in one-dimensional dynamics" by S. Day, H. Kokubu, S. Luzzatto, K. Mischaikow, H. Oka, P. Pilarczyk, published in Nonlinearity, Vol. 21, No. 9 (2008), 1967-1987, doi: 10.1088/0951-7715/21/9/002.
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Uniform expansion estimates in the quadratic map as a function of the partition size, using the “derivative” partition type
Open Research DataThis dataset contains selected results of numerical computations described in the paper "Quantitative hyperbolicity estimates in one-dimensional dynamics" by S. Day, H. Kokubu, S. Luzzatto, K. Mischaikow, H. Oka, P. Pilarczyk, published in Nonlinearity, Vol. 21, No. 9 (2008), 1967-1987, doi: 10.1088/0951-7715/21/9/002.
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Uniform expansion estimates in the cubic map as a function of the parameter
Open Research DataThis dataset contains selected results of numerical computations described in the paper "Quantitative hyperbolicity estimates in one-dimensional dynamics" by S. Day, H. Kokubu, S. Luzzatto, K. Mischaikow, H. Oka, P. Pilarczyk, published in Nonlinearity, Vol. 21, No. 9 (2008), 1967-1987, doi: 10.1088/0951-7715/21/9/002.
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Uniform expansion estimates in the quadratic map with the smallest critical neighborhood for which the expansion exponent λ is positive
Open Research DataThis dataset contains selected results of numerical computations described in the paper "Quantitative hyperbolicity estimates in one-dimensional dynamics" by S. Day, H. Kokubu, S. Luzzatto, K. Mischaikow, H. Oka, P. Pilarczyk, published in Nonlinearity, Vol. 21, No. 9 (2008), 1967-1987, doi: 10.1088/0951-7715/21/9/002.
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Hydrodynamic reanalysis of water temperature and salinity in the Baltic Sea using the PM3D model
Open Research DataThe dataset contains the results of numerical modeling of water temperature and salinity in the Baltic Sea since 1998. A long-term reanalysis was performed using the three-dimensional hydrodynamic model PM3D (Kowalewski and Kowalewska-Kalkowska, 2017), a new version of the M3D model (Kowalewski, 1997). A numerical dynamic-thermodynamic model of sea...