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Search results for: PROTEIN STRUCTURE PREDICTION, MULTISCALE MODELING, UNRES FORCE FIELD, FREE AND BIOINFORMATICS-ASSISTED MODELING, REPLICA-EXCHANGE MOLECULAR DYNAMICS
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Nonlinear free and forced vibrations of a dielectric elastomer-based microcantilever for atomic force microscopy
PublicationThe majority of atomic force microcode (AFM) probes work based on piezoelectric actuation. However, some undesirable phenomena such as creep and hysteresis may appear in the piezoelectric actuators that limit their applications. This paper proposes a novel AFM probe based on dielectric elastomer actuators (DEAs). The DE is modeled via the use of a hyperelastic Cosserat model. Size effects and geometric nonlinearity are included...
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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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An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12
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Fiber-optic Fabry-Pérot sensors – modeling versus measurements results
PublicationThis paper describes how parameters of investigated substances and the fiber-optic Fabry-Pérot sensing interferometer affect the spectrum of the optical radiation at the output of the sensor. First, the modeling of the operation of the sensing interferometer was conducted. Most important parameters and effects that were taken into account are: dependences of the refractive indices of the core and the cladding, as well the mode...
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Catalytic Mechanism of Non-Target DNA Cleavage in CRISPR-Cas9 Revealed by Ab Initio Molecular Dynamics
PublicationCRISPR-Cas9 is a cutting-edge genome editing technology, which uses the endonuclease Cas9 to introduce mutations at desired sites of the genome. This revolutionary tool is promising to treat a myriad of human genetic diseases. Nevertheless, the molecular basis of DNA cleavage, which is a fundamental step for genome editing, has not been established. Here, quantum–classical molecular dynamics (MD) and free energy methods are used...
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Modeling of Performance, Reliability and Energy Efficiency in Large-Scale Computational Environments
PublicationLarge scale of complexity of distributed computational systems imposes special challenges for prediction of quality in such systems. Existing quality models for lower-scale systems include functionality, performance, reliability, flexibility and usability. Among these attributes, performance and reliability have a particular significance to the large-scale systems computing quality modeling due to their strong dependence on the...
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Mathematical modeling and prediction of pit to crack transition under cyclic thermal load using artificial neural network
PublicationThe formation of pitting is a major problem in most metals, which is caused by extremely localized corrosion that creates small holes in metal and subsequently, it changes into cracks under mechanical load, thermo-mechanical stress, and corrosion process factors. This research aims to study pit to crack transition phenomenon of steel boiler heat tubes under cyclic thermal load, and mathematical modeling...
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Two-Stage Variable-Fidelity Modeling of Antennas with Domain Confinement
PublicationSurrogate modeling has become the method of choice in solving an increasing number of antenna design tasks, especially those involving expensive full-wave electromagnetic (EM) simulations. Notwithstanding, the curse of dimensionality considerably affects conventional metamodeling methods, and their capability to efficiently handle nonlinear antenna characteristics over broad ranges of the system parameters is limited. Performance-driven...
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Advanced Modeling of Management Processes in Information Technology
PublicationThis book deals with the issues of modeling management processes of information technology and IT projects while its core is the model of information technology management and its component models (contextual, local) describing initial processing and the maturity capsule as well as a decision-making system represented by a multi-level sequential model of IT technology selection, which acquires a fuzzy rule-based implementation...
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Modeling lubricant flow between thrust-bearing pads
PublicationInlet temperature is one of the main inputs in all models for the analysis of fluid film bearing performance. At the same time, inlettemperature distribution and also oil velocity distribution at the inlet are the result of flow phenomena in the gap between the bearingpads. These phenomena are complex and in many cases further affected by any special arrangements of forced oil supply to the gapbetween pads. The reason for such...
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Video DATA - Traffic generation modeling for discount shops - Chrobrego Street
Open Research DataThe data includes video traffic data (vehicles, pedestrians, cyclists) registered at 75 Chrobrego street in Gdansk. The data covers the day 01.10.2020 at 6:00-22:00. The video camera was installed at the parking area belonging to the discount store Lidl. The data obtained was used in analysis, providing information about the modal split, the number...
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Video DATA - Traffic generation modeling for discount shops - Czerska Street
Open Research DataThe data includes video traffic data (vehicles, pedestrians, cyclists) registered at 71 Czerska street in Gdansk. The data covers the day 01.10.2020 at 6:00-22:00. The video camera was installed at the parking area belonging to the discount store Lidl. The data obtained was used in analysis, providing information about the modal split, the number of...
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Video DATA - Traffic generation modeling for discount shops - Gdanska Street
Open Research DataThe data includes video traffic data (vehicles, pedestrians, cyclists) registered at 21C Gdanska street in Gdansk. The data covers the day 01.10.2020 at 6:00-22:00. The video camera was installed at the parking area belonging to the discount store Lidl. The data obtained was used in analysis, providing information about the modal split, the number of...
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Video DATA - Traffic generation modeling for discount shops - Dragana Street
Open Research DataThe data includes video traffic data (vehicles, pedestrians, cyclists) registered at 27 Dragana street in Gdansk. The data covers the day 01.10.2020 at 6:00-22:00. The video camera was installed at the parking area belonging to the discount store Lidl. The data obtained was used in analysis, providing information about the modal split, the number of...
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Application of mesh deformation for modeling of conformal RF components with 3D FEM
PublicationIn this paper, a method of analysis of conformal RF components has been proposed. In this approach, modeling of a curved structure is based on mesh deformation of planar objects rather than the construction of conformal geometry at CSG level. Since the model is represented as a 3D mesh, the deformation only requires the calculation of nodes position in the bent structure. The results of the proposed algorithm have been validated...
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Dynamic Bayesian Networks for Symbolic Polyphonic Pitch Modeling
PublicationSymbolic pitch modeling is a way of incorporating knowledge about relations between pitches into the process of an- alyzing musical information or signals. In this paper, we propose a family of probabilistic symbolic polyphonic pitch models, which account for both the “horizontal” and the “vertical” pitch struc- ture. These models are formulated as linear or log-linear interpo- lations of up to fi ve sub-models, each of which is...
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Toolchain Modeling: Comprehensive Engineering Plans for Industry 4.0
PublicationThe fourth industrial revolution (Industry 4.0) elevates the complexity and autonomy of industrial systems and engineering environments to levels not seen before. The novel challenges involve not only the software running on the partaking autonomous devices, but also architectural considerations and the technological infrastructure around the entire engineering process. In this paper, complementing the trends in industrial systems...
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ENVIRONMENTAL MODELING & ASSESSMENT
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Journal of Mathematical Modeling
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Statistics & Risk Modeling
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Computer Research and Modeling
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Computational Mathematics and Modeling
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Mathematical Modeling and Computing
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NATURAL RESOURCE MODELING
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Journal for Modeling in Ophthalmology
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MODELING IDENTIFICATION AND CONTROL
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Software and Systems Modeling
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Scientific Modeling and Simulations
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Molecular dynamics study of 4-OH-phenylacetyl- D -Y(Me)FQNRPR-NH 2 selectivity to V1a receptor
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A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. III. Determination of scale-consistent backbone-local and correlation potentials in the UNRES force field and force-field calibration and validation
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Performance-Based Nested Surrogate Modeling of Antenna Input Characteristics
PublicationUtilization of electromagnetic (EM) simulation tools is mandatory in the design of contemporary antenna structures. At the same time, conducting designs procedures that require multiple evaluations of the antenna at hand, such as parametric optimization or yield-driven design, is hindered by a high cost of accurate EM analysis. To certain extent, this issue can be addressed by utilization of fast replacement models (also referred...
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Modeling and Evaluation of Electric Treeing Phenomena in Polymeric Cable Insulation
PublicationThis paper investigates the treeing phenomenon in polymeric materials such as crosslinked polyethylene (XLPE) that is widely used in medium and high voltage power cables as primary insulation. The modeling of electrical tree growth in the insulation from its initiation to breakdown is significant research work that illustrates the discharge dynamics and its impact on aging process in polymeric insulation. This study utilizes pulse...
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Modeling pragmatics for visual modeling language evaluation
PublicationPodczas oceny użyteczności języków modelowania wizualnego istnieje potrzeba uwzględnienia ich pragmatyki. Języki modelowania wizualnego mogą być stosowane w różnym kontekście, co powoduje różnice w wymaganiach, które są im stawiane. Jawny opis kontekstu użycia ułatwia precyzyjną ocenę. Pragmatyka składa się ze zbioru profili, które opisują konkretne konteksty użycia. W referacie podjęto próbę zastosowania modeli zadań do opisu...
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Low-Cost Behavioral Modeling of Antennas by Dimensionality Reduction and Domain Confinement
PublicationBehavioral modeling has been rising in importance in modern antenna design. It is primarily employed to diminish the computational cost of procedures involving massive full-wave electromagnetic (EM) simulations. Cheaper alternative offer surrogate models, yet, setting up data-driven surrogates is impeded by, among others, the curse of dimensionality. This article introduces a novel approach to reduced-cost surrogate modeling of...
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Mechanical Properties of Twisted Carbon Nanotube Bundles with Carbon Linkers from Molecular Dynamics Simulations
PublicationThe manufacturing of high-modulus, high-strength fibers is of paramount importance for real-world, high-end applications. In this respect, carbon nanotubes represent the ideal candidates for realizing such fibers. However, their remarkable mechanical performance is difficult to bring up to the macroscale, due to the low load transfer within the fiber. A strategy to increase such load transfer is the introduction of chemical linkers...
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Modeling the debonding process of osseointegrated implants due to coupled adhesion and friction
PublicationCementless implants have become widely used for total hip replacement surgery. The long-term stability of these implants is achieved by bone growing around and into the rough surface of the implant, a process called osseointegration. However, debonding of the bone–implant interface can still occur due to aseptic implant loosening and insufficient osseointegration, which may have dramatic consequences. The aim of this work is to...
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Changes of Conformation in Albumin with Temperature by Molecular Dynamics Simulations
PublicationThis work presents the analysis of the conformation of albumin in the temperature range of 300K – 312K, i.e., in the physiological range. Using molecular dynamics simulations, we calculate values of the backbone and dihedral angles for this molecule. We analyze the global dynamic properties of albumin treated as a chain. In this range of temperature, we study parameters of the molecule and the conformational entropy derived from...
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Modeling the global atmospheric transport and deposition of mercury to the Great Lakes
PublicationMercury contamination in the Great Lakes continues to have important public health and wildlife ecotoxicology impacts, and atmospheric deposition is a significant ongoing loading pathway. The objective of this study was to estimate the amount and source-attribution for atmospheric mercury deposition to each lake, information needed to prioritize amelioration efforts. A new global, Eulerian version of the HYSPLIT-Hg model was used...
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Energy Consumption Modeling in SPMD and DAC Applications
PublicationIn this chapter, we show a study of energy consumption during execution of SPMD and DAC application – the same applications which time of execution we modeled in the previous two chapters. We measured an average power usage at a single node of the GALERA+ cluster during application execution and then we modeled the total energy consumption by the application. Next we simulated the applications using MERPSYS and we compared the...
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Propagation Path Loss Modeling in Container Terminal Environment
PublicationThis paper describes novel method of path loss modeling for radio communication channels in container port area. Multi-variate empirical model is presented, based on multidimensional regression analysis of real path loss measurements from container terminal environment. The measurement instruments used in propagation studies in port area are also described.
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An insight into the mixed quantum mechanical-molecular dynamics simulation of a ZnII-Curcumin complex with a chosen DNA sequence that supports experimental DNA binding investigations
PublicationAn important aspect of research pertaining to Curcumin (HCur) is the need to arrest its degradation in aqueous solution and in biological milieu. This may be achieved through complex formation with metal ions. For this reason, a complex of HCur was prepared with ZnII, that is not likely to be active in redox pathways, minimizing further complications. The complex is monomeric, tetrahedral, with one HCur, an acetate and a molecule...
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An interactive system for remote modeling and design validation of hybrid photovoltaic systems
PublicationIn the paper a multi-functional demonstrator of the interactive system designed to modeling, monitoring and validation of hybrid photovoltaic systems assisted by fuel cells and thermoelectric generators is presented. The purpose of this paper is to report the system solution expressed in the form of a block diagram. Technical parameters of demonstrator components such as: silicon photovoltaic modules, fuel cells, thermoelectric...
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Free surface flow modeling in numerical estimation of flood risk zones: a case study
PublicationNa przykładzie doliny Wisły w Warszawie przedstawiono metodę wyznaczenia stref zagrożenia powodziowego. Symulowana numerycznie powódź wywołana została potencjalnym przerwaniem obwałowania rzeki w okolicach Saskiej Kępy. Do obliczeń zastosowano opracowany w Katedrze Hydrotechniki Wydziału Inżynierii Lądowej i Środowiska Politechniki Gdańskiej model dwuwymiarowego, płaskiego przepływu wody ze swobodną powierzchnią.
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Sławomir Jerzy Ambroziak dr hab. inż.
PeopleSławomir J. Ambroziak was born in Poland, in 1982. He received the M.Sc., Ph.D. and D.Sc. degrees in radio communication from Gdańsk University of Technology (Gdańsk Tech), Poland, in 2008, 2013, and 2020 respectively. Since 2008 he is with the Department of Radiocommunication Systems and Networks of the Gdańsk Tech: 2008-2013 as Research Assistant, 2013-2020 as Assistant Professor, and since 2020 as Associate Professor. He is...
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Modeling of multi-cavity Fabry-Perot optical fiber sensors
PublicationReflectance characteristics of a two-cavity extrinsic Fabry-Perot optical fiber sensor were investigated using computer modeling. Calculations were performed using a plane wave-based approach, selected for clarity of results. Based on the modeling results, it can be concluded that the two-cavity Fabry-Perot interferometer can be used to measure two different quantities, such as refractive index and temperature, independently. It...
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Interaction of amphotericin B and its selected derivatives with membranes: molecular modeling studies
PublicationJest to praca przeglądowa obejmująca krytyczną analizę danych dotyczących oddziaływania amfoterycyny B (AmB) i jej wybranych, mniej toksycznych pochodnych, z błonami lipidowymi. Amfoterycyna B jest antybiotykiem przeciwgrzybowym ale ze względu na jej toksyczność trwają prace nad modyfikacjami chemicznymi tego związku. Celem molekularnym dla tego antybiotyku jest błona lipidowa i dlatego różnicowe powinowactwo AmB i jej pochodnych...
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Modeling lignin extraction with ionic liquids using machine learning approach
PublicationLignin, next to cellulose, is the second most common natural biopolymer on Earth, containing a third of the organic carbon in the biosphere. For many years, lignin was perceived as waste when obtaining cellulose and hemicellulose and used as a biofuel for the production of bioenergy. However, recently, lignin has been considered a renewable raw material for the production of chemicals and materials to replace petrochemical resources....
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Prediction of coking dynamics for wet coal charge
PublicationA one-dimensional transient mathematical model describing thermal and flow phenomena during coal coking in an oven chamber was studied in the paper. It also accounts for heat conduction in the ceramic oven wall when assuming a constant temperature at the heating channel side. The model was solved numerically using partly implicit methods for gas flow and heat transfer problems. The histories of temperature, gas evolution and internal...
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Molecular dynamics and verisimilitude - to what extent can one trust a computational simulation?
PublicationFor the last several tens of years, computer simulations have become of undeniable importance. Molecular Dynamics (MD) simulation techniques are used to examine the phenomena which occur at the level that cannot be observed directly. Thus, they can be successfully exploited in many different scientific fields such as: materials science, applied mathematics and theoretical physics, biochemistry, biophysics or drug design. Despite...
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Modeling and simulation of tool cycle in manufacturing cell
PublicationThe paper addresses issues concerning modeling and analysis of tool flow within a three-machine manufacturing cell used for small batch manufacturing of a definite spectrum of prismatic parts. The approach utilizes a method for job and tool allocation to work centers with limited number of machines and capacity of tool resources, based on the analysis of formalized relations: job - tool sets required. Selected tool flow control...