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Search results for: PROTEIN-STRUCTURE MODELING, COARSE GRAINING, UNRES MODEL OF POLYPEPTIDE CHAINS, MOLECULAR DYNAMICS, DATA-ASSISTED SIMULATIONS
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Elastic-contractile model proteins: Physical chemistry, protein function and drug design and delivery
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The Boltzmann sequence-structure channel
PublicationWe rigorously study a channel that maps binary sequences to self-avoiding walks in the two-dimensional grid, inspired by a model of protein statistics. This channel, which we also call the Boltzmann sequence-structure channel, is characterized by a Boltzmann/Gibbs distribution with a free parameter corresponding to temperature. In our previous work, we verified experimentally that the channel capacity has a phase transition for...
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Dependence between Ionic Liquid Structure and Mechanism of Visible-Light-Induced Activity of TiO2 Obtained by Ionic-Liquid-Assisted Solvothermal Synthesis
PublicationBecause of the tremendous structural diversityof ionic liquids (ILs), simple transfer of observations performed for one IL used for IL-TiO2 preparation on different samples is not possible. Therefore, four ionic liquids, all containing distinct nitrogen-bearing organic cations (pyridinium, pyrrolidinium, ammonium, imidazolium), were used for the first time for the preparation of IL-TiO2 composites. The role of the individual IL...
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Indirect adaptive controller based on a self-structuring fuzzy system for nonlinear modeling and control
PublicationIn this paper, a unified nonlinear modeling and control scheme is presented. A self-structuring Takagi-Sugeno (T-S) fuzzymodel is used to approximate the unknown nonlinear plant based on I/O data collected on-line. Both the structure and theparameters of the T-S fuzzy model are updated by an on-line clustering method and a recursive least squares estimation(RLSE) algorithm. The rules of the fuzzy model can be added, replaced or...
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Selection and Setting of an Intelligent Fuzzy Regulator based on Nonlinear Model Simulations of a Helicopter in Hover
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Anisotropic stochastic dispersion model for large-eddy simulations of particle-laden turbulent flows
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Model test and numerical simulations of earth pressure of non-cohesive soil in 3D formulation.
PublicationW pracy przedstawiono wyniki badań modelowych i obliczeń numerycznych parcia gruntu niespoistego w układzie przestrzennym działajacego na sztywną ścia- nę oporową. Podstawowe schematy wyznaczenia parcia gruntu na sztywną ścianę oporową opatre sa na obrocie ściany wokół jej wierzchołka i podstawy. Uzys- kane wyniki obliczeń przedstawiono jako rozkład składowych statycznych i normalnych wzdłuż sciany. Podano również wypadową parcia...
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Effect of steel fibres on concrete behavior in 2D and 3D simulations using lattice model.
PublicationW artykule przedstawiono wyniki numerycznej symulacji betonu zbrojonego włóknami stalowymi. Beton został opisany w skali mezo jako materiał 3-fazowy przy zastosowaniu modelu sieciowego. Obliczenia wykonano dla rozciągania jednoosiowego. Porównano ze sobą wyniki dwu- i trójwymiarowe.
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Asking Data in a Controlled Way with Ask Data Anything NQL
PublicationWhile to collect data, it is necessary to store it, to understand its structure it is necessary to do data-mining. Business Intelligence (BI) enables us to make intelligent, data-driven decisions by the mean of a set of tools that allows the creation of a potentially unlimited number of machine-generated, data-driven reports, which are calculated by a machine as a response to queries specified by humans. Natural Query Languages...
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Expedited Trust-Region-Based Design Closure of Antennas by Variable-Resolution EM Simulations
PublicationThe observed growth in the complexity of modern antenna topologies fostered a widespread employment of numerical optimization methods as the primary tools for final adjustment of the system parameters. This is mainly caused by insufficiency of traditional design closure approaches, largely based on parameter sweeping. Reliable evaluation of complex antenna structures requires full-wave electromagnetic (EM) analysis. Yet, EM-driven...
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Chitosan-protein scaffolds loaded with lysostaphin as potential antistaphylococcal wound dressing materials.
PublicationAIMS: The development of technology for preparing chitosan-protein scaffolds loaded with lysostaphin, which potentially could be used as dressing for wound treatment and soft tissue infections caused by Staphylococcus aureus. METHODS AND RESULTS: The unique technology of chitosan solubilization using gaseous CO(2) instead of organic or inorganic acids was used for the incorporation of lysostaphin, the enzyme that exhibits bactericidal...
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Fractional Calculus Evaluation of Hyaluronic Acid Crosslinking in a Nanoscopic Part of Articular Cartilage Model System
PublicationThis work presents a study of the mechanism of physical crosslinking of hyaluronic acid in the presence of common phospholipids in synovial joint organ systems. Molecular dynamic simulations have been executed to understand the formation of hyaluronan networks at various phospholipid concentrations. The results of the simulations suggest that the mechanisms exhibit subdiffusion characteristics. Transportation quantities derive...
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Data librarian and data steward – new tasks and responsibilities of academic libraries in the context of Open Research Data implementation in Poland
PublicationThesis/Objective – The policy of Open Access (OA) for researching resources in Europe has been implemented for more than 10 years. The first recommendations concerning providing OA to scientific materials were defined during the implementation of the 7th Framework Programme. Introducing another set of recommendations concerning OA to research data was the next stage. The recommendations were transformed into obligations under the...
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Surrogate-Assisted Design of Checkerboard Metasurface for Broadband Radar Cross-Section Reduction
PublicationMetasurfaces have been extensively exploited in stealth applications to reduce radar cross section (RCS). They rely on the manipulation of backward scattering of electromagnetic (EM) waves into various oblique angles. However, arbitrary control of the scattering properties poses a significant challenge as a design task. Yet it is a principal requirement for making RCS reduction possible. This article introduces a surrogate-based...
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Molecular Simulation Study of the Potentials of Mean Force for the Interactions between Models of Like-Charged and between Charged and Nonpolar Amino Acid Side Chains in Water
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Evaluating experimental molecular physics studies of radiation damage in DNA*
PublicationThe field of Atomic and Molecular Physics (AMP) is a mature field exploring the spectroscopy, excitation, ionisation of atoms and molecules in all three phases. Understanding of the spectroscopy and collisional dynamics of AMP has been fundamental to the development and application of quantum mechanics and is applied across a broad range of disparate disciplines including atmospheric sciences, astrochemistry, combustion and environmental...
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Mathematical Modeling of Hydrodynamics in Bioreactor by Means of CFD-Based Compartment Model
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GIS-based hydrodynamic modeling for urban flood mitigation in fast-growing regions: a case study of Erbil, Kurdistan Region of Iraq
PublicationFloods threaten urban infrastructure, especially in residential neighborhoods and fast-growing regions. Flood hydrodynamic modeling helps identify flood-prone locations and improve mitigation plans' resilience. Urban floods pose special issues due to changing land cover and a lack of raw data. Using a GIS-based modeling interface, input files for the hydrodynamic model were developed. The physical basin's properties were identified...
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Automated Valuation Model based on fuzzy and rough set theory for real estate market with insufficient source data
PublicationObjective monitoring of the real estate value is a requirement to maintain balance, increase security and minimize the risk of a crisis in the financial and economic sector of every country. The valuation of real estate is usually considered from two points of view, i.e. individual valuation and mass appraisal. It is commonly believed that Automated Valuation Models (AVM) should be devoted to mass appraisal, which requires a large...
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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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Self-healing mechanism of metallopolymers investigated by QM/MM simulations and Raman spectroscopy
PublicationThe thermally induced self-healing mechanisms in metallopolymers based on bisterpyridine complexes of iron(II) sulfate and cadmium(II) bromide, respectively, were studied by means of combined quantum mechanical/molecular mechanical (QM/MM) simulations and Raman spectroscopy. Two possible healing schemes, one based on a decomplexation of the cross-linking complexes and a second one relying on the dissociation of ionic clusters,...
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Coarse-Grained Models of Proteins: Theory and Applications
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"Creating a numerical model of noise conditions based on the analysis of traffic volume changes in cities with low and medium structure.
PublicationThe subject of this research study is to analyze noise conditions of the selected area in the city of Gdańsk using data related to traffic volume changes during a day. This is because daily distribution of noise levels is much more helpful for noise control and reduction than traditional maps with Lden levels indicated. Calculations are made with the use of a numerical model developed at the Gdansk Univ. of Technology and implemented...
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"Creating a numerical model of noise conditions based on the analysis of traffic volume changes in cities with low and medium structure.
PublicationThe subject of this research study is to analyze noise conditions of the selected area in the city of Gdańsk using data related to traffic volume changes during a day. This is because daily distribution of noise levels is much more helpful for noise control and reduction than traditional maps with Lden levels indicated. Calculations are made with the use of a numerical model developed at the Gdansk Univ. of Technology and implemented...
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Protein thermal stabilization in aqueous solutions of osmolytes
PublicationProteins’ thermal stabilization is a significant problem in various biomedical, biotechnological, and technological applications. We investigated thermal stability of hen egg white lysozyme in aqueous solutions of the following stabilizing osmolytes: Glycine (GLY), N-methylglycine (NMG), N,N-dimethylglycine (DMG), N,N,N-trimethylglycine (TMG), and trimethyl-N-oxide (TMAO). Results of CD-UV spectroscopic investigation were compared...
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Analysis of Reconstituted Tripartite Complex Supports Avidity-based Recruitment of Hsp70 by Substrate Bound J-domain Protein
PublicationHsp70 are ubiquitous, versatile molecular chaperones that cyclically interact with substrate protein(s). The initial step requires synergistic interaction of a substrate and a J-domain protein (JDP) cochaperone, via its J-domain, with Hsp70 to stimulate hydrolysis of its bound ATP. This hydrolysis drives conformational changes in Hsp70 that stabilize substrate binding. However, because of the transient nature of substrate and JDP...
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Modeling BIM Objects From Point Clouds. Examples
PublicationThe article presents several ways to obtain BIM (Building Information Modeling) models from point clouds using standard commands in Revit 2018. In Revit geometric forms are possible to obtain in project, family or conceptual environments. Efficient modeling requires knowledge of methods of creating families and components in these environments and ways to combine them. Modeling methods with system and loadable families are presented,...
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Membrane structure and interactions of peptide hormones with model lipid bilayers
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Mechanical model of fascia-implant structure. Finite element simulation.
PublicationPraca dotyczy modelowania i symulacji syntetycznych implantów chirurgicznych stosowanych w leczeniu przepulin brzusznych metodą laparoskowpową. Prponowane są modele matematyczne a ich prawidłowość weryfikowana jest na podstawie badań doświadczalnych zachowania się modeli fizycznych wszczepionych implantów pod wpływem obciążeń wynikających z fizjologii człowieka. Nakreślona jest metodologia oceny trwałości połączenia siatki chirurgicznej...
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Combining Road Network Data from OpenStreetMap with an Authoritative Database
PublicationComputer modeling of road networks requires detailed and up-to-date dataset. This paper proposes a method of combining authoritative databases with OpenStreetMap (OSM) system. The complete route is established by finding paths in the graph constructed from partial data obtained from OSM. In order to correlate data from both sources, a method of coordinate conversion is proposed. The algorithm queries road data from OSM and provides...
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Reliability Modeling for SPMD and DAC Applications in MERPSYS
PublicationIn this chapter we shall see a method for modeling of reliability of application execution in the MERPSYS system, and the results of reliability simulation of the same SPMD and DAC application which we have previously presented in this book. Unlike energy usage modeling and modeling of execution efficiency we could not compare the reliability model and simulation results to real experiment just because the experiment would last too...
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An interactive system for remote modeling and design validation of hybrid photovoltaic systems
PublicationAbstract: A multi-functional demonstrator of the interactive system is presented. The demostrator enables modeling, monitoring and design validation of hybrid photovoltaic systems assisted by fuel cells and thermoelectric generators, as well as experimentation and scientific research. A block diagram of the system is presented and the selection of its components is discussed. Availability of the system via Ethernet or GSM...
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Band structure, Born effective charges, and lattice dynamics of CuInS2 from ab initio calculations
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Microwave-assisted synthesis of zinc derivatives of potato starch
PublicationZincatated potato starch was prepared in a solid-state, microwave-assisted reaction using generated in situ sodium tetrahydroxozincate [Na2Zn(OH)4]. For comparison, zincatation of starch was also carriedout on convectional heating. Depending on the irradiation conditions, the products of either mono- or crosslinking esterification were formed. Higher power applied at shorter exposition offered products ofmonoesterification, and...
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Data regarding a new, vector-enzymatic DNA fragment amplification-expression technology for the construction of artificial, concatemeric DNA, RNA and proteins, as well as biological effects of selected polypeptides obtained using this method
PublicationApplications of bioactive peptides and polypeptides are emerging in areas such as drug development and drug delivery systems. These compounds are bioactive, biocompatible and represent a wide range of chemical properties, enabling further adjustments of obtained biomaterials. However, delivering large quantities of peptide derivatives is still challenging. Several methods have been developed for the production of concatemers –...
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Molecular simulation study of cooperativity in hydrophobic association
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Rigid finite elements and multibody modeling in analyses of a robot shaped elastic/plastic deformations of a beam
PublicationDynamics analysis of a system composed of a parallel manipulator and of an elastic beam is presented in the paper. Classic 3RRR parallel manipulator is considered and used to deform the beam. Elasto-plastic deformations are investigated. Rigid-finite-elements technique is employed to deal with dynamics of the beam. A multibody structure is associated with the introduced hybrid system in order to model its dynamics. Idea of the...
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Construction and purification of his6-Thermus thermophilus MutS protein
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Construction and purification of his6-Thermus thermophilus MutS protein.
PublicationGen mutS z termofilnej bakterii Thermus thermophilus zamplifikowano przy użyciu PCR, sklonowano i przeprowadzono jego ekspresję w E. coli. Rekombinantowe białko MutS zawierające oligohistydynową domenę na N-końcu oczyszczono w jednoetapowej procedurze przy wykorzystaniu chromatografii powinowactwaNi(2+). Zdolność do rozpoznania niekomplementarności białka his(6)-MutS potwierdzono w eksperymentach ochrony DNA przed trawieniem...
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Molecular Characterization of Growth Hormone-producing Tumors in the GC Rat Model of Acromegaly
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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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Reversed-Phase TLC and HPLC Retention Data in Correlation Studies with in Silico Molecular Descriptors and Druglikeness Properties of Newly Synthesized Anticonvulsant Succinimide Derivatives
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Density functional theory calculations on entire proteins for free energies of binding: Application to a model polar binding site
PublicationIn drug optimization calculations, the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method can be used to compute free energies of binding of ligands to proteins. The method involves the evaluation of the energy of configurations in an implicit solvent model. One source of errors is the force field used, which can potentially lead to large errors due to the restrictions in accuracy imposed by its empirical nature....
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Speed estimation of a car at impact with a W-beam guardrail using numerical simulations and machine learning
PublicationThis paper aimed at developing a new method of estimating the impact speed of a passenger car at the moment of a crash into a W-beam road safety barrier. The determination of such a speed based on the accident outcomes is demanding, because often there is no access to full accident data. However, accurate determination of the impact speed is one of the key elements in the reconstruction of road accidents. A machine learning algorithm...
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<title>Cavity control system advanced modeling and simulations for TESLA linear accelerator and free electron laser</title>
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Modeling an Industrial Revolution: How to Manage Large-Scale, Complex IoT Ecosystems?
PublicationAdvancements around the modern digital industry gave birth to a number of closely interrelated concepts: in the age of the Internet of Things (IoT), System of Systems (SoS), Cyber-Physical Systems (CPS), Digital Twins and the fourth industrial revolution, everything revolves around the issue of designing well-understood, sound and secure complex systems while providing maximum flexibility, autonomy and dynamics. The aim of the...
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Modeling and Designing Acoustical Conditions of the Interior – Case Study
PublicationThe primary aim of this research study was to model acoustic conditions of the Courtyard of the Gdańsk University of Technology Main Building, and then to design a sound reinforcement system for this interior. First, results of measurements of the parameters of the acoustic field are presented. Then, the comparison between measured and predicted values using the ODEON program is shown. Collected data indicate a long reverberation...
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Self-assembly and interactions of short antimicrobial cationic lipopeptides with membrane lipids: ITC, FTIR and molecular dynamics studies
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Pro-Cognitive Properties of the Immunomodulatory Polypeptide Complex, Yolkin, from Chicken Egg Yolk and Colostrum-Derived Substances: Analyses Based on Animal Model of Age-Related Cognitive Deficits
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Stochastic model of the process of starting piston combustion engines and the practical use of the process
PublicationW artykule zaproponowano model procesu rozruchu silników o zapłonie samoczynnym, w formie procesu semimarkowskiego, dyskretnego w stanach i ciągłego w czasie eksploatacji. Stanami tego procesu są: stan zimny silnika (s1), stan ciepły silnika (s2) i stan gorący silnika (s3). Zaproponowano również koncepcję zastosowania opracowanego modelu do określenia ilości substancji szkodliwych, jakie emitowane są w spalinach podczas rozruchu...