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Search results for: molecular dynamic simulation
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Molecular Dynamics to Predict Cryo-EM: Capturing Transitions and Short-Lived Conformational States of Biomolecules
PublicationSingle-particle cryogenic electron microscopy (cryo-EM) has revolutionized the field of the structural biology, providing an access to the atomic resolution structures of large biomolecular complexes in their near-native environment. Today’s cryo-EM maps can frequently reach the atomic-level resolution, while often containing a range of resolutions, with conformationally variable regions obtained at 6 Å or worse. Low resolution...
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Dynamic risk assessment in autonomous vehicles motion planning
PublicationArguing that an autonomous mobile system is sufficiently safe to operate in presence of other vehicles and objects is an important element in development of such systems. Traditional approach to assure safety is to distinguish between safe and unsafe area and prevent the autonomous vehicle from entering the unsafe area. The paper presents a model of autonomous vehicle control system which uses risk assessment...
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Analysis of hull, propeller and engine interactions in regular waves by a combination of experiment and simulation
PublicationAnalysis of hull, propeller and engine interactions in regular waves by a combination of experiment and simulation
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Wideband Off-Body Channel Characteristics with Dynamic User
PublicationThis paper presents the preliminary results of a dynamic off-body channel characterisation study, based on wideband measurements at 5.8 GHz in an indoor environment. The Channel Impulse Response (CIR) was measured for a scenario with the user approaching and departing from the off-body antenna. A CIR deconvolution procedure was performed jointly in two polarisations, and the received signal power, Cross-Polarisation Discrimination...
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Positron collisions with molecular hydrogen: cross sections and annihilation parameters calculated using theR-matrix with pseudo-states method
PublicationThe molecular R-matrix with pseudo-states (MRMPS) method is employed to study positron collisions with H2. The calculations employ pseudo-continuum orbital sets containing up to h (l = 5) functions. Use of these high l functions is found to give converged eigenphase sums. Below the positronium formation threshold, the calculated cross sections agree with other high-accuracy theories and generally with the measurements. Calculation...
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Effect of pavement roughness and vehicle dynamic loads on decrease of fatigue life of flexible pavements
PublicationDue to the fact that pavement surfaces are not ideally even, dynamic loads of vehicle axles deviate from static loads. Higher dynamic loads contribute to faster pavement distress. The distribution of dynamic loads is similar to normal distribution and can be described by static load and factors DI (dynamic impact) and DLC (dynamic load coefficient). With the deterioration of pavement condition its evenness decreases as well and...
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Chitosan-Based Membranes as Gentamicin Carriers for Biomedical Applications — Influence of Chitosan Molecular Weight
PublicationOver the past decade, much attention has been paid to chitosan as a potential drug carrier because of its non-toxicity, biocompatibility, biodegradability and antibacterial properties. The effect of various chitosan characteristics on its ability to carry different antibiotics is discussed in the literature. In this work, we evaluated the influence of the different molecular weights of this polymer on its potential as an antibacterial...
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Paweł Możejko dr hab.
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Simulation of fluid structure interaction in a novel design of high pressure axial piston pump
PublicationA novel type of an axial, piston-driven high pressure hydraulic pump with variable capacity marks a significant improvement in the area of the hydraulic machinery design. Total discharge from hydrostatic forces eliminates a need for a servomechanism, thus simplifying operation, reducing weight and introducing the possibility of the pump displacement control by computer. PWK-type pumps, invented in the Gdansk University of Technology,...
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Verification of the Analytical Traffic Model of a Multidomain IMS/NGN Using the Simulation Model
PublicationIn this paper we verify the previously proposed analytical traffic model of a multidomain Next Generation Network (NGN), which is standardized for delivering multimedia services based on the IP Multimedia Subsystem (IMS). For this reason a proper simulation model used, in which not theoretical queuing system models but the operation of real network elements and standardized call scenarios are accurately implemented. Consequently,...
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On time-dependent nonlinear dynamic response of micro-elastic solids
PublicationA new approach to the mechanical response of micro-mechanic problems is presented using the modified couple stress theory. This model captured micro-turns due to micro-particles' rotations which could be essential for microstructural materials and/or at small scales. In a micro media based on the small rotations, sub-particles can also turn except the whole domain rotation. However, this framework is competent for a static medium....
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The Multiplatform Environment for Simulation and Features Estimation of Mixed-Signal Devices
PublicationThe use of simulation laboratories is gaining popularity in thedomains of engineering programs. However, the experience in teaching showsthat the simulation itself is not very effective in didactic processes. Teachingprocesses in thefield of specialist subjects, designed for students of technicaluniversities, should be based on direct operations performed by the student onreal devices. At the same time, at the later stages of didactic...
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History-based dynamic weight voting for multi-agent systems
PublicationTaking decision in multi-agent systems may involve voting. Two basic voting protocols are surveyed in the paper. Then, a new history-based dynamic weight voting is proposed. This voting protocol allows for identification of the agents which contribute to the correct system decision. The proposed solution is contrasted with majority voting and with weighted average voting, to show its advantages
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Simulation model for assessment of IMS-based NGN call processing performance
PublicationIn current telecommunications it is assumed that demands of information society for quickly delivered services will be satisfied by Next Generation Network (NGN) architecture, which includes IP Multimedia Subsystem (IMS) elements. To guarantee Quality of Service (QoS), proper design and dimensioning of NGN is absolutely necessary, for which appropriate models have to be proposed. As NGN architecture is very complicated, the most...
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A structure and simulation-driven design of compact CPW-fed UWB antenna
PublicationIn this letter, a structure of a miniaturized ultra-wideband CPW-fed antenna and its design proce-dure are presented. The antenna is a modified version of the design previously proposed in the literature, with additional degrees of freedom introduced in order to improve the structure flexibility. The small size is achieved by executing a rigorous optimization procedure that consists of two stages: (i) smart random search carried...
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Molecular Oncology
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MOLECULAR PHARMACOLOGY
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Identification of diagnostic parameter sensitivity during dynamic processes of a marine engine
PublicationChanging some parameters of the engine structure alters the emission of harmful components in the exhaust gas. This applies in particular to the damage of charge exchange system as well as fuel system and engine supercharger. These changes are much greater during the dynamic states and their accompanying transitional processes. The different sensitivity of diagnostic parameters to the same force, coming from the engine structure, but...
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MULTISCALE MODELING & SIMULATION
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Thermo-Mechanical Simulation of Underwater Friction Stir Welding of Low Carbon Steel
PublicationThis article investigates the flow of materials and weld formation during underwater friction stir welding (UFSW) of low carbon steel. A thermo-mechanical model is used to understand the relation between frictional heat phenomena during the welding and weld properties. To better understand the effects of the water environment, the simulation and experimental results were compared with the sample prepared by the traditional friction...
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Fading Modelling in Dynamic Off-Body Channels
PublicationThis paper presents an off-body fading channel model for Body Area Networks (BANs) in indoor environments. The proposed model, which is based on both simulations and measurements in a realistic environment, consists of three components: mean path loss, body shadowing, and multipath fading. Seven scenarios in an indoor environment (a medium-size room with furniture, mostly consisting of wooden tables and chairs) have been measured:...
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Mechanical-Level Hardware-In-The-Loop and Simulation in Validation Testing of Prototype Tower Crane Drives
PublicationIn this paper, the static and dynamic simulations, and mechanical-level Hardware-In-the-Loop (MHIL) laboratory testing methodology of prototype drive systems with energy-saving permanent-magnet electric motors, intended for use in modern construction cranes is proposed and described. This research was aimed at designing and constructing a new type of tower crane by Krupiński Cranes Company. The described research stage was necessary...
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Molecular Umbrellas Modulate the Selective Toxicity of Polyene Macrolide Antifungals
PublicationAntifungal polyene macrolide antibiotics Amphotericin B (AmB) and Nystatin (NYS) were conjugated through the ω-amino acid linkers with diwalled “molecular umbrellas” composed of spermidine-linked deoxycholic or cholic acids. The presence of “umbrella” substituents modulated biological properties of the antibiotics, especially their selective toxicity. Some of the AmB-umbrella conjugates demonstrated antifungal in vitro activity...
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The consequences of dynamic BPM
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Effect of Chitosan Deacetylation on Its Affinity to Type III Collagen: A Molecular Dynamics Study
PublicationThe ability to form strong intermolecular interactions by linear glucosamine polysaccharides with collagen is strictly related to their nonlinear dynamic behavior and hence bio-lubricating features. Type III collagen plays a crucial role in tissue regeneration, and its presence in the articular cartilage affects its bio-technical features. In this study, the molecular dynamics methodology was applied to evaluate the effect of...
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Real-Time PCR: molecular technique of many applications
PublicationReal-Time PCR is a sensitive DNA amplification technique initially applied in genetics and molecular biology. It enables in vivo copying of the selected DNA fragment (flanked by two primers) by the thermostable polymerase (in the presence of magnesium ions and deoxynucleotide triphosphates) and simultaneous measurement of the fluorescence. For one or more specific sequences in a DNA sample, real-time PCR enables both detection...
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Development of dynamic method for evaluation of inhibition efficiency on the example of 8-hydroxyquinolin
PublicationSelection of a proper inhibitor should be based on the evaluation of its mechanism and effective concentrations. Mechanism of inhibition usually has dynamic character due to changing physicochemical conditions of the environment and corroding metal surface. Most of actually used methods are stationary or contain assumptions which highly influences obtained values. Development of new dynamic method, based on modified EIS, allows...
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Dynamic Analysis of the Turnout Diverging Track for HSR with Variable Curvature Sections
PublicationThe paper presents an analytical method of identifying the curvature of the turnout diverging track consisting of sections of varying curvature. Both linear and nonlinear (polynomial) curvatures of the turnout diverging track are identified and evaluated in the paper. The presented method is a universal one, it enables to assume curvature values at the beginning and end point of the geometrical layout of the turnout. The results...
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Quest for the Molecular Basis of Improved Selective Toxicity of All-Trans Isomers of Aromatic Heptaene Macrolide Antifungal Antibiotics
PublicationThree aromatic heptaene macrolide antifungal antibiotics, Candicidin D, Partricin A (Gedamycin) and Partricin B (Vacidin) were subjected to controlled cis-trans to all trans photochemical isomerization. The obtained all-trans isomers demonstrated substantially improved in vitro selective toxicity in the Candida albicans cells: human erythrocytes model. This effect was mainly due to the diminished hemotoxicity. The molecular modeling...
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Composite sandwich footbridge - measured dynamic response vs. FEA
PublicationThe paper describes a process of in situ dynamic tests of a composite sandwich footbridge before its accepta-tion for exploitation in real traffic conditions. It is only a part of a big research task that includes design, manufacture and introduce practical application of the bridge. The in situ measured natural modes and fre-quencies are compared with numerically determined ones. Finite element analysis is established to estimate...
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Thermodynamics and kinetics of amphotericin B self-association in aqueous solution characterized in molecular detail
PublicationAmphotericin B (AmB) is a potent but toxic drug commonly used to treat systemic mycoses. Its efficiency as a therapeutic agent depends on its ability to discriminate between mammalian and fungal cell membranes. The association of AmB monomers in an aqueous environment plays an important role in drug selectivity, as oligomers formed prior to membrane insertion – presumably dimers – are believed to act differently on fungal (ergosterol-rich)...
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Capillary Electrophoresis in Determination of Low Molecular Mass Organic Acids
PublicationThis paper presents overviews the capabilities of capillary electrophoretic techniques to determine low molecular mass organic acids in a variety of aqueous, gas and solid samples. It mainly focuses on short - chain carboxylic acids containing one or more carboxylic groups and possibly some other functional groups (hydroxyl, keto-, amino- etc.). Finally the procedures applied to the determine the acids in different matrices are...
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COMMUNICATIONS IN STATISTICS-SIMULATION AND COMPUTATION
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International Journal of Tomography and Simulation
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Journal of Building Performance Simulation
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Journal of Computational Simulation and Modeling
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International Journal of Modelling and Simulation
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JOURNAL OF STATISTICAL COMPUTATION AND SIMULATION
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SPECTRAL DYNAMIC ANALYSIS OF A STATIONARY JACK-UP PLATFORM
PublicationThe paper refers to the dynamic short-term response analysis of the Baltic steel drilling platform (see Fig.2) in a random sea-state represented by one-dimensional wave spectrum proposed by Striekalov and Massel and it is recommended for the Baltic Sea area. The Baltic drilling platform is a jack-up type platform for the exploration and exploitation of oil under the Baltic Sea. The analysis presented deals with the stationary...
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ortho-Fluorobenzanilides and ortho-fluorothiobenzanilides: Molecular conformations and crystal packing
PublicationSeries of 2-fluoro and 2,6-difluorobenzanilides and their thiobenzanilide analogs have been synthesized to investigate the influence of the fluorine atom on their crystal structures and self-assembly in the crystal lattice. The X-ray analysis of the single crystal revealed that the synthesized molecules adopt a geometry being deflected from planarity. The deflection was investigated by analysis of dihedral angles between mean planes...
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DISCRETE EVENT DYNAMIC SYSTEMS-THEORY AND APPLICATIONS
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Possible uses of crisis situation aiding system in virtual world simulation
PublicationMany of the real world crisis situations like spreading fire, hostile units attack, flood, and etc. are commonly used in computer games where a simulation of extensive virtual world is crucial. This paper presents some ideas for possible uses of existing crisis situation aiding system in such environments. Moreover it shows how this kind of system can be taught during subsequent games with a large number of players.
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Building Simulation
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On–line Parameter and Delay Estimation of Continuous–Time Dynamic Systems
PublicationThe problem of on-line identification of non-stationary delay systems is considered. The dynamics of supervised industrial processes are usually modeled by ordinary differential equations. Discrete-time mechanizations of continuous-time process models are implemented with the use of dedicated finite-horizon integrating filters. Least-squares and instrumental variable procedures mechanized in recursive forms are applied for simultaneous...
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Evolutionary Sets of Safe Ship Trajectories: simulation results
PublicationThe Evolutionary Sets of Safe Ship Trajectories is a method solving multi-ship encounter situations. For given positions and motion parameters the method finds a near optimal set of safe trajectories of all ships involved in an encounter. The paper briefly presents foundations of the method and focuses on simulation results for selected test cases based on the Baltic Basin. The computer simulations cover both open waters and restricted...
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Simulation of fluid structure interaction in a novel design of high pressure axial piston hydraulic pump
PublicationA novel type of an axial, piston-driven high pressure hydraulic pump with variable capacity marks a significant improvement in the area of the hydraulic machinery design. Total discharge from hydrostatic forces eliminates a need for a servomechanism, thus simplifying operation, reducing weight and introducing the possibility of the pump displacement control by computer. PWK-type pumps, invented in the Gdansk University of Technology,...
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Quantitative Active Dynamic Thermal IR-Imaging and Thermal Tomography in Medical Diagnostic
PublicationPrinciples of Active dynamic thermal (ADT) IR-imaging and Thermal Tomography are described in details. Basic medical applications of this new modality are also discussed.
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Simulation of the Dynamics of Renewable Energy Sources with Energy Storage Systems
PublicationThe intermittency of renewable energy sources (RES) constitutes a challenge for effective power system control. Fossil-fuel-based units offering ancillary power services to meet the short-term power imbalance are a financial and environmental burden for the society. Energy storage systems (ESS) can be the solution in view of the electricity market development and growing environmental concern. The major questions are, in what circumstances...
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Simulation of influence of the air gap asymmetryon voltage waveforms of a synchronous machine
PublicationResults of simulation of a synchronous generator with the air gap asymmetry characterised by eccentricity are presented in the paper. The Lagrange's energy method has been used in derivation of the model equations. Analysis of influence of the air gap asymmetry on characteristics of self and mutual inductances of windings, as well as analysis of induced voltage waveforms as a function of the air gap asymmetry have been performed....
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Hybrid quantum-classical approach for atomistic simulation of metallic systems
PublicationThe learn-on-the-fly (LOTF) method [G. Csanyi et al., Phys. Rev. Lett. 93, 175503 (2004)] serves to seamlessly embed quantum-mechanical computations within a molecular-dynamics framework by continual local retuning of the potential's parameters so that it reproduces the quantum-mechanical forces. In its current formulation, it is suitable for systems where the interaction is short-ranged, such as covalently bonded semiconductors....