Wyniki wyszukiwania dla: Molecular docking and simulation study
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Novel application of terminal restriction fragments length polymorphism method (t-RFLP) for identification of six clinically important Candida sp.
PublikacjaTerminal restriction fragments length polymorphism method (t-RFLP) is a modified classical RFLP method. The main difference is based on carrying out PCR using a fluorescently labeled primer or primers. The result of such modification is that after digestion of amplicons only terminal fragments of PCR product (containing fluorescent dye) are visualized. T-RFLP method has found application in environmental microbiology and epidemiology....
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Influence of a Lighting Column in the Working Width of a W-Beam Barrier on TB51 Crash Test
PublikacjaRoad equipment, such as, e.g., road safety barriers and lighting columns, are subject to certification according to the EN1317 standard to be allowed for use on European roads. In engineering practice, due to the terrain conditions, there are cases where other road equipment is installed within the working width of road safety barriers. Such situations are not considered during the certification process. Hence, the aim of this...
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Searching for Solvents with an Increased Carbon Dioxide Solubility Using Multivariate Statistics
PublikacjaIonic liquids (ILs) are used in various fields of chemistry. One of them is CO2 capture, a process that is quite well described. The solubility of CO2 in ILs can be used as a model to investigate gas absorption processes. The aim is to find the relationships between the solubility of CO2 and other variables—physicochemical properties and parameters related to greenness. In this study, 12 variables are used to describe a dataset...
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Structure of liquid gold from tight-binding driven molecular-dynamics
PublikacjaPraca przedstawia wyniki symulacji ciekłego złota w nadkomórce periodycznej przy użyciu stworzonego przez autorów programu komputerowego, za pomocą połączonych metod dynamiki molekularnej (MD) i ciasnego wiązania (TB). Omówiono strukturę tak symulowanej cieczy, porównując ją z dostępnymi danymi doświadczalnymi oraz wynikami innych symulacji, pod kątem radialnej i kątowej funkcji rozkładu i elektronowej gęstości stanów.A tight-binding...
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Milena Marycz dr inż.
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Implementation of Non-Probabilistic Methods for Stability Analysis of Nonlocal Beam with Structural Uncertainties
PublikacjaIn this study, a non-probabilistic approach based Navier’s Method (NM) and Galerkin Weighted Residual Method (GWRM) in term of double parametric form has been proposed to investigate the buckling behavior of Euler-Bernoulli nonlocal beam under the framework of the Eringen's nonlocal elasticity theory, considering the structural parameters as imprecise or uncertain. The uncertainties in Young’s modulus and diameter of the beam are...
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An optimal designed experiment for the alkaline hydrolysis of feather keratin
PublikacjaFeathers, burdensome waste from the poultry industry, can be a cheap source of keratin, a protein with excellent physico- chemical, biological, and mechanical properties. Acid and alkaline hydrolyses are usually adopted for isolation of keratin from its natural resources. This study aimed at assessing the statistically significant effect of input variables in the alkaline hydrolysis of keratin from chicken feathers on the process...
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Identification of ship’s hull mathematical model with numerical methods
PublikacjaThe modern maritime industry is moving toward the development of technology that will allow for full or partial autonomy of ship operation. This innovation places high demands on ship performance prediction techniques at the design stage. The researchwork presented in the article is related to the design stage of the ship and concerns methods for prognosis and evaluation of the specific operational condition of the ship, namely...
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Modeling and Simulation for Exploring Power/Time Trade-off of Parallel Deep Neural Network Training
PublikacjaIn the paper we tackle bi-objective execution time and power consumption optimization problem concerning execution of parallel applications. We propose using a discrete-event simulation environment for exploring this power/time trade-off in the form of a Pareto front. The solution is verified by a case study based on a real deep neural network training application for automatic speech recognition. A simulation lasting over 2 hours...
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Solvent Exchange around Aqueous Zn(II) from Ab Initio Molecular Dynamics Simulations
PublikacjaHydrated zinc(II) cations, due to their importance in biological systems, are the subject of ongoing research concerning their hydration shell structure and dynamics. Here, ab initio molecular dynamics (AIMD) simulations are used to study solvent exchange events around aqueous Zn2+, for which observation in detail is possible owing to the considerable length of the generated trajectory. While the hexacoordinated Zn(H2O)62+ is the...
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Supporting development of the smart ship technology by CFD simulation of ship behavior in close to real operational conditions
PublikacjaThe shipping industry is at the milestone of technological development – autonomous ships. Involving smart technologies accelerates development of green and safe shipping. Also IMO regulations, especially EEDI en-hanced application of new technologies. Meeting economic and ecological requirements future ships need to be designed with respect to increased reliability and operational performance. Design process of ships may be improved...
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Simulating Malware with MAlSim
PublikacjaThis paper describes MAlSim - Mobile Agent Malware Simulator - a mobile agent framework developed to address one of the most important problems related to the simulation of attacks against information systems i.e. the lack of adequate tools for reproducing behaviour of malicious software (malware). The framework can be deployed over the network of an arbitrary information system and it aims at simulating behaviour of each instance...
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Simulating malware with MAlSim
PublikacjaThis paper describes MAlSim - Mobile Agent Malware Simulator - a mobile agent framework developed to address one of the most important problems related to the simulation of attacks against information systems, i.e. the lack of adequate tools for reproducing behaviour of malicious software (malware). The framework can be deployed over the network of an arbitrary information system and it aims at simulating behaviour of each instance...
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Analysis of electromagnetic disturbances in DC network of grid connected building-integrated photovoltaic system
PublikacjaThis paper focuses on conducted electromagnetic interference (EMI) emissions and propagation in the DC network of grid connected building integrated photovoltaic (PV) system. The investigated PV system, consists of ten solar panels, cabling and the grid-connected one phase inverter. The EMI simulation model of the real PV system has been developed with the aid of impedance analyzer measurements of solar panels and the DC network...
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Why do G-quadruplexes dimerize through the 5’-ends? Driving forces for G4 DNA dimerization examined in atomic detail
PublikacjaG-quadruplexes (G4) are secondary structures formed by guanine-rich nucleic acid sequences and shown to exist in living cells where they participate in regulation of gene expression and chromosome maintenance. G-quadruplexes with solvent-exposed guanine tetrads show the tendency to associate together through cofacial stacking, which may be important for packaging of G4-forming sequences and allows for the design of higher-order...
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Albumin–Hyaluronan Interactions: Influence of Ionic Composition Probed by Molecular Dynamics
PublikacjaThe lubrication mechanism in synovial fluid and joints is not yet fully understood. Nevertheless, intermolecular interactions between various neutral and ionic species including large macromolecular systems and simple inorganic ions are the key to understanding the excellent lubrication performance. An important tool for characterizing the intermolecular forces and their structural consequences is molecular dynamics. Albumin...
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Diaryl Sulfide Derivatives as Potential Iron Corrosion Inhibitors: A Computational Study
PublikacjaThe present work aimed to assess six diaryl sulfide derivatives as potential corrosion inhibitors. These derivatives were compared with dapsone (4,4′-diaminodiphenyl sulfone), a common leprosy antibiotic that has been shown to resist the corrosion of mild steel in acidic media with a corrosion efficiency exceeding 90%. Since all the studied compounds possess a common molecular backbone (diphenyl sulfide), dapsone was taken as the...
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Adaptive Multiplex Resource Allocation Method for DAB+ Broadcast System
PublikacjaIn this paper an adaptive multiplex resource allocation method for the DAB+ broadcast system is presented. An analysis of content transmitted over different radio programs with respect to their profile is discussed. Simulation results of an adaptive multiplexer, as well as the technological demonstrator, fully compatible with the DAB+ standard, are described. The concept is verified by a subjective quality assessment study of real-time...
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Fractional Calculus Evaluation of Hyaluronic Acid Crosslinking in a Nanoscopic Part of Articular Cartilage Model System
PublikacjaThis 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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Electron impact fragmentation of pyrrole molecules studied by fluorescence emission spectroscopy
PublikacjaThe fluorescence emission spectroscopy using electron impact excitation technique was employed to study fragmentation processes of the gas phase pyrrole molecules. The following excited fragmentation species were observed by detection of their fluorescence decay: the atomic hydrogen H(n), n = 4-7 and the diatomic CH(A2Δ), CN(B2Σ+), NH(A3Π) and C2(d3Πg) fragments. These atomic and molecular products differ from those previously...
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Multifunctional PID Neuro-Controller for Synchronous Generator
PublikacjaThis paper deals with a PID Neuro-Controller (PIDNC) for synchronous generator system. The controller is based on artificial neural network and adaptive control strategy. It ensures two functions: maintaining the generator voltage at its desired value and damping electromechanical oscillations. The performance of the proposed controller is evaluated on the basis of simulation tests. A comparative study of the results obtained with...
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Dominant Pathways of Adenosyl Radical-Induced DNA Damage Revealed by QM/MM Metadynamics
PublikacjaBrominated nucleobases sensitize double stranded DNA to hydrated electrons, one of the dominant genotoxic species produced in hypoxic cancer cells during radiotherapy. Such radiosensitizers can therefore be administered locally to enhance treatment efficiency within the solid tumor while protecting the neighboring tissue. When a solvated electron attaches to 8-bromoadenosine, a potential sensitizer, the dissociation of bromide...
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Optimal Rotating Receiver Angles Estimation for Multicoil Dynamic Wireless Power Transfer
PublikacjaThis study proposed an approach to dynamic wireless charging that uses a rotating receiver coil. Our simulation study focused on the verification of a novel way of increasing the coupling coefficient and power transfer stability by following the flux of the transmitting coils. To obtain the highest possible coupling by means of the FEM analysis, we studied the optimization of the trajectory of the angular velocity of the rotating...
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Mechanism of Binding of Antifungal Antibiotic Amphotericin B to Lipid Membranes: An Insight from Combined Single-Membrane Imaging, Microspectroscopy, and Molecular Dynamics
PublikacjaAmphotericin B is a lifesaving polyene antibiotic used in the treatment of systemic mycoses. Unfortunately, the pharmacological applicability of this drug is limited because of its severe toxic side effects. At the same time, the lack of a well-defined mechanism of selectivity hampers the efforts to rationally design safer derivatives. As the drug primarily targets the biomembranes of both fungi and humans, new insights into the...
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Monitoring of CRT by means of impedance multiple measurements - simulation studies
PublikacjaCardiac resynchronization therapy (CRT) is a very promising treatment for patients with congestive heart failure. An Impedance Cardiography (ICG) is used for evaluation of heart mechanical activity. A simulation study with the use of a FEM model was performed. The developed realistic model of the thorax, based on CT data obtained from examination of a 68-year-old man, consisted of 212 000 tetrahedral elements. Different configurations...
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Modified Inductive Multi-Coil Wireless Power Transfer Approach Based On Z-Source Network
PublikacjaThis article presents a non-conventional approach to a multi-coil wireless power transfer system based on a Z-source network. The novelty of the approach lies in the use of a Z-source as a voltage source for energy transmission through the wireless power transfer coils. The main advantage is in a reduced number of semiconductors. This paper provides the design approach, simulation and experimental study. Feasibility and possible...
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Fuzzy Divisive Hierarchical Clustering of Solvents According to Their Experimentally and Theoretically Predicted Descriptors
PublikacjaThe present study describes a simple procedure to separate into patterns of similarity a large group of solvents, 259 in total, presented by 15 specific descriptors (experimentally found and theoretically predicted physicochemical parameters). Solvent data is usually characterized by its high variability, dierent molecular symmetry, and spatial orientation. Methods of chemometrics can usefully be used to extract and explore accurately...
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A new open-source software developed for numerical simulations usingdiscrete modeling methods
PublikacjaThe purpose of this work is to present the development of an open-source software based on a discrete description of matter applied to study the behavior of geomaterials. This software uses Object Oriented Programming techniques, and its methodology design uses three different methods, which are the Discrete Element Method (DEM) [F. Donzé, S.A. Magnier, Formulation of a three-dimensional numerical model of brittle behavior, Geophys....
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Numerical Modeling of Water and Ice Dynamics for Analysis of Flow Around the Kiezmark Bridge Piers
PublikacjaThis paper presents the results of a numerical model study on the effect of ice on the proposed bridge piers in the Vistula River outlet and its effect on flow conditions in the river. The model DynaRICE is used in this study, which is a two-dimensional hydro-ice dynamic numerical model developed for dynamic ice transport and jamming in rivers. To simulate river hydrodynamics in the vicinity of the bridge piers, 2-dimensional numerical...
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Approach to security assessment of critical infrastructures' information systems
PublikacjaThis study presents an approach to the security assessment of the information systems of critical infrastructures. The approach is based on the faithful reconstruction of the evaluated information system in a computer security laboratory followed by simulations of possible threats against the system. The evidence collected during the experiments, stored and organised using a proprietary system InSAW, may later be used for the creation...
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Environmental exposure to cadmium in breast cancer – association with the Warburg effect and sensitivity to tamoxifen
PublikacjaThe association between cadmium and breast cancer remains unexplained due to inconsistent epidemiological data and unknown underlying mechanisms. This study aimed to assess the relationship between environmental exposure to cadmium and the Warburg effect in breast cancer and, thus, its possible interference with breast cancer treatment. The observational study in two groups of breast cancer patients indicated a positive correlation between...
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Early Stages of RNA-Mediated Conversion of Human Prions
PublikacjaPrion diseases are characterized by the conversion of prion proteins from a PrPC fold into a disease-causing PrPSC form that is self-replicating. A possible agent to trigger this conversion is polyadenosine RNA, but both mechanism and pathways of the conversion are poorly understood. Using coarse-grained molecular dynamic simulations we study the time evolution of PrPC over 600 μs. We find that both the D178N mutation and interacting...
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New PCR test for detection of Candida glabrata based on the molecular target chosen by the RAPD technique
PublikacjaRapid, reliable diagnosis is a necessary condition for the successful treatment of infections. Such diagnostic assays are continually being developed. #e paper presents a method for selecting the molecular target for PCR-based diagnostics based on the comparison of RAPD patterns. A sequence encoding Candida glabrata CBS138 hypothetical protein was selected. The limit of detection for PCR and real-time PCR reactions with DNA extracted...
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Taq DNA polymerase fused with DNA binding protein with increased resistance to inhibitors from clinical samples
PublikacjaNowadays PCR method is commonly used in molecular diagnostic. However, in many cases PCR is limited, by the presence of inhibitory substances in biological, soil or food samples Efficiency and fidelity of amplification is strongly connected with DNA polymerase and reaction conditions. To meet the requirements of modern diagnostic methods it is essential to seeking for new DNA polymerases with better properties useful in these field....
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The use of mathematical models for diagnosis of activated sludge systems in WWTP
PublikacjaIn this study diagnosis of activated sludge systems in wastewater treatment plant (WWTP) was investigated. Diagnosis of technical objects can be realized in many ways. One of the divisions of the diagnostic methods include modelling with or without a model of the object. The first of these is the analysis of the symptoms for which, based on the parameter values, the abnormality in the diagnosed objects are sought. Another way is...
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ASYNCHRONICZNE METODY RADIOLOKALIZACYJNE
PublikacjaW pracy przedstawiono wybrane problemy lokalizowania obiektów w asynchronicznych sieciach radiowych. W pierwszej kolejności zostały zdefiniowane kryteria jakościowe do oceny efektywności pracy opracowanych metod oraz przedstawiono model symulacyjny, który został użyty do badań. W kolejnych trzech rozdziałach szczegółowo opisano trzy oryginalne asynchroniczne metody radiolokalizacyjne w różnych wariantach. Przeprowadzono analizę...
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Intermolecular Interactions as a Measure of Dapsone Solubility in Neat Solvents and Binary Solvent Mixtures
PublikacjaDapsone is an effective antibacterial drug used to treat a variety of conditions. However, the aqueous solubility of this drug is limited, as is its permeability. This study expands the available solubility data pool for dapsone by measuring its solubility in several pure organic solvents: N-methyl-2-pyrrolidone (CAS: 872-50-4), dimethyl sulfoxide (CAS: 67-68-5), 4-formylmorpholine (CAS: 4394-85-8), tetraethylene pentamine (CAS:...
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Improving SBR Performance Alongside with Cost Reduction through Optimizing Biological Processes and Dissolved Oxygen Concentration Trajectory
PublikacjaAuthors of this paper take under investigation the optimization of biological processes during the wastewater treatment in sequencing batch reactor (SBR) plant. A designed optimizing supervisory controller generates the dissolved oxygen (DO) trajectory for the lower level parts of the hierarchical control system. Proper adjustment of this element has an essential impact on the efficiency of the wastewater treatment process as well...
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Accurate modeling of quasi-resonant inverter fed IM drive
PublikacjaIn this paper wide-band modeling methodology of a parallel quasi-resonant dc link inverter (PQRDCLI) fed induction machine (IM) is presented. The modeling objective is early-design stage prediction of conductive electromagnetic interference (EMI) emissions of the considered converter fed IM drive system. Operation principles of the selected topology of PQRDCLI feeding IM drive are given. Modeling of the converter drive system is...
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Effects of Noncontact Shoulder Tool Velocities on Friction Stir Joining of Polyamide 6 (PA6)
PublikacjaIn this study, the effects of the traverse and rotational velocities of the noncontact shoulder tool on the heat generation and heated flux during the friction stir joining of high-density polyamide 6 (PA6) polymer were investigated. The computational fluid dynamics (CFD) method was employed to simulate the thermomechanical phenomena during the friction stir joining (FSJ) process of PA6. A developed model was used to consider the...
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Theoretical designing of selenium heterocyclic non-fullerene acceptors with enhanced power conversion efficiency for organic solar cells: a DFT/TD-DFT-based prediction and understanding
PublikacjaIn this study, we have designed and explored a new series of non-fullerene acceptors for possible applications in organic solar cells. We have designed four molecules named as APH1 to APH4 after end-capped modification of recently synthesized Y6-Se-4Cl molecule. Density functional theory and time dependent-density functional theory have been employed for computing geometric and photovoltaic parameters of the designed molecules....
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Experimental and Theoretical Insights into the Intermolecular Interactions in Saturated Systems of Dapsone in Conventional and Deep Eutectic Solvents
PublikacjaSolubility is not only a crucial physicochemical property for laboratory practice but also provides valuable insight into the mechanism of saturated system organization, as a measure of the interplay between various intermolecular interactions. The importance of these data cannot be overstated, particularly when dealing with active pharmaceutical ingredients (APIs), such as dapsone. It is a commonly used anti-inflammatory and...
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Parameter and delay estimation of linear continuous-time systems
PublikacjaIn this paper the problem of on-line identification of non-stationary delay systems is considered. Dynamics of supervised industrial processes is described by ordinary differential equations. Discrete-time mechanization of their continuous-time representations is based on dedicated finite-horizon integrating filters. Least-squares and instrumental variable procedures implemented in recursive forms are applied for simultaneous identification...
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A novel hierarchically-porous diamondized polyacrylonitrile sponge-like electrodes for acetaminophen electrochemical detection
PublikacjaA novel composite electrode material consisting of tangled fibrous polyacrylonitrile-based hierarchically-struc- tured nanocomposites has been produced by wet-spinning, carbonized and decorated with a carbon nano- architecture by microwave plasma-enhanced chemical vapor deposition and investigated as a metal-free electrode for the enhanced electrochemical detection of acetaminophen. Surprisingly, the hierarchical fiber ar- chitecture...
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A Model of Thermal Energy Storage According to the Convention of Bond Graphs (BG) and State Equations (SE)
PublikacjaThe main advantage of the use of the Bond Graphs method and State Equations for modeling energy systems with a complex structure (marine power plants, hybrid vehicles, etc.) is the ability to model the system components of different physical nature using identical theoretical basis. The paper presents a method of modeling thermal energy storage, which is in line with basic BG theory. Critical comments have been put forward concerning...
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Real-time PCR approach in dermatophyte detection and Trichophyton rubrum identification
PublikacjaDermatophytes are keratinophilic molds that infect human hair, nails and skin. Diagnosis of dermatophytosis is based on morphological, serological and biochemical features. However, identification is difficult and laborious due to similarities between microorganisms. Thus, there is considerable interest to develop mycological diagnostic procedures based on molecular biology methods. In this study, fast, two-step DNA extraction...
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Average Size of a Suffix Tree for Markov Sources
PublikacjaWe study a suffix tree built from a sequence generated by a Markovian source. Such sources are more realistic probabilistic models for text generation, data compression, molecular applications, and so forth. We prove that the average size of such a suffix tree is asymptotically equivalent to the average size of a trie built over n independentsequences from the same Markovian source. This equivalenceis only known for memoryless...
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Two Time-Scale Hierarchical Control of Integrated Quantity and Quality in Drinking Water Distribution Systems
PublikacjaThe paper considers a feedback optimising control of drinking water distribution systems (DWDS). Although the optimised pump and valves scheduling and disinfectant injection control attracted considerable attention over last two decades most of the contributions were limited to an open-loop optimisation repetitively performed during the DWDS operation. Also, while a strong interaction between the water quantity and quality exists...
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Molecular Dynamics simulations of thermal conductivity of penta-graphene
PublikacjaThe thermal conductivity of penta-graphene (PG), a new two dimensional carbon allotrope and its dependence on temperature, strain, and direction are studied in this paper. The thermal conductivity of PG is investigated using a non-equilibrium molecular dynamics simulation (NEMD) with the Two Region Method by applying the optimized Tersoff interatomic potential. Our study shows that the thermal conductivity of PG (determined for...
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Performance and Emission Modelling and Simulation of Marine Diesel Engines using Publicly Available Engine Data
PublikacjaTo analyse the behaviour of marine diesel engines in unsteady states for different purposes, for example to determine the fuel consumption or emissions level, to adjust the control strategy, to manage the maintenance, etc., a goal-based mathematical model that can be easily implemented for simulation is necessary. Such a model usually requires a wide range of operating data, measured on a test stand. This is a time-consuming process...