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Wyniki wyszukiwania dla: Molecular dynamics simulations
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Technological capability dynamics through cluster organizations
PublikacjaPurpose – The purpose of the paper is to portrait how members of cluster organizations (COs) perceive the role of COs in enabling them to accumulate technological capability (TC) significant for their innovation. Design/methodology/approach – The authors report the findings from their qualitative study based on an analysis of four COs. The organizational inertia and absorptive capacity (AC) theories are the theoretical underpinning...
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GPR simulations for diagnostics of a reinforced concrete beam
PublikacjaThe most popular technique for modelling of an electromagnetic field, the finite difference time domain (FDTD) method, has recently become a popular technique as an interpretation tool for ground penetrating radar (GPR) measurements. The aim of this study is to detect the size and the position of damage in a reinforced concrete beam using GPR maps. Numerical simulations were carried out using the finite differ-ence time domain...
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The importance of the shape of the protein–water interface of a kinesin motor domain for dynamics of the surface atoms of the protein
PublikacjaA single kinesin motor domain immersed in water has been investigated using molecular dynamics. It has been found that local properties of water in the solvation shell change along with the nature of the neighboring protein surface. However, a detailed analysis leads to the conclusion that the geometrical features of hydrogen bonds and overall structure of kinesin hydration water are not very different from bulk water. The local...
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The importance of the shape of the protein-water interface of a kinesin motor domain for dynamics of the surface atoms of the protein
PublikacjaSingle kinesin motor domain immersed in water has been investigated using molecular dynamics. It has been found that local properties of water in solvation shell change along with the nature of neighboring protein surface. However, a detailed analysis leads to the conclusion that the geometrical features of hydrogen bonds and overall structure of kinesin hydration water is not very different from bulk water. The local values of...
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Constant vs. Variable Efficiency of Electric Drive in Train Run Simulations
PublikacjaTrain run simulations, which focus on various power- and energy-oriented aspects, should reflect the losses in the electric powertrain. In general, the powertrain efficiency varies with respect to load and speed. Including this relation in simulation requires knowledge about detailed drivetrain parameters, which are often unavailable. This paper verifies the possibility to approximate the drivetrain efficiency in train run simulations...
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Advanced Potential Energy Surfaces for Molecular Simulation
PublikacjaAdvanced potential energy surfaces are defined as theoretical models that explicitly include many-body effects that transcend the standard fixed-charge, pairwise-additive paradigm typically used in molecular simulation. However, several factors relating to their software implementation have precluded their widespread use in condensed-phase simulations: the computational cost of the theoretical models, a paucity of approximate models...
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Optimization of Hydrogen - Evolving Photochemical Molecular Devices
PublikacjaA molecular photocatalyst consisting of a RuII photocenter, a tetrapyridophenazine bridging ligand, and a PtX2 (X=Cl or I) moiety as the catalytic center functions as a stable system for light-driven hydrogen production. The catalytic activity of this photochemical molecular device (PMD) is significantly enhanced by exchanging the terminal chlorides at the Pt center for iodide ligands. Ultrafast transient absorption spectroscopy...
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Utilizing pulse dynamics for non-invasive Raman spectroscopy of blood analytes
PublikacjaNon-invasive measurement methods offer great benefits in the field of medical diagnostics with molecular-specific techniques such as Raman spectroscopy which is increasingly being used for quantitative measurements of tissue biochemistry in vivo. However, some important challenges still remain for label-free optical spectroscopy to be incorporated into the clinical laboratory for routine testing. In particular, non-analyte-specific...
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Numerical simulations of novel GFRP sandwich footbridge
PublikacjaIn the following paper some aspects of numerical analysis and designing stages of a footbridge made of composite materials are elucidated. Because of the used materials the design process in this case is not ordinary and requires the development of concepts, material selections, identification of material properties, numerical simulations, strength calculations, serviceability and durability analyses. This contribution presents...
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Molecular Targets for Anticandidal Chemotherapy
PublikacjaA relatively small number of anticandidal chemotherapeutics used in clinical practice is at least in part consequence of a limited number of their molecular targets: ergosterol in the membrane, lanosterol demethylase, b(1!3) glucan synthase, and DNA/RNA biosynthesis. Much more potential novel targets have been revealed by the comparative genomic studies identifying essential genes unique for Candida albicans or resulted from recognition...
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Mesoscopic simulations of crack propagation in concrete using cohesive elements
PublikacjaThe paper presents results of two-and three-dimensional meso-scale simulations of fracture in notched concrete beams subjected to three-point bending test. Concrete was assumed as a 3-phase material composed of aggregate grains placed in the cement matrix with Interfacial Transitional Zones (ITZs) between then. In 2D simulations macro-voids were also taken into account. The particle distribution was taken from real concrete beams...
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The surface photoconductivity in molecular layers
PublikacjaW pracy przedstawiono rezultaty analizy fotoprądów powierzchniowych w cienkich warstwach tetracenu i pentacenu. W szczególności badano wpływ obecności defektów strukturalnych w warstwach na charakterystyki fotoprądów i transport nośników ładunku.
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Some Optimization Methods for Simulations in Volunteer and Grid Systems
PublikacjaIn this chapter, some optimization methods have been presented for improving performance of simulations in the volunteer and grid computing system called Comcute. Some issues related to the cloud computing can be solved by presented approaches as well as the Comcute platform can be used to simulate execution of expensive and energy consuming long-term tasks in the cloud environment. In particular, evolutionary algorithms as well...
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Design and computational fluid dynamics analysis of the last stage of innovative gas-steam turbine
PublikacjaResearch regarding blade design and analysis of flow has been attracting interest for over a century. Meanwhile new concepts and design approaches were created and improved. Advancements in information technologies allowed to introduce computational fluid dynamics and computational flow mechanics. Currently a combination of mentioned methods is used for the design of turbine blades. These methods enabled us to improve flow efficiency...
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Molecular Design Using Selected Concentration Effects in Optically Activated Fluorescent Matrices
PublikacjaMolecular physics plays a pivotal role in various fields, including medicine, pharmaceuticals, and broader industrial applications. This study aims to enhance the methods for producing specific optically active materials with distinct spectroscopic properties at the molecular level, which are crucial for these sectors, while prioritizing human safety in both production and application. Forensic science, a significant socio-economic...
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Power System Dynamics. Stability and Control. 3rd edition
PublikacjaComprehensive, state-of-the-art review of information on the electric power system dynamics and stability. It places the emphasis first on understanding the underlying physical principles before proceeding to more complex models and algorithms. The book explores the influence of classical sources of energy, wind farms and virtual power plants, power plants inertia and control strategy on power system stability. The book cover...
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Discussing daylight simulations in a proposal for online daylighting education.
PublikacjaThere is increasing interest concerning daylighting in the building sector. However, such knowledge is difficult to penetrate the curricula of architects and designers as existing educational programmes often do not provide sufficient training on BPS. This also leads to superficial use of daylight simulations. This paper presents a proposal for a needs-based education package on daylighting design, that mixes modular eLearning...
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Circular saw vibrations or dynamics of the spindle
PublikacjaSawing of wood with circular saws is a typical example of cutting with multi-blade tools. In that kind of cutting, theposition accuracy of following tool blades is a crucial factor which affects the cutting process and machining final effects.Position tooth errors may cause deterioration in cutting conditions, changes in loads of individual teeth and the tool as a whole,and also a decrease in accuracy and surface quality after...
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Introduction in to tyre simulations
PublikacjaW artykule przedstawiono wyniki symulacji komputerowej zachowania się opony w czasie badania jej oporów toczenia w oparciu o program LMS Virtual Lab. Przedstawiono także wnioski wynikające z przeprowadzonej symulacji.
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Acceleration of Electromagnetic Simulations on Reconfigurable FPGA Card
PublikacjaIn this contribution, the hardware acceleration of electromagnetic simulations on the reconfigurable field-programmable-gate-array (FPGA) card is presented. In the developed implementation of scientific computations, the matrix-assembly phase of the method of moments (MoM) is accelerated on the Xilinx Alveo U200 card. The computational method involves discretization of the frequency-domain mixed potential integral equation using...
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Searching for Critical Conditions During Lifeboat Launching – Simulations
PublikacjaThe article describes numerical simulations of the process of lifeboat launching at the ship’s side. The research is aimed at finding the values of ship motion parameters which appear to be most dangerous for people in the lowered lifeboat due to the generated accelerations. The simplified model of ship hull motion adopted at this research stage bases on a superposition of harmonic motions with given amplitudes and periods in six...
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Dynamics of Field Line Mappings in Magnetic Flux Tubes
PublikacjaWe study the topological constraints on the dynamics of magnetic field lines in flux tubes. Our approach is based on the application of the topological invariant: fixed point index. We consider periodic flux tubes and find various restrictions on the field lines that come from the sequence of fixed point indices of iterations. We also analyze the case of a tube with a cylindrical obstacle, deducing some special dynamical properties...
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Towards detecting programmers’ stress on the basis of keystroke dynamics
PublikacjaThe article describes the idea of detecting stress among programmers on the basis of keystroke dynamics. An experiment with a group of students of artificial intelligence classes was performed. Two samples of keystroke data were recorded for each case, the first while programming without stress, the second under time pressure. A number of timing and frequency parameters were calculated for each sample. Then statistical analysis...
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Keystroke Dynamics Patterns While Writing Positive and Negative Opinions
PublikacjaThis paper deals with analysis of behavioural patterns in human–computer interaction. In the study, keystroke dynamics were analysed while participants were writing positive and negative opinions. A semi-experiment with 50 participants was performed. The participants were asked to recall the most negative and positive learning experiences (subject and teacher) and write an opinion about it. Keystroke dynamics were captured and...
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Structural Control of Photoinduced Dynamics in 4H-Imidazole- Ruthenium Dyes
PublikacjaThe photoinduced dynamics of a series ofterpyridine 4H-imidazole-ruthenium complexes, which constitutea new family of panchromatic dyes, is investigated. Thedynamics involves two excited states localized within the 4Himidazolesphere. Upon MLCT excitation, an excited state ispopulated, which is localized on the central part of the 4Himidazoleligand caused by its nonplanar conformation. Thepopulation of the second excited state is...
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Computational Fluid Dynamics Simulation of Gas–Liquid Multiphase Flow in T-junction for CO2 Separation
PublikacjaThe article presents the results of a computational fluid dynamics (CFD) analysis of gas-liquid multiphase flow. The simulation was conducted using CFD code and the Euler–Euler approach. The presented study relates to the non–reactive, steady-state, turbulent flow of water and carbon dioxide mixture in a 3D pipe. Separation phenomenon between phases is observed. The solution was obtained using a mixture model. Different values...
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Prediction of coking dynamics for wet coal charge
PublikacjaA 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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The Dynamics of Trade Relations between Ukraine and Romania: Modelling and Forecasting
PublikacjaThe article examines the monthly dynamics of exports, imports and balance of trade between Ukraine and Romania in the period from 2005 to 2021. Time series from 2015 to 2021 were used for modelling and forecasting (since the date the European Union–Ukraine Association Agreement took effect). Adequate models of the dynamics series of the Box-Jenkins methodology were built: additive models with seasonal component ARIMA (Autoregressive...
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Generating optimal paths in dynamic environments using RiverFormation Dynamics algorithm
PublikacjaThe paper presents a comparison of four optimisation algorithms implemented for the purpose of finding the shortest path in static and dynamic environments with obstacles. Two classical graph algorithms –the Dijkstra complete algorithm and A* heuristic algorithm – were compared with metaheuristic River Formation Dynamics swarm algorithm and its newly introduced modified version. Moreover, another swarm algorithm has been compared...
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Molecular properties with dual basis set methods
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Numerical solution of threshold problems in epidemics and population dynamics
PublikacjaA new algorithm is proposed for the numerical solution of threshold problems in epidemics and population dynamics. These problems are modeled by the delay-differential equations, where the delay function is unknown and has to be determined from the threshold conditions. The new algorithm is based on embedded pair of continuous Runge–Kutta method of order p = 4 and discrete Runge–Kutta method of order q = 3 which is used for the...
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Analysis of dynamics of a map-based neuron model via Lorenz maps
PublikacjaModeling nerve cells can facilitate formulating hypotheses about their real behavior and improve understanding of their functioning. In this paper, we study a discrete neuron model introduced by Courbage et al. [Chaos 17, 043109 (2007)], where the originally piecewise linear function defining voltage dynamics is replaced by a cubic polynomial, with an additional parameter responsible for varying the slope. Showing that on a large...
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A NUMERICAL STUDY ON THE DYNAMICS OF DENGUE DISEASE MODEL WITH FRACTIONAL PIECEWISE DERIVATIVE
PublikacjaThe aim of this paper is to study the dynamics of Dengue disease model using a novel piecewise derivative approach in the sense of singular and non-singular kernels. The singular kernel operator is in the sense of Caputo, whereas the non-singular kernel operator is the Atangana–Baleanu Caputo operator. The existence and uniqueness of a solution with piecewise derivative are examined for the aforementioned problem. The suggested...
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Positron binding to alkali-metal hydrides: The role of molecular vibrations
PublikacjaThe bound vibrational levels for J=0 have been computed for the series of alkali-metal hydride molecules from LiH to RbH, including NaH and KH. For all four molecules the corresponding potential-energy curves have been obtained for each isolated species and for its positron-bound complex (e+XH). It is found that the calculated positron affinity values strongly depend on the molecular vibrational state for which they are obtained...
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Usefulness of Keystroke Dynamics Features in User Authentication and Emotion Recognition
PublikacjaThe study presented in the article focuses on keystroke dynamics analysis applied to recognize emotional states and to authenticate users. An overview of some studies and applications in these areas is presented. Then, an experiment is described, i.e. the way of collecting data, extracting features, training classifiers and finding out the most appropriate feature subsets. The results show that it is difficult to indicate a universal...
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Directed electromagnetic pulse dynamics: projecting operators method
PublikacjaIn this article, we consider a one-dimensional model of electromagnetic pulse propagation in isotropic media, takinginto account a nonlinearity of the third order. We introduce a method for Maxwell's equation transformation on thebasis of a complete set of projecting operators. The operators correspond to wave dispersion branches including thedirection of propagation. As the simplest result of applying the method, we derive a system...
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Hopping or Tunneling? Tailoring the Electron Transport Mechanisms through Hydrogen Bonding Geometry in the Boron-Doped Diamond Molecular Junctions
PublikacjaMechanisms of charge transport in molecular junctions involving hydrogen bonds are complex and remain mostly unclear. This study is focused on the elucidation of the electron transfer in a molecular device consisting of two boron-doped diamond interfaces bound with an aromatic linker and a hydrogen bonding surrogating molecule. The projected local density of states (PLODS) analysis coupled with transmission spectra and current−voltage...
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Dynamics of Antimicrobial Peptide Encapsulation in Carbon Nanotubes: The Role of Hydroxylation
PublikacjaIntroduction: Carbon nanotubes (CNTs) have been widely employed as biomolecule carriers, but there is a need for further functionalization to broaden their therapeutic application in aqueous environments. A few reports have unraveled biomolecule–CNT interactions as a measure of response of the nanocarrier to drug-encapsulation dynamics. Methods: Herein, the dynamics of encapsulation of the antimicrobial peptide HA-FD-13 (accession...
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The dynamics of the total output of the fishery sector: The case of Indonesia
PublikacjaThe purpose of this study is to analyze the dynamics of the total output of the Indonesian fishery industry when the changes of the final demand occur. This study employs a demand-pull Input-Output (IO) quantity model, one of the calculation tools in the IO analysis, as an analysis instrument. Two conditions are noticed in calculation and analysis parts, namely (1) “whole sector change”, and (2) “pure change”. An initial period...
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Are the short cationic lipopeptides bacterial membrane disruptors? Structure-Activity Relationship and molecular dynamic evaluation
PublikacjaShort cationic lipopeptides are amphiphilic molecules that exhibit antimicrobial activity mainly against Grampositives. These compounds bind to bacterial membranes and disrupt their integrity. Here we examine the structure-activity relation (SAR) of lysine-based lipopeptides, with a prospect to rationally design more active compounds. The presented study aims to explain how antimicrobial activity of lipopeptides is affected by...
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Improvement of ships seakeeping performance by application of the full-scale cfd simulations
PublikacjaThe ship’s fuel economy is increasingly important. The paper presents the effect of redesigning a case study ship for increasing seakeeping performance. Selected wave parameters reflect very difficult operational conditions existing on the North Sea and the Baltic Sea. The analyzed variants of a case study ship represent the latest developments of modern hull forms. The concepts similar to V-shaped bulbous bow, X-bow, X-aft, B-bow...
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Simulations of air and water flow in a model dike during overflow experiments
PublikacjaFlow in flood dikes, earth dams, and embankments occurs in variably saturated conditions, with pores of the earth material filled partly with water and partly with air. In routine engineering analysis, the influence of pore air is neglected and the air pressure is assumed equal to atmospheric. In some circumstances, for example, during overtopping of the dike by water, the effect of pore air on water flow and stability of the structure...
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Dynamics of Chains as a Tool to Study Thermomechanical Properties of Proteins.
PublikacjaPolymer dynamics can be formulated on different levels of detail. One approach eliminates microscopic degrees of freedom and a polymer molecule is represented by a simplified structure—a chain. In the simplest case monomers of ideal chain have fixed length, and their orientation is independent of the orientations and positions of neighbouring monomers. This is reason that two monomers can co-exist at the same place. Ideal chain...
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Membrane model of human abdominal wall. Simulations vs. in vivo measurements
PublikacjaThe study presents a methodology of defining a numerical model of human abdominal wall based on the experimentally registered data of the abdomen geometry due to variations of the intraabdominal pressure. The abdominal wall is modelled here as a simple homogeneous membrane structure made of linear orthotropic material The displacements registered during the increase of pressure are compared with the re-sults of the model static...
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A Subspace-Splitting Moment-Matching Model-Order Reduction Technique for Fast Wideband FEM Simulations of Microwave Structures
PublikacjaThis article describes a novel model-order reduction (MOR) approach for efficient wide frequency band finite-element method (FEM) simulations of microwave components. It relies on the splitting of the system transfer function into two components: a singular one that accounts for the in-band system poles and a regular part that has no in-band poles. In order to perform this splitting during the reduction process, the projection...
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Simulations of Shear Zones and Cracks in Engineering Materials Using eXtended Finite Element Method
PublikacjaNumerical simulations of cracks and shear zones in quasi-brittle materials are presented. Extended Finite Element Method is used to describe both cracks and shear zones. In a description of tensile cracks, a Rankine criterion is assumed. A discrete Mohr-Coulomb law is adopted for simulations of shear zones. Results of simple numerical tests: unixial tension, bending and biaxial compression are demonstrated.
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From flow to jamming: Lattice Gas Automaton simulations in granular materials
PublikacjaWe introduce the first extension of a Lattice Gas Automaton (LGA) model to accurately replicate observed emergent phenomena in granular materials with a special focus on previously unexplored jamming transitions by incorporating gravitational effects, energy dissipation in particle collisions, and wall friction. We successfully reproduce flow rate evolution, density wave formation, and jamming transition observed in experiments....
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Finite Resolution Dynamics
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Molecular structures of two E-azobenzocrown ethers
PublikacjaRentgenowska analiza strukturalna monokryształów posłużyła do scharakteryzowania struktury izomerów E dwóch azobenzokoron: 13- i 16-członowej. Oba związki krystalizują w układzie jednoskośnym. W komórce elementarnej, w każdym przypadku znajdują się dwie niezależne cząsteczki, różniące się konformacją, szczególnie łańcucha eterowego. Porównując konformacje ''wolnych'' makrocykli z konformacjami ich kompleksów z jonami metali wskazano,...
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Experimental investigations and simulations of the microturbine unit with permanent magnet generator
PublikacjaIn dispersed power generation, low power devices are used for local combined generating of heat end electric power. There are developing concepts of micropower plants with electric generators driven by steam or gas microturbines. The paper presents the results of an experimental investigations of the microturbine set consists of the turbine with partial admission, permanent magnet generator and three phase AC-to-DC rectifier. The...