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Search results for: QM/MM
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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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Mutually polarizable QM/MM model with in situ optimized localized basis functions
PublicationWe extend our recently developed quantum-mechanical/molecular mechanics (QM/MM) approach [Dziedzic et al., J. Chem. Phys. 145, 124106 (2016)] to enable in situ optimization of the localized orbitals. The quantum subsystem is described with ONETEP linear-scaling density functional theory and the classical subsystem – with the AMOEBA polarizable force field. The two subsystems interact via multipolar electrostatics and are fully...
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Dominant Pathways of Adenosyl Radical-Induced DNA Damage Revealed by QM/MM Metadynamics
PublicationBrominated 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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TINKTEP: A fully self-consistent, mutually polarizable QM/MM approach based on the AMOEBA force field
PublicationWe present a novel quantum mechanical/molecular mechanics (QM/MM) approach in which a quantum subsystem is coupled to a classical subsystem described by the AMOEBA polarizable force field. Our approach permits mutual polarization between the QM and MM subsystems, effected through multipolar electrostatics. Self-consistency is achieved for both the QM and MM subsystems through a total energy minimization scheme. We provide an expression...
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Badania składu chemicznego materiału rury 323,90x12,70 mm
PublicationWykonano badania składu chemicznego materiału rury i dokonano oceny zgodności z atestem i normą.
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Performance of the AMOEBA Water Model in the Vicinity of QM Solutes: A Diagnosis Using Energy Decomposition Analysis
PublicationThe importance of incorporating solvent polarization effects into the modeling of solvation processes has been well-recognized, and therefore a new generation of hybrid quantum mechanics/molecular mechanics (QM/MM) approaches that accounts for this effect is desirable. We present a fully self-consistent, mutually polarizable QM/MM scheme using the AMOEBA force field, in which the total energy of the system is variationally minimized...
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On the design of planar high directivity proximity couplers in the mm-wave range
PublicationPrzedyskutowano problemy projektowania sprzęgaczy zbliżeniowych wykonywanych w technologii planarnej i przeznaczonych do pracy w zakresie fal milimetrowych. Zasadniczym celem badań było zaprojektowanie, wykonanie i przebadanie układu sprzęgacza o wysokiej kierunkowości i umiarkowanym poziomie sprzężenia pracującego w zakresie 40-50GHz. Przedyskutowano i zamodelowano różne konfiguracje sprzęgaczy. Stwierdzono, że znane zasady projektowania...
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Towards modelling of the environmental fate of pharmaceuticals using the QSPR-MM scheme
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Survivin expression in invasive pituitary gland adenomas with a diameter exceeding 20 mm
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Badania składu chemicznego i własności mechanicznych materiału rury fi 323,85x12,7 mm
PublicationWykonano badania składu chemicznego i właściwości mechanicznych materiału (stal nierdzewna typu 316L)
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Flow boiling of R1233zd(E) in a 3 mm vertical tube at moderate and high reduced pressures
PublicationThe results of flow boiling of R1233zd(E) in a 3 mm vertical stainless steel tube are presented at moderate and high saturation temperatures. Integral flow characteristics in the form of pressure drop and heat transfer coefficient are discussed for saturation temperatures ranging from 115 to 145 °C (corresponding reduced pressures from 0.2 to 0.7), mass velocity of 800 kg/m2s and heat flux of 20 kW/m2. All of the obtained heat...
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Molecular dynamics simulation and MM-PBSA analysis of Oxytricha nova TEBP ternary complex with ssDNA
PublicationPraca dotyczy badań metodami chemii obliczeniowej właściwości elektrostatycznych i termodynamicznych kompleksu telomerowego białka TEBP pochodzącego z organizmu Oxytricha z jednoniciowym telomerowym DNA (ssDNA).
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Design of mm-wave MIC frequency multiplayers and mixers using simple microstrip high-pass filters
PublicationPrzedyskutowano podstawowe wymagania dotyczące impedancji elementów półprzewodnikowych wykorzystywanych w mieszaczach i powielaczach częstotliwości projektowanych dla zakresu fal milimetrowych. Określono typy układów filtrujących niezbędnych w różnych częściach układów, podkreślając znaczenie filtrów górnoprzepustowych. Mikropaskowy filtr ze zwartym brzegiem został wykonany i zaimplementowany w mieszaczu pracującym w zakresie 20-40GHz.
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Rozkład naprężeń mechanicznych w łyżce o szerokości 500 mm, przeznaczonej do koparki podsiębiernej
PublicationW artykule zaprezentowano optymalizację kształtu łyżki koparki przedsiębiernej z wykorzystaniem analizy wytrzymałościowej. Analizę oparto na trójwymiarowym modelu konstrukcji łyżki z zastosowaniem metody elementów skończonych (MES). Opracowanie wspomnianej metody pozwoliło na modyfikację konstrukcji łyżki, która dała w efekcie obniżenie naprężeń złożonych w newralgicznych obszarach konstrukcji łyżki. Przedstawiona analiza okazała...
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Ekspertyza przyczyn korozji złącza spawanego rury ze szwem 129x3,0 mm z instalacji flokulatora
PublicationCelem pracy było ustalenie przyczyn korozji złącza spawanego rury ze szwem 130x3,0 mm z instalacji flokulatora. Instalacja była wykonana ze stali nierdzewnej AISI 316L. Zakres pracy obejmował: wykonanie analizy EDX składu chemicznego spoiny oraz nalotów obecnych na rurociągu, wykonanie badań próbek metalograficznych wraz z określeniem mikrostruktury
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MM/PBSA analysis of molecular dynamics simulations of bovine beta-lactoglobulin: free energy gradients in conformational transitions?
PublicationPraca dotyczy pH zależnych zmian konformacyjnych EF pętli beta-laktoglobuliny. Zmiany te są śledzone za pomocą metod obliczeniowych chemii (dynamika molekularna oraz metody MM/PBSA).
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Investigations on mixture preparation for two phase adiabatic pressure drop of R134a flowing in 5 mm diameter channel
PublicationThe article presents detailed two-phase adiabatic pressure drops data for refrigerant R134a. Study cases have been set for a mass flux varying from 200 to 400 kg/m2 s, at the saturation temperature of 19.4 ◦C. Obtained experimental data was compared with the available correlations from the literature for the frictional pressure drop during adiabatic flow. Influence of mixture preparation on pressure drop was investigated, for...
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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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SU‐GG‐T‐208: 3‐D Dosimetric Comparison of IMRT with 2.5 Mm HD120 MLC Using Optical CT Based Polymer Gel and PRESAGE Dosimeters
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Detailed experimental investigations on frictional pressure drop of R134a during flow boiling in 5 mm diameter channel: The influence of acceleration pressure drop component =Études expérimentales détaillées sur la chute de pression frictionnelle du R134a lors de l'ébullition en écoulement dans un canal de 5 mm de diamètre : influence de la composante d'accélération de la chute de pression
PublicationThis article presents detailed two-phase diabatic pressure drop data for refrigerant R134a at a saturation pressure of 5.5 bar corresponding to the saturation temperature of 19.4 °C. Study cases have been set for a mass flux varying from 100 to 500 kg m−2 s−1. The obtained data are used as a validation of the void fraction literature models, a set of graphs shows comparisons, for a representative set of experimental conditions,...
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The assessment of metrological properties of segmental orifice based on simulations and experiments
PublicationSegmental orifices are often used to measure flows of heterogeneous mixtures, especially in flow meters in the power industry, for example. The orifice (with module m= 0.25) was installed in a stainless-steel pipe with internal diameter of 50 mm, placed in a hydraulic water system. The research was performed for Reynolds numbers ranging from 9,000 to 17,000. The flow characteristics of this orifice obtained based on simulation...
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OPINIA TECHNICZNA O BUDOWLI PRZEZNACZONEJ DO PROWADZENIA RUCHU KOLEJOWEGO – PODKŁAD DREWNIANY NOWY TYPU IIIB DLA TORÓW O SZEROKOŚCI 750 MM ZASTOSOWANY W TORACH KROŚNICKIEJ KOLEI WĄSKOTOROWEJ
PublicationZlecenie obejmuje wykonanie badań koniecznych przez jednostkę upoważnioną i przedstawienie opinii jednostki upoważnionej celem uzyskania świadectwa dopuszczenia do eksploatacji typów budowli przeznaczonych do prowadzenia ruchu kolejowego: szyny kolejowej, systemu przytwierdzeń, podkładu kolejowego, rozjazdu kolejowego (Rozporządzenie Ministra Transportu, Budownictwa i Gospodarki Morskiej z dnia 7 sierpnia 2012 r. w sprawie wykazu...
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Fabrication of exfoliated graphite reinforced silicone rubber composites - Mechanical, tribological and dielectric properties
PublicationThe effect of exfoliated graphite (EG) on the mechanical, tribological and dielectric properties of the silicone rubber (QM) composites has been systematically investigated and analysed. Morphological analysis of the composites helps to understand the interfacial interaction between the filler and the rubber matrix as well as wear mechanism respectively. An enhancement in the mechanical, tribological and dielectric properties was...
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Fabrication of exfoliated graphite reinforced silicone rubber composites - Mechanical, tribological and dielectric properties
PublicationThe effect of exfoliated graphite (EG) on the mechanical, tribological and dielectric properties of the silicone rubber (QM) composites has been systematically investigated and analysed. Morphological analysis of the composites helps to understand the interfacial interaction between the filler and the rubber matrix as well as wear mechanism respectively. An enhancement in the mechanical, tribological and dielectric properties was...
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Sprawozdanie naukowe z badania nośności pala CFA Nr T13 mm metodą próbnego obciążenia statycznego z pomiarem rozkładu siły osiowej wzdłuż trzonu na terenie budowy Inteligentnego Centrum Logistycznego w Pustyni k. Dębicy
PublicationOpracowanie wyników badania nośności pala wierconego świdrem ciągłym CFA ∅630 mm, nr T13, wykonanego na terenie budowy Inteligentnego Centrum Logistycznego dla Nutrifarm Sp. z o.o., zlokalizowanego w miejscowości Pustynia k. Dębicy. Badanie pala wykonano metodą próbnego obciążenia statycznego z pomiarem rozkładu siły osiowej wzdłuż trzonu pala, zrealizowanym za pomocą ekstensometrów strunowych.
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Ocena nośności pali wierconych fi 880 mm wykonanych pod posadowienie podpór wiaduktu na podstawie próbnych obciążeń statycznych pali. Budowa wiaduktu nad torami PKP relacji Gdańsk - Tczew (E-65) w km 310+773.
PublicationWykonano ocenę nośności fundamentów palowych posadowionych na palach wierconych o średnicy 880 mm na podstawie badań statycznych tych pali.
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Opinia naukowo-techniczna dotycząca przyczyn obniżonej nośności pali CFA 800 mm wykonanych pod posadowienie podpory P10 wiaduktu drogowego nad linią kolejową w Cieplewie k. Pruszcza Gdańskiego wraz z propozycją zapewnienia nośności fundamentu podpory
PublicationPrzeprowadzono analizę wyniku próbnego obciążenia pala CFA pod posadowienie przyczółka wiaduktu. Przeanalizowano budowę podłoża gruntowego na podstawie dokumentacji archiwalnych i na podstawie własnych badań metodą CPT. Określono przyczyny obniżonej nośności wykonanych pali. Zaproponowano sposób zapewnienia wymaganej nośności fundamentu przyczółka.
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Opinia naukowo-techniczna dotycząca nośności pali wierconych fi 1500 mm wykonanych pod podpory wiaduktu C-4 na podstawie badań statycznych. Budowa Północnego Obejścia Krakowa w ciągu Drogi Krajowej nr 94 na odcinku Węzeł Radzikowskiego - Węzeł Modlnica.
PublicationOpinia dotycząca nośności pali wierconych o średnicy 1500 mm wykonanych pod podpory wiaduktu C-4 w ciągu Drogi Krajowej nr 94 na odcinku Węzeł Radzikowskiego - Węzeł Modlnica na podstawie próbnych obciążeń statycznych.
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Unraveling the role of boron dimers in the electrical anisotropy and superconductivity in boron-doped diamond
PublicationWe use quantum mechanics (QM) to determine the states formed by B dopants in diamond. We find that isolated B sites prefer to form BB dimers and that the dimers pair up to form tetramers (BBCBB) that prefer to aggregate parallel to the (111) surface in the <110> direction, one double layer below the H-terminated surface double layer. These tetramers lead to metallic character (Mott metal Insulator Transition) with holes in the...
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Better polynomial algorithms for scheduling unit-length jobs with bipartite incompatibility graphs on uniform machines
PublicationThe goal of this paper is to explore and to provide tools for the investigation of the problems of unit-length scheduling of incompatible jobs on uniform machines. We present two new algorithms that are a significant improvement over the known algorithms. The first one is Algorithm 2 which is 2-approximate for the problem Qm|p j = 1, G = bisubquartic|Cmax . The second one is Algorithm 3 which is 4-approximate for the problem Qm|p...
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Opinia naukowo-techniczna dotycząca nośności pali wierconych fi 1500 mm wykonanych pod podpory wiaduktu C-3 (jezdnia prawa) na podstawie badań statycznych. Budowa Północnego Obejścia Krakowa w ciągu Drogi Krajowej nr 94 na odcinku Węzeł Radzikowskiego - Węzeł Modlnica.
PublicationOpinia dotycząca nośności pali wierconych o średnicy 1500 mm wykonanych pod podpory wiaduktu C-3 (jezdnia prawa) w ciągu Drogi Krajowej nr 94 na odcinku Węzeł Radzikowskiego - Węzeł Modlnica na podstawie badań statycznych.
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A socially responsible university - an attempt to approach the system
PublicationIt is the author's thesis that social responsibility of university is an integrated system of both knowledge management (KM), quality management (QM) and organizational development (OD) processes. The author determined that the university "bond" is an institutional culture (IC). An integrated system is the way to create university an open system co-operated and co-opetited with stakeholders. The stakes are high in game - both students...
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APPLICATION OF NUMERICAL SIMULATIONS ON X10CRWMOVNB9-2 STEEL MULTILAYER WELDING
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Uniwersytet społecznie odpowiedzialny - próba podejścia systemowego. [ wersja polska artykułu rejestrowanego pod nr 86628]
PublicationW artykule postawiono tezę, że uniwersytet społecznie odpowiedzialny to taki, w którym przenikać się będą: rozwójorganizacyjny (OD), doskonalenie procesów zarządzania wiedzą (KM) i doskonalenie zarządzania jakością (QM. Spoiwem uniwersytetu jest jego kultura organizacyjna (instytucjonalna. Uniwersytet społecznie odpowiedzialny tootwarty system współpracujący z otoczeniem, w którym toczy się gra o studenta (słuchacza) oraz o finanse....
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The ONETEP linear-scaling density functional theory program
PublicationWe present an overview of the ONETEP program for linear-scaling density functional theory (DFT) calculations with large basis set (planewave) accuracy on parallel computers. The DFT energy is computed from the density matrix, which is constructed from spatially localized orbitals we call Non-orthogonal Generalized Wannier Functions (NGWFs), expressed in terms of periodic sinc (psinc) functions. During the calculation, both the...
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The Role of Electrostatics in Enzymes: Do Biomolecular Force Fields Reflect Protein Electric Fields?
PublicationPreorganization of large, directionally oriented, electric fields inside protein active sites has been proposed as a crucial contributor to catalytic mechanism in many enzymes, and it may be efficiently investigated at the atomistic level with molecular dynamics simulations. Here, we evaluate the ability of the AMOEBA polarizable force field, as well as the additive Amber ff14SB and Charmm C36m models, to describe the electric...
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Concomitant consumption of Aronia melanocarpa aqueous extract and low cadmium doses improve serum and bone antioxidative status in a rat model
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Advanced Potential Energy Surfaces for Molecular Simulation
PublicationAdvanced 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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Electronically Excited States in Solution via a Smooth Dielectric Model Combined with Equation-of-Motion Coupled Cluster Theory
PublicationWe present a method for computing excitation energies for molecules in solvent, based on the combination of a minimal parameter implicit solvent model and the equation-of-motion coupled-cluster singles and doubles method (EOM-CCSD). In this method, the solvent medium is represented by a smoothly varying dielectric function, constructed directly from the quantum mechanical electronic density using only two tunable parameters. The...
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Influence of the laser remelting parameters on the thickness of surface layers created on the stainless steel X5CrNi18-10
PublicationIn this work the surface of austenitic stainless steel type X5CrNi18-10 was treated by using laser. Laser remelting was done by means of laser MLT 2500 CO2 with different parameters of treatment: P - power beam (800 [W], 1000 [W], 1100 [W], 1200 [W]); v - scanning velocity (6 [mm/s], 7 [mm/s], 8 [mm/s]); diameter of laser beam (1.4 [mm], 1.6 [mm]). The influence of these parameters on the thickness and shape of layers in manufacturing...
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Wavelet analysis of frequency of air bubble departure
PublicationPrzedstawiono wyniki nieliniowej analizy częstotliwośći generowania pęcherzyków powietrza z dysz o średnicy 0.75 mm, 1.61 mm oraz 2.76 mm umieszczonych 15 cm poniżej poziomu wody.
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Stability and phase transition investigation of olanzapine polymorphs
PublicationWe use electrical embedded-fragment QM method with both DFT/ωB97XD/6-31G* and MP2/6-31G* to investigate the phase transformations of olanzapine. Gibbs free energy calculations predict that form I is always the most stable structure and form II is the least stable one, while form IV is more stable than form III below about 200 K but less stable above this temperature, implying a polymorphic phase transformation. This may account...
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Mitigation of the Flow Maldistribution in Minichannel and Minigap Heat Exchangers by Introducing Threshold in the Manifolds
PublicationIn the present paper, a detailed numerical investigation has been carried out to analyze the flow maldistribution in 50 parallel rectangular cross-section (1 mm depth and 1 mm width) minichannels and minigap section (1 mm depth and 99 mm width) with rectangular/trapezoidal manifolds in Z-type flow configuration. The author carried out numerical investigation with various mass flowrates, namely 0.05 kg/s, 0.1 kg/s and 0.2 kg/s which...
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Experimental and comparative study on the two-phase pressure drop of air-water mixture in U-bend and straight pipe annuli
PublicationIn this paper, the experimental and theoretical analysis of pressure drop in singlephase and two phase-flow were presented for straight and U-bend smooth tube annulus and tube annulus with wire coil insert. Experiments for various boundary conditions were performed. In case of U-tube and straight tube with and without turbulator, tests were made for the water-water and air-water systems. The study covered a wide measuring range,...
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Experimental Investigations on the Influence of Coil Arrangement on Melting/Solidification Processes
PublicationThe latent heat thermal energy storage units are very popular because of their high energy density and almost close to constant temperature during the charging/discharging. In the present study has been proposed new shell-and-coil geometry with a shifted coil position to enhance the performance of phase change thermal magazine. The experimental investigations have been performed both for the melting and solidification process of...
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Degradation of Gel-Coat Layer in Glass/Polyester Laminate in Seawater Environment
PublicationGlass/polyester laminate coated with gelcoat layer of different thickness 0,5; 1,5; 3 mm was studied in terms of blistering behaviour and water sorption in hot water environment. Blistering was found to be accelerated for thin (0,5 mm) gel-coat layer compared to the thick (1,5; 3 mm), however no significant difference in blistering behaviour was observed between the laminates with gel-coat thickness 1,5 and 3 mm which may suggest...
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Protective impact of extract from Aronia melanocarpa berries against low-level exposure to cadmium-induced lipid peroxidation in the bone tissue: a study in a rat model
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Effect of polyphenols from Aronia melanocarpa on the total oxidative and antioxidative bone status of cadmium-exposed rats
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Experimental investigation of heat transfer enhancement in straight and U-bend double-pipe heat exchanger with wire insert
PublicationIn this paper, the possibility of heat transfer enhancement in the U-bend exchanger was presented. Experimental research has been carried out for four individual heat exchanger constructions i.e. plain tube in tube, turbulized tube in tube, plain U-bend and U-bend with turbulator. Also, heat transfer experiments for various boundary conditions were performed to obtain reference values. In case of U-bend exchanger with and without...
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Thermal and economic investigation of straight and U-bend double tube heat exchanger with coiled wire turbulator
PublicationExperimental research has been carried out for four individual heat exchanger constructions, i.e., plain double tube, turbulized double tube, plain U-bend and U-bend with turbulator. Tests were made for the water-water system. The study covered a wide measuring range, i.e., Re = 800–9000 – on the shell side, for a constant cold water temperature of 9 ◦C and hot water of 50 ◦C. The heat exchangers were made from copper tubes with...