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Search results for: QM/MM FREE ENERGY SIMULATIONS
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Variable-fidelity shape optimization of dual-rotor wind turbines
PublicationPurpose Dual-rotor wind turbines (DRWTs) are a novel type of wind turbines that can capture more power than their single-rotor counterparts. Because their surrounding flow fields are complex, evaluating a DRWT design requires accurate predictive simulations, which incur high computational costs. Currently, there does not exist a design optimization framework for DRWTs. Since the design optimization of DRWTs requires numerous model...
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Wind resource assessment and energy yield prediction for the small wind turbine on the Szubieniczne Hill
PublicationThe goal of this study is to preliminary assess the wind resources on the Szubieniczne Hill in order to predict the annual energy production for planned small wind turbine. The analyzed site is located close to the Gdańsk University of Technology campus, in complex urban environment additionally surrendered by forested hills. The assessment is based on Computational Fluid Dynamics simulations which allow to evaluate the wind energy potential...
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Effect of osmolytes on the thermal stability of proteins: replica exchange simulations of Trp-cage in urea and betaine solutions
PublicationAlthough osmolytes are known to modulate the folding equilibrium, the molecular mechanism of their effect on thermal denaturation of proteins is still poorly understood. Here, we simulated the thermal denaturation of a small model protein (Trp-cage) in the presence of denaturing (urea) and stabilizing (betaine) osmolytes, using the all-atom replica exchange molecular dynamics simulations. We found that urea destabilizes Trp-cage...
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Towards Carbon Neutral Settlements. The Importance of Early-Stage Urban and Energetic Optimizations
PublicationThe aim of the research was to verify the essence of interdisciplinary energy optimizations in earlystage urban design process. A further aim was to the find most optimal design variant and scenario in terms of urban energy efficiency for the future development in Nowy Port, located in Gdansk, Poland - a place requiring complex revitalization. The research combined qualitative and quantitative approaches; an urban design layer...
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A Concept for Safe and Less Expensive Acceleration of a Marine Steam Turbine Start-up
PublicationThis paper analyses the issue of accelerated start-up of a marine steam turbine, which is an important problem because the start-up of a steam machine involves the combustion of fuel that is not transformed into useful energy. To find novel technologies that offer improvements in this aspect is essential due to restrictions on reducing ship emissions. Thus, the shorter the start-up time, the better for the environment and economy....
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Prediction of consumer electricity needs based on Internet weather forecasts
PublicationElectrical energy is considered both as an important driver for producing and transporting goods in companies, as well as a good in itself which requires planning and management for generating and delivering it to consumers in proper time and amounts. Weather information can be considered to convey part of the data on energy delivery needs of consumers. Free meteorological data sources on the Web do not offer consistent data to...
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Physics-Based Coarse-Grained Modeling in Bio- and Nanochemistry
PublicationCoarse-grained approaches, in which groups of atoms are represented by single interaction sites, are very important in biological and materials sciences because they enable us to cover the size- and time-scales by several orders of magnitude larger than those available all-atom simulations, while largely keeping the details of the systems studied. The coarse-grained approaches differ by the scheme of reduction and by the origin...
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How proteins bind to DNA: target discrimination and dynamic sequence search by the telomeric protein TRF1
PublicationTarget search as performed by DNA-binding proteins is a complex process, in which multiple factors contribute to both thermodynamic discrimination of the target sequence from overwhelmingly abundant off-target sites and kinetic acceleration of dynamic sequence interrogation. TRF1, the protein that binds to telomeric tandem repeats, faces an intriguing variant of the search problem where target sites are clustered within short fragments...
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Non-destructive inspection of ground anchors using guided wave propagation
PublicationThis paper deals with numerical and experimental investigations of specific problems of guided wave propagation in ground anchors. The research focuses on recognizing the phenomenon of the energy transfer between anchor components. Particular attention is paid to characteristic features of guided waves propagating in free and embedded parts of the tendon, at the interface between the tendon and the surrounding anchor body as well...
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On the use of uniaxial one-parameter damage laws for estimating fatigue life under multiaxial loading
PublicationThe goal of this paper is to evaluate the capabilities of different one-parameter fatigue laws to estimate crack initiation in notched components under multiaxial loading. Fatigue damage is accounted for through stress-based, strain-based, and energy-based approaches while the cyclic plasticity at the notch-controlled process zone is estimated using linear-elastic simulations. The results show that energy-based formulations established...
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Anti-plane waves in an elastic thin strip with surface energy
PublicationWe consider anti-plane motions of an elastic plate taking into account surface energy within the linear Gurtin–Murdoch surface elasticity. Two boundary-value problems are considered that describe complete shear dynamics of a plate with free faces or with free and clamped faces, respectively. These problems correspond to anti-plane dynamics of an elastic film perfectly or non-perfectly attached to a rigid substrate. Detailed analysis...
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Membrane Sterols Modulate the Binding Mode of Amphotericin B without Affecting Its Affinity for a Lipid Bilayer
PublicationMembrane-active antibiotics are known to selectively target certain pathogens based on cell membrane properties, such as fluidity, lipid ordering, and phase behavior. These are in turn modulated by the composition of a lipid bilayer and in particular by the presence and type of membrane sterols. Amphotericin B (AmB), the golden standard of antifungal treatment, exhibits higher activity toward ergosterol-rich fungal membranes, which...
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Chip suction system in circular sawing machine: empirical research and computational fluid dynamics numerical simulations
PublicationThe experimental analysis of the wood chip removing system during its redesigning in the existing sliding table circular saw and computational fluid dynamic (CFD) numerical simulations of the air flow process is presented in the paper. The attention was focused on the extraction hood and the bottom shelter of the actual existing system. The main aim was to perform experimental research on the pressure distribution inside the...
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Electrochemically directed biofunctionalization of a lossy-mode resonance optical fiber sensor
PublicationIn this work, we present a direct electrochemical biofunctionalization of an indium-tin-oxide-coated lossy-mode resonance optical fiber sensor. The functionalization using a biotin derivative was performed by cyclic voltammetry in a 10 mM biotin hydrazide solution. All stages of the experiment were simultaneously verified with optical and electrochemical techniques. Performed measurements indicate the presence of a poly-biotin...
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Balancing Energy Inputs/Outputs and GHG Emissions for Sustainable Wastewater Treatment – a Case Study
PublicationThe aim of the study is a model-based evaluation of the selected operating modes and technological upgrades on the energy balance and greenhouse gas (GHG) emissions in a large wastewater treatment plant in the city of Slupsk (northern Poland). The considered scenarios focus on energy savings for aeration, increasing energy recovery via biogas cogeneration and reduction of the CO2 equivalent emission from both direct processes (related...
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Numerical Estimation of Hull Hydrodynamic Derivatives in Ship Maneuvering Prediction
PublicationPrediction of the maneuvering characteristics of the ship at the design stage can be done by means of model tests, computational simulations or a combination of both. The model tests can be realized as direct simulation of the standard maneuvers with the free running model, which gives the most accurate results, but is also the least affordable as it requires very large tank or natural lake, as well as complex equipment of the...
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Rotation Triggers Nucleotide-Independent Conformational Transition of the Empty β Subunit of F1-ATPase
PublicationF1-ATPase (F1) is the catalytic portion of ATP synthase, a rotary motor protein that couples proton gradients to ATP synthesis. Driven by a proton flux, the F1 asymmetric γ subunit undergoes a stepwise rotation inside the α3β3 headpiece and causes the β subunits’ binding sites to cycle between states of different affinity for nucleotides. These concerted transitions drive the synthesis of ATP from ADP and phosphate. Here, we study...
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ENERGY EFFICIENT SMALL INLAND PASSENGER SHUTTLE FERRY WITH HYBRID PROPULSION - CONCEPT DESIGN, CALCULATIONS AND MODEL TESTS
PublicationIn recent years, there has been a significant development in “green” and energy efficient propulsion systems, which fits into the general trend of environmentally friendly “green shipping”. The pursued goal is to construct a safe passenger ship that is low in energy demand and equipped with a highly energy efficient, emission-free propulsion system. The paper presents main problems encountered by designers of a small, hybrid-powered...
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Molecular dynamics simulations of the affinity of chitin and chitosan for collagen: the effect of pH and the presence of sodium and calcium cations
PublicationChitosan and chitin are promising biopolymers used in many areas including biomedical applications, such as tissue engineering and viscosupplementation. Chitosan shares similar properties with hyaluronan, a natural component of synovial fluid, making it a good candidate for joint disease treatment. The structural and energetic consequences of intermolecular interactions are crucial for understanding the biolubrication phenomenon...
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Role of cholesterol in substrate recognition by -secretase
Publication-Secretase is an enzyme known to cleave multiple substrates within their transmembrane domains, with the amyloid precursor protein of Alzheimer’s Disease among the most prominent examples. The activity of -secretase strictly depends on the membrane cholesterol content, yet the mechanistic role of cholesterol in the substrate binding and cleavage remains unclear. In this work, we used all-atom molecular dynamics simulations to examine...
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Mechanism of recognition of parallel G-quadruplexes by DEAH/RHAU helicase DHX36 explored by molecular dynamics simulations
PublicationBecause of high stability and slow unfolding rates of G-quadruplexes (G4), cells have evolved specialized helicases that disrupt these non-canonical DNA and RNA structures in an ATP-dependent manner. One example is DHX36, a DEAH-box helicase, which participates in gene expression and replication by recognizing and unwinding parallel G4s. Here, we studied the molecular basis for the high affinity and specificity of DHX36 for parallel-type...
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Understanding the formation of metastable furan dication in collisions with ions
PublicationThis work relies on complementary theoretical and experimental studies of the processes induced by ion-furan collisions. Results of the Molecular Dynamics simulations and exploration of the energy profiles combined with coincidence mass spectrometry provide complete picture of the fragmentation of furan dication.
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Game theory-based virtual machine migration for energy sustainability in cloud data centers
PublicationAs the demand for cloud computing services increases, optimizing resource allocation and energy consumption has become a key factor in achieving sustainability in cloud environments. This paper presents a novel approach to address these challenges through an optimized virtual machine (VM) migration strategy that employs a game-theoretic approach based on particle swarm optimization (PSO) (PSO-GTA). The proposed approach leverages...
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Hydraulic analysis of causes of washout of Gdynia-Orłowo seashore during the flood in the Kacza river estuary
PublicationIn July 2016 in the Three-city agglomeration a rainfall episode of over a day duration and 150 mm summary rainfall height, occurred. This situation, extreme as for Polish conditions, caused significant freshets in rivers and streams running into Gdansk Bay, the Baltic Sea, and serving as collectors of rainfall waters for the sea-coast towns. In many areas of the Three-city flood phenomena and overflows took place. The flood also...
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Design of new cholinesterase inhibitors based on phosphorus analogs of tacrine as potential anti-Alzheimer’s disease agents
PublicationBased on the analysis of the determined free binding energy (using the AutoDock Vina 1.1.2 docking program), the most potent cholinesterase inhibitors were selected. Moreover, studies of 3D visualization of the results of molecular modeling led to the identification of potential sites for the interaction of new potential inhibitors with amino acid residues building active sites of investigated cholinesterases.
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Strategies for Achieving Energy Neutrality in Biological Nutrient Removal Systems – a Case Study of the Slupsk WWTP (northern Poland)
PublicationThe paper presents a model-based evaluation of technological upgrades on the energy and cost balance in a large biological nutrient removal wastewater treatment plant (WWTP) in the city of Slupsk (northern Poland). The proposed upgrades include chemically enhanced primary sludge removal and reduction of the nitrogen load in the deammonification process employed for reject water treatment. Simulations enabled to estimate the increased...
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Strategies for achieving energy neutrality in biological nutrient removal systems - a case study of the Slupsk WWTP (northern Poland)
PublicationThe paper presents a model-based evaluation of technological upgrades on the energy and cost balance in a large biological nutrient removal wastewater treatment plant (WWTP) in the city of Slupsk (northern Poland). The proposed upgrades include chemically enhanced primary sludge removal and reduction of the nitrogen load in the deammonification process employed for reject water treatment. Simulations enabled to estimate the increased...
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Experimental and numerical study of thermal and electrical potential of BIPV/T collector in the form of air-cooled photovoltaic roof tile
PublicationAmong renewable energy sources, Building-Integrated Photovoltaic/Thermal (BIPV/T) systems are gaining increasing interest. To improve their economic competitiveness, technologies that increase their efficiency are searched for. The paper is devoted to evaluating the impact of various air-cooling configurations on the thermal and electrical performance of a photovoltaic roof tile. A numerical model of the own experimental system...
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Theoretical Encapsulation of Fluorouracil (5-FU) Anti-Cancer Chemotherapy Drug into Carbon Nanotubes (CNT) and Boron Nitride Nanotubes (BNNT)
PublicationIntroduction: Chemotherapy with anti-cancer drugs is considered the most common approach for killing cancer cells in the human body. However, some barriers such as toxicity and side effects would limit its usage. In this regard, nano-based drug delivery systems have emerged as cost-effective and efficient for sustained and targeted drug delivery. Nanotubes such as carbon nanotubes (CNT) and boron nitride nanotubes (BNNT) are promising...
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Estimation of Vehicle Energy Consumption at Intersections Using Microscopic Traffic Models
PublicationThis paper addresses issues related to modeling energy consumption and emissions using microscopic traffic simulations. This paper develops a method in which a traffic model is used to calculate the energy needed to travel through selected types of intersections. This paper focuses on energy consumption and derived values of calculated energy, which can be, for example, carbon dioxide emissions. The authors present a review of...
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N-phosphonomethylglycine utilization by the psychrotolerant yeast Solicoccozyma terricola M 3.1.4.
PublicationSolicoccozymaterricolaM 3.1.4., the yeast strain isolated from soil sample from blueberry cultivation in MiedzyrzecPodlaski in Poland, is capable to split of phosphorus to nitrogen and nitrogen to carbon bonds inN-phosphono-methylglycine (PMG, glyphosate). The biodegradation process proceeds in the phosphate-independent manner. Itis the first example of a psychrotolerant yeast strain able to degrade PMGviaCeN bond cleavage accompanied...
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COMPUTER ANALYSIS OF HYDRAULIC CONDITIONS IN A SANITARY CHAMBER
PublicationThis paper presents analysis of hydraulic conditions of sewage flow down the slipway (ramp) in the collecting sanitary chamber connecting 3 collectors on the inlet: ⌀600, ⌀800 and ⌀1400 and one on the outlet ⌀1600 mm, with a maximum difference of elevation 5 m. The mathematical model has been made and hydraulic calculations were carried out in steady flow conditions. Then wastewater surface elevation, energy grade line elevation,...
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The Efficacious Benefit of 25-Hydroxy Vitamin D to Prevent COVID-19: An In-Silico Study Targeting SARS-CoV-2 Spike Protein
PublicationThe environment has rapidly looked at proven specialist task forces in the aftermath of the COVID-19 pandemic to build public health policies and measures to mitigate the effects of emerging coronaviruses. According to the researchers, taking 10 μg of 25-hydroxy vitamin D daily is recommended to keep us safe. There have been several studies recently indicating that there is a reduced risk of contracting Coronavirus by 25-hydroxy...
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CFD-based evaluation of current-carrying capacity of power cables installed in free air
PublicationEvaluation of current-carrying capacity of power cables and selection of cross-sectional area of their conductors are mainly performed in accordance with requirements of EN, IEC or IEEE standards. However, these standards do not provide all methods of cables installation and location which occur in practice. Thus, in some cases, performance of advanced modeling of various thermal phenomena, affecting power cables current-carrying...
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Energy Modeling of Single-Family Houses in the Conceptual Phase
PublicationThe aim of the article is to identify the potential impact of the latest commercial digital tools for building energy analysis on the everyday architectural practice in Poland in the context of typology and energy optimization of single –family houses. The reason for this survey is that “architect friendly” interfaces simulation results’ visualization and energy analysis tools are not given deserved attention in the architectural...
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Hyaluronic acid/tannic acid films for wound healing application
PublicationIn this study, thin films based on hyaluronic acid (HA) with tannic acid (TA) were investigated in three different weight ratios (80HA/20TA, 50HA/50TA, 20HA/80TA) for their application as materials for wound healing. Surface free energy, as well as their roughness, mechanical properties, water vapor permeability rate, and antioxidant activity were determined. Moreover, their compatibility with blood and osteoblast cells was investigated....
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The Possibility of Phase Change Materials (PCM) Usage to Increase Efficiency of the Photovoltaic Modules
PublicationSolar energy is widely available, free and inexhaustible. Furthermore this source of energy is the most friendly to the environment. For direct conversion of solar energy into useful forms like of electricity and thermal energy, respectively photovoltaic cells and solar collectors are being used. Forecast indicate that the first one solution will soon have a significant part in meeting the global energy demand. Therefore it is...
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INFLUENCE OF THE HULL SHAPE ON THE ENERGY DEMAND OF A SMALL INLAND VESSEL WITH HYBRID PROPULSION
PublicationRecently, there has been a significant development of ecological propulsion systems, which is in line with the general trend of environmentally friendly “green shipping”. The main aim is to build a safe, low-energy passenger ship with a highly efficient, emission-free propulsion system. This can be achieved in a variety of ways. The article presents the main problems encountered by designers and constructors already at the stage...
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Interaction of cisplatin and two potential antitumoral platinum(ii) complexes with a model lipid membrane: a combined NMR and MD study
PublicationIn this study, the interaction of cisplatin (1) and two potential antitumoral Pt(II) complexes (2 and 3) with a model DMPC bilayer was investigated by multinuclear NMR spectroscopy and MD simulations in order to understand its implication for the different antitumoral properties shown by the three complexes. In particular, 31P, 13C and 2H solid state NMR experiments were performed to obtain information on the phase structure, phase...
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Telomere uncapping by common oxidative guanine lesions: Insights from atomistic models
PublicationOxidative damage to DNA is widely known to contribute to aging and disease. This relationship has been extensively studied for telomeres – structures that cap chromosome ends – due to their role in cell proliferation and senescence, and exceptional susceptibility to oxidation. Indeed, the repetitive telomeric DNA sequence contains the 5′-GGG-3′ motif that has the lowest ionization potential of all trinucleotides. Accordingly, experiments...
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A Numerical Study on Baseline-Free Damage Detection Using Frequency Steerable Acoustic Transducers
PublicationIn structural health monitoring (SHM) a considerable amount of damage detection algorithms based on guided waves (GW) have been developed. Most of them rely on extensive transducer networks, besides preliminary reference measurements of the structures. This originated a growing demand for hardware simplification and cost reduction of the wave-based SHM methods, driving the conception of new solutions enabling both: the reduction...
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Experimental-Numerical Analysis of the Effect of Bar Diameter on Bond in Pull-Out Test
PublicationBar diameter is one of the basic factors affecting bond behavior, which is still of interest due to opposing opinions regarding its effect on bond behavior in the pull-out test. This paper presents an experimental and numerical bond analysis of ribbed reinforcing bar in concrete. The aim was to experimentally evaluate the effect of bar diameter on the bond behavior in the pull-out test and to perform numerical simulations of the...
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Correlation between partial inhibition of hydrogen evolution using thiourea and catalytic activity of AB5-type hydrogen storage alloy towards borohydride electrooxidation
PublicationDirect borohydride fuel cells (DBFCs) are devices which directly convert the chemical energy stored in the borohydride ion and oxidant into electrical energy as a result of redox reactions. Unfortunately, a significant amount of fuel is lost as a result of the undesirable hydrolysis reaction. The selection of an efficient borohydride hydrolysis inhibitor requires detailed knowledge regarding the interaction mechanism between the...
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A novel dual-band rectifier circuit with enhanced bandwidth for RF energy harvesting applications
PublicationIn recent years, a rapid development of low-power sensor networks, enabling machine-to-machine communication in applications such as environmental monitoring, has been observed. Contemporary sensors are normally supplied by an external power source, typically in a form of a battery, which limits their lifespan and increases the maintenance costs. This problem can be addressed by harvesting and converting ambient RF energy into...
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Design and Evaluation of the Compact and Autonomous Energy Subsystem of a Wave Energy Converter
PublicationThis paper presents the results of the design process focused on the development of the energy subsystem (ES) of a wave energy converter (WEC). The ES is an important electrical part that significantly affects the energy reliability and energy efficiency of the entire WEC device. The designed ES was intended for compact WECs powering IoT network devices working in the distributed grid. The developed ES is an electronic circuit...
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Measurements and visualization of sound field distribution around organ pipe
PublicationMeasurements and visualization of acoustic field around an organ pipe are presented. Sound intensity technique was applied for this purpose. Measurements were performed in free field. The organ pipe was activated with a constant air flow, produced by an external compressor, aimed at obtaining long-term steady state responses of generated acoustic signal. Sound energy distribution was measured in a defined fixed grid of points...
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A dynamic vehicle-bridge model based on the modal identification results of an existing EN57 train and bridge spans with non-ballasted tracks
PublicationThis paper addresses the methodology of the bridge-vehicle dynamic model definition based on the free response measurements of an existing train and existing bridge spans. In the case of the railway vehicle, the methodology uses the impulse excitations of a single car by means of the wedge method. In the case of the bridge spans, free responses are collected after the passages of trains. The global modal parameters (frequencies...
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Effect of Microplastics Pollution on Hydrogen Production from Biomass: A Comprehensive Review
PublicationHydrogen production from biomass and organic wastes is considered as a potential alternative energy source and is known as a clean and CO2-free fuel energy carrier. H2 is considered very promising among the other energy sources; therefore, the effective conversion of biomass and organic solid waste to this secondary energy source is urgently sought. As a result, it is of importance to assess the impact of the existence of microplastics...
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Determination of the Bending Properties of Wire Rope Used in Cable Barrier Systems
PublicationThis paper presents research on the bending properties of 3 × 7 19-mm wire rope commonly used in road cable barriers. A total of 19 experimental tests were conducted. In addition, two nonlinear 3D numerical models of the wire rope using beam and solid finite elements were developed. Based on these models, four numerical simulations were carried out. The numerical results were validated against the experimental ones and a very good...
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Rapid redesign of multiband antennas with respect to operating conditions and material parameters of substrate
PublicationThis work addresses geometry parameter scaling of multi-band antennas for Internet of Things applications. The presented approach is comprehensive and permits re-design of the structure with respect to both the operating frequencies and material parameters of the dielectric substrate. A two-step procedure is developed with the initial design obtained from an inverse surrogate model constructed using a set of appropriately prepared...