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Wyniki wyszukiwania dla: coarse graining, molecular dynamics, openmp, parallel algorithms, unres
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Guanosine Dianions Hydrated by One to Four Water Molecules
PublikacjaIntermolecular interactions such as those present in molecule···water complexes may profoundly influence the physicochemical properties of molecules. Here, we carried out an experimental–computational study on doubly deprotonated guanosine monophosphate···water clusters, [dGMP – 2H]2–·nH2O (n = 1–4), using a combination of negative anion photoelectron spectroscopy (NIPES) with molecular dynamics (MD) and quantum chemical (QM) calculations....
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Closer look into the structures of tetrabutylammonium bromide–glycerol-based deep eutectic solvents and their mixtures with water
PublikacjaIn recent years, deep eutectic solvents (DES) and it’s mixture with water have become more and more attention as green solvents used in chemistry. However, there are only a few theoretical studies on the mechanisms of pure DES and DES-water complex formation. Therefore, the structural properties of tetrabutylammonium bromide–glycerol-based deep eutectic solvents and their mixtures with water have been investigated by means of Molecular...
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Membrane Sterols Modulate the Binding Mode of Amphotericin B without Affecting Its Affinity for a Lipid Bilayer
PublikacjaMembrane-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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Performance of electrochemical immunoassays for clinical diagnostics of SARS-CoV-2 based on selective nucleocapsid N protein detection: Boron-doped diamond, gold and glassy carbon evaluation
PublikacjaThe 21st century has already brought us a plethora of new threats related to viruses that emerge in humans after zoonotic transmission or drastically change their geographic distribution or prevalence. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first spotted at the end of 2019 to rapidly spread in southwest Asia and later cause a global pandemic, which paralyzes the world since then. We have designed novel...
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Accelerated Gradient-Based Optimization of Antenna Structures Using Multi-Fidelity Simulations and Convergence-Based Model Management Scheme
PublikacjaThe importance of numerical optimization has been steadily growing in the design of contemporary antenna structures. The primary reason is the increasing complexity of antenna topologies, [ a typically large number of adjustable parameters that have to be simultaneously tuned. Design closure is no longer possible using traditional methods, including theoretical models or supervised parameter sweeping. To ensure reliability, optimization...
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Dynamic coloring of graphs
PublikacjaDynamics is an inherent feature of many real life systems so it is natural to define and investigate the properties of models that reflect their dynamic nature. Dynamic graph colorings can be naturally applied in system modeling, e.g. for scheduling threads of parallel programs, time sharing in wireless networks, session scheduling in high-speed LAN's, channel assignment in WDM optical networks as well as traffic scheduling. In...
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Influence and development of new kinematic systems in flat surface lapping
PublikacjaThe face grinding and lapping technology is widely used in the field of the precise and ultraprecise manufacturing. It has become an indispensable technology in the manufacture of many parts. An absence of material restrictions allows machining both metal and non-metallic materials, including technical ceramics [1]. Nowadays there are mainly two kinematic systems in lapping machines [2]. The machining plane-parallel surfaces is...
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Performance evaluation of unified memory and dynamic parallelism for selected parallel CUDA applications
PublikacjaThe aim of this paper is to evaluate performance of new CUDA mechanisms—unified memory and dynamic parallelism for real parallel applications compared to standard CUDA API versions. In order to gain insight into performance of these mechanisms, we decided to implement three applications with control and data flow typical of SPMD, geometric SPMD and divide-and-conquer schemes, which were then used for tests and experiments. Specifically,...
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Further Developments of the Online Sound Restoration System for Digital Library Applications
PublikacjaNew signal processing algorithms were introduced to the online service for audio restoration available at the web address: www.youarchive.net. Missing or distorted audio samples are estimated using a specific implementation of the Jannsen interpolation method. The algorithm is based on the autoregressive model (AR) combined with the iterative complementation of signal samples. Since the interpolation algorithm is computationally...
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Condition-Based Monitoring of DC Motors Performed with Autoencoders
PublikacjaThis paper describes a condition-based monitoring system estimating DC motor degradation with the use of an autoencoder. Two methods of training the autoencoder are evaluated, namely backpropagation and extreme learning machines. The root mean square (RMS) error in the reconstruction of successive fragments of the measured DC motor angular-frequency signal, which is fed to the input of autoencoder, is used to determine the health...
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Molecular Insights into the Interactions Between Human Serum Albumin and Phospholipid Membranes
PublikacjaIn this study, molecular dynamics simulations were employed to analyze interactions between phospholipid membranes and human serum albumin (HSA) in the presence of mono- and divalent cations. Two types of membranes, composed of dipalmitoyl phosphatidylcholine (DPPC) and dipalmitoyl phosphatidylethanolamine (DPPE), were utilized. The results revealed that both systems exhibited high stability. The DPPE complexes displayed a greater...
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Telomere uncapping by common oxidative guanine lesions: Insights from atomistic models
PublikacjaOxidative 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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Molecular hydrogen solvated in water – A computational study
PublikacjaThe aqueous hydrogen molecule is studied with molecular dynamics simulations at ambient temperature and pressure conditions, using a newly developed flexible and polarizable H2 molecule model. The design and implementation of this model, compatible with an existing flexible and polarizable force field for water, is presented in detail. The structure of the hydration layer suggests that first-shell water molecules accommodate the...
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Deep eutectic solvents – Ideal solution for clean air or hidden danger?
PublikacjaThe industrial sector is one of the fastest-growing sources of greenhouse gases, due to its excessive energy consumption to meet the rapidly growing demand for energy-intensive products. The use of deep eutectic solvents (DESs) has been studied extensively in order to cope with these harmful gases, but their usage can be an issue in respect to ecological reasons. Do deep eutectic solvents harm the atmosphere? Yes, these solvents...
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Expedited constrained multi-objective aerodynamic shape optimization by means of physics-based surrogates
PublikacjaIn the paper, computationally efficient constrained multi-objective design optimization of transonic airfoil profiles is considered. Our methodology focuses on fixed-lift design aimed at finding the best possible trade-offs between the two objectives: minimization of the drag coefficient and maximization of the pitching moment. The algorithm presented here exploits the surrogate-based optimization principle, variable-fidelity computational...
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Multi-core processing system for real-time image processing in embedded computer vision applications
PublikacjaW artykule opisano architekturę wielordzeniowego programowalnego systemu do przetwarzania obrazów w czasie rzeczywistym. Dane obrazu są przetwarzane równocześnie przez wszystkie procesory. System umożliwia niskopoziomowe przetwarzanie obrazów,np. odejmowanie tła, wykrywanie obiektów ruchomych, transformacje geometryczne, indeksowanie wykrytych obiektów, ocena ich kształtu oraz podstawowa analiza trajektorii ruchu. Ang:This paper...
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Extracting functional groups of ALLINI to design derivatives of FDA‐approved drugs: Inhibition of HIV‐1 integrase
PublikacjaHIV‐1 integrase (IN) is crucial for integration of viral DNA into the host genome and a promising target in development of antiretroviral inhibitors. In this work, six new compounds were designed by linking the structures of two different class of HIV‐1 IN inhibitors (active site binders and allosteric IN inhibitors (ALLINIs)). Among newly designed compounds, INRAT10b was found most potent HIV‐1 IN inhibitor considering different...
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Communication: Inside the water wheel: Intrinsic differences between hydrated tetraphenylphosphonium and tetraphenylborate ions
PublikacjaTetraphenylphosphonium tetraphenylborate (TPTB) is a common reference electrolyte in physical chemistry of solutions allowing for a convenient partitioning of thermodynamic properties into single-ion contributions. Here, we compute on the basis of ab initio molecular dynamics simulations the infrared (IR) spectra for hydrated constituent ions of the TPTB assumption. Using spectral decomposition techniques, we extract important...
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Theoretical calculation of the physico-chemical properties of 1-butyl-4-methylpyridinium based ionic liquids
PublikacjaACCEPTED MAIonic liquids (ILs) have attracted much attention for their unique physicochemical properties, which can be designed as needed by altering the ion combinations. Besides experimental work, numerous computational studies have been concerned with prediction of physical properties of ILs. The results of molecular dynamics simulations of ILs depend strongly on the proper force field parameterization. Classical force fields...
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Unique agreement of experimental and computational infrared spectroscopy: a case study of lithium bromide solvation in an important electrochemical solvent
PublikacjaInfrared (IR) spectroscopy is a widely used and invaluable tool in the studies of solvation phenomena in electrolyte solutions. Using state-of-the-art chemometric analysis of a spectral series measured in a concentration-dependent manner, the spectrum of the solute-affected solvent can be extracted, providing a detailed view of the structural and energetic states of the solvent molecules influenced by the solute. Concurrently,...
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Mechanism of antifreeze protein functioning and the “anchored clathrate water” concept
PublikacjaIn liquid water, there is a natural tendency to form aggregates that consist of water molecules linked by hydrogen bonds. Such spontaneously formed aggregates are surrounded by a "sea" of disordered water molecules, with both forms remaining in equilibrium. The process of creating water aggregates also takes place in the solvation water of proteins, but in this case the interactions of water molecules with the protein surface shift...
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Investigating the disease- modifying properties of sclerotiorin in Alzheimer's therapy using acetylcholinesterase inhibition
PublikacjaAlzheimer's disease (AD) is a progressive neurodegenerative disorder caused due to the damage and loss of neurons in specific brain regions. It is the most common form of dementia observed in older people. The symptoms start with memory loss and gradually cause the inability to speak and do day-to-day activities. The cost of caring for those affected individuals is huge and is probably beyond most developing countries capability....
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Laser-Induced Graphitization of Polydopamine on Titania Nanotubes
PublikacjaSince the discovery of laser-induced graphite/graphene, there has been a notable surge of scientific interest in advancing diverse methodologies for their synthesis and applications. This study focuses on the utilization of a pulsed Nd:YAG laser to achieve graphitization of polydopamine (PDA) deposited on the surface of titania nanotubes. The partial graphitization is corroborated through Raman and XPS spectroscopies and supported...
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Modeling and control of a redundantly actuated variable mass 3RRR planar manipulator controlled by a model-based feedforward and a model-based-proportional-derivative feedforward–feedback controller
PublikacjaIn the paper, dynamics of a complex mechatronics system is considered. A redundantly actuated planar manipulator is the base of the mechanical part of it. It is a 3RRR 1 platform based parallel manipulator. To control its trajectory, a model-based feedforward controller is employed. Three aspects are fundamental in the presented investigations. The first focus is on development of an accurate numerical model used to solve the inverse...
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Enhanced Charge Storage Mechanism And Long-Term Cycling Stability In Diamondized Titania Nanocomposite Supercapacitors Operating In Aqueous Electrolytes
PublikacjaThe long cycle life stability jointly with high energy density are limiting broader feasible applications of supercapacitors. The novel diamondized titania nanocomposite supercapacitors deliver high power and energy densities along with high capacitance retention rates. Supercapacitor electrodes were fabricated utilizing a combination of Ti anodization followed by chemical vapor deposition resulting in simultaneous growth of complex...
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Modelling of wastewater treatment plant for monitoring and control purposes by state - space wavelet networks
PublikacjaMost of industrial processes are nonlinear, not stationary, and dynamical with at least few different time scales in their internal dynamics and hardly measured states. A biological wastewater treatment plant falls into this category. The paper considers modelling such processes for monitorning and control purposes by using State - Space Wavelet Neural Networks (SSWN). The modelling method is illustrated based on bioreactors of...
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Detection of anomalies in bee colony using transitioning state and contrastive autoencoders
PublikacjaHoneybees plays vital role for the environmental sustainability and overall agricultural economy. Assisting bee colonies within their proper functioning brings the attention of researchers around the world. Electronics systems and machine learning algorithms are being developed for classifying specific undesirable bee behaviors in order to alert about upcoming substantial losses. However, classifiers could be impaired when used...
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Intercalation complex of imidazoacridinone C-1311, a potential anticancer drug, with DNA helix d(CGATCG)2: stereostructural studies by 2D NMR spectroscopy.
PublikacjaImidazoacridinone C-1311 (Symadex®) is a powerful antitumor agent, which successfully made its way through the Phase I clinical trials and has been recommended for Phase II few a years ago. It has been shown experimentally that during the initial stage of its action C-1311 forms a relatively stable intercalation complex with DNA, yet it has shown no base-sequence specificity while binding to DNA. In this paper, the d(CGATCG)2:C-1311...
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Continuum contact model for friction between graphene sheets that accounts for surface anisotropy and curvature
PublikacjaUnderstanding the interaction mechanics between graphene layers and co-axial carbon nanotubes (CNTs) is essential for modeling graphene and CNT-based nanoelectromechanical systems. This work proposes a new continuum contact model to study interlayer interactions between curved graphene sheets. The continuum model is calibrated and validated using molecular dynamics (MD) simulations. These are carried out employing the reactive...
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PTD4 Peptide Increases Neural Viability in an In Vitro Model of Acute Ischemic Stroke
PublikacjaIschemic stroke is a disturbance in cerebral blood flow caused by brain tissue ischemia and hypoxia. We optimized a multifactorial in vitro model of acute ischemic stroke using rat primary neural cultures. This model was exploited to investigate the pro-viable activity of cell-penetrating peptides: arginine-rich Tat(49–57)-NH2 (R49KKRRQRRR57-amide) and its less basic analogue, PTD4 (Y47ARAAARQARA57-amide). Our model included glucose...
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Theoretical examination of the fracture behavior of BC3 polycrystalline nanosheets: Effect of crack size and temperature
Publikacja2D carbon graphene nanostructures are elements of advanced materials and systems. This theoretical survey provides explanation to the mechanical and fracture behavior of mono- and polycrystalline BC3 nanosheets (denoted as MC- and PCBC3NS, respectively) as a function of temperature and the type of crack defects. The mechanical performance of PCBC3NS at elevated temperatures was monitored varying the number of grain boundaries (the...
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A novel one-variable first-order shear deformation theory for biaxial buckling of a size-dependent plate based on Eringen’s nonlocal differential law
PublikacjaPurpose – This paper aims to present a new one-variable first-order shear deformation theory (OVFSDT) using nonlocal elasticity concepts for buckling of graphene sheets. Design/methodology/approach – The FSDT had errors in its assumptions owing to the assumption of constant shear stress distribution along the thickness of the plate, even though by using the shear correction factor (SCF), it has been slightly corrected, the errors...
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Enhanced susceptibility of SARS-CoV-2 spike RBD protein assay targeted by cellular receptors ACE2 and CD147: Multivariate data analysis of multisine impedimetric response
PublikacjaSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) enters the cells through the binding of spike protein to the host cell surface-expressing angiotensin-converting enzyme 2 (ACE2) or by endocytosis mediated by extracellular matrix metalloproteinase inducer (CD147). We present extended statistical studies of the multisine dynamic electrochemical impedance spectroscopy (DEIS) revealing interactions between Spike RBD and...
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Molecular transformation of dissolved organic matter in manganese ore-mediated constructed wetlands for fresh leachate treatment
PublikacjaThe organic matter (OM) and nitrogen in Fresh leachate (FL) from waste compression sites pose environmental and health risks. Even though the constructed wetland (CW) can efficiently remove these pollutants, the molecular-level transformations of dissolved OM (DOM) in FL remain uncertain. This study reports the molecular dynamics of DOM and nitrogen removal during FL treatment in CWs. Two lab-scale vertical-flow CW systems were...
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A new deterministic PSO algorithm for real-time systems implemented on low-power devices
PublikacjaThe paper presents a novel, deterministic particle swarm optimization (PSO) algorithm, facilitating its implementation in low-power application specific integrated circuits (ASIC) realized in CMOS technology. The PSO algorithms are commonly used in a variety of optimization problems. They allow to search for a global extreme in a selected fitness function, which is used for numerical modeling of specific optimized problems. The...
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A novel hybrid adaptive framework for support vector machine-based reliability analysis: A comparative study
PublikacjaThis study presents an innovative hybrid Adaptive Support Vector Machine - Monte Carlo Simulation (ASVM-MCS) framework for reliability analysis in complex engineering structures. These structures often involve highly nonlinear implicit functions, making traditional gradient-based first or second order reliability algorithms and Monte Carlo Simulation (MCS) time-consuming. The application of surrogate models has proven effective...
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Reduced-Cost Microwave Design Closure by Multi-Resolution EM Simulations and Knowledge-Based Model Management
PublikacjaParameter adjustment through numerical optimization has become a commonplace of contemporary microwave engineering. Although circuit theory methods are ubiquitous in the development of microwave components, the initial designs obtained with such tools have to be further tuned to improve the system performance. This is particularly pertinent to miniaturized structures, where the cross-coupling effects cannot be adequately accounted...
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Algorithms and Tools for Intelligent Control of Critical Infrastructure Systems
PublikacjaCritical Infrastructure Systems (CIS) are spatially distributed and of a network structure. The dynamics are nonlinear, uncertain and with several time scales. There is a variety of different objectives to be reliably met under a wide range of operational conditions. The operational conditions are influenced by the disturbance inputs, operating ranges of the CIS, faults in the sensors and actuators and abnormalities occurring in...
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Graph Neural Networks and Structural Information on Ionic Liquids: A Cheminformatics Study on Molecular Physicochemical Property Prediction
PublikacjaIonic liquids (ILs) provide a promising solution in many industrial applications, such as solvents, absorbents, electrolytes, catalysts, lubricants, and many others. However, due to the enormous variety of their structures, uncovering or designing those with optimal attributes requires expensive and exhaustive simulations and experiments. For these reasons, searching for an efficient theoretical tool for finding the relationship...
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Degradation of a nano-cutting tool: an MD simulation
PublikacjaW pracy przedstawiono wyniki symulacji wielokrotnego oddziaływania realistycznie ukształtowanego ostrza tnącego z modelowym, nieskończenie twardym ziarnem, przy zastosowaniu metody dynamiki molekularnej. Ostrze składało się z kilkuset tysięcy atomów metalu fcc, traktowanego za pomocą potencjału Suttona-Chena, przesuwane było ze stałą prędkością 20 m/s. Obserwowane deformacje plastyczne pojawiające się na skutek kontaktu ostrza...
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Correlation between the number of Pro-Ala repeats in the EmrA homologue of Acinetobacter baumannii and resistance to netilmicin, tobramycin, imipenem and ceftazidime
PublikacjaAcinetobacter baumannii coccobacilli are dangerous to patients in intensive care units because of their multidrug resistance to antibiotics, developed mainly in the past decade. This study aimed to examine whether there is a significant correlation between the number of Pro-Ala repeats in the CAP01997 protein, the EmrA homologue of A. baumannii, and resistance to antibiotics. A total of 79 multidrug-resistant A. baumannii strains...
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Two bacterial small heat shock proteins, IbpA and IbpB, form a functional heterodimer
PublikacjaSmall heat shock proteins (sHsps) are a conserved class of ATP-independent chaperones which in stress conditions bind to unfolded protein substrates and prevent their irreversible aggregation. Substrates trapped in sHsps-containing aggregates are efficiently refolded into native structures by ATP-dependent Hsp70 and Hsp100 chaperones. Most γ-proteobacteria possess a single sHsp (IbpA), while in a subset of Enterobacterales, as...
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Energy landscape and structural transformations of C38 penta-fullerene: The stabilizing role of octagons and insights into penta-octa-penta-fullerene
PublikacjaTheoretical investigations were conducted to study the stability and energy landscape of C38 penta-fullerene, a structure comprising six penta-graphene unit cells. Vibrational analysis at the B3LYP/def2SVP level revealed 18 negative frequencies, indicating the dynamic instability of penta-fullerene. Analyzing the energy profiles for these vibrational modes led to the identification of six energetically favourable isomers, featuring...
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A Novel Cryptic Clostridial Peptide That Kills Bacteria by a Cell Membrane Permeabilization Mechanism
PublikacjaThis work reports detailed characteristics of the antimicrobial peptide Intestinalin (P30), which is derived from the LysC enzyme of Clostridium intestinale strain URNW. The peptide shows a broader antibacterial spectrum than the parental enzyme, showing potent antimicrobial activity against clinical strains of Gram-positive staphylococci and Gram-negative pathogens and causing between 3.04 ± 0.12 log kill for Pseudomonas aeruginosa...
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Understanding the Electronic Structure and Optical Properties of Vacancy-Ordered Double Perovskite A2BX6 for Optoelectronic Applications
PublikacjaOver the past few years, metal halide perovskite solar cells have made significant advances. Currently, the single-junction perovskite solar cells reach a conversion efficiency of 25.7%. Perovskite solar cells with a wide band gap can also be used as top absorber layers in multi-junction tandem solar cells. We examined the dynamical and thermal stability, electronic structure, and optical features of In2PtX 6 (X = Cl, Br, and I)...
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Generalized regression neural network and fitness dependent optimization: Application to energy harvesting of centralized TEG systems
PublikacjaThe thermoelectric generator (TEG) system has attracted extensive attention because of its applications in centralized solar heat utilization and recoverable heat energy. The operating efficiency of the TEG system is highly affected by operating conditions. In a series-parallel structure, due to diverse temperature differences, the TEG modules show non-linear performance. Due to the non-uniform temperature distribution (NUTD) condition,...
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Multi-region fuzzy logic controller with local PID controllers for U-tube steam generator in nuclear power plant
PublikacjaIn the paper, analysis of multi-region fuzzy logic controller with local PID controllers for steam generator of pressurized water reactor (PWR) working in wide range of thermal power changes is presented. The U-tube steam generator has a nonlinear dynamics depending on thermal power transferred from coolant of the primary loop of the PWR plant. Control of water level in the steam generator conducted by a traditional PID controller...
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Fire Protection and Materials Flammability Control by Artificial Intelligence
PublikacjaFire safety has become a major challenge of materials developers because of the massive production of organic materials, often combustibles, and their use for different purposes. In this sense, fire safety is critically considered in the development of engineering materials [1, 2]. The multiplicity of parameters contributing to the development of formulation of flame-retardant materials from one side and the sustainability concerns...
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Zintegrowane sterowanie systemami zaopatrzenia w wodę pitną
PublikacjaOptymalne ekonomicznie zaspokojenie w miastach bieżącego zapotrzebowania na wodę pitną tak, aby spełnione były wymagania jakości dostaw oraz jakości samej wody jest złożonym zadaniem. Zarówno aspekty aplikacyjne jak i teoretyczne tego problemu są przedmiotem intensywnych prac prowadzanych w sektorach naukowych i przemysłowych na całym świecie. Prace te finansowane są przez przemysł, komitety naukowe oraz Programy Ramowe Unii Europejskiej....
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Problem of aggregation in dye-DNA interaction, calorimetry studies
PublikacjaNucleic acids are the biological target for many antimicrobial, antitumor and antiviral drugs. Ligand-DNA interactions can be classified into two major categories: 1. covalent binding, which can provide to intermolecular adducts, 2. physico-chemical interactions, which can be divided into intercalation (e.g. adriamycin) or groove binding (e.g. dystamycin). There are several methods to investigate interactions between drug and DNA....