Search results for: Molecular docking and simulation study
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Modelling of Abdominal Wall Under Uncertainty of Material Properties
PublicationThe paper concerns abdominal wall modelling. The accurate prediction and simulation of abdominal wall mechanics are important in the context of optimization of ventral hernia repair. The shell Finite Element model is considered, as the one which can be used in patient-specific approach due to relatively easy geometry generation. However, there are uncertainties in this issue, e.g. related to mechanical properties since the properties...
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Improved maximum power point tracking algorithms by using numerical analysis techniques for photovoltaic systems
PublicationSolar photovoltaic (PV) panels generate optimal electricity when operating at the maximum power point (MPP). This study introduces a novel MPP tracking algorithm that leverages the numerical prowess of the predictor-corrector method, tailored to accommodate voltage and current fluctuations in PV panels resulting from variable environmental factors like solar irradiation and temperature. This paper delves into the intricate dynamics...
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Teloxantron inhibits the processivity of telomerase with preferential DNA damage on telomeres
PublicationTelomerase reactivation is one of the hallmarks of cancer, which plays an important role in cellular immortalization and the development and progression of the tumor. Chemical telomerase inhibitors have been shown to trigger replicative senescence and apoptotic cell death both in vitro and in vivo. Due to its upregulation in various cancers, telomerase is considered a potential target in cancer therapy. In this study, we identified...
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Green TPUs from Prepolymer Mixtures Designed by Controlling the Chemical Structure of Flexible Segments
PublicationThis study concerns green thermoplastic polyurethanes (TPU) obtained by controlling the chemical structure of flexible segments. Two types of bio-based polyether polyols—poly(trimethylene glycol)s—with average molecular weights ca. 1000 and 2700 Da were used (PO3G1000 and PO3G2700, respectively). TPUs were prepared via a two-step method. Hard segments consisted of 4,4?- diphenylmethane diisocyanates and the bio-based 1,4-butanodiol...
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Changes of Conformation in Albumin with Temperature by Molecular Dynamics Simulations
PublicationThis work presents the analysis of the conformation of albumin in the temperature range of 300K – 312K, i.e., in the physiological range. Using molecular dynamics simulations, we calculate values of the backbone and dihedral angles for this molecule. We analyze the global dynamic properties of albumin treated as a chain. In this range of temperature, we study parameters of the molecule and the conformational entropy derived from...
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Interaction of 4-nitrothiophenol with low energy electrons: Implications for plasmon mediated reactions
PublicationThe reduction of 4-nitrothiophenol (NTP) to 4-4′-dimercaptoazobenzene (DMAB) on laser illuminated noble metal nanoparticles is one of the most widely studied plasmon mediated reactions. The reaction is most likely triggered by a transfer of low energy electrons from the nanoparticle to the adsorbed molecules. Besides the formation of DMAB, dissociative side reactions of NTP have also been observed. Here, we present a crossed electron-molecular...
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How do sterols determine the antufungal activitiy of amphotericin B? Free energy of binding between the drug and its membrane targets.
PublicationAmphotericin B (AmB) is a well-known polyene antibiotic used to treat systemic fungal infections. It is commonly accepted that the presence of sterols in the membrane is essential for the AmB biological activity, that is, for the formation of transmembrane ion channels. The selective toxicity of AmB for fungal cells is attributed to the fact that it is more potent against fungal cell membranes containing ergosterol than against...
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The importance of anchoring ligands of binuclear sensitizers on electron transfer processes and photovoltaic action in dye-sensitized solar cells
PublicationThe relatively low photon-to-current conversion efficiency of dye-sensitized solar cells is their major drawback limiting widespread application. Light harvesting, followed by a series of electron transfer processes, is the critical step in photocurrent generation. An in-depth understanding and fine optimization of those processes are crucial to enhance cell performance. In this work, we synthesize two new bi-ruthenium sensitizers...
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Jerzy H. Czembor Prof. dr hab.
PeopleYear of birth: 1965, Poland, Work address: Plant Breeding and Acclimatization Institute –National research Institute (IHAR-PIB), Radzikow, 05-870 Blonie, Poland. Scientific disciplines: agricultural sciences, plant pathology, plant physiology, genetics. Specialization: phytopathology, mycology, plant genetics, molecular genetics, plant breeding, breeding for disease resistance, biotechnology, evaluation of genetic resources,...
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Electrochemical simulation of metabolic reduction and conjugation reactions of unsymmetrical bisacridine antitumor agents, C-2028 and C-2053
PublicationElectrochemistry (EC) coupled with analysis techniques such as liquid chromatography (LC) and mass spectrometry (MS) has been developed as a powerful tool for drug metabolism simulation. The application of EC in metabolic studies is particularly favourable due to the low matrix contribution compared to in vitro or in vivo biological models. In this paper, the EC(/LC)/MS system was applied to simulate phase I metabolism of the representative...
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Analysis of cyclone separator solutions depending on SEC outlet conditions in nCO2PP
PublicationUtilization of spray ejector condenser in order to carry out direct-contact condensation of vapour with inert gas (CO2) on a spray of subcooled liquid integrated with separator (to make pure CO2) has been proposed for the task of condensation and CO2 separation in the negative CO2 emission gas power plant. Condensation and separation has a significant impact on the thermodynamic efficiency of the entire negative CO2 emission gas...
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Effective Formula for Impact Damping Ratio for Simulation of Earthquake-induced Structural Pounding
PublicationStructural pounding during earthquakes may cause substantial damage to colliding structures. The phenomenon is numerically studied using different models of collisions. The aim of the present paper is to propose an effective formula for the impact damping ratio, as a parameter of the impact force model used to study different problems of structural pounding under seismic excitations. Its accuracy has been verified by four various...
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Comparative analysis of three‐phase dual active bridge converter with different transformer topology and modern universal control for DC microgrids
PublicationThe presented work discusses issues related to the use of modern multiphase topologies of Dual Active Bridge (DAB)-type converters. Converters of this type are widely used in most DC microgrid applications. The introduction emphasizes a comparative analysis between single-phase and multi-phase DAB topologies within high-power DC microgrids, delving into their respective advantages, drawbacks, design procedures, and considerations...
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Three-dimensional modeling and automatic analysis of the human nasal cavity and paranasal sinuses using the computational fluid dynamics method
PublicationPurpose The goal of this study was to develop a complete workflow allowing for conducting computational fluid dynam- ics (CFD) simulation of airflow through the upper airways based on computed tomography (CT) and cone-beam computed tomography (CBCT) studies of individual adult patients. Methods This study is based on CT images of 16 patients. Image processing and model generation of the human nasal cavity and paranasal sinuses...
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Stochastic optimisation algorithm for optimisation of controller parameters for control of dissolved oxygen in wastewater treatment plant
PublicationWastewater treatment plants (WWTPs) are very important facilities for mankind. They enable the removal and neutralisation of man-made pollutants. Therefore, it is important for wastewater treatment plants to operate as efficiently as possible so that the level of pollutants in the treated wastewater meets specific requirements. This paper concerns the design of a hierarchical nonlinear adaptive control system for dissolved oxygen...
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On reliability assessment of ship machinery system in different autonomy degree; A Bayesian-based approach
PublicationAnalyzing the reliability of autonomous ships has recently attracted attention mainly due to epistemic uncertainty (lack of knowledge) integrated with automatic operations in the maritime sector. The advent of new random failures with unrecognized failure patterns in autonomous ship operations requires a comprehensive reliability assessment specifically aiming at estimating the time in which the ship can be trusted to be left unattended....
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Ensuring sustainable development of urban public transport: A case study of the trolleybus system in Gdynia and Sopot (Poland)
PublicationElectromobility is a vital tool in reducing the environmental impact of transportation. A technologically mature means of public transport is the trolleybus. Based on a case study of the Polish cities of Gdynia and Sopot, this paper explores the factors that influence the development of the trolleybus system. Recent developments of in-motion charging (IMC) technology are analysed what provides a new analytical framework for the...
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Adaptive dynamic control allocation for dynamic positioning of marine vessel based on backstepping method and sequential quadratic programming
PublicationIt is generally assumed in dynamic positioning of over-actuated marine vessels that the control effectiveness matrix (input matrix) is known and constant, or, in case of fault information, it is estimated by the fault detection and diagnosis system. The purpose of the study is to develop the adaptive dynamic positioning control system for an over-actuated marine vessel in the presence of uncertainties and with emphasis on limited...
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Experimental and numerical investigation of mercury removal from flue gas by sorbent polymer composite
PublicationThis paper presents an experimental and numerical investigation of the performance of a sorbent polymer composite (SPC) material used for removing mercury from the flue gases in a full-scale industrial installation. The investigated material is an attractive alternative to activated carbon, which is commonly used for this purpose. While the application of the SPC is characterized by high capital expenditures, this technology offers...
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On Reduced-Cost Design-Oriented Constrained Surrogate Modeling of Antenna Structures
PublicationDesign of contemporary antenna structures heavily relies on full-wave electromagnetic (EM) simulation models. Such models are essential to ensure reliability of evaluating antenna characteristics, yet, they are computationally expensive and therefore unsuitable for handling tasks that require multiple analyses, e.g., parametric optimization. The cost issue can be alleviated by using fast surrogate models. Conventional data-driven...
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Nonlinear Fuzzy Control System for Dissolved Oxygen with Aeration System in Sequencing Batch Reactor
PublicationBiological processes at a wastewater treatment plant are complex, multivariable, time varying and nonlinear. Moreover, interactions between the components are very strong. Control of dissolved oxygen is one of most important task at the plant. The level of dissolved oxygen in aerobic tanks has significant influence on behaviour and activity of microorganisms at the plant. Air for aerated tanks is supplied by the aeration system...
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Structural, physicochemical and anticancer study of Zn complexes with pyridyl-based thiazolyl-hydrazones
PublicationThiazolyl-hydrazones (THs) exhibit a wide spectrum of biological activity that can be enhanced by complexation with various metal ions. Zn(II) complexes with α-pyridine-1,3-TH ligands may represent an alternative to the standard platinum-based chemotherapeutics. In addition, they show photoluminescence properties and thus can be regarded as multifunctional materials. In this study, we synthesized and characterized three neutral...
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Interactions of telomeric proteins with nucleic acids: sequence recognition on intact and oxidatively damaged telomeres
PublicationTelomeres are complex nucleoprotein assemblies that play a vital role in the maintenance of functional ends of linear chromosomes. Telomeric DNA, composed of tandem repeats of the 5'-TTAGGG-3' motif, solves the so-called end replication problem: as chromosomes shorten with each cell division, no information is lost, and the telomere can be re-extended. In the cell, many protein factors regulate telomere length, nuclear positioning...
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The Toolbox of Methods for Multidirectional Characterization of Dietary Nucleic Acids; Verification for Raw and Processed Food Products
PublicationCurrently, the nutritional value of food is associated mainly with components such as proteins, carbohydrates, and lipids. However, another important macromolecules present in many foods are dietary nucleic acids (dietNA), i.e., DNA as well as both coding and non-coding RNAs. In the context of food chemistry and nutrition, dietNA are nowadays vastly neglected. In consequence, there are no dedicated methodologies to characterize...
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The role of hydrogen bonding on tuning hard-soft segments in bio-based thermoplastic poly(ether-urethane)s
PublicationThis work describes the preparation of bio-based thermoplastic poly(ether-urethane)s (TPU) via a prepolymer method and investigates the effect of varying the interphase hydrogen-bonding (H-bonding) on physicochemical, thermal and mechanical properties. This was achieved by varying the glycol type and molar ratio of [NCO]/[OH] groups used during the prepolymer chain extending step. The TPUs’ chemical structure was analyzed by Fourier...
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The Product of Matrix Metalloproteinase Cleavage of Doxorubicin Conjugate for Anticancer Drug Delivery: Calorimetric, Spectroscopic, and Molecular Dynamics Studies on Peptide–Doxorubicin Binding to DNA
PublicationMatrix metalloproteinases (MMPs) are extracellular matrix degradation factors, promoting cancer progression. Hence, they could provide an enzyme-assisted delivery of doxorubicin (DOX) in cancer treatment. In the current study, the intercalation process of DOX and tetrapeptide-DOX, the product of the MMPs' cleavage of carrier-linked DOX, into dsDNA was investigated using stationary and time-resolved fluorescence spectroscopy, UV-Vis...
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INVESTIGATION OF THE EFFECT OF THE ROCKET'S SUBORBITAL FLIGHT ON BIOFILM, ENZYMES AND BIOSYNTHESIS ON AUTONOMOUS, MODULAR AND SCALABLE PLATFORM FOR CONDUCTING EXPERIMENTS OF AN ASTROBIOTECHNOLOGICAL NATURE
PublicationWith new incentives for human space exploration, biotechnological experiments in orbit became imperative.Answering this need, we build an autonomous, modular, and scalable platform that enables those experiments onrockets. We called it AMBER. The aim of the payload of the R6 suborbital rocket is to perform an experiment tostudy the influence of rocket flights on biofilm, molecular...
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The influence of reactions conditions on aggregation of dyes used in biochemistry
PublicationSelf-association of dyes and related substances is a very important phenomenon in many fields of applied chemistry. It is also fundamental model reaction of many kinds of molecular interactions such as the micelle formation of amphiphilic substances and the binding of small organic molecules to macromolecules. In spite of many studies concerning the dimerization equilibria of dyes and related substances, the mechanism seems not...
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Semicrystalline Polyesters Based on a Novel Renewable Building Block
PublicationIsohexides, like e.g. isosorbide, are well-known carbohydrate-based rigid diols which are capable of dramatically increasing the glass transition temperature of polyesters. However, their relatively low reactivity has thus far hampered large-scale industrial applications in the polymer field. Recently, with the aim to increase reactivity while at the same time retain rigidity, we have developed a new isoidide dicarboxylic acid...
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Texture or Linker? Competitive Patterning of Receptor Assembly toward Ultra-Sensitive Impedimetric Detection of Viral Species at Gold-Nanotextured Titanium Surfaces
PublicationIn this work, we study the electrodes with a periodic matrix of gold particles pattered by titanium dimples and modified by 3-mercaptopropionic acid (MPA) followed by CD147 receptor grafting for specific impedimetric detection of SARS-CoV-2 viral spike proteins. The synergistic DFT and MM/MD modeling revealed that MPA adsorption geometries on the Au–Ti surface have preferential and stronger binding patterns through the carboxyl...
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Laser-Induced Graphitization of Polydopamine on Titania Nanotubes
PublicationSince 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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Deep Eutectic Solvents as Agents for Improving the Solubility of Edaravone: Experimental and Theoretical Considerations
PublicationIn this study, both practical and theoretical aspects of the solubility of edaravone (EDA) in Deep Eutectic Solvents (DESs) were considered. The solubility of edaravone in some media, including water, can be limited, which creates the need for new efficient and environmentally safe solvents. The solubility of EDA was measured spectrophotometrically and the complex intermolecular interactions within the systems were studied with...
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Deep Eutectic Solvents as Agents for Improving the Solubility of Edaravone: Experimental and Theoretical Considerations
PublicationIn this study, both practical and theoretical aspects of the solubility of edaravone (EDA) in Deep Eutectic Solvents (DESs) were considered. The solubility of edaravone in some media, including water, can be limited, which creates the need for new efficient and environmentally safe solvents. The solubility of EDA was measured spectrophotometrically and the complex intermolecular interactions within the systems were studied with...
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Modeling lignin extraction with ionic liquids using machine learning approach
PublicationLignin, next to cellulose, is the second most common natural biopolymer on Earth, containing a third of the organic carbon in the biosphere. For many years, lignin was perceived as waste when obtaining cellulose and hemicellulose and used as a biofuel for the production of bioenergy. However, recently, lignin has been considered a renewable raw material for the production of chemicals and materials to replace petrochemical resources....
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Targeting yeast topoisomerase II by imidazo and triazoloacridinone derivatives resulting in their antifungal activity
PublicationFungal pathogens are considered as serious factors for deadly diseases and are a case of medical concern. Invasive fungal infections also complicate the clinical course of COVID-19, leading to a significant increase in mortality. Furthermore, fungal strains' multidrug resistance has increased the demand for antifungals with a different mechanism of action. The present study aimed to identify antifungal compounds targeting yeast...
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Genotyping Techniques for Determining the Diversity of Microorganisms
PublicationTyping of microbial pathogens, or identifying bacteria at the strain level, is particularly important for diagnosis, treatment, and epidemiological surveillance of bacterial infections. This is especially the case for bacteria exhibiting high levels of antibiotic resistance or virulence, and those involved in nosocomial or pandemic infections. Strain typing also has applications in studying bacterial population dynamics. The part...
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Impact of Propeller Emergence on Hull, Propeller, Engine, and Fuel Consumption Performance in Regular Head Waves
PublicationIn this study, the impact of propeller emergence on the performance of a ship (speed), propeller (thrust, torque, and RPM), a diesel engine (torque and RPM) and fuel consumption are analysed under severe sea conditions. The goal is to describe the variation in the system variables and fuel consumption rather than analysing the motion of the ship or the phenomenon of propeller ventilation in itself. A mathematical model of the...
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Novel molecules containing structural features of NSAIDs and 1,2,3-triazole ring: Design, synthesis and evaluation as potential cytotoxic agents
PublicationFor the first time the template containing structural features of more than one NSAIDs and the 1,2,3-triazole ring was explored for the identification of potential cytotoxic agents. These new and complex molecules were predicted to be effective inhibitors of PDE4B by molecular modelling studies in silico. The multi-step synthesis of these compounds were carried out starting from the well-known drug nimesulide and involved the use...
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Organic solvents aggregating and shaping structural folding of protein, a case study of the protease enzyme
PublicationLow solubility of reactants or products in aqueous solutions can result in the enzymatic catalytic reactions that can occur in non-aqueous solutions. In current study we investigated aqueous solutions containing different organic solvents / deep eutectic solvents (DESs) that can influence the protease enzyme's activity, structural, and thermal stabilities. Retroviral aspartic protease enzyme is responsible for the cleavage of the...
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Relationship between Telomere Length, TERT Genetic Variability and TERT, TP53, SP1, MYC Gene Co-Expression in the Clinicopathological Profile of Breast Cancer
PublicationThe molecular mechanisms of telomerase reverse transcriptase (TERT) upregulation in breast cancer (BC) are complex. We compared genetic variability within TERT and telomere length with the clinical data of patients with BC. Additionally, we assessed the expression of the TERT, MYC, TP53 and SP1 genes in BC patients and in BC organoids (3D cell cultures obtained from breast cancer tissues). We observed the same correlation in the...
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Torsional elasticity and energetics of F1-ATPase
PublicationFoF1-ATPase is a rotary motor protein synthesizing ATP from ADP driven by a cross-membrane proton gradient. The proton flow through the membrane-embedded Fo generates the rotary torque that drives the rotation of the asymmetric shaft of F1. Mechanical energy of the rotating shaft is used by the F1 catalytic subunit to synthesize ATP. It was suggested that elastic power transmission with transient storage of energy in some compliant...
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Increased concentration of Taq DNA polymerase as a solution for GC-rich templates from clinical and environmental samples
PublicationDNA polymerase is an enzyme which plays crucial role in replication and DNA repair. It found application in PCR (polymerase chain reaction) where catalyses process of in vitro DNA synthesis. To meet the demands posed by mod- ern diagnostic, molecular biology or genetic engineering it is necessary to improve DNA polymerases to obtain new or better features useful in these fields. So far implemented modifications in majority are...
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Structure-property relationships disclosed in the family of acridinium esters – chemiluminogenic molecules of great practical importance
PublicationAcridinium esters (AE), since their introduction to the analytics 30 years ago, make one of the most important groups of chemiluminogenic (CL) systems, that have been employed in medical diagnostics and environmental analysis today. So far, however, no systematic studies on the structureproperty relationships were carried out in this family of compounds. The latter features likely determine their practical utility and facilitate...
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Novel primosomal protein B from Clostridium pastuerianum
PublicationPriB is a primosomal protein that catalyzes DNA replication in Procaryota. The replication pathway starts with PriA protein - the initiator protein that binds to a DNA replication fork, unwinds double-stranded DNA and role of PriB is to stabilize PriA on the DNA. However there are many biochemical differences in replication mechanism in bacteria and only some of them use PriB proteins. A few of PriB proteins were published and...
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Novel primosomal protein B from Clostridium pasteurianum
PublicationPriB is a primosomal protein that catalyzes DNA replication in Procaryota. The replication pathway starts with PriA protein - the initiator protein that binds to a DNA replication fork, unwinds double-stranded DNA and role of PriB is to stabilize PriA on the DNA. However there are many biochemical differences in replication mechanism in bacteria and only some of them use PriB proteins. A few of PriB proteins were published and...
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Continuum contact model for friction between graphene sheets that accounts for surface anisotropy and curvature
PublicationUnderstanding 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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Incorporating installation effects into the probability analysis of controlled modulus columns
PublicationThis technical report presents the probabilistic analysis which integrates the Monte Carlo simulation (MCS) with random field theory to model the load–displacement behavior of Controlled Modulus Columns (CMCs) in overconsolidated Poznań clay. Presented study focuses on the practical aspects of statistical analysis of geotechnical data, numerical model development, and results evaluation. Variability and spatial distribution of...
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Size effect at aggregate level in microCT scans and DEM simulation – Splitting tensile test of concrete
PublicationThe paper describes an experimental and numerical study of size effect on concrete cylindrical specimens in splitting tensile test. Own experimental campaign was performed on specimens with 5 various diameters from D = 74, 105, 150, 192 and 250 mm with hardboard loading strips (distributed load according to standard methods) scaled proportionally to the specimen diameter. The crack opening-control system was applied to obtain the...
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Comparative Analysis of Reactive Power Compensation Devices in a Real Electric Substation
PublicationA constant worldwide growing load stress over a power system compelled the practice of a reactive power injection to ensure an efficient power network. For this purpose, multiple technologies exist in the knowledge market out of which this paper emphasizes the usage of the flexible alternating current transmission system (FACTS) and presents a comparative study of the static var compensator (SVC) with the static synchronous compensator...
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Parametric Study on a Performance of a Small Counter-Rotating Wind Turbine
PublicationA small Counter-Rotating Wind Turbine (CRWT) has been proposed and its performancehas been investigated numerically. Results of a parametric study have been presented in this paper.As parameters, the axial distance between rotors and a tip speed ratio of each rotor have been selected.Performance parameters have been compared with reference to a Single Rotor Wind Turbine (SRWT).Simulations were carried out with Computational Fluids...