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Search results for: Molecular docking and simulation study
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Effects of Salvia officinalis and Thymus vulgaris on oxidant-induced DNA damage and antioxidant status in HepG2 cells
PublicationSalvia officinalis (SO) and Thymus vulgaris (TV) are medicinal plants well known for their curative powers. However, the molecular mechanisms responsible for these abilities of sage and thyme have not been fully understood yet. In this study we investigated the composition and the quantitative estimation of plant extracts, the protective effects of plant extracts against hydrogen peroxide- and 2,3-dimethoxy-1,4 naphthoquinone-induced...
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Configurations of H 3 + (H2)n clusters and their energies
PublicationThe H-3(+) ion plays an important role in low temperature astrophysical and laboratory plasmas. It is considered as the initiator of many ion-molecule chemistries. Also its clusters with H-2 are quite interesting. We study configurations of the H-3(+)(H-2)(n) clusters for n = 1 up to n = 12 as a simple test system. Total energies for these structures, with zero point vibration corrections have been calculated. Stabilization energies...
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Silver(I) complexes with nitrile ligands: New materials with versatile applications
PublicationIn the present study, the structure, thermal stability, conductive properties, and antimicrobial activity of silver(I) complexes with nitrile ligands were investigated. For the construction of the materials, 2-cyanopyridine (2-cpy), 4-cyanopyridine (4-cpy), 1,2-dicyanobenzene (1,2-dcb), and 1,3-dicyanobenzene (1,3-dcb) were used in addition to the silver nitrite and nitrate. Four new compounds were isolated and structurally characterized:...
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Characterization of GM3 Gangliosides in Human Milk throughout Lactation: Insights from the Analysis with the Use of Reversed-Phase Liquid Chromatography Coupled to Quadrupole Time-Of-Flight Mass Spectrometry
PublicationGangliosides are complex lipids found in human milk that play important structural and biological functions. In this study, we utilized reversed-phase liquid chromatography coupled to quadrupole time-of-flight mass spectrometry to evaluate the molecular distribution of GM3 in human milk samples collected at distinct lactation stages, ranging from colostrum to advanced lactation samples. Throughout lactation, GM3 d40:1 emerged as...
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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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Mass spectrometry based identification of geometric isomers during metabolic stability study of a new cytotoxic sulfonamide derivatives supported by quantitative structure-retention relationships
PublicationA set of 15 new sulphonamide derivatives, presenting antitumor activity have been subjected to a metabolic stability study. The results showed that besides products of biotransformation, some additional peaks occurred in chromatograms. Tandem mass spectrometry revealed the same mass and fragmentation pathway, suggesting that geometric isomerization occurred. Thus, to support this hypothesis, quantitative structure-retention relationships...
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A Model-Based Improved Control of Dissolved Oxygen Concentration in Sequencing Wastewater Batch Reactor
PublicationBiochemical processes at wastewater treatment plant are complex, nonlinear, time varying and multivariable. Moreover, relationships between processes are very strong. One of the most important issues is exerting proper control over dissolved oxygen levels during nitrification phase. This parameter has a very large impact on activity of microorganisms in activated sludge and on quality of pollution removal processes. Oxygen is supplied...
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Practical Eco-Driving Strategy for Suburban Electric Multiple Unit
PublicationIn this paper, a practical approach to velocity profile optimization for electric multiple unit was presented. The study focuses on a case of fast urban railway, which is a popular mean of transport across Tricity, Poland. Based on observations and measurements, a potential for improvement of energy efficiency by modifying the speed profile was recognized. In order to conduct necessary calculations, simulation model of railway...
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Rapid design of miniaturised branch-line couplers through concurrent cell optimisation and surrogate-assisted fine-tuning
PublicationIn this study, the authors introduce a methodology for low-cost simulation-driven design optimisation of highly miniaturised branch-line couplers (BLCs). The first stage of their design approach exploits fast concurrent optimisation of geometrically dependent, but electromagnetically isolated cells that constitute a BLC. The cross-coupling effects between the cells are taken into account in the second stage, where a surrogate-assisted...
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Application of advanced CFD simulations in seakeeping analysis of ships (case study)
PublicationThe novel design process of many types of ships needs estimation of seakeeping properties. Especially ships like Offshore Supply Vessels, Wind Farm Support Vessels, Research Vessels, ferries, military vessels, rescue vessels require extended analysis of ship behavior on rough sea. The main reason for improving ships operability in different sea conditions is need of rising efficiency of propulsion system, reducing hull added resistance,...
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Areas of Updraft Air Motion in an Idealised Weather Research and Forecasting Model Simulation of Atmospheric Boundary Layer Response to Different Floe Size Distributions
PublicationPresented dataset is part of a numerical modelling study focusing on the analysis of the influence of sea ice floe size distribution (FSD) on the horizontal and vertical structure of convection in the atmosphere. The total area and spatial arrangement of the up-drafts indicates that the FSD affects the total moisture content and the values of area averaged turbulent fluxes in the model domain. In fact, while convective updrafts...
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Experimental and numerical analysis of the modified TB32 crash tests of the cable barrier system
PublicationRoad restraint systems, including safety barriers, are one of the means used to improve road safety. Currently, they can be allowed to general use after passing the specific crash tests. However, it is always important and desirable to evaluate their performance under various realistic conditions, which can happen on the roads. In this study, the behaviour of the cable barrier system in impact conditions different than assumed...
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The literature review on boundary conditions of use for non-residential buildings
PublicationThis paper describes the results of qualitative and quantitative literature reviews on boundary conditions within educational buildings, emphasising the users' perspective. The reviews were performed before and during the COVID-19 pandemic using Scopus, Taylor& Francis, Web of Science databases. The boundary conditions understood as special characteristics for use and or precondition, determining specific features of buildings...
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The literature review on boundary conditions of use for non-residential buildings. Educational buildings.
PublicationThis paper describes the results of qualitative and quantitative literature reviews on boundary conditions within educational buildings, emphasising the users' perspective. The studies were performed before and during the COVID-19 pandemic using Scopus, Taylor& Francis, and Web of Science databases. The boundary conditions are understood as special characteristics for use and or precondition, determining specific features of...
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Modeling of Electrodynamic Phenomena in an Ultra-Rapid Inductive–Dynamic Actuator as Applied to Hybrid Short-Circuit Breakers - A Review Study
PublicationThis article is a study of the research development of electrodynamic phenomena occurring in ultra-fast electrodynamic drives. These types of linear drives are among the fastest, not only because of the huge accelerations achieved, but, above all, because of the extremely short reaction time. For this reason, electrodynamic drives are used in hybrid short-circuit breakers. The phenomena occurring in this type of drive are actually...
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Evaluation of fire hazard in electrical installations due to unfavorable ambient thermal conditions
PublicationEvaluation of fire hazard caused by electrical installations is a difficult and important topic, and it limits the possibility of loss of life or health of people, as well as the occurrence of significant property damage. In particular, this hazard was caused by power cables and especially photovoltaic (PV) installations. The authors proved that power cables directly exposed to strong solar radiation are likely to exceed maximum...
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Application 2D Descriptors and Artificial Neural Networks for Beta-Glucosidase Inhibitors Screening
PublicationBeta-glucosidase inhibitors play important medical and biological roles. In this study, simple two-variable artificial neural network (ANN) classification models were developed for beta-glucosidase inhibitors screening. All bioassay data were obtained from the ChEMBL database. The classifiers were generated using 2D molecular descriptors and the data miner tool available in the STATISTICA package (STATISTICA Automated Neural...
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Utilizing pulse dynamics for non-invasive Raman spectroscopy of blood analytes
PublicationNon-invasive measurement methods offer great benefits in the field of medical diagnostics with molecular-specific techniques such as Raman spectroscopy which is increasingly being used for quantitative measurements of tissue biochemistry in vivo. However, some important challenges still remain for label-free optical spectroscopy to be incorporated into the clinical laboratory for routine testing. In particular, non-analyte-specific...
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Towards sugar-derived polyamides as environmentally friendly materials
PublicationAs part of our ongoing study investigating isohexide-based polyamides, we have synthesized isosorbide(bis(propan-1-amine)) (DAPIS) and studied its reactivity in the polymerization towards fully biobased polyamides. Polycondensation of nylon salts with various contributions of DAPIS afforded a family of homo- and copolyamides, which were characterized using complementary spectroscopic techniques. The chemical structure of the materials...
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Inhibition of T-type calcium channel disrupts Akt signaling and promotes apoptosis in glioblastoma cells.
PublicationGlioblastoma multiforme (GBM) are brain tumors that are exceptionally resitant to both radio- and chemotherapy regimens and novel approaches to treatment are needed. T-type calcium channels are one type of low voltage-gated channel (LVCC) involved in embryonic cell proliferation and differentiation; however they are often over-expressed in tumors, including GBM. In this study, we found that inhibition of T-type Ca channels in GBM...
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Investigation of the Effect of the Rocket's Suborbital Flight on Biofilm, Enzymes and Biosynthesis on Autonomous, Modular and Scalable Platforms 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 on rockets. We called it AMBER. The aim of the payload of the R6 suborbital rocket is to perform an experiment to study the influence of rocket flights on biofilm, molecular biology enzymes and biosynthesis using our platform....
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Guanosine Dianions Hydrated by One to Four Water Molecules
PublicationIntermolecular 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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MODELOWANIE TURBINY WIATROWEJ Z DWOMA PRZECIWBIEŻNIE OBRACAJĄCYMI SIĘ WIRNIKAMI
PublicationW artykule przedstawiono sposoby modelowania dwuwirnikowej turbiny wiatrowej z wykorzystaniem technik Obliczeniowej Mechaniki Płynów. Omówiono uproszczone metody modelowania Actuator Disc i Actuator Line Method oraz aspekty związane z dokładnym odwzorowaniem turbiny na siatce obliczeniowej. Zaprezentowano przykładowe wyniki obliczeń turbiny dwuwirnikowej złożonej z wirników NREL o mocy nominalnej 5 MW każdy. Do wykonania badań...
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Influence of an Interview Location on Opinions about the Ecosystem Services Provided by Trees
PublicationCollecting opinions regarding environmental management is essential, particularly in urban areas where space is limited, and interests often collide. However, the impact of the conditions in which the research is conducted on opinions and preferences elicited via surveys and interviews about the environment is usually taken for granted. The recent development of computer-aided survey methods allows a simulation of an environment,...
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Developing the Urban Blue-Green Infrastructure as a Tool for Urban Air Quality Management
PublicationUrban structure is an important factor that shapes the process of urban ventilation and pollution dispersion. With proper planning of the urban spatial layout, city breathability can be effectively regulated, contributing to urban air quality improvement. This paper investigates the development and current management of urban systems of green and open spaces in four Polish cities: Gda ´nsk, Warsaw, Pozna ´n and Wrocław, with a...
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Biomechanics of Lumbar Spine Injury in Road Barrier Collision–Finite Element Study
PublicationLiterature and field data from CIREN database have shown that lumbar spine injuries occur during car crashes. There are multiple hypotheses regarding how they occur; however, there is no biomechanical explanation for these injuries during collisions with road safety barriers (RSBs). Therefore, the objective of this study was to investigate the mechanics of vertebral fractures during car collisions with concrete RSBs. The finite...
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Electrochemistry meets enzymes: Investigation of the biotransformation pathway of C-1311 based on electrochemical simulation in comparison to in vitro methods.
PublicationThe knowledge of the metabolic pathways and the biotransformation of new drugs is one of the major challenges in pharmaceutical research. It is crucial for elucidation of degradation routes of the new biologically active compounds, especially in the area of possible toxicity. Conventional in vitro drug metabolism studies are based on incubating drug candidate with e.g. hepatocytes or, most importantly, liver cell microsomes and...
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Identification of defected sensors in an array of amperometric gas sensors
PublicationPurpose Amperometric gas sensors are commonly used in air quality monitoring in long-term measurements. Baseline shift of sensor responses and power failure may occur over time, which is an obstacle for reliable operation of the entire system. The purpose of this study is to check the possibility of using PCA method to detect defected samples, identify faulty sensor and correct the responses of the sensor identified as faulty. Design/methodology/approach In...
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Electrochemical simulation of metabolism for antitumor-active imidazoacridinone C-1311 and in silico prediction of drug metabolic reactions
PublicationThe metabolism of antitumor-active 5-diethylaminoethylamino-8-hydroxyimidazoacridinone (C-1311) has been investigated widely over the last decade but some aspects of molecular mechanisms of its metabolic transformation are still not explained. In the current work, we have reported a direct and rapid analytical tool for better prediction of C-1311 metabolism which is based on electrochemistry (EC) coupled on-line with electrospray...
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Highly Conserved Homotrimer Cavity Formed by the SARS-CoV-2 Spike Glycoprotein: A Novel Binding Site
PublicationAn important stage in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) life cycle is the binding of the spike (S) protein to the angiotensin converting enzyme-2 (ACE2) host cell receptor. Therefore, to explore conserved features in spike protein dynamics and to identify potentially novel regions for drugging, we measured spike protein variability derived from 791 viral genomes and studied its properties by molecular...
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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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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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Model of optical phantoms thermal response upon irradiation with 975 nm dermatological laser
PublicationWe have developed a numerical model describing the optical and thermal behavior of optical tissue phantoms upon laser irradiation. According to our previous studies, the phantoms can be used as substitute of real skin from the optical, as well as thermal point of view. However, the thermal parameters are not entirely similar to those of real tissues thus there is a need to develop mathematical model, describing the thermal and...
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Novel hierarchical nonlinear control algorithm to improve dissolved oxygen control in biological WWTP
PublicationWastewater treatment is a problem known to humankind for centuries. The quality of treated sewage determines the condition of reservoirs around the world. Control of such a complex and nonlinear system as a wastewater treatment plant requires thorough knowledge of the process. The paper presents a hierarchical control system of a Sequencing Batch Reactor (SBR) in Wastewater Treatment Plant (WWTP) taking into account a model based...
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Scalability of surrogate-assisted multi-objective optimization of antenna structures exploiting variable-fidelity electromagnetic simulation models
PublicationMulti-objective optimization of antenna structures is a challenging task due to high-computational cost of evaluating the design objectives as well as large number of adjustable parameters. Design speedup can be achieved by means of surrogate-based optimization techniques. In particular, a combination of variable-fidelity electromagnetic (EM) simulations, design space reduction techniques, response surface approximation (RSA) models,...
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DETERMINING THE TIME CONSTANT USING TWO METHODS AND DEFINING THE THERMOCOUPLE RESPONSE TO SINE EXCITATION OF GAS TEMPERATURE
PublicationThis paper describes the two methods of determining the time constant of type K thermocouple, for two construction solutions: the exposed weld and the mantle fillet weld. This is an important parameter indicating the response time of the thermocouple on the recorded signal. The first method consists of determining the value of τ in the way of numerical simulation of heat exchange between the thermocouple and the current of gas...
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Towards improved energy efficiency of future smart ships by application of advanced CFD simulations – case study
PublicationThe international trade plays crucial role in today’s globally developed world’s economy. Many people are unaware of the unimaginable volume of cargo being transported every year by oceans and seas. For most of the time invisible from land the shipping industry preserves its strong position of the most cost-efficient and environmental friendly mean of transport. However during last years the shipping industry is under great pressure...
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Computer vision techniques applied for reconstruction of seafloor 3D images from side scan and synthetic aperture sonars data
PublicationThe Side Scan Sonar and Synthetic Aperture Sonar are well known echo signal processing technologies that produce 2D images of the seafloor. Both systems combines a number of acoustic pings to form a high resolution image of seafloor. It was shown in numerous papers that 2D images acquired by such systems can be transformed into 3D models of seafloor surface by algorithmic approach using intensity information, contained in a grayscaled...
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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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Minichannel and minigap classification criteria based on the aspect ratio of the minigeometry: A numerical study
PublicationA detailed numerical investigation has been carried out to analyze the diabatic flow distribution and velocity profile in 18 minigeometries with various aspect ratios for V-type and I-type flow configurations (for 36 cases) assuming ethanol as a working fluid. The aim of the study is to distinguish the value of the aspect ratio for which the flow in minigeometry starts to be two-dimensional (minigap). Cases with a constant Reynolds...
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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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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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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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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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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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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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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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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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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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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...