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Search results for: MECHANISTIC MODEL
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Analyzing and improving a mechanistic model for the Microthrix parvicella in activated sludge systems
PublicationW pracy przedstawiono wyniki estymacji parametrów dla mechanistycznego modelu bakterii Microthrix parvicella w systemach osadu czynnego. W tym celu wykorzystano dane z oczyszczalni ścieków w Szwajcarii oraz wyniki dodatkowych badań laboratoryjnych w reaktorze nieprzepływowym. Model właściwie prognozował szybkość poboru tlenu (mierzoną dla różnych substratów) oraz zawartść bakterii Microthrix w biomasie osadu czynnego.
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A mechanistic model for fate and removal of estrogens in biological nutrient removal activated sludge systems
PublicationTwo estrogen fate and transformation models were integrated with a comprehensive activated sludge model (ASM) to predict estrogen removal based on biomass and solids production. Model predictions were evaluated against published full-scale plant data as well as results from a laboratory-scale sequencing batch reactor (SBR) fed synthetic wastewater. The estrogen fate model relating the rate of total estrogen degradation to soluble...
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Application of a hybrid mechanistic/machine learning model for prediction of nitrous oxide (N2O) production in a nitrifying sequencing batch reactor
PublicationNitrous oxide (N2O) is a key parameter for evaluating the greenhouse gas emissions from wastewater treatment plants. In this study, a new method for predicting liquid N2O production during nitrification was developed based on a mechanistic model and machine learning (ML) algorithm. The mechanistic model was first used for simulation of two 15-day experimental trials in a nitrifying sequencing batch reactor. Then, model predictions...
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Application of mechanistic and data-driven models for nitrogen removal in wastewater treatment systems
PublicationIn this dissertation, the application of mechanistic and data-driven models in nitrogen removal systems including nitrification and deammonification processes was evaluated. In particular, the influential parameters on the activity of the Nitrospira activity were assessed using response surface methodology (RSM). Various long-term biomass washout experiments were operated in two parallel sequencing batch reactor (SBR) with a different...
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How to Tackle Bacteriophages: The Review of Approaches with Mechanistic Insight
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Hypertension and coronary artery disease: Mechanistic insights and therapeutic challenges
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Arylation of enelactams using TIPSOTf: reaction scope and mechanistic insight
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Characterization of aggregate interlocking in hot mix asphalt by mechanistic performance tests
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Equivalent temperature for design of airport pavements using mechanistic-empirical methods
PublicationThe paper presents implementation of equivalent temperature for design of airport asphalt pavements. The calculation methods of equivalent temperature: the Shell method, the French method and method that use the Asphalt Institute fatique criteria were presented. An example of calculations of equivalent temperature for Gdansk Airport was introduced and discussed. It was shown that methods of calculation of equivalent temperature...
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Biologically active compounds based on the carbazole scaffold - synthetic and mechanistic aspects
PublicationDoctoral dissertation is divided into three main parts: introduction, results and discussion and experimental. The introduction is divided into four main parts which describe: 5-hydroxytryptamine receptors, the most popular antidepressants, new compounds based on the carbazole structure with affinity for serotonin receptors, telomeres and telomerase with their functions, telomerase inhibition strategies, carbazoles approved in...
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Reactions of Plasmodium falciparum Ferredoxin:NADP+ Oxidoreductase with Redox Cycling Xenobiotics: A Mechanistic Study
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DNA restriction analysis as a supportive tool in mechanistic studies carried out by 32P-postlabelling
PublicationNumerous antitumor and carcinogenic compounds are able to modify DNA by forming covalent bonds with its constituents, while some anticarcinogenic compounds are known to prevent such a modification. All these processes are of vital biological import_ance, though deeper inside into factors influencing formation of DNA adducts is difficult due to the low level of their occurrence. 32P-Postlabelling approach ensures very sensitive...
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Insights into interplay of immunopathophysiological events and molecular mechanistic cascades in psoriasis and its associated comorbidities
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Mechanistic studies of the hydrolysis of p-nitrophenyl sulfate catalyzed by arylsulfatase from Helix pomatia
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Redox reactions of the FAD-containing apoptosis-inducing factor (AIF) with quinoidal xenobiotics: A mechanistic study
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Synthesis, characteristics and mechanistic insight into the clays and clay minerals-biochar surface interactions for contaminants removal-A review
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Triplet–Triplet Annihilation Upconverting Liposomes: Mechanistic Insights into the Role of Membranes in Two-Dimensional TTA-UC
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Photodegradation of phenol by UV/TiO2 and Vis/N,C-TiO2 processes: Comparative mechanistic and kinetic studies
PublicationPorównano drogę fotodegradacji w dwóch systemach badawczych: UV/TiO2 i Vis/N,C-TiO2. Zbadano efektywność degradacji fenolu, powstające produkty pośrednie oraz generowanie rodników hydoksylowych w przygotowanych układach badawczych. Wyniki badań wykazały porównywalne efektywności degradacji fenolu w zawiesinach: domieszkowany TiO2/Vis i TiO2 P-25/UV. Uzyskane wyniki wskazują również na odmienne drogi degradacji zanieczyszczeń w...
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Triplet–Triplet Annihilation Upconverting Liposomes: Mechanistic Insights into the Role of Membranes in Two-Dimensional TTA-UC
PublicationTriplet−triplet annihilation upconversion (TTA-UC) implemented in nanoparticle assemblies is of emerging interest in biomedical applications, including in drug delivery and imaging. As it is a bimolecular process, ensuring sufficient mobility of the sensitizer and annihilator to facilitate effective collision in the nanoparticle is key. Liposomes can provide the benefits of two-dimensional confinement and condensed concentration...
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Model-Based Evaluation of N2O Production Pathways in the Anammox-Enriched Granular Sludge Cultivated in a Sequencing Batch Reactor
PublicationA mechanistic model was developed as an extension of the Activated Sludge Model No. 1 to describe three nitrous oxide (N2O) production pathways in a laboratory-scale anammox-enriched granular sequencing batch reactor. Heterotrophic denitrification and two processes mediated by ammonia oxidizing bacteria (AOB), that is, ammonia (NH4+) oxidation via hydroxylamine (NH2OH) and autotrophic denitrification, were considered. A systematic...
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Integrated model for the fast assessment of flood volume: Modelling – management, uncertainty and sensitivity analysis
PublicationThe specific flood volume is an important criterion for assessing the performance of sewage networks. It has been shown that its value is greatly influenced by the layout of the sewers in the catchment area, which is usually expressed by a fractal dimension. Currently, only mechanistic models (such as SWMM) enable the determination of the impact of the layout of the sewers on flooding volume, but they require additional and robust...
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Robust and highly efficient electrocatalyst based on ZIF-67 and Ni2+ dimers for oxygen evolution reaction: In situ mechanistic insight
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Quantitative structure activity relationships for the electron transfer reactions ofAnabaenaPCC 7119 ferredoxin-NADP+oxidoreductase with nitrobenzene and nitrobenzimidazolone derivatives: mechanistic implications
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Practical Method for the Preparation of 2,2-Dimethyl-5- {aryl[(hetero)aryl]methyl}-1,3-dioxane-4,6-diones: Synthesis and Mechanistic Study
PublicationAn efficient practical synthetic procedure has been developed for the synthesis of 2,2-dimethyl-5-{aryl[(hetero)aryl]methyl}- 1,3-dioxane-4,6-diones through Friedel–Crafts alkylation. The scope and limitation of the reaction of 2,2-dimethyl-5-arylidene-1,3-dioxane- 4,6-diones with π-excess aromatic systems have been delineated.
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Mechanistic insights and atmospheric implications of the degradation reaction of 3-methoxy-1-propanol by reaction with hydroxyl radicals and identification of the end products in the presence of O2/NO
PublicationThe study investigated the degradation of 3-methoxy-1-propanol (3M1P) by OH using the M06-2X/6-311++G(d,p) level, with CCSD(T) single-point corrections. We focused on hydrogen atom abstraction from various alkyl groups within the molecule. The rate coefficient for 3M1P degradation was calculated from the sum of the rate coefficients corresponding to the removal of H-atoms from primary (-CH3), secondary (-CH2-), tertiary (-CH<),...
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Mechanistic insights into the reactive radicals-assisted degradation of sulfamethoxazole via calcium peroxide activation by manganese-incorporated iron oxide–graphene nanocomposite: Formation of radicals and degradation pathway
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Perfluorooctanoic acid induces transgenerational modifications in reproduction, metabolism, locomotor activity, and sleep behavior in Drosophila melanogaster and deleterious effects in human cancer cells
PublicationPerfluorooctanoic acid (PFOA) has been widely documented to affect various aspects of health, including development, metabolism and neuronal function in a variety of organisms. Despite numerous reports detailing these effects, a comprehensive mechanistic model remains elusive, especially with regard to the long-term effects of PFOA, as it bioaccumulates in food chains with a long half-life. In this study, we evaluated the impact...
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Molecular mechanism of proton-coupled ligand translocation by the bacterial efflux pump EmrE
PublicationThe current surge in bacterial multi-drug resistance (MDR) is one of the largest challenges to public health, threatening to render ineffective many therapies we rely on for treatment of serious infections. Understanding different factors that contribute to MDR is hence crucial from the global “one health” perspective. In this contribution, we focus on the prototypical broad-selectivity proton-coupled antiporter EmrE, one of the...
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Mathematical modelling and computer simulation of activated sludge systems.Second edition
PublicationMathematical Modelling and Computer Simulation of Activated Sludge Systems – Second Edition, provides, from the process engineering perspective, a comprehensive and up-to-date overview regarding various aspects of the mechanistic (“white box”) modelling and simulation of advanced activated sludge systems performing biological nutrient removal. In the new edition of the book, a special focus is given to nitrogen removal and an overview...
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Modeling the pH effects on nitrogen removal in the anammox-enriched granular sludge
PublicationThe aim of the study was to determine the pH effects on nitrogen removal in the anammox-enriched granular sludge. The experimental data were extracted from a 4L completely-mixed batch reactor with the granular sludge at different initial pH values (6.5, 7, 7.5, 8, 8.5, 9, 9.5, 10, 10.5) and constant temperature T=30℃. Simulations were run in GPS-X 6.4 using a comprehensive mechanistic model Mantis2. Two kinetic parameters, including...
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MODELING THE pH EFFECTS ON NITROGEN REMOVAL IN THE ANAMMOX-ENRICHED GRANULAR SLUDGE
PublicationThe aim of the study was to determine the pH effects on nitrogen removal in the anammox-enriched 10 granular sludge. The experimental data were extracted from a 4L completely-mixed batch reactor with the 11 granular sludge at different initial pH values (6.5, 7, 7.5, 8, 8.5, 9, 9.5, 10, 10.5) and constant temperature 12 T=30℃. Simulations were run in GPS-X 6.4 using a comprehensive mechanistic model Mantis2. Two 13 kinetic parameters,...
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Two-step mechanism of J-domain action in driving Hsp70 function
PublicationJ-domain proteins (JDPs), obligatory Hsp70 cochaperones, play critical roles in protein homeostasis. They promote key allosteric transitions that stabilize Hsp70 interaction with substrate polypeptides upon hydrolysis of its bound ATP. Although a recent crystal structure revealed the physical mode of interaction between a J-domain and an Hsp70, the structural and dynamic consequences of J-domain action once bound and how Hsp70s...
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Analysis of pavement structure sensitivity to passage of oversized heavy duty vehicle in terms of bearing capacity
PublicationOversized heavy duty vehicles occur in traffic very rarely but they reach extremely high weights, even up to 800 tonne. The detrimental impact of these vehicles on pavement structure is much higher than in case of commercial vehicles that comprise typical traffic, thus it is necessary to assess the sensitivity of pavement structure to passage of oversized vehicles. The paper presents results of sample calculations of load equivalency factor...
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Transition-Metal-Promoted Oxidative Cyclization To Give 1,2,4-Trisubstituted Carbazole Scaffolds
PublicationHerein, we describe the synthesis of a 1,2,4-trisubstituted carbazole core from 5-(1H-indol-3-yl)-3-oxopentanoic acid esters or amides. For oxidative cyclization, we tested two different approaches. First, we used manganese triacetate as a conventional moderate oxidizer to ensure the radical course of the reaction. Second, we examined the use of a more complex oxidizing agent I2/Me(OTf)3. In both cases, formation of a fused-ring...
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Structural design and sensitivity analysis of semi-rigid pavement of a motorway
PublicationThis paper presents application of mechanistic-empirical methods in design of semi-rigid pavement for a section of a motorway in Poland. The stage construction was assumed. Three fatigue criteria were applied in the design. For asphalt fatigue cracking and subgrade soil the criteria from the Asphalt Institute (USA) were applied. For fatigue cracking of cement stabilized bases the Dempsey (USA) and De Beer (South Africa) criteria...
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Does the coordinated development of two-way FDI increase the green energy efficiency of Chinese cities? Evidence from Chinese listed companies
PublicationBased on the evidence from listed company microdata and data from 285 cities in China, this paper studies the coordinated development of two-way FDI (CDFDI) in improving green energy efficiency (GEE). In particular, this paper examines the spatial heterogeneity effects of CDFDI on GEE. The results showed that CDFDI had a positive impact on the GEE of local and surrounding cities. Mechanistic examinations show that the effects...
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The CON−H…+NH2 Blue-Shifting H-Bond Stabilizing Effect on Z Secondary Amides and Cyclic System Conformational Rearrangement through an Alkylamine-Chain Migration Pathway
PublicationThe paper is focusing on the amide linkage exceptional properties and usage of chemistry (conformational rearrangement, geometrical stereoisomers, spectroscopic blue shift phenomenon, protonation and deprotonation reactions, synthetic scope, and mechanistic implications). Hydrogen-bond-stabilized acylation reactions of a diamine with thioamides or nitriles reveal how substituents influence both the outcome of stereoselectivity...
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Isolation and structure of a covalent cross-link adduct between mitomycin C and DNA
PublicationA DNA cross-link adduct of the antitumor agent mitomycin C (MC) to DNA has been isolated and characterized; the results provide direct proof for bifunctional alkylation of DNA by MC. Exposure of MC to Micrococcus luteus DNA under reductive conditions and subsequent nuclease digestion yielded adducts formed between MC and deoxyguanosine residues. In addition to the two known monoadducts, a bisadduct was obtained. Reductive MC activation...
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Determinants of Directionality and Efficiency of the ATP Synthase Fo Motor at Atomic Resolution
PublicationFo subcomplex of ATP synthase is a membrane-embedded rotary motor that converts proton motive force into mechanical energy. Despite a rapid increase in the number of high-resolution structures, the mechanism of tight coupling between proton transport and motion of the rotary c-ring remains elusive. Here, using extensive all-atom free energy simulations, we show how the motor’s directionality naturally arises from the interplay...
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Silica In Silico: A Molecular Dynamics Characterization of the Early Stages of Protein Embedding for Atom Probe Tomography
PublicationA novel procedure for the application of atom probe tomography (APT) to the structural analysis of biological systems, has been recently proposed, whereby the specimen is embedded by a silica matrix and ablated by a pulsed laser source. Such a technique, requires that the silica primer be properly inert and bio-compatible, keeping the native structural features of the system at hand, while condensing into an amorphous, glass-like...
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Integration of protein tethering in a rapid and label-free SERS screening platform for drugs of abuse
PublicationSurface enhanced Raman spectroscopy (SERS) has emerged as a promising technique for the rapid and ultrasensitive detection of molecular species such as drugs of abuse in biofluids. Yet, it remains a significant challenge to create a viable screening tool for multiple drug classes, owing to the lack of affinity of certain species for the SERS substrate and to the matrix interference in complex media. Here we report a protein tethering...
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Study on the accuracy of axle load spectra used for pavement design
PublicationWeigh-in-Motion (WIM) systems are used in order to reduce the number of overloaded vehicles. Data collected from WIM provide characteristics of vehicle axle loads that are crucial for pavement design as well as for the development of pavement distress prediction models. The inaccuracy of WIM data lead to erroneous estimation of traffic loads and in consequence inaccurate prediction of pavement distress process. The objective of...
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The Role of Electrostatics in Enzymes: Do Biomolecular Force Fields Reflect Protein Electric Fields?
PublicationPreorganization of large, directionally oriented, electric fields inside protein active sites has been proposed as a crucial contributor to catalytic mechanism in many enzymes, and it may be efficiently investigated at the atomistic level with molecular dynamics simulations. Here, we evaluate the ability of the AMOEBA polarizable force field, as well as the additive Amber ff14SB and Charmm C36m models, to describe the electric...
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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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Principles of target DNA cleavage and the role of Mg2+ in the catalysis of CRISPR–Cas9
PublicationAt the core of the CRISPR–Cas9 genome-editing technology, the endonuclease Cas9 introduces site-specific breaks in DNA. However, precise mechanistic information to ameliorate Cas9 function is still missing. Here, multimicrosecond molecular dynamics, free energy and multiscale simulations are combined with solution NMR and DNA cleavage experiments to resolve the catalytic mechanism of target DNA cleavage. We show that the conformation...
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Structural Design and Sensitivity Analysis of Semi-Rigid Pavement of a Motorway
PublicationThis paper presents application of mechanistic-empirical methods in design of semi-rigid pavement for a section of a motorway in Poland. The stage construction was assumed. Three fatigue criteria were applied in the design. For asphalt fatigue cracking and subgrade soil the criteria from the Asphalt Institute (1981) were applied. For fatigue cracking of cement stabilized bases the Dempsey (1984) and De Beer (1992) criteria were...
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Green Polymer Nanocomposites for Skin Tissue Engineering
PublicationFabrication of an appropriate skin scaffold needs to meet several standards related to the mechanical and biological properties. Fully natural/green scaffolds with acceptable biodegradability, biocompatibility, and physiological properties quite often suffer from poor mechanical properties. Therefore, for appropriate skin tissue engineering and to mimic the real functions, we need to use synthetic polymers and/or additives as complements...
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Snapshot of micro-animals and associated biotic and abiotic environmental variables on the edge of the south-west Greenland ice sheet
PublicationMicroinvertebrates play a role as top consumers on glaciers. In this study we tested what kind of cryoconite material the animals inhabit (mud vs granules) on the edge of the Greenland ice sheet (GrIS) in the south-west. We also tested the links between the densities of micro-fauna in cryoconite material and selected biotic (algae, cyanobacteria, bacterial abundances) and abiotic (water depth, pH, ion content, radionuclides) factors....
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An attempt to mechanistically explain the viscoelastic behavior of transparent epoxy/starch-modified ZnO nanocomposite coatings
PublicationThe effects of bare and starch-modified ZnO (ZnO-St) nanoparticles on viscoelastic and mechanical properties are studied by dynamic mechanical and tensile analyses. Transparent epoxy-based nanocomposite films are prepared by incorporating bare or starch-modified ZnO particles into the epoxy matrix. The results demonstrated that ZnO particles hindered the curing reactions and hence the final properties of the cured epoxy. As a result,...
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ANTIOXIDANT POWER SERIES (APS) AS A TOOL FOR RATIONAL DESIGN AND ASSESSMENT OF HEALTH PROMOTING PROPERTIES OF FUNCTONAL FOODS BASED ON ANTIOXIDANT PHYTOCHEMICALS
PublicationOver past decades, plantborne antioxidants dominated so called "translational research" in the area of food, nutrition, and disease prevention. Among consumers and producers, such phytochemicals are synonyms of nutriceuticals. Popularity and commercial success of antioxidants stems from mechanistic studies suggesting the involvement of reactive oxygen species in etiology of chronic diseases. However, epidemiology failed to provide...