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Search results for: interactions modeling
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Improvements and new functionalities of UNRES server for coarse-grained modeling of protein structure, dynamics, and interactions
PublicationIn this paper we report the improvements and extensions of the UNRES server (https://unres-server.chem.ug.edu.pl) for physics-based simulations with the coarse-grained UNRES model of polypeptide chains. The improvements include the replacement of the old code with the recently optimized one and adding the recent scale-consistent variant of the UNRES force field, which performs better in the modeling of proteins with the β and the...
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Modeling the impact of surface currents in a harbor using graph theory
PublicationEnsuring security in a harbor requires research into its infrastructure using spatial environmental data. This paper presents a methodology that defines the design of a graph for modeling the interactions between surface currents and moving objects. Combining this graph with port charts that integrate electronic navigation charts with coastal orthophotographs allows us to perform a multidimensional analysis. In addition, the complete...
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Expedited Variable-Resolution Surrogate Modeling of Miniaturized Microwave Passives in Confined Domains
PublicationDesign of miniaturized microwave components is largely based on computational models, primarily, full-wave electromagnetic (EM) simulations. EM analysis is capable of giving an accurate account for cross-coupling effects, substrate and radiation losses, or interactions with environmental components (e.g., connectors). Unfortunately, direct execution of EM-based design tasks such as parametric optimization or uncertainty quantification,...
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Intermolecular Interactions as a Measure of Dapsone Solubility in Neat Solvents and Binary Solvent Mixtures
PublicationDapsone is an effective antibacterial drug used to treat a variety of conditions. However, the aqueous solubility of this drug is limited, as is its permeability. This study expands the available solubility data pool for dapsone by measuring its solubility in several pure organic solvents: N-methyl-2-pyrrolidone (CAS: 872-50-4), dimethyl sulfoxide (CAS: 67-68-5), 4-formylmorpholine (CAS: 4394-85-8), tetraethylene pentamine (CAS:...
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Double-Blind Reputation vs. Intelligent Fake VIP Attacks in Cloud-Assisted Interactions
PublicationWe consider a generic model of Client-Server interactions in the presence of Sender and Relay, conceptual agents acting on behalf of Client and Server, respectively, and modeling cloud service providers in the envisaged "QoS as a Service paradigm". Client generates objects which Sender tags with demanded QoS level, whereas Relay assigns the QoS level to be provided at Server. To verify an object's right to a QoS level, Relay detects...
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Low-Cost Modeling of Microwave Components by Means of Two-Stage Inverse/Forward Surrogates and Domain Confinement
PublicationFull-wave electromagnetic (EM) analysis is one of the most important tools in the design of modern microwave components and systems. EM simulation permits reliable evaluation of circuits at the presence of cross-coupling effects or substrate anisotropy, as well as for accounting for interactions with the immediate environment. However, repetitive analyses required by EM-driven procedures, such as parametric optimization or statistical...
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Development of Strategies for AOB and NOB Competition Supported by Mathematical Modeling in Terms of Successful Deammonification Implementation for Energy-Efficient WWTPs
PublicationNovel technologies such as partial nitritation (PN) and partial denitritation (PDN) could be combined with the anammox-based process in order to alleviate energy input. The former combination, also noted as deammonification, has been intensively studied in a frame of lab and full-scale wastewater treatment in order to optimize operational costs and process efficiency. For the deammonification process, key functional microbes include...
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Editorial for the special issue on advances in forward and inverse surrogate modeling for high-frequency design
PublicationThe design of modern‐day high‐frequency devices and circuits, including microwave/RF, antenna and photonic components, historically has relied on full‐wave electromagnetic (EM) simulation tools. Initially used for design verification, EM simulations are nowadays used in the design process itself, for example, for finding optimum values of geometry and/or material parameters of the structures of interest. In a growing number of...
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Modeling nutrient removal and energy consumption in an advanced activated sludge system under uncertainty
PublicationActivated sludge models are widely used to simulate, optimize and control performance of wastewater treatment plants (WWTP). For simulation of nutrient removal and energy consumption, kinetic parameters would need to be estimated, which requires an extensive measurement campaign. In this study, a novel methodology is proposed for modeling the performance and energy consumption of a biological nutrient removal activated sludge system...
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Innovations in Wastewater Treatment: Harnessing Mathematical Modeling and Computer Simulations with Cutting-Edge Technologies and Advanced Control Systems
PublicationThe wastewater treatment landscape in Central Europe, particularly in Poland, has undergone a profound transformation due to European Union (EU) integration. Fueled by EU funding and rapid technological advancements, wastewater treatment plants (WWTPs) have adopted cutting-edge control methods to adhere to EU Water Framework Directive mandates. WWTPs contend with complexities such as variable flow rates, temperature fluctuations,...
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Rengel Cane Sia Doctoral Candidate
PeopleI’m Rengel, born and raised in the Philippines. As an undergraduate I did kinetic modeling on Copper-catalyzed atom transfer radical addition (ATRA). Then I was inspired to do both theoretical and experimental studies, which led me to propose my master’s thesis on Synthesis, Computational, Electrochemical, and Photoconductivity Studies on Naphthalene and its derivatives. This led to a master’s degree in Chemistry in the Mindanao...
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Karol Grębowski dr inż.
PeopleKarol Grębowski (M.Sc.) works as an assistant at the Department of Technical Fundamentals of Architecture Design of the Faculty of Architecture at Gdansk University of Technology. His scientific research deals with dynamic phenomena occurring during the vibration of structures, bridges, and studies the design methodology of the elements forming passive protection system of the vehicles degraded by struck or explosion in the context...
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Numerical solutions for large deformation problems in geotechnical engineering
PublicationThe problem of large deformations often occurs in geotechnical engineering. Numerical modeling of such issues is usually complex and tricky. The chosen solution has to implicate soil-soil and soil-structure interactions. In this paper, a review of the most popular numerical methods for large deformation problems is presented. The Coupled Eulerian-Lagrangian (CEL) method, the Arbitrary Lagrangian-Eulerian (ALE) method, the Smoothed...
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Particle Shape Effect on Macroscopic Behaviour of Underground Structures: Numerical and Experimental Study
PublicationAbstract: The mechanical performance of underground flexible structures such as buried pipes or culverts made of plastics depend not only on the properties of the structure, but also on the material surrounding it. Flexible drains can deflect by 30% with the joints staying tight, or even invert. Large deformations of the structure are difficult to model in the framework of Finite Element Method, but straightforward in Discrete...
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Particle Shape Effect on Macroscopic Behaviour of Underground Structures: Numerical and Experimental Study
PublicationThe mechanical performance of underground flexible structures such as buried pipes or culverts made of plastics depend not only on the properties of the structure, but also the material surrounding it. Flexible drains can deflect by 30% with the joints staying tight, or even invert. Large deformations of the structure are difficult to model in the framework of Finite Element Method, but straightforward in Discrete Element Methods....
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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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Quest for the Molecular Basis of Improved Selective Toxicity of All-Trans Isomers of Aromatic Heptaene Macrolide Antifungal Antibiotics
PublicationThree aromatic heptaene macrolide antifungal antibiotics, Candicidin D, Partricin A (Gedamycin) and Partricin B (Vacidin) were subjected to controlled cis-trans to all trans photochemical isomerization. The obtained all-trans isomers demonstrated substantially improved in vitro selective toxicity in the Candida albicans cells: human erythrocytes model. This effect was mainly due to the diminished hemotoxicity. The molecular modeling...
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The Mediation Function of Job Satisfaction's between Organizational Culture Dimensions and Knowledge Sharing
PublicationIt is commonly acknowledged that organizational culture is a valuable element of intellectual capital and as a hidden source of competitive advantage can considerably affect the achieving of strategic business goals. The axiological dimension of organizational culture is mostly identified with a set of shared assumptions and values, while work practices mainly define its behavioral dimension. Both these dimensions influence, among...
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Eu2Mg3Bi4: Competing Magnetic Orders on a Buckled Honeycomb Lattice
PublicationThe honeycomb lattice and its derived variants provide information on modeling and designing quantum magnets. A novel magnetic material, Eu2Mg3Bi4, which stabilizes in a previously unknown buckled honeycomb lattice, was discovered by high-pressure and high-temperature methods. We report here on the synthesis exploration of pure single crystals, structural determination of the buckled honeycomb lattice of europium moments, and experimental observation...
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Naturally-derived hydrogels for 3D pancreatic tumor models: A short review
PublicationStatistics suggest a high proportion of mortality rate by pancreatic cancer, which is a solid tumor characterized by high heterogeneity and the presence of a complex extracellular matrix. The very low effectiveness of pancreatic cancer treatment roots in the high metastatic potential and drug resistance of this tumor. Therefore, the quest for efficient cellular models enabling precise mimicking in vivo conditions, and anticancer...
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Retention modeling of some saccharides separated on an amino column.
PublicationUsing an amino column (Supelcosil LC-NH2) and different mixtures of acetonitrile-water, quantitative structure-retention relationship models are discussed. These models are based on computed molecular descriptors representing numerically structured features of some saccharides. The obtained results are underlining the lipophilicity/hydrophilicity balance, and how this is controlling the separation of the saccharides. The resulting...
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Role of Oligosaccharide Chain Polarity in Protein–Glycosaminoglycan Interactions
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Computational studies of intermolecular interactions in aqueous solutions of poly(vinylmethylether)
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The particle method for simulation of self-organization phenomena
PublicationThe aim of the work was to design, implement, and use, in a number of experiments, an abstract software environment (an artificial world)suitable for modelling systems consisting of many moving and interactingobjects distributed in space. The environment, named DigiHive, is directed towards modeling of complex systems manifested by processes of self-organization, self-reproduction and self modifications. The environment is mainly...
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Study of the Interactions between Neurophysin II and Dipeptide Ligand by Means of Molecular Dynamics
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A unified coarse-grained model of biological macromolecules based on mean-field multipole–multipole interactions
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Data-Driven Modeling of Mechanical Properties of Fiber-Reinforced Concrete: A Critical Review
PublicationFiber-reinforced concrete (FRC) is extensively used in diverse structural engineering applications, and its mechanical properties are crucial for designing and evaluating its performance. The compressive, flexural, splitting tensile, and shear strengths of FRCs are among the most important attributes, which have been discussed more extensively than other properties. The accurate prediction of these properties, which are required...
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Free volume in physical absorption of carbon dioxide in ionic liquids: Molecular dynamics supported modeling
PublicationUnderstanding the mechanisms underlying the carbon dioxide (CO2) absorption in ionic liquids (ILs) is the key to their efficient utilization in industrial flue gas treatment. One of the parameters considered substantially important in the process is the Free Volume. In this study, the Fractional Free Volume (FFV) of 73 ILs was calculated using Molecular Dynamics (MD). A quantitative Structure-Property Relationship (QSPR) study...
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Synthesis and biological evaluation of fluorinated N-benzoyl and N-phenylacetoyl derivatives of 3-(4-aminophenyl)-coumarin-7-O-sulfamate as steroid sulfatase inhibitors
PublicationIn the present work, we report convenient methods for the synthesis of 3-(4-aminophenyl)-coumarin-7-O-sulfamate derivatives N-acylated with fluorinated analogues of benzoic or phenylacetic acid as steroid sulfatase (STS) inhibitors. The design of these potential STS inhibitors was supported by molecular modeling techniques. Additionally, computational docking methods were used to determine the binding modes of the synthesized inhibitors...
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Workers, Firms and Task Heterogeneity in International Trade Analysis: An Example of Wage Effects of Trade Within GVC.
PublicationObjective: The main aim of this article is to present how the heterogeneity of workers, firms, and tasks can be incorporated into empirical international trade analysis. In particular, we provide an empirical example in which we aim to quantify the reliance on foreign value added (FVA) within Global Value Chains (GVC) on wages. Research Design & Methods: We estimate a Mincerian wage model augmented with a measure of foreign value...
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Evaluating Industry 4.0 Implementation Challenges Using Interpretive Structural Modeling and Fuzzy Analytic Hierarchy Process
PublicationThe fourth industrial revolution known as Industry 4.0 is reshaping and evolving the way industries produce products and individuals live and work therefore, gaining massive attraction from academia, business and politics. The manufacturing industries are optimistic regarding the opportunities Industry 4.0 may offer such as, improved efficiency, productivity and customization. The present research contributes to the Industry 4.0...
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The impact of precipitation and external carbon source addition on biological nutrient removal in activated sludge systems - experimentalinvestigation and mathematical modeling
PublicationThe aim of this study was to determine the effects of chemical precipitation and addition of external carbonsources on the denitrification capability and enhanced biological phosphorus removal (EBPR) interactions atthe 'Wschod' WWTP (600,000 PE) in Gdansk (northern Poland). For this purpose, different kinds of batch experimentswere carried out with the settled wastewater (without pretreatment and after coagulation-flocculation)and...
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The impact of precipitation and external carbon source addition on biological nutrient removal in activated sludge systems – experimental investigation and mathematical modeling
PublicationThe aim of this study was to determine the effects of chemical precipitation and addition of external carbonsources on the denitrification capability and enhanced biological phosphorus removal (EBPR) interactions atthe ‘Wschod’ WWTP (600,000 PE) in Gdansk (northern Poland). For this purpose, different kinds of batch experimentswere carried out with the settled wastewater (without pretreatment and after coagulation-flocculation)and...
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An insight into the mixed quantum mechanical-molecular dynamics simulation of a ZnII-Curcumin complex with a chosen DNA sequence that supports experimental DNA binding investigations
PublicationAn important aspect of research pertaining to Curcumin (HCur) is the need to arrest its degradation in aqueous solution and in biological milieu. This may be achieved through complex formation with metal ions. For this reason, a complex of HCur was prepared with ZnII, that is not likely to be active in redox pathways, minimizing further complications. The complex is monomeric, tetrahedral, with one HCur, an acetate and a molecule...
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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
PublicationThe 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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Modeling of soft N, M and L X-ray lines from tungsten relevant to plasma parameters in the WEST tokamak
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Stateczność i niezawodność pełnomorskich platform wiertniczych
PublicationW pracy przedstawiono wieloletnie doświadczenia Autora w zakresie wybranych aspektów numerycznej analizy pełnomorskich platform wiertniczych, w szczególności stacjonarnych platform stalowych poddanych działaniu fal wiatrowych i wiatru. W opisie zachowania się platform uwzględniono współoddziaływanie trzech ośrodków: materiału konstrukcji, morskich fal wiatrowych i podłoża gruntowego. Przyjęcie do opisu stochastycznych właściwości...
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Wiktoria Wojnicz dr hab. inż.
PeopleDSc in Mechanics (in the field of Biomechanics) - Lodz Univeristy of Technology, 2019 PhD in Mechanics (in the field of Biomechanics) - Lodz Univeristy of Technology, 2009 (with distinction) List of papers (2009 - ) Wojnicz W., Wittbrodt E., Analysis of muscles' behaviour. Part I. The computational model of muscle. Acta of Bioengineering and Biomechanics, Vol. 11, No.4, 2009, p. 15-21 Wojnicz W., Wittbrodt E., Analysis of...
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Novel 2-(2-arylmethylthio-4-chloro-5-methylbenzenesulfonyl)-1-(1,3,5-triazin-2-ylamino)guanidine derivatives: Inhibition of human carbonic anhydrase cytosolic isozymes I and II and the transmembrane tumor-associated isozymes IX and XII, anticancer activity, and molecular modeling studies
PublicationA series of novel 2-(2-arylmethylthio-4-chloro-5-methylbenzenesulfonyl)-1-(6-substituted-4-chloro-1,3,5-triazin-2-ylamino)guanidine derivatives 9–20 have been synthesized by substitution of chlorine atom at the 1,3,5-triazine ring in compounds 5–8 with 3- or 4-aminobenzenesulfonamide and 4-(aminomethyl)benzenesulfonamide hydrochloride. All the synthesized compounds were evaluated for their inhibitory activity toward hCA I, II,...
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On the origin of surface imposed anisotropic growth of salicylic and acetylsalicylic acids crystals during droplet evaporation
PublicationIn this paper droplet evaporative crystallization of salicylic acid (SA) and acetylsalicylic acid (ASA) crystals on different surfaces, such as glass, polyvinyl alcohol (PVA), and paraffin was studied. The obtained crystals were analyzed using powder X-ray diffraction (PXRD) technique. In order to better understand the effect of the surface on evaporative crystallization, crystals deposited on glass were scraped off. Moreover,...
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Exploring the cocrystallization potential of urea and benzamide
PublicationThe cocrystallization landscape of benzamide and urea interacting with aliphatic and aromatic carboxylic acids was studied both experimentally and theoretically. Ten new cocrystals of benzamide were synthesized using an oriented samples approach via a fast dropped evaporation technique. Information about types of known bi-component cocrystals augmented with knowledge of simple binary eutectic mixtures was used for the analysis...
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Modeling of pharmaceuticals mixtures toxicity with deviation ratio and best-fit functions models
PublicationThe present study deals with assessment of ecotoxicological parameters of 9 drugs (diclofenac (sodium salt), oxytetracycline hydrochloride, fluoxetine hydrochloride, chloramphenicol, ketoprofen, progesterone, estrone, androstenedione and gemfibrozil), present in the environmental compartments at specific concentration levels, and theirmutual combinations by couples against Microtox® and XenoScreen YES/YAS® bioassays. As the quantitative...