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Search results for: protein structure prediction, multiscale modeling, unres force field, free and bioinformatics-assisted modeling, replica-exchange molecular dynamics
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Recent Advances in Accelerated Multi-Objective Design of High-Frequency Structures using Knowledge-Based Constrained Modeling Approach
PublicationDesign automation, including reliable optimization of engineering systems, is of paramount importance for both academia and industry. This includes the design of high-frequency structures (antennas, microwave circuits, integrated photonic components), where the appropriate adjustment of geometry and material parameters is crucial to meet stringent performance requirements dictated by practical applications. Realistic design has...
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Structure of solvation water around the active and inactive regions of a type III antifreeze protein and its mutants of lowered activity
PublicationWater molecules from the solvation shell of the ice-binding surface are considered important for the antifreeze proteins to perform their function properly. Herein, we discuss the problem whether the extent of changes of the mean properties of solvation water can be connected with the antifreeze activity of the protein. To this aim, the structure of solvation water of a type III antifreeze protein from Macrozoarces americanus (eel...
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Modeling Methodologies for the Environment EE Msc sem. II r.a. 23/24
e-Learning CoursesZrozumienie procesów które mają wpływ na migrację i przemiany zanieczyszczeń w środowisku (ze szczególnym uwzględnieniem wód powierzchniowych). Zajęcia dotyczą podstaw i zasad budowy modeli jakości wody oraz służą pokazaniu jak te modele mogą być wykorzystywane do rozwiązywania problemów w inżynierii środowiska.
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Rigid finite elements and multibody modeling in analyses of a robot shaped elastic/plastic deformations of a beam
PublicationDynamics analysis of a system composed of a parallel manipulator and of an elastic beam is presented in the paper. Classic 3RRR parallel manipulator is considered and used to deform the beam. Elasto-plastic deformations are investigated. Rigid-finite-elements technique is employed to deal with dynamics of the beam. A multibody structure is associated with the introduced hybrid system in order to model its dynamics. Idea of the...
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Achieving Efficient and Stable Deammonification at Low Temperatures—Experimental and Modeling Studies
PublicationThe short-term effects of temperature on deammonification sludge were evaluated in a laboratory-scale sequencing batch reactor (SBR). Mathematical modeling was used for further evaluations of different intermittent aeration strategies for achieving high and stable deammonification performance at decreasing temperatures. As for the biomass cultivated at high temperatures (e.g., 30 C), a higher temperature dependency (the adjusted...
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The protocol for using elastic wall model in modeling blood flow within human artery
PublicationMedical diagnostic tools will play a major role in the future for an effective patient treatment and reduction their mortality, related to the cardiovascular system diseases (CVDs). There is an urgent need for developing diagnostic procedure to be robust, reliable, accurate and efficient, in the framework of a paradigm shift. Application of numerical techniques is seen as a perspective tool for such purpose. Nevertheless, existing...
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Optical method supported by machine learning for dynamics of C‐reactive protein concentrations changes detection in biological matrix samples
PublicationIn this article we present the novel spectroscopy method supported with machine learning for real-time detection of infectious agents in wastewater. In the case of infectious diseases, wastewater monitoring can be used to detect the presence of inflammation biomarkers, such as the proposed C-reactive protein, for monitoring inflammatory conditions and mass screening during epidemics for early detection in communities of concern,...
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Comparative molecular modelling of biologically active sterols
PublicationMembrane sterols are targets for a clinically important antifungal agent – amphotericin B. The relatively specific antifungal action of the drug is based on a stronger interaction of amphotericin B with fungal ergosterol than with mammalian cholesterol. Conformational space occupied by six sterols has been defined using the molecular dynamics method to establish if the conformational features correspond to the preferential interaction...
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Effect of Chitosan Deacetylation on Its Affinity to Type III Collagen: A Molecular Dynamics Study
PublicationThe ability to form strong intermolecular interactions by linear glucosamine polysaccharides with collagen is strictly related to their nonlinear dynamic behavior and hence bio-lubricating features. Type III collagen plays a crucial role in tissue regeneration, and its presence in the articular cartilage affects its bio-technical features. In this study, the molecular dynamics methodology was applied to evaluate the effect of...
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Weather Hazard Avoidance in Modeling Safety of Motor-Driven Ship for Multicriteria Weather Routing
PublicationWeather routing methods find the most suitable ocean?s route for a vessel, taking into account changeable weather conditions and navigational constraints. In the multicriteria approach based on the evolutionary SPEA algorithm one is able to consider a few constrained criteria simultaneously. The approach applied for a ship with hybrid propulsions has already been presented by one of the authors on previous TransNav?2009. This time...
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Modeling of Surface Roughness in Honing Processes by UsingFuzzy Artificial Neural Networks
PublicationHoning processes are abrasive machining processes which are commonly employed to improve the surface of manufactured parts such as hydraulic or combustion engine cylinders. These processes can be employed to obtain a cross-hatched pattern on the internal surfaces of cylinders. In this present study, fuzzy artificial neural networks are employed for modeling surface roughness parameters obtained in finishing honing operations. As...
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Rapid Design of 3D Reflectarray Antennas by Inverse Surrogate Modeling and Regularization
PublicationReflectarrays (RAs) exhibit important advantages over conventional antenna arrays, especially in terms of realizing pencil-beam patterns without the employment of the feeding networks. Unfortunately, microstrip RA implementations feature narrow bandwidths, and are severely affected by losses. A considerably improved performance can be achieved for RAs involving grounded dielectric layers, which are also easy to manufacture using...
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Modeling N2O behavior during denitrification with different carbon sources and electron acceptors
PublicationA mathematical model was developed for identification of the most important mechanism leading to nitrous oxide (N2O) accumulation in denitrifying activated sludge systems. The activated sludge model No. 2d (ASM2d) was extended to include intermediate three steps of the denitrification process. The formation and accumulation of nitric oxide (NO) was assumed to be very low in the performed laboratory experiments. These experiments...
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Modeling by finite element methods of impact of erosion on frequency of normal modes of L-0 blade
PublicationAfter some time of exploitation steam turbine rotors blades in energetic industry they are being eroded and also their frequency of normal modes is changed. Those changes can cause to unwanted shift of blades normal mode frequencies. It is necessary to find quick method of rating changes of frequency in connection of mass loss due erosion. The evaluation of this dependence was made by finite element modeling method using HyperWorks...
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Surrogate modeling of impedance matching transformers by means of variable‐fidelity electromagnetic simulations and nested cokriging
PublicationAccurate performance evaluation of microwave components can be carried out using full‐wave electromagnetic (EM) simulation tools, routinely employed for circuit verification but also in the design process itself. Unfortunately, the computational cost of EM‐driven design may be high. This is especially pertinent to tasks entailing considerable number of simulations (eg, parametric optimization, statistical analysis). A possible...
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Nested Kriging with Variable Domain Thickness for Rapid Surrogate Modeling and Design Optimization of Antennas
PublicationDesign of modern antennas faces numerous difficulties, partially rooted in stringent specifications imposed on both electrical and field characteristics, demands concerning various functionalities (circular polarization, pattern diversity, band-notch operation), but also constraints imposed upon the physical size of the radiators. Conducting the design process at the level of full-wave electromagnetic (EM) simulations, otherwise...
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On dynamics of the question mark shell structure
PublicationW pracy prezentuje się problemy analizy dynamicznej nieregularnej konstrukcji powłokowej na przykładzie powłoki w kształcie znaku zapytania. Badania oparto na sześcioparametrowej nieliniowej teorii powłok, która pozwala na dyskretyzację modelu metodą elementów skończonych zawierających sześć stopni swobody w węźle. Ta teoria daje możliwość poprawnego modelowania nieregularności oraz rozgałęzień i ortogonalnych przecięć, jak również...
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Furan Fragmentation in the Gas Phase: New Insights from Statistical and Molecular Dynamics Calculations
PublicationWe present a complete exploration of the different fragmentation mechanisms of furan (C4H4O) operating at low and high energies. Three different theoretical approaches are combined to determine the structure of all possible reaction intermediates, many of them not described in previous studies, and a large number of pathways involving three types of fundamental elementary mechanisms: isomerization, fragmentation, and H/H2 loss...
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Uniform sampling in constrained domains for low-cost surrogate modeling of antenna input characteristics
PublicationIn this letter, a design of experiments technique that permits uniform sampling in constrained domains is proposed. The discussed method is applied to generate training data for construction of fast replacement models (surrogates) of antenna input characteristics. The modeling process is design-oriented with the surrogate domain spanned by a set of reference designs optimized with respect to the performance figures and/or operating...
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Modeling the Influence of Salts on the Critical Micelle Concentration of Ionic Surfactants
PublicationWe show for the first time that a phenomenological, augmented volume-based thermodynamics (aVBT) model is capable to predict the critical micelle concentrations of ionic surfactants, including ionic liquids, with added salts. The model also adjusts for the type of salt added by including its molecular volume, which might form a connection to the Hofmeister effect. The other physico-chemically relevant quantities included in the...
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Journal of Advances in Modeling Earth Systems
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International Journal of Economics and Business Modeling
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Advanced Modeling and Simulation in Engineering Sciences
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Journal of Applied Structural Equation Modeling
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ACM Transactions on Modeling and Computer Simulation
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International Journal of Numerical Analysis and Modeling
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Structural Equation Modeling: A Multidisciplinary Journal
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USER MODELING AND USER-ADAPTED INTERACTION
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Molecular modeling of Gram-positive bacteria peptidoglycan layer, selected glycopeptide antibiotics and vancomycin derivatives modified with sugar moieties
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Influence of bulky 3,3′-diphenylalanine enantiomers replacing position 2 of AVP analogues on their conformations: NMR and molecular modeling studies
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Accurate Modeling of Frequency Selective Surfaces Using Fully-Connected Regression Model with Automated Architecture Determination and Parameter Selection Based on Bayesian Optimization
PublicationSurrogate modeling has become an important tool in the design of high-frequency structures. Although full-wave electromagnetic (EM) simulation tools provide an accurate account for the circuit characteristics and performance, they entail considerable computational expenditures. Replacing EM analysis by fast surrogates provides a way to accelerate the design procedures. Unfortunately, modeling of microwave passives is a challenging...
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Lipid-protein interactions in membranes: a molecular modelling study
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Hydration of N-Hydroxyurea from Ab Initio Molecular Dynamics Simulations
PublicationN-Hydroxyurea (HU) is an important chemotherapeutic agent used as a first-line treatment in conditions such as sickle cell disease and β-thalassemia, among others. To date, its properties as a hydrated molecule in the blood plasma or cytoplasm are dramatically understudied, although they may be crucial to the binding of HU to the radical catalytic site of ribonucleotide reductase, its molecular target. The purpose of this work...
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Expedited Acquisition of Database Designs for Reduced-Cost Performance-Driven Modeling and Rapid Dimension Scaling of Antenna Structures
PublicationFast replacement models have been playing an increasing role in high-frequency electronics, including the design of antenna structures. Their role is to improve computational efficiency of the procedures that normally entail large numbers of expensive full-wave electromagnetic (EM) simulations, e.g., parametric optimization or uncertainty quantification. Recently introduced performance-driven modeling methods, such as the nested...
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Depression as is Seen by Molecular Spectroscopy. Phospholipid- Protein Balance in Affective Disorders and Dementia
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An advanced tool integrating failure and sensitivity analysis into novel modeling of the stormwater flood volume
PublicationAn innovative tool for modeling the specific flood volume was presented that can be applied to assess the need for stormwater network modernization as well as for advanced flood risk assessment. Field measurements for a catchment area in Kielce, Poland, were used to apply the model and demonstrate its usefulness. This model extends the capability of recently developed statistical and machine learning hydrodynamic models developed...
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Modeling of light propagation in canine gingiva
PublicationThis study is a preliminary evaluation of the effectivenes of laser-based surgery of maxillary and mandibular bone in dogs. Current methods of gingivial surgery in dogs require the use of general anaesthesia.1, 2 The proposed methods of laser surgery can be performed on conscious dogs, which substantially reduces the associated risks. Two choices of lasers, Nd:YAG and a 930 nm semiconductor lasers were evaluated. The former is...
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Alternative Modeling of Volunteer Based Systems
PublicationThe canonical approach to model a flow of a voluntary based computing, as presented in Chapter 7 may tax the capacity of the simulator, especially when a more complex model of Voluntary Computing, proposed in [1], is used which would imply that, for typical heterogeneous groups of volunteers, several thousands of threads would have to be run inside the simulator, to mimic closely the behaviour of every volunteer. This chapter presents...
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Computer modeling and testing of structural metamaterials
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The CFD modeling in bioreactor tracer studies
PublicationW artykule zaprezentowano badania traserowe w bioreaktorach z osadem czynnym. Przedstawiono efekty działania procesu dyspersji na podstawie obliczonych podłużnych profili koncentracji znacznika w komorach osadu czynnego zlokalizowanych na Oczyszczalni Ścieków "Wschód" w Gdańsku. W ramach badań wykonano symulację przepływu substancji nieaktywnej (bazując na pomierzonych profilach stężenia znacznika) stosując jednowymiarowe równanie...
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Modeling of nonlinear generation in a bubble layer
PublicationPraca prezentuje numeryczne podejście do zagadnienia liniowego i nieliniowego rozpraszania w warstwie z pęcherzykami. Badania numeryczne niekoherentnego rozpraszania wykonano stosując metodę Monte Carlo. Propagację i wsteczne rozpraszanie sygnałów badano w oparciu o równanie Rayleigha-Plesseta.
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Systems modeling and simulation for environmental management.
PublicationW pracy omówiono podstawy systemowego modelowania i symulacji w szerokim zakresie zagadnień związanych z zarządzaniem przepływami informacji w środowisko naturalnym.
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On constitutive modeling for technical woven fabric
PublicationW pracy przestawiono kilka modeli konstytutywnych przyjmowanych do opisu zachowania się tkanin technicznych. Oprócz modeli zaczerpniętych z literatury autorzy prezentują własną koncepcje modelu stanowiąca rozszerzenie modelu sieci gęstej.This paper describes several types of the constitutive models used for the technical woven fabric description. Besides of the literatures examples of the constitutive models, the authors presented...
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A methodology of visual modeling language evaluation
PublicationMetody oceny jakości metod modelowania są istotnym elementem inżynierii języków modelowania wizualnego. W referacie zaproponowano metodę oceny języków modelowania wizualnego na podstawie wymiarów poznawczych. Zaprezentowano metodologiczną dyskusję zastosowania nauk psychologicznych do oceny metod modelowania, metodologię CD-VML, powiązaną z nią metodę CD-VML-UC do oceny przypadków użycia oraz weryfikację metodologii.
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Application of muscle model to the musculoskeletal modeling
PublicationThe purpose of this paper is to investigate new fusiform muscle models. Each of these models treats a muscle as a system composedof parts characterized by different mechanical properties. These models explain the influence of differences in the stiffness of lateral parts and the degree of muscle model discretization. Each muscle model is described by a system of differential equations and a single integro-differential equation....
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Modeling DAC Application Execution Time
PublicationAn application written in the Divide And Conquer paradigm is more difficult to model than SPMD application because of complex algorithm, causing use of many coefficients in a computational complexity function. Processors are divided into various layers, each layer contains different number of processors. Data packets processed in different layers and transferred between layers have different length. Moreover first layer processors use...
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Modeling bioaugmentation with nitrifiers in membrane bioreactors
PublicationBioaugmentation with nitrifiers was studied using two pilot-scale membrane bioreactors, with the purpose of assessing the suitability of state-of-the-art activated sludge models (ASMs) in predicting the efficiency of bioaugmentation as a function of operating conditions. It was demonstrated that the temperature difference between seeding and seeded reactors (ΔT) affects bioaugmentation efficiency. Experimental data were accurately...
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Theoretical designing of selenium heterocyclic non-fullerene acceptors with enhanced power conversion efficiency for organic solar cells: a DFT/TD-DFT-based prediction and understanding
PublicationIn this study, we have designed and explored a new series of non-fullerene acceptors for possible applications in organic solar cells. We have designed four molecules named as APH1 to APH4 after end-capped modification of recently synthesized Y6-Se-4Cl molecule. Density functional theory and time dependent-density functional theory have been employed for computing geometric and photovoltaic parameters of the designed molecules....
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Multiscale model for blood flow after a bileaflet artificial aortic valve implantation
PublicationCardiovascular diseases are the leading cause of mortality in the world, mainly due to atherosclerosis and its consequences. The article presents the numerical model of the blood flow through artificial aortic valve. The overset mesh approach was applied to simulate the valve leaflets motion and to realize the moving mesh, in the aortic arch and the main branches of cardiovascular system. To capture the cardiac system’s response...
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Finite element modeling of plastic hinges based on ductility demand-capacity method using nonlinear material for dynamic analysis
PublicationThe article discusses modeling plastic hinges in reinforced concrete interme-diate supports using finite elements methods. The ductility demand-capacitymethod was used to determine the geometrical parameters of cross-section plas-ticization zones, their ability to move and rotate, as well as their ductility. Dueto the varied geometry and stiffness of the supports and their nonlinear behav-ior under dynamic load, this method was...