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Search results for: PROTEIN-STRUCTURE MODELING, COARSE GRAINING, UNRES MODEL OF POLYPEPTIDE CHAINS, MOLECULAR DYNAMICS, DATA-ASSISTED SIMULATIONS
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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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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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Structural elucidation of transmembrane transporter protein bilitranslocase: Conformational analysis of the second transmembrane region TM2 by molecular dynamics and NMR spectroscopy
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Nutrient transport and acquisition by diatom chains in a moving fluid
PublicationThe role of fluid motion in delivery of nutrients to phytoplankton cells is a fundamental question in biological and chemical oceanography. In the study of mass transfer to phytoplankton, diatoms are of particular interest. They are non-motile, are often the most abundant components in aggregates and often form chains, so they are the ones expected to benefit most from enhancement of nutrient flux due to dissipating turbulence....
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Global Surrogate Modeling by Neural Network-Based Model Uncertainty
PublicationThis work proposes a novel adaptive global surrogate modeling algorithm which uses two neural networks, one for prediction and the other for the model uncertainty. Specifically, the algorithm proceeds in cycles and adaptively enhances the neural network-based surrogate model by selecting the next sampling points guided by an auxiliary neural network approximation of the spatial error. The proposed algorithm is tested numerically...
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Accelerated Gradient-Based Optimization of Antenna Structures Using Multi-Fidelity Simulations and Convergence-Based Model Management Scheme
PublicationThe importance of numerical optimization has been steadily growing in the design of contemporary antenna structures. The primary reason is the increasing complexity of antenna topologies, [ a typically large number of adjustable parameters that have to be simultaneously tuned. Design closure is no longer possible using traditional methods, including theoretical models or supervised parameter sweeping. To ensure reliability, optimization...
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Integration of thermographic data with the 3D object model
PublicationThe aim of the paper is to present new method for merging the 3D model data of the measured object with thermograms. Our technique is based on the combination of visual 3D imaging technique and thermal imaging technique, which maps the 2D thermograms on to 3D anatomical mesh model. The combination of these imaging modalities allows the generation of combined 3D and thermal data from which thermal signatures can be verified and...
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Reduced model of gyroscopic system
PublicationThe paper presents the method of model reduction for the system with gyroscopic interactions. Two methods were used to obtain the approximate discrete models of the continuous structure: the modal decomposition method and the rigid finite element method. The first approach is used for this part of a system for which it is easy to formulate orthogonality conditions, meanwhile the second one is used for other part. The method enables...
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Determination of viscosity changes of protein hydrolyzate solutions depending on shear rate
Open Research DataRheological characteristics of connective tissue protein solutions were made on the basis of viscosity measurement using a Brookfield viscometer using LV SC4 - 27 spindles and shear rate of 85 s-1 (Fig. 1). Solutions of protein hydrolysates with a concentration of 2% in 0.5M acetic acid were prepared.
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Takagi-Sugeno Fuzzy Model of Dissolved Oxygen Concentration Dynamics in a Bioreactor at WWTP
PublicationThe importance of dissolved oxygen concentration controlinaerationtanksofabioreactoratflow-throughwastewater treatment plant (WWTP) can easily be justified by technological requirements as well as simple economics. Firstly, appropriate levels of dissolved oxygen concentration are essential for the vitality of microorganisms that comprise the bioreactor. Secondly, the costs of dissolved oxygen concentration control related to the...
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Simulations of the Derecho Event in Poland of 11th August 2017 Using WRF Model
PublicationThis series contains datasets related to the forecasting of a severe weather event, a derecho, in Poland on 11 August 2017. The simulations were conducted using the Weather Research and Forecasting (WRF) model version 4.2.1 with different initial and boundary conditions of the pressure and model levels derived from 5 global models: Global Forecast System (GFS), Global Data Assimilation System (GDAS), European Centre for Medium-Range...
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Ultrasound assisted synthesis of 3-alkynyl substituted 2-chloroquinoxaline derivatives: Their in silico assessment as potential ligands for N-protein of SARS-CoV-2
PublicationIn view of recent global pandemic the 3-alkynyl substituted 2-chloroquinoxaline framework has been explored as a potential template for the design of molecules targeting COVID-19. Initial in silico studies of representative compounds to assess their binding affinities via docking into the N-terminal RNA-binding domain (NTD) of N-protein of SARS-CoV-2 prompted further study of these molecules. Thus building of a small library of...
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Data on wages, gender wage gap and global value chains measured on the European Structure of Earnings Survey and World Input-Output Database.
Open Research DataThis data article describes the data and merging procedure used by Nikulin and Wolszczak-Derlacz (Nikulin and Wolszczak-Derlacz, 2022).
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Comparative molecular dynamics study of dimeric and monomeric forms of HIV-1 protease in ligand bound and unbound state
PublicationHuman immunodeficiency virus type 1 protease (HIV-1 PR) is a viral-encoded enzyme that forms a homodimer. HIV-1 PR is essential for replication and assembly of the virus and inactivation of HIV-1 PR enzyme causes production of immature, noninfectious viral particles and thus HIV-1 PR is an attractive target in anti-AIDS drug design. In our current work, we performed molecular dynamics (MD) calculations (500 ns) for two different...
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Global value chains, wages, employment and labour production in China: A regional approach
PublicationIn this study we analyse the relationship of trade and global value chains (GVCs) to the labour market in 31 Chinese provinces for 25 sectors, by means of a system of structural equations. We firstly distinguish between provincial value chains (PVCs) and interprovincial value chains (PRVCs) in order to outline their distribution and evolution over time. Then, we investigate to what extent participation in GVCs, PVCs and PRVCs –...
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Collagen type II–hyaluronan interactions – the effect of proline hydroxylation: a molecular dynamics study
PublicationHyaluronan–collagen composites have been employed in numerous biomedical applications. Understanding the interactions between hyaluronan and collagen is particularly important in the context of joint cartilage function and the treatment of joint diseases. Many factors affect the affinity of collagen for hyaluronan. One of the important factors is the ratio of 3- or 4-hydroxy proline to proline residues. This article presents...
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THE 3D MODEL OF WATER SUPPLY NETWORK WITH APPLICATION OF THE ELEVATION DATA
Publication3D visualization is a key element of research and analysis and as the source used by experts in various fields e.g.: experts from water and sewage systems. The aim of this study was to visualize in three-dimensional space model of water supply network with relief. The path of technological development of GESUT data (Geodezyjna Ewidencja Sieci Uzbrojenia Terenu – geodetic records of public utilities) for water supply and measurement...
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Enhanced uniform data sampling for constrained data‐driven modeling of antenna input characteristics
PublicationData-driven surrogates are the most popular replacement models utilized in many fields of engineering and science, including design of microwave and antenna structures. The primary practical issue is a curse of dimensionality which limits the number of independent parameters that can be accounted for in the modelling process. Recently, a performance-driven modelling technique has been proposed where the constrained domain of the...
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VEHICLE DYNAMICS (2024)
e-Learning Courses(W) Vehicle dynamics (W-Lecture) - DAPE - WIMiO The course entitled "Vehicle dynamcs" (VD) is conducted for the DAPE WIMiO Students. The VD course is to discuss the following problems: - major problems of vehicle dynamics from the application point of view, - definition of working environment, - types of vehicles, - parameters and characteristics of vehicles, - assessment of performance of vehicles towards design, -...
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MOLECULAR SIMULATIONS OF NEOCARZINOSTATIN CHROMOPHORE RELEASE MECHANISM
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Quantum corrections to 4 model solutions and applications to Heisenberg chain dynamics
PublicationThe Heisenberg spin chain is considered in φ^4 model approximation. Quantum corrections to classical solutions of the one-dimensional φ^4 model within the correspondent physics are valuated with account of rest d − 1 dimensions of a d-dimensional theory. A quantization of the model is considered in terms of space- time functional integral. The generalized zeta-function formalism is used to renormalize and evaluate the functional...
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Conformational studies of [Nphe5]SFTI-1 by means of 2D NMR spectroscopy in conjunction with molecular dynamics calculations
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Joanna Raczek dr inż.
PeopleEmployment 2003 -- 2019: Faculty of Applied Physics and Mathematics, Gdańsk University of Technology. 2019 - present: Faculty of Electronic, Informatics and Telecominications, Gdańsk University of Technology. Education May 2007: Doctor of Philosophy in Mathematics, University of Gdańsk. Doctoral dissertation: "Paired domination and doubly domination in graphs". Supervisor: dr hab. Jerzy Topp. 2000 -- 2004 Bachelor of Science...
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A material model of asphalt mixtures based on Monte Carlo simulations
PublicationThe paper aims to numerically reflect mineral-asphalt mixture structure by a standard FEM software. Laboratory test results are presented due to bending tests of circular notched elements. The result scatter is relatively high. An attempt was made to form a random aggregate distribution in order to obtain various results corresponding to laboratory tests. The material structure calibration, its homogenization and finite element...
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Numerical Simulations and Tracer Studies as a Tool to Support Water Circulation Modeling in Breeding Reservoirs
PublicationThe article presents a proposal of a method for computer-aided design and analysis of breeding reservoirs in zoos and aquariums. The method applied involves the use of computer simulations of water circulation in breeding pools. A mathematical model of a pool was developed, and a tracer study was carried out. A simplified model of two-dimensional flow in the form of a biharmonic equation for the stream function (converted into...
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PROTEIN EXPRESSION AND PURIFICATION
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Static Load Test on Instrumented Pile – Field Data and Numerical Simulations
PublicationFor some time (since 8-10 years in Poland) a special static load tests on instrumented piles are carried out. Such studies are usually of a scientific nature and provide detailed quantitative data on the load transfer into the ground and characteristics of particular soil layers interaction with a pile shaft and pile base. Deep knowledge about the pile-subsoil interaction can be applied for a various design purposes, e.g. numerical...
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Molecular dynamics study of 4-OH-phenylacetyl- D -Y(Me)FQNRPR-NH 2 selectivity to V1a receptor
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Molecular biology
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Molecular biology
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Molecular dynamics simulation of polymerization of p-xylylene
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Nonlinear Modeling in Time Domain Numerical Analysis of Stringed Instrument Dynamics
PublicationMusical instruments are very various in terms of sound quality with their timbre shaped by materials and geometry. Materials' impact is commonly treated as dominant one by musicians, while it is unclear whether it is true or not. The research proposed in the study focuses on determining influence of both these factors on sound quality based on their impact on harmonic composition. Numerical approach has been chosen to allowed independent...
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FE simulations of a soil structure interface.
PublicationPrzedstawiono warunki brzegowe do opisu szorstkości ściany konstrukcji w kontakcie z gruntem. Wykonano doświadczenia i symulacje MES na bazie mikropolarnego prawa hipoplastycznego.
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Molecular Modeling of Meta II Rhodopsin
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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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A Comprehensive Review: Applications of the Kozeny–Carman Model in Engineering with Permeability Dynamics
PublicationIn this review article, we investigate the dynamic nature of the Kozeny–Carman Model concerning permeability and its application in engineering contexts. Providing insights into the changing dynamics of permeability within mining, petroleum, and geotechnical engineering, among other engineering applications. While some are complex and require additional modifcations to be applicable, others are simple and still function in specifc...
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ANALYSIS OF THE p53 PROTEIN GENE EXPRESSION MODEL
PublicationWe study the asymptotic behaviour of the solutions of the p53-Mdm2 model proposed by Monk (2003). The p53 gene is crucial for cellular inhibition of the angiogenesis process, while Mdm2 is a negative regulator of the p53 tumor-suppressor. We investigate the stability of the positive steady state and perform some numerical experiments.
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Temperature-dependent structure-property modeling of viscosity for ionic liquids
PublicationIn this paper we present the methodology for assessing the ionic liquids' viscosity at six temperature points (25, 35, 45, 50, 60 and 70 [C]), which utilizes only the in silico approach. The main idea of such assessment is based on the "correction equation" describing the correlation between experimentally measured viscosity and theoretically derived density (calculated with use of molecular mechanics), given at 6 different temperature...
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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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Global Value Chains and Wages: International Evidence from Linked Worker-Industry Data
PublicationUsing a rich dataset on over 110,000 workers from nine European countries and the USA we study the wage response to industry dependence on foreign value added. We estimate a Mincerian wage model augmented with an input-output interindustry linkages measure accounting for task heterogeneity across workers. Low and mediumeducated workers and those performing routine tasks experience (little) wage decline due to major dependency of...
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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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Jan Franz dr hab.
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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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Quantum corrections to phi^4 model solutions and applications to Heisenberg chain dynamics
PublicationThe Heisenberg spin chain is considered in φ^4 model approximation. Quantum corrections to classical solutions of the one-dimensional φ^4 model within the correspondent physics are evaluated with account of rest d−1 dimensions of a d-dimensional theory. A quantization of the model is considered in terms of spacetime functional integral. The generalized zeta-function formalism is used to renormalize and evaluate the functional integral...
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JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM
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Working Conditions in Global Value Chains: Evidence for European Employees
PublicationThis article investigates a sample of almost nine million workers from 24 European countries in 2014 to conclude how involvement in global value chains (GVCs) affects working conditions. We use employer–employee data from the Structure of Earnings Survey merged with industry-level statistics on GVCs based on the World Input-Output Database. Given the multidimensional nature of the dependent variable, we compare estimates of the...
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Generating molecular entities as structured data
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Lipid-protein interactions in membranes: a molecular modelling study
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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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Molecular hydrogen solvated in water – A computational study
PublicationThe aqueous hydrogen molecule is studied with molecular dynamics simulations at ambient temperature and pressure conditions, using a newly developed flexible and polarizable H2 molecule model. The design and implementation of this model, compatible with an existing flexible and polarizable force field for water, is presented in detail. The structure of the hydration layer suggests that first-shell water molecules accommodate the...