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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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Thermodynamics and kinetics of amphotericin B self-association in aqueous solution characterized in molecular detail
PublicationAmphotericin B (AmB) is a potent but toxic drug commonly used to treat systemic mycoses. Its efficiency as a therapeutic agent depends on its ability to discriminate between mammalian and fungal cell membranes. The association of AmB monomers in an aqueous environment plays an important role in drug selectivity, as oligomers formed prior to membrane insertion – presumably dimers – are believed to act differently on fungal (ergosterol-rich)...
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Brain Structure & Function
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CELL STRUCTURE AND FUNCTION
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Catalysis Structure & Reactivity
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Food Structure-Netherlands
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Journal of Social Structure
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ARTHROPOD STRUCTURE & DEVELOPMENT
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TREES-STRUCTURE AND FUNCTION
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A Triplet-learnt Coarse-to-Fine Reranking for Vehicle Re-identification
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Grand Challenges on the Theory of Modeling and Simulation
PublicationModeling & Simulation (M&S) is used in many different fields and has made many significant contributions. As a field in its own right, there have been many advances in methodologies and technologies. In 2002 a workshop was held in Dagstuhl, Germany, to reflect on the grand challenges facing M&S. Ten years on, a series of M& S Grand Challenge activities are marking a decade of progress and are providing an opportunity to reflect...
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Modeling lubricant flow between thrust-bearing pads
PublicationInlet temperature is one of the main inputs in all models for the analysis of fluid film bearing performance. At the same time, inlettemperature distribution and also oil velocity distribution at the inlet are the result of flow phenomena in the gap between the bearingpads. These phenomena are complex and in many cases further affected by any special arrangements of forced oil supply to the gapbetween pads. The reason for such...
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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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Performance and Power-Aware Modeling of MPI Applications for Cluster Computing
PublicationThe paper presents modeling of performance and power consumption when running parallel applications on modern cluster-based systems. The model includes basic so-called blocks representing either computations or communication. The latter includes both point-to-point and collective communication. Real measurements were performed using MPI applications and routines run on three different clusters with both Infiniband and Gigabit Ethernet...
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Synergic Effect of Selected Ingredients and Calcium Chloride on the Technological, Molecular and Microbial Usefulness of Eggshells and Their Impact on Sensory Properties in a Food Model System
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Towards an efficient multi-stage Riemann solver for nuclear physics simulations
PublicationRelativistic numerical hydrodynamics is an important tool in high energy nuclear science. However, such simulations are extremely demanding in terms of computing power. This paper focuses on improving the speed of solving the Riemann problem with the MUSTA-FORCE algorithm by employing the CUDA parallel programming model. We also propose a new approach to 3D finite difference algorithms, which employ a GPU that uses surface memory....
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Wodociągi - model. komput., stacjon., I sem mgr 2023/2024
e-Learning CoursesKurs dotyczy przedmiotu Modelowanie systemów wodociągowych na Kierunku Inżynieria Środowiska, studia stacjonarne II stopnia, sem.I. W ramach przedmiotu (wykłady, ćwiczenia, projektowanie) dostarczana jest studentom uporządkowana, możliwie kompletna wiedza umożliwiająca wykonywanie prac projektowych i analitycznych dla systemów transportu i dystrybucji wody wodociągowej (STiDW) z wykorzystaniem modelowania komputerowego przepływów ...
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Molecular picture of hydroxide anion hydration in aqueoussolutions studied by FT-IR ATR spectroscopy
PublicationHydratacja anionu hydroksylowego w wodnych roztworach wodorotlenków metali alkalicznych (LiOH, NaOH, KOH) została zbadana metodą spektroskopii oscylacyjnej FT-IR całkowitego wewnętrznego odbicia (ATR). Widma oscylacyjne wody dostarczają cennych informacji na temat stanu strukturalnego cząsteczek wody w sferach hydratacyjnych, wynikających ze sprzężeń oscylatorów w układzie. Wykazano, że drganie normalne rozciągające cząsteczki...
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Objectivity in the non-Markovian spin-boson model
PublicationObjectivity constitutes one of the main features of the macroscopic classical world. An important aspect of the quantum-to-classical transition issue is to explain how such a property arises from the microscopic quantum theory. Recently, within the framework of open quantum systems, there has been proposed such a mechanism in terms of the so-called spectrum broadcast structures. These are multipartite quantum states of the system...
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Multi-Fidelity Local Surrogate Model for Computationally Efficient Microwave Component Design Optimization
PublicationIn order to minimize the number of evaluations of high-fidelity (“fine”) model in the optimization process, to increase the optimization speed, and to improve optimal solution accuracy, a robust and computational-efficient multi-fidelity local surrogate-model optimization method is proposed. Based on the principle of response surface approximation, the proposed method exploits the multi-fidelity coarse models and polynomial interpolation...
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The Bridge of Data Project Objectives
PublicationOpen Research Data (ORD) is one of the emerging trends for researchers across the globe. However, it has to be stressed that the level of implementation and awareness of ORD varies between countries. Many initiatives have been created in Polish scientific institutions to support the process of opening publications. These are mainly Open Access (OA) repositories, implementing the so-called green road of OA. However, only a few universities...
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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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Molecular modeling of Gram-positive bacteria peptidoglycan layer, selected glycopeptide antibiotics and vancomycin derivatives modified with sugar moieties
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Thin-walled frames and grids - statics and dynamics
PublicationFrames and grids assembled with thin-walled beams of open cross-section are widely applied in various civil engineering and vehicle or machine structures. Static and dynamic analysis of theses structures may be carried out by means of different models, startingfrom the classical models made of beam elements undergoing the Kirchhoff assumptions to the FE discretization of whole frame into plane elements. The former model is very...
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Modeling and analysis of the effectiveness of the guard systemswith dynamic graphs
PublicationIn the following paper it will be presented a new model for analysis (in polynomial time) of the effectiveness of the guard systems. Therewill be presented its practical applications in problems such as searching for the weakest points of the system, planning guards' paths or cameras deployment, switching image from multiple cameras on several monitors, or interception of the intruder. This model is based on describing the guarded...
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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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Structure–activity relationships study on biological activity of peptides as dipeptidyl peptidase IV inhibitors by chemometric modeling
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How the “Liquid Drop” Approach Could Be Efficiently Applied for Quantitative Structure–Property Relationship Modeling of Nanofluids
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Technological capability dynamics through cluster organizations
PublicationPurpose – The purpose of the paper is to portrait how members of cluster organizations (COs) perceive the role of COs in enabling them to accumulate technological capability (TC) significant for their innovation. Design/methodology/approach – The authors report the findings from their qualitative study based on an analysis of four COs. The organizational inertia and absorptive capacity (AC) theories are the theoretical underpinning...
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Numerical modeling of hydrodynamics and sediment transport—an integrated approach
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Two-state dynamics for replicating two-strand systems
PublicationDynamika dwustanowa została zastosowana do opisów układów dwuniciowych, analogicznych do DNA.
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New PCR test for detection of Candida glabrata based on the molecular target chosen by the RAPD technique
PublicationRapid, reliable diagnosis is a necessary condition for the successful treatment of infections. Such diagnostic assays are continually being developed. #e paper presents a method for selecting the molecular target for PCR-based diagnostics based on the comparison of RAPD patterns. A sequence encoding Candida glabrata CBS138 hypothetical protein was selected. The limit of detection for PCR and real-time PCR reactions with DNA extracted...
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The assessment of metrological properties of segmental orifice based on simulations and experiments
PublicationSegmental orifices are often used to measure flows of heterogeneous mixtures, especially in flow meters in the power industry, for example. The orifice (with module m= 0.25) was installed in a stainless-steel pipe with internal diameter of 50 mm, placed in a hydraulic water system. The research was performed for Reynolds numbers ranging from 9,000 to 17,000. The flow characteristics of this orifice obtained based on simulation...
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Assessment of cardiovascular risk in assisted living
PublicationWady i choroby układu krążenia są jedną z podstawowych przyczyn problemów zdrowotnych oraz przyczyn śmierci. Wczesne ich wykrycie jest szczególnie cenne jako, że może zapobiec przez poważnymi incydentami (np. zawał, udar, itp.). W artykule przedstawiono nasobny system pomiarowy integrujący wiele pomiarów przydatnych do oceny problemów kardiologicznych.Disorders of the heart and blood vessels are the leading cause of health problems...
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Video-Assisted Thoracic Surgery
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JOURNAL OF COMPUTER ASSISTED LEARNING
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Efficient Surrogate Modeling and Design Optimization of Compact Integrated On-Chip Inductors Based on Multi-Fidelity EM Simulation Models
PublicationHigh-performance and small-size on-chip inductors play a critical role in contemporary radio-frequency integrated circuits. This work presents a reliable surrogate modeling technique combining low-fidelity EM simulation models, response surface approximations based on kriging interpolation, and space mapping technology. The reported method is useful for the development of broadband and highly accurate data-driven models of integrated...
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Numerical Modeling of Cone Penetration Test in Slightly Overconsolidated Clay with Arbitrary Lagrangian-Eulerian Formulation
PublicationIn this paper the results of the cone penetration test (CPT) modeling with the arbitrary Lagrangian-Eulerian (ALE) formulation provided by Abaqus software package have been presented. The study compares the cone resistance and sleeve friction obtained in numerical analysis with values measured in soundings performed in the uniform layer of clayey soil in the Koszalin area. The clay layer was found to be slightly overconsolidated...
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MACHINE DYNAMICS PROBLEMS
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The hydrogen bond network structure within the hydration shell around simple osmolytes: Urea, tetramethylurea, and trimethylamine-N-oxide, investigated using both a fixed charge and a polarizable water model
PublicationDespite numerous experimental and computer simulation studies, a controversy still exists regarding the effect of osmolytes on the structure of surrounding water. There is a question, to what extent some of the contradictory results may arise from differences in potential models used to simulate the system or parameters employed to describe physical properties of the mixture and interpretation of the results. Bearing this in mind,...
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The hydrogen bond network structure within the hydration shell around simple osmolytes: Urea, tetramethylurea, and trimethylamine-N-oxide, investigated using both a fixed charge and a polarizable water model
PublicationDespite numerous experimental and computer simulation studies, a controversy still exists regarding the effect of osmolytes on the structure of surrounding water. There is a question, to what extent some of the contradictory results may arise from differences in potential models used to simulate the system or parameters employed to describe physical properties of the mixture and interpretation of the results. Bearing this in mind,...
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Wave Method for Structural Health Monitoring: Testing Using Full-Scale Shake Table Experiment Data
PublicationAn algorithm of the wave method for structural health monitoring (SHM) is tested and calibrated using shake table experiment data of a full-scale, seven-story, reinforced-concrete building slice. The method is based on monitoring changes in the velocity of waves propagating vertically through the structure, identified by least-squares (LSQ) fit of beam models. The experiment was conducted by a team from the University of California,...
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Experimental investigations and simulations of the microturbine unit with permanent magnet generator
PublicationIn dispersed power generation, low power devices are used for local combined generating of heat end electric power. There are developing concepts of micropower plants with electric generators driven by steam or gas microturbines. The paper presents the results of an experimental investigations of the microturbine set consists of the turbine with partial admission, permanent magnet generator and three phase AC-to-DC rectifier. The...
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Micelle-bound conformations of neurohypophyseal hormone analogues modified with a Cα-disubstituted residue: NMR and molecular modelling studies
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Methodology of Selecting the Optimal Receptor to Create an Electrochemical Immunosensor for Equine Arteritis Virus Protein Detection
PublicationThe study reports a methodology of selecting the optimal receptor to create an electrochemical immunosensor for equine arteritis virus (EAV) protein detection. The detection was based on antigen recognition by antibodies immobilized on gold electrodes. Modification steps were controlled by electrochemical impedance spectroscopy and cyclic voltammetry measurements. In order to obtain the impedance immunosensor with the best parameters,...
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On Accuracy Modeling of Gas Turbine Cycles by the In-house COM-GAS Code
PublicationIn this paper, a comparison of accuracy modeling of gas turbine cycles between the basic (classical) model and the in-house COM-GAS code has been presented. The basic model uses a semi-perfect gas and well known projecting assumption. On the other hand, the computational flow mechanics (CFM) basis on a real gas by using thermodynamic tables. The thermodynamic analysis of thermal cycles, simply gas cycle GT8C and gas turbine cycle...
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Synthesis, structure and properties of novel poly(hydroxyurethane)s obtained by non-isocyanate route
PublicationNon-isocyanate polyurethanes (NIPUs) can be synthesized by polyaddition of five-membered bis(cyclic carbonate)s and primary diamines. NIPUs are an alternative for the commonly used (in the form of foams, elastomers, coatings or fibers) in the industry polyurethanes obtained using toxic and moisture sensitive diisocyanates, polyols and low-molecular weight chain extenders. The main aim of this work was to synthesize non-isocyanate...
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A structure and design of a novel compact UWB MIMO antenna
PublicationIn the paper, a concept and design procedure of a novel compact MIMO slot antenna is presented. In order to achieve a better filling of available space, individual antennas are constrained to a triangular shape and optimized for a reduced size. The MIMO structure is then assembled using the two of previously designed antennas in orthogonal arrangement. Surrogate-assisted numerical optimization involving variable-fidelity electromagnetic...
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New propagation model for wireless monitoring systems in the container terminal environment
PublicationW artykule został poddany analizie problem szacowania tłumienia propagacyjnego na obszarze terminala kontenerowego. Została opisana kampania pomiarowa, której rezultatem było opracowanie nowego modelu propagacyjnego dla łącza radiowego pracującego w warunkach LOS i NLOS.
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Methodology of Selecting the Optimal Receptor to Create an Electrochemical Immunosensor for Equine Arteritis Virus Protein Detection
PublicationThe study reports a methodology of selecting the optimal receptor to create an electrochemical immunosensor for equine arteritis virus (EAV) protein detection. The detection was based on antigen recognition by antibodies immobilized on gold electrodes. Modification steps were controlled by electrochemical impedance spectroscopy and cyclic voltammetry measurements. In order to obtain the impedance immunosensor with the best parameters,...
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Chosen aspects of skeletal system modeling: Numerical solid and shell models of femur part
PublicationThe purpose of this paper is to present a new method of femur part modeling by using the finite element method. This method treats a femur part as a system composed of cortical and trabecular bone. For the purpose of determining a proper shape of femur part model there were created three models: a) the first one describes a femur part as a solid structure; b) the second one describes a femur part as a connection of cortical bone...