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Docking simulations, Molecular properties and ADMET studies of novel Chromane6,7diol analogues as potential inhibitors of Mushroom tyrosinase
PublicationResearch on inhibition of tyrosinase enzyme has attained significant value, because tyrosinase inhibitors have potential applications in medicine, cosmetics (as whitening agents) and in agriculture (as bioinsecticides). Determination and elucidation of new tyrosinase inhibitors are not only beneficial for medical purposes, but their promising applications in improving food quality and nutritional...
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Efficient Simulation-Based Global Antenna Optimization Using Characteristic Point Method and Nature-Inspired Metaheuristics
PublicationAntenna structures are designed nowadays to fulfil rigorous demands, including multi-band operation, where the center frequencies need to be precisely allocated at the assumed targets while improving other features, such as impedance matching. Achieving this requires simultaneous optimization of antenna geometry parameters. When considering multimodal problems or if a reasonable initial design is not at hand, one needs to rely...
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A study on microcrack monitoring in concrete: discrete element method simulations of acoustic emission for non-destructive diagnostics
PublicationThe research is focused on the monitoring of fracture evolution in concrete beams under three-point bending using the acoustic emission technique and the discrete element method. The main objective of the study was to numerically and experimentally investigate the mechanism behind the generation of elastic waves during acoustic emission events and their interaction with micro- and macro-cracking in concrete beams under monotonic...
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A multiparameter simulation-driven analysis of ship turning trajectory concerning a required number of irregular wave realizations
PublicationIn times of progressive automation of the marine industry, accurate modeling of ship maneuvers is of utmost importance to all parties involved in maritime transportation. Despite the existence of modern collisionavoidance algorithms using 6DOF motion models to predict ship trajectories in waves, the impact of stochastic realization of irregular waves is usually neglected and remains under-investigated. Therefore, herein, this phenomenon...
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UNRES-GPU for Physics-Based Coarse-Grained Simulations of Protein Systems at Biological Time- and Size-Scales
PublicationThe dynamics of the virus like particles (VLPs) corresponding to the GII.4 Houston, GII.2 SMV, and GI.1 Norwalk strains of human noroviruses (HuNoV) that cause gastroenteritis was investigated by means of long-time (about 30 μs in the laboratory timescale) molecular dynamics simulations with the coarse-grained UNRES force field. The main motion of VLP units turned out to be the bending at the junction between the P1 subdomain (that...
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Globalized Knowledge-Based Simulation-Driven Antenna Miniaturization Using Domain-Confined Surrogates and Dimensionality Reduction
PublicationDesign of contemporary antenna systems encounters multifold challenges, one of which is a limited size. Compact antennas are indispensable for the new fields of application such as inter-net of things or 5G/6G mobile communication. Still, miniaturization generally undermines elec-trical and field performance. When attempted through numerical optimization, it turns into a constrained problem with costly constraints requiring electromagnetic...
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Assessment of the Speed Management Impact on Road Traffic Safety on the Sections of Motorways and Expressways Using Simulation Methods
PublicationMethods used to evaluate the impact of Intelligent Transport System (ITS) services on road safety are usually based on expert assessments or statistical studies. However, commonly used methods are challenging to apply in the planning process of ITS services. This paper presents the methodology of research using surrogate safety measures calculated and calibrated with the use of simulation techniques and a driving simulator. This...
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Reduced-Cost Microwave Design Closure by Multi-Resolution EM Simulations and Knowledge-Based Model Management
PublicationParameter adjustment through numerical optimization has become a commonplace of contemporary microwave engineering. Although circuit theory methods are ubiquitous in the development of microwave components, the initial designs obtained with such tools have to be further tuned to improve the system performance. This is particularly pertinent to miniaturized structures, where the cross-coupling effects cannot be adequately accounted...
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Expedited Gradient-Based Design Closure of Antennas Using Variable-Resolution Simulations and Sparse Sensitivity Updates
PublicationNumerical optimization has been playing an increasingly important role in the design of contemporary antenna systems. Due to the shortage of design-ready theoretical models, optimization is mainly based on electromagnetic (EM) analysis, which tends to be costly. Numerous techniques have evolved to abate this cost, including surrogate-assisted frameworks for global optimization, or sparse sensitivity updates for speeding up local...
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Chip suction system in circular sawing machine: empirical research and computational fluid dynamics numerical simulations
PublicationThe experimental analysis of the wood chip removing system during its redesigning in the existing sliding table circular saw and computational fluid dynamic (CFD) numerical simulations of the air flow process is presented in the paper. The attention was focused on the extraction hood and the bottom shelter of the actual existing system. The main aim was to perform experimental research on the pressure distribution inside the...
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Simulation of the number of storm overflows considering changes in precipitation dynamics and the urbanisation of the catchment area: a probabilistic approach
PublicationThis paper presents a probabilistic methodology that allows the study of the interactions between changes in rainfall dynamics and impervious areas in urban catchment on a long- and short-term basis. The proposed probabilistic model predict future storm overflows while taking into account the dynamics of changes in impervious areas and rainfall. In this model, a logistic regression method was used to simulate overflow resulting...
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Mechanism of recognition of parallel G-quadruplexes by DEAH/RHAU helicase DHX36 explored by molecular dynamics simulations
PublicationBecause of high stability and slow unfolding rates of G-quadruplexes (G4), cells have evolved specialized helicases that disrupt these non-canonical DNA and RNA structures in an ATP-dependent manner. One example is DHX36, a DEAH-box helicase, which participates in gene expression and replication by recognizing and unwinding parallel G4s. Here, we studied the molecular basis for the high affinity and specificity of DHX36 for parallel-type...
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Computational fluid dynamics simulation of heat transfer from densely packed gold nanoparticles to isotropic media
PublicationThis work aims to determine and compare heat generation and propagation of densely packed gold nanoparticles (Au NPs) induced by a resonant laser beam (532 nm) according to the Mie theory. The heat flux propagation is transferred into the materials, which here are: silica glass; soda-lime-silica glass; borosilicate glass; polymethyl methacrylate (PMMA); polycarbonate (PC); and polydimetylosiloxane (PDMS). This analysis aims to...
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Low-Cost Quasi-Global Optimization of Expensive Electromagnetic Simulation Models by Inverse Surrogates and Response Features
PublicationConceptual design of contemporary high-frequency structures is typically followed by a careful tuning of their parameters, predominantly the geometry ones. The process aims at improving the relevant performance figures, and may be quite expensive. The reason is that conventional design methods, e.g., based on analytical or equivalent network models, often only yield rough initial designs. This is especially the case for miniaturized...
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Operation of the Hybrid Photovoltaic-Battery System on the Electricity Market—Simulation, Real-Time Tests and Cost Analysis
PublicationThis paper presents research on a hybrid photovoltaic-battery energy storage system, declaring its hourly production levels as a member of a balancing group submitting common scheduling unit to the day-ahead market. It also discusses the variability of photovoltaic system generation and energy storage response. The major research questions were whether the operation of a hybrid photovoltaic-battery energy storage system is viable...
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Prediction of cast-in-place concrete strength of the extradosed bridge deck based on temperature monitoring and numerical simulations
PublicationThe work is devoted to the implementation of a monitoring system for high performance concrete embedded in the span of an extradosed bridge deck using a modified maturity method augmented by numerical simulations conducted by the authors’ FEM code. The paper presents all research stages of bridge construction and considers the conclusions drawn from the results of laboratory tests, field measurements, and numerical calculations....
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Modeling, simulation, and validation of a TB41 crash test of the H2/W5/B concrete vehicle restraint system
PublicationThe paper addresses numerical simulations of a concrete vehicle restraint system. The model is described in detail. The advanced material law of the continuous surface cap model was used to analyze the damage locations in concrete barrier segments. The results were validated against the TB41 full-scale crash test. The test was conducted in compliance with European standard EN 1317, and the validation was performed in accordance...
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Broadening the scope of measurement and analysis of vibrations of an organ pipe employing intensity probe, simulations, and highspeed camera
PublicationThis paper shows an integrated approach to measure, analyze, and model phenomena occurring in an organ pipe driven by pressurized air. The aim of this paper is two-fold, i.e., to measure the pressure signal and the intensity field around the mouth by means of an intensity probe and to visualize and observe the motion of the air jet, which represents the excitation mechanism of the system. This is realized through two techniques,...
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Efficient parallel implementation of crowd simulation using a hybrid CPU+GPU high performance computing system
PublicationIn the paper we present a modern efficient parallel OpenMP+CUDA implementation of crowd simulation for hybrid CPU+GPU systems and demonstrate its higher performance over CPU-only and GPU-only implementations for several problem sizes including 10 000, 50 000, 100 000, 500 000 and 1 000 000 agents. We show how performance varies for various tile sizes and what CPU–GPU load balancing settings shall be preferred for various domain...
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Electrochemical simulation of metabolism for antitumor-active imidazoacridinone C-1311 and in silico prediction of drug metabolic reactions
PublicationThe metabolism of antitumor-active 5-diethylaminoethylamino-8-hydroxyimidazoacridinone (C-1311) has been investigated widely over the last decade but some aspects of molecular mechanisms of its metabolic transformation are still not explained. In the current work, we have reported a direct and rapid analytical tool for better prediction of C-1311 metabolism which is based on electrochemistry (EC) coupled on-line with electrospray...
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Full-scale CFD simulations for the determination of ship resistance as a rational, alternative method to towing tank experiments
PublicationResults of ship resistance predictions obtained from towing tank experiments are affected by the method used to extrapolate from a model scale to a ship scale. Selection of method to determine a form factor is subjective and the extrapolation method is accurate for typical hull forms. For innovative hull forms the proper method for calculating the form factor is questionable. Moreover, the influence of the extrapolation method...
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Numerical Simulation of Catastrophic Flood: the Case Study of Hypothetical Failure of the Bielkowo Hydro–Power Plant Reservoir
PublicationThe numerical modeling of flood wave propagation following the hypo-thetical breaks of the embankments of the Bielkowo hydro–power plant storage reservoir (Kolbudy II Reservoir) on the Radunia River in Poland have been presented. The results of computations were used to estimate the parameters of the flood waves, which are indispensable for the flood zone determination and mapping and then for the flood risk analysis. When estimating...
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3D DEM simulations of monotonic interface behaviour between cohesionless sand and rigid wall of different roughness
PublicationArtykuł omawia wyniki metodą elementów dyskretnych (DEM) dotyczace zachowania się strefy kontaktu między bezkohezyjnym piaskiem a sztywną scianą o różnej szorstkości. Obliczenia wykonano dla dla różnej wysokości, nachylenia i rozstawu rowków wzdłuż sciany, które symulowały jej szorstkość. W symulacjach zmieniano dodatkowo ciśnienie pionowe i początkowy wskaźnik porowatosci piasku. Nacisk położono na wpływ szorstkości na mobilizowany...
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Simulations of hydro-fracking in rock mass at meso-scale using fully coupled DEM/CFD approach
PublicationThe paper deals with two-dimensional (2D) numerical modelling of hydro-fracking (hydraulic fracturing) in rocks at the meso-scale. A numerical model was developed to characterize the properties of fluid-driven fractures in rocks by combining the discrete element method (DEM) with computational fluid dynamics (CFD). The mechanical behaviour of the rock matrix was simulated with DEM and the behaviour of the fracturing fluid flow...
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Meat Proteins as Dipeptidyl Peptidase IV Inhibitors and Glucose Uptake Stimulating Peptides for the Management of a Type 2 Diabetes Mellitus In Silico Study
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Quantifying Contextuality
PublicationContextuality is central to both the foundations of quantum theory and to the novel information processing tasks. Despite some recent proposals, it still faces a fundamental problem: how to quantify its presence? In this work, we provide a universal framework for quantifying contextuality. We conduct two complementary approaches: (i) the bottom-up approach, where we introduce a communication game, which grasps the phenomenon of...
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Dimethyl(3,3,3-trifluoropropyl)silyldiethylamine—A new silylating agent for the derivatization of β-blockers and β-agonists in environmental samples
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Application of the finite element methods in long-term simulation of the multi-physics systems with large transient response differences
PublicationApplication of the Finite Element Method (FEM) and the Multibody Dynamics Method allows analyzing of complex physical systems. Complexity of the system could be related both to the geometry and the physical description of phenomenon. The metod is the excellent tool for analyzing statics or dynamics of the mechanical systems, and permits tracking of Multi Body System (MBS) transient response for the long-term simulations and application...
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The Impact of Selected Parameters on the efficiency of PV Installations - Simulation Test of the 1 MW PV Farm in the PVSyst Program
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Numerical Simulation and Experimental Analysis of Thermal Cycles and Phase Transformation Behavior of Laser-Welded Advanced Multiphase Steel
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New trim configurations for laser trimmed thick-film resistors - theoretical analysis, numerical simulation and experimential verification
PublicationW pracy przedstawiono nowe podejście do korekcji rezystorów warstwowych polegające na wytwarzaniu dodatkowego kontaktu w celu rozszerzenia zakresu korekcji i uproszczenia projektowania. Ponadto zaprezentowano nową szybką metodę wyznaczania charakterystyk korekcyjnych a także weryfikację eksperymentalną. Przedstawiono wyniki w postaci zakresów korekcji i względnych przyrostów rezystancji w funkcji kształtu dodatkowego kontaktu oraz...
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Extension of the Unres Package for Physics-Based Coarse-Grained Simulations of Proteins and Protein Complexes to Very Large Systems
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Implementations of Nosé–Hoover and Nosé–Poincaré thermostats in mesoscopic dynamic simulations with the united-residue model of a polypeptide chain
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Comparison the heat load as the results of tests on human subject in a hot environment with the results obtained from numerical simulation
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<title>Cavity control system advanced modeling and simulations for TESLA linear accelerator and free electron laser</title>
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Molecular Simulations Using Boltzmann’s Thermally Activated Diffusion - Implementation on ARUZ – Massively-parallel FPGA-based Machine
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Cutting forces and temperature measurements in cryogenic assisted turning of AA2024-T351 alloy: An experimentally validated simulation approach
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Performance of extended Lagrangian schemes for molecular dynamics simulations with classical polarizable force fields and density functional theory
PublicationIterative energy minimization with the aim of achieving self-consistency is a common feature of Born-Oppenheimer molecular dynamics (BOMD) and classical molecular dynamics with polarizable force fields. In the former, the electronic degrees of freedom are optimized, while the latter often involves an iterative determination of induced point dipoles. The computational effort of the self-consistency procedure can be reduced by re-using...
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Surrogate-assisted EM-driven miniaturization of wideband microwave couplers by means of co-simulation low-fidelity models
PublicationThis article proposes a methodology for rapid design optimization of miniaturized wideband couplers. More specifically, a class of circuits is considered, in which conventional transmission lines are replaced by their abbreviated counterparts referred to as slow-wave compact cells. Our focus is on explicit reduction of the structure size as well as on reducing the CPU cost of the design process. For the sake of computational feasibility,...
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Recent advances in rapid multiobjective optimization of expensive simulation models in microwave and antenna engineering by Pareto front exploration
PublicationPractical engineering design problems are inherently multiobjective, that is, require simultaneous control of several (and often conflicting) criteria. In many situations, genuine multiobjective optimization is required to acquire comprehensive information about the system of interest. The most popular solution techniques are populationbased metaheuristics, however, they are not practical for handling expensive electromagnetic...
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Multi-fidelity EM simulations and constrained surrogate modelling for low-cost multi-objective design optimisation of antennas
PublicationIn this study, a technique for low-cost multi-objective design optimisation of antenna structures has been proposed. The proposed approach is an enhancement of a recently reported surrogate-assisted technique exploiting variable-fidelity electromagnetic (EM) simulations and auxiliary kriging interpolation surrogate, the latter utilised to produce the initial approximation of the Pareto set. A bottleneck of the procedure for higher-dimensional...
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Comparison of the exponential thermal transient parameterization methods with the SMTP method in the unipedicled DIEP flap computer modelling and simulation
PublicationThe aim of this paper is to compare the spatial contrast of the image descriptors obtained via three different thermal transient parameterization methods in Active Dynamic Thermography. The thermal constants and amplitude values of the one- and two- exponential parametrization are compared to the Simplified Magnitude-Temporal Parametrization method (SMTP). The comparison is performed using the data obtained by simulating the cold...
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Combining X-ray tomogrpahy imaging and DEM simulations to investigate granular material flow during silo discharging
PublicationEven after few decades of research, the study of particle motion taking place during silo discharging hasn’t been fully addressed, both experimentally and numerically, because of nontrivial behaviors that occur during associated flow patterns. For instance, discrete element method (DEM) has shown good qualitative prediction potential of velocity profile, but, on the other hand, frequently failed to match quantitatively experimental...
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MM/PBSA analysis of molecular dynamics simulations of bovine beta-lactoglobulin: free energy gradients in conformational transitions?
PublicationPraca dotyczy pH zależnych zmian konformacyjnych EF pętli beta-laktoglobuliny. Zmiany te są śledzone za pomocą metod obliczeniowych chemii (dynamika molekularna oraz metody MM/PBSA).
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Simulation of static response of thin walled bars with changed design parameters by means of second order sensitivity analysis.
PublicationZa pomocą analizy wrażliwości drugiego rzędu wyznaczono przybliżone wartości sił wewnętrznych i przemieszczeń pręta cienkościennego dla zmieniających się parametrów projektowych. W przykładzie numerycznym wyznaczono pierwszą i drugą wariację bimomentu w funkcji grubości półek skręcanego dwuteownika. Zbadano dokładność rozwiązania uzyskanego za pomocą analizy wrażliwości z rozwiązaniem ścisłym.
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Comparison of two model concepts for simulation of nitrogen removal at a full-scale biological nutrient removal pilot plant
PublicationCelem badań było porównanie zdolności predykcyjnych dwóch mechanistycznych modeli procesu osadu czynnego (ASM1 i ASM3). W tym celu wykorzystano bazę danych empirycznych z pilotowej oczyszczalni ścieków Gummerwald w Hanowerze (Niemcy). Oba badane modele prognozowały szczytowe stężenia azotu amonowego na poziomie >8 gN/m3 w ciągu, którego obciążenie hydrauliczne wzrastało czterokrotnie w porównaniu do okresu bezdeszczowego. Prognozowany...
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Experimental study and numerical simulation on porosity dependent direct reducibility of high-grade iron oxide pellets in hydrogen
PublicationThe transition to more environmentally friendly steel production methods has intensified research into hydrogen-based direct reduction (HyDR) of iron oxide pellets. The aim of this study is to systematically investigate the kinetics of the reduction process, the evolution of porosity and the resulting microstructural changes on the reduction behavior of high-quality pellets during HyDR of iron ore at different temperatures. A modified...
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Scalability of surrogate-assisted multi-objective optimization of antenna structures exploiting variable-fidelity electromagnetic simulation models
PublicationMulti-objective optimization of antenna structures is a challenging task due to high-computational cost of evaluating the design objectives as well as large number of adjustable parameters. Design speedup can be achieved by means of surrogate-based optimization techniques. In particular, a combination of variable-fidelity electromagnetic (EM) simulations, design space reduction techniques, response surface approximation (RSA) models,...
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Electrochemistry meets enzymes: Investigation of the biotransformation pathway of C-1311 based on electrochemical simulation in comparison to in vitro methods.
PublicationThe knowledge of the metabolic pathways and the biotransformation of new drugs is one of the major challenges in pharmaceutical research. It is crucial for elucidation of degradation routes of the new biologically active compounds, especially in the area of possible toxicity. Conventional in vitro drug metabolism studies are based on incubating drug candidate with e.g. hepatocytes or, most importantly, liver cell microsomes and...
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Model Management for Low-Computational-Budget Simulation-Based Optimization of Antenna Structures Using Nature-Inspired Algorithms
PublicationThe primary objective of this study is investigation of the possibilities of accelerating nature-inspired optimization of antenna structures using multi-fidelity EM simulation models. The primary methodology developed to achieve acceleration is a model management scheme which the level of EM simulation fidelity using two criteria: the convergence status of the optimization algorithm, and relative quality of the individual designs...