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Wyniki wyszukiwania dla: computational models of emotions
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Ergodicity and model quality in template-restrained canonical and temperature/Hamiltonian replica exchange coarse-grained molecular dynamics simulations of proteins
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Kinetic flux vector splitting scheme for solving non-reactive multi-component flows
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Protein structure prediction with the UNRES force-field using Replica-Exchange Monte Carlo-with-Minimization; Comparison with MCM, CSA, and CFMC
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An efficient molecular docking using conformational space annealing
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Conformation of six fentanyls revisited
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Frequency bands selection of the Portevin-LeChatelier
PublikacjaEfekt Portevina-LeChateliera ujawnia się w postaci skokowych zmian naprężenia w trakcie procesu odkształcenia próbek pewnych stopów. Zjawisko PLC występuje w kilku odmianach charakteryzujących się istotnymi różnicami zarówno w przestrzennym rozkładzie pasm odkształcenia jak też przebiegu krzywej naprężeniowej. Przebiegi odpowiadające różnym odmianom serration charakteryzują się odmiennymi właściwościami rozkładu energetycznego...
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Quadratic Cohen representations in spectral analysis of serration process in Al–Mg alloys
PublikacjaImportant from mechanical point of view the Portevin–Le Chatelier serration phenomenon is being characterized by a complicated spectral profile. As a typical example of nonstationary processes it demands a special treatment allowing to follow the evolution of energy of stress fluctuations as a function of strain. The authors suggest the utilization of a compact system of quadratic transformations, known as Cohen class, as a technique...
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Metal salts reduction during parylenes polymerization
PublikacjaPublikacja o wynikach obliczeń kwantowych o możliwości redukcji niektórych soli metali przy pomocy rodników parylenu w czasie jego polimeryzacji.
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Structure and properties of liquid Al–Cu alloys: Empirical potentials compared
PublikacjaWe report on the structure and mass transport properties of liquid Al–Cu alloys predicted by two recently-developed empirical many-body potentials: MEAM (Jelinek et al., 2012) and EAM-ADP (Apostol and Mishin, 2011), and by the well-known Gupta potential. Total and partial pair correlation functions, angular distribution functions, densities, coordination numbers and self-diffusion coefficients are compared with published experimental...
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Applying molecular dynamics simulation to take the fracture fingerprint of polycrystalline SiC nanosheets
PublikacjaGraphene-like nanosheets are the key elements of advanced materials and systems. The mechanical behavior of the structurally perfect 2D nanostructures is well documented, but that of polycrystalline ones is less understood. Herein, we applied molecular dynamics simulation (MDS) to take the fracture fingerprint of polycrystalline SiC nanosheets (PSiCNS), where monocrystalline SiC nanosheets (MSiCNS) was the reference nanosheet....
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Molecular mechanism of proton-coupled ligand translocation by the bacterial efflux pump EmrE
PublikacjaThe current surge in bacterial multi-drug resistance (MDR) is one of the largest challenges to public health, threatening to render ineffective many therapies we rely on for treatment of serious infections. Understanding different factors that contribute to MDR is hence crucial from the global “one health” perspective. In this contribution, we focus on the prototypical broad-selectivity proton-coupled antiporter EmrE, one of the...
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Optimization of parallel implementation of UNRES package for coarse‐grained simulations to treat large proteins
PublikacjaWe report major algorithmic improvements of the UNRES package for physics-based coarse-grained simulations of proteins. These include (i) introduction of interaction lists to optimize computations, (ii) transforming the inertia matrix to a pentadiagonal form to reduce computing and memory requirements, (iii) removing explicit angles and dihedral angles from energy expressions and recoding the most time-consuming energy/force terms...
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Structure-based design and evaluation of novel N-phenyl-1H-indol-2-amine derivatives for fat mass and obesity-associated (FTO) protein inhibition
PublikacjaFat mass and obesity-associated (FTO) protein contributes to non-syndromic human obesity which refers to excessive fat accumulation in human body and results in health risk. FTO protein has become a promising target for anti-obesity medicines as there is an immense need for the rational design of potent inhibitors to treat obesity. In our study, a new scaffold N-phenyl-1H-indol-2-amine was selected as a base for FTO protein inhibitors...
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Multi-agent large-scale parallel crowd simulation with NVRAM-based distributed cache
PublikacjaThis paper presents the architecture, main components and performance results for a parallel and modu-lar agent-based environment aimed at crowd simulation. The environment allows to simulate thousandsor more agents on maps of square kilometers or more, features a modular design and incorporates non-volatile RAM (NVRAM) with a fail-safe mode that can be activated to allow to continue computationsfrom a recently analyzed state in...
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Why do G-quadruplexes dimerize through the 5’-ends? Driving forces for G4 DNA dimerization examined in atomic detail
PublikacjaG-quadruplexes (G4) are secondary structures formed by guanine-rich nucleic acid sequences and shown to exist in living cells where they participate in regulation of gene expression and chromosome maintenance. G-quadruplexes with solvent-exposed guanine tetrads show the tendency to associate together through cofacial stacking, which may be important for packaging of G4-forming sequences and allows for the design of higher-order...
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Generating optimal paths in dynamic environments using RiverFormation Dynamics algorithm
PublikacjaThe paper presents a comparison of four optimisation algorithms implemented for the purpose of finding the shortest path in static and dynamic environments with obstacles. Two classical graph algorithms –the Dijkstra complete algorithm and A* heuristic algorithm – were compared with metaheuristic River Formation Dynamics swarm algorithm and its newly introduced modified version. Moreover, another swarm algorithm has been compared...
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In-depth characterization of icosahedral ordering in liquid copper
PublikacjaThe presence of icosahedral ordering in liquid copper at temperatures close to the melting point is now well-established both experimentally and through computer simulation. However, a more elaborate analysis of local icosahedral and icosahedron-like structures, together with a system for classifying such structures based on some measure of "icosahedrity", has so far been conspicuously absent in the literature. Similarly, the dynamics...
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ESCASA : Analytical estimation of atomic coordinates from coarse‐grained geometry for nuclear‐magnetic‐resonance ‐assisted protein structure modeling. I. Backbone and Hβ protons
PublikacjaA method for the estimation of coordinates of atoms in proteins from coarse-grained geometry by simple analytical formulas (ESCASA), for use in nuclear-magnetic-resonance (NMR) data-assisted coarse-grained simulations of proteins is proposed. In this paper, the formulas for the backbone Hα and amide (HN) protons, and the side-chain Hβ protons, given the Cα-trace, have been derived and parameterized, by using the interproton distances...
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Two-step mechanism of J-domain action in driving Hsp70 function
PublikacjaJ-domain proteins (JDPs), obligatory Hsp70 cochaperones, play critical roles in protein homeostasis. They promote key allosteric transitions that stabilize Hsp70 interaction with substrate polypeptides upon hydrolysis of its bound ATP. Although a recent crystal structure revealed the physical mode of interaction between a J-domain and an Hsp70, the structural and dynamic consequences of J-domain action once bound and how Hsp70s...
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Long‐time scale simulations of virus‐like particles from three human‐norovirus strains
PublikacjaThe 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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Generalization of Phylogenetic Matching Metrics with Experimental Tests of Practical Advantages
PublikacjaThe ability to quantify a dissimilarity of different phylogenetic trees is required in various types of phylogenetic studies, for example, such metrics are used to assess the quality of phylogeny construction methods and to define optimization criteria in supertree building algorithms. In this article, starting from the already described concept of matching metrics, we define three new metrics for rooted phylogenetic trees. One...
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On the joint time-frequency characteristics of chemical oscillations
PublikacjaZaprezentowano rezultaty analizy czasowo-częstotliwościowej rejestrów potencjałowych oscylacyjnej reakcji Biełousowa-Żabotyńskiego (BŻ). Wybraną reprezentację czasowo-częstotliwościową w postaci algorytmu STFT zastosowano do analizy typowych przebiegów reakcji BŻ, prowadzonej w układzie zamkniętym. Zaprezentowano spektrogramy STFT ukazujące czasowo-częstotliwościową strukturę oscylacji regularnych, mieszanych i chaotycznych. Na...
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Proximal primal–dual best approximation algorithm with memory
PublikacjaWe propose a new modified primal–dual proximal best approximation method for solving convex not necessarily differentiable optimization problems. The novelty of the method relies on introducing memory by taking into account iterates computed in previous steps in the formulas defining current iterate. To this end we consider projections onto intersections of halfspaces generated on the basis of the current as well as the previous...
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Analysis of High Resolution Clouds of Points as a Source of Biometric Data
PublikacjaThe article presents the analysis devoted to human face data obtained by means of precise photographic scanners. Collected point clouds were used to make high precision meshes of human face. The essence of these studies is the comparison of relative features as well as the comparison of absolute models which require as precisely as possible matching of face models. The article focuses on the analysis of various parts of the human...
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Outlier detection method by using deep neural networks
PublikacjaDetecting outliers in the data set is quite important for building effective predictive models. Consistent prediction can not be made through models created with data sets containing outliers, or robust models can not be created. In such cases, it may be possible to exclude observations that are determined to be outlier from the data set, or to assign less weight to these points of observation than to other points of observation....
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Wind resource assessment and energy yield prediction for the small wind turbine on the Szubieniczne Hill
PublikacjaThe goal of this study is to preliminary assess the wind resources on the Szubieniczne Hill in order to predict the annual energy production for planned small wind turbine. The analyzed site is located close to the Gdańsk University of Technology campus, in complex urban environment additionally surrendered by forested hills. The assessment is based on Computational Fluid Dynamics simulations which allow to evaluate the wind energy potential...
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Hybridized Space-Vector Pulsewidth Modulation for Multiphase Two-Level Voltage Source Inverter
PublikacjaIn space vector pulsewidth modulation (SVPWM) algorithms for multiphase two-level voltage source inverters (VSI), the components of active vectors in all orthogonal spaces have to be calculated within the processor and stored in its memory. These necessitate intensive computational efforts of the processor and large memory space. This article presents a hybridized SVPWM for multiphase two-level VSI. In this algorithm, elements...
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Binary-Encounter Model for Direct Ionization of Molecules by Positron-Impact
PublikacjaWe introduce two models for the computation of direct ionization cross sections by positron impact over a wide range of collision energies. The models are based on the binary-encounter-Bethe model and take into account an extension of the Wannier theory. The cross sections computed with these models show good agreement with experimental data. The extensions improve the agreement between theory and experiment for collision energies...
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Accurate Modeling of Antenna Structures by Means of Domain Confinement and Pyramidal Deep Neural Networks
PublikacjaThe importance of surrogate modeling techniques has been gradually increasing in the design of antenna structures over the recent years. Perhaps the most important reason is a high cost of full-wave electromagnetic (EM) analysis of antenna systems. Although imperative in ensuring evaluation reliability, it entails considerable computational expenses. These are especially pronounced when carrying out EM-driven design tasks such...
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Cost-Efficient Globalized Parameter Optimization of Microwave Components through Response-Feature Surrogates and Nature-Inspired Metaheuristics
PublikacjaDesign of contemporary microwave devices predominantly utilizes computational models, including both circuit simulators, and full-wave electromagnetic (EM) evaluation. The latter constitutes the sole generic way of rendering accurate assessment of the system outputs that considers phenomena such as cross-coupling or radiation and dielectric losses. Consequently, for reliability reasons, the final tuning of microwave device parameters...
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A concept of zero-dimensional and three-dimensional thermodynamic modelling of steam storage in a steam cycle
PublikacjaThis work presents the thermodynamic model of steam storage in a steam cycle. The innovative steam storage is an integral part of the unit and thus responds quickly to changes in load. This enhances the primary control reserve while maintaining high efficiency of energy conversion. With regard to power plants, it improves the operational safety of generation units, as it prevents boiler and turbines overload in the case of steep...
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Real‐Time PPG Signal Conditioning with Long Short‐Term Memory (LSTM) Network for Wearable Devices
PublikacjaThis paper presents an algorithm for real‐time detection of the heart rate measured on a person’s wrist using a wearable device with a photoplethysmographic (PPG) sensor and accelerometer. The proposed algorithm consists of an appropriately trained LSTM network and the Time‐Domain Heart Rate (TDHR) algorithm for peak detection in the PPG waveform. The Long Short‐Term Memory (LSTM) network uses the signals from the accelerometer...
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Assessment of Trajectories of Non-bankrupt and Bankrupt Enterprises
PublikacjaThe aim of this study is to show how long-term trajectories of enterprises can be used to increase the forecasting horizon of bankruptcy prediction models. The author used seven popular forecasting models (two from Europe, two from Asia, two from North America and one from Latin America). These models (five multivariate discriminant analysis models and two logit models) were used to develop 17-year trajectories separately for non-bankrupt...
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Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment
PublikacjaWe present the results for CAPRI Round 50, the 4th joint CASP-CAPRI protein assembly prediction challenge. The Round comprised a total of 12 targets, including 6 dimers, 3 trimers, and 3 higher-order oligomers. Four of these were easy targets, for which good structural templates were available either for the full assembly, or for the main interfaces (of the higher-order oligomers). Eight were difficult targets for which only distantly...
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Biocatalytic Functionalities of Lignin Peroxidase‑Based Systems in Lignin Depolymerization and Pollutants Removal from Environmental Matrices
PublikacjaPurpose of Review In the presented review, we have summarized and highlighted recent developments in the use of lignin peroxidase (LiP) to remove a variety of pollutants from water matrices. The high redox potential of LiP is underlined by its excellent catalytic functionalities in the elimination of pharmaceuticals, phenolics, dyes, polycyclic aromatic hydrocarbons (PAHs), endocrine-disrupting chemicals (EDCs), and other miscellaneous...
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Biocatalytic Functionalities of Lignin Peroxidase-Based Systems in Lignin Depolymerization and Pollutants Removal from Environmental Matrices
PublikacjaPurpose of Review In the presented review, we have summarized and highlighted recent developments in the use of lignin peroxidase (LiP) to remove a variety of pollutants from water matrices. The high redox potential of LiP is underlined by its excellent catalytic functionalities in the elimination of pharmaceuticals, phenolics, dyes, polycyclic aromatic hydrocarbons (PAHs), endocrine-disrupting chemicals (EDCs), and other miscellaneous...
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Taking advantage of symmetries: Gathering of many asynchronous oblivious robots on a ring
PublikacjaOne of the recently considered models of robot-based computing makes use of identical, memoryless mobile units placed in nodes of an anonymous graph. The robots operate in Look-Compute-Move cycles; in one cycle, a robot takes a snapshot of the current configuration (Look), takes a decision whether to stay idle or to move to one of the nodes adjacent to its current position (Compute), and in the latter case makes an instantaneous...
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Inverse Modeling and Optimization of CSRR-based Microwave Sensors for Industrial Applications
PublikacjaDesign optimization of multivariable resonators is a challenging topic in the area of microwave sensors for industrial applications. This paper proposes a novel methodology for rapid re-design and parameter tuning of complementary split-ring resonators (CSRRs). Our approach involves inverse surrogate models established using pre-optimized resonator data as well as analytical correction techniques to enable rapid adjustment of geometry...
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Machine learning-based prediction of seismic limit-state capacity of steel moment-resisting frames considering soil-structure interaction
PublikacjaRegarding the unpredictable and complex nature of seismic excitations, there is a need for vulnerability assessment of newly constructed or existing structures. Predicting the seismic limit-state capacity of steel Moment-Resisting Frames (MRFs) can help designers to have a preliminary estimation and improve their views about the seismic performance of the designed structure. This study improved data-driven decision techniques in...
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Optimum number of actuators to minimize the cross-sectional area of prestressable cable and truss structures
PublikacjaThis paper describes a new computational method for determining the optimum number of actuators to design the optimal and economic cross-sectional area of pin-jointed assemblies based on the conventional force method. The most active members are selected to be prestressed to redistribute stress in the whole structure, resulting in regulating the internal force of bars that face high stress. Reducing stress in critical members allows...
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Limiting distribution of the three-state semi-Markov model of technical state transitions of ship power plant machines and its applicability in operational decision-making.
PublikacjaThe article presents the three-state semi-Markov model of the process {W(t): t 0} of state transitions of a ship power plant machine, with the following interpretation of these states: s1 – state of full serviceability, s2 – state of partial serviceability, and s3 – state of unserviceability. These states are precisely defined for the ship main engine (ME). A hypothesis is proposed which explains the possibility of application...
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Optimization of hybrid parallel application execution in heterogeneous high performance computing systems considering execution time and power consumption
PublikacjaMany important computational problems require utilization of high performance computing (HPC) systems that consist of multi-level structures combining higher and higher numbers of devices with various characteristics. Utilizing full power of such systems requires programming parallel applications that are hybrid in two meanings: they can utilize parallelism on multiple levels at the same time and combine together programming interfaces...
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Multi-objective design optimization of antenna structures using sequential domain patching with automated patch size deter-mination
PublikacjaIn this paper, a simple yet efficient and reliable technique for fully automated multi-objective design optimization of antenna structures using sequential domain patching (SDP) is discussed. The optimization procedure according to SDP is a two-step process: (i) obtaining the initial set of Pareto-optimal designs representing the best possible trade-offs between considered conflicting objectives, and (ii) Pareto set refinement...
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Expedited Trust-Region-Based Design Closure of Antennas by Variable-Resolution EM Simulations
PublikacjaThe observed growth in the complexity of modern antenna topologies fostered a widespread employment of numerical optimization methods as the primary tools for final adjustment of the system parameters. This is mainly caused by insufficiency of traditional design closure approaches, largely based on parameter sweeping. Reliable evaluation of complex antenna structures requires full-wave electromagnetic (EM) analysis. Yet, EM-driven...
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Cost-Efficient Surrogate Modeling of High-Frequency Structures Using Nested Kriging with Automated Adjustment of Model Domain Lateral Dimensions
PublikacjaSurrogate models are becoming popular tools of choice in mitigating issues related to the excessive cost of electromagnetic (EM)-driven design of high-frequency structures. Among available techniques, approximation modeling is by far the most popular due to its versatility. In particular, the surrogates are exclusively based on the sampled simulation data with no need to involve engineering insight or problem-specific knowledge....
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MEMORY EFFECT ANALYSIS USING PIECEWISE CUBIC B-SPLINE OF TIME FRACTIONAL DIFFUSION EQUATION
PublikacjaThe purpose of this work is to study the memory effect analysis of Caputo–Fabrizio time fractional diffusion equation by means of cubic B-spline functions. The Caputo–Fabrizio interpretation of fractional derivative involves a non-singular kernel that permits to describe some class of material heterogeneities and the effect of memory more effectively. The proposed numerical technique relies on finite difference approach and cubic...
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One-Dimensional Modeling of Flows in Open Channels
PublikacjaIn this chapter, modeling of the unsteady open channel flow using one-dimensional approach is considered. As this question belongs to the well-known and standard problems of open channel hydraulic engineering, comprehensively presented and described in many books and publications, our attention is focused on some selected aspects only. As far as the numerical solution of the governing equations is considered, one can find out that...
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Residual MobileNets
PublikacjaAs modern convolutional neural networks become increasingly deeper, they also become slower and require high computational resources beyond the capabilities of many mobile and embedded platforms. To address this challenge, much of the recent research has focused on reducing the model size and computational complexity. In this paper, we propose a novel residual depth-separable convolution block, which is an improvement of the basic...
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Study on the Influence of an Axial Distance Between Rotors on a Performance of a Small Counter-Rotating Wind Turbine
PublikacjaIn this paper, results of the investigation on the performance of a small counter-rotating wind turbinehas been presented. Computational Fluid Dynamics methodshave been used forwind turbine simulations. Rotors representation were introduced into computational domain by means of Actuator Line Model. Influence of an axial distance of CRWTrotorshas been investigated. In all studied configurations rotors were counter-rotating...
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Study on population dynamics for triple-linked food chain using a simulation-based approach
PublikacjaThe procedures based on simulation have become a feasible testing method that does not require investing valuable resources to create a concrete prototype, especially with the increasing computational power of computers. Thus, design changes can be adopted and design errors can be fixed before it is too late. Simulation turns to be a cheap, safe and often more acceptable from an ethical perspective. In our work we summarize the...