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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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Modeling Dynamics of Autonomous Underwater Vehicle.
PublicationArtykuł dotyczy budowy modelu autonomicznego pojazdu podwodnego do celów syntezy układu sterowania pojazdem. Rozważany pojazd ma długośc ok. 1 m i 30 cm średnicy. Wyposażony jest w 5 pędników, które pozwalają na sterowanie w pięciu stopniach swobody. Do badań wykorzystano model o 4 stopniach swobody. Dokonano identyfikacji parametrycznej modelu. Model zrealizowano w środowisku programowym Matlab/Simulink.
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The Product of Matrix Metalloproteinase Cleavage of Doxorubicin Conjugate for Anticancer Drug Delivery: Calorimetric, Spectroscopic, and Molecular Dynamics Studies on Peptide–Doxorubicin Binding to DNA
PublicationMatrix metalloproteinases (MMPs) are extracellular matrix degradation factors, promoting cancer progression. Hence, they could provide an enzyme-assisted delivery of doxorubicin (DOX) in cancer treatment. In the current study, the intercalation process of DOX and tetrapeptide-DOX, the product of the MMPs' cleavage of carrier-linked DOX, into dsDNA was investigated using stationary and time-resolved fluorescence spectroscopy, UV-Vis...
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Open Data Capability Architecture - An Interpretive Structural Modeling Approach
PublicationDespite of increasing availability of open data as a vital organizational resource, large numbers of startups and organizations fail when it comes to utilizing open data effectively. This shortcoming is attributable to the poor understanding of what types of capabilities are required to successfully conduct data related activities. At the same time, research on open data capabilities and how they relate to one another remains sparse....
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Processing of point cloud data retrieved from terrestrial laser scanning for structural modeling by Finite Element Method
PublicationFinite Element Method is one most popular contemporary method of strength analysis. The method is an advanced method for solving differential equations, based on discretization, which means that area is divided into finite elements. Each finite element has a solution of the equation approximated by specific functions and performing the actual calculations only for nodes of this division. Finite Element Method is widely used in...
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Au–Si plasmonic platforms: synthesis, structure and FDTD simulations
PublicationPlasmonic platforms based on Au nanostructures have been successfully synthesized by directional solidification of a eutectic from Au and the substrate. In order to determine homogeneous shape and space distribution, the influence of annealing conditions and the initial thickness of the Au film on the nanostructures was analyzed. For the surface morphology studies, SEM and AFM measurements were performed. The structure of platforms...
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Combining tight-binding and molecular dynamics methods to model the behaviour of metals in the plastic regime
PublicationOpisujemy zastosowanie metody dwuskalowej (kwantowo-klasycznej) w zastosowaniu do metali. Region energetycznie najważniejszy jest traktowany kwantowo, podczas gdy reszta układu jest traktowana klasycznie. Wprowadzamy własną implementację metody oraz przedstawiamy uzyskane wyniki dla metali.
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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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Comparative molecular modelling of biologically active sterols
PublicationMembrane sterols are targets for a clinically important antifungal agent – amphotericin B. The relatively specific antifungal action of the drug is based on a stronger interaction of amphotericin B with fungal ergosterol than with mammalian cholesterol. Conformational space occupied by six sterols has been defined using the molecular dynamics method to establish if the conformational features correspond to the preferential interaction...
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A Data Driven Model for Predicting RNA-Protein Interactions based on Gradient Boosting Machine
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Molecular Dynamics Study of the Internal Water Molecules in Vasopressin and Oxytocin Receptors
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A simplified behavioral MOSFET model based on parameters extraction for circuit simulations.
PublicationThe paper presents results on behavior modeling of general purpose Metal-Oxide Semiconductor Field-Effect Transistor (MOSFET) for simulation of power electronics systems requiring accuracy both in steady-state and in switching conditions. Methods of parameters extraction including nonlinearity of parasitic capacitances and steady-state characteristics are based on manufacturer data sheet and externally measurable characteristics....
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A NUMERICAL STUDY ON THE DYNAMICS OF DENGUE DISEASE MODEL WITH FRACTIONAL PIECEWISE DERIVATIVE
PublicationThe aim of this paper is to study the dynamics of Dengue disease model using a novel piecewise derivative approach in the sense of singular and non-singular kernels. The singular kernel operator is in the sense of Caputo, whereas the non-singular kernel operator is the Atangana–Baleanu Caputo operator. The existence and uniqueness of a solution with piecewise derivative are examined for the aforementioned problem. The suggested...
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Molecular dynamics study of the influence of calcium ions on the conformation of gelsolin S2 domain
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Intramolecular transformation of an antifungal antibiotic nystatin A1 into its isomer, iso-nystatin A1 - structural and molecular modeling studies
PublicationNystatin A1, a polyene macrolide antifungal antibiotic, in a slightly basic or acidic solution undergoes an intramolecular transformation, yielding a structural isomer, the translactonization product, iso-nystatin A1 with lactone ring diminished by two carbon atoms. Structural evidence is provided by advanced NMR and Mass Spectrometry (MS) studies. Molecular dynamics simulations and quantum mechanics calculations gave the insight...
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Simulations of air and water flow in a model dike during overflow experiments
PublicationFlow in flood dikes, earth dams, and embankments occurs in variably saturated conditions, with pores of the earth material filled partly with water and partly with air. In routine engineering analysis, the influence of pore air is neglected and the air pressure is assumed equal to atmospheric. In some circumstances, for example, during overtopping of the dike by water, the effect of pore air on water flow and stability of the structure...
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Nilpotent singularities and chaos: Tritrophic food chains
PublicationLocal bifurcation theory is used to prove the existence of chaotic dynamics in two well-known models of tritrophic food chains. To the best of our knowledge, the simplest technique to guarantee the emergence of strange attractors in a given family of vector fields consists of finding a 3-dimensional nilpotent singularity of codimension 3 and verifying some generic algebraic conditions. We provide the essential background regarding...
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Understanding the interactions between protein stabilizers and the peptide bond through the analysis of the volumetric and compressibility properties for the model systems
PublicationThis work confirms our earlier supposition, that volumetric and acoustic parameters for simple model proposed by us are directly related to stabilizing/destabilizing effect of osmolytes on proteins structure. The apparent molar volumes, V and the apparent molar isentropic compressions, KS,, of glycine and N,N,N –trimethylglycine (betaine) were determined from densities and speed of sound measurements in aqueous solution of N-methylacetamide...
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A concept of heterogeneous numerical model of concrete for GPR simulations
PublicationThe Ground Penetrating Radar (GPR) method, which is increasingly being used in the non-destructive diagnostics of reinforced concrete structures, often needs more accurate interpretation tools for analysis of experimental data. Recently, there has been growing interest in developing of various numerical models for exhaustive understanding of GPR data. This paper presents the concept of a heterogeneous numerical model of concrete,...
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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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A Multi-Fidelity Surrogate-Model-Assisted Evolutionary Algorithm for Computationally Expensive Optimization Problems
PublicationIntegrating data-driven surrogate models and simulation models of different accuracies (or fideli-ties) in a single algorithm to address computationally expensive global optimization problems has recently attracted considerable attention. However, handling discrepancies between simulation models with multiple fidelities in global optimization is a major challenge. To address it, the two major contributions of this paper include:...
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Enhanced susceptibility of SARS-CoV-2 spike RBD protein assay targeted by cellular receptors ACE2 and CD147: Multivariate data analysis of multisine impedimetric response
PublicationSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) enters the cells through the binding of spike protein to the host cell surface-expressing angiotensin-converting enzyme 2 (ACE2) or by endocytosis mediated by extracellular matrix metalloproteinase inducer (CD147). We present extended statistical studies of the multisine dynamic electrochemical impedance spectroscopy (DEIS) revealing interactions between Spike RBD and...
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Effect of Nanohydroxyapatite on Silk Fibroin–Chitosan Interactions—Molecular Dynamics Study
PublicationFibroin–chitosan composites, especially those containing nanohydroxyapatite, show potential for bone tissue regeneration. The physicochemical properties of these biocomposites depend on the compatibility between their components. In this study, the intermolecular interactions of fibroin and chitosan were analyzed using a molecular dynamics approach. Two types of systems were investigated: one containing acetic acid and the other...
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Mathematical Modeling of Ice Dynamics as a Decision Support Tool in River Engineering
PublicationThe prediction of winter flooding is a complicated task since it is affected by many meteorological and hydraulic factors. Typically, information on river ice conditions is based on historical observations, which are usually incomplete. Recently, data have been supplemented by information extracted from satellite images. All the above mentioned factors provide a good background of the characteristics of ice processes, but are not...
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Evaluation of the scale-consistent UNRES force field in template-free prediction of protein structures in the CASP13 experiment
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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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Mechanism of Binding of Antifungal Antibiotic Amphotericin B to Lipid Membranes: An Insight from Combined Single-Membrane Imaging, Microspectroscopy, and Molecular Dynamics
PublicationAmphotericin B is a lifesaving polyene antibiotic used in the treatment of systemic mycoses. Unfortunately, the pharmacological applicability of this drug is limited because of its severe toxic side effects. At the same time, the lack of a well-defined mechanism of selectivity hampers the efforts to rationally design safer derivatives. As the drug primarily targets the biomembranes of both fungi and humans, new insights into the...
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Keep It Flexible: Driving Macromolecular Rotary Motions in Atomistic Simulations with GROMACS
PublicationWe describe a versatile method to enforce the rotation of subsets of atoms, e.g., a protein subunit, in molecular dynamics (MD) simulations. In particular, we introduce a “flexible axis” technique that allows realistic flexible adaptions of both the rotary subunit as well as the local rotation axis during the simulation. A variety of useful rotation potentials were implemented for the GROMACS 4.5 MD package. Application to the...
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Molecular Dynamics Studies on Amyloidogenic Proteins
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Molecular Dynamics Studies on Amyloidogenic Proteins
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Low-Cost Data-Driven Surrogate Modeling of Antenna Structures by Constrained Sampling
PublicationFull-wave electromagnetic (EM) analysis has become one of the major design tools for contemporary antenna structures. Although reliable, it is computationally expensive which makes automated simulation-driven antenna design (e.g., parametric optimization) difficult. This difficulty can be alleviated by utilization of fast and accurate replacement models (surrogates). Unfortunately, conventional data-driven modeling of antennas...
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Effect of osmolytes on the thermal stability of proteins: replica exchange simulations of Trp-cage in urea and betaine solutions
PublicationAlthough osmolytes are known to modulate the folding equilibrium, the molecular mechanism of their effect on thermal denaturation of proteins is still poorly understood. Here, we simulated the thermal denaturation of a small model protein (Trp-cage) in the presence of denaturing (urea) and stabilizing (betaine) osmolytes, using the all-atom replica exchange molecular dynamics simulations. We found that urea destabilizes Trp-cage...
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Instrument detection and pose estimation with rigid part mixtures model in video-assisted surgeries
PublicationLocalizing instrument parts in video-assisted surgeries is an attractive and open computer vision problem. A working algorithm would immediately find applications in computer-aided interventions in the operating theater. Knowing the location of tool parts could help virtually augment visual faculty of surgeons, assess skills of novice surgeons, and increase autonomy of surgical robots. A surgical tool varies in appearance due to...
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Applying molecular dynamics simulation to take the fracture fingerprint of polycrystalline SiC nanosheets
PublicationGraphene-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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Asymptotic behaviour in the set of nonhomogeneous chains of stochastic operators
PublicationWe study different types of asymptotic behaviour in the set of (infinite dimensional) nonhomogeneous chains of stochastic operators acting on L1(μ) spaces. In order to examine its structure we consider different norm and strong operator topologies. To describe the nature of the set of nonhomogeneous chains of Markov operators with a particular limit behaviour we use the category theorem of Baire. We show that the geometric structure...
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Nuclear Power Plant Steam Turbine - Modeling for Model Based Control Purposes
PublicationThe nature of the processes taking place in a nuclear power plant (NPP) steam turbine is the reason why their modeling is very difficult, especially when the model is intended to be used for on-line optimal model based process control over a wide range of operating conditions, caused by changing electrical power demand e.g. when combined heat and power mode of work is utilized. The paper presents three nonlinear models of NPP steam...
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Influence of a lipid bilayer on the conformational behavior of amphotericin B derivatives - A molecular dynamics study.
PublicationAmphotericin B (AmB) is an effective but very toxic antifungal antibiotic. In our laboratory a series of AmB derivatives of improved selectivity of action was synthesized and tested. To understand molecular basis of this improvement, comparative conformational studies of amphotericin B and its two more selectivederivatives were carried out in an aqueous solution and in a lipid membrane. These molecular simulation studies revealed...
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Numerical simulations of overflow experiments on a model dike
PublicationDike failure due to overtopping is one of the important factors, which should be considered in the dike designing process. Although the overflow is characterized by the relatively low risk of occurrence, in many cases dikes are totally destroyed or seriously damaged. An interesting phenomenon occurring during overflow is the trapping of air in pores of the unsaturated soil material. As the infiltration progresses from all sides,...
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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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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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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...