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Search results for: MOLECULAR MECHANICS
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Molecular dynamics simulations of the growth of poly (chloro-para-xylylene) films.
PublicationParylene C, poly(chloro-para-xylylene) is the most widely used member of the parylene family due to its excellent chemical and physical properties. In this work we analyzed the formation of the parylene C film using molecular mechanics and molecular dynamics methods. A five unit chain is necessary to create a stable hydrophobic cluster and to adhere to a covered surface. Two scenarios were deemed to take place. The obtained results...
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Evaluating experimental molecular physics studies of radiation damage in DNA*
PublicationThe field of Atomic and Molecular Physics (AMP) is a mature field exploring the spectroscopy, excitation, ionisation of atoms and molecules in all three phases. Understanding of the spectroscopy and collisional dynamics of AMP has been fundamental to the development and application of quantum mechanics and is applied across a broad range of disparate disciplines including atmospheric sciences, astrochemistry, combustion and environmental...
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Geometry optimization of steroid sulfatase inhibitors - the influence on the free binding energy with STS
PublicationIn the paper we review the application of two techniques (molecular mechanics and quantum mechanics) to study the influence of geometry optimization of the steroid sulfatase inhibitors on the values of descriptors coded their chemical structure and their free binding energy with the STS protein. We selected 22 STS-inhibitors and compared their structures optimized with MM+, PM7 and DFT B3LYP/6–31++G* approaches considering separately...
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Computational methods for calculation of binding free energy for ligand-receptor complexes
PublicationAccurate description of the molecular complexes energetic influence is required for understanding of many biological functions carried out by proteins. Therefore, estimation of binding free energy for ligand-receptor complexes is of highest importance for structure-based ligand design and drug discovery approaches.Experimental methods of determination of difference in Gibbs'es free energy have many limitations. Thus, computational...
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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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Mechanism of reaction of RNA-dependent RNA polymerase from SARS-CoV-2
PublicationWe combine molecular dynamics, statistical mechanics, and hybrid quantum mechanics/molecular mechanics simulations to describe mechanistically the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA-dependent RNA polymerase (RdRp). Our study analyzes the binding mode of both natural triphosphate substrates as well as remdesivir triphosphate (the active form of drug), which is bound preferentially over ATP by RdRp while...
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Principles of target DNA cleavage and the role of Mg2+ in the catalysis of CRISPR–Cas9
PublicationAt the core of the CRISPR–Cas9 genome-editing technology, the endonuclease Cas9 introduces site-specific breaks in DNA. However, precise mechanistic information to ameliorate Cas9 function is still missing. Here, multimicrosecond molecular dynamics, free energy and multiscale simulations are combined with solution NMR and DNA cleavage experiments to resolve the catalytic mechanism of target DNA cleavage. We show that the conformation...
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Mechanics of Micro- and Nano-Size Materials and Structures
PublicationNanotechnology knowledge is always looking to expand its boundaries to achieve the mostsignificant benefit to human life and meet the growing needs of today. In this case, we can refer tomicro- and nanosensors in micro/nano-electromechanical systems (MEMS/NEMS). These electricaldevices can detect minimal physical stimuli up to one nanometer in size. Today, micro/nano-sensordevices are widely used in the...
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Negative Poisson’s ratio from pentagons: A new auxetic structure combining three different auxetic mechanisms
PublicationA novel class of two-dimensional auxetic structures based on the pentagon motif is proposed. Their mechanical properties are investigated by combining molecular mechanics simulations with a simple three-parameter mechanical model which assumes perfectly elastic behavior. It is predicted that the proposed structures – termed as double re-entrant honeycomb – may possess unique mechanical characteristics, which include complete and...
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Performance of the AMOEBA Water Model in the Vicinity of QM Solutes: A Diagnosis Using Energy Decomposition Analysis
PublicationThe importance of incorporating solvent polarization effects into the modeling of solvation processes has been well-recognized, and therefore a new generation of hybrid quantum mechanics/molecular mechanics (QM/MM) approaches that accounts for this effect is desirable. We present a fully self-consistent, mutually polarizable QM/MM scheme using the AMOEBA force field, in which the total energy of the system is variationally minimized...
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Temperature-dependent structure-property modeling of viscosity for ionic liquids
PublicationIn this paper we present the methodology for assessing the ionic liquids' viscosity at six temperature points (25, 35, 45, 50, 60 and 70 [C]), which utilizes only the in silico approach. The main idea of such assessment is based on the "correction equation" describing the correlation between experimentally measured viscosity and theoretically derived density (calculated with use of molecular mechanics), given at 6 different temperature...
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TINKTEP: A fully self-consistent, mutually polarizable QM/MM approach based on the AMOEBA force field
PublicationWe present a novel quantum mechanical/molecular mechanics (QM/MM) approach in which a quantum subsystem is coupled to a classical subsystem described by the AMOEBA polarizable force field. Our approach permits mutual polarization between the QM and MM subsystems, effected through multipolar electrostatics. Self-consistency is achieved for both the QM and MM subsystems through a total energy minimization scheme. We provide an expression...
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Continuum contact model for friction between graphene sheets that accounts for surface anisotropy and curvature
PublicationUnderstanding the interaction mechanics between graphene layers and co-axial carbon nanotubes (CNTs) is essential for modeling graphene and CNT-based nanoelectromechanical systems. This work proposes a new continuum contact model to study interlayer interactions between curved graphene sheets. The continuum model is calibrated and validated using molecular dynamics (MD) simulations. These are carried out employing the reactive...
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Density functional theory calculations on entire proteins for free energies of binding: Application to a model polar binding site
PublicationIn drug optimization calculations, the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method can be used to compute free energies of binding of ligands to proteins. The method involves the evaluation of the energy of configurations in an implicit solvent model. One source of errors is the force field used, which can potentially lead to large errors due to the restrictions in accuracy imposed by its empirical nature....
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Nonlocal Models of Plates and Shells with Applications in Micro- and Nanomechanics
PublicationNowadays, the use of small-scale structures in micro/nanomachines has become more and more widespread. The most important applications of such small-sized parts are in micro-electro-mechanical systems (MEMS) as well as nano-electro-mechanical systems (NEMS) as actuators, sensors, energy harvesters. For example, nanosensors are nanoscale devices that measure physical quantities and convert these to signals that can be detected and...
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Mutually polarizable QM/MM model with in situ optimized localized basis functions
PublicationWe extend our recently developed quantum-mechanical/molecular mechanics (QM/MM) approach [Dziedzic et al., J. Chem. Phys. 145, 124106 (2016)] to enable in situ optimization of the localized orbitals. The quantum subsystem is described with ONETEP linear-scaling density functional theory and the classical subsystem – with the AMOEBA polarizable force field. The two subsystems interact via multipolar electrostatics and are fully...
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From fluid mechanics backgrounds to modern field theory
PublicationOur presentation keeps a historical line of reasoning, since we start from old concepts of fluid mechanics and finish on concepts of modern field theory. We want to show that some facts from the nature phenomena, which have firstly been discovered on the ground of fluid mechanics, were next incorporated into physics and later become the important pattern for whole mathematical physics. Especially, well-known continuum models, which...
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Analytical predictions for the buckling of a nanoplate subjected to non-uniform compression based on the four-variable plate theory
PublicationIn the present study, the buckling analysis of the rectangular nanoplate under biaxial non-uniform compression using the modified couple stress continuum theory with various boundary conditions has been considered. The simplified first order shear deformation theory (S-FSDT) has been employed and the governing differential equations have been obtained using the Hamilton’s principle. An analytical approach has been applied to obtain...
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Quantum origins of objectivity
PublicationIn spite of all of its successes, quantum mechanics leaves us with a central problem: How does nature create a bridge from fragile quanta to the objective world of everyday experience? Here we find that a basic structure within quantum mechanics that leads to the perceived objectivity is a so-called spectrum broadcast structure. We uncover this based on minimal assumptions, without referring to any dynamical details or a concrete...
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Performance of isotropic constitutive laws in simulating failure mechanisms in scaled RC beams
PublicationResults of numerical calculations of reinforced concrete (RC) beams are presented. Based on experimental results on longitudinally reinforced specimens of different sizes and shapes are investigated. Four different continuum constitutive laws with isotropic softening are used: one defined within continuum damage mechanics, an elasto-plastic with the Rankine criterion in tension and the Drucker-Prager criterion in compression, a...
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On Invariants of Fluid Mechanics Tensors
PublicationThis paper presents physical interpretations of the first and second invariants of tensors of fluid mechanics. Some examples of elementary applications and meanings are also given.
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New approaches to cutting resistance estimation of wood cutting process with circular-saw blades
PublicationTheoretical and experimental determination of values of cutting resistance belongs to the basic and simultaneously the most developed field of mechanics of this process. Energetic effects of wood sawing process are mainly calculated on the basis of the specific cutting resistance which, in wood cutting, is a function on a lot of factors. In this paper new method for calculation of cutting resistance is described. The latter method...
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Designing effective educational games - a case study of a project management game
PublicationThis paper addresses the issues of designing effective educational games. We aim at investigating how the cognitive, behavioral and emotional aspects of the games influence their educational effectiveness. The results were obtained with an observational user experience study extended with affect analysis carried out for a project management game GraPM. We analyzed the...
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Report of Eurocode 7 application for pile foundation design in Poland
PublicationThe EC7 rules of geotechnical design are in use in Poland for several years, even though there is no National annex. With regard to pile foundations, there are valid EC7 recommendations concerning design approaches, load partial coefficients, correlation coefficients and capacity partial coefficients. Polish designers can be quite flexible when it comes to choose a method for static, bearing capacity and settlement calculations....
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Multidimensional Monitoring System of State Machines
PublicationTechnical systems are more complex every day as their electronics and mechanics. Technical advances tend to be autonomous in its performance and perform an auto-diagnosis that allows determining an abnormality existence in a component or subsystem and deciding if the system has to be stopped or not.
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CUTTING POWER FORECASTING WHILE WOOD SAWING: FRACTURE MECHANICS APPROACH AND AXELSSON’S MODEL COMPARISON
PublicationIn the classical approach, energetic effects (cutting forces and cutting power) of wood sawing process are generally calculated on the basis of the specific cutting resistance, which is in the case of wood cutting the function of more or less important factors. On the other hand, cutting forces (power) could be considered from a point of view of modern fracture mechanics. Another way is to forecast cutting power consumption on...
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A new open-source software developed for numerical simulations usingdiscrete modeling methods
PublicationThe purpose of this work is to present the development of an open-source software based on a discrete description of matter applied to study the behavior of geomaterials. This software uses Object Oriented Programming techniques, and its methodology design uses three different methods, which are the Discrete Element Method (DEM) [F. Donzé, S.A. Magnier, Formulation of a three-dimensional numerical model of brittle behavior, Geophys....
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Framework for gamification of specialized subjects within engineering studies
PublicationGamification is a relatively new term forged along with the occurrence of new information technology, especially easy access to internet and smartphones. Gamification is a use of game mechanics, to modify the behavior of people in non-games situations to increase the involvement of individuals. The method is based on the pleasure that comes from overcoming the obstacles to reach next achievable level, which consists of challenges,...
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Numerical Simulation of two dimensional flow past a bridge cross section
PublicationThis work presents some numerical results concerning application of CFD in civil engineering problems. Selected theoretical aspects of fluid mechanics are elucidated. In the second part of the paper a cross section of upper footbridge of the Bella Sky Hotel in Copenhagen is analysed numerically in the field of wind action.
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Extended micropolar approach within the framework of 3M theories and variations thereof
PublicationAs part of his groundbreaking work on generalized continuum mechanics, Eringen proposed what he called 3M theories, namely the concept of micromorphic, microstretch, and micropolar materials modeling. The micromorphic approach provides the most general framework for a continuum with translational and (internal) rotational degrees of freedom (DOF), whilst the rotational DOFs of micromorphic and micropolar continua are subjected...
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Fundamentals of classical and analytical mechanics
PublicationThe book is a monographic description of the present attempt to Newtonian and Lagrangian mechanics. But also, it could be found as a supplementary educational material useful for the graduate courses in mechanics taken by students majoring in mechanical engineering, physics or physical science. In the book you can find a brief introduction to concepts and principles of algebra of vectors; Kinematics of particles, mainly focused...
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Charge dependence of fragmentation process induced by ion collisions with furan molecule
PublicationThe goal of this work is to describe the system evolution after ion-molecule interaction. We combine different quantum chemistry and statistical mechanics approaches in order to give extended description of the process. Herein we report on a recent study of the fragmentation mechanism of neutral, singly- and doubly-ionized furan molecule in the gas phase.
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On the material symmetry group for micromorphic media with applications to granular materials
PublicationWithin the framework of the theory of nonlinear elastic micromorphic continua we introduce the new definition of the local material symmetry group. The group consists of ordered triples of second- and third-order tensors describing such changes of a reference placement that cannot be recognized with any experiment. Using the definition we characterize the micromorphic isotropic media, micromorphic fluids, solids and special intermediate...
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THE METHODS OF TEACHING / LEARNING STRUCTURAL MECHANICS
PublicationStructural mechanics is a key issue to study for engineers. A high rank and high social responsibility profession requires both a high graded and intuitive approach. The evolution of learning / teaching methodology follows the novel technical achievements of every decade. The aim remains the same: to produce a professional to perform advanced relevant analysis and safe, optimal structural design
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BJS-03 DO WE NEED FIXATION OF THE MESH IN LAPAROENDOSCOPIC TECHNIQUES FOR M3 INGUINAL DEFECTS? AN EXPERIMENTAL STUDY
PublicationThe authors conducted a research experiment to verify the hypothesis that it is possible to preserve the mesh in the operating field in large direct hernias (M3) without the need to use fixing materials. The results showed that mesh fixation is not the only alternative to preventing recurrence in complex defects and that the type of implant seems to be a key factor from the point of view of mechanics and biophysics.
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Duhem and Natanson: Two Mathematical Approaches to Thermodynamics
PublicationIn this article, the previously unrecognized contributions of Pierre Duhem and Ladislavus Natanson in thermodynamics are shown. The mathematical remodelling of a few of their principal ideas is taken into consideration, despite being neglected in the literature. To emphasize these ideas in an appropriate epistemological order, it would be crucial to first revalue and reconstruct some underrepresented parts of the proceedings process...
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SAWING PROCESS AS A NEW ALTERNATIVE WAY OF DETERMINING SOME WOOD PROPERTIES
PublicationCutting forces (power) could be considered from a point of view of modern fracture mechanics. The developed cutting model, derived from fracture mechanics, includes work of separation (fracture toughness) in addition to plasticity and friction, and also dullness of the cutting edge described by the cutting edge radius. Moreover, forecasting of the shear plane angle for the cutting models, broaden possibilities of energetic effects...
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Minimal surfaces and conservation laws for bidimensional structures
PublicationWe discuss conservation laws for thin structures which could be modeled as a material minimal surface, i.e., a surface with zero mean curvatures. The models of an elastic membrane and micropolar (six-parameter) shell undergoing finite deformations are considered. We show that for a minimal surface, it is possible to formulate a conservation law similar to three-dimensional non-linear elasticity. It brings us a path-independent...
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A New Quaternion Encryption Scheme for Image Transmission
PublicationQuaternions are hypercomplex number of rank 4. They are often applied to mechanics in three-dimensional space and considered as one of the best ways to represent rotations. In this paper a new encryption scheme, based on the rotation of data vector in three-dimensional space around another quaternion (key) is proposed. A computer-based simulation was created to analyze the potential of the proposed encryption technique.
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Report for the Short Term Scientific Mission within COST Action FP1101: development of the in-field sensor for estimation of fracture toughness and shear strength by measuring cutting forces
PublicationKnowledge on the fracture properties of materials is essential to assure structural integrity and proper design of mechanical connections in timber constructions. Measurement of this property is, however, a very challenging task. The linear fracture mechanics is usually used for its assessment assisted with experimental data acquired by means of various techniques, usually of destructive nature. The cutting force is an energetic...
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An innovative approach to the forecasting of energetic effects while wood sawing
PublicationIn the classical approach, energetic effects (cutting forces and cutting power) of wood sawing process are generally calculated on the basis of the specific cutting resistance, which is in the case of wood cutting the function of more or less important factors. On the other hand, the cutting forces (power) problem may be tackled with an innovative, up-to-date fundamental analysis of the mechanics of sawing based on modern fracture...
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An Innovative Approach to the Forecasting of Energetic Effects While Wood Sawing
PublicationIn the classical approach, energetic effects (cutting forces and cutting power) of wood sawing process are generally calculated on the basis of the specifi c cutting resistance, which is in the case of wood cutting the function of more or less important factors. On the other hand, the cutting forces (power) problem may be tackled with an innovative, up-to-date fundamental analysis of the mechanics of sawing based on modern fracture mechanics....
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A compartment model of alveolar–capillary oxygen diffusion with ventilation–perfusion gradient and dynamics of air transport through the respiratory tract
PublicationThis paper presents a model of alveolar–capillary oxygen diffusion with dynamics of air transport through the respiratory tract. For this purpose electrical model representing the respiratory tract mechanics and differentia equations representing oxygen membrane diffusion are combined. Relevant thermodynamic relations describing the mass of oxygen transported into the human body are proposed as the connection between these models,...
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Professor Jan Kruszewski-Majewski (1929-2012)
PublicationIn this obituary, we present the life and achievements of an outstanding Polish scientist, Professor Jan Kruszewski-Majewski, who passed away in 2012. Professor Jan Kruszewski-Majewski was one of the pioneers in introducing modern numerical methods in mechanics. He created and developed an original, Polish method of modellings called the rigid finite element method. He was ont only an outstanding scientist, but also a person of...
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Quaternion Encryption Method for Image and Video Transmission
PublicationQuaternions are hyper-complex numbers of rank 4. They are often applied to mechanics in 3D space and are considered to be one of the best ways of representing rotations. In this paper a quaternion encryption method, based on algorithm by Nagase et al. (2004) has been proposed. According to a computer-based simulation the results of the performed research yield a high level of security, which is additionally strengthened by the...
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On the exact equilibrium conditions of irregular shells reinforced by beams along the junctions
PublicationThe exact, resultant equilibrium conditions for irregular shells reinforced by beams along the junctions are formulated. The equilibrium conditions are derived by performing direct integration of the global equilibrium conditions of continuum mechanics. New, exact resultant static continuity conditions along the singular curve modelling reinforced junction are presented. The results do not depend on shell thickness, internal through-the-thickness...
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Optymalne ciśnienie kondensacji w odwróconym obiegu Braytona
PublicationMotywacją do podjęcia niniejszej pracy jest potrzeba rozwijania obiegów termodynamicznych charakteryzujących się niskoemisyjnością, takich jak podwójny obieg Braytona z zastosowaniem oksyspalania. Celem przeprowadzonej analizy termodynamicznej było znalezienie optymalnego ciśnienia kondensacji w odwróconym obiegu Braytona. W artykule przybliżono również zagadnienie kondensacji oraz przedstawiono wyniki obliczeń numerycznych wykonanych...
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On coertia and inertia in aspects of Natanson’s nonlinear extended thermodynamics
PublicationIn this article, the previously underrepresented contributions of Natanson to the field of thermodynamics have been presented. In order to identify a source of irreversibility at Nature, Natanson introduced the concept of Coertia, which is similar to inertia. Natanson’s Coertia is a fundamental property of space that is responsible for every irreversible phenomena in matter, as well as in the electromagnetic and gravitational fields....
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Arch bridges under test loadings
PublicationThis paper illustrates experience in arch bridges test loadings of the research team of Department of Structural Mechanics and Bridge Structures from the Gdansk University of Technology. The presented calculations results constist the analysis of spatial construction schemes made using the finite elements method (FEM) and its comparison to the field studies. Arch bridges with the longest spans, visualisation of the computational...
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Test loading of the longest span arch bridge in Poland
PublicationBridge structures undergo thorough examination during test loading before they come into use. The aim of the examination is to check the correctness of the working structure and construction design assumptions. Test loading on the bridge is preceded by examination specification. This paper describes computational model and test loading results carried out during examibation of the bridge over the Vistula within the bypass of Puławy...