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Search results for: MOLECULAR DYNAMICS METHOD
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Katarzyna Merkel dr hab.
PeopleOver the past 15 years, my work has mainly been related to the study of liquid crystal compounds with a diverse structure (discotic, dendrimeric, banana, bimedogenic, uniaxial and biaxial nematics and smectics) as well as polymeric materials (biopolymers, nano-composites) and biological materials. My work concerned mainly the issues of organization, observation of orientation effects, studying the dynamics of molecular processes...
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Coarse-grained simulation - an efficient approach for studying motions of large proteins
PublicationOne of the most important challenges in performing Molecular Dynamics (MD) simulations of large protein complexes is to accommodate the model accuracy and the simulation timescale. Hitherto, for the most relevant dynamics of protein aggregates in an explicit aqueous environment, the timescale reachable for the all-atoms simulations is of hundreds of nanoseconds. This range is four to six orders of magnitude smaller than processes...
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Study of Icosahedral Clusters in Close-packed Simple Liquids
PublicationThe local structure of liquid copper was determined using Steinhardt order parameters, with particular attention paid to icosahedral clusters. The positions of atoms were obtained from three sets of molecular dynamics simulations, with the forces obtained from: the Sutton-Chen (SC) potential, the Naval Research Laboratory total energy tight-binding (NRL-TB) method and the divide-and-conquer learn-on-the-fly (DCLOTF) method, respectively....
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A coarse‐grained approach to NMR ‐data‐assisted modeling of protein structures
PublicationThe ESCASA algorithm for analytical estimation of proton positions from coarse-grained geometry developed in our recent work has been implemented in modeling protein structures with the highly coarse-grained UNRES model of polypeptide chains (two sites per residue) and nuclear magnetic resonance (NMR) data. A penalty function with the shape of intersecting gorges was applied to treat ambiguous distance restraints, which automatically...
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In-depth characterization of icosahedral ordering in liquid copper
PublicationThe 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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Water Behavior Near the Lipid Bilayer
PublicationIn this chapter, we focus on the dynamics of water molecules situated in the vicinity of a phospholipid bilayer. Using a molecular dynamics simulation method, we studied interactions between water and the bilayer and tracked trajectories of the water molecules. Based on the hypothesis that molecules trapped inside the bilayer make different motions than the ones which are either attached to the surface or move freely in the water...
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Kazi Amirul Hossain
PeopleI am a PhD graduate from Gdańsk University of Technology and currently a postdoctoral researcher at IRB Barcelona (Prof. Modesto Orozco lab). My academic focus is on computational biophysics, particularly Molecular Dynamics (MD) and statistical mechanics. I also have expertise in molecular modeling techniques like Molecular Docking, Homology Modeling, and QSAR. I hold an M.S. (Pharm) from NIPER, Kolkata, where I was awarded the...
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Paweł Możejko dr hab.
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Entropy of water calculated from harmonic approximation: estimation of the accuracy of method
PublicationSome molecular dynamics simulations were performed for liquid TIP4P and SPC water at a constant density (1.00 g/cm(3)) and within the temperature range of 5-90 degrees C. By using harmonic approximation, both the entropy of water S-H and the specific heat c(v) were calculated, and the results were compared to literature data. It was found that harmonic approximation overestimates absolute entropy of TIP4P water by 5.6 J/mol K (similar...
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Non-ergodic fragmentation upon collision-induced activation of cysteine–water cluster cations
PublicationCysteine–water cluster cations Cys(H2O)3,6 + and Cys(H2O)3,6H+ are assembled in He droplets and probed by tandem mass spectrometry with collision-induced activation. Benchmark experimental data for this biologically important system are complemented with theory to elucidate the details of the collisioninduced activation process. Experimental energy thresholds for successive release of water are compared to water dissociation energies...
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A novel hierarchically-porous diamondized polyacrylonitrile sponge-like electrodes for acetaminophen electrochemical detection
PublicationA novel composite electrode material consisting of tangled fibrous polyacrylonitrile-based hierarchically-struc- tured nanocomposites has been produced by wet-spinning, carbonized and decorated with a carbon nano- architecture by microwave plasma-enhanced chemical vapor deposition and investigated as a metal-free electrode for the enhanced electrochemical detection of acetaminophen. Surprisingly, the hierarchical fiber ar- chitecture...
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Why is TASK Quarterly a Significant Journal to Publish Your Article? —A Bibliometric Analysis of a Scientific and Technical Journal
PublicationA bibliometric analysis of TASK Quarterly in the years 1997-2021 in terms of various bibliometric indicators was performed to celebrate the 25th anniversary of the publication of the first issue of the journal. The number of publications and citations increased over the mentioned span of years. The leading countries in terms of the greatest number of papers published in TASK Quarterly are Poland, Italy, Germany, Ukraine, USA and...
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Refined theoretical study of radiative association: Cross sections and rate constants for the formation of SiN
PublicationRadiative association of silicon mononitride (SiN) in its two lowest molecular electronic states is studied through quantum and classical dynamics. Special attention is paid to the behavior of the cross section at high collision energies. A modified expression for the semiclassical cross section is presented which excludes transitions to continuum states. This gives improved agreement with quantum mechanical perturbation theory...
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Kamil Andrzej Rybacki mgr inż.
PeopleBorn on 23 October 1993 in Gdańsk. In 2017, I have received the M.Sc. Degree at the Faculty of Applied Physics and Mathematics, Gdańsk University of Technology, Poland. My main fields of interest include computer simulations of molecular systems, parallel computing in application to computational physics methods and development of various simulation software. Currently, my research is focused on the development of hybrid Molecular...
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Hybrid quantum-classical approach for atomistic simulation of metallic systems
PublicationThe learn-on-the-fly (LOTF) method [G. Csanyi et al., Phys. Rev. Lett. 93, 175503 (2004)] serves to seamlessly embed quantum-mechanical computations within a molecular-dynamics framework by continual local retuning of the potential's parameters so that it reproduces the quantum-mechanical forces. In its current formulation, it is suitable for systems where the interaction is short-ranged, such as covalently bonded semiconductors....
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Theoretical studies of fragmentation processes of neutral and ionized furan molecule
PublicationThis PhD thesis focuses on the fragmentation mechanism of the furan molecule in the gas phase. The approach taken in this work comprised of three theoretical methodologies considering the dynamical, energetical and entropic aspects of the studied process. First, molecular dynamics simulations were performed. Next, the potential energy surfaces were explored at the DFT/B3LYP level of theory. Finally, a new statistical Microcanonical...
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Unusual Influence of Fluorinated Anions on the Stretching Vibrations of Liquid Water
PublicationInfrared (IR) spectroscopy is a commonly used and invaluable tool in the studies of solvation phenomena in aqueous solutions. Concurrently, ab initio molecular dynamics (AIMD) simulations deliver the solvation shell picture at a molecular detail level and allow for a consistent decomposition of the theoretical IR spectrum into underlying spatial correlations. Here, we demonstrate how the novel spectral decomposition techniques...
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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
PublicationA 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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The ONETEP linear-scaling density functional theory program
PublicationWe present an overview of the ONETEP program for linear-scaling density functional theory (DFT) calculations with large basis set (planewave) accuracy on parallel computers. The DFT energy is computed from the density matrix, which is constructed from spatially localized orbitals we call Non-orthogonal Generalized Wannier Functions (NGWFs), expressed in terms of periodic sinc (psinc) functions. During the calculation, both the...
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The OpenMolcas Web: A Community-Driven Approach to Advancing Computational Chemistry
Open Research DataThe developments of the open-source OpenMolcas chemistry software environment since spring 2020 are described, with a focus on novel functionalities accessible in the stable branch of the package or via interfaces with other packages. These developments span a wide range of topics in computational chemistry and are presented in thematic sections: electronic...
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A BODIPY‐Based Molecular Rotor in Giant Unilamellar Vesicles: A Case Study by Polarization‐Resolved Time‐Resolved Emission and Transient Absorption Spectroscopy
PublicationBODIPY and BODIPY-derived systems are widely applied as fluorophores and as probes for viscosity detection in solvents and biological media. Their orientational and rotational dynamics in biological media are thus of vital mechanistic importance and extensively investigated. In this contribution, polarization-resolved confocal microscopy is used to determine the orientation of an amphiphilic BODIPY-cholesterol derivative in homogeneous...
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Correlation between the number of Pro-Ala repeats in the EmrA homologue of Acinetobacter baumannii and resistance to netilmicin, tobramycin, imipenem and ceftazidime
PublicationAcinetobacter baumannii coccobacilli are dangerous to patients in intensive care units because of their multidrug resistance to antibiotics, developed mainly in the past decade. This study aimed to examine whether there is a significant correlation between the number of Pro-Ala repeats in the CAP01997 protein, the EmrA homologue of A. baumannii, and resistance to antibiotics. A total of 79 multidrug-resistant A. baumannii strains...
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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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Genotyping Techniques for Determining the Diversity of Microorganisms
PublicationTyping of microbial pathogens, or identifying bacteria at the strain level, is particularly important for diagnosis, treatment, and epidemiological surveillance of bacterial infections. This is especially the case for bacteria exhibiting high levels of antibiotic resistance or virulence, and those involved in nosocomial or pandemic infections. Strain typing also has applications in studying bacterial population dynamics. The part...
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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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Autocorrelation function for the chosen effective potential of the diatomic silver anion
Open Research DataThe process of a two-channel decay of the diatomic silver anion (Ag2-), namely the spontaneous electron ejection giving Ag2 + e- and the dissociation leading to Ag- + Ag is theoretically studied. The ground state potential energy curves (PECs) of the neutral silver dimer and anionic silver diatomic molecule are calculated using the single reference...
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Non-adiabatic coupling elements between the diatomic silver anion and neutral silver dimer plus continuum electron
Open Research DataThe process of a two-channel decay of the diatomic silver anion (Ag2-), namely the spontaneous electron ejection giving Ag2 + e- and the dissociation leading to Ag- + Ag is theoretically studied. The ground state potential energy curves (PECs) of the neutral silver dimer and anionic silver diatomic molecule are calculated using the single reference...
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Quantum-classical calculations of the nanomechanical properties of metals
PublicationTradycyjnie symulacje komputerowe układów w skali atomowej prowadzone są przy użyciu klasycznej metody dynamiki molekularnej (MD) bądź kwantowych metod ab initio. Główną wadą ujęcia klasycznego jest jego empiryczna natura, a co za tym idzie - niewielka przenośność, jego prostota natomiast pozwala na przeprowadzanie symulacji układów zawierających miliony atomów. W wyniku zastosowania metod kwantowych otrzymuje się bardziej wiarygodne...
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Joanna Janczewska prof. dr hab.
PeopleJoanna Janczewska obtained her PhD degree at the University of Gdansk in 2002. From October 1999 to September 2004 she was an assistant at the University of Gdansk. Since October 2004 she has been an assistant professor at the Gdansk University of Technology. Moreover, from October 2008 to September 2010 she had a visiting position in the Institute of Mathematics of the Polish Academy of Sciences. Her mathematical interests...
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Mixed, quantum-classical description of electron density transfer in the collision process
PublicationIn this work, we investigate an ion-atom model describing the time-dependent evolution of electron density during the collision. For a S3+- H system, numerical simulations are based on classical trajectory calculations, and the electron density behaviour is described with the time-dependent Schrödinger equation. We apply the finite difference method to obtain quantitative insights into the charge transfer dynamics, providing detailed...
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Wybrane elementy nieliniowej dynamiki struktur kratowych
PublicationW pracy jest dyskutowany problem nieliniowej dynamiki struktur kratowych. Zastosowano stacjonarny opis Lagrange'a (ang. Total Lagrange), pokazano silne i słabe sformułowanie dla pręta kratowego, jego aplikację do MES. W zakresie całkowania równań ruchu przedstawiono metodę Newmarka i metodę-a dla problemów liniowych i nieliniowych. Załączony przykład numeryczny ilustruje cechy przedstawionych metod.
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Karolina Lademann mgr
PeopleCurriculum vitae
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Niebezpieczeństwo ukryte w żywności-aminy biogenne. Cz. II. Metody oznaczania i wyzwania.
PublicationZe względu na aktywność biologiczną amin biogennych ich oznaczanie zarówno jakościowe, jak i ilościowe w żywności ma istotne znaczenie w celu zapewnienia ochrony zdrowia i życia ludzkiego. Obecnie do monitoringu amin biogennych w żywności najczęściej wykorzystuje się: wysokosprawną chromatografię cieczową (HPLC), chromatografię cienkowarstwową (TLC) oraz absorpcyjną spektrofotometrię cząsteczkową. Są to jednak techniki czasochłonne,...
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Piotr Płotka dr hab. inż.
PeoplePiotr Płotka received the M.Sc. and D.Eng. degrees in electronic engineering from the Gdansk University of Technology, Poland, in 1976 and 1985. In 2008 he received D.Sc. (Dr.Hab.) degree, also in electronic engineering, from the Institute of Electron Technology at Warsaw, Poland. From 1977 he was with Academy of Technology and Agriculture at Bydgoszcz, Poland and from 1981 with the Gdansk University of Technology. In cooperation...
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VEHICLE DYNAMICS (2024)
e-Learning Courses(W) Vehicle dynamics (W-Lecture) - DAPE - WIMiO The course entitled "Vehicle dynamcs" (VD) is conducted for the DAPE WIMiO Students. The VD course is to discuss the following problems: - major problems of vehicle dynamics from the application point of view, - definition of working environment, - types of vehicles, - parameters and characteristics of vehicles, - assessment of performance of vehicles towards design, -...
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Molecular biology
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Molecular biology
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Efektywna metoda wyznaczania trasy statków żaglowych
PublicationZaproponowano metodę wyznaczania suboptymalnej trasy statków żaglowych poruszających się w ograniczonym akwenie morskim. Uwzględniono przy tym dynamikę tego środowiska w tym warunki pogodowe oraz charakterystyki prędkościowe statków żaglowych. Jako kryterium optymalizacji przyjęto czas żeglugi T oraz liczbę wykonanych manewrów ω. Zaprojektowano heurystyczny algorytm oraz odpowiednią aplikację wyznaczania trasy dla ustalonych punktów...
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Rengel Cane Sia Doctoral Candidate
PeopleI'm Rengel, born and raised in the Philippines. As an undergraduate I did kinetic modeling on Copper-catalyzed atom transfer radical addition (ATRA). Then I was inspired to do both theoretical and experimental studies, which led me to propose my master's thesis on Synthesis, Computational, Electrochemical, and Photoconductivity Studies on Naphthalene and its derivatives. This led to a master's degree in Chemistry in the Mindanao...
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ANALIZA CECH HYDRO-AERODYNAMICZNYCH BEZZAŁOGOWEGO POJAZDU NAWODNO-POWIETRZNEGO Z WYKORZYSTANIEM EFEKTU PRZYPOWIERZCHNIOWEGO
PublicationW artykule przedstawiono problematykę badań dotyczących opracowania demonstratora technologii bezzałogowego pojazdu nawodno-powietrznego z wykorzystaniem efektu przypowierzchniowego. Opisano podstawowe problemy badawcze związane z analizą cech hydro-aerodynamicznych pojazdu. Opisano przedmiot badań, bezzałogowy pojazd nawodno-powietrzny typu USV-UAV-WIG. Opisano metodę badań. Przeprowadzono wstępną analizę osiągów i zachowania...
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Marek Czachor prof. dr hab.
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Wykorzystanie algorytmów ewolucyjnych do doboru wzmocnień rozszerzonego obserwatora prędkości maszyny indukcyjnej
PublicationW pracy opisano sposób doboru wzmocnień rozszerzonego obserwatora prędkości maszyny indukcyjnej przy wykorzystaniu algorytmów ewolucyjnych. Zaproponowano funkcję celu opartą na rozkładzie biegunów obserwatora. Ze względu na wpływ prędkości maszyny na dynamikę obserwatora zaproponowano dobór wzmocnień obserwatora dla różnych przedziałów prędkości. Dla poszczególnych przedziałów zaprezentowano wyniki doboru wzmocnień w postaci tabel...
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SELECTED PROBLEMS OF MACHINE DYNAMICS (2024)
e-Learning CoursesThe course is devoted towards lectures assocuated with the novel issues of machine and structures dynamics. The following lectures will be given during the SPMD course: - introduction to selected problems of machine dynamics, - definition of the machine and structure working environment, - internal and external loads on machines and structures, - dynamics of machines and structures, - strength of machines and structures, - special...
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Molecular biology GT
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Fuzyjne polimerazy DNA – otrzymywanie, charakterystyka i zastosowanie
PublicationObecnie reakcje PCR (ang. Polymerase Chain Reaction) wykazują bardzo szerokie zastosowanie w diagnostyce medycznej, biologii molekularnej czy inżynierii genetycznej. Efektywność tych reakcji rozumiana jako wydajność i wierność przeprowadzonej amplifikacji jest nieodłącznie związana ze stosowaną polimerazą DNA i warunkami prowadzenia reakcji PCR. Aby sprostać wymaganiom stawianym przez nowoczesne metody diagnostyczne oraz współczesną...
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Selected Problems of Machine Dynamics
e-Learning CoursesThe following set of lectures is performed: 1. LECTURE No.1 - INTRODUCTION TO SELECTED PROBLEMS OF MACHINE DYNAMICS. STRUCTURES and MACHINES 2. LECTURE No.2 - ENVIRONMENT, LOADS ON STRUCTURES and MACHINES 3. LECTURE No.3 - DYNAMICS of STRUCTURES and MACHINES 4. LECTURE No.4 - STRENGTH of STRUCTURES and MACHINES 5. LECTURE No.5 - SPECIAL PROBLEMS ASSOCIATED with DYNAMICS and STRENGTH of STRUCTURES and MACHINES
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Mathematical and numerical modelling,W,IDE-EMSS,IIst,sem.01,lato,2023/24 (PG_00057379)
e-Learning CoursesModelling of controlled mechanical systems by the mixed method of rigid and flexible finite elements: The finite element volume problems. Dynamics of multibody systems. Modelling of stationary closed loop systems. Modelling of systems whose configuration changes with time. Modelling of nonlinear controlled systems. Optimal control at energy performance index: Control of continuous nonstationary systems in domain of generalised...
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Mathematical and Numerical Modelling, L, IDE IInd, sem.01, summer, 2022/23(00057379)
e-Learning CoursesModelling of controlled mechanical systems by the mixed method of rigid and flexible finite elements: The finite element volume problems. Dynamics of multibody systems. Modelling of stationary closed loop systems. Modelling of systems whose configuration changes with time. Modelling of nonlinear controlled systems. Optimal control at energy performance index: Control of continuous nonstationary systems in domain of generalised...
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Finite Element Method
e-Learning CoursesItem Name : Finite Element Method- Abaqus learning Field of study : Civil Engineering Faculty : Faculty of Civil and Environmental Engineering Education level : Second degree studies Form of studies : Full-time studies Year of studies : 1 Study semester : 2 Start of the semester : November 2021 Academic year of the course : 2021/2022 Form of classes : Lecture, Laboratory
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Selected Problems of Machine Dynamics II
e-Learning CoursesThe following set of lectures is performed: 1. LECTURE No.1 - INTRODUCTION TO SELECTED PROBLEMS OF MACHINE DYNAMICS. STRUCTURES and MACHINES 2. LECTURE No.2 - ENVIRONMENT, LOADS ON STRUCTURES and MACHINES 3. LECTURE No.3 - DYNAMICS of STRUCTURES and MACHINES 4. LECTURE No.4 - STRENGTH of STRUCTURES and MACHINES 5. LECTURE No.5 - SPECIAL PROBLEMS ASSOCIATED with DYNAMICS and STRENGTH of STRUCTURES and MACHINES