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Selected Problems of Machine Dynamics - advances
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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Simulation of the number of storm overflows considering changes in precipitation dynamics and the urbanisation of the catchment area: a probabilistic approach
PublicationThis paper presents a probabilistic methodology that allows the study of the interactions between changes in rainfall dynamics and impervious areas in urban catchment on a long- and short-term basis. The proposed probabilistic model predict future storm overflows while taking into account the dynamics of changes in impervious areas and rainfall. In this model, a logistic regression method was used to simulate overflow resulting...
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Conformational Studies of Two Bradykinin Antagonists by Using Two-dimensional NMR Techniques and Molecular Dynamics Simulations
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Independent dynamics of slow, intermediate, and fast intracranial EEG spectral activities during human memory formation
PublicationA wide spectrum of brain rhythms are engaged throughout the human cortex in cognitive functions. How the rhythms of various low and high frequencies are spatiotemporally coordinated across the human brain during memory processing is inconclusive. They can either be coordinated together across a wide range of the frequency spectrum or induced in specific bands. We used a large dataset of human intracranial electroencephalography...
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Catalytic Mechanism of Non-Target DNA Cleavage in CRISPR-Cas9 Revealed by Ab Initio Molecular Dynamics
PublicationCRISPR-Cas9 is a cutting-edge genome editing technology, which uses the endonuclease Cas9 to introduce mutations at desired sites of the genome. This revolutionary tool is promising to treat a myriad of human genetic diseases. Nevertheless, the molecular basis of DNA cleavage, which is a fundamental step for genome editing, has not been established. Here, quantum–classical molecular dynamics (MD) and free energy methods are used...
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Low-energy positron scattering from gas-phase tetrahydrofuran: A quantum treatment of the dynamics and a comparison with experiments
PublicationIn this paper we report new quantum calculations of the dynamics for low-energy positrons interacting with gaseous molecules of tetrahydrofuran. The new quantum scattering cross sections are differential and integral cross sections at collision energies between 1.0 and 25.0 eV and include a careful treatment of the additional effects on the scattering process brought about by the permanent dipole moment of the target molecule....
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Unraveling Energy Transfer and Fluorescence Quenching Dynamics in Biomolecular Complexes: A Comprehensive Study of Imiquimod-Rifampicin Interaction.
PublicationIn nature, numerous biomolecules are implicated in charge transfer (CT) and energy transfer (ET) mechanisms crucial for fundamental processes such as photosynthesis. Unveiling these mechanisms is pertinent to multiple disciplines including chemistry, engineering and biochemistry. This letter presents a study involving two molecules forming a model system with efficient ET properties. Specifically, their complex exhibits dark quenching...
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Collagen Type II—Chitosan Interactions as Dependent on Hydroxylation and Acetylation Inferred from Molecular Dynamics Simulations
PublicationChitosan–collagen blends have been widely applied in tissue engineering, joints diseases treatment, and many other biomedical fields. Understanding the affinity between chitosan and collagen type II is particularly relevant in the context of mechanical properties modulation, which is closely associated with designing biomaterials suitable for cartilage and synovial fluid regeneration. However, many structural features influence...
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Molecular dynamics simulations of the affinity of chitin and chitosan for collagen: the effect of pH and the presence of sodium and calcium cations
PublicationChitosan and chitin are promising biopolymers used in many areas including biomedical applications, such as tissue engineering and viscosupplementation. Chitosan shares similar properties with hyaluronan, a natural component of synovial fluid, making it a good candidate for joint disease treatment. The structural and energetic consequences of intermolecular interactions are crucial for understanding the biolubrication phenomenon...
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Optimization of hydrodynamic vortex separator for removal of sand particles from storm water by computational fluid dynamics
PublicationStorm water treatment has been gradually acknowledged for the removal of pollutants from urban areas using the hydro cyclone separation technique. The separation efficiency of the hydrodynamic vortex separator (HDVS) is a complex phenomenon. With the aim enhance the separation potency of HDVS for storm runoff to get rid of sand particles, the HDVS with different structural configurations was studied by computational fluid dynamics....
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Computational fluid dynamics simulation of heat transfer from densely packed gold nanoparticles to isotropic media
PublicationThis work aims to determine and compare heat generation and propagation of densely packed gold nanoparticles (Au NPs) induced by a resonant laser beam (532 nm) according to the Mie theory. The heat flux propagation is transferred into the materials, which here are: silica glass; soda-lime-silica glass; borosilicate glass; polymethyl methacrylate (PMMA); polycarbonate (PC); and polydimetylosiloxane (PDMS). This analysis aims to...
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Mechanism of recognition of parallel G-quadruplexes by DEAH/RHAU helicase DHX36 explored by molecular dynamics simulations
PublicationBecause of high stability and slow unfolding rates of G-quadruplexes (G4), cells have evolved specialized helicases that disrupt these non-canonical DNA and RNA structures in an ATP-dependent manner. One example is DHX36, a DEAH-box helicase, which participates in gene expression and replication by recognizing and unwinding parallel G4s. Here, we studied the molecular basis for the high affinity and specificity of DHX36 for parallel-type...
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Chip suction system in circular sawing machine: empirical research and computational fluid dynamics numerical simulations
PublicationThe experimental analysis of the wood chip removing system during its redesigning in the existing sliding table circular saw and computational fluid dynamic (CFD) numerical simulations of the air flow process is presented in the paper. The attention was focused on the extraction hood and the bottom shelter of the actual existing system. The main aim was to perform experimental research on the pressure distribution inside the...
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Modelling of a medium-term dynamics in a shallow tidal sea, based on combined physical and neural network methods
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Impact of climate and humans on the range dynamics of the woolly mammoth (Mammuthus primigenius) in Europe during MIS 2
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Regional effects of amphetamine, cocaine, nomifensine and GBR 12909 on the dynamics of dopamine release and metabolism in the rat brain
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Interfaces with Structure Dynamics of the Workhorses from Cells Revealed through Cross-Linking Mass Spectrometry (CLMS)
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Mechanism of recognition of parallel G-quadruplexes by DEAH/RHAU helicase DHX36 explored by molecular dynamics simulations
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Transcriptome Dynamics Underlying Planticine®-Induced Defense Responses of Tomato (Solanum lycopersicum L.) to Biotic Stresses
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Low-energy positron scattering from gas-phase pyrimidine: A quantum treatment of the dynamics and a comparison with experiments
PublicationWe are reporting detailed quantum scattering calculations that describe the diffusion of a beam of low-energy positrons interacting with the pyrimidine target as a gas-phase partner. The calculations have employed an essentially ab initio model for the short-range correlation interaction and for the electrostatic interaction of an impinging positron and the electron+nuclear structure of the target molecule at its equilibrium geometry.
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Conformational studies of [Nphe5]SFTI-1 by means of 2D NMR spectroscopy in conjunction with molecular dynamics calculations
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Scale-consistent approach to the derivation of coarse-grained force fields for simulating structure, dynamics, and thermodynamics of biopolymers
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Molecular dynamics study of a gelsolin-derived peptide binding to a lipid bilayer containing phosphatidylinositol 4,5-bisphosphate
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Independent dynamics of slow, intermediate, and fast intracranial EEG spectral activities during human memory formation
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Structure determination of UL49.5 transmembrane protein from bovine herpesvirus 1 by NMR spectroscopy and molecular dynamics
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Multiple β-sheet molecular dynamics of amyloid formation from two ABl-SH3 domain peptides
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Spin probe dynamics in relation to free volume in crystalline organics from ESR and PALS: N-tridecane
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Gluten-Free Bread with Cricket Powder—Mechanical Properties and Molecular Water Dynamics in Dough and Ready Product
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Measurement Of The Dynamics Of The Sheave Block Of Shipyard Crane With 1000 T Lifting Capacity For Verification Of The Laboratory Stand
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Effect of the Relative Position of the Face Milling Tool towards the Workpiece on Machined Surface Roughness and Milling Dynamics
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Ammonium sorption from aqueous solutions by the natural zeolite Transcarpathian clinoptilolite studied under dynamics conditons
PublicationPrzeprowadzone badania z wykorzystaniem wodnych roztworów modelowych amoniaku mogą stanowić podstawę do następujących wniosków:- maksymalna pojemność sorpcyjna klinoptylolitu w stosunku do jonów NH4+ w warunkach dynamicznych jest zdecydowanie wyższa niż w warunkach statycznych,- proces usuwania jonów amonowych podlega intensyfikacji w przypadku zastosowania frakcji zeolitu o mniejszej średnicy ziaren,- istotną rolę w procesie sorpcji...
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New possibilities of the passive layer cracking dynamics detection using a new Dynamic Electrochemical Impedance Spectroscopy.
PublicationNowa metoda Dynamicznej Elektrochemicznej Spektroskopii Impedancyjnej opracowana w Katedrze Elektrochemii, Korozji i Inżynierii Materiałowej Politechniki Gdańskiej daje możliwości określania charakterystyki impedancyjnej w dziedzinie czasu podczas procesu pękania ochronnej warstwy pasywnej. Fakt ten jest związany z procedurą analizującą wspomnianej techniki, która umożliwia selektywną analizę czasowo-częstotliwościową uzyskanych...
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Orientational order and dynamics of the dendritic liquid crystal organo-siloxane tetrapodes determined using dielectric spectroscopy
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Increasing Energy Efficiency and Productivity of the Comminution Process in Tumbling Mills by Indirect Measurements of Internal Dynamics—An Overview
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Investigation on the effect of anti-pitch fins for reducing the motion and acceleration of ships using computational fluid dynamics
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Combining the MARTINI and Structure-Based Coarse-Grained Approaches for the Molecular Dynamics Studies of Conformational Transitions in Proteins
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Dynamics of changes in the concentration levels of organic pollutants in the proglacial waters of the Scott River (Spitsbergen, SW Svalbard)
PublicationThe study area covered the NW part of the Wedel Jarlsberg Land. The present study concerns participation of organic pollutants inflow from glacier and seaside plane of Calypsostranda to proglacial waters of the Scott River due to occurrence of precipitation. Concentration ranges for phenols and formaldehyde in water samples are respectively:
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Conformation analysis and semiclassical dynamics study of charge exchange process induced by collision of C2+ ions with tetrahydrofuran
PublicationWe present the results of recent investigations of charge transfer processes in the collisions of C²⁺ ions with heterocyclic molecules of tetrahydrofuran.
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Dynamics of Asymmetric Conflict: Pathways toward Terrorism and Genocide
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SAE International Journal of Vehicle Dynamics Stability and NVH
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Dynamics of Continuous, Discrete and Impulsive Systems Series A: Mathematical Analysis
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Performance of extended Lagrangian schemes for molecular dynamics simulations with classical polarizable force fields and density functional theory
PublicationIterative energy minimization with the aim of achieving self-consistency is a common feature of Born-Oppenheimer molecular dynamics (BOMD) and classical molecular dynamics with polarizable force fields. In the former, the electronic degrees of freedom are optimized, while the latter often involves an iterative determination of induced point dipoles. The computational effort of the self-consistency procedure can be reduced by re-using...
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Independent dynamics of low, intermediate, and high frequency spectral intracranial EEG activities during human memory formation
PublicationA wide spectrum of brain rhythms are engaged throughout the human cortex in cognitive functions. How the rhythms of various frequency ranges are coordinated across the space of the human cortex and time of memory processing is inconclusive. They can either be coordinated together across the frequency spectrum at the same cortical site and time or induced independently in particular bands. We used a large dataset of human intracranial...
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Long range molecular dynamics study of regulation of eukaryotic glucosamine-6-phosphate synthase activity by UDP-GlcNAc
PublicationGlucosamine-6-phosphate (GlcN-6-P) synthase catalyses the first and practically irreversible step in hexosamine metabolism. The final product of this pathway, uridine 5' diphospho N-acetyl-D-glucosamine (UDPGlcNAc), is an essential substrate for assembly of bacterialand fungal cell walls. Moreover, the enzyme is involved in phenomenon of hexosamine induced insulin resistance in type II diabetes, which makes it a potential target...
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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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High frequency dynamics of an isotropic Timoshenko periodic beam by the use of the Time-domain Spectral Finite Element Method
PublicationIn this work results of numerical simulations and experimental measurements related to the high frequency dynamics of an aluminium Timoshenko periodic beam are presented. It was assumed by the authors that the source of beam structural periodicity comes from periodical alterations to its geometry due to the presence of appropriately arranged drill-holes. As a consequence of these alterations dynamic characteristics of the beam...
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On the Possibility of the Amphotericin B-Sterol Complex Formation in Cholesterol- and Ergosterol-Containing Lipid Bilayers: A Molecular Dynamics Study
PublicationAmphotericin B (AmB) is a well-known membrane-active antibiotic that has been used to treat systemicfungal infections for more than 45 years. Therapeutic application of AmB is based on the fact that it is moreactive against ergosterol-containing membranes of fungal cells than against mammalian membranes withcholesterol. In this paper, we examine the hypothesis according to which the selectivity of the AmB's membraneaction originates...
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Effect of the Catalytic Center on the Electron Transfer Dynamics in Hydrogen-Evolving Ruthenium-Based Photocatalysts Investigated by Theoretical Calculations
PublicationThe light-induced relaxation pathways in the molecular photocatalyst [(tbbpy)2Ru(tpphz)PtCl2]2+ are investigated with time-dependent density functional theory calculations together with the Marcus theory of electron transfer (ET). The calculations show that metal (Ru) to ligand (tpphz) charge transfer (MLCT) triplet states are populated following an excitation in the longer wavelength range of the absorption spectrum, but that an...
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Expansion and population dynamics of a non-native invasive species: the 40-year history of American mink colonisation of Poland
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Diagnostics of UV Nanosecond Laser Generated Plasma Plume Dynamics in Ambient Air Using Time-Resolved Imaging
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