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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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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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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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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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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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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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Trust Dynamics Analysis of CTR Scheme Subversion under Virtual Anonymity and Trust-Unaware Partner Selection
PublicationWe propose a framework to study Markovian trust value dynamics in a centralized Computational Trust and Reputation (CTR) scheme under trust-unaware partner selection using a mean-value approximation. Analytically founded answers are sought to questions like: Can dishonest agents subvert the CTR scheme (i.e., acquire higher trust values than honest agents)? Is indirect reciprocity incentivized? Is there a qualitative impact of a...
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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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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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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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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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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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Investigating the Ischaemic Phase of Skin NADH Fluorescence Dynamics in Recently Diagnosed Primary Hypertension: A Time Series Analysis
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LF NMR spectroscopy analysis of water dynamics and texture of Gluten-Free bread with cricket powder during storage
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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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Expansion and population dynamics of a non-native invasive species: the 40-year history of American mink colonisation of Poland
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Application of Multiplexed Replica Exchange Molecular Dynamics to the UNRES Force Field: Tests with α and α+β Proteins
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Self-assembly and interactions of short antimicrobial cationic lipopeptides with membrane lipids: ITC, FTIR and molecular dynamics studies
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A systematic approach to understand hydrogeochemical dynamics in large river systems: Development and application to the River Ganges (Ganga) in India
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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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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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Diagnostics of UV Nanosecond Laser Generated Plasma Plume Dynamics in Ambient Air Using Time-Resolved Imaging
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Dynamics of cutting power during sawing with circular saw blades as an effect of wood properties changes in the cross section
PublicationIn the paper the effect of the method calculation upon the cutting power is presented. In computations were used models in which fracture toughness was incorporated. The comparison concerned models as follows: FM-CM – classic model in which the sum of all uncut chip thicknesses of the simultaneously teeth engaged represented the mean uncut chip thickness, FM-FDM – full dynamical model in which besides variable uncut chip thickness...
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Dipole-driven dynamics for near-threshold electron/positron interactions with pyrimidinic DNA bases: a path to compound formations
PublicationCalculations are reported for electron and positron scattering from isolated cytosine and thymine, where the two pyrimidinic single-ring DNA bases, in the gas-phase at energies near the elastic threshold, they reveal the special features of the dipole-driven scattering states. All molecules examined exhibit, in fact, supercritical (>1.67 D) permanent dipoles which can therefore also support, below threshold, excited bound compound...
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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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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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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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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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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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Programmable dynamically changing RC model for evaluation of Dynamic EIS methods and instrumentation
PublicationThe paper concerns the RC equivalent circuit of electrochemical cell with the impedance changed during the experiment. The model was constructed using the digital potentiometers controlled by the microcontroller. This solution allows to control the model impedance by the software means. By creating adequate changes of the impedance spectrum as a time function, the different impedance measurement method can be tested to find out...
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Do global brands contribute to the economy of their country of origin? A dynamic spatial approach
PublicationPurpose - Brand positioning based on the brand’s country of origin is at the centre of attention in international marketing. It is evident that global brands constitute critical intangible assets for businesses and places. However, it is not clear how they contribute to national economies. This paper aims to discuss the significance of brands as contributing to the value of their companies but also helping to leverage national...
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Dynamic analysis of temporary steel grandstand equipped with different types of bracing system
PublicationIn the paper, behaviour of a temporary steel grandstand equipped with two different types of bracing system has been analysed through the numerical study. A typical solution concerning application of a diagonal tubular members has been compared with elements proposed by authors and called polymer dampers. A polymer element consists of two L-shape steel members bonded with polymer mass. The aim of the paper is to verify the effectiveness...
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Determination of the optimal curvature of the turnout diverging track for HSR using dynamic analysis
PublicationThe paper presents an analytical method of identifying the curvature of the turnout diverging track consisting of sections of varying curvature. Such turnout is mainly applied on High Speed Railway. Both linear and nonlinear (polynomial) curvatures of the turnout diverging track are considered in the paper. Obtained solutions enable to assume curvature values at the beginning and end point of the geometrical layout of the turnout.The...
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Modified nanodiamond particle size studies by means of dynamic light scattering technique
PublicationThe Methods Utilizing the Phenomena of Light Scattering to Measure Particle Size distribution in different solvent, such as deionise water and alcohol and also to study the various structural formation when nanodiamond solution is placed on silicon surface. The purpose of this research project is divided into two parts to configure the measurement units for examining modified nanodiamond particles, examination...
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Modified nanodiamond particle size studies by means of dynamic light scattering technique
PublicationThe Methods Utilizing the Phenomena of Light Scattering to Measure Particle Size distribution in different solvent, such as deionise water and alcohol and also to study the various structural formation when nanodiamond solution is placed on silicon surface. The purpose of this research project is divided into two parts to configure the measurement units for examining modified nanodiamond particles, examination...
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Evaluation of fouling potential of nanofiltration membranes based on the dynamic contact angle measurements
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Time Domain Modeling of Propeller Forces due to Ventilation in Static and Dynamic Conditions
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Image Quality Assessment Tool for Conventional and Dynamic Magnetic Resonance Imaging Acquisitions
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Analysis od dynamic loads on lightweight footbridge caused by lorry passing underneath
PublicationW artykule przedstawiono analizę drgań lekkiej kładki dla pieszych wywołanych przejazdem ciężarówki z dużą prędkością pod spodem konstrukcji.
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Quantitative active dynamic thermal ir-imaging and thermal tomography in medical diagnostics
PublicationPraca dotyczy nowych technik obrazowania w diagnostyce medycznej, wykorzystując przetwarzanie obrazów termicznych rejestrowanych w podczerwieni. Opisano właściwości termiczne tkanek biologicznych, omówiono medele termiczne i zdefiniowano zastępcze parametry syntetyczne, metody pomiarów i stosowane urządzenia. Omówiono procedury akwizycji danych i ich przetwarzania. Wprowadzono pojęcie tomografii termicznej. Opisano przeprowadzone...
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Simulation Results of Dynamic Capacity Reallocation in Hierarchical Cell Structure of UMTS Network
PublicationIn the paper simulation results of dynamic capacity reallocation between different layers of hierarchical cell structure of UMTS network has been described. This approach for load management seems to be useful for improving the resource utilization perfmorance.
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From the Dynamic Lattice Liquid Algorithm to the Dedicated Parallel Computer – mDLL Machine
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Web-based GIS technologies dedicated for presenting semi-dynamic geospatial data
PublicationSieciowe technologie prezentacji danych przestrzennych przeżywają aktualnie rozkwit spowodowany między innymi spadającymi cenami sprzętu komputerowego. Wynikający z tego wzrost wydajności domowych i biurowych stacji roboczych pozwala na praktyczne zastosowanie czasochłonnych algorytmów wizualizacji i przetwarzania skomplikowanych danych rastrowych i wektorowych. Niniejszy artykuł omawia wybrane technologie sieciowej prezentacji...
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Improved estimation of dynamic modulus for hot mix asphalt using deep learning
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Static and dynamic superheated water extraction of essential oil components fromThymus vulgarisL.
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The method of improving the dynamic range of jitter analyzers in optical-fiber transmission systems
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Dynamic Analysis of an Enhanced Multi-Frequency Inertial Exciter for Industrial Vibrating Machines
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Static and dynamic properties of light PU foam for building the shallow river barges
PublicationPrzedstawiono wyniki badań wytrzymałości statycznej na rozciąganie, ściskanie i ścinanie oraz zmęczeniowej przy obciążeniach ściskających jednostronnie tętniących pian poliuretanowych o gęstości 53 i 62 kg/m3, mierzonych w kierunku podłużnym i prostopadłym do kierunku wzrostu piany w procesie jej otrzymywania. Stwierdzono wyraźną anizotropię własności mechanicznych piany. Obserwowano znacznie silniejsze zniszczenie zmęczeniowe...
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Dynamic control of the receiving beam horizontal cross-section in the side scan sonar
PublicationW skonstruowanych przed kilkunastu laty a obecnie modernizowanych sonarach bocznych jako jeden z zabiegów modernizacyjnych wprowadzono dynamiczną regulację kąta rozwarcia odbiorczej charakterystyki kierunkowej w przekroju horyzontalnym. Regulacja taka zapewnia quasi-stałą rozdzielczość liniową sonaru (zamiast stałej rozdzielczości kątowej) przy odbiorze sygnałów echa ze wzrastających odległości od wykrywanych celów. W efekcie tego...