Search results for: molecular-dynamics
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Theoretical Investigation of the Electron-Transfer Dynamics and Photodegradation Pathways in a Hydrogen-Evolving Ruthenium-Palladium Photocatalyst
PublicationTime-dependent density functional theory calcula- tions combinedwith the Marcus theory of electron transfer (ET) were app lied on the molecular photocatalys t [(tbbpy) 2 Ru(tpph z)PdC l 2 ] 2 + in order to elucidate thelight-in- duced relaxation pathways populated upon excitation in the longer wavelength range of its absorption spectrum. The computational resultsshow that after the initial excitation, metal (Ru) to ligand (tpphz)chargetransfer...
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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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Degradation of a nano-cutting tool: an MD simulation
PublicationW pracy przedstawiono wyniki symulacji wielokrotnego oddziaływania realistycznie ukształtowanego ostrza tnącego z modelowym, nieskończenie twardym ziarnem, przy zastosowaniu metody dynamiki molekularnej. Ostrze składało się z kilkuset tysięcy atomów metalu fcc, traktowanego za pomocą potencjału Suttona-Chena, przesuwane było ze stałą prędkością 20 m/s. Obserwowane deformacje plastyczne pojawiające się na skutek kontaktu ostrza...
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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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Understanding the Electronic Structure and Optical Properties of Vacancy-Ordered Double Perovskite A2BX6 for Optoelectronic Applications
PublicationOver the past few years, metal halide perovskite solar cells have made significant advances. Currently, the single-junction perovskite solar cells reach a conversion efficiency of 25.7%. Perovskite solar cells with a wide band gap can also be used as top absorber layers in multi-junction tandem solar cells. We examined the dynamical and thermal stability, electronic structure, and optical features of In2PtX 6 (X = Cl, Br, and I)...
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A Novel Cryptic Clostridial Peptide That Kills Bacteria by a Cell Membrane Permeabilization Mechanism
PublicationThis work reports detailed characteristics of the antimicrobial peptide Intestinalin (P30), which is derived from the LysC enzyme of Clostridium intestinale strain URNW. The peptide shows a broader antibacterial spectrum than the parental enzyme, showing potent antimicrobial activity against clinical strains of Gram-positive staphylococci and Gram-negative pathogens and causing between 3.04 ± 0.12 log kill for Pseudomonas aeruginosa...
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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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Recent Developments in Data-Assisted Modeling of Flexible Proteins
PublicationMany proteins can fold into well-defined conformations. However, intrinsically-disordered proteins (IDPs) do not possess a defined structure. Moreover, folded multi-domain proteins often digress into alternative conformations. Collectively, the conformational dynamics enables these proteins to fulfill specific functions. Thus, most experimental observables are averaged over the conformations that constitute an ensemble. In this...
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Theoretical Encapsulation of Fluorouracil (5-FU) Anti-Cancer Chemotherapy Drug into Carbon Nanotubes (CNT) and Boron Nitride Nanotubes (BNNT)
PublicationIntroduction: Chemotherapy with anti-cancer drugs is considered the most common approach for killing cancer cells in the human body. However, some barriers such as toxicity and side effects would limit its usage. In this regard, nano-based drug delivery systems have emerged as cost-effective and efficient for sustained and targeted drug delivery. Nanotubes such as carbon nanotubes (CNT) and boron nitride nanotubes (BNNT) are promising...
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Rotation Triggers Nucleotide-Independent Conformational Transition of the Empty β Subunit of F1-ATPase
PublicationF1-ATPase (F1) is the catalytic portion of ATP synthase, a rotary motor protein that couples proton gradients to ATP synthesis. Driven by a proton flux, the F1 asymmetric γ subunit undergoes a stepwise rotation inside the α3β3 headpiece and causes the β subunits’ binding sites to cycle between states of different affinity for nucleotides. These concerted transitions drive the synthesis of ATP from ADP and phosphate. Here, we study...
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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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H2O˙+ and OH+ reactivity versus furan: experimental low energy absolute cross sections for modeling radiation damage
PublicationRadiotherapy is one of the most widespread and efficient strategies to fight malignant tumors. Despite its broad application, the mechanisms of radiation-DNA interaction are still under investigation. Theoretical models to predict the effects of a particular delivered dose are still in their infancy due to the difficulty of simulating a real cell environment, as well as the inclusion of a large variety of secondary processes. This...
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Extreme bottom velocities induced by wind wave and currents in the Gulf of Gdańsk
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Numerical modeling of hydrodynamics and sediment transport—an integrated approach
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An evaluation and implementation of the regional coupled ice-ocean model of the Baltic Sea
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Diurnal variability of atmospheric water vapour, precipitation and cloud top temperature across the global tropics derived from satellite observations and GNSS technique
PublicationThe diurnal cycle of convection plays an important role in clouds and water vapour distribution across the global tropics. In this study, we utilize integrated moisture derived from the global navigation satellite system (GNSS), satellite precipitation estimates from TRMM and merged infrared dataset to investigate links between variability in tropospheric moisture, clouds development and precipitation at a diurnal time scale. Over...
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Nonlinear planar modeling of massive taut strings travelled by a force-driven point-mass
PublicationThe planar response of horizontal massive taut strings, travelled by a heavy point-mass, either driven by an assigned force, or moving with an assigned law, is studied. A kinematically exact model is derived for the free boundary problem via a variational approach, accounting for the singularity in the slope of the deflected string. Reactive forces exchanged between the point-mass and the string are taken into account via Lagrange...
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Statistical properties of a modified standard map in quantum and classical regimes
PublicationWe present a model—a modified standard map. This model has interesting properties that allow quantum–classical correspondences to be studied. For some range of parameters in the classical phase space of this model, there exist large accelerator modes. We can create a family of maps that have large accelerator modes.
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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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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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Modelling of planar movement dynamics of upper limb
PublicationThe original model describing planar movement dynamics of upper limb is presented. The upper limb is modelled as two-joints system loaded by external forces and internal forces of striated skeletal muscles. A behaviour of each muscle is modelled as a system composed of serially linked rheologic fragments that have different mechanical properties. These muscle models allow us to simulate a behaviour of short fusiform muscle (3DOF...
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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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Towards better understanding of context-aware knowledge transformation
PublicationConsidering different aspects of knowledge functioning, context is poorly understood in spite of intuitively identifying this concept with environmental recognition. For dynamic knowledge, context especially seems to be an essential factor of change. Investigation on the impact of context on knowledge dynamics or more generally on the relationship between knowledge and its contextual interpretation is important in order to understand...
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Rigid finite elements and multibody modeling in analyses of a robot shaped elastic/plastic deformations of a beam
PublicationDynamics analysis of a system composed of a parallel manipulator and of an elastic beam is presented in the paper. Classic 3RRR parallel manipulator is considered and used to deform the beam. Elasto-plastic deformations are investigated. Rigid-finite-elements technique is employed to deal with dynamics of the beam. A multibody structure is associated with the introduced hybrid system in order to model its dynamics. Idea of the...
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Two examples of Quantum Dynamical Semigroups
PublicationThe Hamiltonians of the considered bi-partite systems are of the form $$ H_{S,R} = H_S /times 1_R + Q_{S} /times M_R + 1_S /times H_R $$ Subindex $S$ corresponds to the observed system and $R$ to the reservoir (the enviroment of $S$). Two classes of systems are distinguished: the discrete-continuous...
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Periodic and chaotic dynamics in a map‐based neuron model
PublicationMap-based neuron models are an important tool in modeling neural dynamics and sometimes can be considered as an alternative to usually computationally costlier models based on continuous or hybrid dynamical systems. However, due to their discrete nature, rigorous mathematical analysis might be challenging. We study a discrete model of neuronal dynamics introduced by Chialvo in 1995. In particular, we show that its reduced one-dimensional...
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Robust Monitoring of Water Quality in Drinking Water Distribution System
PublicationThe paper develops a novel open loop set bounded observer for robust estimation of water quality in DWDS based on the advanced nonlinear quality dynamics model including disinfections by-products (DBPs). The observer utilises a cooperativeness of the quality dynamics model and is computationally efficient, hence applicable to on-line quality monitoring. The simulation results illustrate its good and sustainable performance.
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Cosmic-Time Quantum Mechanics and the Passage-of-Time Problem
PublicationA new dynamical paradigm merging quantum dynamics with cosmology is discussed.
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On finite element modelling of architectural fabrics for hanging roofs
PublicationArtykuł dotyczy modelowania konstytutywnego i identyfikacji parametrów materiałowych dla tkanin technicznych powszechnie stosowanych w konstrukcjach membranowo-cięgnowych. Autorzy przedstawiają krótką charakterystyke modeli stosowanych w opisie zachowania sie tkanin technicznych. Opisano metodę do idetyfikacji nieliniowo-sprężystych właściwości tkanin technicznych. Dodatkowo dokonao porówania wyników z prób jednoosiowego rozciągania...
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Identification of nonlinear viscoelastic properties of the ''Panama'' fabric
PublicationTkanina techniczna Panama wytwarzana przez firmę Sattler (Niemcy)wykazuje cechy nieliniowe w tym właściwości lepkosprężyste w czasie testów długoterminowych. Na podstawie jednoosiowych testów płynięcia i regeneracji przeprowadzonych dla pięciu poziomów obciążenia przeprowadzono identyfikacje nieliniowych lepkosprężystych właściwości tkaniny. Do opisu zależności konstytutywnych użyto całkowego modelu Schapery'ego. Zastosowano funkcję...
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Identification of inertia, damping and stiffness parameters for low pressure steam turbine framework.
PublicationW pracy przedstawiono metodę identyfikacji masy tłumienia i sztywności kadłuba części niskoprężnej turbiny parowej 200MW.
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Symbolic multibody models for digital-twin applications
PublicationSymbolic generation of multibody systems equations of motion appeared in the 1980s. In addition to their computational advantage over their numerical counterparts, symbolic models can be very easily and straightforwardly interfaced with a wide range of software environments and hardware devices. These two features place this approach in a pole position to participate and intervene in the design of digital twins for systems such...
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Rheological Problems of Technical Fabirc
PublicationW pracy przedstawiono wyniki identyfikacji modeli Chaboche'a i Schapery dla tkaniny technicznej Panama.
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Methods of material parameters identification for isotropic damage in viscoplastic flow conditions
PublicationW pracy zaprezentowano trzy metody identyfikacji parametrów materiałowych dla izotropowego zniszczenia w warunkach lepkoplastycznego płynięcia. Przedstawiono wyniki identyfikacji dla dwóch stopów aluminium, które następnie zweryfikowano porównując wyniki symulacji numerycznych z wynikami eksperymentalnymi.
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Experimental research on technical fabric of the Forest Opera Roof in Sopot
PublicationThe experimental analysis of the technical fabric Valmex is presented. The study involves uniaxial tensile, cyclic, rheological and biaxial tests. Some of the main differencies between two types of the analysed material have been identified. Mechanical properties of the textile have been modeled by the viscoelastic standard model with quite good effect.
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Constructional properties of polycarbonate plates for EURO 2012 Gdansk stadium
PublicationPrzedstawiono wyniki badań doświadczalnych dla płyt z poliwęglanu litego, które miały zostać wykorzystane jako materiał konstrukcyjno-osłonowy stadionu piłkarskiego na mistrzostwa Euro 2012 w Gdańsku. Zidentyfikowano moduł Younga oraz Poissona, wykonano próby cykliczne oraz pełzania. Właściwości mechaniczne poliwęglanu litego oceniono jako dobre, choć obawy budzą mikrorysy pojawiające się podczas badań w strukturze materiału.
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Regression points in non-intrusive polynomial chaos expansion method and D-optimal design
PublicationThe paper addresses selected issues of uncertainty quantification in the modelling of a system containing surgical mesh used in ventral hernia repair. Uncertainties in the models occur e.g. due to variability of abdominal wall properties among others. In order to include them, a non-intrusive regression-based polynomial chaos expansion method is employed. Its accuracy depends on the choice of regression points. In the study a relation...
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Drivetrain of a Wind Turbine
PublicationIn a most commonly met design of a wind turbine the power is transmitted from the rotor to the generator through the system composed of the main shaft, friction connection, multiplying gearbox and a flexible coupling. The driving system comprises almost a complete set of the machine elements being described during machine design lectures and can serve as an interesting illustration...
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Novel method of estimation of inertial and dissipative parameters of a railway pantograph model
PublicationAn increase in electric railway vehicles service velocity requires that correct interaction between the pantograph and the catenary is ensured. This implies the need for developing mathematical models of pantographs and catenaries and determining their parameters. The article presents a method to determine parameters of mechanical joints of a railway pantograph based on analysis of pantograph subassemblies in swinging motion. The...
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Numerical modelling of moored floating structures using SPH. Preliminary results
PublicationThis article presents partial results of the works carried out under the research project "The development of the methodof modeling the dynamics of the floating (offshore) objects subjected to the environment influence", which aims at developing computational methods for modeling the dynamics of offshore structures.The article contains the description of the method of modeling the hydrodynamic impacts using SPH method and the description...
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What drives sustainable investing? Adoption determinants of sustainable investing exchange-traded funds in Europe
PublicationDespite the growing interest in various topics related to sustainable (ESG) investing, some issues remain understudied, such as the determinants of their utilization at the macro level. This paper contributes to the state of knowledge two-directionally. First, it shows the development of sustainable investing exchange-traded funds (ETFs) in European countries. Second, it traces the significant determinants of adopting sustainable...
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Analysis and characterization of coordination compounds by resonance Raman spectroscopy
PublicationResonance Raman spectroscopy has become a powerful tool to study excited-state geometries, excited-state charge distributions and photoinduced reaction dynamics in coordination compounds. Due to their rich photophysical properties coordination compounds are utilized for a variety of applications ranging from DNA sensing to photocatalysis. This review features recent applications of various resonance Raman scattering techniques...
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Hierarchical dissolved oxygen control for activated sludge processes
PublicationA hierarchical controller for tracking the dissolved oxygen reference trajectory in activated sludge processes is proposed and investigated. The removal of nitrogen and phosphorous from wastewater is considered. Typically, an aeration system itself is a complicated hybrid nonlinear dynamical system with faster dynamics compared to the internal dynamics of the dissolved oxygen in a biological reactor. It is a common approach to...
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Firing map for periodically and almost-periodically driven integrate-and-fire models: a dynamical systems approach
PublicationWe consider the Leaky Integrate-and-Fire and Perfect Integrator models of neuron’s dynamics with the input function being periodic and almost-periodic (in the sense of Stepanov). In particular we analyze properties and dynamics of the so-called firing map, which iterations give timings of consecutive spikes of a neuron. In case of a periodic input function we provide a detailed description of the sequence of interspike-intervals,...
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Analytical modeling of electric drives for vehicle traction control systems
PublicationWheel-torque control bandwidth in vehicle dynamics model is crucial in evaluating optimal tracking ability of tire slip and in analysis of control system stability. Electric drives’ control dynamics are influenced by timing of digital control events, e.g. by sampling instant of motor currents. Reflecting this timing in drive analytical models is therefore important for analysis of vehicle traction systems. The paper considers five...
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Experimental and numerical analysis of the pyrolysis dynamics of a single wood particle: presentation of the radiographic technique
PublicationPyrolysis is an oxygen-free process for the thermal decomposition of raw materials. The heat conduction and flow of pyrolysis products (i.e., the gas fraction and liquid vapour generated during pyrolysis) influence the process and products. In this work, the influence of the orientation of wooden particle fibres with respect to the direction of the heat source on the dynamics of the process was investigated, where there were two...
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Frequency and time domain characteristics of digital control of electric vehicle in-wheel drives
PublicationIn-wheel electric drives are promising as actuators in active safety systems of electric and hybrid vehicles. This new function requires dedicated control algorithms, making it essential to deliver models that reflect better the wheel-torque control dynamics of electric drives. The timing of digital control events, whose importance is stressed in current research, still lacks an analytical description allowing for modeling its...
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Fitting the mobile device characteristics to the user's hearing preferences
PublicationA method for fitting the mobile computer audio characteristics to the user's hearing preferences is proposed. The process consists of two stages: calibration and dynamics processing. During the calibration phase the user performs a loudness scaling test giving their response regarding the perceived loudness. The dynamics processing made on above basis sets the loudness to the most comfortable level. The processing accounts both...