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Wyniki wyszukiwania dla: RIVER ICE DYNAMICS
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The river water influence on cationic and anionic dyes collection by nickel foam with carbonized metal-organic frameworks and carbon nanotubes
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Tideless estuaries in brackish seas as possible freshwater‐marine transition zones for bacteria: the case study of the Vistula river estuary
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CPLFD-GDPT5: High-resolution gridded daily precipitation and temperature data set for two largest Polish river basins
PublikacjaThe CHASE-PL (Climate change impact assessment for selected sectors in Poland) Forcing Data–Gridded Daily Precipitation & Temperature Dataset–5 km (CPLFD-GDPT5) consists of 1951–2013 daily minimum and maximum air temperatures and precipitation totals interpolated onto a 5 km grid based on daily meteorological observations from the Institute of Meteorology and Water Management (IMGW-PIB; Polish stations), Deutscher Wetterdienst...
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The Product of Matrix Metalloproteinase Cleavage of Doxorubicin Conjugate for Anticancer Drug Delivery: Calorimetric, Spectroscopic, and Molecular Dynamics Studies on Peptide–Doxorubicin Binding to DNA
PublikacjaMatrix metalloproteinases (MMPs) are extracellular matrix degradation factors, promoting cancer progression. Hence, they could provide an enzyme-assisted delivery of doxorubicin (DOX) in cancer treatment. In the current study, the intercalation process of DOX and tetrapeptide-DOX, the product of the MMPs' cleavage of carrier-linked DOX, into dsDNA was investigated using stationary and time-resolved fluorescence spectroscopy, UV-Vis...
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Crystal structure, hydrogen bonds, and lattice dynamics in kanemite from first-principles calculations
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Combining tight-binding and molecular dynamics methods to model the behaviour of metals in the plastic regime
PublikacjaOpisujemy zastosowanie metody dwuskalowej (kwantowo-klasycznej) w zastosowaniu do metali. Region energetycznie najważniejszy jest traktowany kwantowo, podczas gdy reszta układu jest traktowana klasycznie. Wprowadzamy własną implementację metody oraz przedstawiamy uzyskane wyniki dla metali.
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Dynamic Formation and Breaking of Disulfide Bonds in Molecular Dynamics Simulations with the UNRES Force Field
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Thermodynamics, size, and dynamics of zwitterionic dodecylphosphocholine and anionic sodium dodecyl sulfate mixed micelles
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An automatic selection of optimal recurrent neural network architecture for processes dynamics modelling purposes
PublikacjaA problem related to the development of algorithms designed to find the structure of artificial neural network used for behavioural (black-box) modelling of selected dynamic processes has been addressed in this paper. The research has included four original proposals of algorithms dedicated to neural network architecture search. Algorithms have been based on well-known optimisation techniques such as evolutionary algorithms and...
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An adaptive-noise Augmented Kalman Filter approach for input-state estimation in structural dynamics
PublikacjaThe establishment of a Digital Twin of an operating engineered system can increase the potency of Structural Health Monitoring (SHM) tools, which are then bestowed with enhanced predictive capabilities. This is particularly relevant for wind energy infrastructures, where the definition of remaining useful life is a main driver for assessing the efficacy of these systems. In order to ensure a proper representation of the physical...
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Tool Life and Process Dynamics in High Speed Ball End Milling of Hardened Steel
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Triticale extrudates – Changes of macrostructure, mechanical properties and molecular water dynamics during hydration
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MEL zeolite nanosheet membranes for water purification: insights from molecular dynamics simulations
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Dynamics of Microbiome Changes in the Endometrium and Uterine Cervix during Embryo Implantation: A Comparative Analysis
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Population dynamics of Baltic herring since the Viking Age revealed by ancient DNA and genomics
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Multimodal analysis of traction forces and the temperature dynamics of living cells with a diamond-embedded substrate
PublikacjaCells and tissues are constantly exposed to chemical and physical signals that regulate physiological and pathological processes. This study explores the integration of two biophysical methods: traction force microscopy (TFM) and optically detected magnetic resonance (ODMR) to concurrently assess cellular traction forces and the local relative temperature. We present a novel elastic substrate with embedded nitrogen-vacancy microdiamonds...
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Influence of a lipid bilayer on the conformational behavior of amphotericin B derivatives - A molecular dynamics study.
PublikacjaAmphotericin B (AmB) is an effective but very toxic antifungal antibiotic. In our laboratory a series of AmB derivatives of improved selectivity of action was synthesized and tested. To understand molecular basis of this improvement, comparative conformational studies of amphotericin B and its two more selectivederivatives were carried out in an aqueous solution and in a lipid membrane. These molecular simulation studies revealed...
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Non-linearity of multibody dynamic equations with respect to Lagrange multipliers: application to railway dynamics
PublikacjaPraca koncentruje się na dynamice układów wieloczłonowych z zamkniętymi łańcuchami członów. Głównym punktem zainteresowania jest modelowanie układów z występującymi nieliniowymi zależnościami opisującymi wpływ siły mnożników Lagrange'a na dynamikę układu (nieliniowe modele siły tarcia.). Aby zbudować model dynamiki układu zawierającego zamknięte łańcuchy członów, wspomniane łańcuchy są "rozcinane" i budowana jest struktura drzewa...
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Dynamics of productivity in higher education: cross-european evidence based on bootstrapped Malmquist indices
PublikacjaAbstract This study examines patterns of productivitychange in a large set of 266 public higher educationinstitutions (HEIs) in 7 European countries across the timeperiod 2001-2005. We adopt consistent bootstrap estimationprocedures to obtain confidence intervals for Malmquistindices of HEI productivity and their components.Consequently, we are able to assess the statistical significanceof changes in HEI productivity, efficiency...
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Fractional neutron point kinetics equations for nuclear reactor dynamics – Numerical solution investigations
PublikacjaThis paper presents results concerning numerical solutions to a fractional neutron point kinetics model for a nuclear reactor. The paper discusses and expands on results presented in (Espinosa-Paredes et al., 2011). The fractional neutron point kinetics model with six groups of delayed neutron precursors was developed and a numerical solution using the Edwards’ method was proposed (Edwards et al., 2002). The mathematical model...
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Source-related Wavefields in Fluids and Dielectrics: A new way of Thinking about Medium Dynamics
PublikacjaAcoustic and electromagnetic wave phenomena may seem to have a proper formal representation in field theory dating from the 19th century, founded on the mathematics of complex functions. This paper shows, however, that when replacing the classical spectrum-domain approach related to the assumption of harmonic timeform of signals, with a time-domain approach imposingnorestrictionastotheclassoftimeevolutionofsourceandfieldsignals,...
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Smart modeling support for managing complexities and dynamics of knowledge-based systems - part 2
PublikacjaPrzedstawiono i poddano analizie najnowsze trendy w zakresie kierunków badań dotyczących inteligentnego wspomagania zarządzania dynamiką i kompleksowością systemów opartych na wiedzy.
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Dynamics of productivity in higher education. Cross-European evidence based on bootstrapped Malmquist indices
PublikacjaThis study presents patterns of productivity change in a large set of 266 public higher education institutions (HEIs) from 7 European countries across the time period 2001-2005. We adopt consistent bootstrap estimation procedures to obtain confidence intervals for Malmquist indices of HEI productivity and their components. Consequently, we are able to assess statistical significance of the changes in HEIs' productivity, efficiency...
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Dynamics analysis of footbridge mode shapes the s8 expressway on the basis of the results of in situ tests
PublikacjaNon-destructive diagnostics for structure may use dynamic measurements realized during vibrations of a facility induced by dynamic environmental impact, enforced by the use of inductors or impulse impact. Dynamic tests and the analysis were undertaken for a footbridge situated over the expressway S8. The studies in situ allowed for dynamic characteristics to be determined: frequency, shape modes and damping for respective frequency...
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Bistability in a One-Dimensional Model of a Two-Predators-One-Prey Population Dynamics System
PublikacjaIn this paper, we study a classical two-predators-one-prey model. The classical model described by a system of three ordinary differential equations can be reduced to a one-dimensional bimodalmap. We prove that this map has at most two stable periodic orbits. Besides, we describe the bifurcation structure of the map. Finally, we describe a mechanism that leads to bistable regimes. Taking this mechanism into account, one can easily...
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Furan Fragmentation in the Gas Phase: New Insights from Statistical and Molecular Dynamics Calculations
PublikacjaWe present a complete exploration of the different fragmentation mechanisms of furan (C4H4O) operating at low and high energies. Three different theoretical approaches are combined to determine the structure of all possible reaction intermediates, many of them not described in previous studies, and a large number of pathways involving three types of fundamental elementary mechanisms: isomerization, fragmentation, and H/H2 loss...
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Influence of Protonation State on the Excited State Dynamics of a Photobiologically Active Ru(II) Dyad
PublikacjaThe influence of ligand protonation on the photophysics of a ruthenium (Ru) dyad bearing the 2-(1-pyrenyl)-1H-imidazo[4,5-f][1,10]-phenanthroline (ippy) ligand was investigated by time-resolved transient absorption spectroscopy. It was found that changes in the protonation state of the imidazole group led to changes in the electronic configuration of the lowest lying excited state. Formation of the fully deprotonated imidazole...
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Anisotropic mechanical behavior and auxeticity of penta-graphene: Molecular statics/molecular dynamics studies
PublikacjaWe investigate the mechanical properties of penta-graphene (PG), a recently proposed two-dimensional carbon allotrope using atomistic simulation techniques combined with the empirical description of interatomic interactions. We report on the dependence of its three in-plane mechanical moduli (i.e. Young's modulus, Poisson's ratio and shear modulus) on the deformation direction, strain and temperature. We show that PG displays a...
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Study on population dynamics for triple-linked food chain using a simulation-based approach
PublikacjaThe procedures based on simulation have become a feasible testing method that does not require investing valuable resources to create a concrete prototype, especially with the increasing computational power of computers. Thus, design changes can be adopted and design errors can be fixed before it is too late. Simulation turns to be a cheap, safe and often more acceptable from an ethical perspective. In our work we summarize the...
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Fem and time stepping procedures in non-linear dynamics of flexible branched shell structures.
PublikacjaW pracy dyskutowano problemy całkowania równań ruchu, sformułowanych w ramach nieliniowej sześcioparametrowej teorii powłok. Główne myśli dotyczą zbieżności rozwiązań uzyskanych w procesie aproksymacji przestrzennej i czasowej oraz analizy stabilności rozwiązań MES.
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Molecular aspects of the interaction between amphotericin B and a phospholipid bilayer: molecular dynamics studies.
PublikacjaAmfoterycyna B jest antybiotykiem z grupy polienów makrolidowych. Stosowany jest on w leczeniu układowych infekcji grzybowych. Wiadomo że związek ten oddziałuje ze składnikami błon lipidowych i tworzy kanały. W przedstawianej pracy prezentowane są wyniki symulacji przeprowadzonej dynamiką molekularną układu składającego się z 200 cząsteczek lipidów DMPC i jednej cząsteczki amfoterycyny ułożonej na powierzchni błony. Z przeprowadzonej...
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Phylogenetic relationship and antimicrobial resistance in Escherichia coli isolated from the Reda River and the Oliwski Stream, Northern Poland = Lekooporność i przynależność filogenetyczna szczepów Escherichia Coli izolowanych z rzeki Redy i Potoku Oliwskiego
PublikacjaThe high abundance of fecal bacteria in surface water is usually related to poor agricultural practice, pollution caused by domesticated and wild animals as well as with septic tank failures. Identification of fecal contamination sources seems to be crucial in order to effectively estimate the inherent risk. In this study, the phylogenetic relationship of 30 isolates of E. coli, originated from surface water, was estimated by employing...
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Identification of 1H‐indene‐(1, 3, 5, 6)‐tetrol derivatives as potent pancreatic lipase inhibitors using molecular docking and molecular dynamics approach
PublikacjaPancreatic lipase is a potential therapeutic target to treat diet-induced obesity in humans, as obesity-related diseases continue to be a global problem. Despite intensive research on finding potential inhibitors, very few compounds have been introduced to clinical studies. In this work, new chemical scaffold 1H-indene-(1,3,5,6)-tetrol was proposed using knowledge-based approach, and 36 inhibitors were derived by modifying its...
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First occurrence of thinlip grey mullet, Liza ramada (Risso, 1827) in the Odra River estuary (NW Poland): genetic identification
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First record of the leopard pleco, <I>Pterygoplichthys gibbiceps</I> (Actinopterygii, Loricariidae) in the Brda River in the centre of Bydgoszcz (northern Poland)
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Volatile organic pollutants in the Odra river - sources. Lotne związki organiczne obecne w wodach rzeki Odry - próba identyfikacji.
PublikacjaPrzedstawiono wyniki oznaczania i identyfikacji lotnych związków organicznych obecnych w wodach Odry. Próbki do analiz pobierano w ramach Międzynarodowego Programu Odra. W badaniach wykorzystano zestaw do jednoczesnego wymywania i wychwytywania analitów na stałym sorbencie (Purge and Trap)Oznaczenia końcowe wykonano z wykorzystaniem techniki chromatografii gazowej połączonej ze spektrometrem mas. W wodach zidentyfikowano szeroką...
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Spectroscopic studies on physicochemical properties of selected unsymmetrical bisacridine derivatives and NMR analysis of their interactions with the model sequence Pu22 aided by molecular dynamics
PublikacjaIn recent years, new promising acridine derivatives have appeared, belonging to the unsymmetrical bisacridines (UAs) family with high anticancer activity. Both their physicochemical properties and their mechanism of action at the molecular level have not been thoroughly analyzed so far. Four derivatives were selected for the study, termed as: C-2028, C-2041, C-2045 and C-2053. The first aim of this work was to determine the protonation...
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An insight into the mixed quantum mechanical-molecular dynamics simulation of a ZnII-Curcumin complex with a chosen DNA sequence that supports experimental DNA binding investigations
PublikacjaAn important aspect of research pertaining to Curcumin (HCur) is the need to arrest its degradation in aqueous solution and in biological milieu. This may be achieved through complex formation with metal ions. For this reason, a complex of HCur was prepared with ZnII, that is not likely to be active in redox pathways, minimizing further complications. The complex is monomeric, tetrahedral, with one HCur, an acetate and a molecule...
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Band structure, Born effective charges, and lattice dynamics of CuInS2 from ab initio calculations
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Molecular dynamics simulation of human neurohypophyseal hormone receptors complexed with oxytocin—modeling of an activated state
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Orientational Order and Dynamics of Nematic Multipodes Based on Carbosilazane Cores Using Optical and Dielectric Spectroscopy
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UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics
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Improvements and new functionalities of UNRES server for coarse-grained modeling of protein structure, dynamics, and interactions
PublikacjaIn this paper we report the improvements and extensions of the UNRES server (https://unres-server.chem.ug.edu.pl) for physics-based simulations with the coarse-grained UNRES model of polypeptide chains. The improvements include the replacement of the old code with the recently optimized one and adding the recent scale-consistent variant of the UNRES force field, which performs better in the modeling of proteins with the β and the...
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Pre‐exascale HPC approaches for molecular dynamics simulations. Covid‐19 research: A use case
PublikacjaExascale computing has been a dream for ages and is close to becoming a reality that will impact how molecular simulations are being performed, as well as the quantity and quality of the information derived for them. We review how the biomolecular simulations field is anticipating these new architectures, making emphasis on recent work from groups in the BioExcel Center of Excellence for High Performance Computing. We exemplified...
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Adsorption dynamics of chlorinated hydrocarbons from multi-component aqueous solution onto activated carbon
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On dynamics of flexible branched shell structures undergoing large overall motion using finite elements
PublikacjaZaprezentowano autorski algorytm do analizy dynamicznej powłok sprężystych oparty na niejawnym schemacie Newmarka. Rozważania dotyczą całkowania po czasie dynamicznych równań ruchu sformułowanych w ramach nieliniowej sześcioparametrowej teorii powłok. Opracowanie zawiera pewne elementy analizy statycznej, poprzedzającej badania dynamiczne. Przykłady numeryczne prezentują zastosowanie algorytmu stanowią podstawową część pracy.
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Study of Direct Methanol Fuel Cell Process Dynamics Using Dynamic Electrochemical Impedance Spectroscopy
PublikacjaA new technique, which was developed to characterize the direct methanol fuel cell under work conditions, has been presented in this paper. The impedance measurements were made using dynamic electrochemical impedance spectroscopy research technique in the galvanostatic mode, using multiple sinusoidal excitation. Obtained results show, that together with an increase of the temperature and working load, the global impedance...
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Editorial: smart modeling support for managing complexities and dynamics of knowledge-based systems-part 1
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Theoretical Investigation of the Electron-Transfer Dynamics and Photodegradation Pathways in a Hydrogen-Evolving Ruthenium-Palladium Photocatalyst
PublikacjaTime-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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Early stages of condensation from the gaseous phase in a H2O-N2 system: a molecular dynamics study.
PublikacjaW pracy przedstawiono wyniki symulacji wczesnych etapów kondensacji z fazy gazowej w układzie xH2O (1-x)N2. Przeanalizowano całkowitą liczbę klastrów, średni rozmiar klastra i rozmiar klastra maksymalnego w funkcji czasu.