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Wyniki wyszukiwania dla: DYNAMICS OF IONS INTERACTION
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Effect of Starch Phosphorylation on Interaction With Chromium Ions in Aqueous Solutions
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Influence of magnetic interaction on lattice dynamics of FeBO 3
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Interaction of selected divalent metal ions with human ataxin-3 Q36
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Interaction of modes in nonlinear acoustics: theory and applications to pulse dynamics.
PublikacjaOgólna teoria oddziaływania modów hydrodynamicznych opiera się na wyprowadzeniu równań różniczkowych nieliniowych. Mody rozumiane są tu jako wektory własnych układów praw zachowań hydrodynamicznych. Rozpatrywano zjawiska towarzyszące fali akustycznej w przepływie lepkim nieliniowym. Uwzględniono płyny w każdym fizycznym równaniu stanu.
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Effects of Coulomb interaction on the electronic structure and lattice dynamics of the Mott insulatorFe2SiO4spinel
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Investigation of influence of space mopdes interaction on nonlinear dynamics of sound beams
PublikacjaOperatory rzutu na mody są zdefiniowane w dynamice płynów trójwymiarowych. Zostały wyprowadzone równania ewolucyjne. Rezultaty obliczeń numerycznych przedstawione.
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Interaction of amphotericin B with phospholipids in the model membrane - molecular dynamics study.
PublikacjaAmfoterycyna B jest antybiotykiem używanym w leczeniu układowych infekcji grzybowych. Jej mechanizm działania polega na tworzeniu kanałów wewnątrz błon lipidowych. W przedstawianej pracy publikowane są wyniki symulacji przeprowadzonej dynamiką molekularną monomerycznej i dimerycznej formy antybiotyku wewnątrz błony lipidowej zbudowanej z cząsteczek DMPC. Wyniki te wskazują, że powinowactwo cząsteczek amfoterycyny wewnątrz dimeru...
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Molecular dynamics study of the influence of calcium ions on the conformation of gelsolin S2 domain
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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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Formation of Protein Networks between Mucins: Molecular Dynamics Study Based on the Interaction Energy of the System
PublikacjaMolecular dynamics simulations have been performed for a model aqueous solution of mucin. As mucin is a central part of lubricin, a key component of synovial fluid, we investigate its ability to form cross-linked networks. Such network formation could be of major importance for the viscoelastic properties of the soft-matter system and crucial for understanding the lubrication mechanism in articular cartilage. Thus,the inter- and...
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Conformation analysis and semiclassical dynamics study of charge exchange process induced by collision of C2+ ions with tetrahydrofuran
PublikacjaWe 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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Beyond the helium buffer: 12C−2 rotational cooling in cold traps with H2 as a partner gas: interaction forces and quantum dynamics
Publikacjaabstract = { The scattering cross-sections and corresponding rate coefficients for rotationally inelastic collisions of $^{12}$C$_2$^-$ ($^2 \Sigma_g^+$) with H$_2$ ($^1 \Sigma_g^+$) are presented over a broad range of cold-trap temperatures. They have been calculated using quantum scattering theory that employs a new ab initio potential energy surface. The rate coefficients for the inelastic processes in the anionic partner are...
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In silico modelling for predicting the cationic hydrophobicity and cytotoxicity of ionic liquids towards the Leukemia rat cell line, Vibrio fischeri and Scenedesmus vacuolatus based on molecular interaction potentials of ions
PublikacjaIn this study we present prediction models for estimating in silico the cationic hydrophobicity and the cytotoxicity (log [1/EC50]) of ionic liquids (ILs) towards the Leukemia rat cell line (IPC-81), the marine bacterium Vibrio fischeri and the limnic green algae Scenedesmus vacuolatus using linear free energy relationship (LFER) descriptors computed by COSMO calculations. The LFER descriptors used for the prediction model (i.e....
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Lower rim substituted p-tert-butyl-calix[4]arene. Part 16. Synthesis of 25,26,27,28-tetrakis(piperidinylthiocarbonylmethylene)-p-tert-butylcalix[4]arene and its interaction with metal ions
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Lower Rim Substituted p-tert-Butyl-Calix[4]arene. Part 16. Synthesis of 25, 26, 27, 28-tetrakis(piperidinethiocarbonylmethylene)-p-tert-butylcalix[4]arene and its interaction with metal ions
PublikacjaThe synthesis, characterisation and X-ray crystal structures of p-tert-butyl-calix[4]arenethioamide L and its complex with lead L-Pb2+ is reported. The cation-binding properties in solution have been assessed by liquid-liquid extraction of the metal picrates from water into dichloromethane and by stability constants determination in acetonitrile using UV-absorption spectrophotometry or potentiometry. The compound was used as active...
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Jan Franz dr hab.
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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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H2O˙+ and OH+ reactivity versus furan: experimental low energy absolute cross sections for modeling radiation damage
PublikacjaRadiotherapy 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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Albumin–Hyaluronan Interactions: Influence of Ionic Composition Probed by Molecular Dynamics
PublikacjaThe lubrication mechanism in synovial fluid and joints is not yet fully understood. Nevertheless, intermolecular interactions between various neutral and ionic species including large macromolecular systems and simple inorganic ions are the key to understanding the excellent lubrication performance. An important tool for characterizing the intermolecular forces and their structural consequences is molecular dynamics. Albumin...
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Communication: Inside the water wheel: Intrinsic differences between hydrated tetraphenylphosphonium and tetraphenylborate ions
PublikacjaTetraphenylphosphonium tetraphenylborate (TPTB) is a common reference electrolyte in physical chemistry of solutions allowing for a convenient partitioning of thermodynamic properties into single-ion contributions. Here, we compute on the basis of ab initio molecular dynamics simulations the infrared (IR) spectra for hydrated constituent ions of the TPTB assumption. Using spectral decomposition techniques, we extract important...
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Solvent Exchange around Aqueous Zn(II) from Ab Initio Molecular Dynamics Simulations
PublikacjaHydrated zinc(II) cations, due to their importance in biological systems, are the subject of ongoing research concerning their hydration shell structure and dynamics. Here, ab initio molecular dynamics (AIMD) simulations are used to study solvent exchange events around aqueous Zn2+, for which observation in detail is possible owing to the considerable length of the generated trajectory. While the hexacoordinated Zn(H2O)62+ is the...
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Paweł Możejko dr hab.
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Effect of Ion and Binding Site on the Conformation of Chosen Glycosaminoglycans at the Albumin Surface
PublikacjaAlbumin is one of the major components of synovial fluid. Due to its negative surface charge, it plays an essential role in many physiological processes, including the ability to form molecular complexes. In addition, glycosaminoglycans such as hyaluronic acid and chondroitin sulfate are crucial components of synovial fluid involved in the boundary lubrication regime. This study presents the influence of Na+, Mg2+ and Ca2+ ions...
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Marek Czachor prof. dr hab.
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Catalytic Mechanism of Non-Target DNA Cleavage in CRISPR-Cas9 Revealed by Ab Initio Molecular Dynamics
PublikacjaCRISPR-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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Modelling charge transfer processes in C2+ -tetrahydrofuran collision for ion-induced radiation damage in DNA building blocks
PublikacjaInvestigations of collision-induced processes involving carbon ions and molecules of biological interest in particular DNA building blocks, are crucial to model the effect of radiation on cells in order to improve medical treatments for cancer therapy. Using carbon ions appears to be one of the most efficient ways to increase biological effectiveness to damage cancerous cells by irradiating deep-seated tumors. Therefore, interest...
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Effect of Nanohydroxyapatite on Silk Fibroin–Chitosan Interactions—Molecular Dynamics Study
PublikacjaFibroin–chitosan composites, especially those containing nanohydroxyapatite, show potential for bone tissue regeneration. The physicochemical properties of these biocomposites depend on the compatibility between their components. In this study, the intermolecular interactions of fibroin and chitosan were analyzed using a molecular dynamics approach. Two types of systems were investigated: one containing acetic acid and the other...
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Seashore sediment and water chemistry at the Admiralty Bay (King George Island, Maritime Antarctica) – geochemical analysis and correlations between the concentrations of chemical species
PublikacjaThis study covers water and sediment chemical characteristics by the western shore of Admiralty Bay (King George Island, Antarctica) in 2016. Chemical processes between sediment and water have been described based on the determination of ions, metals, non-metals, and TOC concentrations. Rock weathering is an important source of Fe, Ni, Co, Al in the seashore area. The PCA shows the impact of acidification in the release metals...
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Analiza drgań przewodu jezdnego sieci trakcyjnej w aspekcie oceny jej stanu technicznego.
PublikacjaGórna sieć trakcyjna jest nadal najefektywniejszym sposobem zasilania kolejowych pojazdów elektrycznych. Sieć jezdna nie ma możliwości technicznych redundancji, co wymaga okresowej oceny stanu technicznego w celu zapewnienia prawidłowej współpracy z odbierakami prądu pojazdów. W artykule przedstawiono aspekty oceny stanu technicznego górnej sieci trakcyjnej na podstawie modelowania matematycznego i wybranych badań laboratoryjnych....
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The Role of Electrostatics in Enzymes: Do Biomolecular Force Fields Reflect Protein Electric Fields?
PublikacjaPreorganization of large, directionally oriented, electric fields inside protein active sites has been proposed as a crucial contributor to catalytic mechanism in many enzymes, and it may be efficiently investigated at the atomistic level with molecular dynamics simulations. Here, we evaluate the ability of the AMOEBA polarizable force field, as well as the additive Amber ff14SB and Charmm C36m models, to describe the electric...
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Understanding ion–ion and ion–solvent interactions in aqueous solutions of morpholinium ionic liquids with N-acetyl-L-alaninate anion through partial molar properties and molecular dynamics simulations
PublikacjaAmino acid ionic liquids (AAILs) provide a low toxicity, biodegradable alternative to conventional ionic liquids, while also maintaining solubility in water. Densities and sound velocities of aqueous solutions of four amino acid ionic liquids (AAILs), based on the N-alkyl-N-methylmorpholinium ([Mor1,R], R = 2, 3, 6, 8) cation and N-acetyl-L-alaninate ([N-Ac-L-Ala]) anion were measured at T = (293.15–313.15) K and at atmospheric...
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VEHICLE DYNAMICS (2024)
Kursy Online(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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Theoretical calculation of the physico-chemical properties of 1-butyl-4-methylpyridinium based ionic liquids
PublikacjaACCEPTED MAIonic liquids (ILs) have attracted much attention for their unique physicochemical properties, which can be designed as needed by altering the ion combinations. Besides experimental work, numerous computational studies have been concerned with prediction of physical properties of ILs. The results of molecular dynamics simulations of ILs depend strongly on the proper force field parameterization. Classical force fields...
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Autocorrelation function for the chosen effective potential of the diatomic silver anion
Dane BadawczeThe 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
Dane BadawczeThe 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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Directed pulse dynamics
PublikacjaIntroducing a projection method into a one-dimensional model of a pulse propagation in isotropic media, we derive and investigate a system of equation describing dynamics ultrashort pulses of opposite directions ofpropagation and ones with interaction of directed pulses with different polarization.
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SELECTED PROBLEMS OF MACHINE DYNAMICS (2024)
Kursy OnlineThe 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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Unusual Influence of Fluorinated Anions on the Stretching Vibrations of Liquid Water
PublikacjaInfrared (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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Understanding the Electronic Structure and Optical Properties of Vacancy-Ordered Double Perovskite A2BX6 for Optoelectronic Applications
PublikacjaOver 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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Selected Problems of Machine Dynamics
Kursy OnlineThe 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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Dynamics of quantum entanglement
PublikacjaA model of discrete dynamics of entanglement of a bipartite quantum state is considered. It involves a global unitary dynamics of the system and periodic actions of local bistochastic or decaying channel. For initially pure states the decay of entanglement is accompanied by an increase of von Neumann entropy of the system. We observe and discuss revivals of entanglement due to unitary interaction of subsystems. For some mixed states...
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The rovibrational energy levels of the diatomic silver anion and neutral silver dimer
Dane BadawczeThe 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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Mixed conductivity in tungstenite-phosphate glasses containing alkali metal ions
PublikacjaThe conductivity of glasses in the 50WO3-(50-x)P2O5-xA2O (A = Na, K, Cs) system has been investigated as a function of composition. It is shown that in tungstenite-phosphate glasses containing different alkali metal ions the conductivity decreases with an increase in the alkali metal ion content. A decrease in conductivity is larger for heavier ions and reaches more than seven orders of magnitude in the case of glass containing...
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Selected Problems of Machine Dynamics II
Kursy OnlineThe 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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Selected Problems of Machine Dynamics - advances
Kursy OnlineThe 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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Selected Problems of Machine Dynamics - advances
Kursy OnlineThe 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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Human Computer Interaction
Kursy Online -
Marcin Sikorski prof. dr hab. inż.
OsobyMarcin Sikorski jest profesorem w Katedrze Informatyki w Zarządzaniu na Wydziale Zarządzania i Ekonomii Politechniki Gdańskiej. Wcześniej odbył liczne pobyty w instytucjach naukowych, m.in. w Niemczech (Uniwersytety w Bonn i w Heidelbergu), Szwajcarii (ETH Zurich), Holandii (TU Eindhoven) i USA (Harvard University). Prof. Sikorski jest przedstawicielem Polski w komitecie TC13 Human-Computer-Interaction w międzynarodowej organizacji...
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Hydration of Oxometallate Ions in Aqueous Solution
PublikacjaThe strength of hydrogen bonding to and structure of hydrated oxometallate ions in aqueous solution have been studied by double difference infrared (DDIR) spectroscopy and large-angle X-ray scattering (LAXS), respectively. Anions are hydrated by accepting hydrogen bonds from the hydrating water molecules. The oxygen atom of the permanganate and perrhenate ions form weaker and longer hydrogen bonds to water than the hydrogen bonds...
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Potential energy curves and spectroscopic parameters of the diatomic silver anion and neutral silver dimer
Dane BadawczeThe 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...