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Wyniki wyszukiwania dla: AB INITIO CALCULATIONS
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Probing the Magnetic Anisotropy of Co(II) Complexes Featuring Redox-Active Ligands
PublikacjaCoordination complexes that possess large magnetic anisotropy (otherwise known as zero-field splitting, ZFS) have possible applications in the field of magnetic materials, including single molecule magnets (SMMs). Previous studies have explored the role of coordination number and geometry in controlling the magnetic anisotropy and SMM behavior of high-spin (S = 3/2) Co(II) complexes. Building upon these efforts, the present work...
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Modeling the Structure, Dynamics, and Transformations of Proteins with the UNRES Force Field
PublikacjaThe physics-based united-residue (UNRES) model of proteins ( www.unres.pl ) has been designed to carry out large-scale simulations of protein folding. The force field has been derived and parameterized based on the principles of statistical-mechanics, which makes it independent of structural databases and applicable to treat nonstandard situations such as, proteins that contain D-amino-acid residues. Powered by Langevin dynamics...
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The role of low-energy electrons in the charging process of LISA test masses
PublikacjaThe estimate of the total electron yield is fundamental for our understanding of the test-mass charging associated with cosmic rays in the Laser Interferometer Space Antenna (LISA) Pathfinder mission and in the forthcoming gravitational wave observatory LISA. To unveil the role of low energy electrons in this process owing to galactic and solar energetic particle events, in this work we study the interaction of keV and sub-keV...
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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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Dissociative ionization dynamics of dielectric gas C3F7CN
PublikacjaFluoronitrile C3F7CN is a promising candidate for the replacement of SF6 dielectric gas in high-voltage insulation. We present a combined experimental and theoretical study on its ionization dynamics probed in the 0-100 eV energy range. We exploited the total ion collection technique to determine the absolute ionization cross section, mass spectrometry to determine the fragment branching ratios and ab initio nonadiabatic molecular...
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Multi-mode vibronic interactions in the five lowest electronic states of the fluorobenzene radical cation
PublikacjaThe multi-mode vibronic interactions between the five lowest electronic states of the fluorobenzene radical cation are investigated theoretically, based on ab initio electronic structure data, and employing the linear vibronic coupling model. Low-energy conical intersections, and strong vibronic couplings are found to prevail within the set of X-A and B-C-D cationic states, while the interactions between these two sets of states...
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Hydration of simple amides. FTIR spectra of HDO and theoretical studies
PublikacjaZastosowano metodę ważonych widm różnicowych do opisu hydratacji amidów w roztworach wodnych: formamidu, N-metyloformamidu, N,N-dimetyloformaidu, acetamidu, N-metyloacetamidu, N,N-dimetyloacetamidu. Narzędziem wspomagającym interpretację wyników eksperymentalnych są struktury agregatów solwatacyjnych wokół cząsteczki substancji rozpuszczonej uzyskane na podstawie obliczeń teoretycznych metodą ab initio z korelacją elektronową...
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Principles of target DNA cleavage and the role of Mg2+ in the catalysis of CRISPR–Cas9
PublikacjaAt the core of the CRISPR–Cas9 genome-editing technology, the endonuclease Cas9 introduces site-specific breaks in DNA. However, precise mechanistic information to ameliorate Cas9 function is still missing. Here, multimicrosecond molecular dynamics, free energy and multiscale simulations are combined with solution NMR and DNA cleavage experiments to resolve the catalytic mechanism of target DNA cleavage. We show that the conformation...
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The influence of intermolecular correlations on the infrared spectrum of liquid dimethyl sulfoxide
PublikacjaDimethyl sulfoxide (DMSO) is routinely applied as an excellent, water-miscible solvent and chemical reagent. Some of the most important data concerning its liquid structure were obtained using infrared (IR) spectroscopy. However, the actual extent of intermolecular correlations that connect the isolated monomer spectrum to the IR response of the bulk liquid is poorly studied thus far. Using ab initio molecular dynamics (AIMD) simulations,...
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Cytocompatibility of stabilized black phosphorus nanosheets tailored by directly conjugated polymeric micelles for human breast cancer therapy
PublikacjaThe novel procedure of few-layer black phosphorus (FLBP) stabilization and functionalisation was here proposed. The cationic polymer PLL and non-ionic PEG have been involved into encapsulation of FLBP to allow sufficient time for further nanofabrication process and overcome environmental degradation. Two different spacer chemistry was designed to bind polymers to tumor-homing peptides. The efficiency of functionalisation was examined...
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Low-Barrier Hydrogen Bond Determines Target-Binding Affinity and Specificity of the Antitubercular Drug Bedaquiline
PublikacjaThe role of short strong hydrogen bonds (SSHB) in ligand-target binding remains largely unexplored, thereby hin- dering a potentially important avenue in the rational drug de- sign. Here, we investigate the interaction between bedaquiline (Bq), a potent anti-tuberculosis drug, and the mycobacterial ATP synthase, to unravel the role of a specific hydrogen bond to a conserved acidic residue in the target affinity and specificity....
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Enhanced photocatalytic properties of lanthanide-TiO2 nanotubes: An experimental and theoretical study
PublikacjaA series of Er-, Yb-, Ho-, Tb-, Gd-, Pr-TiO2 nanotubes (RE-NTs) was prepared via an electrochemical method. The as-prepared photocatalysts were characterized by X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), UV–vis absorption, scanning electron microscopy (SEM) and luminescent spectroscopy. The experiments demonstrated that toluene in the gas phase was successfully degraded under visible light (LEDs λmax = 465...
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Linking optical and electronic properties to photoresponse of heterojunctions based on titania nanotubes and chromium, molybdenum, and tungsten oxides
PublikacjaThe development of photosensitization strategies for titanium dioxide is necessary for the enhancement of its optical and electronic properties towards its application potential in solar photoelectrochemistry. In this work, significant differences in the photosensitizing capability of the 6th group transition metal oxides applied on the surface of titania nanotubes are reported. For the first time, correlations between the experimentally...
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How acidic amino acid residues facilitate DNA target site selection
PublikacjaDespite the negative charge of the DNA backbone, acidic residues (Asp/Glu) commonly participate in the base readout, with a strong preference for cytosine. In fact, in the solved DNA/protein structures, cytosine is recognized almost exclusively by Asp/Glu through a direct hydrogen bond, while at the same time, adenine, regardless of its amino group, shows no propensity for Asp/Glu. Here, we analyzed the contribution of Asp/Glu...
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Structure and properties of liquid Al–Cu alloys: Empirical potentials compared
PublikacjaWe report on the structure and mass transport properties of liquid Al–Cu alloys predicted by two recently-developed empirical many-body potentials: MEAM (Jelinek et al., 2012) and EAM-ADP (Apostol and Mishin, 2011), and by the well-known Gupta potential. Total and partial pair correlation functions, angular distribution functions, densities, coordination numbers and self-diffusion coefficients are compared with published experimental...
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Unique agreement of experimental and computational infrared spectroscopy: a case study of lithium bromide solvation in an important electrochemical solvent
PublikacjaInfrared (IR) spectroscopy is a widely used and invaluable tool in the studies of solvation phenomena in electrolyte solutions. Using state-of-the-art chemometric analysis of a spectral series measured in a concentration-dependent manner, the spectrum of the solute-affected solvent can be extracted, providing a detailed view of the structural and energetic states of the solvent molecules influenced by the solute. Concurrently,...
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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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Studies on the solid-liquid equilibria and intermolecular interactions Urea binary mixtures with Sulfanilamide and Sulfacetamide
PublikacjaThe binary phase diagrams of Sulfanilamide-Urea (SN-U) and Sulfacetamide-Urea (SC-U) were measured using differential scanning calorimetry technique (DSC). Both examined mixtures were found to form simple binary eutectics. The limited miscibility in the solid state observed by DSC, proving inability of co-crystallization in new multi-molecular form, was also confirmed using PXRD and FTIR-ATR measurements of solid dispersions...
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Charge Distribution and Hyperfine Interactions in GdBa2Cu3O7 from First Principles
PublikacjaW rozdziale przedstawiono wyniki obliczeń "z zasad pierwszych" (''ab initio'') struktury elektronowej, rozkładu ładunku i struktury nadsubtelnej, w szczególności gradientu pola elektrycznego (EFG) i składnika kontaktowego pola nadsubtelnego (HFF), nadprzewodnika wysokotemperaturowego o wzorze GdBa2Cu3O7 (Gd123). Do obliczeń wykorzystano metodę FP-LAPW (full-potential linearized augmented plane wave). Efekty związane z oddziaływaniami...
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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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Conformational analysis of N-isopropylbenzohydroxamic acids:Crystal structure, DFT and NMR studies
PublikacjaCelem pracy było znalezienie różnic strukturalnych dwóch wybranych kwasów N-izopropylobenzhydroksamowych, które rzutują na ich zaobserwowaną wcześniej zróżnicowaną reaktywność wobec odczynników elektrofilowych i porównanie ich budowy z budową znanych kwasów N-metylobenzhydroksamowych. Na podstawie analizy rentgenostrukturalnej monokryształu, obliczeń kwantowo-mechanicznych metodami ab initio oraz DFT w fazie gazowej oraz wyników...
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Molecular level interpretation of excess infrared spectroscopy
PublikacjaInfrared (IR) spectroscopy is an invaluable tool in studying intermolecular interactions in solvent mixtures. The deviation of the IR spectrum of a mixture from the spectra of its pure components is a sensitive measure of the non-ideality of solutions and the modulation of intermolecular interactions introduced by mutual influence of the components. Excess IR spectroscopy, based on the established notion of excess thermodynamic...
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Deep learning for ultra-fast and high precision screening of energy materials
PublikacjaSemiconductor materials for energy storage are the core and foundation of modern information society and play important roles in photovoltaic system, integrated circuit, spacecraft technology, lighting applications, and other fields. Unfortunately, due to the long experiment period and high calculation cost, the high-precision band gap (the basic characteristic parameter) of semiconductor is difficult to obtain, which hinders the...
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Rare earth ions doped K 2 Ta 2 O 6 photocatalysts with enhanced UV–vis light activity
PublikacjaNew rare earth-doped K2Ta2O6 photocatalysts were successfully synthesized by hydrothermal method. The effect of dopant type (Y,Yb,Ho,Pr,Er) and amount of rare earth precursor (2,4,8 and 10 mol%) on the physicochemical and photocatalytic properties of RE-K2Ta2O6 have been investigated. All as-prepared materials were characterized by UV–vis diffuse reflectance spectroscopy, Brunauer-Emmett-Teller specific surface area measurement,...
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Structural properties of hypothetical CeBa2Cu3O7 compound from LSDA+DMFT calculations
PublikacjaThe hypothetical stoichiometric CeBa2Cu3O7 (Ce123) compound, which has not been synthesized as a single phase yet, was studied by the density functional theory (DFT). We utilized a method which merges the local spin density approximation (LSDA) with the dynamical mean-field theory (DMFT) to account for the electronic correlations. The LSDA+DMFT calculations were performed in the high-temperature range. The particular emphasis was...
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Ab initiocharacterization of magneticCuFeS2
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Earthwork calculations in various field conditions
PublikacjaThe article characterizes the continuation of ongoing work on the MUGO computer program. The analyzes refer to the modernization of railway lines and directly to the earthwork calculations. The methodology of calculating the earthwork size in the areas of fills and cuts is discussed in detail.
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TERMODYNAMIC CALCULATIONS OF TURBINE STEAM PARAMETERS
PublikacjaIn this work a heat balance was made for the nominal conditions of a block working with 18K370 turbine. For the parameters obtained, the thermal-flow calculations of the steam turbine were performed, maintaining the actual geometry of its flow system. Based on the nominal values obtained, iterative thermal and flow calculations were made for both the heat cycle of the power plant block and the steam turbine itself, seeking to obtain...
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The hydrodynamic pressure field of the ship Zodiak, measurements and calculations
PublikacjaThe article presents the results of measurements of the slowly changing hydrodynamic pressure field HPF generated by the movement of the ship, Zodiak, in the Bay of Gdansk. The measurement results have been obtained in the framework of the program of the work in Siramis, under the auspices of the European Defence Administration of the EU, by the research team of the Naval Academy in Gdynia. The measurement results were compared with...
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Discrete random variables in reliability calculations of a reticulated shell
PublikacjaImplementation of the Point Estimation Method (PEM) in the reliability analysis of a three-dimensional truss structure is presented in the paper. The influence of geometric and material random parameters on the truss load-carrying capacity was investigated. The analysis was performed for different combinations of basic variables. Symmetric and asymmetric cases of snow load were taken to assess the structural reliability. Sensitivity...
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Static and dynamic concrete calculations: Breakable aggregates in DEM model
PublikacjaThe paper deals with the calculations of a 3-point bending beam under static and dynamic loads. The real microstructure was obtained from laboratory tests using micro-tomography images. The quasi-static results were compared directly with experimental data at both macro and micro levels. Subsequently, higher strain rates were applied to investigate dynamic effects. The study focused on the influence of dynamic loading on the macroscopic...
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DESIGN AND STRENGTH CALCULATIONS OF THE TRIPOD SUPPORT STRUCTURE FOR OFFSHORE POWER PLANT
PublikacjaThe support structure being the object of the analysis presented in the article is Tripod. According to the adopted assumptions, it is a foundation gravitationally set in the water region of 60 m in depth, not fixed to the seabed, which can be used for installing a 7MW wind turbine. Due to the lack of substantial information on designing and strength calculations of such types of structures in the world literature, authors have...
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1D Model Callibration on the Basis on 3D calculations for Tesla Turbine
PublikacjaThe paper presents the system of equations for axisymmetriclaminar flow, after averaging, through the width of interdisk slit ofTesla turbine. Coefficients were introduced, as a result ofaveraging, that improve the efficiency of 1D model. The minimalnumber of such coefficients was determined. The 1D modelmakes it possible to attain analytical solutions to an accuracylimited by these coefficients. Calibration of 1D model depends...
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Calculations of Short-Circuit Current Flows in Earth Wires of HV Lines
PublikacjaThis paper presents a method which enables calculating flows of short-circuit currents in earth wires of high voltage transmission lines, and its implementation in the form of a computer programme. The algorithm enables performing calculations for a double-fed line and starconnected lines (three terminal lines). The developed programme enables verifying dimensioning of earth wires in the context of their short-circuit thermal withstand...
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A 0.5-V bulk-driven voltage follower / DC level shifter and its application in class AB output stage
PublikacjaA simple realization of a 0.5-V bulk-driven voltage follower/DC level shifter, designed in a 0.18um CMOS technology is presented in the paper. The circuit is characterized by large input and output voltage swings, and a DC voltage gain close to unity. The DC voltage shift between input and output terminals can be regulated in a certain interval around zero, by means of biasing current sinks. An application of the proposed voltage...
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Ab initioheat capacity and atomic temperature factors of chalcopyrites
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Large hydrodynamic thrust bearing: Comparison of the calculations and measurements
PublikacjaHydrodynamic thrust bearings, used to carry axial loads in heavily loaded shafts of water power plants hydro turbines, can reach outer diameters even exceeding 5 m. In such large objects scale effect could be observed. According to this, allowable bearing specific load assuring safe operation of the bearings has to be decreased, which increases thrust bearing dimensions. This effect is caused by excessive thermal deflections of...
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DL_MG: A Parallel Multigrid Poisson and Poisson–Boltzmann Solver for Electronic Structure Calculations in Vacuum and Solution
PublikacjaThe solution of the Poisson equation is a crucial step in electronic structure calculations, yielding the electrostatic potential -- a key component of the quantum mechanical Hamiltonian. In recent decades, theoretical advances and increases in computer performance have made it possible to simulate the electronic structure of extended systems in complex environments. This requires the solution of more complicated variants of the...
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Electron-scattering cross sections for selected alkyne molecules: Measurements and calculations
PublikacjaWe report cross-section results from experimental and theoretical studies on electron collisions with 1-butyne (HC≡C–CH2CH3) and acetylene (HC≡CH) molecules and from computations for a propyne (HC≡C–CH3) molecule. Absolute grand -total electron-scattering cross sections (TCSs) were measured at impact energies ranging from about 0.5 to 300 eV using the linear electron-transmission method. The TCS energy curve for 1-butyne has a...
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Computed vibrational excitation ofCF4by low-energy electrons and positrons: Comparing calculations and experiments
PublikacjaQuantum calculations for the excitation of the asymmetric modes of the CF4 target gas, ν3 and ν4, by impact of low-energy electrons and positrons are carried out in the energy range around 1 eV and are compared with recent experimental findings. The similarities and differences between the two types of projectiles, and the two different modes, are analyzed and discussed vis à vis the present accord with the experimental results.
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Computer-Aided Calculations of Earth Potential Rise in High Voltage Overhead Lines
PublikacjaHigh voltage overhead power lines with earth wires comprise towers made of conductive material. Some towers are in locations where people can be expected to be either for a long time or for a short time but very frequently. Evaluation of shock hazard near such towers requires calculation of line-to-earth short-circuit current, earth current and especially earth potential rise. Number of towers in high voltage power lines can exceed...
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JMATRIX - a package for relativistic J-matrix calculations in elastic scattering of electrons from model potentials
PublikacjaWe present a software package JMATRIX, consisting of two computer codes written in FORTRAN 95 and parallelized with OpenMP, implementing the so-called J-matrix method, applied to elastic scattering of electrons on the radial potential, vanishing faster than Coulomb one. In the J-matrix method, physical scattering problem is replaced by using well-defined model, which is solved analytically. Presented software implements both non-relativistic...
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LattE- first-principles lattice energy calculations
PublikacjaCrystal engineering is currently attracting much interest. Its aim is to create materials of predefined properties fulfilling the requirements imposed by the applications. There are several parameters describing crystal structures, but the most important one is probably the energy of a crystal lattice. It is the energy released by the system when crystalline solid is formed out of molecules or ions in gaseous phase. Approximate...
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First-principles calculations of the lattice dynamics of CuInSe2
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Displacements of chimney in the light of computer calculations and surveying
PublikacjaThe article presents the numerical analysis of reinforced concrete chimney displacements, which was carried out geodetic measurements.
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A Novel Ru(II) Polypyridine Black Dye Investigated by Resonance Raman Spectroscopy and TDDFT Calculations
PublikacjaThe optical properties of a new(bipyridine)2Ru(4H-imidazole) complex presenting a remarkablebroad absorption in the visible range are investigated. Thestrong overlap of the absorption with the solar radiationspectrum renders the studied complex promising as a blackabsorber and hence as a starting structure for applications inthe field of dye-sensitized solar cells. The correlations betweenstructural and electronic features for...
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Effect of the Catalytic Center on the Electron Transfer Dynamics in Hydrogen-Evolving Ruthenium-Based Photocatalysts Investigated by Theoretical Calculations
PublikacjaThe 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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Weak hydrogen bonding interaction S-H···O=C studied by FT-IR spectroscopy and DFT calculations
PublikacjaInteractions between the thiolate group of tri-tert-butoxysilanethiol (TBST) and carbonyl group of acetone are studied with the use of FT-IR spectroscopy and DFT calculations.
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Density functional theory calculations on entire proteins for free energies of binding: Application to a model polar binding site
PublikacjaIn drug optimization calculations, the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method can be used to compute free energies of binding of ligands to proteins. The method involves the evaluation of the energy of configurations in an implicit solvent model. One source of errors is the force field used, which can potentially lead to large errors due to the restrictions in accuracy imposed by its empirical nature....
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Properties of Oxygen Vacancy and Hydrogen Interstitial Defects in Strontium Titanate: DFT + Ud,p Calculations
PublikacjaThis work presents extensive theoretical studies focused on the mixed ion-electron transport in cubic strontium titanate (STO). A new approach to the description of this difficult system was developed within the framework of linear-scaling Kohn–Sham density functional theory, as realized in the ONETEP program. The description we present is free of any empirical parameters and relies on the Hubbard U and Hund’s J corrections applied...