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Search results for: QUANTUM DYNAMICS, NUMERICAL METHODS, TIME-DEPENDENT HAMILTONIAN, COUPLED SCHRÖDINGER EQUATIONS, FIELD-MOLECULE INTERACTION, PHOTOASSOCIATION, POWER-LAW DECAY, DIATOMIC MOLECULE, SPIN-ORBIT COUPLING, TRANSITION DIPOLE MOMENT
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Entropic Measures of Complexity of Short-Term Dynamics of Nocturnal Heartbeats in an Aging Population
PublicationTwo entropy-based approaches are investigated to study patterns describing differences in time intervals between consecutive heartbeats. The first method explores matrices arising from networks of transitions constructed following events represented by a time series. The second method considers distributions of ordinal patterns of length three, whereby patterns with repeated values are counted as different patterns. Both methods provide...
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Mechanochemical Energy Transduction during the Main Rotary Step in the Synthesis Cycle of F1-ATPase
PublicationF1-ATPase is a highly efficient molecular motor that can synthesize ATP driven by a mechanical torque. Its ability to function reversibly in either direction requires tight mechanochemical coupling between the catalytic domain and the rotating central shaft, as well as temporal control of substrate binding and product release. Despite great efforts and significant progress, the molecular details of this synchronized and fine-tuned...
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Krzywa przejściowa z wygładzoną krzywizną dla dróg kolejowych
PublicationW pracy przedstawiono koncepcję nowej postaci krzywej przejściowej, o liniowym przebiegu krzywizny na długości i wygładzonymi rejonami skrajnymi. Może ona stanowić alternatywę dla tzw. gładkich krzywych przejściowych, o nieliniowym przebiegu krzywizny na całej długości. Została tutaj wykorzystana uniwersalna metoda identyfikacji krzywych przejściowych za pomocą równań różniczkowych. Wyznaczono ogólne równania krzywizny oraz odpowiednie...
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Hydration of N-Hydroxyurea from Ab Initio Molecular Dynamics Simulations
PublicationN-Hydroxyurea (HU) is an important chemotherapeutic agent used as a first-line treatment in conditions such as sickle cell disease and β-thalassemia, among others. To date, its properties as a hydrated molecule in the blood plasma or cytoplasm are dramatically understudied, although they may be crucial to the binding of HU to the radical catalytic site of ribonucleotide reductase, its molecular target. The purpose of this work...
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Structural and dynamic changes adopted by EmrE, multidrug transporter protein—Studies by molecular dynamics simulation
PublicationEmrE protein transports positively charged aromatic drugs (xenobiotics) in exchange for two protons and thus provides bacteria resistance to variety of drugs. In order to understand how this protein may recognize ligands, the monomer and asymmetric apo-form of the EmrE dimer embedded in a heterogeneous phospholipid (POPE + POPG) membrane were studied by molecular dynamics simulations. Dimer is regarded as a functional form of the...
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Predicting the viscosity and electrical conductivity of ionic liquids on the basis of theoretically calculated ionic volumes
PublicationSelected physical properties of the ionic liquids might be quantitatively predicted based on the volumes of the ions these systems are composed of. It is demonstrated that the ionic volumes calculated using relatively simple theoretical quantum chemistry methods can be utilised to estimate the viscosities and electrical conductivities of various commonly used ionic liquids. The fitting formulas of the exponential form are offered...
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A spectroscopic study of the cis/trans-isomers of penta-2,4-dienoic acid attached to gold nanoclusters
PublicationIn this theoretical work, we present a spectroscopic analysis of the cis/trans-isomers of a molecular switch, penta-2,4-dienoic acid, attached to gold clusters of different size (1, 2 and 20 gold atoms). We have simulated 4 different spectroscopic techniques: Infrared spectroscopy, normal Raman scattering, absorption spectra and resonance Raman scattering. We discuss how the position and the conformation of the molecule determine...
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FDTD Simulations on Disjoint Domains with the Use of Discrete Green's Function Diakoptics
PublicationA discrete Green's function (DGF) approach to couple disjoint domains in the finite-difference time-domain (FDTD) grid is developed. In this method, total-field/scattered-field (TFSF) FDTD domains are associated with simulated objects whereas the interaction between them is modeled with the use of the DGF propagator. Hence, source and scatterer are simulated in separate domains and updating of vacuum cells, being of little interest,...
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The equations for interactions of polarization modes in optical fibres including the kerr effect
PublicationWe have derived coupled nonlinear Schro¨ dinger equations (CNLSE) for arbitrary polarized light propagation in a single-mode fibre employing electromagnetic field complete description. We used a basis of transverse eigenmodes with appropriate projecting; hence, the nonlinear constants depend on the waveguide geometry. Accounting for a weak nonlinearity, which is connected to the Kerr effect, we have given explicit expressions for...
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An isogeometric finite element formulation for boundary and shell viscoelasticity based on a multiplicative surface deformation split
PublicationThis work presents a numerical formulation to model isotropic viscoelastic material behavior for membranes and thin shells. The surface and the shell theory are formulated within a curvilinear coordinate system,which allows the representation of general surfaces and deformations. The kinematics follow from Kirchhoff–Love theory and the discretization makes use of isogeometric shape functions. A multiplicative split of the surface...
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Electrical Simulations of the SIS100 Superconducting Dipole and Quadrupole Circuits: Transients, Earthing and Failure Modes
PublicationThe 100 Tm superconducting synchrotron SIS100 is the main accelerator of the international Facility for Antiproton and Ion Research (FAIR) currently under advanced construction in Darmstadt, Germany. The SIS100 dipole circuit which creates the magnetic field required to bend the beam, consists of 108 dipoles distributed over six arc sections of the ring. The magnetic field for the beam focusing is generated by three individual...
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Eu2Mg3Bi4: Competing Magnetic Orders on a Buckled Honeycomb Lattice
PublicationThe honeycomb lattice and its derived variants provide information on modeling and designing quantum magnets. A novel magnetic material, Eu2Mg3Bi4, which stabilizes in a previously unknown buckled honeycomb lattice, was discovered by high-pressure and high-temperature methods. We report here on the synthesis exploration of pure single crystals, structural determination of the buckled honeycomb lattice of europium moments, and experimental observation...
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Photophysics of Soret-Excited Tin(IV) Porphyrins in Solution
PublicationThe photophysics of low-chlorin tin(IV) tetraphenylporphyrin dihydroxide, a core building block for axially substituted supramolecular tin porphyrin constructs, has been studied in a variety of hydrogen-bonding, nonpolar, and aprotic polar solvents using steady-state, nanosecond, and femtosecond time-resolved emission, and femtosecond time-resolved absorption methods. In hydrogen-bonding solvents the metalloporphyrin exists as...
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Endohedral gallide cluster superconductors and superconductivity in ReGa5
PublicationWe present transition metal-embedded (T@Gan) endohedral Ga clusters as a favorable structural motif for superconductivity and develop empirical, molecule-based, electron counting rules that govern the hierarchical architectures that the clusters assume in binary phases. Among the binary T@Gan endohedral cluster systems, Mo8Ga41, Mo6Ga31, Rh2Ga9, and Ir2 Ga9 are all previously known superconductors. The well-known exotic superconductor...
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Dynamics of Ice Jam Formation and Release
PublicationThe numerical model DynaRICE and its application to ice jam formation and release is presented. The model is a two-dimensional coupled flow and ice dynamic model. The ice dynamic component, which includes both the internal ice resistance and boundary friction on ice motion, uses a Lagrangian SPH method. The hydrodynamic component of the model uses a streamline upwind finite element method, which is capable of simulating trans-critical...
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<i>N,N</i>'-diphenylthiourea acetone monosolvate
PublicationIn the title compound, C13H12N2S·C3H6O, the phenyl rings of the thiourea molecule are in syn and anti positions in relation to the C=S bond. Two molecules are connected by N-HS=C hydrogen bonds into a centrosymmetric dimer. An additional N-HO=C hydrogen bond to the acetone solvent molecule and some weak C-H interactions reinforce the crystal structure.
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On the Equations of the Surface Elasticity Model Based on the Theory of Polymeric Brushes
PublicationMotivating by theory of polymers, in particular, by the models of polymeric brushes we present here the homogenized (continual) two-dimensional (2D) model of surface elasticity. A polymeric brush consists of an system of almost aligned rigid polymeric chains. The interaction between chain links are described through Stockmayer potential, which take into account also dipole-dipole interactions. The presented 2D model can be treated...
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Instantaneous Heating and Cooling Caused by Periodic or Aperiodic Sound of Any Characteristic Duration in a Gas with Vibrational Relaxation
PublicationThermodynamic relaxation of internal degrees of a molecule's freedom in a gas occurs with some characteristic time. This makes wave processes in a gas behave differently depending on the ratio of characteristic duration of perturbations and the relaxation time. In particular, generation of the secondary non-wave modes by intense sound in a nonlinear flow dependens on frequency. These kinds of interaction are considered in this...
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Pressure effects on the electronic structure and superconductivity of (TaNb)0.67(HfZrTi)0.33 high entropy alloy
PublicationEffects of pressure on the electronic structure, electron-phonon interaction, and superconductivity of the high entropy alloy ( TaNb ) 0.67 ( HfZrTi ) 0.33 are studied in the pressure range 0–100 GPa. The electronic structure is calculated using the Korringa-Kohn-Rostoker method with the coherent potential approximation. Effects of pressure on the lattice dynamics are simulated using the Debye-Grüneisen model and the Grüneisen...
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Extending the Frequency Limit of Microstrip-Coupled CSRR Using Asymmetry
PublicationAbstract— This article explains the frequency limitation in designing microstrip circuits based on a complementary split-ring resonator (CSRR) and reports a novel technique for increasing its operating frequency, which makes the CSRR suitable for high-frequency applications. This study helps in synthesizing the dimensions of symmetric CSRR (SCSRR) and asymmetric CSRR (ACSRR) circuits, which shows the applicability of the proposed...
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Low-energy positron scattering from DNA nucleobases: the effects from permanent dipoles
PublicationAb initio quantum calculations for low-energy positron scattering from gas-phase isolated molecular nucleobases which are part of the DNA structure are presented and discussed over the range of 1 eV to 25 eV. The calculations report the integral cross sections (ICSs) and the momentum-transfer cross sections (MTCSs) for Adenine, Guanine, Thymine and Cytosine. The calculations show very clearly the important role of the dominant...
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Superconductivity in the superhard boride WB4.2
PublicationWe show that the superhard boride WB4.2 is a superconductor with a Tc of 2.05(5) K. Temperature-dependent magnetic susceptibility, electrical resistivity, and specific heat measurements were used to characterize the superconducting transition. The Sommerfeld constant γ for WB4.2 is 2.07(3) mJ mol−1 K−2 and the ΔC/γTc=1.56, which is somewhat higher than what is expected for weakly coupled Bardeen–Cooper–Schrieffer type superconductors....
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Interaction Between Storm Water Conduit And Surface Flow For Urban Flood Inundation Modelling
PublicationRapid development of urban areas always comes with great side effects. One of them is the occurrence of urban floods. Growth of impervious surfaces in cities leads to increasing run-off values. This together with difficulties connected with sewage modernization in cities marks urban inundations as being one of the most important issues concerning urban water. Accurate prediction of a phenomenon is difficult as it is highly dependent...
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Współczynniki strat energetycznych w elementach napędu hydrostatycznego
PublicationW każdym układzie napędowym należy zastąpić obraz przepływu mocy opisany dotychczas powszechnie stosowanym wykresem Sankey’a spadku mocy zgodnego z kierunkiem przepływu mocy proponowanym przez autora wykresem wzrostu mocy w układzie przeciwnego do kierunku przepływu mocy. Należy więc opisywać straty i sprawność energetyczną a także pole pracy każdego silnika i układu napędowego jako zależne od wielkości fizycznych niezależnych...
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Hyperelastic Microcantilever AFM: Efficient Detection Mechanism Based on Principal Parametric Resonance
PublicationThe impetus of writing this paper is to propose an efficient detection mechanism to scan the surface profile of a micro-sample using cantilever-based atomic force microscopy (AFM), operating in non-contact mode. In order to implement this scheme, the principal parametric resonance characteristics of the resonator are employed, benefiting from the bifurcation-based sensing mechanism. It is assumed that the microcantilever is made...
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Electron collisions with cyanoacetylene HC3N : Vibrational excitation and dissociative electron attachment
PublicationWe experimentally probe electron collisions with HC3N in the energy range from 0 to 10 eV with the focus on vibrational excitation and dissociative electron attachment. The vibrational excitation cross sections show a number of resonances which are mode specific: the two dominant π∗ resonances are visible in the excitation of all the vibrational modes; however, broad σ ∗ resonances are visible only in certain bond-stretching vibrational...
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Computational methods for calculation of binding free energy for ligand-receptor complexes
PublicationAccurate description of the molecular complexes energetic influence is required for understanding of many biological functions carried out by proteins. Therefore, estimation of binding free energy for ligand-receptor complexes is of highest importance for structure-based ligand design and drug discovery approaches.Experimental methods of determination of difference in Gibbs'es free energy have many limitations. Thus, computational...
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Influence of Installation Effects on Pile Bearing Capacity in Cohesive Soils – Large Deformation Analysis Via Finite Element Method
PublicationIn this paper, the whole process of pile construction and performance during loading is modelled via large deformation finite element methods such as Coupled Eulerian Lagrangian (CEL) and Updated Lagrangian (UL). Numerical study consists of installation process, consolidation phase and following pile static load test (SLT). The Poznań site is chosen as the reference location for the numerical analysis, where series of pile SLTs...
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Muramyl dipeptide-based analogs as potential anticancer compounds: Strategies to improve selectivity, biocompatibility, and efficiency
PublicationAccording to the WHO, cancer is the second leading cause of death in the world. This is an important global problem and a major challenge for researchers who have been trying to find an effective anticancer therapy. A large number of newly discovered compounds do not exert selective cytotoxic activity against tumorigenic cells and have too many side effects. Therefore, research on muramyl dipeptide (MDP) analogs has attracted interest...
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Numerical investigation on the performance of a small counter-rotating wind turbine
PublicationThe article presents the results of the investigation on the performance of a small counter-rotating wind turbine. The wind turbine has been simulated using Computational Fluid Dynamics methods. Actuator Line Model has been successfully used to represent rotors in the computational domain. A parametric study has been carried out, taking into account changes in the tip speed ratio of the rotors while maintaining a constant distance...
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CFD analysis of fluid flow through the labyrinth seal
PublicationSteam and gas turbines are some of the fundamental means of power generation. The energy efficiency of the turbines, however, is not satisfactory. Ever since the start-up of the first turbine in the world, engineers have been striving for their increased efficiency. Multiple solutions to the problem of steam loss in an operating turbine are available. The use of seals is one of them. Empirical methods or numerical calculations...
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Mapping the Structural and Dynamic Determinants of pH-Sensitive Heparin Binding to Granulocyte Macrophage Colony Stimulating Factor
PublicationGranulocyte macrophage colony stimulating factor (GMCSF) is an immunomodulatory cytokine that is harnessed as a therapeutic. GMCSF is known to interact with other clinically important molecules, such as heparin, suggesting that endogenous and administered GMCSF has the potential to modulate orthogonal treatment outcomes. Thus, molecular level characterization of GMCSF and its interactions with biologically active compounds is critical...
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Dopants and gas modifiers in ion mobility spectrometry
PublicationThe ion mobility techniques, including the most commonly used drift-tube ion mobility spectrometry (IMS) and differential mobility spectrometry (DMS), are used successfully for the detection of a wide range of organic compounds in the gas phase. In order to improve detection quality, admixtures are added to gas streams flowing through the detector. Dopants mostly prevent the ionization of interfering chemicals however, better detection...
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A review on analytical models of brushless permanent magnet machines
PublicationThis study provides an in-depth investigation of the use of analytical and numerical methods in analyzing electrical machines. Although numerical models such as the finite-element method (FEM) can handle complex geometries and saturation effects, they have significant computational burdens, are time-consuming, and are inflexible when it comes to changing machine geometries or input values. Analytical models based on magnetic equivalent...
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Production of singlet oxygen atoms by photodissociation of oxywater
PublicationQuantum chemical calculations are reported for the energies of the few lowest electronic singlet states of oxywater along dissociation of the oxygen-oxygen bond into water and singlet oxygen using multistate multireference second-order Møller–Plesset perturbation theory. We compute an energy of 21 kcal/mol to remove one oxygen atom in the lowest singlet state. The two lowest excited singlet states have vertical excitation energies...
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On the plastic buckling of curved carbon nanotubes
PublicationThis research, for the first time, predicts theoretically static stability response of a curved carbon nanotube (CCNT) under an elastoplastic behavior with several boundary conditions. The CCNT is exposed to axial compressive loads. The equilibrium equations are extracted regarding the Euler–Bernoulli displacement field by means of the principle of minimizing total potential energy. The elastoplastic stress-strain is concerned...
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Acoustic heating produced in the thermoviscous flow of a bingham plastic
PublicationThis study is devoted to the instantaneous acoustic heating of a Bingham plastic. The model of the Bingham plastic's viscous stress tensor includes the yield stress along with the shear viscosity, which differentiates a Bingham plastic from a viscous Newtonian fluid. A special linear combination of the conservation equations in differential form makes it possible to reduce all acoustic terms in the linear part of of the final equation...
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Acoustic heating produced in the thermoviscous flow of a Bingham plastic
PublicationThis study is devoted to the instantaneous acoustic heating of a Bingham plastic. The model of the Bingham plastic's viscous stress tensor includes the yield stress along with the shear viscosity, which differentiates a Bingham plastic from a viscous Newtonian fluid. A special linear combination of the conservation equations in differential form makes it possible to reduce all acoustic terms in the linear part of of the final equation...
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Catalytic Mechanism of Non-Target DNA Cleavage in CRISPR-Cas9 Revealed by Ab Initio Molecular Dynamics
PublicationCRISPR-Cas9 is a cutting-edge genome editing technology, which uses the endonuclease Cas9 to introduce mutations at desired sites of the genome. This revolutionary tool is promising to treat a myriad of human genetic diseases. Nevertheless, the molecular basis of DNA cleavage, which is a fundamental step for genome editing, has not been established. Here, quantum–classical molecular dynamics (MD) and free energy methods are used...
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Core–shell excitation of isoxazole at the C, N, and O K-edges – an experimental NEXAFS and theoretical TD-DFT study
PublicationThe near-edge X-ray absorption fine structure (NEXAFS) spectra of the gas-phase isoxazole molecule have been measured by collecting total ion yields at the C, N, and O K-edges. The spectral structures have been interpreted using time-dependent density functional theory (TD-DFT) with the short-range corrected SRC2-BLYP exchange–correlation functional. Experimental and calculated energies of core excitations are generally in good...
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Multi-state multi-reference Møller-Plesset second-order perturbation theory for molecular calculations
PublicationThis work presents multi‐state multi‐reference Møller–Plesset second‐order perturbation theory as a variant of multi‐reference perturbation theory to treat electron correlation in molecules. An effective Hamiltonian is constructed from the first‐order wave operator to treat several strongly interacting electronic states simultaneously. The wave operator is obtained by solving the generalized Bloch equation within the first‐order...
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Nieliniowa statyka 6-parametrowych powłok sprężysto plastycznych. Efektywne obliczenia MES
PublicationGłównym zagadnieniem omawianym w monografii jest sformułowanie sprężysto-plastycznego prawa konstytutywnego w nieliniowej 6-parametrowej teorii powłok. Wyróżnikiem tej teorii jest występujący w niej w naturalny sposób tzw. stopień 6 swobody, czyli owinięcie (drilling rotation). Podstawowe założenie pracy to przyjęcie płaskiego stanu naprężenia uogólnionego na ośrodek typu Cosseratów. Takie podejście stanowi oryginalny aspekt opracowania....
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Guanosine Dianions Hydrated by One to Four Water Molecules
PublicationIntermolecular interactions such as those present in molecule···water complexes may profoundly influence the physicochemical properties of molecules. Here, we carried out an experimental–computational study on doubly deprotonated guanosine monophosphate···water clusters, [dGMP – 2H]2–·nH2O (n = 1–4), using a combination of negative anion photoelectron spectroscopy (NIPES) with molecular dynamics (MD) and quantum chemical (QM) calculations....
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Detection and time/frequency analysis of electric fields in the ground
PublicationThis paper sets out to detect and characterize electric fields in the ground (such as stray current fields) using a tandem time/frequency method of signal analysis. Results were obtained from investigations performed in the presence of a generated electric field with controlled variable characteristics, and in the presence of an electric field generated by a tramline. The analysis of measurement registers was performed using Short‐Time...
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Geometrically Nonlinear Analysis of Functionally Graded Shells Based on 2-D Cosserat Constitutive Model
PublicationIn this paper geometrically nonlinear analysis of functionally graded shells in 6-parameter shell theory is presented. It is assumed that the shell consists of two constituents: ceramic and metal. The mechanical properties are graded through the thickness and are described by power law distribution. Formulation based on 2-D Cosserat constitutive model is used to derive constitutive relation for functionally graded shells. Numerical...
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Role of the Solvation Water in Remote Interactions of Hyperactive Antifreeze Proteins with the Surface of Ice
PublicationMost protein molecules do not adsorb onto ice, one of the exceptions being so-called antifreeze proteins. In this paper, we describe that there is a force pushing an antifreeze protein molecule away from the ice surface when it is not oriented with its ice-binding plane toward the ice and that this pushing force may be also present even when the protein is oriented with its ice-binding plane toward the ice. This force is absent...
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SPECTRAL RESPONSE OF STATIONARY JACK-UP PLATFORMS LOADED BY SEA WAVES AND WIND USING PERTURBATION METHOD
PublicationThe paper addresses non-linear vibrations of offshore jack-up drilling platforms loaded by sea waves and wind in their stationary condition using the perturbation method. Non-linearity of dynamic equations of motion for fixed offshore platforms yields from two factors. The first is load excitation generating non-linear velocity coupling in a dynamic system. This coupling is inherent in the modified Morison equation, involving the...
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The imidazoacridinone C-1311 induces p53-dependent senescence or p53-independent apoptosis and sensitizes cancer cells to radiation
PublicationC-1311 is a small molecule, which has shown promise in a number of preclinical and clinical studies. However, the biological response to C-1311 exposure is complicated and has been reported to involve a number of cell fates. Here, we investigated the molecular signaling which determines the response to C-1311 in both cancer and non-cancer cell lines. For the first time we demonstrate that the tumor suppressor, p53 plays a key role...
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On the non-linear dynamics of torus-shaped and cylindrical shell structures
PublicationIn this study, the non-linear dynamic analysis of torus-shaped and cylindrical shell-like structures has been studied. The applied material is assumed as the functionally graded material (FGM). The structures are considered to be used for important machines such as wind turbines. The effects of some environmental factors on the analysis like temperature and humidity have been considered. The strain field has been calculated in...
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Trichloridobis(ethyldiphenylphosphine)-(tetrahydrofuran)molybdenum(III)
PublicationIn the mononuclear title compound, [MoCl3(C4H8O)(C14H15P)2], obtained by the reaction of trichlorotris(tetrahydrofuran)molybdenum(III) and ethyldiphenylphosphine in tetrahydrofuran (THF) solution, the MoIII atom is six-coordinated by one O atom of a THF molecule, two P atoms from two ethyldiphenylphosphine ligands and three Cl atoms in a distorted octahedral geometry. The C atoms of the THF molecule are disordered over two positions...