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Search results for: WATER CLUSTERS, MOLECULAR INTERACTIONS, HYDROGEN BONDS, AB INITIO CALCULATIONS, ELASTIC SCATTERING, DIRAC-HARTREE-FOCK SELF-CONSISTENT FIELD, GAUSSIAN FUNCTION BASIS SE
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New Two-center Ellipsoidal Basis Function Neural Network for Fault Diagnosis of Analog Electronic Circuits
PublicationIn the paper a new fault diagnosis-oriented neural network and a diagnostic method for localization of parametric faults in Analog Electronic Circuits (AECs) with tolerances is presented. The method belongs to the class of dictionary Simulation Before Test (SBT) methods. It utilizes dictionary fault signatures as a family of identification curves dispersed around nominal positions by component tolerances of the Circuit Under Test...
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Joint experimental and theoretical study on low-energy elastic electron scattering by gaseous alkynes: Differential cross sections, shape resonances, and methylation effects
PublicationA detailed comparison of experimental and theoretical elastic cross sections for low-energy electron scattering by ethyne, taken earlier in our group by Gauf et al. [Phys. Rev. A 87, 012710 (2013)], and some of its methylated derivatives, propyne, and the isomers 1-butyne and 2-butyne, taken here, are presented. The present differential cross sections were measured at incident electron energies ranging from 1 eV to 30 eV and...
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Electric-field-induced magnetic quadrupole moment in the ground state of the relativistic hydrogenlike atom: Application of the Sturmian expansion of the generalized Dirac-Coulomb Green function
PublicationStosując rozwinięcie sturmowskie uogólnionej funkcji Greena-Diraca-Coulomba, znaleziono wyrażenie analityczne dla magnetycznego momentu kwadrupolowego, indukowanego przez zewnętrzne słabe, stałe, jednorodne pole elektryczne w stanie podstawowym relatywistycznego atomujednoelektronowego.
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Thermodynamics and kinetics of amphotericin B self-association in aqueous solution characterized in molecular detail
PublicationAmphotericin B (AmB) is a potent but toxic drug commonly used to treat systemic mycoses. Its efficiency as a therapeutic agent depends on its ability to discriminate between mammalian and fungal cell membranes. The association of AmB monomers in an aqueous environment plays an important role in drug selectivity, as oligomers formed prior to membrane insertion – presumably dimers – are believed to act differently on fungal (ergosterol-rich)...
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Molecular properties with dual basis set methods
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Furan Fragmentation in the Gas Phase: New Insights from Statistical and Molecular Dynamics Calculations
PublicationWe 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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Properties of Oxygen Vacancy and Hydrogen Interstitial Defects in Strontium Titanate: DFT + Ud,p Calculations
PublicationThis 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...
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Dual functionality of amphiphilic 1-alkyl-3-methylimidazolium hydrogen sulfate ionic liquids: surfactants with catalytic function
PublicationA series of amphiphilic 1-alkyl-3-methylimidazolium hydrogen sulfate ionic liquids were synthesized. Acidic hydrogen sulfate ionic liquids with the alkyl chains C6–C14 are characterized by good surface properties. Their surface properties (adsorption and micellization parameters, degree of ionization of micelles, Krafft temperatures and thermodynamic parameters) were determined. Synthesized ionic liquids were applied as a co-catalyst...
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Effect of the Catalytic Center on the Electron Transfer Dynamics in Hydrogen-Evolving Ruthenium-Based Photocatalysts Investigated by Theoretical Calculations
PublicationThe light-induced relaxation pathways in the molecular photocatalyst [(tbbpy)2Ru(tpphz)PtCl2]2+ are investigated with time-dependent density functional theory calculations together with the Marcus theory of electron transfer (ET). The calculations show that metal (Ru) to ligand (tpphz) charge transfer (MLCT) triplet states are populated following an excitation in the longer wavelength range of the absorption spectrum, but that an...
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First Evidence of Rhombic (NaCl)2-. Ab Initio Reexamination of the Sodium Chloride Dimer Anion
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Ab Initio Analysis of a Quantum Dot Induced by a Local External Potential in a Semiconducting Carbon Nanotube
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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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Method of reconstructing two-dimensional velocity fields on the basis of temperature field values measured with a thermal imaging camera
PublicationThis paper describes a novel numerical reconstruction procedure (NRP) of the velocity field during natural convective heat transfer from a two-sided, isothermal, heated vertical plate based only on the known temperature field obtained, e.g. with a thermal imaging camera. It has been demonstrated that with a knowledge of temperature distributions, the NRP enables the reconstruction of velocity fields by solving the Navier-Stokes...
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Fast Basis Function Estimators for Identification of Nonstationary Stochastic Processes
PublicationThe problem of identification of a linear nonsta-tionary stochastic process is considered and solved using theapproach based on functional series approximation of time-varying parameter trajectories. The proposed fast basis func-tion estimators are computationally attractive and yield resultsthat are better than those provided by the local least squaresalgorithms. It is shown that two...
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The significance of the properties of water for the working cycle of the kinesin molecular motor
PublicationExplicit solvent molecular dynamics simulations were performed in this study to investigate and discuss several aspects of the influence of the properties of water on the working cycle of a molecular motor from the kinesin superfamily. The main objects of attention were: the binding of the neck linker and the association of the kinesin and the tubulin. The docking of the neck linker is considered a crucial event during the working...
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Measurements of inelastic electron scattering from molecular oxygen at high scattering angles
PublicationBadano procesy wzbudzenia oscylacyjnego poziomów v = 1-9 stanu podstawowego X3 sigma g oraz v=0 stanu wzbudzonego a1 delta g cząsteczki tlenu dla energii 10eV w przedziale kąta rozproszenia od 90 do 180 st. Dla pomiaru v=1 stanu X3 sigma g wyznaczono różniczkowy przekrój czynny na wzbudzenie. W pomiarach wykorzystano podwójny hemisferyczny spektrometr elektrostatyczny wykorzystujący nowozaprojektowane źródło lokalnego pola magnetycznego.
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Differential cross section minima in elastic scattering of electrons fromzinc
PublicationZostały obliczone położenia minimów różniczkowych przekrojów czynnych na sprężyste rozpraszanie elektronów na atomach cynku. Metoda obliczeniowa oparta jest na równaniach relatywistycznej mechaniki kwantowej. Wyniki obliczeń zostały porównane z ostatnimi danymi doświadczalnymi grupy z Uniwersytetu Belgradzkiego.
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Critical minima in elastic scattering of electrons from Ar and Zn.
PublicationDokonano obliczeń różniczkowych przekrojów czynnych na sprężyste rozpraszanie elektronów na atomach argonu i cynku. Otrzymane minimum krytyczne z tych przekrojów porównano z niedawno otrzymanymi danymi doświadczalnymi.
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The high-energy critical minimum in elastic electron scattering by argon.
PublicationZostało zbadane położenie wysokoenergetycznego minimum krytycznego w rozpraszaniu elektronów na argonie. W celu przeprowadzenia dyskusji zachowania się czynnego przekroju różniczkowego w okolicy minimum krytycznego przeprowadzono analizę położenia minimum zarówno dla energii, jak i kątów.
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Water clusters in liquid organic matrices of different polarity
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Hydrogen assisted cracking of 2205 duplex stainless steel in synthetic sea water
PublicationThe cracking behavior of 2205 duplex stainless steels (DSSs) in synthetic sea water under cathodic polarization condition was investigated. (SSRT) method was employed in aim to evaluate the susceptibility to hydrogen assisted cracking. The results showed that the reduction in the uniform elongation (UEL) and the reduction of area (RA) varied with the applied cathodic current density. Significant reductions in ductility were found,...
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Ab-initio investigations for structural, mechanical, optoelectronic, and thermoelectric properties of Ba2SbXO6 (X Nb, Ta) compounds
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Dimeric structure of the N-terminal domain of PriB protein from Thermoanaerobacter tengcongensis solved ab initio
PublicationPriB is one of the components of the bacterial primosome, which catalyzes the reactivation of stalled replication forks at sites of DNA damage. The N-terminal domain of the PriB protein from the thermophilic bacterium Thermoanaerobacter tengcongensis (TtePriB) was expressed and its crystal structure was solved at the atomic resolution of 1.09 Å by direct methods. The protein chain, which encompasses the first 104 residues of the...
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Molecular dynamics study on the role of solvation water in the adsorption of hyperactive AFP to the ice surface
PublicationUsing computer simulations, the early stages of the adsorption of the CfAFP molecule to the ice surface were analyzed. We found that the ice and the protein interact at least as early as when the protein is about 1 nm away from the ice surface. These interactions are mediated by interfacial solvation water and are possible thanks to the structural ordering of the solvent. This ordering leads to positional preference of the protein...
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Experimental Research on Insufficient Water Lubrication of Marine Stern Tube Journal Bearing with Elastic Polymer Bush
PublicationWater-lubricated bearings with polymer bushes are steadily gaining popularity due to their advantages, including environmental friendliness, relatively simple construction and long-term operation. Nevertheless, in practice instances of damage to such bearings occur due to insufficient or absent flow of the lubricating agent. In this study, experimental tests established that elastic polymer bush bearing is capable of operating...
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Fast recursive basis function estimators for identification of time-varying processes
PublicationW pracy wprowadzono nową kategorię filtrów adaptacyjnych opartych na metodzie funkcji bazowych i wykorzystujących koncepcję postfiltracji. Proponowane algorytmy pozwalają połączyć niską złożoność obliczeniową i dobre właściwości śledzące.
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Cross sections for electron scattering from furan molecules; measurements and calculations
PublicationZmierzono i policzono przekroje czynne (TCS) na rozproszenie elektronów na drobinach furanu (C4H4O). Całkowite przekroje czynne zmierzono metodą transmisyjną w zakresie energii 0.6 - 400 eV. Sprężysty i jonizacyjny przekrój czyny obliczono dla energii zderzenia do 4 keV; powyżej 70 eV suma obu przekrojów pozostaje w dobrej zgodności z mierzonymi wartościami TCS.
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Electron scattering from hexafluoroacetone molecules: cross section measurements and calculations
PublicationZmierzono absolutne całkowite przekroje czynne na zderzenie elektronów z drobinami hexafluoroacetonu (HFA). Pomiary przeprowadzono dla energii zderzenia od 1 do 400 eV. Zależność energetyczna przekroju czynnego wykazała obecność struktur związanych z procesami o charakterze rezonansowym. Wykonano obliczenia sprężystego i jonizacyjnego przekroju czynnego dla drobin HFA i acetonu. Suma obliczonych przekrojów wykazuje dużą zgodność...
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Cross section calculations for electron scattering from DNA and RNA bases.
PublicationPoliczono różniczkowy i scałkowany przekrój czynny na rozproszenie sprężyste elektronów (w przybliżeniu atomów niezależnych) na uracylu, cytozynie, guaninie, adeninie i tyminie w zakresie energii od 50-4000 eV. W przybliżeniu modelu BEB policzono również przekroje czynne na jonizację tych molekuł.
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Crystallographic study of self-organization in the solid state including quasi-aromatic pseudo-ring stacking interactions in 1-benzoyl-3-(3,4-dimethoxyphenyl)thiourea and 1-benzoyl-3-(2-hydroxypropyl)thiourea
Publication1-Benzoylthioureas contain both carbonyl and thiocarbonyl functional groups and are of interest for their biological activity, metal coordination ability and involvement in hydrogen-bond formation. Two novel 1-benzoylthiourea derivatives, namely 1-benzoyl-3-(3,4-dimethoxyphenyl)thiourea, C₁₆H₁₆N₂O₃S, (I), and 1-benzoyl-3-(2-hydroxypropyl)thiourea, C₁₁H₁₄N₂O₂S, (II), have been synthesized and characterized. Compound (I) crystallizes...
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Quest for the Molecular Basis of Improved Selective Toxicity of All-Trans Isomers of Aromatic Heptaene Macrolide Antifungal Antibiotics
PublicationThree aromatic heptaene macrolide antifungal antibiotics, Candicidin D, Partricin A (Gedamycin) and Partricin B (Vacidin) were subjected to controlled cis-trans to all trans photochemical isomerization. The obtained all-trans isomers demonstrated substantially improved in vitro selective toxicity in the Candida albicans cells: human erythrocytes model. This effect was mainly due to the diminished hemotoxicity. The molecular modeling...
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Self-assembly, stability and conductance of amphotericin B channels: bridging the gap between structure and function
PublicationAmphotericin B (AmB), one of the most powerful but also toxic drugs used to treat systemic mycoses, is believed to selectively permeabilize fungal cell membranes to ions in a sterol-dependent manner. Unfortunately, the structure of the biologically active AmB channels has long eluded researchers, obstructing the design of safer alternatives. Here, we investigate the structural and thermodynamic aspects of channel formation, stability,...
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The hydrogen bond network structure within the hydration shell around simple osmolytes: Urea, tetramethylurea, and trimethylamine-N-oxide, investigated using both a fixed charge and a polarizable water model
PublicationDespite numerous experimental and computer simulation studies, a controversy still exists regarding the effect of osmolytes on the structure of surrounding water. There is a question, to what extent some of the contradictory results may arise from differences in potential models used to simulate the system or parameters employed to describe physical properties of the mixture and interpretation of the results. Bearing this in mind,...
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The hydrogen bond network structure within the hydration shell around simple osmolytes: Urea, tetramethylurea, and trimethylamine-N-oxide, investigated using both a fixed charge and a polarizable water model
PublicationDespite numerous experimental and computer simulation studies, a controversy still exists regarding the effect of osmolytes on the structure of surrounding water. There is a question, to what extent some of the contradictory results may arise from differences in potential models used to simulate the system or parameters employed to describe physical properties of the mixture and interpretation of the results. Bearing this in mind,...
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Neutral Dissociation of Pyridine Evoked by Irradiation of Ionized Atomic and Molecular Hydrogen Beams
PublicationThe interactions of ions with molecules and the determination of their dissociation patterns are challenging endeavors of fundamental importance for theoretical and experimental science. In particular, the investigations on bond-breaking and new bond-forming processes triggered by the ionic impact may shed light on the stellar wind interaction with interstellar media, ionic beam irradiations of the living cells, ion-track nanotechnology,...
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Palladium versus Platinum: The Metal in the Catalytic Center of a Molecular Photocatalyst Determines the Mechanism of the Hydrogen Production with Visible Light
PublicationTo develop highly efficient molecular photocatalysts for visible light-driven hydrogen production, a thorough understanding of the photophysical and chemical processes in the photocatalyst is of vital importance. In this context, in situ X-ray absorption spectroscopic (XAS) investigations show that the nature of the catalytically active metal center in a (N^N)MCl2 (M=Pd or Pt) coordination sphere has a significant impact on the...
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Elastic electron scattering by argon in the vicinity of the high-energy critical minimum.
PublicationZostały obliczone różniczkowe przekroje czynne na sprężyste rozpraszanie elektronów na argonie. Przedział energetyczny rozpraszanych elektronów został tak dobrany, aby zbadać położenie tzw. minimum krytycznego.
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Maximizing Bio-Hydrogen and Energy Yields Obtained in a Self-Fermented Anaerobic Bioreactor by Screening of Different Sewage Sludge Pretreatment Methods
PublicationEgypt faces significant challenges in managing its sewage sludge generated in large quantities from wastewater treatment plants. This study investigates the feasibility of utilizing sewage sludge as a renewable resource for hydrogen production through anaerobic digestion at the 100 L bioreactor level. Hydrogen is considered a promising alternative energy source due to its high energy content and environmental benefits. To optimize...
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Multigap superconducting state in molecular metallic hydrogen
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Chiral and achiral crystals, charge-assisted hydrogen-bond patterns and self-organization of selected solid diaminium thiosulfates
PublicationAbstract A series of diaminium thiosulfates, derivatives of diamines: NH2CH2CH(CH3)NH2 (1) and NH2(CH2)nNH2, n = 3-6 (2-5 respectively)and thiosulfuric acid were prepared and their structures determined by crystal X-ray diffraction analysis. Compounds 1, 2 and 4 turned out to be hydrates. The crystal structure of 1,2-proylenediaminium thiosulfate is chiral and exhibits spontaneous resolution. Crystals for both enantiomers...
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Ab initio study of phenyl benzoate: structure, conformational analysis, dipole moment, IR and Raman vibrational spectra
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Ab initio studies of the structure, physicochemical properties and behavior of lead chlorides and chloroplumbate anions in gaseous and aqueous phases
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Ab initio electronic structure of HCN− and HNC− dipole-bound anions and a description of electron loss upon tautomerization
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Parkinson’s disease: Etiopathogenesis, molecular basis and potential treatment opportunities
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Evaluation of the scale-consistent UNRES force field in template-free prediction of protein structures in the CASP13 experiment
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Polarisation effects in low-energy positron–molecule scattering
PublicationThe UK molecular R-matrix method has been adapted to treat positron collisions from polyatomic targets. A simple empirical enhancement factor which corrects for the underestimation of electron–positron polarisation and correlation effects in the calculations performed with the static-plus-polarization model at low scattering energies is presented. Application of this model to positron scattering from carbon dioxide at energies...
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Lipid-protein interactions in membranes: a molecular modelling study
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Gradient based basis function algorithms for identification of quasi periodically varying processes.
PublicationW pracy przedstawiono problem identyfikacji systemów, których parametry zmieniają się w sposób pseudookresowy. Pokazano sposób, w jaki można modelować takie systemy przy zastosowaniu metody harmonicznych funkcji bazowych.Przedstawiono dwa sposoby dekompozycji (struktura szeregowa i równoległa) takich układów na elementy związane z poszczególnymi funkcjami bazowymi. Zaprezentowany został sposób śledzenia częstotliwości funkcji...
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Molecular simulation study of cooperativity in hydrophobic association: clusters of four hydrophobic particles
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Early stage of critical clusters growth in phenomenological and Molecular Dynamic simulation models
PublicationW artykule opisano wzrost klastrów krytycznych w ramach klasycznego podejścia fenomenologicznego oraz dynamiczno-molekularnego (MD). Została wyprowadzona nowa formuła opisujaca liczbę klastrów krytycznych. Sformułowano równania opisujace wczesne etapy wzrostu kropli o rozmiarach krytycznych. Opisano wyniki symulacji dynamiczno-molekularnych powstawania klastrów w jednorodnej parze przesyconej oraz podano czasowe zmiany rozkładu...