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Search results for: atomic and molecular physics
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Measurements of Subnanometer Molecular Layers
PublicationSelected methods of formation and detection of nanometer and subnanometer molecular layers were shown. Additionally, a new method of detection and measurement with subnanometer resolution of layers adsorbed or bonded to the gate dielectric of the ion selective field effect transistor (ISFET) was presented.
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Molecular Umbrella as A Nanocarrier for Antifungals
PublicationA molecular umbrella composed of two O‐sulfated cholic acid residues was applied for the construction of conjugates with cispentacin, containing a “trimethyl lock” (TML) or o‐dithiobenzylcarbamoyl moiety as a cleavable linker. Three out of five conjugates demonstrated antifungal in vitro activity against C. albicans and C. glabrata but not against C. krusei, with MIC90 values in the 0.22–0.99 mM range and were not hemolytic. Antifungal...
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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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Physics 2, DaPE, sem. 2, W, lato 2021/2022
e-Learning CoursesPhysics 2
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Molecular hydrogen solvated in water – A computational study
PublicationThe aqueous hydrogen molecule is studied with molecular dynamics simulations at ambient temperature and pressure conditions, using a newly developed flexible and polarizable H2 molecule model. The design and implementation of this model, compatible with an existing flexible and polarizable force field for water, is presented in detail. The structure of the hydration layer suggests that first-shell water molecules accommodate the...
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AFM (atomic force microscopy) images of borophene after sonication of boron
Open Research DataThese data include AFM (atomic force microscopy) images of borophene obtained after sonication in aceton of boron, collected in order to estimate lateral size of the nanoflakes.
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Albumin–Hyaluronan Interactions: Influence of Ionic Composition Probed by Molecular Dynamics
PublicationThe 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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Molecular level interpretation of excess infrared spectroscopy
PublicationInfrared (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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BULLETIN OF THE ATOMIC SCIENTISTS
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The effect of a miniature argon flow rate on the spectral characteristics of a direct current atmospheric pressure glow micro-discharge between an argon microjet and a small sized flowing liquid cathode
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Ultrasonic nebulization atmospheric pressure glow discharge — Preliminary study
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A measurement system for nonlinear surface spectroscopy with an atomic force microscope during corrosion process monitoring
PublicationIn addition to traditional imaging the surface, atomic force microscopy (AFM) enables wide variety of additional measurements. One of them is higher harmonic imaging. In tapping mode the nonlinear contact between tip and specimen results in higher frequency vibrations. More information available from the higher harmonics analysis proves to be helpful for more detailed imaging. Such visualization is espe-cially useful for heterogeneous...
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A Direct Modulation for Matrix Converters based on the Onecycle Atomic operation developed in Verilog HDL.
PublicationThis paper presents a fast direct Pulse Width Modulation (PWM) algorithm for the Conventional Matrix Converters (CMC) developed in Verilog Hardware Description language (HDL). All PWM duty cycle calculations are performed in one cycle by an atomic operation designed as a digital module using FPGA basic blocks. The algorithm can be extended to any number of output phase. The improved version of the discontinuous Direct Analytic...
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Molecular Imaging and Nanotechnology—Emerging Tools in Diagnostics and Therapy
PublicationPersonalized medicine is emerging as a new goal in the diagnosis and treatment of diseases. This approach aims to establish differences between patients suffering from the same disease, which allows to choose the most effective treatment. Molecular imaging (MI) enables advanced insight into molecule interactions and disease pathology, improving the process of diagnosis and therapy and, for that reason, plays a crucial role in personalized...
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Determination of total mercury in raw petrol using cold vapour atomic absorption spectrometry
PublicationPresence of different forms of mercury in petroleum based products may impair the proper operation of the equipment or led to poisoning of automotive catalysts. However much more important problem is environmental pollution with mercury emitted from different types of fossil fuels. Although the average mercury concentration in petroleum based products (automotive fuels) is on the level around 1 ppb, taking into account annual...
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Study of the atomic structure and morphology of the Pt3Co nanocatalyst
PublicationThe local structure and chemical disorder of a commercially available Pt3Co nanocatalyst supported on high surface area carbon were investigated. High-quality XAFS spectra were collected at the ELETTRA synchrotron XAFS 11.1 beamline. XAFS spectra analysis have been performed accounting for the reduction of the coordination number and degeneracy of three-body configurations, resulting from transmission electron microscopy (TEM)...
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RESTful atomic services for distributed digital libraries
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AFM (Atomic Force Microscopy) analysis of surface topography loaded with nickel nanoparticles.
Open Research DataThis dataset presents AFM (Atomic Force Microscopy) images depicting the surface topography loaded with nickel powdered nanoparticles. The detailed equipment and measurement data was described in "AFM readme.txt" file
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Non-Newtonian Mathematics Instead of Non-Newtonian Physics: Dark Matter and Dark Energy from a Mismatch of Arithmetics
PublicationNewtonian physics is based on Newtonian calculus applied to Newtonian dynamics. New paradigms such as ‘modified Newtonian dynamics’ (MOND) change the dynamics, but do not alter the calculus. However, calculus is dependent on arithmetic, that is the ways we add and multiply numbers. For example, in special relativity we add and subtract velocities by means of addition β1⊕β2=tanh(tanh−1(β1)+tanh−1(β2)), although multiplication β1⊙β2=tanh(tanh−1(β1)⋅tanh−1(β2)),...
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Potential of novel atomic emission techniques as a tool for investigation of the possibilities of using industrial waste as additives in construction materials
PublicationNowadays, due to the global ecological crisis and ways to prevent a climate disaster, more and more attention is paid to green techno-logies and green Chemistry, which are part of the so-called “The Green Deal.” The main assumption is the optimization of the processes of producing necessary goods and the implementation of methods of managing postproduction waste in the least environmentally harmful manner. In the presented research,...
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ATOMIC DATA AND NUCLEAR DATA TABLES
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The effect of chitosan concentration and molecular weight on endotoxin content
Open Research DataThe dataset includes results to determine the effect of chitosan concentration and molecular weight on endotoxin content as well as the effect of purification methods. The endotoxin concentration was determined using the PyroGene Recombinant Factor C Endpoint Fluorescent Assay. Chitosan 0.6% in 0.1M glycolic acid from Chemat LMW, MMW, and HMW were used...
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Nonlinear free and forced vibrations of a dielectric elastomer-based microcantilever for atomic force microscopy
PublicationThe majority of atomic force microcode (AFM) probes work based on piezoelectric actuation. However, some undesirable phenomena such as creep and hysteresis may appear in the piezoelectric actuators that limit their applications. This paper proposes a novel AFM probe based on dielectric elastomer actuators (DEAs). The DE is modeled via the use of a hyperelastic Cosserat model. Size effects and geometric nonlinearity are included...
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Structural and dynamic insights on the EmrE protein with TPP+ and related substrates through molecular dynamics simulations
PublicationEmrE is a bacterial transporter protein that forms an anti-parallel homodimer with four transmembrane helices in each monomer. EmrE transports positively charged aromatic compounds, such as TPP+ and its derivatives. We performed molecular dynamics (MD) simulations of EmrE in complex with TPP+, MeTPP+, and MBTPP+ embedded in a membrane. The detailed molecular properties and interactions were analysed for all EmrE-ligand complexes....
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Molecular dynamics studies of polyurethane nanocomposite hydrogels
PublicationPolyurethane PEO-based hydrogels have a broad range of biomedical applicability. They are attractive for drug-controlled delivery systems, surgical implants and wound healing dressings. In this study, a PEO based polyurethane hydrogels containing Cloisite R 30B, an organically modified clay mineral, was synthesized. Structure of nanocomposite hydrogels was determined using XRD technique. Its molecular dynamics was studied by means...
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Dye-sensitized solar cells, in: Physics of Nanostructured Solar Cells
PublicationRozwój nanotechnologii otwiera coraz szersze horyzonty w dziedzinie zastosowania nowych materiałów w istniejących technologiach. Po tranzystorach także inne urządzenia wchodzą w erę nanotechnologii, w tym także te, dla których podstawowym materiałem są półprzewodniki i materiały organiczne. Ogniwa słoneczne nie są w tym zakresie wyjątkiem. W książce przedstawiono różne rodzaje ogniwa fotowoltaicznych i związane z ich eksploatacją...
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Metrological Aspects of Accelerator Technology and High Energy Physics Experiments
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Optimization of Hydrogen - Evolving Photochemical Molecular Devices
PublicationA molecular photocatalyst consisting of a RuII photocenter, a tetrapyridophenazine bridging ligand, and a PtX2 (X=Cl or I) moiety as the catalytic center functions as a stable system for light-driven hydrogen production. The catalytic activity of this photochemical molecular device (PMD) is significantly enhanced by exchanging the terminal chlorides at the Pt center for iodide ligands. Ultrafast transient absorption spectroscopy...
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Molecular Targets for Anticandidal Chemotherapy
PublicationA relatively small number of anticandidal chemotherapeutics used in clinical practice is at least in part consequence of a limited number of their molecular targets: ergosterol in the membrane, lanosterol demethylase, b(1!3) glucan synthase, and DNA/RNA biosynthesis. Much more potential novel targets have been revealed by the comparative genomic studies identifying essential genes unique for Candida albicans or resulted from recognition...
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UNRES-GPU for Physics-Based Coarse-Grained Simulations of Protein Systems at Biological Time- and Size-Scales
PublicationThe dynamics of the virus like particles (VLPs) corresponding to the GII.4 Houston, GII.2 SMV, and GI.1 Norwalk strains of human noroviruses (HuNoV) that cause gastroenteritis was investigated by means of long-time (about 30 μs in the laboratory timescale) molecular dynamics simulations with the coarse-grained UNRES force field. The main motion of VLP units turned out to be the bending at the junction between the P1 subdomain (that...
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The surface photoconductivity in molecular layers
PublicationW pracy przedstawiono rezultaty analizy fotoprądów powierzchniowych w cienkich warstwach tetracenu i pentacenu. W szczególności badano wpływ obecności defektów strukturalnych w warstwach na charakterystyki fotoprądów i transport nośników ładunku.
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Performance of extended Lagrangian schemes for molecular dynamics simulations with classical polarizable force fields and density functional theory
PublicationIterative energy minimization with the aim of achieving self-consistency is a common feature of Born-Oppenheimer molecular dynamics (BOMD) and classical molecular dynamics with polarizable force fields. In the former, the electronic degrees of freedom are optimized, while the latter often involves an iterative determination of induced point dipoles. The computational effort of the self-consistency procedure can be reduced by re-using...
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Time-of-flight electron scattering from molecular hydrogen: Benchmark cross sections for excitation of the X1Σ+g→b3Σ+u transition
PublicationThe electron impact X1Σ+g to b3Σ+u transition in molecular hydrogen is one of the most important dissociation pathways to forming atomic hydrogen atoms, and is of great importance in modeling astrophysical and industrial plasmas where molecular hydrogen is a substantial constituent. Recently it has been found that the convergent close-coupling (CCC) cross sections of Zammit et al. [Phys. Rev. A 95, 022708 (2017)] are up to a factor...
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Application of dynamic impedance spectroscopy to atomic force microscopy
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Ab initioheat capacity and atomic temperature factors of chalcopyrites
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Atomic substitution and carbon isotope effect in superconducting MgCNi3
PublicationW pracy analizowany jest wpływ domieszkowania zarówno pozycji niklu, jak i węgla w nadprzewodzącym związku międzymetalicznym MgCNi3. Dodatkowo dyskutowany jest węglowy nadprzewodzący efekt izotopowy.
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Application of dynamic impedance spectroscopy to atomic force microscopy
PublicationMikroskopia sił atomowych jest uniwersalną techniką obrazowania powierzchni podczas gdy spektroskopia impedancyjna jest fundamentalną metodą charakteryzowania właściwości elektrycznych materiałów. Z powyższego względu użyteczne jest połączenie powyższych technik dla uzyskania przestrzennego rozkładu wektora impedancji. W pracy autorzy proponują nowe podejście polegające na połączeniu multiczęstotliwościowego pomiaru impedancyjnego...
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Visualization and characterization of prolamellar bodies with atomic force microscopy
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MOLECULAR PHARMACEUTICS
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Density functional theory-based simulations of sum frequency generation spectra involving methyl stretching vibrations: effect of the molecular model on the deduced molecular orientation and comparison with an analytical approach
PublicationThe knowledge of the first hyperpolarizability tensor elements of molecular groups is crucial for a quantitative interpretation of the sum frequency generation (SFG) activity of thin organic films at interfaces. Here, the SFG response of the terminal methyl group of a dodecanethiol (DDT) monolayer has been interpreted on the basis of calculations performed at the density functional theory (DFT) level of approximation. In particular,...
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JOURNAL OF PHYSICS D-APPLIED PHYSICS
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Brygida Mielewska dr
PeopleBorn on 1 December 1972 in Gdynia. Education and professional experience:June 1997 MSc in Physics, Gdańsk University, Faculty of Mathematics and Physics; October 1997 – August 2003 – Assistant at Gdańsk University of Technology (GUT), Faculty of Applied Physics nad Technical Mathematics, Department of Physics of Electronic Phenomena;June 2003 – PhD in Physics, thesis advisor prof. dr hab. Mariusz Zubek; September 2003- January...
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Evolution of physics-based methodology for exploring the conformational energy landscape of proteins
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Towards an efficient multi-stage Riemann solver for nuclear physics simulations
PublicationRelativistic numerical hydrodynamics is an important tool in high energy nuclear science. However, such simulations are extremely demanding in terms of computing power. This paper focuses on improving the speed of solving the Riemann problem with the MUSTA-FORCE algorithm by employing the CUDA parallel programming model. We also propose a new approach to 3D finite difference algorithms, which employ a GPU that uses surface memory....
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E-experiments in physics. Proper business process management, collaborative development process and project management guidance – remedy for avoiding the main IT project’s failure
PublicationOnly a few of learning aids and simulations of physical phenomena allow for building interactive experiments; experiments similar to those that should be conducted in physics laboratories at schools. Group of staff from Gdansk University of Technology decided to fill this market niche by designing and constructing a set of virtual experiments – so called e-experiments. To avoid common problems that a lot of IT products brought...
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Titania Nanotubes/Hydroxyapatite Nanocomposites Produced with the Use of the Atomic Layer Deposition Technique: Estimation of Bioactivity and Nanomechanical Properties
PublicationTitanium dioxide nanotubes/hydroxyapatite nanocomposites were produced on a titanium alloy (Ti6Al4V/TNT/HA) and studied as a biocompatible coating for an implant surface modification. As a novel approach for this type of nanocomposite fabrication, the atomic layer deposition (ALD) method with an extremely low number of cycles was used to enrich titania nanotubes (TNT) with a very thin hydroxyapatite coating. X-ray diffraction (XRD)...
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Positron binding to alkali-metal hydrides: The role of molecular vibrations
PublicationThe bound vibrational levels for J=0 have been computed for the series of alkali-metal hydride molecules from LiH to RbH, including NaH and KH. For all four molecules the corresponding potential-energy curves have been obtained for each isolated species and for its positron-bound complex (e+XH). It is found that the calculated positron affinity values strongly depend on the molecular vibrational state for which they are obtained...
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Molecular Recognition in Complexes of TRF Proteins with Telomeric DNA
PublicationTelomeres are specialized nucleoprotein assemblies that protect the ends of linear chromosomes. In humans and many other species, telomeres consist of tandem TTAGGG repeats bound by a protein complex known as shelterin that remodels telomeric DNA into a protective loop structure and regulates telomere homeostasis. Shelterin recognizes telomeric repeats through its two major components known as Telomere Repeat-Binding Factors, TRF1...
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Sensing the onset of epoxy coating degradation with combined Raman spectroscopy/atomic force microscopy/electrochemical impedance spectroscopy
PublicationThe paper presents the results of investigation on epoxy resin durability upon 12-week exposure to UV radiation. The aim was early determination of the onset of epoxy degradation and for this purpose an epoxy film on steel substrate systems were periodically inspected using Raman spectroscopy, atomic force microscopy and electrochemical impedance spectroscopy. The behaviour of examined polymer could be divided into three periods: immunity,...
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Mechanism of Binding of Antifungal Antibiotic Amphotericin B to Lipid Membranes: An Insight from Combined Single-Membrane Imaging, Microspectroscopy, and Molecular Dynamics
PublicationAmphotericin B is a lifesaving polyene antibiotic used in the treatment of systemic mycoses. Unfortunately, the pharmacological applicability of this drug is limited because of its severe toxic side effects. At the same time, the lack of a well-defined mechanism of selectivity hampers the efforts to rationally design safer derivatives. As the drug primarily targets the biomembranes of both fungi and humans, new insights into the...