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    Wyświetlanie 1-9 z 9
    Tytuł:
    15N magnetic relaxation study of backbone dynamics of the ribosome-associated cold shock response protein Yfia of Escherichia coli
    Autorzy:
    Zhukov, Igor
    Bayer, Peter
    Schölermann, Beate
    Ejchart, Andrzej
    Powiązania:
    https://bibliotekanauki.pl/articles/1040866.pdf
    Data publikacji:
    2007
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    anisotropic overall molecular diffusion
    model-free approach
    15N NMR spectroscopy
    stress adaptation
    disordered polypetide chain motion
    protein Y
    Opis:
    In the solution structure of the ribosome-associated cold shock response protein Yfia of Escherichia coli in the free state two structural segments can be distinguished: a well structured, rigid N-terminal part displaying a βαβββα topology and a flexible C-terminal tail comprising last 20 amino-acid residues. The backbone dynamics of Yfia protein was studied by 15N nuclear magnetic relaxation at three magnetic fields and analyzed using model-free approach. The overall diffusional tumbling of the N-terminal part is strongly anisotropic with a number of short stretches showing increased mobility either on a subnanosecond time scale, or a micro- to millisecond time scale, or both. In contrast, the unstructured polypeptide chain of the C-terminal part, which cannot be regarded as a rigid structure, shows the predominance of fast local motions over slower ones, both becoming faster closer to the C-terminus.
    Źródło:
    Acta Biochimica Polonica; 2007, 54, 4; 769-775
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Application of the molecular dynamics method for modelling of mass transfer on the border of Ni-Al bimetal
    Zastosowanie metody dynamiki molekularnej do modelowania transferu masy na granicy bimetalu Ni-Al
    Autorzy:
    Starostenkov, M.
    Demina, I.
    Popova, G.
    Denisova, N.
    Smolarz, A.
    Powiązania:
    https://bibliotekanauki.pl/articles/408811.pdf
    Data publikacji:
    2012
    Wydawca:
    Politechnika Lubelska. Wydawnictwo Politechniki Lubelskiej
    Tematy:
    modelowanie komputerowe
    proces dyfuzji
    wakans
    metoda dynamiki molekularnej
    atom międzywęzłowy
    sieć krystaliczna
    transport masy
    method of computer modelling
    diffusion process
    vacancy
    method of molecular dynamics
    internodal atom
    crystalline lattice
    mass transfer
    Opis:
    One of the basic issues of examination of process of interaction of two-component alloys is the study of the mass transfer process in the presence of dot flaws: internodal atoms and vacancies. The study of this process in real experiments is impossible; therefore it is reasonable to apply computer modelling. The authors present a model of Ni-Al bimetal diffusion process produced by the method of molecular dynamics.
    Jednym z podstawowych zagadnień analizy procesu interakcji stopów dwuskładnikowych jest badanie procesu wymiany masy w obecności defektów punktowych: atomów międzywęzłowych i wakansów. Badania tego procesu w rzeczywistych eksperymentach jest niemożliwe, dlatego uzasadnione jest zastosowanie modelowania komputerowego. Autorzy przedstawiają model procesu dyfuzji w bimetalu Ni-Al stworzony metodą dynamiki molekularnej.
    Źródło:
    Informatyka, Automatyka, Pomiary w Gospodarce i Ochronie Środowiska; 2012, 1; 36-38
    2083-0157
    2391-6761
    Pojawia się w:
    Informatyka, Automatyka, Pomiary w Gospodarce i Ochronie Środowiska
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Comparison of the free volume sizes and shapes determined from crystallographic and PALS data
    Autorzy:
    Tydda, M.
    Jasińska, B.
    Powiązania:
    https://bibliotekanauki.pl/articles/146378.pdf
    Data publikacji:
    2015
    Wydawca:
    Instytut Chemii i Techniki Jądrowej
    Tematy:
    benzenediols
    free volume
    molecular crystals olanzapine
    positron annihilation
    positronium
    positronium diffusion coefficient
    Opis:
    Two different classes of molecular crystals were investigated. The first group was benzenediols, which are characterized by the same chemical composition but a different organization of their crystallographic structures; all of the compounds from this group have only one kind of free volumes. The second class was represented by olanzapine, which has more complex chemical composition and two kinds of free volumes in the structure. The o-Ps lifetime values determined from positron annihilation lifetime spectroscopy (PALS) measurements agree quite well with those calculated for sizes found from crystallographic data for benzenediols (agreement within 10% of the lifetime values). For olanzapine, a good agreement is observed in the case of cuboidal free volumes, while for the other kind of void, the agreement is less satisfactory. Positronium diffusion coefficient determined from o-Ps redistribution in olanzapine agrees with these found for polymers.
    Źródło:
    Nukleonika; 2015, 60, No. 4, part 1; 771-775
    0029-5922
    1508-5791
    Pojawia się w:
    Nukleonika
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Mikromieszanie w układzie dwufazowym w warunkach przepływu laminarnego
    Micromixing in a two-phase system in laminar flow
    Autorzy:
    Rożeń, A.
    Powiązania:
    https://bibliotekanauki.pl/articles/2071114.pdf
    Data publikacji:
    2010
    Wydawca:
    Stowarzyszenie Inżynierów i Techników Mechaników Polskich
    Tematy:
    mieszanie
    przepływ laminarny
    dyfuzja molekularna
    napięcie międzyfazowe
    układ dwufazowy
    mixing
    laminar flow
    molecular diffusion
    interfacial tension
    two-phase system
    Opis:
    Praca poświęcona jest mieszaniu na skalę molekularną (mikromieszaniu) płynów w układzie dwufazowym. Przedstawiono w niej wyniki modelowania deformacji kropel fazy rozproszonej w liniowym polu prędkości oraz dyfuzji molekularnej inertnego znacznika na zewnątrz kropel. Symulacje mikromieszania wykonano przyjmując, że przepływ jest izotermiczny i stabilny do momentu rozpadu kropel lub do chwili uzyskania przez nie stałego kształtu. Wyznaczono wpływ napięcia międzyfazowego na czas mikromieszania dla różnych wartości szybkości ścinania i współczynnika dyfuzji molekularnej znacznika. Tę metodę można wykorzystać do optymalizacji procesów mieszania, w których miesza się ciecze o dużej lepkości.
    This work is concerned with mixing on the molecular scale (micromixing) of fluids in a two-phase system. Modeling results dealing with the deformation of dispersed phase drops in a linear flow field and molecular diffusion of inert tracer outside the drops are presented. Micromixing simulations were conducted under the assumption that flow is isothermal and stable until disruption of drops or until obtaining by them a stable shape. The effect of interfacial tension on micromixing time for different values of shear rate and tracer molecular diffusivity coefficient was determined. This method can be applied to optimize mixing processes in which liquids of high viscosity are mixed.
    Źródło:
    Inżynieria i Aparatura Chemiczna; 2010, 3; 105-106
    0368-0827
    Pojawia się w:
    Inżynieria i Aparatura Chemiczna
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Molecular dynamics simulation of copolymers
    Autorzy:
    Banaszak, M.
    Powiązania:
    https://bibliotekanauki.pl/articles/1964087.pdf
    Data publikacji:
    2001
    Wydawca:
    Politechnika Gdańska
    Tematy:
    molecular dynamics
    computer simulation
    copolymer
    diblock
    ionic copolymer
    diffusion
    structure factor
    equation of state
    thermodynamic properties
    Opis:
    A series of representative molecular dynamics simulations of model Lennard-Jones copolymer chains is presented. We report measurements of thermodynamic, structural and dynamic properties of our model copolymers. For neutral copolymers we confirm our version of thermodynamic perturbation theory of the first order, while for ionic copolymers we demonstrate microphase formation and the anisotropy of the counterion diffusion.
    Źródło:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2001, 5, 1; 17-27
    1428-6394
    Pojawia się w:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Properties of water hydrating the galactolipid and phospholipid bilayers: a molecular dynamics simulation study
    Autorzy:
    Markiewicz, Michał
    Baczyński, Krzysztof
    Pasenkiewicz-Gierula, Marta
    Powiązania:
    https://bibliotekanauki.pl/articles/1038986.pdf
    Data publikacji:
    2015
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    molecular modelling
    hydrogen bonds
    water diffusion
    water dipole orientation
    inter-lamellar water
    Opis:
    Molecular dynamics simulations of 1,2-di-O-acyl-3-O-β-D-galactopyranosyl-sn-glycerol (MGDG) and 1,2-dioleoyl-sn-glycero-3-phosphatidylcholine (DOPC) bilayers were carried out to compare the effect of the lipid head group's chemical structure on the dynamics and orientational order of the water molecules hydrating the bilayer. The effect of the bilayers on the diffusion of water is strong for the neighbouring water molecules i.e., those located not further than 4 Å from any bilayer atom. This is because the neighbouring water molecules are predominantly hydrogen bonded to the lipid oxygen atoms and their mobility is limited to a confined spatial volume. The choline group of DOPC and the galactose group of MGDG affect water diffusion less than the polar groups located deeper in the bilayer interface, and similarly. The latter is an unexpected result since interactions of water with these groups have a vastly different origin. The least affected by the bilayer lipids is the lateral diffusion of unbound water in the bilayer plane (x,y-plane) - it is because the diffusion is not confined by the periodic boundary conditions, whereas that perpendicular to the plane is. Interactions of water molecules with lipid groups also enforce certain orientations of water dipole moments. The profile of an average water orientation along the bilayer normal for the MGDG bilayer differs from that for the DOPC bilayer. In the DOPC bilayer, the ordering effect of the lipid head groups extends further into the water phase than in the MGDG bilayer, whereas inside the bilayer/water interface, ordering of the water dipoles in the MGDG bilayer is higher. It is possible that differences in the profiles of an average water orientation across the bilayer in the DOPC and MGDG bilayers are responsible for differences in the lateral pressure profiles of these bilayers.
    Źródło:
    Acta Biochimica Polonica; 2015, 62, 3; 475-481
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Small high density lipoprotein subclasses: some of their physico-chemical properties and stability in solution.
    Autorzy:
    Atmeh, Ragheb
    Abd Elrazeq, Issa
    Powiązania:
    https://bibliotekanauki.pl/articles/1041440.pdf
    Data publikacji:
    2005
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    small high density lipoproteins
    diffusion coefficient
    surface charge
    molecular shape
    coefficient of friction
    stability
    Opis:
    Small high density lipoproteins (SHDL) contribute to the protection from atherosclerosis, but detailed information about their properties is not available yet. We isolated four of the smallest HDL subclasses that contain apoA-I alone, the small lipoprotein A-I (SLpAI), by their separation on gradient polyacrylamide gel followed by electroelution. Their physico-chemical properties were calculated from their displacement in non-denaturing gradient polyacrylamide gel under the effect of electrical potential. The properties are: Stokes' radii 2.96-3.56 nm; molecular masses 42-70 kDa; net negative charge 7.2-13.5; surface charge densities 3139-4069 -esu∙˙cm^(-2); surface potentials 10.6-15.7 -mV; coefficients of friction 5.74-6.90 × 10-8 g∙˙s^(-1); and diffusion coefficients 5.76-6.94 7× 10-7 cm^2∙˙s^(-1). We found that these particles were of low stability as they underwent molecular transformation into larger particles on storage. The estimated dimensions of these particles do not support ellipsoidal shape, therefore, the most probable shape is spherical; consequently, their hydrated characteristics were estimated. We conclude that these particles have high values of negative surface charge and diffusion coefficients, and are of low stability. Their small Stokes' radii were similar to each other and they are spherical and highly hydrated.
    Źródło:
    Acta Biochimica Polonica; 2005, 52, 2; 515-525
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Statistical properties of a polymer chain in the environment with low concentration of nanoparticles
    Autorzy:
    A. Tsehay, Dessalegne
    Luo, Meng-Bo
    Powiązania:
    https://bibliotekanauki.pl/articles/1050809.pdf
    Data publikacji:
    2018-05
    Wydawca:
    Polska Akademia Nauk. Instytut Fizyki PAN
    Tematy:
    diffusion
    conformation
    polymer chain
    nanoparticles
    molecular dynamics
    Opis:
    We have investigated the statistical properties of polymer in the environment with low concentration of nanoparticles by using large-scale molecular dynamics simulations. The scaling law for the mean square radius of gyration was examined and simulation results for the polymer lengths 64≤N≤144 yielding a reasonably accurate value of the Flory exponent ν=0.58 at weak polymer-nanoparticle interaction ε_{PN}. Within the same range of N, the mean asphericity of the chain is independent of N. We found that the polymer behaves like a self-avoiding walk chain at small ε_{PN} and a compact sphere at large ε_{PN}. The results are attributed to the increase in the contact between polymer and nanoparticles with increasing ε_{PN}. Normal diffusions of polymer are always observed at whatever ε_{PN} and size and concentration of nanoparticles. Our result shows that the normal diffusion behavior of polymer is independent of polymer's state even though there is a phase transition from a desorbed polymer phase at small ε_{PN} to an adsorbed polymer phase at large ε_{PN}.
    Źródło:
    Acta Physica Polonica A; 2018, 133, 5; 1274-1280
    0587-4246
    1898-794X
    Pojawia się w:
    Acta Physica Polonica A
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Surface diffusion and cluster formation of gold on the silicon (111)
    Autorzy:
    Plechystyy, V.
    Shtablavyi, I.
    Rybacki, K.
    Winczewski, S.
    Mudry, S.
    Rybicki, J.
    Powiązania:
    https://bibliotekanauki.pl/articles/952460.pdf
    Data publikacji:
    2020
    Wydawca:
    Stowarzyszenie Komputerowej Nauki o Materiałach i Inżynierii Powierzchni w Gliwicach
    Tematy:
    molecular dynamics
    surface diffusion
    clusters
    atomic monolayer
    activation energy
    dynamika molekularna
    dyfuzja powierzchniowa
    klastry
    monowarstwa atomowa
    energia aktywacji
    Opis:
    Purpose: Investigation of the gold atoms behaviour on the surface of silicon by molecular dynamics simulation method. The studies were performed for the case of one, two and four atoms, as well as incomplete and complete filling of gold atoms on the silicon surface. Design/methodology/approach: Investigations were performed by the method of molecular dynamics simulation using the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS). MEAM potential of interatomic interaction was used for modelling. Molecular dynamic simulations were carried out in isothermal-isobaric ensemble (NpT) with a timestep 1.0 fs. Findings: As a result of studies, the preferred interaction between gold atoms and the formation of clusters at temperatures up to 800 K was revealed. Analysis of the temperature dependences of the number of large jumps of atoms made it possible to calculate the activation energy of a single jump. It was found that activation energy of single atomic displacement decreases with increasing number of gold atoms. Research limitations/implications: Only a limited number of sets of atoms were used in the study. It is possible that for another combination of atoms and a larger substrate surface, the formation of gold nanoislands on the silicon surface can be observed, which requires further research. Practical implications: The research results can be used to select the modes of gold sputtering to create gold nanoislands or nanopillars on the silicon surface. Originality/value: Computer modelling of the behaviour of gold atoms on the surface of silicon with the possibility of their self-organization and cluster formation was performed for the first time.
    Źródło:
    Journal of Achievements in Materials and Manufacturing Engineering; 2020, 101, 2; 49-59
    1734-8412
    Pojawia się w:
    Journal of Achievements in Materials and Manufacturing Engineering
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
      Wyświetlanie 1-9 z 9

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