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1
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Influence of Dipole-Dipole Interactions on Structural Properties of Gay-Berne Particles

100%
Gwóźdź E., Bródka A.
Acta Physica Polonica A
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2000
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vol. 98
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issue 5
645-649
EN
Molecular dynamics simulations were performed for a liquid crystal system composed of the Gay-Berne particles with terminal transverse dipole moments. When the dipole-dipole interactions are weak, the isotropic-smectic transition is observed and the transition point shifts towards lower densities as the dipole moment increases. For higher dipole moments the system shows isotropic structure in the whole range of density, and strong dipole-dipole interactions produce two types of dimers that cannot be accommodated into smectic layers.
2
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Survey of the Excited State Dissociation οf Gas-Phase Bromine Monochloride in the Visible-Near UV Wavelength Region

80%
Zhang D.
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issue 3
457-465
EN
The spectroscopic transitions and photoabsorption/dissociation processes of bromine monochloride (BrCl) via several low-lying covalently bound electronic states and repulsive states have been investigated by performing electronic structure calculations and wave packet simulations of nuclear motion. The absorption spectra for 52-electron singlet systems are obtained by employing time-dependent propagation methods or the real-time propagation of the time-dependent Schrödinger equations in the adiabatically exact approximation. Based on the elastic scattering calculations, the results of angular distributions of the products of photodissociation of BrCl molecules are examined on two aspects: (1) the nature of the state that is prepared by excitation from a bound level into a continuum, and (2) under avoided crossing cases, the influences of nonadiabatic coupling processes on the fragmentation process are evaluated by virtue of a semiclassical Landau-Zener model, which treats an avoided crossing between two states of a given nature and evaluates a nonadiabatic effect relevant to the molecule during photodissociation. The model qualitatively reproduces the key aspects of the full processes related to the transfer of dissociating flux between states of 0+ symmetry, indicating that the proposed coupling scheme is generally correct.
3
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Ab Initio Study of CH₄, CH₃, and CO₂ Affinity to the (001) MgO Surface

80%
Siklitskaya A., Majewski J.
Acta Physica Polonica A
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2016
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vol. 129
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issue 1a
A-145-A-147
EN
The dynamics of the methane, methyl, and carbon dioxide adsorption to the (001) surface of cubic magnesium oxide (periclase) has been studied within the ab initio molecular dynamics in the temperature range between 0 and 1000 K. For methane, neither chemisorption nor physisorption has been observed in the considered temperature range, whereas methyl group and carbon dioxide build chemical bond to the MgO surface at temperatures 350 K and 450 K, with adhesive energies of 0.218 and 0.935 eV, respectively.
4
Content available remote

Computational determination of radiation damage effects on DNA structure

80%
Pinak M.
Open Physics
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2003
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vol. 1
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issue 1
179-190
EN
Molecular dynamics (MD) studies of several radiation originated lesions on the DNA molecules are presented. The pyrimidine lesions (cytosinyl radical, thymine dimer, thymine glycol) and purine lesion (8-oxoguanine) were subjected to the MD simulations for several hundred picoseconds using MD simulation code AMBER 5.0 (4.0). The simulations were performed for fully dissolved solute molecules in water. Significant structural changes in the DNA double helical structure were observed in all cases which may be categorized as: a) the breaking of hydrogen bonds network between complementary bases and resulted opening of the double helix (cytosinyl, radical, 8-oxoguanine); b) the sharp bending of the DNA helix centered at the lesion site (thymine dimer, thymine glycol); and c) the flippingout of adenine on the strand complementary to the lesion (8-oxoguanine). These changes related to the overall collapsing of the double helical structure around the lesion, are expected to facilitate the docking of the repair enzyme into the DNA in the formation of DNA-enzyme complex. The stable DNA-enzyme complex is a necessary condition for the onset of the enzymatic repair process. In addition to structural changes, specific values of electrostatic interaction energy were determined at several lesion sites (thymine dimer, thymine glycol and 8-oxoguanine). This lesion-specific electrostatic energy is a factor that enables repair enzyme to discriminate lesion from the native site during the scanning of the DNA surface.
5
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Large-Scale Nanosecond Simulations of the Dynamics of the Xe + H_2O System

70%
Kholmurodov K., Seifert Z., Rączkiewicz K., Nitka J.
Acta Physica Polonica A
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2006
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vol. 110
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issue 6
759-767
EN
Large-scale molecular dynamics simulations of the high-pressure transformations of the xenon/water system were performed involving special purpose molecular dynamics machines. We investigated several systems of different sizes and geometry at the suitable simulational conditions (density, temperature, etc.), which are similar to the experiments conducted on the xenon hydrates. A binary mixture (ice water + Xe) undergoes at high pressure a long evolution and the Xe-guest atoms, enclosed inside the water molecules, were observed and analyzed. Even for the thin slabs, starting with the capture of the guest atoms by the water molecules, the water clusters around the xenon atoms are formed. The results show that such a hydrate-like formation preserves its structural stability over a long period of the simulation time of order of nanosecond. The molecular dynamics simulations were performed on a basis of the MDGRAPE-2 modifications of the DL_POLY general purposes package, with the efficient treatment of the Ewald real and reciprocal-space components of the Coulombic and Van der Waals forces. The MDGRAPE-2 accelerates the calculations of the Coulomb and Van der Waals forces, without applying a spherical cut of a fixed distance. 31.15.Qg, 61.20.-p, 61.50.Ah, 81.10.Aj, 91.60.Gf
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