Dipole-driven dynamics for near-threshold electron/positron interactions with pyrimidinic DNA bases: a path to compound formations

ABSTRACT

Calculations are reported for electron and positron scattering from isolated cytosine and thymine, where the two pyrimidinic single-ring DNA bases, in the gas-phase at energies near the elastic threshold, they reveal the special features of the dipole-driven scattering states. All molecules examined exhibit, in fact, supercritical (>1.67 D) permanent dipoles which can therefore also support, below threshold, excited bound compound states (M·e^? and M·e⁺) classified as dipole-bound states. The possible paths for going from above to below the energy threshold to form whole, unfragmented bound complexes are discussed for both leptonic projectiles.     

激光辐照均匀性与相息相位板计算研究

分析激光聚变中的辐照均匀性(光滑化)原理和方法,对相息相位板(KinoformPhasePlateKPP)进行理论分析和计算研究。结果表明,最佳集能效率可到96%,最小的不均匀性可到14%。对我国激光聚变中的辐照均匀性提出一些看法。     

Structure and dynamics of a dense dipolar system in an electric field and their relevance to electrorheological fluids

Results of computer simulations of a dense system of dipolar spheres in an electric field are summarized. Dissipative and Hamiltonian dynamics algorithms have been used to find energy minima of the system for varying particle densities. The structures obtained by these simulations are in reasonable agreement with experimentally observed structures in electrorheological (ER) fluids. Qualitative agreement is also obtained with the limited available experimental observations on the dynamics of ER fluids.     

Stabilization of the long-range magnetic ordering by dipolar and magnetoelastic interactions in two-dimensional ferromagnets

The possibility of the long-range magnetic order stabilization in two-dimensional ferromagnets with the account of dipolar and magnetoelastic interactions is investigated. The mechanisms of the magnetic order stabilization by both types of interactions are studied. The Curie temperature is estimated. The comparisons with experimental data are made. Received 22 June 2001 and Received in final form 17 January 2002     

Build-up processes of an optical cavity enclosing an absorbent thin film: computational study by the CIP method

Propagation of monochromatic light is analyzed by numerical calculations for an optical cavity enclosing a thin absorbent film. The computational study is performed by the CIP (constrained interpolation profile) method, which is shown to be able to solve temporal evolution of Maxwell’s equations even in a strongly absorbing medium. Simulations on build-up processes reveal that such a cavity exhibits transmittance even higher than the intrinsic transmissivity of the absorbent, i.e., the absorbent is virtually transparent, when the following requirements are satisfied: the film is much thinner than the wavelength, it is located at a node of a standing wave, and the cavity consists of a pair of mirrors with optimal reflectivity depending on the film thickness. Optimal conditions are discussed as well for maximizing absorption in the film.     

Structure and dynamics of octamethyl-ethinyl-ferrocene: an organometallic rotator phase

The onset of dynamics and the structural changes of octamethyl–ethinyl-ferrocene around a solid–solid phase transition at 248 K have been investigated using the novel technique of quasielastic nuclear forward scattering (QNFS) in a temperature range between 61 and 257 K at a photon energy of 14.413 keV, as well as X-ray powder diffraction at various energies. A pronounced hysteresis for both the dynamical and the structural properties is observed and confirmed by differential-scanning calorimetry. We assign the observed phenomena to a first-order transition from a low-symmetry low-temperature phase to a high-symmetry high-temperature plastically crystalline phase with nearly cubic symmetry. Possible mechanisms for this transition are discussed in the light of our results.     

Molecular dynamics and interactions of human ceruloplasmin: A spin labelling study

Summary Ceruloplasmin, a paramagnetic copper-containing protein, has been spin labelled with different nitroxide spin labels in order to study its molecular dynamics and to gain further information about its interaction with other biosystems. Spin labelling with a maleimide derivative resulted in an electron spin resonance spectrum which was a superposition of two different absorptions due to paramagnetic species in different microenvironments. The first one, a three-line isotropic spectrum, is due to a fast-moving spin label (with a rotational correlation time τ_c≃10^-9s); the second one is an anisotropic, asymmetrical signal arising from an immobilized spin in a slow-motion domain (τ_c=10^-7). The assumption of a spherical shape for the molecule provided, through the Stokes-Einstein relation, an estimate of the molecular-radius value consistent with smallangle neutron scattering measurements. The interaction with other biosystems, as deduced from the protein molecule dynamics, is discussed.

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Riassunto La ceruloplasmina, una proteina umana contenente ioni Cu⁺⁺ paramagnetici, è stata marcata con differenti spin labels per studiarne la dinamica molecolare e la sua interazione con altri biosistemi. Il marcaggio mediante spin labels di tipo maleimidico ha portato ad uno spettro di risonanza elettronica di spin composto da due differenti gruppi di righe dovuti a specie paramagnetiche in differenti microambienti. Il primo segnale è costituito da un tripletto isotropico dovuto ad uno spin label in rapida rotazione (τ_c≃10^-9s), mentre il secondo è alquanto asimmetrico (anisotropico) e deriva da uno spin label ruotante in un dominio temporale piuttosto lento (τ_c=10^-7). L'assunzione di una forma sferica per la proteina in soluzione ha portato, attraverso la relazione di Stokes-Einstein, ad una determinazione del raggio molecolare in buon accordo con il risultato di misure di diffrazione a basso angolo di neutroni. Si discute inoltre l'interazione con altri biosistemi come desunta dalla dinamica molecolare della proteina.

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Резюме Церулоплазмин, человеческий белок, содержащий парамагнитные ионы меди Cu⁺⁺, помечается с помощью различных спиновых меток для исследования молекулярной динамики и взаимодействий с другими биосистемами. Спиновая метка в случае производной меламида приводит к спектру электронного спинового резонанса, который представляет суперпозицию двух различных групп линий, обусловленных парамагнитными разновидностями при различных микро-окружениях. Первый спектр, изотропный триплет линий, обусловлен быстро движущейся спиновой меткой (с временем ротационной корреляции (τ_c≃10^-9 c); второй спектр представляет анизотропный асимметричный сигнал, возникающий от медленно движущейся спиновой метки (τ_c=10^-7 c). Предположение сферической формы бекла в растворе, которое следует из соотношения Стокса-Эйнштейна, позволяет оценить радиус молекулы, величина которого хорошо согласуется с измерениями малоуг лового рассеяния нейтронов. Обсуждается взаимодействие с другими биосистемами на основе анализа динамики молекул белка.

     

Characterization of the structure and dynamics of an aqueous Hg solution by an ab initio molecular dynamics study

Quantum mechanical charge field (QMCF) MD simulation has been performed to investigate the structure and dynamics of Hg²⁺ hydrate. The first-shell hexacoordinated [Hg(H₂O)₆]²⁺ complex with an average Hg²⁺-O distance of 2.40 Å is dominantly found, which corresponds to the neutron diffraction and extended X-ray absorption fine structure (EXAFS) experiments. Other species, in particular the 7-fold coordinated complexes, can be formed transiently, according to the water exchange processes with an associative interchange (I_a) mechanism. The second hydration shell exhibits a Hg²⁺-O distance of 4.6 Å with a coordination number of ~ 14. The mean residence times (MRTs) of first- and second-shell waters clearly indicate a strong “structure-forming” ability of Hg²⁺ in aqueous solution.     

A new application for an old concept: Constant time (CT)-REDOR for an accurate determination of second moments in multiple spin systems with strong heteronuclear dipolar couplings

In this contribution we present a constant time version of the well known REDOR pulse sequence which enables us to determine the second moments in multiple spin systems with strong dipolar couplings. From the resulting dipolar evolution curves, accurate values for the second moments can be obtained without the need to incorporate the full information about the detailed spin geometry of the multiple spin systems into the simulation protocol.     

Structure and dynamics of the plastic crystal tetramethylammonium dicyanamide—a molecular dynamics study

A molecular dynamics study of the organic ionic plastic crystal tetramethylammonium dicyanamide is reported here. An all atom force field, based on CHARMM parameters, has been used, and calculations were carried out under NPT conditions at several temperatures ranging from the rigid lattice (200 K) up to well above the melt (600 K). The volume expansion, radial distribution functions and the onset of different rotational and translational motions has been simulated and are discussed both in terms of plastic crystals in general as well as compared to experimental results previously obtained for this particular system.     

Simulation study for the orientation of the driven vortex lattice in an amorphous superconductor

We investigate the orientation of the vortex lattice driven by an applied current by means of numerical simulations based on the time-dependent Ginzburg–Landau (TDGL) theory. A lattice order is restored by a current driving of vortices under the influence of random vortex pinnings. The orientation of the moving vortex lattice is different between the presence and the absence of vortex pinnings. We show results of TDGL simulations for these phenomena.     

Phase dynamics of a relativistic electron driven by the potential field of a wave packet: Poincaré transformation dynamics

We investigate the Poincaré transformation dynamics describing the stochastic motion of a relativistic electron in the regular electrostatic field of a wave packet. The conditions of local instability of the phase trajectories are determined: it is shown that the system is a structurally stable Y system with an attracting set of the hyperbolic type. The relationship between the dynamics at the strange attractor characterized by Lyapunov indices and its statistical structure described by the Kolmogorov entropy is discussed. The fractal dimension of the phase space of the system is determined. The results of a numerical simulation of the effect are presented and discussed. Altai State University. Translated from Izvestiya Vysshikh Uchebnykh Zavedenii, Fizika, No. 6, pp. 15–20, June, 1998.     

Investigations of polymer dynamics in nanoporous media by field cycling NMR relaxometry and the dipolar correlation effect

The chain dynamics of short-chain perfluoropolyether melts confined in Vycor nanoporous media has been characterized by field cycling nuclear magnetic resonance relaxometry and the dipolar correlation effect. The slowdown of motions under confinement, leading to larger residual dipolar couplings, has been probed by looking at the quotient of stimulated and primary echoes. Using field cycling relaxometry, it has been shown that there is strong evidence of reptation-like motion, even for such short-chain polymers as shown by the frequency and molecular weight dependences of the spin-lattice relaxation time.     

Lattice dynamics of an anharmonic crystal: evidence for interactions between atomic vibrations at high temperatures

In studying the lattice dynamics of a strongly anharmonic crystal, we solve a set of nonlinear Langevin equations for interacting oscillators while a multiwell potential is calculated in the displacive limit from the first principles. The model applied to the peculiar vibrations of beta-Zr along [111] allows us to analyze all contributions to the spectral density and their influence on each other. We predict the effect of induced anharmonicity for quick vibrations due to their interaction with intrinsically anharmonic slow vibrations. This effect results in the broadband distribution in energy of inelastic neutron scattering known as the symmetry-forbidden phonon-branch splitting.     

Kinetics and mechanism for the oxidation of anilines by ClO2: a combined experimental and computational study

The oxidation of para‐substituted anilines (X–C₆H₄NH₂, X = –CH₃, –H, –Cl, –NO₂) with chlorine dioxide was studied as a means of eliminating these pollutants. The oxidation rate decreases from that for 4‐methylaniline to that for 4‐nitroanilinem in agreement with the Hammett plot; the oxidation kinetics is second order in aniline and first order in ClO₂, for which a possible mechanism is proposed. Liquid chromatography and gas chromatography mass spectrometry results show that benzoquinone is formed as the major intermediate in aniline/ClO₂ oxidation, and the reaction is pH‐dependent as the rate constant increases with increasing pH. To further support our proposed mechanism, Density Functional Theory (DFT) computations at both B3LYP/6‐311 + G(d,p) level with the polarizable continuum model with an integral equation formalism solvation model (i.e., with water) were carried out, showing that activation energy barriers predict the same reactivity trend as shown by the kinetics experiments. Copyright © 2014 John Wiley & Sons, Ltd.     

Bond breaking and temporary anion states in uracil and halouracils: implications for the DNA bases

Low energy electrons are capable of breaking bonds in gas phase DNA bases by means of the dissociative electron attachment process. With the aid of new total scattering data in the halouracils and input from quantum chemical calculations, we describe the dipole bound and valence anion states in these compounds and present assignments for the two types of structure appearing in the cross sections. A clear distinction between the two mechanisms for bond breaking is necessary for an understanding of electron induced damage to DNA.     

A study of dipolar interactions and dynamic processes of water molecules in tendon by 1H and 2H homonuclear and heteronuclear multiple-quantum-filtered NMR spectroscopy

The effect of proton exchange on the measurement of 1H-1H, 1H-2H, and 2H-2H residual dipolar interactions in water molecules in bovine Achilles tendons was investigated using double-quantum-filtered (DQF) NMR and new pulse sequences based on heteronuclear and homonuclear multiple-quantum filtering (MQF). Derivation of theoretical expressions for these techniques allowed evaluation of the 1H-1H and 1H-2H residual dipolar interactions and the proton exchange rate at a temperature of 24 degrees C and above, where no dipolar splitting is evident. The values obtained for these parameters at 24 degrees C were 300 and 50 Hz and 3000 s-1, respectively. The results for the residual dipolar interactions were verified by repeating the above measurements at a temperature of 1.5 degrees C, where the spectra of the H2O molecules were well resolved, so that the 1H-1H dipolar interaction could be determined directly from the observed splitting. Analysis of the MQF experiments at 1.5 degrees C, where the proton exchange was in the intermediate regime for the 1H-2H dipolar interaction, confirmed the result obtained at 24 degrees C for this interaction. A strong dependence of the intensities of the MQF signals on the proton exchange rate, in the intermediate and the fast exchange regimes, was observed and theoretically interpreted. This leads to the conclusion that the MQF techniques are mostly useful for tissues where the residual dipolar interaction is not significantly smaller than the proton exchange rate. Dependence of the relaxation times and signal intensities of the MQF experiments on the orientation of the tendon with respect to the magnetic field was observed and analyzed. One of the results of the theoretical analysis is that, in the fast exchange regime, the signal decay rates in the MQF experiments as well as in the spin echo or CPMG pulse sequences (T2) depend on the orientation as the square of the second-rank Legendre polynomial.