Molecular dynamics simulations of the oligonucleotide with the modified phosphate/phosphonate internucleotide linkage

Impact of the internucleotide linkage modification by inserting a methylene group to the P-O bond (—O—PO ₂ ^— —O— chain changed for —O—PO ₂ ^— —CH₂—O—), on the modified oligonucleotide binding ability to the natural DNA strand was studied by molecular dynamics simulation. Complex of (dT)₁₁ with a deoxyadenosine undecamer containing alternating modified and natural internucleotide linkage was studied as a model system. The Amber force field was completed by a set of new parameters needed to model the modified part of the nucleotide. The simulations confirmed existence of a double-helical complex the melting point of which is considerably higher than 300 K. While the thymidine (unmodified) strand possesses a B-type secondary structure, the conformation of the adenosine (modified) strand is not stable at 300 K. The -ggt conformation of the modified linkages is highly preferred, temporary jumps to the -g-gt and ggt conformations were, however, observed.     

Parahydrogen-Induced Polarization in Heterogeneous Hydrogenations over Silica-Immobilized Rh Complexes

The use of heterogeneous catalysts for parahydrogen-induced polarization (PHIP) of nuclear spins opens new horizons for production of hyperpolarized substances. Immobilization of homogeneous hydrogenation catalysts is a promising approach for designing the efficient heterogeneous catalytic systems capable of PHIP generation. Herein, we study the formation of PHIP in the gas-phase and in the liquid-phase hydrogenations of propyne and propylene catalyzed by silica-immobilized Rh complexes synthesized by the ligand-exchange anchoring of the Wilkinson’s complex RhCl(PPh₃)₃, the binuclear complex Rh₂Cl₂(C₈H₁₂)₂ and the cationic complex [Rh(C₈H₁₂)₂]⁺[BF₄]^? to the phosphine-modified silica gel. We consider the stability and the mechanistic aspects of the hydrogenation over the immobilized Wilkinson’s catalyst in terms of PHIP observation. Using a PASADENA (parahydrogen and synthesis allow dramatically enhanced nuclear alignment) effect, it is found, in particular, that liquid-phase propyne hydrogenation over the immobilized Wilkinsons’s catalyst at 70°C proceeds in a stable regime with a stereoselective cis addition of a hydrogen molecule, while in the gas phase at the same temperature the hydrogenation stereoselectivity is observed only for a short time after the reaction is started, and then the catalyst rapidly loses its activity. The reasons of the catalyst deactivation are discussed based on the literature data, the results of infrared spectroscopy study, and the comparison to the behavior of the immobilized binuclear and cationic Rh complexes. In addition, it is shown that the immobilized Wilkinson’s catalyst is reduced as temperature increases in the range of 90–130°C, as confirmed by X-ray photoelectron spectroscopy.     

Nonlinear optoacoustic transformation in the system of dielectric substrate/submicron metal coating/liquid

The optoacoustic method has been shown to be an accurate technique for the measurement of the properties of submicron metal coatings deposited on a dielectric substrate, i.e., mirrors. The method has been previously theoretically described in terms of a linear model of optoacoustic transformation in a system substrate/coating/liquid. The goal of the present work was to determine the limits at which the linear model is still applicable. The modification of the laser induced acoustic signal profiles and transfer functions of optoacoustic transformation versus the laser fluence was studied for two liquids: ethanol and water.     

Two-zone elastic-plastic single shock waves in solids

By decoupling time and length scales in moving window molecular dynamics shock-wave simulations, a new regime of shock-wave propagation is uncovered characterized by a two-zone elastic-plastic shock-wave structure consisting of a leading elastic front followed by a plastic front, both moving with the same average speed and having a fixed net thickness that can extend to microns. The material in the elastic zone is in a metastable state that supports a pressure that can substantially exceed the critical pressure characteristic of the onset of the well-known split-elastic-plastic, two-wave propagation. The two-zone elastic-plastic wave is a general phenomenon observed in simulations of a broad class of crystalline materials and is within the reach of current experimental techniques.     

Wake effect in doped graphene due to moving external charge

We use the dielectric-response formalism to evaluate the induced density of charge carriers in supported graphene due to an external moving charged particle in terms of its velocity and distance from graphene for several equilibrium charge carrier densities due to graphene doping. We show that, when the particle speed exceeds a threshold value, an oscillatory wake effect develops in the induced charge density trailing the particle. Strong effects are observed in the wake pattern due to finite size of the graphene–substrate gap, as well as due to strong coupling effects, and plasmon damping of graphene?s π electrons.     

Exoelectron emission from solid nitrogen

Solid nitrogen was investigated by activation spectroscopy methods – thermally stimulated luminescence and thermally stimulated exoelectron emission (TSL and TSEE) in combination with luminescence analysis. TSEE from solid nitrogen pre-irradiated by an electron beam was measured and investigated for the first time. A set of peaks both in TSL and TSEE were observed. It was found that one of the peaks in the TSEE curve is caused by release of electrons in the course of the α-β phase transition of solid nitrogen. The corresponding activation energy was estimated.     

Hawking radiation by Kerr black holes and conformal symmetry

The exponential blueshift associated with the event horizon of a black hole makes conformal symmetry play a fundamental role in accounting for its thermal properties. Using a derivation based on two-point functions, we show that the full spectrum of thermal radiation of scalar particles by Kerr black holes can be explicitly derived on the basis of a conformal symmetry arising in the wave equation near the horizon. The simplicity of our approach emphasizes the depth of the connection between conformal symmetry and black hole radiance.     

Semi-passivity and synchronization of diffusively coupled neuronal oscillators

We discuss synchronization in networks of neuronal oscillators which are interconnected via diffusive coupling, i.e. linearly coupled via gap junctions. In particular, we present sufficient conditions for synchronization in these networks using the theory of semi-passive and passive systems. We show that the conductance based neuronal models of Hodgkin-Huxley, Morris-Lecar, and the popular reduced models of FitzHugh-Nagumo and Hindmarsh-Rose all satisfy a semi-passivity property, i.e. that is the state trajectories of such a model remain oscillatory but bounded provided that the supplied (electrical) energy is bounded. As a result, for a wide range of coupling configurations, networks of these oscillators are guaranteed to possess ultimately bounded solutions. Moreover, we demonstrate that when the coupling is strong enough the oscillators become synchronized. Our theoretical conclusions are confirmed by computer simulations with coupled Hindmarsh-Rose and Morris-Lecar oscillators. Finally we discuss possible “instabilities” in networks of oscillators induced by the diffusive coupling.