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.     

Luttinger liquid with asymmetric dispersion

We present an extension of the Tomonaga-Luttinger model in which left and right-moving particles have different Fermi velocities. We derive expressions for one-particle Green's functions, momentum-distributions, density of states, charge compressibility and conductivity as functions of both the velocity difference ε and the strength of the interaction β. This allows us to identify a novel restricted region in the parameter space in which the system keeps the main features of a Luttinger liquid but with an unusual behavior of the density of states and the static charge compressibility κ. In particular κ diverges on the boundary of the restricted region, indicating the occurrence of a phase transition. Received 20 May 2002 / Received in final form 23 August 2002 Published online 19 November 2002     

A branching process model for sand avalanches

An analytically solvable model for sand avalanches of noninteracting grains of sand, based on the Chapman-Kolmogorov equations, is presented. For a single avalanche, distributions of lifetimes, sizes of overflows and avalanches, and correlation functions are calculated. Some of these are exponentials, some are power laws. Spatially homogeneous distributions of avalanches are also studied. Computer simulations of avalanches of interacting grains of sand are compared to the solutions to the Chapman-Kolmogorov equations. We find that within the range of parameters explored in the simulation, the approximation of noninteracting grains of sand is a good one.     

XPS and XAES study of the interaction of palladium and copper overlayers with fullerene films

X-ray photoelectron and Auger spectroscopies were used to examine surface bonding and overlayer growth during palladium and copper deposition onto films of fullerene, C₆₀ The results were consistent with metal cluster formation on C₆₀. The observed positive core electron binding energy shifts in small metallic clusters supported on C₆₀ were shown to originate in metal-fullerene interaction accompanied by charge transfer. Palladium-fullerene intermixing at temperatures as low as ss 50°C was observed for small Pd coverages.     

Singular terms of helicity amplitudes at one loop in QCD and the soft limit of the cross sections of multi-parton processes

We describe a general method that enables us to obtain all the singular terms of helicity amplitudes of n-parton processes at one loop. The algorithm uses helicity amplitudes at tree level and simple color algebra. We illustrate the method by calculating the singular part of the one-loop helicity amplitudes of all 2 → 3 parton subprocesses. The results are used to derive the soft gluon limit of the cross sections of all 2 → 4 parton scattering subprocesses which provide a useful initial condition for the angular ordering approximation to coherent multiple soft gluon emission, incorporated in existing Monte Carlo simulation programs.     

The first ruthenium-alkyne-dihydride reported is now recognized as an intermediate in the homogeneous hydrogenation of diphenylacetylene: Crystal structure of (μ-H)2Ru3(CO)9(μ3-η2-∥-C2Ph2)

The title complex (complex1) was the first alkyne-substituted triruthenium dihydrido cluster to be reported and was characterized by spectroscopy as a triangular cluster with the alkyne parallel to a Ru-Ru edge. Recently, we have found that1 is a key intermediate in the homogeneous hydrogenation of diphenylacetylene catalyzed by tetrahedral Ru₄ and FeRu₃ clusters. Since the discovery of1, a great number of complexes with alkynes parallel to a cluster edge have been reported; at present this is the more common bonding mode for alkynes on trinuclear clusters. The structural features of1 allow a comparison with those of other ruthenium-containing derivatives and help to draw suggestions of the role of1 in hydrogenation catalysis.     

Spatial Vector Solitons in Nonlinear Photonic Crystal Fibers

We study spatial vector solitons in a photonic crystal fiber (PCF) made of a material with the focusing Kerr nonlinearity. We show that such two-component localized nonlinear waves consist of two mutually trapped components confined by the PCF linear and the self-induced nonlinear refractive indices, and they bifurcate from the corresponding scalar solitons. We demonstrate that, in a sharp contrast with an entirely homogeneous nonlinear Kerr medium where both scalar and vector spatial solitons are unstable and may collapse, the periodic structure of PCF can stabilize the otherwise unstable two-dimensional spatial optical solitons. We apply the matrix criterion for stability of these two-parameter solitons, and verify it by direct numerical simulations.     

Efficient synthesis of an aldehyde‐capped polythiophene containing fluorinated electron‐withdrawing groups

To incorporate an acceptor type polythiophene segment onto a supramolecular block copolymer for potential light harvesting applications, effective synthetic routes for the end‐functionalized and acceptor‐substituted polythiophenes are critical. The Ullmann coupling reaction can be utilized to obtain electron‐deficient polythiophenes and to attach terminal thiophene units that carry functional groups. In this article, the reactions involving a 2,5‐dibromothiophene monomer containing an electron‐withdrawing fluorinated ester and 5‐bromo‐2‐thiophenecarboxaldehyde (the end‐capper) were studied in detail. It was found that the Ullmann coupling reaction of the dibromide is very fast (completed in a few minutes) and the terminal bromine group does not survive long under the reaction condition. These findings lead to the development of an effective procedure for aldehyde end‐capping of electron‐deficient polythiophenes. Polymers with molecular weights around 4000 Da are routinely obtained. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 41–47, 2007