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.     

A Simple Bi-directional Mode Expansion Propagation Algorithm Based on Modes of a Parallel-plate Waveguide

The bi-directional mode expansion propagation algorithm (BEP) is known to be an accurate and efficient method for modelling field distribution in high-index contrast waveguide structures with strong back-reflections like Bragg gratings and photonic crystals. The main difficulty of this method is that for lossy structures, the propagation constants of modes are to be searched in the complex plane. To speed-up this procedure, a two-step algorithm for eigenmode calculation based on the expansion into the modes of an empty metallic waveguide has recently been proposed. Proper truncation rules possessing good convergence of the expansion method for both TE and TM modes have also been recently published. In this contribution, both these approaches are combined in the development of an extremely simple version of the two-dimensional BEP method that makes use of the field expansion into the eigenmodes of a parallel-plate waveguide. The method is strictly reciprocal and appeared to be computationally reliable also for strongly lossy structures. High numerical stability is ensured using the scattering matrix formalism, and an efficient method of calculating Bloch modes for symmetric as well as asymmetric periodic waveguide structures is adopted. A wide range of applicability of the method is demonstrated by a few examples.     

Fractional Hamiltonian Monodromy

We introduce fractional monodromy in order to characterize certain non-isolated critical values of the energy–momentum map of integrable Hamiltonian dynamical systems represented by nonlinear resonant two-dimensional oscillators. We give the formal mathematical definition of fractional monodromy, which is a generalization of the definition of monodromy used by other authors before. We prove that the 1:( − 2) resonant oscillator system has monodromy matrix with half-integer coefficients and discuss manifestations of this monodromy in quantum systems. Communicated by Eduard Zehnder Submitted: February 25, 2005; Accepted: November 17, 2005     

Scientist up to the highest level

Dr. Miroslav Kyrš, DrSc. passed away prematurely and unexpectedly in August 2006 at age of 75. He was a leading person of the Czech radiochemistry during the second half of the 20th century and his results have of world-wide impact. His diligence, intelligence and permanent activity led him to be at first a laboratory chief and subsequently for about 25 years to be a chief of the Radiochemical Department of Czech Nuclear Research Institute (NRI) at Řež near Prague.     

Parton-hadron duality in event generators

The validity of local parton-hadron duality within the framework of HERWIG and JETSET event generators is investigated. We concentrate one ⁺ e ^– annihilations in LEP 2 energy range as these interactions provide theoretically the cleanest condition for the discussion of this concept. We conclude that the concept of local parton-hadron duality is not valid in either of the two generators considered.