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.     

The Eta Invariant of Pin Manifolds with Cyclic Fundamental Groups

Periodica Mathematica Hungarica - Let ?= 2ν &;gt; 1. Let M be an orientable manifold of odd dimension m with $\pi _1 (M) = \mathbb{Z}_\ell $ whose universal cover $\tilde M$ is...     

A Survey on Explicit Representation Formulae for Fundamental Solutions of Linear Partial Differential Operators

In the present article, we aim at treating the existence of fundamental solutions of linear partial differential operators with constant coefficients from the viewpoint of setting up explicit formulae yielding fundamental solutions.     

Field optimized initial state based control of photodissociation

A new scheme for controlling photodissociation through preparation of a variationally optimized linear superposition of field free vibrational eigenstates is applied for selective control of IBr and HI dissociation. The dependence of photodissociation on various field parameters and initial conditions is examined to investigate the mechanistic basis of selective control. The parametric equations of motion approach for determining vibrational dynamics as a function of field parameters without having to solve the time dependent Schrödinger equation explicitly for each field parameter separately is outlined and its use to identify field characteristics which will provide the requisite population mix represented by the optimal linear superposition of vibrational states is advocated.     

Properties of nonparametric estimators of autocovariance for stationary random fields

Summary We introduce nonparametric estimators of the autocovariance of a stationary random field. One of our estimators has the property that it is itself an autocovatiance. This feature enables the estimator to be used as the basis of simulation studies such as those which are necessary when constructing bootstrap confidence intervals for unknown parameters. Unlike estimators proposed recently by other authors, our own do not require assumptions such as isotropy or monotonicity. Indeed, like nonparametric function estimators considered more widely in the context of curve estimation, our approach demands only smoothness and tail conditions on the underlying curve or surface (here, the autocovariance), and moment and mixing conditions on the random field. We show that by imposing the condition that the estimator be a covariance function we actually reduce the numerical value of integrated squared error.     

Quantitative electron probe microanalysis for the characterization of thin carbon-boron layers in fusion devices

Summary The first wall of the fusion device TEXTOR at the Forschungszentrum Jülich has been coated in situ with an amorphous hydrogen rich carbon/boron film (a-C/B:H) which reduces plasma impurities caused by the plasma surface interaction. The results of the coating process of the 35 m² large inner wall surface have been controlled by a recently developed modification of the quantitative electron probe microanalysis, which has been applied to 12 samples from specified positions inside the tokamak. The quantification itself is based on a Monte Carlo simulation of electron trajectories providing very accurate results for X-ray intensities emitted by elements present in the electron bombarded sample. The Monte Carlo results are used in the present work to calibrate the measured X-ray intensities emitted by boron and carbon from the a-C/B:H layers deposited on pure silicon substrates. As a result the total deposited mass of the layer per area unit as well as the composition of the layers (except hydrogen) could be determined very accurately. The relative errors were less than 7%. The limit of detectability were found to be in the range of one monolayer for boron as well as for carbon.