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.     

RANDOM EDGE can be exponential on abstract cubes

We prove that RANDOM EDGE, the simplex algorithm that always chooses a random improving edge to proceed on, can take a mildly exponential number of steps in the model of abstract objective functions (introduced by Williamson Hoke [Completely unimodal numberings of a simple polytope, Discrete Appl. Math. 20 (1988) 69-81.] and by Kalai [A simple way to tell a simple polytope from its graph, J. Combin. Theory Ser. A 49(2) (1988) 381-383.] under different names). We define an abstract objective function on the n-dimensional cube for which the algorithm, started at a random vertex, needs at least exp(const·n^1/3) steps with high probability. The best previous lower bound was quadratic. So in order for RANDOM EDGE to succeed in polynomial time, geometry must help.     

Cellulose dimethylphenylcarbamate-bonded carbon-clad zirconia for chiral separation in high performance liquid chromatography.

Porous zirconia particles are very robust material and have received considerable attention as a stationary phase support for HPLC. We prepared cellulose dimethylphenylcarbamate-bonded carbon-clad zirconia (CDMPCCZ) as a chiral stationary phase (CSP) for separation of enantiomers of a set of 14 racemic compounds in normal phase (NP) and reversed-phase (RP) liquid chromatography. Retention and enantioselectivity on CDMPCCZ were compared to those on CDMPC-coated zirconia (CDMPCZ) to see how the change in immobilization method of the chiral selector affects the retention and chiral selectivity. In NPLC, retention was longer and the number of resolved racemates was smaller on CDMPCCZ than on CDMPCZ. However, chiral selectivity factors for some resolved racemates were better on CDMPCCZ than on CDMPCZ. The longer retention on CDMPCCZ is likely due to strong, non-chiral discriminating interactions with the carbon layer on CDMPCZ. In RPLC only two racemates were resolved on CDMPCCZ, but retention times were shorter than, and resolutions were comparable to, those in NPLC, indicating a potential for improving chromatographic performance of the CDMPCCZ column in RPLC with optimized column preparation and separation conditions.     

Changes in the spectrum of Gaussian Schell-model beams propagating through turbulent atmosphere

Based on the extended Huygens-Fresnel principle, the spectrum of Gaussian Schell-model (GSM) beams propagating through turbulent atmosphere is derived analytically. It is shown that, if the scaling law is valid, the normalized spectrum S(ω) of GSM beams propagating through turbulent atmosphere is the same as the normalized source spectrum S⁽⁰⁾(ω), whether GSM source is quasi-homogenous or not. On the other hand, if the scaling law fails, S(ω) of GSM is different from S⁽⁰⁾(ω). The structure constant of the refractive index, transverse coordinate of observation point and spatial correlation length of the source affect the spectrum, which is illustrated numerically.     

Mössbauer and X-ray diffraction characterization of Fe60Al40 coatings prepared by thermal spraying

Microstructured (atomized) and nanostructured (milled) Fe₆₀Al₄₀ powders together with their corresponding coatings synthesized by High Velocity Oxy-fuel (HVOF) or Atmospheric Plasma Spray (APS) thermal spraying techniques have been characterized by Mössbauer Spectroscopy (MS) and X-ray Diffraction (XRD). The evolution of the microstructure and the atomic ordering degree in the powders and coatings are discussed at the light of the various processing conditions. The operational correlation between the parameters of the duplex morphology of coatings and the processing parameters is discussed.     

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.     

Representation surfaces of Young''s modulus and Poisson''s ratio for BCC transition metals

 The general expressions for the compliance , Young's modulus E(h k l) and Poisson's ratio υ(h k l) along an arbitrary direction [h k l] are given for cubic crystals. The representation surfaces, for which the length of the radius vector in the [h k l] direction equals to E(h k l) or υ(h k l), are constructed for seven BCC transition metals Cr, Fe, Mo, Nb, Ta, V and W. Neglecting W, which is isotropic, both representation surfaces of Young's modulus and Poisson's ratio are spherical surfaces. The remaining BCC transition metals may be grouped into two classes. In the first group (Cr, Mo, Nb and V) with negative values of s_A, Young's modulus surface has eight depressed corners and six rounded protuberances at the centers of the faces. In the second group (Fe and Ta) with positive values of s_A, on the contrary, Young's modulus surface has eight rounded protuberance corners and six depressions at the centers of the faces. The contrary conclusions are obtained for Poisson's ratio.     

Ab-initio molecular dynamics simulation on nano-system under external pressure

A new constant-pressure molecular dynamics (MD) method is developed to simulate the dynamic behavior and structure transition of finite system under external pressure. In this method, no artificial parameter is introduced and the computation overheads are very small. As an application, a hard-soft transition of single wall carbon nanotube (SWCNT) under external pressure is found, which is in agreement with the experiments.