Molecular dynamics simulations of single siloxane dendrimers: Molecular structure and intramolecular mobility of terminal groups.

Molecular dynamics simulations of two types of isolated siloxane dendrimers of various generations (from the 2nd to the 8th) have been performed for temperatures ranging from 150 K to 600 K. The first type of dendrimer molecules has short spacers consisting of a single oxygen atom. In the dendrimers of the second type, spacers are longer and comprised of two oxygen atoms separated by a single silicon atom. A comparative analysis of molecular macroscopic parameters such as the gyration radius and the shape factor as well as atom distributions within dendrimer interior has been performed for varying generation number, temperature, and spacer length. It has been found that the short-spacer dendrimers of the 7th and 8th generations have a stressed central part with elongated bonds and deformed valence angles. Investigation of the time evolution of radial displacements of the terminal Si atoms has shown that a fraction of the Si groups have a reduced mobility. Therefore, rather long time trajectories (of the order of tens of nanoseconds) are required to study dendrimer intramolecular dynamics.

Drug kinetics release from Eudragit - Tenofovir@SiOC tablets.

A novel drug release system has been obtained in form of tablets from Eudragit® RS and tenofovir loaded on porous silicon oxycarbide glasses (SiOC). Active carbon (AC) and mesoporous silica (MCM-41) have also been used for comparative purposes. The porous silicon oxycarbide presents a bimodal mesopore size distribution that is maintained after functionalization with amino groups. We have studied the adsorption kinetics and adsorption equilibrium when the materials are loaded with tenofovir and, in all cases, pseudo-second order kinetics and Langmuir isotherm have been revealed as the most representative models describing the kinetic and thermodynamic parameters. Besides, the tenofovir adsorption on these materials turns out to be a favorable process. In vitro release of tenofovir has been studied in simulated vaginal medium by applying different release models. Continuous tenofovir release for >20days has been obtained for the SiOC material functionalized with amine groups. We concluded that the drug release occurs in two steps that involve a drug diffusion step through the material pores and diffusion through the swollen polymer. The interactions between the tenofovir drug and de amine groups of the functionalized silicon oxycarbide also play an important role in the release process.

The "sugar" coarse-grained DNA model.

More than 20 coarse-grained (CG) DNA models have been developed for simulating the behavior of this molecule under various conditions, including those required for nanotechnology. However, none of these models reproduces the DNA polymorphism associated with conformational changes in the ribose rings of the DNA backbone. These changes make an essential contribution to the DNA local deformability and provide the possibility of the transition of the DNA double helix from the B-form to the A-form during interactions with biological molecules. We propose a CG representation of the ribose conformational flexibility. We substantiate the choice of the CG sites (six per nucleotide) needed for the "sugar" GC DNA model, and obtain the potentials of the CG interactions between the sites by the "bottom-up" approach using the all-atom AMBER force field. We show that the representation of the ribose flexibility requires one non-harmonic and one three-particle potential, the forms of both the potentials being different from the ones generally used. The model also includes (i) explicit representation of ions (in an implicit solvent) and (ii) sequence dependence. With these features, the sugar CG DNA model reproduces (with the same parameters) both the B- and A- stable forms under corresponding conditions and demonstrates both the A to B and the B to A phase transitions. Graphical Abstract The proposed coarse-grained DNA model allows to reproduce both the B- and A- DNA forms and the transitions between them under corresponding conditions.

Simulation of melting in crystalline polyethylene.

We carry out a molecular dynamics simulation of the first stages of constrained melting in crystalline polyethylene (PE). When heated, the crystal undergoes two structural phase transitions: from the orthorhombic (O) phase to the monoclinic (M) phase, and then to the columnar (C), quasi-hexagonal, phase. The M phase represents the tendency to the parallel packing of planes of PE zigzags, and the C phase proves to be some kind of oriented melt. We follow both the transitions O→M and M→C in real time and establish that, at their beginning, the crystal tries (and fails) to pass into the partially ordered phases similar to the RI and RII phases of linear alkanes, correspondingly. We discuss the molecular mechanisms and driving forces of the observed transitions, as well as the reasons why the M and C phases in PE crystals substitute for the rotator phases in linear alkanes.

[Computer modeling of the effective search]. / Computernoe modelirovanie éffektivnogo poiska.

A computer model of vector-Brownian processes is proposed, which can be applied to some biophysical problems including the problem of search efficiency. The results obtained suggest that the changes in the ratio of two components (the vector and the Brownian ones) in any process essentially improve the efficiency of search.

[Reassociation of interspersed moderate DNA repeats]. / Reassotsiatsiia peremezhaiushchikhsia umerennykh povtorov DNK.

Reassociation kinetics of the fragments of DNA consisting of interspersed repetitive and non-repetitive nucleotide sequences is considered in this paper. Based on the model, suggested by Gavrilov and Mazo (Mol. biol., 11, 101 1977), which takes into account the random DNA shearing, both reassociation kinetics of the total DNA in the region corresponding to interspersed repeat reassociation and that of the isolated preparation of interspersed repetitive sequences are calculated. In both cases influence of the repeat length on the reassociation rate is demonstrated. The estimation of the repetition frequency of rare repeats from pigeon genome is specified using calculations performed.

[Effect of random shearing of DNA on the reassociation kinetics of repeating sequences]. / Vliianie sluchainogo drobleniia DNK na kinetiku reassotsiatsii povtoriaiushchikhsia posledovatel'nostei.

Influence of random DNA shearing on reassociation of repeated sequences separated by considerably long unique sequences has been considered theoretically. Reassociation kinetic curves have been calculated for repeated sequences of various length. Dependence of the reassociation rate constant and the repeated sequences frequency on the fraction and length of the repeated sequences has been obtained.