Mikhail A. Mazo

Heat conductivity of DNA double helix.

Thermal conductivity of isolated single molecule DNA fragments is of importance for nanotechnology, but has not yet been measured experimentally. Theoretical estimates based on simplified (1D) models predict anomalously high thermal conductivity. To investigate thermal properties of single molecule DNA we have developed a 3D coarse-grained (CG) model that retains the realism of the full all-atom description, but is significantly more efficient. Within the proposed model each nucleotide is represented by 6 particles or grains; the grains interact via effective potentials inferred from classical molecular dynamics (MD) trajectories based on a well-established all-atom potential function. Comparisons of 10 ns long MD trajectories between the CG and the corresponding all-atom model show similar root-mean-square deviations from the canonical B-form DNA, and similar structural fluctuations. At the same time, the CG model is 10 to 100 times faster depending on the length of the DNA fragment in the simulation. Analysis of dispersion curves derived from the CG model yields longitudinal sound velocity and torsional stiffness in close agreement with existing experiments. The computational efficiency of the CG model makes it possible to calculate thermal conductivity of a single DNA molecule not yet available experimentally. For a uniform (polyG-polyC) DNA, the estimated conductivity coefficient is 0.3 W/mK which is half the value of thermal conductivity for water. This result is in stark contrast with estimates of thermal conductivity for simplified, effectively 1D chains (beads on a spring) that predict anomalous (infinite) thermal conductivity. Thus, full 3D character of DNA double-helix retained in the proposed model appears to be essential for describing its thermal properties at a single molecule level.

Molecular Dynamics Simulation of Thermomechanical Properties of Montmorillonite Crystal. 1. Isolated Clay Nanoplate

The structure and mechanical properties of clay nanoparticles is a subject of growing interest because of their numerous applications in engineering. We present the results of molecular dynamics simulation for a single nanoplate of pyrophyllite - a 2:1 clay mineral consisting of two tetrahedral sheets of SiO4 and an intervening octahedral AlO6 sheet. Simulations were performed in the temperature interval from 5 to 750 K using the ionic-type potentials of Cygan et al. On this basis the temperature dependences of structural parameters, characterizing both tetrahedral and octahedral sheets as well as single lamella, have been studied. Two slightly different structures were observed in this wide temperature interval. The mechanical properties of the nanoplate were calculated from stress-strain diagrams, which have been obtained at relatively slow rates of deformation (for molecular simulations). Using different types of loading, we calculated the full elasticity tensor and estimated the influence of temperature on its components. We estimated also the bending and torsion stiffnesses of the nanoplate as specific characteristics of this type of particle. Because the nanoplate is atomically thin, a reasonable determination of the thickness is a nontrivial problem, both in the modeling of mechanical properties and in physical interpretation of the obtained data. We propose a procedure for its calculation.

Molecular dynamics simulation of thermomechanical properties of montmorillonite crystal. 3. montmorillonite crystals with PEO oligomer intercalates.

We present the results of molecular dynamics (MD) simulation of the structure and thermomechanical behavior of Wyoming-type Na+-montmorillonite (MMT) with poly(ethylene oxide) (PEO) oligomer intercalates. Periodic boundary conditions in all three directions and simulation cells containing two MMT lamellae [Si248Al8][Al112Mg16]O640[OH]128 oriented parallel to the XY-plane were used. The interlamellar space, or gallery, between neighboring MMT lamellae was populated by 24 Na+ counterions and PEO macromolecules of different lengths, ranging from 2 up to 240 repeat units. We considered three different loadings of PEO within the gallery: 80, 160, and 240 repeat units, corresponding to 13, 23, and 31 wt % PEO based on total mass of the nanocomposite, respectively. In the cases of 13 and 23 wt %, the polymer chains formed one or two well-defined amorphous layers with interlayer distances of 1.35 and 1.8 nm, respectively. We have observed also formation of a wider monolayer gallery with interlayer distances of 1.6 nm. Three-layer PEO films formed in the case of 31 wt % loading. The thermal properties were analyzed over the range 300-400 K, and the isothermal linear compressibility, transversal moduli, and shear moduli were calculated at 300 K. These properties are compared with the results of our simulation of thermal and mechanical properties of MMT crystal with galleries filled by one or two water layers as well as with those of an isolated clay nanoplate.

Conformational mobility of carbosilane dendrimer: Molecular dynamics simulation

Molecular dynamic simulations were carried out for carbosilane dendrimers of the 5th generation immersed in CCl4 solvent at different temperatures. The calculations were accomplished by using the AMBER force field in the united atom approximation. Lennard-Jones particles were considered as the solvent molecules with potential parameters corresponding to CCl4. There was one molecule of a dendrimer in each calculation cell, and the cells size was large enough to exclude any interaction between dendrimers. The internal structure of the dendrimer (density distributions for both dendrimer and solvent atoms) as well as dynamics of trans–gauche transitions of single bonds and fluctuations of branching points were analysed. It was shown that the one barrier mechanism of conformational transitions observed earlier in linear polymers occurs to be valid also for the conformational rearrangements in dendrimers with the hindered rotation around chain bonds. The contribution of rotational restrictions is essential only for branching points, which are close to the core.

Computer simulation of intramolecular mobility of dendrimers

Structure and intramolecular mobility of a carbosilane dendrimer of the 5th generation has been analysed in a wide temperature range by molecular dynamics. It is shown that in a “poor” solvent, the frequency of conformational transitions, frot, is independent on the conformer position in the macromolecule with the exception of chain end fragments. For the latter, the frequency was 2–3 times higher at all temperatures. In a “good” solvent, frot uniformly increases with a conformer distance from the centre of the molecule. Intramolecular diffusion of chain ends was highly temperature dependent. This allowed to suggest the existence of “liquid-like” and “glassy” states of individual dendrimer molecules.

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.

Molecular dynamic simulation of motion in solid polymers. Rotator phase of n-alkane

The method of molecular dynamic computer simulation is applied for the investigation of structure and dynamics of C10-n-alkane in the solid state. Analyzed is the behaviour of individual molecules as well as of a whole crystal. The investigated system consists of 31 molecules of C10-n-alkane at the temperature 150–275 K. The influence of chemical defects, such as methylene group or chlorine atom, on the dynamics of the system is considered.

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.

2D Chain Models of Nanoribbon Scrolls

We propose a simplified 2D model of the molecular chain that allows to describe molecular nanoribbon’s scrolled packings of various structures as spiral packaging chain. The model allows to obtain the possible stationary states of single-layer nanoribbons scrolls of graphene, graphane, fluorographene, fluorographane, graphone C(_4)H and fluorographone C(_4)F. We show the stability of scrolled packings and calculate the dependence of energy, the number of coils, inner and outer radius of the scrolled packing on the nanoribbon length. It is shown that a scrolled packing is the most energetically favorable conformation for nanoribbons of graphene, graphane, fluorographene, and fluorographane at large lengths. A double-scrolled packing when the nanoribbon is symmetrically rolled into a scroll from opposite ends is more advantageous for longer lengths nanoribbons of graphone and fluorographone. We show the possibility of existence of scrolled packings for nanoribbons of fluorographene and existence of two different types of scrolls for nanoribbons of fluorographane. The simplicity of the proposed model allows to consider the dynamics of molecular nanoribbon scrolls of sufficiently large lengths and at sufficiently large time intervals.

Molecular Simulation of Plastic Deformation of Oligomer Systems

Molecular dynamic simulation of low-temperature uniaxial compression and tension of a glass from 1000 molecules of C13H28 oligomer is carried out. Stress-strain diagrams, an influence of deformation on density of the glass, and connection between local density and atom rearrangements are discussed. The influence of original level of stress on initial rate of stress relaxation are also investigated. The modeling results of mechanical behavior are in good agreement with experimental data for glassy polymers, which allows one to use MD modeling for further in-depth study of glass behavior mechanisms under mechanical actions.