Molecular-dynamics (MD) simulations have been performed for two amorphous polymers with extremely different mechanical properties, atactic polystyrene (PS) and bisphenol A polycarbonate (PC), in the isotropic state and under load. The glass transition temperatures, Young moduli, yield stresses and strain-hardening moduli are calculated and compared to the experimental data. Both chemistry-specific and mode-coupling aspects of the segmental mobility in the isotropic case and under the uniaxial deformation have been identified. The mobility of the PS segments in the deformation direction is increased drastically beyond the yield point. A weaker increase is observed for PC.

Molecular dynamics computer simulations have been carried out of a chemically realistic many-chain nonentangled model of glassy atactic polystyrene under the influence of uniaxial mechanical deformation. Both the initial elastic and the postyield (up to 100% of the deformation) behavior have been simulated. The Poisson ratio, the Young modulus, and the temperature dependence of the yield peak are well reproduced. The simulated strain-hardening modulus is in quantitative agreement with existing experiments. The deformationally induced anisotropy in the global and local segmental orientation is accompanied by an anisotropy of the local translational mobility: the mean-square translational displacement of the individual segments in the direction of the deformation is drastically increased just beyond the yield point as compared to the isotropic sample. The mechanical deformation of a quenched sample leads to an almost complete erasure of the aging history.

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.

We present the results of molecular dynamics simulation of the thermomechanical behavior of Wyomingtype Na + -montmorillonite (MMT) with water intercalates. Montmorillonite is commonly used as a filler in polymer-clay nanocomposites, and calculation of the elastic properties of the composite requires accurate knowledge of the elastic moduli and thermal properties of the components. To calculate the properties of the filler, we used a computational cell containing two MMT lamellae [Si 248 Al 8 ][Al 112 Mg 16 ]O 640 [OH] 128 and periodic boundary conditions in all three directions. The galleries between each pair of MMT lamella were filled with 24 Na + counterions and either one or two water layers (100 and 200 mg/g clay, respectively). The results obtained for the interlayer distance and the number density profiles of water molecules and Na + ions in galleries are in good agreement with experimental data and results of other computer simulations. The thermal properties were analyzed over the range of 300-400 K; the isothermal linear compressibility and all of the components of the elasticity tensor were calculated. It turns out that the elasticity tensor possesses orthotropic symmetry and changes very weakly with temperature in the range 300-350 K. The calculated in-plane Young's moduli of the hydrated MMT are equal at 180 GPa for the case of an intercalated monolayer of water and 150 GPa for that of an intercalated bilayer of water. The shear moduli parallel to the lamellae decrease from 20 GPa for the monolayer case to 2-4 GPa for the bilayer case. The water interlayer significantly alters the linear coefficient of thermal expansion and Young's modulus perpendicular to the clay lamellae in the hydrated crystal. In the monolayer case, the linear coefficient of thermal expansion K T,Z was only slightly larger than that for pyrophyllite but increased noticeably in the bilayer case.

Although stretching of most polymer chains leads to rather featureless force-extension diagrams, some, notably DNA, exhibit nontrivial behavior with a distinct plateau region. Here, we propose a unified theory that connects force-extension characteristics of the polymer chain with the convexity properties of the extension energy profile of its individual monomer subunits. Namely, if the effective monomer deformation energy as a function of its extension has a nonconvex (concave up) region, the stretched polymer chain separates into two phases: the weakly and strongly stretched monomers. Simplified planar and 3D polymer models are used to illustrate the basic principles of the proposed model. Specifically, we show rigorously that, when the secondary structure of a polymer is mostly caused by weak noncovalent interactions, the stretching is two phase, and the force-stretching diagram has the characteristic plateau. We then use realistic coarse-grained models to confirm the main findings and make direct connection to the microscopic structure of the monomers. We show in detail how the two-phase scenario is realized in the α-helix and DNA double helix. The predicted plateau parameters are consistent with single-molecules experiments. Detailed analysis of DNA stretching shows that breaking of Watson-Crick bonds is not necessary for the existence of the plateau, although some of the bonds do break as the double helix extends at room temperature. The main strengths of the proposed theory are its generality and direct microscopic connection.α-helix extension | coarse-grained DNA model | general mechanism | DNA overstretching | polymer force-extension

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.

On the basis of the cell model of dense fluids, we derive the binomial distribution law for a number of solvent particles occupying a given void of excluded volume (a cavity) which arises in a bulk solvent as a fluctuation. It is inserted as a default distribution in the information theory approach (Hummer, G.; Garde, S.; Garcia, A. E.; Paulaitis, M. E.; Pratt, L. R. J. Phys. Chem. B 1998, 102, 10469) for treating the thermodynamics of cavitation; the imaginary process is considered as a component of the total solvation process. Computations of cavitation free energies, entropies, and enthalpies for 11 hydrocarbons in water solvent are compared with results of the computer simulation of these properties reported by E. Gallicchio et al. (Gallicchio, E.; Kubo, M. M.; Levy, R. J. Phys. Chem. B 2000, 104, 6271). A similar analysis of cavitation for model spherical solutes in water in a wide range of cavity radii is also provided. Linear correlation between the cavitation free energy and the cavity volume is observed and justified. The present binomial approach for treating cavitation effects efficiently covers a large range of cavity volumes υ's (102 Å3 < υ <103 Å3).

The molecular dynamics simulation of the structure and molecular mobility of an individual macromolecule of a fourth generation carbosilane dendrimer with terminal cyanobiphenyl groups in a highly diluted chloroform solution in the range 213-323 K is performed. Upon a change in temperature, the den drimer undergoes structural rearrangement that depends on the ability of terminal segments to penetrate into the dendrimer. At temperatures close to the boiling point of the solvent, aliphatic spacers of terminal seg ments can penetrate deep into the dendrimer. As temperature decreases, the terminal segments are grouped only on the surface of the molecule; this leads to a 45% increase in the number of solvent molecules in the treelike part of the macromolecule. These results make it possible to give a new interpretation of temperature effects previously observed in NMR experiments for dilute solutions of these macromolecules.