On calculation of thermal conductivity from Einstein relation in equilibrium molecular dynamics.

In equilibrium molecular dynamics, Einstein relation can be used to calculate the thermal conductivity. This method is equivalent to Green-Kubo relation and it does not require a derivation of an analytical form for the heat current. However, it is not as commonly used as Green-Kubo relationship. Its wide use is hindered by the lack of a proper definition for integrated heat current (energy moment) under periodic boundary conditions. In this paper, we developed an appropriate definition for integrated heat current to calculate thermal conductivity of solids under periodic conditions. We applied this method to solid argon and silicon based systems; compared and contrasted with the Green-Kubo approach.

Power-law creep from discrete dislocation dynamics.

We report two-dimensional discrete dislocation dynamics simulations of combined dislocation glide and climb leading to "power-law" creep in a model aluminum crystal. The approach fully accounts for matter transport due to vacancy diffusion and its coupling with dislocation motion. The existence of quasiequilibrium or jammed states under the applied creep stresses enables observations of diffusion and climb over time scales relevant to power-law creep. The predictions for the creep rates and stress exponents fall within experimental ranges, indicating that the underlying physics is well captured.

Thermal conductivity of Si-Ge quantum dot superlattices.

Quantum dot superlattices (QDSLs) have been proposed for thermoelectric applications as a means of increasing thermal conductivity, σ, and reducing the lattice thermal conductivity, κ(l), to increase the dimensionless thermoelectric figure of merit, ZT. To fully exploit the thermoelectric potential of Si-Ge quantum dot superlattices (QDSLs), we performed a thorough study of the structural interplay of QDSLs with κ(l) using Green-Kubo theory and molecular dynamics. It was found that the resulting κ(l) has less dependence on the arrangement of the dots than to dot size and spacing. In fact, regardless of arrangement or concentration, QDSLs show a minimum κ(l) at a dot diameter of 1.4-1.6 nm and can reach values as low as 0.8-1.0 W mK⁻¹, increasing ZT by orders of magnitude over bulk Si and Ge. The drastic reduction of thermal conductivity in such a crystalline system is shown to be the result of both the stress caused by the dots as well as the quality of the Si-Ge interface.

Atomistic structure simulation of silicon nanocrystals driven with suboxide penalty energies.

The structural control of silicon nanocrystals embedded in amorphous oxide is currently an important technological problem. In this work, an approach is presented to simulate the structural behavior of silicon nanocrystals embedded in amorphous oxide matrix based on simple valence force fields as described by Keating-type potentials. After generating an amorphous silicon-rich-oxide, its evolution towards an embedded nanocrystal is driven by the oxygen diffusion process implemented in the form of a Metropolis algorithm based on the suboxide penalty energies. However, it is observed that such an approach cannot satisfactorily reproduce the shape of annealed nanocrystals. As a remedy, the asphericity and surface-to-volume minimization constraints are imposed. With the aid of such a multilevel approach, realistic-sized silicon nanocrystals can be simulated. Prediction for the nanocrystal size at a chosen oxygen molar fraction matches reasonably well with the experimental data when the interface region is also accounted. The necessity for additional shape constraints suggests the use of more involved force fields including long-range forces as well as accommodating different chemical environments such as the double bonds.

Conformation and proton configuration of pyrimidine deoxynucleoside oxidation damage products in water.

Emerging data strongly suggest that the oxidation of DNA bases can contribute to genomic instability. Structural changes to DNA, induced by base oxidation, may reduce the fidelity of DNA replication and interfere with sequence-specific DNA-protein interactions. We have examined the structures of a series of pyrimidine deoxynucleoside oxidation damage products in aqueous solution. The modified nucleosides studied include the deoxynucleoside derivatives of 5-hydroxyuracil, 5-hydroxycytosine, 5-(hydroxymethyl)uracil, 5-(hydroxymethyl)cytosine, 5-formyluracil, and 5-formylcytosine. The influence of base oxidation on ionization constants, sugar conformation, and tautomeric configuration has been determined on the basis of UV, proton, and nitrogen NMR spectra of the (15)N-enriched derivatives. The potential biological consequences of the structural perturbations resulting from base oxidation are discussed.