A simple monatomic system in two dimensions with a double-well interaction potential is investigated in a wide range of temperatures by molecular-dynamics simulation. The system is melted and equilibrated well above the melting temperature, and then it is quenched to a temperature 88% below the melting temperature at several cooling rates to produce an amorphous state. Various thermodynamic quantities are measured as functions of temperature while the system is heated at a constant rate. The glass transition is observed with a sudden increase in the energy and the glass transition temperature is shown to be an increasing function of the cooling rate in the preparation process of the amorphous state. In a relatively high-temperature region, the system gradually transforms into crystals, and the time-temperature-transformation curve shows a typical nose shape. It is found that the transformation time to a crystalline state is the shortest at a temperature 14-15 % below the melting temperature and that at sufficiently low temperatures the system does not transform into a crystalline state within an observation time in our simulation. This indicates that a long-lived glassy state is realized.

We propose a computational strategy for investigating structural change of tritiumsubstituted macromolecules. Effects of radiation on macromolecules such as polymeric materials and DNA are classified into three categories: (1) direct action, (2) indirect action, and (3) decay effect. In this study, we focus on the decay effect exclusively. After a beta decay of substituted tritium in macromolecules to helium-3, the generated inert helium-3 is assumed to be deleted quickly. To get an insight into the decay effect to the damage of macromolecules, we perform molecular dynamics simulations of tritium-deleted macromolecules and analyze their structural change. Preliminary simulation results of decay effect on polymeric materials and DNA are presented.

All-atom molecular dynamics (MD) simulations are performed to examine the stabilities of a variety of binding configurations of alamethicin, a 20-amino-acid amphipathic peptide, in the bilayers of 1-palmitoyl-2-oleoyl phosphatidylcholine (POPC) and 1,2-dimyristoyl- sn-glycero-3-phosphatidylcholine (DMPC). The binding free energy of alamethicin is calculated through a combination of MD simulation and the energy-representation theory of solutions, and it is seen that the transmembrane configuration is stable in both membranes. A surface-bound state is also found to be stable due to the balance between the attractive and repulsive interactions of the peptide with lipid and water, and the key role of water is pointed out for the stability in the interfacial region. A difference between the POPC and DMPC systems is noted when the polar C-terminal domain is buried in the hydrophobic region of the membrane. In POPC, the peptide is unfavorably located with that configuration due to the loss of electrostatic interaction between the peptide and lipid.

The molecular mechanism through which how beta decays in tritium-substituted species damage DNA and polymeric materials is still unknown. Molecular dynamics simulations of hydrogen-removed polyethylene were performed to predict the structural change of the polyethylene chain after the substituted tritium decays. We calculated the potential energy, the global orientational order parameter, and the average number of consecutive trans bonds. The results are that, the greater the number of removed hydrogen atoms, the higher the potential energy and the lower the value of the global orientational order parameter and the average number of consecutive trans bonds. Thus, after losing hydrogen, polyethylene becomes poorer in terms of both thermal and structural stabilities.