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We clarify the relation between an interatomic potentials and liquid–vapor critical points. For this purpose, we calculate the liquid–vapor coexistence curves of several interatomic model potentials such as the Lennard-Jones n−6 (n=7–32), the Morse, and the modified Stillinger–Weber potentials by the NpT plus test particle method. From these results, we find several universal properties irrespective of the potential type: (1) The law of rectilinear diameter is fulfilled in the density–temperature plane. (2) The coexistence curve scaled by the critical temperature and density almost coincides with one another. On the other hand, we also find some properties which are definitely potential dependent. In order to demonstrate this point, we introduce a new parameter a1=2π/3∫xmin∞x du(x)/dx x2 dx [x: reduced distance, xmin: the minimum position of a potential, u(x): reduced potential] which expresses the effect of the attractive force. By making use of this parameter, we find that the critical temperature Tc and pressure pc change linearly to a1. This means that the wider the attractive part of the potential is, the higher Tc and pc are. In this way, we have discovered a method to estimate the critical point from microscopic information concerning interatomic potentials.

We propose a new method for molecular dynamics and Monte Carlo simulations, which is referred to as the replica-permutation method (RPM), to realize more efficient sampling than the replicaexchange method (REM). In RPM not only exchanges between two replicas but also permutations among more than two replicas are performed. Furthermore, instead of the Metropolis algorithm, the Suwa-Todo algorithm is employed for replica-permutation trials to minimize its rejection ratio.We applied RPM to particles in a double-well potential energy, Met-enkephalin in vacuum, and a C-peptide analog of ribonuclease A in explicit water. For a comparison purposes, replica-exchange molecular dynamics simulations were also performed. As a result, RPM sampled not only the temperature space but also the conformational space more efficiently than REM for all systems.From our simulations of C-peptide, we obtained the α-helix structure with salt-bridges between Gly2 and Arg10 which is known in experiments. Calculating its free-energy landscape, the folding pathway was revealed from an extended structure to the α-helix structure with the salt-bridges.We found that the folding pathway consists of the two steps: The first step is the "salt-bridge formation step", and the second step is the "α-helix formation step". * Electronic address: itoh@ims.ac.jp † Electronic address: hokumura@ims.ac.jp

We describe the disruption of amyloid fibrils of Alzheimer's amyloid-β peptides by ultrasonic cavitation. For this purpose, we performed nonequilibrium all-atom molecular dynamics simulations with sinusoidal pressure and visualized the process with movies. When the pressure is negative, a bubble is formed, usually at hydrophobic residues in the transmembrane region. Most β-strands maintain their secondary structures in the bubble. When the pressure becomes positive, the bubble collapses, and water molecules crash against the hydrophilic residues in the nontransmembrane region to disrupt the amyloid. Shorter amyloids require longer sonication times for disruption because they do not have enough hydrophobic residues to serve as a nucleus to form a bubble. These results agree with experiments in which monodispersed amyloid fibrils were obtained by ultrasonication.