Kentaro Uehara

Structural Phase Transition of Di-Block Polyampholyte

Abstract We have performed both conventional canonical molecular dynamics (MD) and multicanonical MD (MMD) simulations for a single di-block polyampholyte in vacuum to investigate possible structural phase transitions. The conventional canonical MD simulation for temperature T∗ > 0.05 gives reliable results, since these are independent of the initial conformation. The MMD simulation results for temperature T∗ > 0.05 are in good agreement with those of the conventional canonical MD simulation. Glassy-like states are obtained when quenched into temperatures below T∗ > 0.05 with a straight chain structure as an initial conformation. On the other hand a spherical double helical structure is obtained when the temperature is gradually lowered to T∗ > 0.01. Also we find a stretched double helical structure at T∗ ∼ 0.01 which changes to the spherical double helical structure by annealing and quenching.

Structure and Phase Stability of Binary Zintl-Phase Compounds: Lithium–Group 13 Intermetallics and Metal-Doped Group 14 Clathrate Compounds

The structure/bonding relationship in a series of intermetallic phases of Li with Al, Ga, and In was investigated by density functional theory and complemented by a model based on tight-binding theory and the method of moments. The combination of these two approaches provides a simple scheme which allows for both a comprehensive understanding of structural trends and the ability to predict low-energy structures for a given composition. This analysis gives a straightforward picture of phase stability in terms of local geometric features such as triangular, square, and hexagonal arrangements of atoms. The approach was extended to examine the structural properties of metal-doped clathrate compounds of C, Si, Ge, and Sn. Clathrate-type phases based on the frameworks Si172, Ge172, Si40, and Ge40 are not only likely to be energetically favorable but may also exhibit high thermoelectric efficiency.

Large Scale Molecular Dynamics Simulation Using MD-Engine

Recently, demands for computing and designing large complex systems, such as proteins, biomembrain and so on, grow tremendously. For those systems, accurate calculation of non-bonding interactions becomes crucial to predict correct stable structures and thermodynamic properties in molecular dynamics(MD) simulations. However, for examples, truncation of Coulombic interaction must be taken very large and consequently calculation cost scales as O(N2) Special purpose molecular dynamics(MD) hardware accelerator, which is called the MD-Engine, has been used to overcome this difficulty and applied to several complex systems. The MD-Engine consists of custum prosessors that calculate pairwise potentials and forces in parallel. A user just has to send coordinate of atoms and force field parameters, then receive forces and potential energy. Our test calculations show good linear scaling with the system size.

Structural changes of a single polymer chain via multicanonical molecular dynamics simulation

Structural changes and folding properties of 2- and 3-dimensional di-block polyampholytes are investigated via multicanonical molecular dynamics simulations. The restricted free energy of the 2-dimensional system clearly shows double well structure at intermediate temperature region, which is indicative of the structural transition between extended and compact structures. In the 3-dimensional system, only single well structure in the restricted free energy is observed.

First-Principles Calculation of the Electronic Transport Properties of Metals

properties are directly related to the topology of the Fermi surface. In particular, in semi-metal and narrow gap semi-conductor systems, a small amount of electron/hole doping will cause dramatic change in the transport properties. The recent development of highly accurate electronic structure calculation methods and new techniques for band fitting enable us to explore potential candidates of novel materials from first-principles calculations. We have implemented a band interpolation scheme to the WIEN97 full-potential linearized augmented plane-wave (LAPW) band structure package 6), 7) to investigate the electronic transport properties of metals and alloy. The electronic transport coefficients are calculated from Fermi surface integration of the quantities related to band structure, e.g., density of states, Fermi velocity and effective mass tensor. In order to obtain these quantities, we used the modified Shankland-Koelling-Wood (SKW) band interpolation scheme 9) with a simple filtering technique. We applied low-pass filtering function to the interpolation equation in order to suppress high frequency wiggles appearing near band crossing points. The detailed procedure of the calculation will be described in a future paper. 10) The calculated and experimentally observed Hall coefficient for several cubic metals are listed in Table I. Previous theoretical results obtained from tight-binding calculations 8) are also tabulated for comparison. As shown in Table I, the overall agreement between present calculations and experiments is very good except for Fe. In the case of Fe, the band crossing near the ∆ point causes high frequency wiggles in the second derivative of the Fermi surface, which give rise to large numerical error in the unfiltered Hall coefficient. This problem is corrected by the filtering procedure. Figure 1 and 2 show calculated carrier concentration nH and Seebeck coefficient S for β � Sb3Zn4. It is experimentally observed that this compound has highly efficient thermoelectric power measured by a dimensionless figure of merit ZT = σS 2 T/ κ, where σ, T and κ correspond to electrical conductivity, temperature and thermal conductivity, respectively. The non-stoichiometric site occupation number of the compound is taken into account by a rigid band model, i.e., the Fermi level obtained by the calculation for stoichiometric composition is shifted by an amount of +0.027 Ry which yields experimentally observed carrier concentration nH =0 .05 hole/cell. Present result for the Seebeck coefficient shows excellent agreement with experiment and other theoretical calculation. 11) We observed that the calculated thermopower for this compound is very sensitive to the doping level(high hole doping

The Implementation of the Iterative Diagonalization Scheme and ab initio Molecular Dynamics Simulation with the LAPW Method

Abstract A new ab initio molecular dynamics method based on the full-potential linearized-augmented-plane-wave (LAPW) basis set has been implemented. The LAPW basis set has been successfully employed for systems containing localized electrons such as first row atoms and transition metals. In our implementation of the LAPW-MD scheme, iterative residual minimization algorithm is used to solve the electronic states problem. The atoms are moved according to forces derived from the Hellman–Feynman theorem and incomplete basis set correction terms. The performance of the program is further enhanced by parallelization. We will discuss technical details of the program implementation and present results obtained from this code to the equilibrium structures and vibrational properties of simple diatomic molecules.

Soft X-ray fluorescence spectra of photoluminescent layered polysilanes

The electronic structures of layered polysilanes (Si6nH6) derived from the cross-linking of planar (Si6H6) sheets via the elimination of the interplane H atoms are investigated with full-potential LAPW calculations. The electronic band gap energy of the polysilanes is found to be red-shifted with increasing number of stacking sheets and approaches the bulk Si value. The calculated soft X-ray fluorescence difference spectra of polysilanes and bulk Si show features in strong resemblance to those observed in the difference spectrum between porous-silicon and bulk Si. This observation suggests that the nanostructure in the porous Si obtained from the electrochemical etching of an n-Si[100] wafer may exist in a form akin to thin Si6H6 sheets.