Construction of the free energy landscape by the density functional theory

On the basis of the density functional theory, we give a clear definition of the free energy landscape. To show the usefulness of the definition, we construct the free energy landscape for rearrangement of atoms in an FCC crystal of hard spheres. In this description, the cooperatively rearranging region (CRR) is clealy related to the hard spheres involved in the saddle between two adjacent basins. A new concept of the simultaneously rearranging region (SRR) emerges naturally as spheres defined by the difference between two adjacent basins. We show that the SRR and the CRR can be determined explicitly from the free energylandscape.Comment: 11 pages, 3 figures, submitted to J. Chem. Phy

Absence of self-averaging in the complex admittance for transport through random media

A random walk model in a one dimensional disordered medium with an oscillatory input current is presented as a generic model of boundary perturbation methods to investigate properties of a transport process in a disordered medium. It is rigorously shown that an admittance which is equal to the Fourier-Laplace transform of the first-passage time distribution is non-self-averaging when the disorder is strong. The low frequency behavior of the disorder-averaged admittance, $-1 \sim \omega^{\mu}$ where $\mu < 1$, does not coincide with the low frequency behavior of the admittance for any sample, $\chi - 1 \sim \omega$. It implies that the Cole-Cole plot of $$ appears at a different position from the Cole-Cole plots of $\chi$ of any sample. These results are confirmed by Monte-Carlo simulations.Comment: 7 pages, 2 figures, published in Phys. Rev.

Vitrification of a monatomic 2D simple liquid

A monatomic simple liquid in two dimensions, where atoms interact isotropically through the Lennard-Jones-Gauss potential [M. Engel and H.-R. Trebin, Phys. Rev. Lett. 98, 225505 (2007)], is vitrified by the use of a rapid cooling technique in a molecular dynamics simulation. Transformation to a crystalline state is investigated at various temperatures and the time-temperature-transformation (TTT) curve is determined. It is found that the transformation time to a crystalline state is the shortest at a temerature 14% below the melting temperature Tm and that at temperatures below Tv = 0.6 Tm the transformation time is much longer than the available CPU time. This indicates that a long-lived glassy state is realized for T < Tv.Comment: 5pages,5figures,accepted for publication in CEJ

Anisotropic thermally activated diffusion in percolation systems

We present a study of static and frequency-dependent diffusion with anisotropic thermally activated transition rates in a two-dimensional bond percolation system. The approach accounts for temperature effects on diffusion coefficients in disordered anisotropic systems. Static diffusion shows an Arrhenius behavior for low temperatures with an activation energy given by the highest energy barrier of the system. From the frequency-dependent diffusion coefficients we calculate a characteristic frequency $\omega_{c}\sim 1/t_{c}$, related to the time $t_c$ needed to overcome a characteristic barrier. We find that $\omega_c$ follows an Arrhenius behavior with different activation energies in each direction.Comment: 5 pages, 4 figure

Exact Eigenstates of Tight-Binding Hamiltonians on the Penrose Tiling

We investigate exact eigenstates of tight-binding models on the planar rhombic Penrose tiling. We consider a vertex model with hopping along the edges and the diagonals of the rhombi. For the wave functions, we employ an ansatz, first introduced by Sutherland, which is based on the arrow decoration that encodes the matching rules of the tiling. Exact eigenstates are constructed for particular values of the hopping parameters and the eigenenergy. By a generalized ansatz that exploits the inflation symmetry of the tiling, we show that the corresponding eigenenergies are infinitely degenerate. Generalizations and applications to other systems are outlined.Comment: 24 pages, REVTeX, 13 PostScript figures include

Three-Dimensional Quantum Percolation Studied by Level Statistics

Three-dimensional quantum percolation problems are studied by analyzing energy level statistics of electrons on maximally connected percolating clusters. The quantum percolation threshold \pq, which is larger than the classical percolation threshold \pc, becomes smaller when magnetic fields are applied, i.e., \pq(B=0)>\pq(B\ne 0)>\pc. The critical exponents are found to be consistent with the recently obtained values of the Anderson model, supporting the conjecture that the quantum percolation is classified onto the same universality classes of the Anderson transition. Novel critical level statistics at the percolation threshold is also reported.Comment: to appear in the May issue of J. Phys. Soc. Jp

Binary self-similar one-dimensional quasilattices: Mutual local-derivability classification and substitution rules

Self-similar binary one-dimensional (1D) quasilattices (QLs) are classified into mutual local-derivability (MLD) classes. It is shown that the MLD classification is closely related to the number-theoretical classification of parameters which specify the self-similar binary 1D QLs. An algorithm to derive an explicit substitution rule, which prescribes the transformation of a QL into another QL in the same MLD class, is presented. An explicit inflation rule, which prescribes the transformation of the self-similar 1D QL into itself, is obtained as a composition of the explicit substitution rules. Symmetric substitution rules and symmetric inflation rules are extensively discussed.Comment: 24 pages, 4 figures, submitted to PR

Molecular dynamics simulation of the fragile glass former ortho-terphenyl: a flexible molecule model

We present a realistic model of the fragile glass former orthoterphenyl and the results of extensive molecular dynamics simulations in which we investigated its basic static and dynamic properties. In this model the internal molecular interactions between the three rigid phenyl rings are described by a set of force constants, including harmonic and anharmonic terms; the interactions among different molecules are described by Lennard-Jones site-site potentials. Self-diffusion properties are discussed in detail together with the temperature and momentum dependencies of the self-intermediate scattering function. The simulation data are compared with existing experimental results and with the main predictions of the Mode Coupling Theory.Comment: 20 pages and 28 postscript figure

Energy spectra, wavefunctions and quantum diffusion for quasiperiodic systems

We study energy spectra, eigenstates and quantum diffusion for one- and two-dimensional quasiperiodic tight-binding models. As our one-dimensional model system we choose the silver mean or `octonacci' chain. The two-dimensional labyrinth tiling, which is related to the octagonal tiling, is derived from a product of two octonacci chains. This makes it possible to treat rather large systems numerically. For the octonacci chain, one finds singular continuous energy spectra and critical eigenstates which is the typical behaviour for one-dimensional Schr"odinger operators based on substitution sequences. The energy spectra for the labyrinth tiling can, depending on the strength of the quasiperiodic modulation, be either band-like or fractal-like. However, the eigenstates are multifractal. The temporal spreading of a wavepacket is described in terms of the autocorrelation function C(t) and the mean square displacement d(t). In all cases, we observe power laws for C(t) and d(t) with exponents -delta and beta, respectively. For the octonacci chain, 0<delta<1, whereas for the labyrinth tiling a crossover is observed from delta=1 to 0<delta<1 with increasing modulation strength. Corresponding to the multifractal eigenstates, we obtain anomalous diffusion with 0<beta<1 for both systems. Moreover, we find that the behaviour of C(t) and d(t) is independent of the shape and the location of the initial wavepacket. We use our results to check several relations between the diffusion exponent beta and the fractal dimensions of energy spectra and eigenstates that were proposed in the literature.Comment: 24 pages, REVTeX, 10 PostScript figures included, major revision, new results adde

Cloning and heterologous expression of bovine pyroglutamyl peptidase type-1 in Escherichia coli : purification , biochemical and kinetic characterisation

We describe the cloning, expression and purification of the bovine XM866409 form of pyroglutamyl-aminopeptidase I. The amino acid sequence, deduced from the nucleotide sequence, revealed that it consists of 209 amino acid residues and showed to have 98% homology with the human AJ278828 form of the enzyme. Three amino acid residues at positions 81, 205 and 208 were found to vary among the two sequences. The bovine enzyme was expressed in XL10-gold Esherichia coli cells. Immobilizied Ni-ion affinity chromatography was used to purify the expressed protein resulting in a yield of 3.3mg of PAP1 per litre culture. The purified enzyme had a specific activity of 1700 units/ml. SDS-PAGE produced a single band for bovine PAP1 with a molecular weight of ~23-24 kDa which is in good agreement with previously reported data on PAP1. Kinetic constants Km and Kcat were 59μΜ and 3.5s-1, respectively. It possessed an optimum pH between 9-9.5, a temperature of 37°C and showed an absolute requirement for a thiol-reducing agent (10mM DTT). EDTA didn’t prove to have an effect on enzyme activity. Competitive inhibition was seen with pyroglutamyl peptides pGlu-His-Pro-NH2 (TRH; Ki= 44.1 uM), pGlu-Ala- OH (Ki=141 uM) and pGlu-Val-OH (Ki=652.17)