Order-disorder phase change in embedded Si nano-particles

We investigated the relative stability of the amorphous vs crystalline nanoparticles of size ranging between 0.8 and 1.8 nm. We found that, at variance from bulk systems, at low T small nanoparticles are amorphous and they undergo to an amorphous-to-crystalline phase transition at high T. On the contrary, large nanoparticles recover the bulk-like behavior: crystalline at low T and amorphous at high T. We also investigated the structure of crystalline nanoparticles, providing evidence that they are formed by an ordered core surrounded by a disordered periphery. Furthermore, we also provide evidence that the details of the structure of the crystalline core depend on the size of the nanoparticleComment: 8 pages, 5 figure

Analytic Markovian Rates for Generalized Protein Structure Evolution

A general understanding of the complex phenomenon of protein evolution requires the accurate description of the constraints that define the sub-space of proteins with mutations that do not appreciably reduce the fitness of the organism. Such constraints can have multiple origins, in this work we present a model for constrained evolutionary trajectories represented by a Markovian process throughout a set of protein-like structures artificially constructed to be topological intermediates between the structure of two natural occurring proteins. The number and type of intermediate steps defines how constrained the total evolutionary process is. By using a coarse-grained representation for the protein structures, we derive an analytic formulation of the transition rates between each of the intermediate structures. The results indicate that compact structures with a high number of hydrogen bonds are more probable and have a higher likelihood to arise during evolution. Knowledge of the transition rates allows for the study of complex evolutionary pathways represented by trajectories through a set of intermediate structures

Critical Properties of Spectral Functions for the 1D Anisotropic t-J Models with an Energy Gap

We exactly calculate the momentum-dependent critical exponents for spectral functions in the one-dimensional anisotropic t-J models with a gap either in the spin or charge excitation spectrum. Our approach is based on the Bethe ansatz technique combined with finite-size scaling techniques in conformal field theory. It is found that the spectral functions show a power-law singularity, which occurs at frequencies determined by the dispersion of a massive spin (or charge) excitation.We discuss how the nontrivial contribution of a massive excitation controls the singular behavior in optical response functions.Comment: 4 pages, REVTeX, 2 figures(available upon request), accepted for publication in JPSJ 66 (1997) No.

Finite temperature spectral-functions of strongly correlated one-dimensional electron systems

The spectral functions of tJ and tJ_{XY} models in the limit of J/t-> 0 and at finite temperatures T>>t are calculated using the spin-charge factorized wave function. We find that the Luttinger-liquid like scaling behavior for a finite system with L sites is restricted below temperatures of the order T = J/L. We also observe weight redistribution in the photoemission spectral function in the energy range t, which is much larger than the temperature.Comment: revtex, 4 pages, 3 eps figure

Critical Properties in Photoemmision Spectra for One Dimensional Orbitally Degenerate Mott Insulator

Critical properties in photoemission spectra for the one-dimensional Mott insulator with orbital degeneracy are studied by exploiting the integrable {\it t-J} model, which is a supersymmetric generalization of the SU($n$) degenerate spin model. We discuss the critical properties for the holon dispersion as well as the spinon dispersions, by applying the conformal field theory analysis to the exact finite-size energy spectrum. We study the effect of orbital-splitting on the spectra by evaluating the momentum-dependent critical exponents.Comment: 8 pages, REVTeX, 2 figures(available upon request), accepted for publication in JPSJ 68 (1999) No.

Multi-Scale Simulations Provide Supporting Evidence for the Hypothesis of Intramolecular Protein Translocation in GroEL/GroES Complexes

The biological function of chaperone complexes is to assist the folding of non-native proteins. The widely studied GroEL chaperonin is a double-barreled complex that can trap non-native proteins in one of its two barrels. The ATP-driven binding of a GroES cap then results in a major structural change of the chamber where the substrate is trapped and initiates a refolding attempt. The two barrels operate anti-synchronously. The central region between the two barrels contains a high concentration of disordered protein chains, the role of which was thus far unclear. In this work we report a combination of atomistic and coarse-grained simulations that probe the structure and dynamics of the equatorial region of the GroEL/GroES chaperonin complex. Surprisingly, our simulations show that the equatorial region provides a translocation channel that will block the passage of folded proteins but allows the passage of secondary units with the diameter of an alpha-helix. We compute the free-energy barrier that has to be overcome during translocation and find that it can easily be crossed under the influence of thermal fluctuations. Hence, strongly non-native proteins can be squeezed like toothpaste from one barrel to the next where they will refold. Proteins that are already fairly close to the native state will not translocate but can refold in the chamber where they were trapped. Several experimental results are compatible with this scenario, and in the case of the experiments of Martin and Hartl, intra chaperonin translocation could explain why under physiological crowding conditions the chaperonin does not release the substrate protein

Surface characterization and surface electronic structure of organic quasi-one-dimensional charge transfer salts

We have thoroughly characterized the surfaces of the organic charge-transfer salts TTF-TCNQ and (TMTSF)2PF6 which are generally acknowledged as prototypical examples of one-dimensional conductors. In particular x-ray induced photoemission spectroscopy turns out to be a valuable non-destructive diagnostic tool. We show that the observation of generic one-dimensional signatures in photoemission spectra of the valence band close to the Fermi level can be strongly affected by surface effects. Especially, great care must be exercised taking evidence for an unusual one-dimensional many-body state exclusively from the observation of a pseudogap.Comment: 11 pages, 12 figures, v2: minor changes in text and figure labellin

Spectral functions of the 1D Hubbard model in the U -> \infty limit: How to use the factorized wave-function

We give the details of the calculation of the spectral functions of the 1D Hubbard model using the spin-charge factorized wave-function for several versions of the U -> +\infty limit. The spectral functions are expressed as a convolution of charge and spin dynamical correlation functions. A procedure to evaluate these correlation functions very accurately for large systems is developed, and analytical results are presented for the low energy region. These results are fully consistent with the conformal field theory. We also propose a direct method of extracting the exponents from the matrix elements in more general cases.Comment: 15 pages,7 eps figures, RevTeX, needs epsf and multico