73 research outputs found
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() 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
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