25,868 research outputs found
Understanding the determinants of stability and folding of small globular proteins from their energetics
The results of minimal model calculations suggest that the stability and the
kinetic accessibility of the native state of small globular proteins are
controlled by few "hot" sites. By mean of molecular dynamics simulations around
the native conformation, which simulate the protein and the surrounding solvent
at full--atom level, we generate an energetic map of the equilibrium state of
the protein and simplify it with an Eigenvalue decomposition. The components of
the Eigenvector associated with the lowest Eigenvalue indicate which are the
"hot" sites responsible for the stability and for the fast folding of the
protein. Comparison of these predictions with the results of mutatgenesis
experiments, performed for five small proteins, provide an excellent agreement
Competing Humanisms: Debating Cultural Identity in Leonardo Bruni’s "Dialogi ad Petrum Paulum Histrum"
Leonardo Bruni\u2019s Dialogi ad Petrum Paulum Histrum has long been studied as a manifesto of the humanist divergence from medieval culture. This article reconsiders the role of Bruni\u2019s Dialogi in the development of Italian humanism and especially in the development of the humanists\u2019 awareness of their cultural identity as a group. The essay argues that Bruni\u2019s principal aim was not to distance himself from previous traditions, but rather to mark a distinction between two concurrent conceptions of humanism that prevailed in his own time. Through the Dialogi, Bruni criticizes Niccol\uf2 Niccoli\u2019s cultural extremism and advances a moderate ideal of humanism that seeks to revise and incorporate nonhumanist traditions instead of rejecting them outright. In doing so, Bruni also intends to shield his ideal of humanism from the attack of the traditionalist sector of Renaissance culture
Fractional spins and static correlation error in density functional theory
Electronic states with fractional spins arise in systems with large static
correlation (strongly correlated systems). Such fractional-spin states are
shown to be ensembles of degenerate ground states with normal spins. It is
proven here that the energy of the exact functional for fractional-spin states
is a constant, equal to the energy of the comprising degenerate pure spin
states. Dramatic deviations from this exact constancy condition exist with all
approximate functionals, leading to large static correlation errors for
strongly correlated systems, such as chemical bond dissociation and band
structure of Mott insulators. This is demonstrated with numerical calculations
for several molecular systems. Approximating the constancy behavior for
fractional spins should be a major aim in functional constructions and should
open the frontier for DFT to describe strongly correlated systems. The key
results are also shown to apply in reduced density-matrix functional theory.Comment: 6 pages, 4 figure
Multi-Orbital Molecular Compound (TTM-TTP)I_3: Effective Model and Fragment Decomposition
The electronic structure of the molecular compound (TTM-TTP)I_3, which
exhibits a peculiar intra-molecular charge ordering, has been studied using
multi-configuration ab initio calculations. First we derive an effective
Hubbard-type model based on the molecular orbitals (MOs) of TTM-TTP; we set up
a two-orbital Hamiltonian for the two MOs near the Fermi energy and determine
its full parameters: the transfer integrals, the Coulomb and exchange
interactions. The tight-binding band structure obtained from these transfer
integrals is consistent with the result of the direct band calculation based on
density functional theory. Then, by decomposing the frontier MOs into two
parts, i.e., fragments, we find that the stacked TTM-TTP molecules can be
described by a two-leg ladder model, while the inter-fragment Coulomb energies
are scaled to the inverse of their distances. This result indicates that the
fragment picture that we proposed earlier [M.-L. Bonnet et al.: J. Chem. Phys.
132 (2010) 214705] successfully describes the low-energy properties of this
compound.Comment: 5 pages, 4 figures, published versio
Rogue waves and entropy consumption
Based on data from the Japan Sea and the North Sea the occurrence of rogue
waves is analyzed by a scale dependent stochastic approach, which interlinks
fluctuations of waves for different spacings. With this approach we are able to
determine a stochastic cascade process, which provides information of the
general multipoint statistics. Furthermore the evolution of single trajectories
in scale, which characterize wave height fluctuations in the surroundings of a
chosen location, can be determined. The explicit knowledge of the stochastic
process enables to assign entropy values to all wave events. We show that for
these entropies the integral fluctuation theorem, a basic law of
non-equilibrium thermodynamics, is valid. This implies that positive and
negative entropy events must occur. Extreme events like rogue waves are
characterized as negative entropy events. The statistics of these entropy
fluctuations changes with the wave state, thus for the Japan Sea the statistics
of the entropies has a more pronounced tail for negative entropy values,
indicating a higher probability of rogue waves.Comment: 6 pages, 6 figure
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