165 research outputs found
Modelling the Biomacromolecular Structure with Selected Combinatorial Optimization Techniques
Modern approaches to the search of Relative and Global minima of potential
energy function of Biomacromolecular structures include techniques of
combinatorial optimization like the study of Steiner Points and Steiner Trees.
These methods have been successfully applied to the problem of modelling the
configurations of the average atomic positions when they are disposed in the
usual sequence of evenly spaced points along right circular helices. In the
present contribution, we intend to show how these methods can be adapted for
explaining the advantages of introducing the concept of a Steiner Ratio
Function (SRF). We also show how this new concept is adequate for fitting the
results obtained by computing experiments and for providing an improvement to
these results if we use the restriction of working with Full Steiner Trees.Comment: 12 pages, 5 figures; typo correcte
A Combinatorial Optimization Approach to the Stability of Biomacromolecular Structures
The application of optimization techniques derived from the study of
Euclidean full Steiner Trees to macromolecules like proteins is reported in the
present work. We shall use the concept of Euclidean Steiner Ratio Function
(SRF) as a good Lyapunov function in order to perform an elementary stability
analysis.Comment: 13 pages, 4 figure
Magnetic and metal-insulator transitions in coupled spin-fermion systems
We use quantum Monte Carlo to determine the magnetic and transport properties
of coupled square lattice spin and fermionic planes as a model for a
metal-insulator interface. Specifically, layers of Ising spins with an
intra-layer exchange constant interact with the electronic spins of several
adjoining metallic sheets via a coupling . When the chemical potential
cuts across the band center, that is, at half-filling, the N\'eel temperature
of antiferromagnetic () Ising spins is enhanced by the coupling to the
metal, while in the ferromagnetic case () the metallic degrees of freedom
reduce the ordering temperature. In the former case, a gap opens in the
fermionic spectrum, driving insulating behavior, and the electron spins also
order. This induced antiferromagnetism penetrates more weakly as the distance
from the interface increases, and also exhibits a non-monotonic dependence on
. For doped lattices an interesting charge disproportionation occurs where
electrons move to the interface layer to maintain half-filling there.Comment: 12 pages, 15 figure
Dynamical localization and the effects of aperiodicity in Floquet systems
We study the localization aspects of a kicked non-interacting one-dimensional
(1D) quantum system subject to either time-periodic or non-periodic pulses.
These are reflected as sudden changes of the onsite energies in the lattice
with different modulations in real space. When the modulation of the kick is
incommensurate with the lattice spacing, and the kicks are periodic, a well
known dynamical localization in real space is recovered for large kick
amplitudes and frequencies. We explore the universality class of this
transition and also test the robustness of localization under deviations from
the perfect periodic case. We show that delocalization ultimately sets in and a
diffusive spreading of an initial wave packet is obtained when the aperiodicity
of the driving is introduced.Comment: 9 pages, 8 figures, as publishe
The Protein Family Classification in Protein Databases via Entropy Measures
In the present work, we review the fundamental methods which have been
developed in the last few years for classifying into families and clans the
distribution of amino acids in protein databases. This is done through
functions of random variables, the Entropy Measures of probabilities of
occurrence of the amino acids. An intensive study of the Pfam databases is
presented with restrictions to families which could be represented by
rectangular arrays of amino acids with m rows (protein domains) and n columns
(amino acids). This work is also an invitation to scientific research groups
worldwide to undertake the statistical analysis with different numbers of rows
and columns since we believe in the mathematical characterization of the
distribution of amino acids as a fundamental insight on the determination of
protein structure and evolution
Determinant Quantum Monte Carlo Study of the Enhancement of d-wave Pairing by Charge Inhomogeneity
Striped phases, in which spin, charge, and pairing correlations vary
inhomogeneously in the CuO_2 planes, are a known experimental feature of
cuprate superconductors, and are also found in a variety of numerical
treatments of the two dimensional Hubbard Hamiltonian. In this paper we use
determinant Quantum Monte Carlo to show that if a stripe density pattern is
imposed on the model, the d-wave pairing vertex is significantly enhanced. We
attribute this enhancement to an increase in antiferromagnetic order which is
caused by the appearence of more nearly half-filled regions when the doped
holes are confined to the stripes. We also observe a \pi-phase shift in the
magnetic order.Comment: 10 pages, 16 figures To appear in Phys. Rev.
Eigenstate thermalization in the two-dimensional transverse field Ising model
We study the onset of eigenstate thermalization in the two-dimensional
transverse field Ising model (2D-TFIM) in the square lattice. We consider two
non-equivalent Hamiltonians: the ferromagnetic 2D-TFIM and the
antiferromagnetic 2D-TFIM in the presence of a uniform longitudinal field. We
use full exact diagonalization to examine the behavior of quantum chaos
indicators and of the diagonal matrix elements of operators of interest in the
eigenstates of the Hamiltonian. A finite size scaling analysis reveals that
quantum chaos and eigenstate thermalization occur in those systems whenever the
fields are nonvanishing and not too large.Comment: 10 pages, 10 figures, as publishe
Determinant Quantum Monte Carlo Study of d-wave pairing in the Plaquette Hubbard Hamiltonian
Determinant Quantum Monte Carlo (DQMC) is used to determine the pairing and
magnetic response for a Hubbard model built up from four-site clusters -a
two-dimensional square lattice consisting of elemental 2x2 plaquettes with
hopping and on-site repulsion coupled by an inter-plaquette hopping . Superconductivity in this geometry has previously been studied by a
variety of analytic and numeric methods, with differing conclusions concerning
whether the pairing correlations and transition temperature are raised near
half-filling by the inhomogeneous hopping or not. For , DQMC indicates
an optimal at which the pairing vertex is most attractive.
The optimal increases with . We then contrast our results for this
plaquette model with a Hamiltonian which instead involves a regular pattern of
site energies whose large site energy limit is the three band CuO model; we
show that there the inhomogeneity rapidly, and monotonically, suppresses
pairing.Comment: 13 pages, 19 figure
Viral Evolution and Adaptation as a Multivariate Branching Process
In the present work we analyze the problem of adaptation and evolution of RNA
virus populations, by defining the basic stochastic model as a multivariate
branching process in close relation with the branching process advanced by
Demetrius, Schuster and Sigmund ("Polynucleotide evolution and branching
processes", Bull. Math. Biol. 46 (1985) 239-262), in their study of
polynucleotide evolution. We show that in the absence of beneficial forces the
model is exactly solvable. As a result it is possible to prove several key
results directly related to known typical properties of these systems like (i)
proof, in the context of the theory of branching processes, of the lethal
mutagenesis criterion proposed by Bull, Sanju\'an and Wilke ("Theory of lethal
mutagenesis for viruses", J. Virology 18 (2007) 2930-2939); (ii) a new proposal
for the notion of relaxation time with a quantitative prescription for its
evaluation and (iii) the quantitative description of the evolution of the
expected values in four distinct regimes: transient, "stationary" equilibrium,
extinction threshold and lethal mutagenesis. Moreover, new insights on the
dynamics of evolving virus populations can be foreseen.Comment: 39 pages, 3 figures. International Symposium on Mathematical and
Computational Biology, Tempe, Arizona, USA, 6 - 10 November 2012. Fernando
Antoneli, Francisco Bosco, Diogo Castro, And Luiz Mario Janini (2013) Viral
Evolution and Adaptation as a Multivariate Branching Process. Biomat 2012:
pp. 217-243. Ed.: R. P. Mondaini. World Scientific, Singapor
Intramolecular Structure of Proteins as driven by Steiner Optimization Problems
In this work we intend to report on some results obtained by an analytical
modelling of biomacromolecular structures as driven by the study of Steiner
points and Steiner trees with an Euclidean definition of distance.Comment: 2 page
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