387 research outputs found
Exactness of the cluster variation method and factorization of the equilibrium probability for the Wako-Saito-Munoz-Eaton model of protein folding
I study the properties of the equilibrium probability distribution of a
protein folding model originally introduced by Wako and Saito, and later
reconsidered by Munoz and Eaton. The model is a one-dimensional model with
binary variables and many-body, long-range interactions, which has been solved
exactly through a mapping to a two-dimensional model of binary variables with
local constraints. Here I show that the equilibrium probability of this
two-dimensional model factors into the product of local cluster probabilities,
each raised to a suitable exponent. The clusters involved are single sites,
nearest-neighbour pairs and square plaquettes, and the exponents are the
coefficients of the entropy expansion of the cluster variation method. As a
consequence, the cluster variation method is exact for this model.Comment: 14 pages, 1 figur
Cluster Variation Method in Statistical Physics and Probabilistic Graphical Models
The cluster variation method (CVM) is a hierarchy of approximate variational
techniques for discrete (Ising--like) models in equilibrium statistical
mechanics, improving on the mean--field approximation and the Bethe--Peierls
approximation, which can be regarded as the lowest level of the CVM. In recent
years it has been applied both in statistical physics and to inference and
optimization problems formulated in terms of probabilistic graphical models.
The foundations of the CVM are briefly reviewed, and the relations with
similar techniques are discussed. The main properties of the method are
considered, with emphasis on its exactness for particular models and on its
asymptotic properties.
The problem of the minimization of the variational free energy, which arises
in the CVM, is also addressed, and recent results about both provably
convergent and message-passing algorithms are discussed.Comment: 36 pages, 17 figure
CVM ANALYSIS OF CROSSOVER IN THE SEMI-INFINITE ISING MODEL
The crossover behavior of the semi--infinite three dimensional Ising model is
investigated by means of Pad\'e approximant analysis of cluster variation
method results. We give estimates for ordinary critical as well as for
multicritical exponents, which are in very good agreement with extensive Monte
Carlo simulations.Comment: RevTeX, 7 pages + 2 uuencoded PostScript figures. To be published in
J. Magn. Magn. Mat. (substituted raw with encoded PostScript
The Phase Diagram of the Gonihedric 3d Ising Model via CVM
We use the cluster variation method (CVM) to investigate the phase structure
of the 3d gonihedric Ising actions defined by Savvidy and Wegner. The
geometrical spin cluster boundaries in these systems serve as models for the
string worldsheets of the gonihedric string embedded in . The models
are interesting from the statistical mechanical point of view because they have
a vanishing bare surface tension. As a result the action depends only on the
angles of the discrete surface and not on the area, which is the antithesis of
the standard 3d Ising model.
The results obtained with the CVM are in good agreement with Monte Carlo
simulations for the critical temperatures and the order of the transition as
the self-avoidance coupling is varied. The value of the magnetization
critical exponent , calculated with the cluster
variation--Pad\`e approximant method, is also close to the simulation results.Comment: 8 pages text (LaTex) + 3 eps figures bundled together with uufile
NEW TOPOLOGIES IN THE PHASE DIAGRAM OF THE SEMI-INFINITE BLUME-CAPEL MODEL
The phase diagram of the Blume--Capel model on a semi--infinite simple cubic
lattice with a (100) free surface is studied in the pair approximation of the
cluster variation method. Six main topologies are found, of which two are new,
due to the occurrence of a first order surface transition in the phase with
ordered bulk, separating two phases with large and small surface order
parameters. The latter is a new phase and is studied in some detail, giving the
behaviour of the order parameter profiles in two typical cases. A comparison is
made with the results of a low temperature expansion, where these are
available, showing a great increase in accuracy with respect to the mean field
approximation.Comment: RevTeX, 13 pages + 7 uuencoded PostScript figures (substituted raw
with encoded PostScript
Mechanical unfolding and refolding pathways of ubiquitin
Mechanical unfolding and refolding of ubiquitin are studied by Monte Carlo
simulations of a Go model with binary variables. The exponential dependence of
the time constants on the force is verified, and folding and unfolding lengths
are computed, with good agreement with experimental results. Furthermore, the
model exhibits intermediate kinetic states, as observed in experiments.
Unfolding and refolding pathways and intermediate states, obtained by tracing
single secondary structure elements, are consistent with simulations of
previous all-atom models and with the experimentally observed step sizes
Variational approximations for stochastic dynamics on graphs
We investigate different mean-field-like approximations for stochastic
dynamics on graphs, within the framework of a cluster-variational approach. In
analogy with its equilibrium counterpart, this approach allows one to give a
unified view of various (previously known) approximation schemes, and suggests
quite a systematic way to improve the level of accuracy. We compare the
different approximations with Monte Carlo simulations on a reversible
(susceptible-infected-susceptible) discrete-time epidemic-spreading model on
random graphs.Comment: 29 pages, 5 figures. Minor revisions. IOP-style
Pathways of mechanical unfolding of FnIII10: Low force intermediates
We study the mechanical unfolding pathways of the domain of
fibronectin by means of an Ising--like model, using both constant force and
constant velocity protocols. At high forces and high velocities our results are
consistent with experiments and previous computational studies. Moreover, the
simplicity of the model allows us to probe the biologically relevant low force
regime, where we predict the existence of two intermediates with very close
elongations. The unfolding pathway is characterized by stochastic transitions
between these two intermediates
Rigorous results on the local equilibrium kinetics of a protein folding model
A local equilibrium approach for the kinetics of a simplified protein folding
model, whose equilibrium thermodynamics is exactly solvable, was developed in
[M. Zamparo and A. Pelizzola, Phys. Rev. Lett. 97, 068106 (2006)]. Important
properties of this approach are (i) the free energy decreases with time, (ii)
the exact equilibrium is recovered in the infinite time limit, (iii) the
equilibration rate is an upper bound of the exact one and (iv) computational
complexity is polynomial in the number of variables. Moreover, (v) this method
is equivalent to another approximate approach to the kinetics: the path
probability method. In this paper we give detailed rigorous proofs for the
above results.Comment: 25 pages, RevTeX 4, to be published in JSTA
Direction dependent mechanical unfolding and Green Fluorescent Protein as a force sensor
An Ising--like model of proteins is used to investigate the mechanical
unfolding of the Green Fluorescent Protein along different directions. When the
protein is pulled from its ends, we recover the major and minor unfolding
pathways observed in experiments. Upon varying the pulling direction, we find
the correct order of magnitude and ranking of the unfolding forces. Exploiting
the direction dependence of the unfolding force at equilibrium, we propose a
force sensor whose luminescence depends on the applied force.Comment: to appear in Phys Rev
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