Alessandro Pelizzola

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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(More)
A transfer-matrix formalism is introduced to evaluate exactly the partition function of the Muñoz-Eaton model, relating the folding kinetics of proteins of known structure to their thermodynamics and topology. This technique can be used for a generic protein, for any choice of the energy and entropy parameters, and in principle allows the model to be used(More)
Coherent states for a general Lie superalgebra are defined following the method originally proposed by Perelomov. Algebraic and geometrical properties of the systems of states thus obtained are examined, with particular attention to the possibility of defining a Kähler structure over the states supermanifold and to the connection between this supermanifold(More)
We use the cluster variation method (CVM) and Monte Carlo simulations to investigate the phase structure of the 3d gonihedric Ising actions deened by Savvidy and Wegner. This model corresponds to the usual three-dimensional cubic Ising model with nearest, next to the nearest, and plaquette interactions in the region with degenerate lamellar ground states.(More)
Abstract. I study the properties of the equilibrium probability distribution of a protein folding model originally introduced by Wako and Saitô, and later reconsidered by Muñoz 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(More)
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(More)
Mechanical unfolding and refolding of ubiquitin are studied by Monte Carlo simulations of a Gō 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(More)
Recent advances in modeling protein structures at the atomic level have made it possible to tackle "de novo" computational protein design. Most procedures are based on combinatorial optimization using a scoring function that estimates the folding free energy of a protein sequence on a given main-chain structure. However, the computation of the(More)
The authors address the problem of downhill protein folding in the framework of a simple statistical mechanical model, which allows an exact solution for the equilibrium and a semianalytical treatment of the kinetics. Focusing on protein 1BBL, a candidate for downhill folding behavior, and comparing it to the WW domain of protein PIN1, a two-state folder of(More)