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- Alessandro Pelizzola
- ArXiv
- 2005

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)

- M Caraglio, A Imparato, A Pelizzola
- Physical review. E, Statistical, nonlinear, and…
- 2011

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)

- Pierpaolo Bruscolini, Alessandro Pelizzola
- Physical review letters
- 2002

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)

- A Imparato, A Pelizzola
- Physical review letters
- 2008

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)

In this paper we develop a Bethe approximation, based on the cluster variation method, which is apt to study lattice models of branched polymers. We show that the method is extremely accurate in cases where exact results are known as, for instance, in the enumeration of spanning trees. Moreover, the expressions we obtain for the asymptotic number of… (More)

- A Imparato, A Pelizzola, M Zamparo
- Physical review letters
- 2007

The mechanical unfolding of proteins is studied by extending the Wako-Saitô-Muñoz-Eaton model. This model is generalized by including an external force, and its thermodynamics turns out to be exactly solvable. We consider two molecules, the 27th immunoglobulin domain of titin and protein PIN1. We determine equilibrium force-extension curves for the titin… (More)

- Pierpaolo Bruscolini, Alessandro Pelizzola, Marco Zamparo
- Physical review letters
- 2007

Previous research has shown a strong correlation of protein folding rates to the native state geometry, yet a complete explanation for this dependence is still lacking. Here we study the rate-geometry relationship with a simple statistical physics model, and focus on two classes of model geometries, representing ideal parallel and antiparallel structures.… (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)

- Marco Zamparo, Alessandro Pelizzola
- Physical review letters
- 2006

We consider a simplified model of protein folding, with binary degrees of freedom, whose equilibrium thermodynamics is exactly solvable. Based on this exact solution, the kinetics is studied in the framework of a local equilibrium approach, for which we prove that (i) the free energy decreases with time, (ii) the exact equilibrium is recovered in the… (More)

- Mauro Faccin, Pierpaolo Bruscolini, Alessandro Pelizzola
- The Journal of chemical physics
- 2011

We apply the Wako-Saito-Muñoz-Eaton model to the study of myotrophin, a small ankyrin repeat protein, whose folding equilibrium and kinetics have been recently characterized experimentally. The model, which is a native-centric with binary variables, provides a finer microscopic detail than the Ising model that has been recently applied to some different… (More)