Andrea Giansanti

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The melting curves of short heterogeneous DNA chains in solution are calculated on the basis of statistical thermodynamics and compared to experiments. The computation of the partition function is based on the Peyrard-Bishop hamiltonian, which has already been adopted in the theoretical description of the melting of long DNA chains. In the case of short(More)
It is a worthy goal to completely characterize all human proteins in terms of their domains. Here, using the Pfam database, we asked how far we have progressed in this endeavour. Ninety per cent of proteins in the human proteome matched at least one of 5494 manually curated Pfam-A families. In contrast, human residue coverage by Pfam-A families was <45%,(More)
BACKGROUND Natively unfolded proteins lack a well defined three dimensional structure but have important biological functions, suggesting a re-assignment of the structure-function paradigm. To assess that a given protein is natively unfolded requires laborious experimental investigations, then reliable sequence-only methods for predicting whether a sequence(More)
We numerically show that metastable states, similar to the Quasi Stationary States found in the so called Hamiltonian Mean Field Model, are also present in a generalized model in which N classical spins (rotators) interact through ferromagnetic couplings decaying as r −α , where r is their distance over a regular lattice. Scaling laws with N are briefly(More)
Through molecular dynamics, we study the d = 2, 3 classical model of N coupled rotators (inertial XY model) assuming a coupling constant which decays with distance as r −α ij (α ≥ 0). The total energy < H > is asymptotically ∝ N ˜ N with˜N ≡ [N 1−α/d − (α/d)]/[1 − α/d], hence the model is thermodynamically extensive if α/d > 1 and nonextensive otherwise. We(More)
We study the combined influence of amino acid composition and chain length on the thermal stability of protein structures. A new parameterization of the internal free energy is considered, as the sum of hydrophobic effect, hydrogen-bond and dehydration energy terms. We divided a non-redundant selection of protein structures from the Protein Data Bank into(More)
This is a study on the precision of four known protein disorder predictors, ranked among the best-performing ones: DISOPRED2, PONDR VSL2B, IUPred and ESpritz. We address here the problem of a systematic overestimation of the number of disordered proteins recognized through the use of these predictors, considered as a standard. Some of these predictors, used(More)
The α-XY model generalizes, through the introduction of a power-law decaying potential , a well studied mean-field hamiltonian model with attractive long-range interactions. In the α-model, the interaction between classical rotators on a lattice is gauged by the exponent α in the couplings decaying as r α , where r are distances between sites. We review and(More)
Synonymous codons, i.e., DNA nucleotide triplets coding for the same amino acid, are used differently across the variety of living organisms. The biological meaning of this phenomenon, known as codon usage bias, is still controversial. In order to shed light on this point, we propose a new codon bias index, CompAI, that is based on the competition between(More)