arXiv subjects

Michael Bon

Publications and source records attributed to Michael Bon.

3 recordsLinked to original sources

arXiv2012

Temperature Integration: an efficient procedure for calculation of free energy differences

We propose a method, Temperature Integration, which allows an efficient calculation of free energy differences between two systems of interest, with the same degrees of freedom, which may have rough energy landscapes. The method is based on calculating, for each single system, the difference between the values of lnZ at two temperatures, using a Parallel Tempering procedure. If our two systems of interest have the same phase space volume, they have the same values of lnZ at high-T, and we can obtain the free energy difference between them, using the two single-system calculations described above. If the phase space volume of a system is known, our method can be used to calculate its absolute (versus relative) free energy as well. We apply our method and demonstrate its efficiency on a toy model of hard rods on a 1-dimensional ring.

cond-mat.stat-mech↗

arXiv2010

TT2NE: A novel algorithm to predict RNA secondary structures with pseudoknots

We present TT2NE, a new algorithm to predict RNA secondary structures with pseudoknots. The method is based on a classification of RNA structures according to their topological genus. TT2NE guarantees to find the minimum free energy structure irrespectively of pseudoknot topology. This unique proficiency is obtained at the expense of the maximum length of sequence that can be treated but comparison with state-of-the-art algorithms shows that TT2NE is a very powerful tool within its limits. Analysis of TT2NE's wrong predictions sheds light on the need to study how sterical constraints limit the range of pseudoknotted structures that can be formed from a given sequence. An implementation of TT2NE on a public server can be found at http://ipht.cea.fr/rna/tt2ne.php.

q-bio.BM↗

arXiv2006

Topological classification of RNA structures

We present a novel topological classification of RNA secondary structures with pseudoknots. It is based on the topological genus of the circular diagram associated to the RNA base-pair structure. The genus is a positive integer number, whose value quantifies the topological complexity of the folded RNA structure. In such a representation, planar diagrams correspond to pure RNA secondary structures and have zero genus, whereas non planar diagrams correspond to pseudoknotted structures and have higher genus. We analyze real RNA structures from the databases wwPDB and Pseudobase, and classify them according to their topological genus. We compare the results of our statistical survey with existing theoretical and numerical models. We also discuss possible applications of this classification and show how it can be used for identifying new RNA structural motifs.

q-bio.BM↗