439 citations · 2.2k across the 51 of their papers we have counts for
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Folding Rate Optimization Promotes Frustrated Interactions in Entangled Protein Structures
Federico Norbiato, Flavio Seno, Antonio Trovato +1
Many native structures of proteins accomodate complex topological motifs such as knots, lassos, and other geometrical entanglements. How proteins can fold quickly even in the prese…
Exploring the correlation between the folding rates of proteins and the entanglement of their native states
Marco Baiesi, Enzo Orlandini, Flavio Seno +1
The folding of a protein towards its native state is a rather complicated process. However there are empirical evidences that the folding time correlates with the contact order, a…
Bubble-bound state of triple-stranded DNA: Efimov Physics in DNA with repulsion
Jaya Maji, Flavio Seno, Antonio Trovato +1
The presence of a thermodynamic phase of a three-stranded DNA, namely, a mixed phase of bubbles of two bound strands and a single one, is established for large dimensions ($d\geq 5…
Linking in domain-swapped protein dimers
Marco Baiesi, Enzo Orlandini, Antonio Trovato +1
The presence of knots has been observed in a small fraction of single-domain proteins and related to their thermodynamic and kinetic properties. The exchanging of identical structu…
Fibril elongation mechanisms of HET-s prion-forming domain: Topological evidence for growth polarity
Marco Baiesi, Flavio Seno, Antonio Trovato
The prion-forming C-terminal domain of the fungal prion HET-s forms infectious amyloid fibrils at physiological pH. The conformational switch from the non-prion soluble form to the…
When a DNA Triple helix melts: An analog of the Efimov state
Jaya Maji, Somendra M. Bhattacharjee, Flavio Seno +1
The base sequences of DNA contain the genetic code and to decode it a double helical DNA has to open its base pairs. Recent studies have shown that one can use a third strand to id…
Melting a stretched DNA
D. Marenduzzo, A. Maritan, E. Orlandini +2
We study the melting of a double stranded DNA in the presence of stretching forces, via 3D Monte-Carlo simulations, exactly solvable models and heuristic arguments. The resulting f…
On the form of growing strings
D. Marenduzzo, T. X. Hoang, F. Seno +2
Patterns and forms adopted by Nature, such as the shape of living cells, the geometry of shells and the branched structure of plants, are often the result of simple dynamical parad…
Complete Phase Diagram of DNA Unzipping: Eye, Y-fork and triple point
Rajeev Kapri, Somendra M. Bhattacharjee, Flavio Seno
We study the unzipping of double stranded DNA (dsDNA) by applying a pulling force at a fraction from the anchored end. From exact analytical and numerical res…
A new perspective on the analysis of helix-helix packing preferences in globular proteins
A. Trovato, F. Seno
For many years it had been believed that steric compatibility of helix interfaces could be the source of the observed preference for particular angles between neighbouring helices…
Helicase on DNA: A Phase coexistence based mechanism
Somendra M. Bhattacharjee, Flavio Seno
We propose a phase coexistence based mechanism for activity of helicases, ubiquitous enzymes that unwind double stranded DNA. The helicase-DNA complex constitutes a fixed-stretch e…
Dynamical scaling of the DNA unzipping transition
D. Marenduzzo, S. M. Bhattacharjee, A. Maritan +2
We report studies of the equilibrium and the dynamics of a general set of lattice models which capture the essence of the force-induced or mechanical DNA unzipping transition. Besi…
A Measure of data-collapse for scaling
Somendra M. Bhattacharjee, Flavio Seno
Data-collapse is a way of establishing scaling and extracting associated exponents in problems showing self-similar or self-affine characteristics as e.g. in equilibrium or non-equ…
Recurrent oligomers in proteins - an optimal scheme reconciling accurate and concise backbone representations in automated folding and design studies
Cristian Micheletti, Flavio Seno, Amos Maritan
A novel scheme is introduced to capture the spatial correlations of consecutive amino acids in naturally occurring proteins. This knowledge-based strategy is able to carry out opti…
Adsorption-like Collapse of Diblock Copolymers
E. Orlandini, F. Seno, A. L. Stella
A linear copolymer made of two reciprocally attracting N-monomer blocks collapses to a compact phase through a novel transition, whose exponents are determined with extensive MC si…
Determination of Interaction Potentials of Amino Acids from Native Protein Structures: Test on Simple Lattice Models
Jort van Mourik, Cecilia Clementi, Amos Maritan +2
We propose a novel method for the determination of the effective interaction potential between the amino acids of a protein. The strategy is based on the combination of a new optim…