Flavio Seno

Università degli Studi di Padova, Fisica e Astronomia, Faculty Member

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Papers by Flavio Seno

Strange phases in three stranded DNA-models at low dimensionality

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Analysis of series with stochastic coefficients

by Flavio Seno and Raf Dekeyser

Physical Review A, 1990

For functions with power-law singularities we consider series expansions~hose coeKcients have bee... more For functions with power-law singularities we consider series expansions~hose coeKcients have been determined by Monte Carlo simulation. In many practical problems the relative noise of the coefficients is constant or slowly increasing with the order. We modeled real Monte Carlo expansions by test series with known singularity structure where noise with different strength and form is imposed on the coefBcients. The efficiency of different standard methods of series analysis (ratio method, Pade approximants, differental approximants) has been tested together with smoothing methods based on repeated partial summation of the series. We found the Pade method to give reasonable estimates and its accuracy is independent of the smoothing, while the estimates of the ratio and the differential approximant methods are greatly improved when smoothing is applied. Indeed, we found the ratio method with optimally selected smoothing to give the most reliable results.

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Unraveling the Schneeberg garnet puzzle: a numerical model of multiple nucleation and coalescence

by Flavio Seno and Luca Peruzzo

Contributions To Mineralogy and Petrology, 2003

A quantitative kinetic model for the growth of the different garnet porphyroblast microstructures... more A quantitative kinetic model for the growth of the different garnet porphyroblast microstructures (type 1 and type 2) of the Western Schneeberg Complex (WSC) is presented. These porphyroblasts formed by a multiple nucleation and coalescence mechanism. Our numerical simulation shows that at constant diffusion rates: (1) low interface reaction rates result in a fully amalgamated porphyroblast (type 2); (2) intermediate reaction rates result in a porphyroblast, where coalescence of grains closer to the margin prevented amalgamation of those in the centre (similar to type 1 porphyroblasts); and (3) high interface reaction rates result in a porphyroblast microstructure with an atoll form. All three microstructures are characterised by distinctive cluster size distributions. A 2-D cluster size distribution analysis of type 1 porphyroblasts of WSC shows that these did not form because of intermediate interface reaction rates, but because the diffusion rate of nutrients was too low to keep pace with the interface reaction rate.

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An efficient algorithm to perform local concerted movements of a chain molecule

PloS one, 2015

The devising of efficient concerted rotation moves that modify only selected local portions of ch... more The devising of efficient concerted rotation moves that modify only selected local portions of chain molecules is a long studied problem. Possible applications range from speeding the uncorrelated sampling of polymeric dense systems to loop reconstruction and structure refinement in protein modeling. Here, we propose and validate, on a few pedagogical examples, a novel numerical strategy that generalizes the notion of concerted rotation. The usage of the Denavit-Hartenberg parameters for chain description allows all possible choices for the subset of degrees of freedom to be modified in the move. They can be arbitrarily distributed along the chain and can be distanced between consecutive monomers as well. The efficiency of the methodology capitalizes on the inherent geometrical structure of the manifold defined by all chain configurations compatible with the fixed degrees of freedom. The chain portion to be moved is first opened along a direction chosen in the tangent space to the m...

Learning effective amino acid interactions through iterative stochastic techniques

Proteins, Jan 15, 2001

The prediction of the three-dimensional structures of the native states of proteins from the sequ... more The prediction of the three-dimensional structures of the native states of proteins from the sequences of their amino acids is one of the most important challenges in molecular biology. An essential task for solving this problem within coarse-grained models is the deduction of effective interaction potentials between the amino acids. Over the years, several techniques have been developed to extract potentials that are able to discriminate satisfactorily between the native and nonnative folds of a preassigned protein sequence. In general, when these potentials are used in actual dynamical folding simulations, they lead to a drift of the native structure outside the quasinative basin. In this article, we present and validate an approach to overcome this difficulty. By exploiting several numerical and analytical tools, we set up a rigorous iterative scheme to extract potentials satisfying a prerequisite of any viable potential: the stabilization of proteins within their native basin (l...

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Assembly of protein tertiary structures from secondary structures using optimized potentials

We present a simulated annealingbased method for the prediction of the tertiary structures of pro... more We present a simulated annealingbased method for the prediction of the tertiary structures of proteins given knowledge of the secondary structure associated with each amino acid in the sequence. The backbone is represented in a detailed fashion whereas the sidechains and pairwise interactions are modeled in a simplified way, following the LINUS model of Srinivasan and Rose. A perceptron-based technique is used to optimize the interaction potentials for a training set of three proteins. For these proteins, the procedure is able to reproduce the tertiary structures to below 3 Å in root mean square deviation (rmsd) from the PDB targets. We present the results of tests on twelve other proteins. For half of these, the lowest energy decoy has a rmsd from the native state below 6 Å and, in 9 out of 12 cases, we obtain decoys whose rmsd from the native states are also well below 5 Å. Proteins 2003;52:155-165.

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New trends in modern statistical physics

Central European Journal of Physics, 2012

PASTA 2.0: an improved server for protein aggregation prediction

Nucleic acids research, 2014

The formation of amyloid aggregates upon protein misfolding is related to several devastating deg... more The formation of amyloid aggregates upon protein misfolding is related to several devastating degenerative diseases. The propensities of different protein sequences to aggregate into amyloids, how they are enhanced by pathogenic mutations, the presence of aggregation hot spots stabilizing pathological interactions, the establishing of cross-amyloid interactions between co-aggregating proteins, all rely at the molecular level on the stability of the amyloid cross-beta structure. Our redesigned server, PASTA 2.0, provides a versatile platform where all of these different features can be easily predicted on a genomic scale given input sequences. The server provides other pieces of information, such as intrinsic disorder and secondary structure predictions, that complement the aggregation data. The PASTA 2.0 energy function evaluates the stability of putative cross-beta pairings between different sequence stretches. It was re-derived on a larger dataset of globular protein domains. The ...

Gauge model with Ising vacancies

Inverse design of proteins with hydrophobic and polar amino acids

A two amino acid (hydrophobic and polar) scheme is used to perform the design on target conformat... more A two amino acid (hydrophobic and polar) scheme is used to perform the design on target conformations corresponding to the native states of twenty single chain proteins. Strikingly, the percentage of successful identification of the nature of the residues benchmarked against naturally occurring proteins and their homologues is around 75 % independent of the complexity of the design procedure. Typically, the lowest success rate occurs for residues such as alanine that have a high secondary structure functionality. Using a simple lattice model, we argue that one possible shortcoming of the model studied may involve the coarse-graining of the twenty kinds of amino acids into just two effective types.

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Interdisciplinary Physics: Biological Physics, Quantum Information, etc-Protein Structures and Optimal Folding from a Geometrical Variational Principle

Polymers, Biopolymers, and Complex Systems-Determination of interaction potentials of amino acids from native protein structures: Tests on simple lattice models

Self-consistent knowledge-based approach to protein design

A simple and very efficient protein design strategy is proposed by developing some recently intro... more A simple and very efficient protein design strategy is proposed by developing some recently introduced theoretical tools which have been successfully applied to exactly solvable protein models. The design approach is implemented by using three amino acid classes and it is based on the minimization of an appropriate energy function. For a given native state the results of the design procedure are compared, through a statistical analysis, with the properties of an ensemble of sequences folding in the same conformation. If the success rate is computed on those sites designed with high confidence, it can be as high as 80%. The method is also able to identify key sites for the folding process: results for 2ci2 and barnase are in very good agreement with experimental results.

Mechanical denaturation of DNA

by Enzo Orlandini and Flavio Seno

Helicase on DNA

by Somendra Bhattacharjee and Flavio Seno

Stretching of a Polymer Below the Θ Point

... A 35, L233 (2002). [13] M. Cieplak, TX Hoang, and MO Robbins, Proteins 49, 104 (2002); 49, 11... more

An optimal procedure to extract interaction potentials for protein folding

A formidable challenge in molecular biology is the prediction of the three-dimensional structures... more A formidable challenge in molecular biology is the prediction of the three-dimensional structures of the native state of proteins from their sequence of amino acids. An essential step to solve this problem is the extraction of the coarsegrained interaction potentials between the amino acids. Here we outline preliminary results of a strategy that accomplishes such goal with the search of those potentials which are able to recognize the native state of a protein as a stable local minimum. The method is implemented by exploiting several numerical and analytical tools which have been recently developed by our group. The results are extremely promising: despite the fact that we have used simple forms for Hamiltonians, the extracted potentials are able to stabilize simultaneously at least 10 proteins of dierent classes to an average distance (per residue) less than 3 # A from the native state. Ó

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Gauge model with Ising vacancies: Multicritical behavior of self-avoiding surfaces

A openZ2 gauge model with n-component-vector degrees of freedom on a dodecahedral lattice is coup... more A openZ2 gauge model with n-component-vector degrees of freedom on a dodecahedral lattice is coupled to an Ising system on the dual lattice. The statistics of interacting self-avoiding surfaces (SAS) is obtained in the n--&gt;0 limit. At the percolative critical point an exact identification of the SAS critical behavior with that of Ising cluster hulls holds. This condition corresponds to

Vesicles on a hierarchical lattice: an exact renormalization group approach

$Research paper thumbnail of Polymers at the Θ-point on fractals: results of Flory approximations$

Polymers at the Θ-point on fractals: results of Flory approximations

Flavio Seno

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