arXiv subjects

Giuliana Indelicato

Publications and source records attributed to Giuliana Indelicato.

3 recordsLinked to original sources

arXiv2017

Minimum energy paths for conformational changes of viral capsids

In this work we study how a viral capsid can change conformation using techniques of Large Deviations Theory for stochastic differential equations. The viral capsid is a model of a complex system in which many units - the proteins forming the capsomers - interact by weak forces to form a structure with exceptional mechanical resistance. The destabilization of such a structure is interesting both per se, since it is related either to infection or maturation processes, and because it yields insights into the stability of complex structures in which the constitutive elements interact by weak attractive forces. We focus here on a simplified model of a dodecahederal viral capsid, and assume that the capsomers are rigid plaquettes with one degree of freedom each. We compute the most probable transition path from the closed capsid to the final configuration using minimum energy paths, and discuss the stability of intermediate states.

cond-mat.stat-mech↗

arXiv2015

A Ginzburg-Landau model for the expansion of a dodecahedral viral capsid

We propose a Ginzburg-Landau model for the expansion of a dodecahedral viral capsid during infection or maturation. The capsid is described as a dodecahedron whose faces, meant to model rigid capsomers, are free to move independent of each other, and has therefore twelve degrees of freedom. We assume that the energy of the system is a function of the twelve variables with icosahedral symmetry. Using techniques of the theory of invariants, we expand the energy as the sum of invariant polynomials up to fourth order, and classify its minima in dependence of the coefficients of the Ginzburg-Landau expansion. Possible conformational changes of the capsid correspond to symmetry breaking of the equilibrium closed form. The results suggest that the only generic transition from the closed state leads to icosahedral expanded form. Our approach does not allow to study the expansion pathway, which is likely to be non-icosahedral.

math-ph↗

arXiv2009

An algorithm for the arithmetic classification of multilattices

A procedure for the construction and the classification of multilattices in arbitrary dimension is proposed. The algorithm allows to determine explicitly the location of the points of a multilattice given its space group, and to determine whether two multilattices are arithmetically equivalent. The algorithm is based on ideas from integer matrix theory, in particular the reduction to the Smith normal form. Among the applications of this procedure is a software package that allows the classification of complex crystalline structures and the determination of their space groups. Also, it can be used to determine the symmetry of regular systems of points in high dimension, with applications to the study of quasicrystals and sets of points with noncrystallographic symmetry in low dimension, such as viral capsid structures.

math-ph↗