In the present work we give a clear-cut explanation of the unusual pentagonal protein arrangement in viral capsids from the viewpoint of solid state physics, namely theory of quasicrystals (QC). We show that the systems considered represent the first example of matter organization in 2D nanoparticles, in which the regions with a chiral pentagonal quasicrystallineorder of protein positions are arranged in a structure commensurate with the spherical topology and dodecahedral geometry. We establish the relations between the elastic properties of these unconventional QC regions and the unusual structure and geometry of the resulting viral capsid.

Polarity and chirality in NCP mesophases and chromatin fibers

Physical symmetry at nano- and macro-scale : Mechanics of viral capsids, geometry and order in exceptional viruses and Cell positioning, physical constraints and apoptosis process in oocytes

Physical principles of virus structure, self-assembly and maturation

Compared to organisms such as bacteria and eukaryotic cells, viruses have such a low level of complexity that they were at first regarded as being proto-organisms, at the borderline between living and inanimate matter. This view was gradually superseded by the recognition that viruses are highly efficient organisms which have evolved in order to hijack the "active" biological machinery of the infected cells. Recent studies revealed how physical mechanisms are used by the viruses for guiding all salient steps of their "life cycle" This fact has also strongly motivated the recent upsurge of theoretical and experimental studies addressing the molecular basis of the key problems in virology. Specifically, the topics that are presently investigated most intensively include the following: the self-assembly and maturation of viral capsids, the functioning of the molecular motors that loads the viral genome inside preformed capsids, the conformational arrangement of the DNA or RNA inside capsids, the physical forces at play during the ejection of the viral DNA into the host cell, and the electrostatic interactions between the nucleic acids and coat proteins and virus-based nano-composites. The abovementioned efforts in characterizing the key molecular aspects of single viral particles are complemented by the very active research in the modeling of viral epidemics where, again, physics-based statistical mechanical approaches are widely used. A "physical virology" topical conference held at the ICTP in 2012 provided a timely state-of-the art perspective on the subject that is rapidly progressing because of the ongoing advancements in experimental techniques (cryo-EM imaging and single-molecule manipulation) and theoretical ones (large-scale simulations). It came at a very timely junction as the first Gordon conference on physical virology was held in 2009 in Galveston, Texas, and the latest one in Ventura, California, in 2013, which could be taken as the defining events in the establishment of the whole field of physical virology. This special issue of the Journal of Biological Physics is entirely dedicated to physical virology and aims to present a broad overview of the current state of the art in various subtopics of physical virology and stimulate additional activity in this rapidly developing field.

Un des défis majeurs en biologie est de comprendre les lois qui régissent la morphogenèse. L’origine de l’apparition des formes est aujourd’hui généralement considérée comme découlant uniquement de processus moléculaires autonomes plutôt que reposant sur des contraintes physiques et mécaniques comme l’avait suggéré d’Arcy Thompson dès 1917. Dans un organisme modèle, l’œuf de Ciona intestinalis, un processus cellulaire, l’apoptose, est sous le contrôle de cellules géométriquement ordonnées au sein de deux monocouches épithéliales étroitement interconnectées (cellules folliculaires) et recouvrant une sphère (ovocyte). Ces observations suggèrent que des formes préexistantes générées par des contraintes physiques participent au contrôle du déterminisme cellulaire. Ainsi, le positionnement « idéal » des cellules folliculaires est exclusivement lié à la géométrie sphérique de l’ovocyte, et l’optimisation de l’apoptose massive observée dans l’épithélium sous-jacent découle directement de ce positionnement. De ces observations est né le concept d’« organisateur apoptotique » : certaines cellules seraient capables de contrôler le destin d’autres cellules, notamment en coordonnant les processus de mort cellulaire programmée. Ce concept pourrait éclairer d’un jour nouveau l’origine des phases d’apoptose massive et coordonnée nécessaires au bon déroulement de l’embryogenèse (cavitation, interdigitation). Il pourrait également être appliqué à certaines stratégies thérapeutiques anticancéreuses.

We propose crystallization theory of quasicrystalline structures which does not use concepts of multidimensional crystallography for description of quasicrystalline order. On the example of the MnSiAl octagonal quasicrystal structure it is shown that it is possible to calculate the coordinates of corresponding quasilattice (QL) by constrained minimization of Landau free energy. The change from unconstrained to constrained minimization of the free energy is justified by the peculiarities of local atomic order in the considered structure. The proposed theory brings a new physical interpretation to traditional notions of multidimensional crystallography, and can be used to explain quasicrystalline structure formation with different QL.