S.B. Rochal

Extended topological defects as sources and outlets of dislocations in spherical hexagonal crystals

Abstract Extended topological defects (ETDs) arising in spherical hexagonal crystals due to their curvature are considered. These prevalent defects carry a unit total topological charge and are surrounded by scalene pentagonal boundaries. Topological peculiarities of reactions between ETDs and dislocations are considered. Similarly to boundaries of the usual planar crystalline order the ETDs emit and absorb the dislocations without preservation of their dislocational charge. Dislocations located inside the ETD area lose it and the enforced ETD decay can proceed in different ways without conservation of the total Burgers vector of the dislocations emitted.

Two-dimensional elasticity determines the low-frequency dynamics of single- and double-walled carbon nanotubes

We develop a continuous theory of low-frequency dynamics for nanotubes with walls constituted by single-atom monolayer, the topological elasticity of which is not related to its vanishing macroscopic thickness. The applicability region of the theory proposed includes all truly two-dimensional materials such as graphene and MoS2. New comprehensive interpretation and analytical expressions for low-frequency modes in single-walled carbon nanotube (SWCNT) are given. The theory unambiguously relates the radial breathing modes of SWCNT and breathinglike modes of the double-walled carbon nanotube (DWCNT). The existing Raman data on DWCNTs are fitted better than in the frame of previous models.

Hidden symmetry of small spherical viruses and organization principles in “anomalous” and double-shelled capsid nanoassemblies

We propose the principles of structural organization in spherical nanoassemblies with icosahedral symmetry constituted by asymmetric protein molecules. The approach modifies the paradigmatic geometrical Caspar and Klug (CK) model of icosahedral viral capsids and demonstrates the common origin of both the anomalous and conventional capsid structures. In contrast to all previous models of anomalous viral capsids the proposed modified model conserves the basic structural principles of the CK approach and reveals the common hidden symmetry underlying all small viral shells. We demonstrate the common genesis of the anomalous and conventional capsids and explain their structures in the same frame. The organization principles are derived from the group theory analysis of the positional order on the spherical surface. The relationship between the modified CK geometrical model and the theory of two-dimensional spherical crystallization is discussed. We also apply the proposed approach to complex double-shelled capsids and capsids with protruding knob-like proteins. The introduced notion of commensurability for the concentric nanoshells explains the peculiarities of their organization and helps to predict analogous, but yet undiscovered, double-shelled viral capsid nanostructures.

Structures of spherical viral capsids as quasicrystalline tilings

Spherical viral shells with icosahedral symmetry have been considered as quasicrystalline tilings. Similarly to known Caspar-Klug quasi-equivalence theory, the presented approach also minimizes the number of conformations necessary for the protein molecule bonding with its neighbors in the shell, but is based on different geometrical principles. It is assumed that protein molecule centers are located at vertices of tiles with identical edges, and the number of different tile types is minimal. Idealized coordinates of nonequivalent by symmetry protein positions in six various capsid types are obtained. The approach describes in a uniform way both the structures satisfying the well-known Caspar-Klug geometrical model and the structures contradicting this model.

Quasicrystalline and crystalline types of local protein order in capsids of small viruses

Like metal alloys and micellar systems in soft matter, the viral capsid structures can be of crystalline and quasicrystalline types. We reveal the local quasicrystalline order of proteins in small spherical viral capsids using their nets of dodecahedral type. We show that the structure of some of the viral shells is well described in terms of a chiral pentagonal tiling, whose nodes coincide with centers of mass of protein molecules. The chiral protein packing found in these capsids originates from the pentagonal Penrose tiling (PPT), due to a specific phason reconstruction needed to fit the protein order at the adjacent dodecahedron faces. Via examples of small spherical viral shells and geminate capsid of a Maize Streak virus, we discuss the benefits and shortcomings of the usage of a dodecahedral net in comparison to icosahedral one, which is commonly applied for the modeling of viral shells with a crystalline local order.

Theory of morphological transformation of viral capsid shell during the maturation process in the HK97 bacteriophage and similar viruses.

We consider the symmetry and physical origin of collective displacement modes playing a crucial role in the morphological transformation during the maturation of the HK97 bacteriophage and similar viruses. It is shown that the experimentally observed hexamer deformation and pentamer twist in the HK97 procapsid correspond to the simplest irreducible shear strain mode of a spherical shell. We also show that the icosahedral faceting of the bacteriophage capsid shell is driven by the simplest irreducible radial displacement field. The shear field has the rotational icosahedral symmetry group I while the radial field has the full icosahedral symmetry I_{h}. This difference makes their actions independent. The radial field sign discriminates between the icosahedral and the dodecahedral shapes of the faceted capsid shell, thus making the approach relevant not only for the HK97-like viruses but also for the parvovirus family. In the frame of the Landau-Ginzburg formalism we propose a simple phenomenological model valid for the first reversible step of the HK97 maturation process. The calculated phase diagram illustrates the discontinuous character of the virus shape transformation. The characteristics of the virus shell faceting and expansion obtained in the in vitro and in vivo experiments are related to the decrease in the capsid shell thickness and to the increase of the internal capsid pressure.In the frame of the Landau-Ginzburg formalism we propose a minimal phenomenological model for a morphological transformation in viral capsid shells. The transformation takes place during virus maturation process which renders virus infectious. The theory is illustrated on the example of the HK97 bacteriophage and viruses with similar morphological changes in the protective protein shell. The transformation is shown to be a structural phase transition driven by two order parameters. The first order parameter describes the isotropic expansion of the protein shell while the second one is responsible for the shape symmetry breaking and the resulting shell faceting. The group theory analysis and the resulting thermodynamic model make it possible to choose the parameter which discriminates between the icosahedral shell faceting often observed in viral capsids and the dodecahedral one observed in viruses of the Parvovirus family. Calculated phase diagram illustrates the discontinuous character of the virus morphological transformation and shows two qualitatively different paths of the transformation in a function of two main external thermodynamic parameters of the in vitro and in vivo experiments.

Relaxation of interstitials in spherical colloidal crystals

Abstract Spherical colloidal crystals (CCs) self-assemble on the interface between two liquids. These 2D structures unconventionally combine local hexagonal order and spherical geometry. Nowadays CCs are actively studied by altering their structures. However, the statistical analysis of such experiments results is limited by uniqueness of self-assembled structures and their short lifetime. Here we perform numerical experiments to investigate pathways of CC structure relaxation after the intrusion of interstitial. The process is simulated in the frames of overdamped molecular dynamics method. The relaxation occurs due to interaction with extended topological defects (ETDs) mandatory induced in spherical CCs by their intrinsic Gaussian curvature. Types of relaxation pathways are classified and their probabilities are estimated in the low-temperature region. To analyze the structural changes during the relaxation we use a parent phase approach allowing us to describe the global organization of spherical order. This organization is preserved by only the most typical relaxation pathway resulting in filling one of vacancies integrated inside the ETD areas. In contrast with this pathway the other ones shift the ETDs centers and can strongly reconstruct the internal structure of ETDs. Temperature dependence of the relaxation processes and the mechanism of dislocation unbinding are discussed. Common peculiarities in relaxation of spherical structures and particular fragments of planar hexagonal lattice are found.

Tubular lipid membranes pulled from vesicles: Dependence of system equilibrium on lipid bilayer curvature

Conditions of joint equilibrium and stability are derived for a spherical lipid vesicle and a tubular lipid membrane (TLM) pulled from this vesicle. The obtained equations establish relationships between the geometric and physical characteristics of the system and the external parameters, which have been found to be controllable in recent experiments. In particular, the proposed theory shows that, in addition to the pressure difference between internal and external regions of the system, the variable spontaneous average curvature of the lipid bilayer (forming the TLM) also influences the stability of the lipid tube. The conditions for stability of the cylindrical phase of TLMs after switching off the external force that initially formed the TLM from a vesicle are discussed. The loss of system stability under the action of a small axial force compressing the TLM is considered.

Multipole analysis of the strain-mediated coupling between proteins adsorbed at tubular lipid membrane surface

Abstract.The tubular lipid membranes (TLMs) pulled out from vesicles are often used in in vitro studies of the interactions between curvature-inducing proteins and highly curved membranes. The protein molecules adsorbed at the membrane surface deform the TLM and couple with each other due to the induced strain. Here we propose an approach which models the single curvature-inducing protein action on the lipid bilayer by the multipole, the superposition of the point forces applied to the membrane in the region of the protein adsorption. We show that to be localized in the area of the protein size at the TLM surface, the force multipoles satisfying the mechanical equilibrium conditions should be composed of three or more point forces. The protein coupling energy mediated by the membrane strain is studied in detail. In the region of the tubular membrane stability the maximal distance between two neighboring interacting protein-induced force multipoles is estimated to be of the order of the TLM cross section perimeter. In the vicinity of the TLM instability in the region of the vanishing stretching force applied to the TLM, the interaction radius increases drastically. The high affinity of the single curvature-inducing protein molecule to the regions in the vicinity of the TLM ends is explained and related to the boundary conditions in the experimental set-ups. The reasons for the aggregate formation on the membrane surface are also discussed.Graphical abstract

Landau theory of crystallization and self-assembly of octagonal quasicrystals

The theory of crystallization of quasicrystal structures that does not use the concept of multidimensional crystallography for describing the quasicrystal order has been proposed. It has been shown using the structure of the MnSiAl octagonal quasicrystal as an example that the coordinates of the sites in the corresponding quasicrystal lattice can be calculated by conditional minimization of the Landau free energy. The abandonment of the unconditional minimization of the free energy has been justified by special features of the local atomic order in the considered structure. The proposed theory gives a new physical meaning to the traditional concepts of multidimensional crystallography and can also be used for explaining the formation of quasicrystal structures with other quasicrystal lattices.