Symmetry, stability, and dynamics of multidomain and multicomponent protein systems

Symmetry is commonly observed in many biological systems. Here we discuss representative examples of the role of symmetry in structural molecular biology. Point group symmetries are observed in many protein oligomers whose three-dimensional atomic structures have been elucidated by x-ray crystallography. Approximate symmetry also occurs in multidomain proteins. Symmetry often confers stability on the molecular system and results in economical usage of basic components to build the macromolecular structure. Symmetry is also associated with cooperativity. Mild perturbation from perfect symmetry may be essential in some systems for dynamic functions.

Symmetry and the energy landscapes of biomolecules

The role of symmetry in the folding of proteins is discussed using energy landscape theory. An analytical argument shows it is much easier to find sequences with funneled energy landscape capable of fast folding if the structure is symmetric. The analogy with phase transitions of small clusters with magic numbers is discussed.

The role of symmetry in fundamental physics

The role of symmetry in fundamental physics is reviewed.

Symmetry arguments in chemistry

The use (and misuse) of symmetry arguments in constructing molecular models and in the interpretation of experimental observations bearing on molecular structure (spectroscopy, diffraction, etc.) is discussed. Examples include the development of point groups and space groups for describing the external and internal symmetry of crystals, the derivation of molecular symmetry by counting isomers (the benzene structure), molecular chirality, the connection between macroscopic and molecular chirality, pseudorotation, the symmetry group of nonrigid molecules, and the use of orbital symmetry arguments in discussing aspects of chemical reactivity.

Five-fold symmetry in crystalline quasicrystal lattices

To demonstrate that crystallographic methods can be applied to index and interpret diffraction patterns from well-ordered quasicrystals that display non-crystallographic 5-fold symmetry, we have characterized the properties of a series of periodic two-dimensional lattices built from pentagons, called Fibonacci pentilings, which resemble aperiodic Penrose tilings. The computed diffraction patterns from periodic pentilings with moderate size unit cells show decagonal symmetry and are virtually indistinguishable from that of the infinite aperiodic pentiling. We identify the vertices and centers of the pentagons forming the pentiling with the positions of transition metal atoms projected on the plane perpendicular to the decagonal axis of quasicrystals whose structure is related to crystalline η phase alloys. The characteristic length scale of the pentiling lattices, evident from the Patterson (autocorrelation) function, is ∼τ2 times the pentagon edge length, where τ is the golden ratio. Within this distance there are a finite number of local atomic motifs whose structure can be crystallographically refined against the experimentally measured diffraction data.

From symmetry to asymmetry: Phylogenetic patterns of asymmetry variation in animals and their evolutionary significance

Phylogenetic analyses of asymmetry variation offer a powerful tool for exploring the interplay between ontogeny and evolution because (i) conspicuous asymmetries exist in many higher metazoans with widely varying modes of development, (ii) patterns of bilateral variation within species may identify genetically and environmentally triggered asymmetries, and (iii) asymmetries arising at different times during development may be more sensitive to internal cytoplasmic inhomogeneities compared to external environmental stimuli. Using four broadly comparable asymmetry states (symmetry, antisymmetry, dextral, and sinistral), and two stages at which asymmetry appears developmentally (larval and postlarval), I evaluated relations between ontogenetic and phylogenetic patterns of asymmetry variation. Among 140 inferred phylogenetic transitions between asymmetry states, recorded from 11 classes in five phyla, directional asymmetry (dextral or sinistral) evolved directly from symmetrical ancestors proportionally more frequently among larval asymmetries. In contrast, antisymmetry, either as an end state or as a transitional stage preceding directional asymmetry, was confined primarily to postlarval asymmetries. The ontogenetic origin of asymmetry thus significantly influences its subsequent evolution. Furthermore, because antisymmetry typically signals an environmentally triggered asymmetry, the phylogenetic transition from antisymmetry to directional asymmetry suggests that many cases of laterally fixed asymmetries evolved via genetic assimilation.

Symmetry in chemistry from the hydrogen atom to proteins

The last 2 decades have seen discoveries in highly excited states of atoms and molecules of phenomena that are qualitatively different from the “planetary” model of the atom, and the near-rigid model of molecules, characteristic of these systems in their low-energy states. A unified view is emerging in terms of approximate dynamical symmetry principles. Highly excited states of two-electron atoms display “molecular” behavior of a nonrigid linear structure undergoing collective rotation and vibration. Highly excited states of molecules described in the “standard molecular model” display normal mode couplings, which induce bifurcations on the route to molecular chaos. New approaches such as rigid–nonrigid correlation, vibrons, and quantum groups suggest a unified view of collective electronic motion in atoms and nuclear motion in molecules.

Independent determination of symmetry and polarity in the Drosophila eye.

In each facet of the Drosophila compound eye, a cluster of photoreceptor cells assumes an asymmetric trapezoidal pattern. These clusters have opposite orientations above and below an equator, showing global dorsoventral mirror symmetry. However, in the mutant spiny legs, the polarization of each cluster appears to be random, so that no equator is evident. The apparent lack of an equator suggests that spiny legs+ may be involved in the establishment of global dorsoventral identity that might be essential for proper polarization of the photoreceptor clusters. Alternatively, a global dorsoventral pattern could be present, but spiny legs+ may be required for local polarization of individual clusters. Using an enhancer trap strain in which white+ gene expression is restricted to the dorsal field, we show that white+ expression in spiny legs correctly respects dorsoventral position even in facets with inappropriate polarizations; the dorsoventral boundary is indeed present, whereas the mechanism for polarization is perturbed. It is suggested that the boundary is established before the action of spiny legs+ by an independent mechanism.

Thermodynamic glass transition in a spin glass without time-reversal symmetry

Spin glasses are a longstanding model for the sluggish dynamics that appear at the glass transition. However, spin glasses differ from structural glasses in a crucial feature: they enjoy a time reversal symmetry. This symmetry can be broken by applying an external magnetic field, but embarrassingly little is known about the critical behavior of a spin glass in a field. In this context, the space dimension is crucial. Simulations are easier to interpret in a large number of dimensions, but one must work below the upper critical dimension (i.e., in d < 6) in order for results to have relevance for experiments. Here we show conclusive evidence for the presence of a phase transition in a four-dimensional spin glass in a field. Two ingredients were crucial for this achievement: massive numerical simulations were carried out on the Janus special-purpose computer, and a new and powerful finite-size scaling method.

El color como recurso expresivo: análisis de las series de televisión Mad Men y Breaking Bad

La presente investigación tiene como objetivo reconocer y aprender a utilizar el color en el medio audiovisual, es decir, conocer sus cualidades, técnicas y estrategias para, de esta forma, dar justa dimensión a su gran capacidad expresiva. El mirar y, posteriormente, observar permite saber el tipo de atmósferas que son necesarias para sugerir determinados estados. Estas atmósferas se generan gracias a los elementos que las componen, cada uno de ellos con sus formas, colores, ubicación en el espacio, más la interrelación global entre ellos. La composición visual se da a partir del conjunto de elementos distribuidos en el espacio. Que se ven “envueltos” con la luz planteada. Toda esta suma, es la que consigue expresar una emoción por parte del creador y, si se sabe “leer”, una correcta interpretación por parte del espectador. Esta “alfabetización visual” establece nexos entre el creador y el receptor, lo que lleva a unos y otros a un mayor conocimiento en la utilización de las reglas. Ello permite reforzar el texto narrativo, que “se articula en dos niveles: la historia —lo narrado, el qué— y el discurso —el modo de narrarlo, el cómo—, es decir, el plano del contenido y el plano de la expresión” (García, F., 2011, p.12). El creador de la obra audiovisual guía al espectador por los caminos de la historia que está desarrollando, mientras que el espectador, al saber “leer”, puede conocer el camino por donde tiene que transitar para disfrutarlo y entenderlo en su totalidad. Comprender la información que proporciona el color parecería innato al ser humano del siglo XXI, dominado por un entorno netamente visual. Pero no es así. Por lo tanto, si se aprende a conocer los parámetros sobre los que se desarrolla la información que se presenta visualmente, se conseguirá hacer más eficaz la comunicación, a la vez que se fomentará la creatividad, por un lado, y el disfrute visual, por otro...

Hydrogenated graphene nanoribbons for spintronics

We show how hydrogenation of graphene nanoribbons at small concentrations can open venues toward carbon-based spintronics applications regardless of any specific edge termination or passivation of the nanoribbons. Density-functional theory calculations show that an adsorbed H atom induces a spin density on the surrounding π orbitals whose symmetry and degree of localization depends on the distance to the edges of the nanoribbon. As expected for graphene-based systems, these induced magnetic moments interact ferromagnetically or antiferromagnetically depending on the relative adsorption graphene sublattice, but the magnitude of the interactions are found to strongly vary with the position of the H atoms relative to the edges. We also calculate, with the help of the Hubbard model, the transport properties of hydrogenated armchair semiconducting graphene nanoribbons in the diluted regime and show how the exchange coupling between H atoms can be exploited in the design of novel magnetoresistive devices.

Breaking the silence ceiling: how gender violence became into a social problem in Spain through media and politics

This research presents the explanatory model of the process of reconstruction of the ʺsocial problemʺ of Intimate Partner Violence (I.P.V) in Spain during last five years, with special attention to the role of media in this process. Using a content analysis of the three more diffused general newspapers, a content analysis of the minutes of the Parliament, and the statistics of the police reports and murders, from January of 1997 to December of 2001, it observes the relationship between the evolution of the incidence of Intimate Partner Violence (I.P.V) (measured by the number of deaths and the number of police reports) and the evolution of stories about this topic in press. It also studies the interconnection of the two previous variables with the political answer to the problem (measured by the interventions on the I.P.V. in the Senate and in the Congress). Data shows that, even though police reports have increased due to the contribution of politics and media, I.P.V murders keep on growing up.

Breaking down complex saproxylic communities: understanding sub-networks structure and implications to network robustness

Saproxylic insect communities inhabiting tree hollow microhabitats correspond with large food webs which simultaneously are constituted by multiple types of plant-animal and animal-animal interactions, according to the use of trophic resources (wood- and insect-dependent sub-networks), or to trophic habits or interaction types (xylophagous, saprophagous, xylomycetophagous, predators and commensals). We quantitatively assessed which properties of specialised networks were present in a complex networks involving different interacting types such as saproxylic community, and how they can be organised in trophic food webs. The architecture, interacting patterns and food web composition were evaluated along sub-networks, analysing their implications to network robustness from random and directed extinction simulations. A structure of large and cohesive modules with weakly connected nodes was observed throughout saproxylic sub-networks, composing the main food webs constituting this community. Insect-dependent sub-networks were more modular than wood-dependent sub-networks. Wood-dependent sub-networks presented higher species degree, connectance, links, linkage density, interaction strength, and were less specialised and more aggregated than insect-dependent sub-networks. These attributes defined high network robustness in wood-dependent sub-networks. Finally, our results emphasise the relevance of modularity, differences among interacting types and interrelations among them in modelling the structure of saproxylic communities and in determining their stability.

Evidence for non-conservative current-induced forces in the breaking of Au and Pt atomic chains

This experimental work aims at probing current-induced forces at the atomic scale. Specifically it addresses predictions in recent work regarding the appearance of run-away modes as a result of a combined effect of the non-conservative wind force and a ‘Berry force’. The systems we consider here are atomic chains of Au and Pt atoms, for which we investigate the distribution of break down voltage values. We observe two distinct modes of breaking for Au atomic chains. The breaking at high voltage appears to behave as expected for regular break down by thermal excitation due to Joule heating. However, there is a low-voltage breaking mode that has characteristics expected for the mechanism of current-induced forces. Although a full comparison would require more detailed information on the individual atomic configurations, the systems we consider are very similar to those considered in recent model calculations and the comparison between experiment and theory is very encouraging for the interpretation we propose.

Making or Breaking the Republic of Moldova? The Autonomy of Gagauzia. EDAP 02/2013

This article describes the process of self-determination and the creation of a territorial autonomy of the Gagauz people in the Republic of Moldova. It also analyses the situation in the autonomy after the change of government in Chisinau in 2009 and evaluates the current status of accommodation of the Gagauz’ interests in the country. Aspects of state-building and the influence of external actors are explored as well. Gagauzia (Gagauz Yeri) is one of the first post-Soviet autonomies. Since its establishment in 1994, no violent conflict has taken place there. However, the Gagauz language and culture remain relatively unprotected, and incentives as well as support for the integration of the Gagauz are low. The article outlines the potential for future disputes between the central government and local authorities, due to continuous attempts to limit Gagauzia’s self-governance and conflicting interpretations of how the autonomy should work. Furthermore, struggles between Gagauz political leaders and other local realities hamper the successful realization of Gagauz Yeri. With respect to Moldova’s efforts to resolve the Transnistrian conflict and to integrate with the European Union, compromises and cooperation through an ongoing dialogue between the centre and autonomy are clearly due. Resolving the remaining stumbling blocks could make Gagauzia a living, rather than symbolic autonomy.