Raman scattering of perovskite SmScO3 and NdScO3 single crystals

We report an investigation of perovskite-type SmScO3 and NdScO3 single crystals by Raman scattering in various scattering configurations and at different wavelengths. The reported Raman spectra, together with the phonon mode assignment, set the basis for the use of Raman scattering for the structural investigation of RE-scandates. Further to the phonon signature, a fluorescence signal is observed for both scandates and is particularly intense for NdScO3 when using a 488 or 514 nm excitation line. A comparison of Raman spectra of RE-scandates with literature Raman data on orthorhombic perovskites shows that the frequency of particular modes scales with the orthorhombic distortion in terms of the rotation (or tilt) angle of the ScO6 octahedr

Structure, Bonding, and Mineralogy of Carbon at Extreme Conditions

The nature and extent of Earth’s deep carbon cycle remains uncertain. This chapter considers high-pressure carbon-bearing minerals, including those of Earth’s mantle and core, as well as phases that might be found in the interiors of larger planets outside our solar system. These phases include both experimentally produced and theoretically predicted polymorphs of carbon dioxide, carbonates, carbides, silicate-carbonates, as well as very high-pressure phases of pure carbon. One theme in the search for possible high P-T, deep-Earth phases is the likely shift from sp2 bonding (trigonal coordination) to sp3 bonding (tetrahedral coordination) in carbon-bearing phases of the lower mantle and core, as exemplified by the graphite-to-diamond transition (Bundy et al. 1961; Davies 1984). A similar phenomenon has been documented in the preferred coordination spheres of many elements at high pressure. For example, silicon is ubiquitously found in tetrahedral coordination in crustal and upper mantle minerals, but adopts octahedral coordination in many high-pressure phases. Indeed, the boundary between Earth’s transition zone and lower mantle may be described as a crystal chemical shift from 4-coordinated to 6-coordinated silicon (Hazen and Finger 1978; Finger and Hazen 1991). Similarly, magnesium and calcium commonly occur in octahedral 6-coordination in minerals at ambient conditions, but transform to 8- or greater coordination in high-pressure phases, as exemplified by the calcite-to-aragonite transformation of CaCO3 and the pyroxene-to-perovskite and post-perovskite transformations of MgSiO3 (Murakami et al. 2004; Oganov and Ono 2004). Consequently, a principal focus in any consideration of deep-Earth carbon minerals must include carbon in higher coordination, and even more complex bonding at more extreme conditions that characterize the interiors of larger planets

Carbon mineralogy and crystal chemistry

Carbon, element 6, displays remarkable chemical flexibility and thus is unique in the diversity of its mineralogical roles. Carbon has the ability to bond to itself and to more than 80 other elements in a variety of bonding topologies, most commonly in 2-, 3-, and 4-coordination. With oxidation numbers ranging from −4 to +4, carbon is observed to behave as a cation, as an anion, and as a neutral species in phases with an astonishing range of crystal structures, chemical bonding, and physical and chemical properties. This versatile element concentrates in dozens of different Earth repositories, from the atmosphere and oceans to the crust, mantle, and core, including solids, liquids, and gases as both a major and trace element (Holland 1984; Berner 2004; Hazen et al. 2012). Therefore, any comprehensive survey of carbon in Earth must consider the broad range of carbon-bearing phases. / The objective of this chapter is to review the mineralogy and crystal chemistry of carbon, with a focus primarily on phases in which carbon is an essential element: most notably the polymorphs of carbon, the carbides, and the carbonates. The possible role of trace carbon in nominally acarbonaceous silicates and oxides, though potentially a large and undocumented reservoir of the mantle and core (Wood 1993; Jana and Walker 1997; Freund et al. 2001; McDonough 2003; Keppler et al. 2003; Shcheka et al. 2006; Dasgupta 2013; Ni and Keppler 2013; Wood et al. 2013), is not considered here. Non-mineralogical carbon-bearing phases treated elsewhere, including in this volume, include C-O-H-N aqueous fluids (Javoy 1997; Zhang and Duan 2009; Jones et al. 2013; Manning et al. 2013); silicate melts (Dasgupta et al. 2007; Dasgupta 2013; Manning et al. 2013); carbonate melts (Cox 1980; Kramers et al. 1981; Wilson and Head 2007; Walter et al. 2008; Jones et al. 2013); a rich variety of organic molecules, including methane and higher hydrocarbons (McCollom and Simoneit 1999; Kenney et al. 2001; Kutcherov et al. 2002; Sherwood-Lollar et al. 2002; Scott et al. 2004; Helgeson et al. 2009; McCollom 2013; Sephton and Hazen 2013); and subsurface microbial life (Parkes et al. 1993; Gold 1999; Chapelle et al. 2002; D’Hondt et al. 2004; Roussel et al. 2008; Colwell and D’Hondt 2013; Schrenk et al. 2013; Meersman et al. 2013; Anderson et al. 2013). / The International Mineralogical Association (IMA) recognizes more than 380 carbon-bearing minerals (http://rruff.info/ima/), including carbon polymorphs, carbides, carbonates, and a variety of minerals that incorporate organic carbon in the form of molecular crystals, organic anions, or clathrates. This chapter reviews systematically carbon mineralogy and crystal chemistry, with a focus on those phases most likely to play a role in the crust. Additional high-temperature and high-pressure carbon-bearing minerals that may play a role in the mantle and core are considered in the next chapter on deep carbon mineralogy (Oganov et al. 2013)

Transformation Pathways of Silica under High Pressure

Concurrent molecular dynamics simulations and ab initio calculations show that densification of silica under pressure follows a ubiquitous two-stage mechanism. First, anions form a close-packed sub-lattice, governed by the strong repulsion between them. Next, cations redistribute onto the interstices. In cristobalite silica, the first stage is manifest by the formation of a metastable phase, which was observed experimentally a decade ago, but never indexed due to ambiguous diffraction patterns. Our simulations conclusively reveal its structure and its role in the densification of silica.Comment: 14 pages, 4 figure

State of the California current 2012-13: No such thing as an “average” year

This report reviews the state of the California Current System (CCS) between winter 2012 and spring 2013, and includes observations from Washington State to Baja California. During 2012, large-scale climate modes indicated the CCS remained in a cool, productive phase present since 2007. The upwelling season was delayed north of 42°N, but regions to the south, especially 33° to 36°N, experienced average to above average upwelling that persisted throughout the summer. Contrary to the indication of high production suggested by the climate indices, chlorophyll observed from surveys and remote sensing was below average along much of the coast. As well, some members of the forage assemblages along the coast experienced low abundances in 2012 surveys. Specifically, the concentrations of all lifestages observed directly or from egg densities of Pacific sardine, Sardinops sagax, and northern anchovy, Engraulis mordax, were less than previous years’ survey estimates. However, 2013 surveys and observations indicate an increase in abundance of northern anchovy. During winter 2011/2012, the increased presence of northern copepod species off northern California was consistent with stronger southward transport. Krill and small-fraction zooplankton abundances, where examined, were generally above average. North of 42°N, salps returned to typical abundances in 2012 after greater observed concentrations in 2010 and 2011. In contrast, salp abundance off central and southern California increased after a period of southward transport during winter 2011/2012. Reproductive success of piscivorous Brandt’s cormorant, Phalacrocorax penicillatus, was reduced while planktivorous Cassin’s auklet, Ptychoramphus aleuticus was elevated. Differences between the productivity of these two seabirds may be related to the available forage assemblage observed in the surveys. California sea lion pups from San Miguel Island were undernourished resulting in a pup mortality event perhaps in response to changes in forage availability. Limited biological data were available for spring 2013, but strong winter upwelling coastwide indicated an early spring transition, with the strong upwelling persisting into early summer

Universal Sequence Replication, Reversible Polymerization and Early Functional Biopolymers: A Model for the Initiation of Prebiotic Sequence Evolution

Many models for the origin of life have focused on understanding how evolution can drive the refinement of a preexisting enzyme, such as the evolution of efficient replicase activity. Here we present a model for what was, arguably, an even earlier stage of chemical evolution, when polymer sequence diversity was generated and sustained before, and during, the onset of functional selection. The model includes regular environmental cycles (e.g. hydration-dehydration cycles) that drive polymers between times of replication and functional activity, which coincide with times of different monomer and polymer diffusivity. Template-directed replication of informational polymers, which takes place during the dehydration stage of each cycle, is considered to be sequence-independent. New sequences are generated by spontaneous polymer formation, and all sequences compete for a finite monomer resource that is recycled via reversible polymerization. Kinetic Monte Carlo simulations demonstrate that this proposed prebiotic scenario provides a robust mechanism for the exploration of sequence space. Introduction of a polymer sequence with monomer synthetase activity illustrates that functional sequences can become established in a preexisting pool of otherwise non-functional sequences. Functional selection does not dominate system dynamics and sequence diversity remains high, permitting the emergence and spread of more than one functional sequence. It is also observed that polymers spontaneously form clusters in simulations where polymers diffuse more slowly than monomers, a feature that is reminiscent of a previous proposal that the earliest stages of life could have been defined by the collective evolution of a system-wide cooperation of polymer aggregates. Overall, the results presented demonstrate the merits of considering plausible prebiotic polymer chemistries and environments that would have allowed for the rapid turnover of monomer resources and for regularly varying monomer/polymer diffusivities

Degeneracy: a link between evolvability, robustness and complexity in biological systems

A full accounting of biological robustness remains elusive; both in terms of the mechanisms by which robustness is achieved and the forces that have caused robustness to grow over evolutionary time. Although its importance to topics such as ecosystem services and resilience is well recognized, the broader relationship between robustness and evolution is only starting to be fully appreciated. A renewed interest in this relationship has been prompted by evidence that mutational robustness can play a positive role in the discovery of adaptive innovations (evolvability) and evidence of an intimate relationship between robustness and complexity in biology. This paper offers a new perspective on the mechanics of evolution and the origins of complexity, robustness, and evolvability. Here we explore the hypothesis that degeneracy, a partial overlap in the functioning of multi-functional components, plays a central role in the evolution and robustness of complex forms. In support of this hypothesis, we present evidence that degeneracy is a fundamental source of robustness, it is intimately tied to multi-scaled complexity, and it establishes conditions that are necessary for system evolvability

Integrated information increases with fitness in the evolution of animats

One of the hallmarks of biological organisms is their ability to integrate disparate information sources to optimize their behavior in complex environments. How this capability can be quantified and related to the functional complexity of an organism remains a challenging problem, in particular since organismal functional complexity is not well-defined. We present here several candidate measures that quantify information and integration, and study their dependence on fitness as an artificial agent ("animat") evolves over thousands of generations to solve a navigation task in a simple, simulated environment. We compare the ability of these measures to predict high fitness with more conventional information-theoretic processing measures. As the animat adapts by increasing its "fit" to the world, information integration and processing increase commensurately along the evolutionary line of descent. We suggest that the correlation of fitness with information integration and with processing measures implies that high fitness requires both information processing as well as integration, but that information integration may be a better measure when the task requires memory. A correlation of measures of information integration (but also information processing) and fitness strongly suggests that these measures reflect the functional complexity of the animat, and that such measures can be used to quantify functional complexity even in the absence of fitness data.Comment: 27 pages, 8 figures, one supplementary figure. Three supplementary video files available on request. Version commensurate with published text in PLoS Comput. Bio

Energetic Selection of Topology in Ferredoxins

Models of early protein evolution posit the existence of short peptides that bound metals and ions and served as transporters, membranes or catalysts. The Cys-X-X-Cys-X-X-Cys heptapeptide located within bacterial ferredoxins, enclosing an Fe4S4 metal center, is an attractive candidate for such an early peptide. Ferredoxins are ancient proteins and the simple α+β fold is found alone or as a domain in larger proteins throughout all three kingdoms of life. Previous analyses of the heptapeptide conformation in experimentally determined ferredoxin structures revealed a pervasive right-handed topology, despite the fact that the Fe4S4 cluster is achiral. Conformational enumeration of a model CGGCGGC heptapeptide bound to a cubane iron-sulfur cluster indicates both left-handed and right-handed folds could exist and have comparable stabilities. However, only the natural ferredoxin topology provides a significant network of backbone-to-cluster hydrogen bonds that would stabilize the metal-peptide complex. The optimal peptide configuration (alternating αL,αR) is that of an α-sheet, providing an additional mechanism where oligomerization could stabilize the peptide and facilitate iron-sulfur cluster binding