Thermal and convection analyses of the dendrite remelting rocket experiment; Experiment 74-21 in the space processing rocket program

The Dendrite Remelting Rocket Experiment was performed aboard a Black Brant VC Sounding Rocket during a period which gravity levels of approximately 0.00001 g prevailed. The experiment consisted of cooling an aqueous ammonium chloride solution in a manner such that crystallization of ammonium chloride crystals proceeded throughout a three minute period of zero-g. The crystallization process during flight was recorded on 35 mm panatomic-x film. A number of ground crystallizations were similarly recorded for comparison purposes. The convective and thermal conditions in aqueous and metallic liquid systems were assessed under conditions of the flight experiment to help establish the relevance of the rocket experiment to metals casting phenomena. The results indicate that aqueous or metallic convective velocities in the Dendrite Remelting Rocket Experiment cell are of insignificant magnitudes at the 0.0001 to 0.00001 g levels of the experiment. The crystallization phenomena observed in the Rocket Experiment, therefore, may be indicative of how metals will solidify in low-g

Analytical support for SPAR experiment 76-36

The apparatus, materials, and procedures used in an analysis of thermal, convective, and rotational fluid flow for a second series of rocket experiments of dendrite growth are described. A constitutive supercooling criterion was calculated from the thermal data. A convection analysis was made of the various cases to ensure that convective velocities will not exceed about .01 cm/sec in the low-g tests. Damping times for fluid flow generated by rocket spin-up and spin-down were also determined, so that the conditions for this experiment are generally the same as those for the SPAR experiment 74-21 study of ammonium chloride low-g crystallizations

Correcting the Bias of Empirical Frequency Parameter Estimators in Codon Models

Markov models of codon substitution are powerful inferential tools for studying biological processes such as natural selection and preferences in amino acid substitution. The equilibrium character distributions of these models are almost always estimated using nucleotide frequencies observed in a sequence alignment, primarily as a matter of historical convention. In this note, we demonstrate that a popular class of such estimators are biased, and that this bias has an adverse effect on goodness of fit and estimates of substitution rates. We propose a “corrected” empirical estimator that begins with observed nucleotide counts, but accounts for the nucleotide composition of stop codons. We show via simulation that the corrected estimates outperform the de facto standard estimates not just by providing better estimates of the frequencies themselves, but also by leading to improved estimation of other parameters in the evolutionary models. On a curated collection of sequence alignments, our estimators show a significant improvement in goodness of fit compared to the approach. Maximum likelihood estimation of the frequency parameters appears to be warranted in many cases, albeit at a greater computational cost. Our results demonstrate that there is little justification, either statistical or computational, for continued use of the -style estimators

Generalized Rosenfeld scalings for tracer diffusivities in not-so-simple fluids: Mixtures and soft particles

Rosenfeld [Phys. Rev. A 15, 2545 (1977)] noticed that casting transport coefficients of simple monatomic, equilibrium fluids in specific dimensionless forms makes them approximately single-valued functions of excess entropy. This has predictive value because, while the transport coefficients of dense fluids are difficult to estimate from first principles, excess entropy can often be accurately predicted from liquid-state theory. Here, we use molecular simulations to investigate whether Rosenfeld's observation is a special case of a more general scaling law relating mobility of particles in mixtures to excess entropy. Specifically, we study tracer diffusivities, static structure, and thermodynamic properties of a variety of one- and two-component model fluid systems with either additive or non-additive interactions of the hard-sphere or Gaussian-core form. The results of the simulations demonstrate that the effects of mixture concentration and composition, particle-size asymmetry and additivity, and strength of the interparticle interactions in these fluids are consistent with an empirical scaling law relating the excess entropy to a new dimensionless (generalized Rosenfeld) form of tracer diffusivity, which we introduce here. The dimensionless form of the tracer diffusivity follows from knowledge of the intermolecular potential and the transport / thermodynamic behavior of fluids in the dilute limit. The generalized Rosenfeld scaling requires less information, and provides more accurate predictions, than either Enskog theory or scalings based on the pair-correlation contribution to the excess entropy. As we show, however, it also suffers from some limitations, especially for systems that exhibit significant decoupling of individual component tracer diffusivities.Comment: 15 pages, 10 figure

Experimental measurement of stress at a four-domain junction in lead zirconate titanate

A junction between two lamellar bands of ferroelectric domains in a lead zirconate titanate (PZT) ceramic is analysed using Kikuchi diffraction patterns in the transmission electron microscope. Indexing of the diffraction patterns allowed the determination of the 3D relative orientation of the 4 different domains at the junction and thus the characterisation of the domain boundaries. The local c/a ratio could also be determined from the misorientations at the domain boundaries. Analysis of the data showed that large stresses were concentrated at the junction, and that this is inevitable at such band junctions. Such stress concentrations could act as nuclei for cracking of the ceramic under additional loading in service, perhaps particularly as a consequence of extended electromechanical cycling. Moreover, the stresses would increase with increasing c/a making the issues all the more serious for Ti-rich compositions having larger c/a ratios

Plasticity in dormancy behaviour of Calanoides acutus in Antarctic coastal waters

Copepods that enter dormancy, such as Calanoides acutus, are key primary consumers in Southern Ocean food webs where they convert a portion of the seasonal phytoplankton biomass into a longer-term energetic and physiological resource as wax ester (WE) reserves. We studied the seasonal abundance and lipid profiles of pre-adult and adult C. acutus in relation to phytoplankton dynamics on the Western Antarctic Peninsula. Initiation of dormancy occurred when WE unsaturation was relatively high, and chlorophyll a (Chl a) concentrations, predominantly attributable to diatoms, were reducing. Declines in WE unsaturation during the winter may act as a dormancy timing mechanism with increased Chl a concentrations likely to promote sedimentation that results in a teleconnection between the surface and deep water inducing ascent. A late summer diatom bloom was linked to early dormancy termination of females and a second spawning event. The frequency and duration of high biomass phytoplankton blooms may have consequences for the lifespan of the iteroparous C. acutus females (either 1 or 2 years) if limited by a total of two main spawning events. Late summer recruits, generated by a second spawning event, likely benefitted from lower predation and high phytoplankton food availability. The flexibility of copepods to modulate their life-cycle strategy in response to bottom-up and top-down conditions enables individuals to optimize their probability of reproductive success in the very variable environment prevalent in the Southern Ocean

CodonTest: Modeling Amino Acid Substitution Preferences in Coding Sequences

Codon models of evolution have facilitated the interpretation of selective forces operating on genomes. These models, however, assume a single rate of non-synonymous substitution irrespective of the nature of amino acids being exchanged. Recent developments have shown that models which allow for amino acid pairs to have independent rates of substitution offer improved fit over single rate models. However, these approaches have been limited by the necessity for large alignments in their estimation. An alternative approach is to assume that substitution rates between amino acid pairs can be subdivided into rate classes, dependent on the information content of the alignment. However, given the combinatorially large number of such models, an efficient model search strategy is needed. Here we develop a Genetic Algorithm (GA) method for the estimation of such models. A GA is used to assign amino acid substitution pairs to a series of rate classes, where is estimated from the alignment. Other parameters of the phylogenetic Markov model, including substitution rates, character frequencies and branch lengths are estimated using standard maximum likelihood optimization procedures. We apply the GA to empirical alignments and show improved model fit over existing models of codon evolution. Our results suggest that current models are poor approximations of protein evolution and thus gene and organism specific multi-rate models that incorporate amino acid substitution biases are preferred. We further anticipate that the clustering of amino acid substitution rates into classes will be biologically informative, such that genes with similar functions exhibit similar clustering, and hence this clustering will be useful for the evolutionary fingerprinting of genes

Natural growth rates in Antarctic krill (Euphausia superba): II. Predictive models based on food, temperature, body length, sex, and maturity stage

We used the instantaneous growth rate method to determine the effects of food, temperature, krill length, sex, and maturity stage on in situ summer growth of krill across the southwest Atlantic sector of the Southern Ocean. The main aims were to examine the separate effects of each variable and to generate a predictive model of growth based on satellite-derivable environmental data. Both growth increments in length on moulting (GIs) and daily growth rates (DGRs, mm d-1) ranged greatly among the 59 swarms, from 0.58–15% and 0.013–0.32 mm d-1. However, all swarms maintained positive mean growth, even those in the low chlorophyll a (Chl a) zone of the central Scotia Sea. Among a suite of indices of food quantity and quality, large-scale monthly Chl a values from SeaWiFS predicted krill growth the best. Across our study area, the great contrast between bloom and nonbloom regions was a major factor driving variation in growth rates, obscuring more subtle effects of food quality. GIs and DGRs decreased with increasing krill length and decreased above a temperature optimum of 0.5°C. This probably reflects the onset of thermal stress at the northern limit of krill’s range. Thus, growth rates were fastest in the ice edge blooms of the southern Scotia Sea and not at South Georgia as previously suggested. This reflects both the smaller size of the krill and the colder water in the south being optimum for growth. Males tended to have higher GIs than females but longer intermoult periods, leading to similar DGRs between sexes. DGRs of equivalent-size krill tended to decrease with maturity stage, suggesting the progressive allocation of energy toward reproduction rather than somatic growth. Our maximum DGRs are higher than most literature values, equating to a 5.7% increase in mass per day. This value fits within a realistic energy budget, suggesting a maximum carbon ration of ~20% d-1. Over the whole Scotia Sea/South Georgia area, the gross turnover of krill biomass was ~1% d-1

Probing a Complex of Cytochromecand Cardiolipin by Magnetic Circular Dichroism Spectroscopy: Implications for the Initial Events in Apoptosis

Oxidation of cardiolipin (CL) by its complex with cytochrome c (cyt c) plays a crucial role in triggering apoptosis. Through a combination of magnetic circular dichroism spectroscopy and potentiometric titrations, we show that both the ferric and ferrous forms of the heme group of a CL:cyt c complex exist as multiple conformers at a physiologically relevant pH of 7.4. For the ferric state, these conformers are His/Lys- and His/OH–-ligated. The ferrous state is predominantly high-spin and, most likely, His/–. Interconversion of the ferric and ferrous conformers is described by a single midpoint potential of -80 ± 9 mV vs SHE. These results suggest that CL oxidation in mitochondria could occur by the reaction of molecular oxygen with the ferrous CL:cyt c complex in addition to the well-described reaction of peroxides with the ferric form