Lithium-to-calcium ratios in Modern, Cenozoic, and Paleozoic articulate brachiopod shells

Li/Ca ratios in modern brachiopod shells generally correlate inversely with growth temperature, ranging from ∼20 µmol/mol at 30°C to ∼50 µmol/mol at 0°C with no apparent interspecific offsets. Causes of the temperature effect on Li/Ca ratios are not yet understood. Cenozoic brachiopod Li/Ca ratios average ∼30 µmol/mol, similar to the average observed in modern brachiopods. Relatively constant Li/Ca ratios for Eocene to Pleistocene nonluminescent brachiopod shells, consistent with previous observations of Cenozoic planktonic foraminifera, support the conclusion of little variation in Cenozoic seawater Li/Ca. Nonluminescent portions of Permian and Carboniferous brachiopods have Li/Ca ratios substantially lower (generally <10 µmol/mol) than modern, Cenozoic, or Devonian samples. Mass balance considerations, constrained by δ18O of brachiopods, suggest that low Li concentrations in Permo-Carboniferous seawater could be the result of a lower flux of dissolved Li from the continents and/or a higher flux of Li from seawater to clastic marine sediments. Nonluminescent Devonian brachiopods from a single hand specimen have Li/Ca ratios around 70% of the modern average. These Li/Ca ratios can be explained by either somewhat higher temperature with constant seawater Li/Ca, somewhat lower seawater Li/Ca at constant temperature, or a combination of slightly elevated temperature and slightly lower seawater Li/Ca

Noise and Oscillations in Simple Gene Networks

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Stable, Precise, and Reproducible Patterning of Bicoid and Hunchback Molecules in the Early Drosophila Embryo

Precise patterning of morphogen molecules and their accurate reading out are of key importance in embryonic development. Recent experiments have visualized distributions of proteins in developing embryos and shown that the gradient of concentration of Bicoid morphogen in Drosophila embryos is established rapidly after fertilization and remains stable through syncytial mitoses. This stable Bicoid gradient is read out in a precise way to distribute Hunchback with small fluctuations in each embryo and in a reproducible way, with small embryo-to-embryo fluctuation. The mechanisms of such stable, precise, and reproducible patterning through noisy cellular processes, however, still remain mysterious. To address these issues, here we develop the one- and three-dimensional stochastic models of the early Drosophila embryo. The simulated results show that the fluctuation in expression of the hunchback gene is dominated by the random arrival of Bicoid at the hunchback enhancer. Slow diffusion of Hunchback protein, however, averages out this intense fluctuation, leading to the precise patterning of distribution of Hunchback without loss of sharpness of the boundary of its distribution. The coordinated rates of diffusion and transport of input Bicoid and output Hunchback play decisive roles in suppressing fluctuations arising from the dynamical structure change in embryos and those arising from the random diffusion of molecules, and give rise to the stable, precise, and reproducible patterning of Bicoid and Hunchback distributions

Use of correlation matrices in lattice quantum chromodynamics

Thesis (S.B.)--Massachusetts Institute of Technology, Dept. of Physics, 2004.Includes bibliographical references (p. 117).This thesis explores the use of correlation matrices in analyzing Monte Carlo calculations from lattice quantum chromodynamics. Correlation matrices are a powerful tool for examining many problems in which significant correlations exist, and thus offer potential advantages for lattice QCD. Several models were used to study the relative advantages of correlated and uncorrelated analyses. However, when applied to actual lattice data at current statistics, the method appears to be undesirably biased.by David Lepzelter.S.B

Modeling Persistence in Mesenchymal Cell Motility Using Explicit Fibers

[Image: see text] Cell motility is central to a variety of fundamental processes ranging from cancer metastasis to immune responses, but it is still poorly understood in realistic native environments. Previous theoretical work has tended to focus on intracellular mechanisms or on small pieces of interaction with the environment. In this article, we present a simulation which accounts for mesenchymal movement in a 3D environment with explicit collagen fibers and show that this representation highlights the importance of both the concentration and alignment of fibers. We show good agreement with experimental results regarding cell motility and persistence in 3D environments and predict a specific effect on average instantaneous cell speed and persistence. Importantly, we show that a significant part of persistence in 3D is directly dependent on the physical environment, instead of indirectly dependent on the environment through the biochemical feedback that occurs in cell motility. Thus, new models of motility in three dimensions will need to account for the effects of explicit individual fibers on cells. This model can also be used to analyze cellular persistence in both mesenchymal and nonmesenchymal motility in complex three-dimensional environments to provide insights into mechanisms of cell motion seen in various cancer cell types in vivo

Clustered Diffusion of Integrins

AbstractWe discuss the diffusion of clusters of integrins (and other similar membrane proteins) on a cell membrane with a cortical cytoskeleton. We argue that protein clusters—in contrast with normal oligomers, which are forced to pass through cytoskeletal barriers all at once—should be treated essentially as many-legged random walkers that can pass through a cytoskeletal barrier by putting one leg at a time through the fence. We present the mathematics that should describe the phenomenon, which result in a two-parameter model of diffusion that should apply to any cluster size. We also perform and discuss numerical simulations of the effect in the erythrocyte model system