Senescence rates are determined by ranking on the fast-slow life-history continuum

Comparative analyses of survival senescence by using life tables have identified generalizations including the observation that mammals senesce faster than similar-sized birds. These generalizations have been challenged because of limitations of life-table approaches and the growing appreciation that senescence is more than an increasing probability of death. Without using life tables, we examine senescence rates in annual individual fitness using 20 individual-based data sets of terrestrial vertebrates with contrasting life histories and body size. We find that senescence is widespread in the wild and equally likely to occur in survival and reproduction. Additionally, mammals senesce faster than birds because they have a faster life history for a given body size. By allowing us to disentangle the effects of two major fitness components our methods allow an assessment of the robustness of the prevalent life-table approach. Focusing on one aspect of life history - survival or recruitment - can provide reliable information on overall senescence.

From a discrete to a continuum model of cell dynamics in one dimension

Multiscale modeling is emerging as one of the key challenges in mathematical biology. However, the recent rapid increase in the number of modeling methodologies being used to describe cell populations has raised a number of interesting questions. For example, at the cellular scale, how can the appropriate discrete cell-level model be identified in a given context? Additionally, how can the many phenomenological assumptions used in the derivation of models at the continuum scale be related to individual cell behavior? In order to begin to address such questions, we consider a discrete one-dimensional cell-based model in which cells are assumed to interact via linear springs. From the discrete equations of motion, the continuous Rouse [P. E. Rouse, J. Chem. Phys. 21, 1272 (1953)] model is obtained. This formalism readily allows the definition of a cell number density for which a nonlinear "fast" diffusion equation is derived. Excellent agreement is demonstrated between the continuum and discrete models. Subsequently, via the incorporation of cell division, we demonstrate that the derived nonlinear diffusion model is robust to the inclusion of more realistic biological detail. In the limit of stiff springs, where cells can be considered to be incompressible, we show that cell velocity can be directly related to cell production. This assumption is frequently made in the literature but our derivation places limits on its validity. Finally, the model is compared with a model of a similar form recently derived for a different discrete cell-based model and it is shown how the different diffusion coefficients can be understood in terms of the underlying assumptions about cell behavior in the respective discrete models.

A continuum receptor model of hepatic lipoprotein metabolism

A mathematical model describing the uptake of low density lipoprotein (LDL) and very low density lipoprotein (VLDL) particles by a single hepatocyte cell is formulated and solved. The model includes a description of the dynamic change in receptor density on the surface of the cell due to the binding and dissociation of the lipoprotein particles, the subsequent internalisation of bound particles, receptors and unbound receptors, the recycling of receptors to the cell surface, cholesterol dependent de novo receptor formation by the cell and the effect that particle uptake has on the cell's overall cholesterol content. The effect that blocking access to LDL receptors by VLDL, or internalisation of VLDL particles containing different amounts of apolipoprotein E (we will refer to these particles as VLDL-2 and VLDL-3) has on LDL uptake is explored. By comparison with experimental data we find that measures of cell cholesterol content are important in differentiating between the mechanisms by which VLDL is thought to inhibit LDL uptake. We extend our work to show that in the presence of both types of VLDL particle (VLDL-2 and VLDL-3), measuring relative LDL uptake does not allow differentiation between the results of blocking and internalisation of each VLDL particle to be made. Instead by considering the intracellular cholesterol content it is found that internalisation of VLDL-2 and VLDL-3 leads to the highest intracellular cholesterol concentration. A sensitivity analysis of the model reveals that binding, unbinding and internalisation rates, the fraction of receptors recycled and the rate at which the cholesterol dependent free receptors are created by the cell have important implications for the overall uptake dynamics of either VLDL or LDL particles and subsequent intracellular cholesterol concentration. (C) 2008 Elsevier Ltd. All rights reserved.

Selectivity of bis(calix[4]diquinone) ionophores towards metal ions in solvent dimethylsulfoxide: a molecular mechanics and molecular dynamics study

Molecular modelling studies have been carried out on two bis(calix[4]diqu(inone) ionophores, each created from two (calix[4]diquinone)arenes bridged at their bottom rims via alkyl chains (CH2)(n), 1: n = 3, 2; n = 4, in order to understand the reported selectivity of these ligands towards different sized metal ions such as Na+, K+, Rb+, and Cs+ in dmso solution. Conformational. analyses have been carried out which show that in the lowest energy conformations of the two macrocycles, the individual calix[4]diquinones exhibit a combination of partial cone, 1,3-alternate and cone conformations. The interactions of these alkali metals with the macrocycles have been studied in the gas phase and in a periodic box of solvent dmso by molecular mechanics and molecular dynamics calculations. Molecular mechanics calculations have been carried out on the mode of entry of the ions into the macrocycles and suggest that this is likely to occur from the side of the central cavity, rather than through the main axis of the calix[4]diquinones. There are energy barriers of ca. 19 kcal mol(-1) for this entry path in the gas phase, but in solution no energy barrier is found. Molecular dynamics simulations show that in both 1 and 2, though particularly in the latter macrocycle, one or two solvent molecules are bonded to the metal throughout the course of the simulation, often to the exclusion, of one or more of the ether oxygen atoms. By contrast the carbonyl oxygen atoms remain bonded to the metal atoms throughout with bond lengths that remain significantly less than those to the ether oxygen atoms. Free energy perturbation studies have been carried out in dmso and indicate that for 1, the selectivity follows the order Rb+ approximate to K+ > Cs+ >> Na+, which is partially in agreement with the experimental results. The energy differences are small and indeed the ratio between stability constants found for Cs+ and K+ complexes is only 0.60, showing that 1 has only a slight preference for K+. For the larger receptor 2, which is better suited to metal complexation, the binding affinity follows the pattern Cs+ >> Rb+ >> K+ >> Na+, with energy differences of 5.75, 2.61, 2.78 kcal mol(-1) which is perfectly consistent with experimental results.

Quantum mechanics studies of the tautomers of dlhydrodiacetylformoin, an important Maillard intermediate and the synthesis of furaneol

Conformational analyses have been carried out on the acyclic and cyclic forms of dihydrodiacetylformoin, an important Maillard intermediate and precursor for furaneol. For the acyclic forms, the 2,5-dicarbonyl isomers have the lowest energy, while for the cyclic forms, the 3-carbonyl are favoured over the 4-carbonyl isomers. The likely path for cyclisation is investigated and it is shown that the favoured path is dependent upon the relative chiralities of the carbon atoms and in particular that the reaction proceeds more readily if C2 and C3 have different chiralities. After cyclisation, the reaction path to produce furaneol proceeds via the loss of a water molecule. This reaction has been studied with a model including two water molecules and a hydroxide anion and shows relatively low-energy barriers. (C) 2008 Published by Elsevier B.V.

Modelling metal cutting using modern ductile fracture mechanics: Quantitative explanations for some longstanding problems

The assumption that negligible work is involved in the formation of new surfaces in the machining of ductile metals, is re-examined in the light of both current Finite Element Method (FEM) simulations of cutting and modern ductile fracture mechanics. The work associated with separation criteria in FEM models is shown to be in the kJ/m2 range rather than the few J/m2 of the surface energy (surface tension) employed by Shaw in his pioneering study of 1954 following which consideration of surface work has been omitted from analyses of metal cutting. The much greater values of surface specific work are not surprising in terms of ductile fracture mechanics where kJ/m2 values of fracture toughness are typical of the ductile metals involved in machining studies. This paper shows that when even the simple Ernst–Merchant analysis is generalised to include significant surface work, many of the experimental observations for which traditional ‘plasticity and friction only’ analyses seem to have no quantitative explanation, are now given meaning. In particular, the primary shear plane angle φ becomes material-dependent. The experimental increase of φ up to a saturated level, as the uncut chip thickness is increased, is predicted. The positive intercepts found in plots of cutting force vs. depth of cut, and in plots of force resolved along the primary shear plane vs. area of shear plane, are shown to be measures of the specific surface work. It is demonstrated that neglect of these intercepts in cutting analyses is the reason why anomalously high values of shear yield stress are derived at those very small uncut chip thicknesses at which the so-called size effect becomes evident. The material toughness/strength ratio, combined with the depth of cut to form a non-dimensional parameter, is shown to control ductile cutting mechanics. The toughness/strength ratio of a given material will change with rate, temperature, and thermomechanical treatment and the influence of such changes, together with changes in depth of cut, on the character of machining is discussed. Strength or hardness alone is insufficient to describe machining. The failure of the Ernst–Merchant theory seems less to do with problems of uniqueness and the validity of minimum work, and more to do with the problem not being properly posed. The new analysis compares favourably and consistently with the wide body of experimental results available in the literature. Why considerable progress in the understanding of metal cutting has been achieved without reference to significant surface work is also discussed.

An investigation into the mechanics of cutting using data from orthogonally cutting Nylon 66

Cutting force data for Nylon 66 has been examined in terms of various different models of cutting. Theory that includes significant work of separation at the tool tip was found to give the best correlation with experimental data over a wide range of rake angles for derived primary shear plane angle. A fracture toughness parameter was used as the measure of the specific work of separation. Variation in toughness with rake angle determined from cutting is postulated to be caused by mixed mode separation at the tool tip. A rule of mixtures using independently determined values of toughness in tension (mode 1) and shear (mode 11) is found to describe well the variation with rake angle. The ratio of modes varies with rake angle and, in turn, with the primary shear plane angle. Previous suggestions that cutting is a means of experimentally determining fracture toughness are now seen to be extended to identify the mode of fracture toughness as well.

Quantum mechanics studies of the tautomers of diacetylformoin, an important maillard product and odorant

Diacetylformoin (3,4-dihydroxy-3-hexene-2,5-dione) has 16 tautomers, many with several possible conformations and all have been geometry optimised using quantum mechanics at the HF/6-31+G* level. Eleven structures have been identified with energies within 10 kcal mol(-1) of the minimum energy structure. Of these eight are acyclic and three cyclic. Calculations of NMR spectra have clarified the identity of the acyclic and cyclic structures found experimentally. The mechanism for cyclisation has been investigated and transition states obtained. The lowest energy reaction path requires the loss and gain of a proton during cyclisation. (c) 2006 Elsevier B.V. All rights reserved.

Laboratory measurements of the water vapor continuum in the 1200–8000 cm−1 region between 293 K and 351 K

Laboratory Fourier transform spectroscopy of pure water vapor and water vapor mixed with air has been conducted between 1200 and 8000 cm−1 and at temperatures between 293 and 351 K with the purpose of detecting and characterizing the water vapor continuum. The spectral features of the continuum within the major water absorption bands are presented and compared where possible to those from previous experimental studies and to the commonly used MT_CKD and CKD models. It was observed that in the main, both models adequately capture the general spectral form of the continuum; however, there were a number of exceptions. Overall, there is no evidence to indicate that MT_CKD is an improvement upon the older CKD model in these spectral regions. There was generally good agreement between our results and those of other experimental investigators. The general mathematical forms of the self-continuum temperature dependence, given by both Roberts et al. (1976) and CKD/MT_CKD, fit well to the experimental continuum in these spectral regions. However, the range of temperatures over which we made measurements is not sufficient to discriminate between these two forms or to exclude the possibility of other forms of temperature dependence being more appropriate. At the same time, the actual parameters currently used in CKD/MT_CKD to describe the temperature dependence in many spectral regions cannot reproduce the observed strong spectral variation in the temperature dependence. It has not been possible to make definitive conclusions about the magnitude of the continuum absorption in the far wings of the absorption bands investigated here.

Whither tube theory: From believing to measuring

This short contribution examines the difficulties that have not yet been fully overcome in the many developments made from the simplest (and original) tube model for entangled polymers. It is concluded that many more length scales have to be considered sequentially when deriving a continuum rheological model from molecular considerations than have been considered in the past. In particular, most unresolved issues of the tube theory are related to the length scales of tube diameter, and molecular dynamics simulations is the perfect route to resolve them. The power of molecular simulations is illustrated by two examples: stress contributions from bonded and non-bonded interaction, and the inter-chain coupling, which is usually neglected in the tube theory.

On the use of geometric moments to examine the continuum of sudden stratospheric warmings

The polar winter stratospheric vortex is a coherent structure that undergoes different types of deformation that can be revealed by the geometric invariant moments. Three moments are used—the aspect ratio, the centroid latitude, and the area of the vortex based on stratospheric data from the 40-yr ECMWF Re-Analysis (ERA-40) project—to study sudden stratospheric warmings. Hierarchical clustering combined with data image visualization techniques is used as well. Using the gap statistic, three optimal clusters are obtained based on the three geometric moments considered here. The 850-K potential vorticity field, as well as the vertical profiles of polar temperature and zonal wind, provides evidence that the clusters represent, respectively, the undisturbed (U), displaced (D), and split (S) states of the polar vortex. This systematic method for identifying and characterizing the state of the polar vortex using objective methods is useful as a tool for analyzing observations and as a test for climate models to simulate the observations. The method correctly identifies all previously identified major warmings and also identifies significant minor warmings where the atmosphere is substantially disturbed but does not quite meet the criteria to qualify as a major stratospheric warming.