Comment on 'Non-equilibrium thermodynamics of light absorption'

A recent paper by Meszéna and Westerhoff (1999 J. Phys. A: Math. Gen. 32 301) has aimed to address what is referred to as a principal question of biological thermodynamics, the possibility of describing photosynthesis in terms of non-equilibrium thermodynamics. The issue is associated with a misrepresentation of the fundamental photophysics involved, and as a result the analysis is invalid

Study and development of acoustic treatment for jet engine tailpipes

A study and development program was accomplished to attenuate turbine noise generated in the JT3D turbofan engine. Analytical studies were used to design an acoustic liner for the tailpipe. Engine ground tests defined the tailpipe environmental factors and laboratory tests were used to support the analytical studies. Furnace-brazed, stainless steel, perforated sheet acoustic liners were designed, fabricated, installed, and ground tested in the tailpipe of a JT3D engine. Test results showed the turbine tones were suppressed below the level of the jet exhaust for most far field polar angles

Encounter complexes and dimensionality reduction in protein-protein association

An outstanding challenge has been to understand the mechanism whereby proteins associate. We report here the results of exhaustively sampling the conformational space in protein–protein association using a physics-based energy function. The agreement between experimental intermolecular paramagnetic relaxation enhancement (PRE) data and the PRE profiles calculated from the docked structures shows that the method captures both specific and non-specific encounter complexes. To explore the energy landscape in the vicinity of the native structure, the nonlinear manifold describing the relative orientation of two solid bodies is projected onto a Euclidean space in which the shape of low energy regions is studied by principal component analysis. Results show that the energy surface is canyon-like, with a smooth funnel within a two dimensional subspace capturing over 75% of the total motion. Thus, proteins tend to associate along preferred pathways, similar to sliding of a protein along DNA in the process of protein-DNA recognition

Part of the D - dimensional Spiked harmonic oscillator spectra

The pseudoperturbative shifted - l expansion technique PSLET [5,20] is generalized for states with arbitrary number of nodal zeros. Interdimensional degeneracies, emerging from the isomorphism between angular momentum and dimensionality of the central force Schrodinger equation, are used to construct part of the D - dimensional spiked harmonic oscillator bound - states. PSLET results are found to compare excellenly with those from direct numerical integration and generalized variational methods [1,2].Comment: Latex file, 20 pages, to appear in J. Phys. A: Math. & Ge

d-Dimensional generalization of the point canonical transformation for a quantum particle with position-dependent mass

The d-dimensional generalization of the point canonical transformation for a quantum particle endowed with a position-dependent mass in Schrodinger equation is described. Illustrative examples including; the harmonic oscillator, Coulomb, spiked harmonic, Kratzer, Morse oscillator, Poschl-Teller and Hulthen potentials are used as reference potentials to obtain exact energy eigenvalues and eigenfunctions for target potentials at different position-dependent mass settings.Comment: 14 pages, no figures, to appear in J. Phys. A: Math. Ge

Topology and energy transport in networks of interacting photosynthetic complexes

We address the role of topology in the energy transport process that occurs in networks of photosynthetic complexes. We take inspiration from light harvesting networks present in purple bacteria and simulate an incoherent dissipative energy transport process on more general and abstract networks, considering both regular structures (Cayley trees and hyperbranched fractals) and randomly-generated ones. We focus on the the two primary light harvesting complexes of purple bacteria, i.e., the LH1 and LH2, and we use network-theoretical centrality measures in order to select different LH1 arrangements. We show that different choices cause significant differences in the transport efficiencies, and that for regular networks centrality measures allow to identify arrangements that ensure transport efficiencies which are better than those obtained with a random disposition of the complexes. The optimal arrangements strongly depend on the dissipative nature of the dynamics and on the topological properties of the networks considered, and depending on the latter they are achieved by using global vs. local centrality measures. For randomly-generated networks a random arrangement of the complexes already provides efficient transport, and this suggests the process is strong with respect to limited amount of control in the structure design and to the disorder inherent in the construction of randomly-assembled structures. Finally, we compare the networks considered with the real biological networks and find that the latter have in general better performances, due to their higher connectivity, but the former with optimal arrangements can mimic the real networks' behaviour for a specific range of transport parameters. These results show that the use of network-theoretical concepts can be crucial for the characterization and design of efficient artificial energy transport networks.Comment: 14 pages, 16 figures, revised versio

Spiked oscillators: exact solution

A procedure to obtain the eigenenergies and eigenfunctions of a quantum spiked oscillator is presented. The originality of the method lies in an adequate use of asymptotic expansions of Wronskians of algebraic solutions of the Schroedinger equation. The procedure is applied to three familiar examples of spiked oscillators

The Structure of Barium in the hcp Phase Under High Pressure

Recent experimental results on two hcp phases of barium under high pressure show interesting variation of the lattice parameters. They are here interpreted in terms of electronic structure calculation by using the LMTO method and generalized pseudopotential theory (GPT) with a NFE-TBB approach. In phase II the dramatic drop in c/a is an instability analogous to that in the group II metals but with the transfer of s to d electrons playing a crucial role in Ba. Meanwhile in phase V, the instability decrease a lot due to the core repulsion at very high pressure. PACS numbers: 62.50+p, 61.66Bi, 71.15.Ap, 71.15Hx, 71.15LaComment: 29 pages, 8 figure

Dislocation interactions mediated by grain boundaries

The dynamics of dislocation assemblies in deforming crystals indicate the emergence of collective phenomena, intermittent fluctuations and strain avalanches. In polycrystalline materials, the understanding of plastic deformation mechanisms depends on grasping the role of grain boundaries on dislocation motion. Here the interaction of dislocations and elastic, low angle grain boundaries is studied in the framework of a discrete dislocation representation. We allow grain boundaries to deform under the effect of dislocation stress fields and compare the effect of such a perturbation to the case of rigid grain boudaries. We are able to determine, both analytically and numerically, corrections to dislocation stress fields acting on neighboring grains, as mediated by grain boundary deformation. Finally, we discuss conclusions and consequences for the avalanche statistics, as observed in polycrystalline samples.Comment: 13 pages, 5 figure

Hemoglobin genotype has minimal influence on the physiological response of juvenile atlantic cod (Gadus morhua) to environmental challenges

Hemoglobin (Hb) polymorphism in cod is associated with temperature‐related differences in biogeographical distribution, and several authors have suggested that functional characteristics of the various hemoglobin isoforms (HbIs) directly influence phenotypic traits such as growth rate. However, no study has directly examined whether Hb genotype translates into physiological differences at the whole animal level. Thus, we generated a family of juvenile Atlantic cod consisting of all three main Hb genotypes (HbI‐1/1, HbI‐2/2, and HbI‐1/2) by crossing a single pair of heterozygous parents, and we compared their metabolic and cortisol responses to an acute thermal challenge (10&deg;C to their critical thermal maximum [CTM] or 22&deg;C, respectively) and tolerance of graded hypoxia. There were no differences in routine metabolism (at 10&deg;C), maximum metabolic rate, metabolic scope, CTM (overall mean 22.9&deg; &plusmn; 0.2&deg;C), or resting and poststress plasma cortisol levels among Hb genotypes. Further, although the HbI‐1/1 fish grew more (by 15%&ndash;30% during the first 9 mo) when reared at 10&deg; &plusmn; 1&deg;C and had a slightly enhanced hypoxia tolerance at 10&deg;C (e.g., the critical O2 levels for HbI‐1/1, HbI‐2/2, and HbI‐1/2 cod were 35.56% &plusmn; 1.24%, and 40.20% &plusmn; 1.99% air saturation, respectively), these results are contradictory to expectations based on HbI functional properties. Thus, our findings (1) do not support previous assumptions that growth rate differences among cod Hb genotypes result from a more efficient use of the oxygen supply&mdash;that is, reduced standard metabolic rates and/or increased metabolic capacity&mdash;and (2) suggest that in juvenile cod, there is no selective advantage to having a particular Hb genotype with regards to the capacity to withstand ecologically relevant environmental challenges.<br /