Extracting chemical energy by growing disorder: Efficiency at maximum power

We consider the efficiency of chemical energy extraction from the environment by the growth of a copolymer made of two constituent units in the entropy-driven regime. We show that the thermodynamic nonlinearity associated with the information processing aspect is responsible for a branching of the system properties such as power, speed of growth, entropy production, and efficiency, with varying affinity. The standard linear thermodynamics argument which predicts an efficiency of 1/2 at maximum power is inappropriate because the regime of maximum power is located either outside of the linear regime or on a separate bifurcated branch, and because the usual thermodynamic force is not the natural variable for this optimization.Comment: 6 pages, 4 figure

Solitons in the Yakushevich model of DNA beyond the contact approximation

The Yakushevich model of DNA torsion dynamics supports soliton solutions, which are supposed to be of special interest for DNA transcription. In the discussion of the model, one usually adopts the approximation $\ell_0 \to 0$, where $\ell_0$ is a parameter related to the equilibrium distance between bases in a Watson-Crick pair. Here we analyze the Yakushevich model without $\ell_0 \to 0$. The model still supports soliton solutions indexed by two winding numbers $(n,m)$; we discuss in detail the fundamental solitons, corresponding to winding numbers (1,0) and (0,1) respectively

The Genetic Code as a Periodic Table: Algebraic Aspects

The systematics of indices of physico-chemical properties of codons and amino acids across the genetic code are examined. Using a simple numerical labelling scheme for nucleic acid bases, data can be fitted as low-order polynomials of the 6 coordinates in the 64-dimensional codon weight space. The work confirms and extends recent studies by Siemion of amino acid conformational parameters. The connections between the present work, and recent studies of the genetic code structure using dynamical symmetry algebras, are pointed out.Comment: 26 pages Latex, 10 figures (4 ps, 6 Tex). Refereed version, small changes to discussion (conclusion unaltered). Minor alterations to format of figures and tables. To appear in BioSystem

Casimir-Polder interaction between an atom and a small magnetodielectric sphere

On the basis of macroscopic quantum electrodynamics and point-scattering techniques, we derive a closed expression for the Casimir-Polder force between a ground-state atom and a small magnetodielectric sphere in an arbitrary environment. In order to allow for the presence of both bodies and media, local-field corrections are taken into account. Our results are compared with the known van der Waals force between two ground-state atoms. To continuously interpolate between the two extreme cases of a single atom and a macroscopic sphere, we also derive the force between an atom and a sphere of variable radius that is embedded in an Onsager local-field cavity. Numerical examples illustrate the theory.Comment: 9 pages, 4 figures, minor addition

Twist solitons in complex macromolecules: from DNA to polyethylene

DNA torsion dynamics is essential in the transcription process; simple models for it have been proposed by several authors, in particular Yakushevich (Y model). These are strongly related to models of DNA separation dynamics such as the one first proposed by Peyrard and Bishop (and developed by Dauxois, Barbi, Cocco and Monasson among others), but support topological solitons. We recently developed a ``composite'' version of the Y model, in which the sugar-phosphate group and the base are described by separate degrees of freedom. This at the same time fits experimental data better than the simple Y model, and shows dynamical phenomena, which are of interest beyond DNA dynamics. Of particular relevance are the mechanism for selecting the speed of solitons by tuning the physical parameters of the non linear medium and the hierarchal separation of the relevant degrees of freedom in ``master'' and ``slave''. These mechanisms apply not only do DNA, but also to more general macromolecules, as we show concretely by considering polyethylene.Comment: New version substantially longer, with new applications to Polyethylene. To appear in "International Journal of Non-Linear Mechanics

Quantum mechanical calculation of the effects of stiff and rigid constraints in the conformational equilibrium of the Alanine dipeptide

If constraints are imposed on a macromolecule, two inequivalent classical models may be used: the stiff and the rigid one. This work studies the effects of such constraints on the Conformational Equilibrium Distribution (CED) of the model dipeptide HCO-L-Ala-NH2 without any simplifying assumption. We use ab initio Quantum Mechanics calculations including electron correlation at the MP2 level to describe the system, and we measure the conformational dependence of all the correcting terms to the naive CED based in the Potential Energy Surface (PES) that appear when the constraints are considered. These terms are related to mass-metric tensors determinants and also occur in the Fixman's compensating potential. We show that some of the corrections are non-negligible if one is interested in the whole Ramachandran space. On the other hand, if only the energetically lower region, containing the principal secondary structure elements, is assumed to be relevant, then, all correcting terms may be neglected up to peptides of considerable length. This is the first time, as far as we know, that the analysis of the conformational dependence of these correcting terms is performed in a relevant biomolecule with a realistic potential energy function.Comment: 37 pages, 4 figures, LaTeX, BibTeX, AMSTe

Efficient Priority Rules

We study the assignment of indivisible objects with quotas (houses, jobs, or offices) to a set of agents (students, job applicants, or professors). Each agent receives at most one object and monetary compensations are not possible. We characterize efficient priority rules by efficiency, strategy-proofness, and renegotiation-proofness. Such a rule respects an acyclical priority structure and the allocations can be determined using the deferred acceptance algorithm.L. Ehlers gratefully acknowledges financial support from the SSHRC (Canada). B. Klaus's research was partly supported by a Ramón y Cajal contract and Research Grant BEC2002-02130 from the Spanish Ministerio de Ciencia y Tecnología and by the Barcelona Economics Program of CREA

Volumetry improves the assessment of the vestibular aqueduct size in inner ear malformation

Objectives: Enlarged vestibular aqueduct (EVA) is a common finding associated with inner ear malformations (IEM). However, uniform radiologic definitions for EVA are missing and various 2D-measurement methods to define EVA have been reported. This study evaluates VA volume in different types of IEM and compares 3D-reconstructed VA volume to 2D-measurements. Methods: A total of 98 high-resolution CT (HRCT) data sets from temporal bones were analyzed (56 with IEM; [cochlear hypoplasia (CH; n = 18), incomplete partition type I (IPI; n = 12) and type II (IPII; n = 11) and EVA (n = 15)]; 42 controls). VA diameter was measured in axial images. VA volume was analyzed by software-based, semi-automatic segmentation and 3D-reconstruction. Differences in VA volume between the groups and associations between VA volume and VA diameter were assessed. Inter-rater-reliability (IRR) was assessed using the intra-class-correlation-coefficient (ICC). Results: Larger VA volumes were found in IEM compared to controls. Significant differences in VA volume between patients with EVA and controls (p < 0.001) as well as between IPII and controls (p < 0.001) were found. VA diameter at the midpoint (VA midpoint) and at the operculum (VA operculum) correlated to VA volume in IPI (VA midpoint: r = 0.78, VA operculum: r = 0.91), in CH (VA midpoint: r = 0.59, VA operculum: r = 0.61), in EVA (VA midpoint: r = 0.55, VA operculum: r = 0.66) and in controls (VA midpoint: r = 0.36, VA operculum: r = 0.42). The highest IRR was found for VA volume (ICC = 0.90). Conclusions: The VA diameter may be an insufficient estimate of VA volume, since (1) measurement of VA diameter does not reliably correlate with VA volume and (2) VA diameter shows a lower IRR than VA volume. 3D-reconstruction and VA volumetry may add information in diagnosing EVA in cases with or without additional IEM. Keywords: 3D segmentation; Cochlear malformation; Diagnosis; Inner ear malformation; Volum

One-phonon coherent neutron scattering from certain polycrystalline materials

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/32012/1/0000054.pd