Which way up? Recognition of homologous DNA segments in parallel and antiparallel alignment

Homologous gene shuffling between DNA promotes genetic diversity and is an important pathway for DNA repair. For this to occur, homologous genes need to find and recognize each other. However, despite its central role in homologous recombination, the mechanism of homology recognition is still an unsolved puzzle. While specific proteins are known to play a role at later stages of recombination, an initial coarse grained recognition step has been proposed. This relies on the sequence dependence of the DNA structural parameters, such as twist and rise, mediated by intermolecular interactions, in particular electrostatic ones. In this proposed mechanism, sequences having the same base pair text, or are homologous, have lower interaction energy than those sequences with uncorrelated base pair texts; the difference termed the recognition energy. Here, we probe how the recognition energy changes when one DNA fragment slides past another, and consider, for the first time, homologous sequences in antiparallel alignment. This dependence on sliding was termed the recognition well. We find that there is recognition well for anti-parallel, homologous DNA tracts, but only a very shallow one, so that their interaction will differ little from the interaction between two nonhomologous tracts. This fact may be utilized in single molecule experiments specially targeted to test the theory. As well as this, we test previous theoretical approximations in calculating the recognition well for parallel molecules against MC simulations, and consider more rigorously the optimization of the orientations of the fragments about their long axes. The more rigorous treatment affects the recognition energy a little, when the molecules are considered rigid. However when torsional flexibility of the DNA molecules is introduced, we find excellent agreement between analytical approximation and simulation.Comment: Paper with supplemental material attached. 41 pages in all, 4 figures in main text, 3 figures in supplmental. To be submitted to Journa

An analysis of type F2 software measurement standards for profile surface texture parameters

This paper reports on an in-depth analysis of ISO 5436 part 2 type F2 reference software for the calculation of profile surface texture parameters that has been performed on the input, implementation and output results of the reference software developed by the National Physical Laboratory (NPL), the National Institute of Standards and Technology (NIST) and Physikalisch-Technische Bundesanstalt (PTB). Surface texture parameters have been calculated for a selection of 17 test data files obtained from the type F1 reference data sets on offer from NPL and NIST. The surface texture parameter calculation results show some disagreements between the software methods of the National Metrology Institutes. These disagreements have been investigated further, and some potential explanations are given

Intelligent sampling for the measurement of structured surfaces

Uniform sampling in metrology has known drawbacks such as coherent spectral aliasing and a lack of efficiency in terms of measuring time and data storage. The requirement for intelligent sampling strategies has been outlined over recent years, particularly where the measurement of structured surfaces is concerned. Most of the present research on intelligent sampling has focused on dimensional metrology using coordinate-measuring machines with little reported on the area of surface metrology. In the research reported here, potential intelligent sampling strategies for surface topography measurement of structured surfaces are investigated by using numerical simulation and experimental verification. The methods include the jittered uniform method, low-discrepancy pattern sampling and several adaptive methods which originate from computer graphics, coordinate metrology and previous research by the authors. By combining the use of advanced reconstruction methods and feature-based characterization techniques, the measurement performance of the sampling methods is studied using case studies. The advantages, stability and feasibility of these techniques for practical measurements are discussed

Unitary relations in time-dependent harmonic oscillators

For a harmonic oscillator with time-dependent (positive) mass and frequency, an unitary operator is shown to transform the quantum states of the system to those of a harmonic oscillator system of unit mass and time-dependent frequency, as well as operators. For a driven harmonic oscillator, it is also shown that, there are unitary transformations which give the driven system from the system of same mass and frequency without driving force. The transformation for a driven oscillator depends on the solution of classical equation of motion of the driven system. These transformations, thus, give a simple way of finding exact wave functions of a driven harmonic oscillator system, provided the quantum states of the corresponding system of unit mass are given.Comment: Submitted to J. Phys.

A dynamical system approach to higher order gravity

The dynamical system approach has recently acquired great importance in the investigation on higher order theories of gravity. In this talk I review the main results and I give brief comments on the perspectives for further developments.Comment: 6 pages, 1 figure, 2 tables, talk given at IRGAC 2006, July 200

Enhancement of superhorizon scale inflationary curvature perturbations

We show that there exists a simple mechanism which can enhance the amplitude of curvature perturbations on superhorizon scales during inflation, relative to their amplitude at horizon crossing. The enhancement may occur even in a single-field inflaton model, and occurs if the quantity $a\dot\phi/H$ becomes sufficiently small, as compared to its value at horizon crossing, for some time interval during inflation. We give a criterion for this enhancement in general single-field inflation models.Comment: 5 pages RevTeX file with 2 figures incorporated v2:Contains important O(k^2) correctio

Shear dynamics in Bianchi I cosmologies with R^n-gravity

We give the equations governing the shear evolution in Bianchi spacetimes for general f(R)-theories of gravity. We consider the case of R^n-gravity and perform a detailed analysis of the dynamics in Bianchi I cosmologies which exhibit local rotational symmetry. We find exact solutions and study their behaviour and stability in terms of the values of the parameter n. In particular, we found a set of cosmic histories in which the universe is initially isotropic, then develops shear anisotropies which approaches a constant value.Comment: 25 pages LaTeX, 6 figures. Revised to match the final version accepted for publication in CQ

Observational constraints on the spectral index of the cosmological curvature perturbation

We evaluate the observational constraints on the spectral index $n$, in the context of the $\Lambda$CDM hypothesis which represents the simplest viable cosmology. We first take $n$ to be practically scale-independent. Ignoring reionization, we find at a nominal 2-$\sigma$ level $n\simeq 1.0 \pm 0.1$. If we make the more realisitic assumption that reionization occurs when a fraction $f\sim 10^{-5}$ to 1 of the matter has collapsed, the 2-$\sigma$ lower bound is unchanged while the 1-$\sigma$ bound rises slightly. These constraints are compared with the prediction of various inflation models. Then we investigate the two-parameter scale-dependent spectral index, predicted by running-mass inflation models, and find that present data allow significant scale-dependence of $n$, which occurs in a physically reasonable regime of parameter space.Comment: ReVTeX, 15 pages, 5 figures and 3 tables, uses epsf.sty Improved treatment of reionization and small bug fixed in the constant n case; more convenient parameterization and better treatment of the n dependence in the CMB anisotropy for the running mass case; conclusions basically unchanged; references adde