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

Large Extra Dimensions from a Small Extra Dimension

Models with extra dimensions have changed our understanding of the hierarchy problem. In general, these models explain the weakness of gravity by diluting gravity in a large bulk volume, or by localizing the graviton away from the standard model. In this paper, we show that the warped geometries necessary for the latter scenario can naturally induce the large volumes necessary for the former. We present a model in which a large volume is stabilized without supersymmetry. We comment on the phenomenology of this scenario and generalizations to additional dimensions.Comment: Some formulae altered, conclusions unchange

Single cell mechanics: stress stiffening and kinematic hardening

Cell mechanical properties are fundamental to the organism but remain poorly understood. We report a comprehensive phenomenological framework for the nonlinear rheology of single fibroblast cells: a superposition of elastic stiffening and viscoplastic kinematic hardening. Our results show, that in spite of cell complexity its mechanical properties can be cast into simple, well-defined rules, which provide mechanical cell strength and robustness via control of crosslink slippage.Comment: 4 pages, 6 figure

Growth and magnetism of self-organized arrays of Fe(110) wires formed by deposition on kinetically grooved W(110)

Homoepitaxy of W(110) and Mo(110) is performed in a kinetically-limited regime to yield a nanotemplate in the form of a uniaxial array of hills and grooves aligned along the [001] direction. The topography and organization of the grooves were studied with RHEED and STM. The nanofacets, of type {210}, are tilted 18° away from (110). The lateral period could be varied from 4 to 12nm by tuning the deposition temperature. Magnetic nanowires were formed in the grooves by deposition of Fe at 150°C on such templates. Fe/W wires display an easy axis along [001] and a mean blocking temperature Tb=100KComment: Proceedings of ECOSS 2006 (Paris

Thermo-mechanic-electrical coupling in phospholipid monolayers near the critical point

Lipid monolayers have been shown to represent a powerful tool in studying mechanical and thermodynamic properties of lipid membranes as well as their interaction with proteins. Using Einstein's theory of fluctuations we here demonstrate, that an experimentally derived linear relationship both between transition entropy S and area A as well as between transition entropy and charge q implies a linear relationships between compressibility \kappa_T, heat capacity c_\pi, thermal expansion coefficient \alpha_T and electric capacity CT. We demonstrate that these couplings have strong predictive power as they allow calculating electrical and thermal properties from mechanical measurements. The precision of the prediction increases as the critical point TC is approached

Production, Decay, and Polarization of Excited Heavy Hadrons

We discuss the production via fragmentation of excited heavy mesons and baryons, and their subsequent decay. In particular, we consider the question of whether a net polarization of the initial heavy quark may be detected, either in a polarization of the final ground state or in anisotropies in the decay products of the excited hadron. The result hinges in part on a nonperturbative parameter which measures the net transverse alignment of the light degrees of freedom in the fragmentation process. We use existing data on charmed mesons to extract this quantity for certain excited mesons. Using this result, we estimate the polarization retention of charm and bottom baryons.Comment: 37 pages, 3 figures available upon request, uses phyzzx forma

New fermions and a vector-like third generation in SU(3)c⊗SU(3)L⊗U(1)NSU(3)_c\otimes SU(3)_L\otimes U(1)_N models

We study two 3-3-1 models with i) five (four) charge 2/3 ($-1/3$) quarks and, ii) four (five) charge 2/3 ($-1/3$) quarks and a vector-like third generation. Possibilities beyond these models are also briefly considered.Comment: 32 pages, Revtex 3.0, no figure

Non-Hermitian Rayleigh-Schroedinger Perturbation Theory

We devise a non-Hermitian Rayleigh-Schroedinger perturbation theory for the single- and the multireference case to tackle both the many-body problem and the decay problem encountered, for example, in the study of electronic resonances in molecules. A complex absorbing potential (CAP) is employed to facilitate a treatment of resonance states that is similar to the well-established bound-state techniques. For the perturbative approach, the full CAP-Schroedinger Hamiltonian, in suitable representation, is partitioned according to the Epstein-Nesbet scheme. The equations we derive in the framework of the single-reference perturbation theory turn out to be identical to those obtained by a time-dependent treatment in Wigner-Weisskopf theory. The multireference perturbation theory is studied for a model problem and is shown to be an efficient and accurate method. Algorithmic aspects of the integration of the perturbation theories into existing ab initio programs are discussed, and the simplicity of their implementation is elucidated.Comment: 10 pages, 1 figure, RevTeX4, submitted to Physical Review

Dynamics of Spreading of Chainlike Molecules with Asymmetric Surface Interactions

In this work we study the spreading dynamics of tiny liquid droplets on solid surfaces in the case where the ends of the molecules feel different interactions with respect to the surface. We consider a simple model of dimers and short chainlike molecules that cannot form chemical bonds with the surface. We use constant temperature Molecular Dynamics techniques to examine in detail the microscopic structure of the time dependent precursor film. We find that in some cases it can exhibit a high degree of local order that can persist even for flexible chains. Our model also reproduces the experimentally observed early and late-time spreading regimes where the radius of the film grows proportional to the square root of time. The ratios of the associated transport coefficients are in good overall agreement with experiments. Our density profiles are also in good agreement with measurements on the spreading of molecules on hydrophobic surfaces.Comment: 12 pages, LaTeX with APS macros, 21 figures available by contacting [email protected], to appear in Phys. Rev.

Inflationary Cosmology: Theory and Phenomenology

This article gives a brief overview of some of the theory behind the inflationary cosmology, and discusses prospects for constraining inflation using observations. Particular care is given to the question of falsifiability of inflation or of subsets of inflationary models.Comment: 11 pages LaTeX file (using iopart) with 4 figures included via EPSF. Article based on a talk presented at ``The Early Universe and Cosmological Observations: a Critical Review'', Cape Town, July 200