Characterization of Knots and Links Arising From Site-specific Recombination on Twist Knots

We develop a model characterizing all possible knots and links arising from recombination starting with a twist knot substrate, extending previous work of Buck and Flapan. We show that all knot or link products fall into three well-understood families of knots and links, and prove that given a positive integer $n$, the number of product knots and links with minimal crossing number equal to $n$ grows proportionally to $n^5$. In the (common) case of twist knot substrates whose products have minimal crossing number one more than the substrate, we prove that the types of products are tightly prescribed. Finally, we give two simple examples to illustrate how this model can help determine previously uncharacterized experimental data.Comment: 32 pages, 7 tables, 27 figures, revised: figures re-arranged, and minor corrections. To appear in Journal of Physics

Single-step method for β-galactosidase assays in Escherichia coli using a 96-well microplate reader

AbstractHistorically, the lacZ gene is one of the most universally used reporters of gene expression in molecular biology. Its activity can be quantified using an artificial substrate, o-nitrophenyl-ß-d-galactopyranoside (ONPG). However, the traditional method for measuring LacZ activity (first described by J. H. Miller in 1972) can be challenging for a large number of samples, is prone to variability, and involves hazardous compounds for lysis (e.g., chloroform, toluene).Here we describe a single-step assay using a 96-well microplate reader with a proven alternative cell permeabilization method. This modified protocol reduces handling time by 90%

Documentation of the data analysis system for the gamma ray monitor aboard OSO-H

The programming system is presented which was developed to prepare the data from the gamma ray monitor on OSO-7 for scientific analysis. The detector, data, and objectives are described in detail. Programs presented include; FEEDER, PASS-1, CAL1, CAL2, PASS-3, Van Allen Belt Predict Program, Computation Center Plot Routine, and Response Function Programs

Topographic controls on dike injection in volcanic rift zones

Author Posting. © Elsevier B.V., 2006. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Earth and Planetary Science Letters 246 (2006): 188-196, doi:10.1016/j.epsl.2006.04.005.Dike emplacement in volcanic rift zones is often associated with the injection of “bladelike” dikes, which propagate long distances parallel to the rift, but frequently remain trapped at depth and erupt only near the tip of the dike. Over geologic time, this style of dike injection implies that a greater percentage of extension is accommodated by magma accretion at depth than near the surface. In this study, we investigate the evolution of faulting, topography, and stress state in volcanic rift zones using a kinematic model for dike injection in an extending 2-D elastic-viscoplastic layer. We show that the intrusion of blade-like dikes focuses deformation at the rift axis, leading to the formation of an axial rift valley. However, flexure associated with the development of the rift topography generates compression at the base of the plate. If the magnitude of these deviatoric compressive stresses exceeds the deviatoric tensile stress associated with far-field extension, further dike injection will be inhibited. In general, this transition from tensile to compressive deviatoric stresses occurs when the rate of accretion in the lower crust is greater than 50-60% of the far-field extension rate. These results indicate that over geologic time-scales the injection of blade-like dikes is a self-limiting process in which dike-generated faulting and topography result in an efficient feedback mechanism that controls the time-averaged distribution of magma accretion within the crust.Funding for this research was provided by NSF Grants OCE 04-43246, OCE 05-50147, OCE 02-42597 and OCE 04-26575, and a Carnegie Postdoctoral Fellowship to M.B

A data comparison between a traditional and the single-step β-galactosidase assay

This article describes reproducibility of a single-step automated β-galactosidase, and the equivalence of its data to the traditional assay ("Experiments in Molecular Genetics" [1]). This was done via a pairwise comparison of both methods using strains with Miller Unit [MU] values ranging from 0 to over 2000. The data presented in this article is associated with the research article entitled "A single-step method for mid to high throughput β-galactosidase assays in Escherichia coli using a microplate reader" [2]

Cellular and molecular phenotypes depending upon the RNA repair system RtcAB of Escherichia coli

Biotechnology and Biological Sciences Research Council (BBSRC) [BB/J00717X/1]; Medical Research Council (MRC) [MR/M017672/1]; Queen's Fellowship (Queen's University Belfast, UK) (to C.E.); Antimicrobial Resistance Cross Council Initiative. Funding for open access charge: BBSRC [BB/J00717X/1]; MRC [MR/M017672/1]

Information and Particle Physics

Information measures for relativistic quantum spinors are constructed to satisfy various postulated properties such as normalisation invariance and positivity. Those measures are then used to motivate generalised Lagrangians meant to probe shorter distance physics within the maximum uncertainty framework. The modified evolution equations that follow are necessarily nonlinear and simultaneously violate Lorentz invariance, supporting previous heuristic arguments linking quantum nonlinearity with Lorentz violation. The nonlinear equations also break discrete symmetries. We discuss the implications of our results for physics in the neutrino sector and cosmology

Bremsstrahlung in Alpha-Decay

We present the first fully quantum mechanical calculation of photon radiation accompanying charged particle decay from a barrier resonance. The soft-photon limit agrees with the classical results, but differences appear at next-to-leading-order. Under the conditions of alpha-decay of heavy nuclei, the main contribution to the photon emission stems from Coulomb acceleration and may be computed analytically. We find only a small contribution from the tunneling wave function under the barrier.Comment: 12 pages, 2 Postscript figure

Possible production of exotic baryonia in relativistic heavy-ion collisions

Properties of a hypothetical baryonium with the quark content (uds\ov{u}\ov{d}\ov{s}) are discussed. The MIT bag model predicts its mass to be unexpectedly low, approximately 1210 MeV. Possible hadronic decay modes of this state are analyzed. Ultrarelativistic heavy-ion collisions provide favorable conditions for the formation of such particles from the baryon-free quark-gluon plasma. We estimate multiplicities of such exotic baryonia on the basis of a simple thermal model.Comment: 8 pages, 1 figur