Numerical studies of the scattering of light from a two-dimensional randomly rough interface between two dielectric media

The scattering of polarized light incident from one dielectric medium on its two-dimensional randomly rough interface with a second dielectric medium is studied. A reduced Rayleigh equation for the scattering amplitudes is derived for the case where p- or s-polarized light is incident on this interface, with no assumptions being made regarding the dielectric functions of the media. Rigorous, purely numerical, nonperturbative solutions of this equation are obtained. They are used to calculate the reflectivity and reflectance of the interface, the mean differential reflection coefficient, and the full angular distribution of the intensity of the scattered light. These results are obtained for both the case where the medium of incidence is the optically less dense medium, and in the case where it is the optically more dense medium. Optical analogues of the Yoneda peaks observed in the scattering of x-rays from metal surfaces are present in the results obtained in the latter case. Brewster scattering angles for diffuse scattering are investigated, reminiscent of the Brewster angle for flat-interface reflection, but strongly dependent on the angle of incidence. When the contribution from the transmitted field is added to that from the scattered field it is found that the results of these calculations satisfy unitarity with an error smaller than $10^{-4}$.Comment: 25 pages, 14 figure

The DNA-binding domain of human papillomavirus type 18 E1. Crystal structure, dimerization, and DNA binding

High risk types of human papillomavirus, such as type 18 (HPV-18), cause cervical carcinoma, one of the most frequent causes of cancer death in women worldwide. DNA replication is one of the central processes in viral maintenance, and the machinery involved is an excellent target for the design of antiviral therapy. The papillomaviral DNA replication initiation protein E1 has origin recognition and ATP-dependent DNA melting and helicase activities, and it consists of a DNA-binding domain and an ATPase/helicase domain. While monomeric in solution, E1 binds DNA as a dimer. Dimerization occurs via an interaction of hydrophobic residues on a single alpha-helix of each monomer. Here we present the crystal structure of the monomeric HPV-18 E1 DNA-binding domain refined to 1.8-A resolution. The structure reveals that the dimerization helix is significantly different from that of bovine papillomavirus type 1 (BPV-1). However, we demonstrate that the analogous residues required for E1 dimerization in BPV-1 and the low risk HPV-11 are also required for HPV-18 E1. We also present evidence that the HPV-18 E1 DNA-binding domain does not share the same nucleotide and amino acid requirements for specific DNA recognition as BPV-1 and HPV-11 E1

Stringent Nucleotide Recognition by the Ribosome at the Middle Codon Position.

Accurate translation of the genetic code depends on mRNA:tRNA codon:anticodon base pairing. Here we exploit an emissive, isosteric adenosine surrogate that allows direct measurement of the kinetics of codon:anticodon University of California base formation during protein synthesis. Our results suggest that codon:anticodon base pairing is subject to tighter constraints at the middle position than at the 5'- and 3'-positions, and further suggest a sequential mechanism of formation of the three base pairs in the codon:anticodon helix

Recurring questions that sustain the sensemaking frame

Many physics instructors aim to support student sensemaking in their classrooms. However, this can be challenging since instances of sensemaking tend to be short-lived, with students often defaulting to approaches based on answer-making or rote mathematical manipulation. In this study, we present evidence that specific recurring questions can serve a key role in the sensemaking process. Using a case-study of two students discussing an E&M thought experiment, we show how students' entry into sensemaking is marked by the articulation of a particular question, based on a perceived gap or inconsistency in understanding and how this question recurs throughout their subsequent explanations, arguing that these recurrences may serve to stabilize and extend the process.Comment: Accepted to the proceedings of the 2018 Physics Education Research Conferenc