Predicting the onset of DNA supercoiling using a non-linear hemitropic elastic rod

Elastic rod models provide a means to interpret single molecule DNA experiments as well as predict DNA behavior under physiological conditions. Here we use an elastic rod model to predict the stability boundary (critical torque vs. applied tension) for single molecule DNA experiments in which the molecule is subjected to applied tension and twist. We discuss the shortcomings of the usual isotropic rod model. We then derive a consistent non-linear material law from the general representation for a hemitropic (chiral) rod. Finally, we present results of a standard bifurcation analysis predicting the stability boundary. We find results from the non-linear hemitropic rod to match the data closely.     

Evolution of the high power THz source program at Jefferson Lab

We report the evolution of the high power THz source program at Jefferson Lab. The source is based on coherent synchrotron radiation in which short bunches of relativistic electrons radiate when traversing a dipolar magnetic field. In our first accelerator we produced 20 W of broadband THz light. Our upgraded accelerator with higher current and improved THz extraction optics will considerably enhance the output power to >100 W. In this paper we describe the source in some detail and present theoretical calculations for the upgrade.     

On subgroups of finite index in compact Hausdorff groups

Let G be a compact Hausdorff group and n a positive integer. It is proved that all subnormal subgroups of G of index dividing n are open if and only if there are only finitely many such subgroups, and that all subgroups of finite index in G are open if and only if there are only countably many such subgroups.     

Synthesis of all diastereomeric methyl 2,5-anhydro-3-deoxy-hexonates: precursors to C-2-deoxynucleosides and THF-templated γ- and δ-amino acids

Efficient syntheses of all diastereomers of methyl 2,5-anhydro-3-deoxy-hexonate from mannono- or gulono-lactones provide precursors for C-nucleosides of 2-deoxyribose and for THF-templated γ- and δ-amino acids.     

Thiol–norbornene materials: Approaches to develop high Tg thiol–ene polymers

The ability to prepare high T_g low shrinkage thiol–ene materials is attractive for applications such as coatings and dental restoratives. However, thiol and nonacrylated vinyl materials typically consist of a flexible backbone, limiting the utility of these polymers. Hence, it is of importance to synthesize and investigate thiol and vinyl materials of varying backbone chemistry and stiffness. Here, we investigate the effect of backbone chemistry and functionality of norbornene resins on polymerization kinetics and glass transition temperature (T_g) for several thiol–norbornene materials. Results indicate that T_gs as high as 94 °C are achievable in thiol–norbornene resins of appropriately controlled chemistry. Furthermore, both the backbone chemistry and the norbornene moiety are important factors in the development of high T_g materials. In particular, as much as a 70 °C increase in T_g was observed in a norbornene–thiol specimen when compared with a sample prepared using allyl ether monomer of analogous backbone chemistry. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 5686–5696, 2007     

A search for fractional electric charge in sea water

The magnetic levitation technique has been used to test for fractional electric charge in sea water, using steel balls coated with sea water residue by evaporation. The objective was to reach concentration levels below 1 g^?1 which might result from cosmic ray interactions. Four stages of increasing sensitivity are reported: (1) residue from direct evaporation of unprocessed sea water, (2) residue from sea water samples enriched by ion exchangen, (3) residue reduced by high temperature evaporation, and (4) hypothetical enrichment by dilution and separation of soluble residue. Stages 1–3 are based on the generally accepted preferential retention of fractional charge during evaporation, but stage 4 limits are subject to uncertainties in the enrichment process. No evidence for fractional charge was found in a total of about 130 samples tested in these four stages. Samples containing positive and negative ions were tested separately, and concentration limits are reported for each of the stages. Levels in the region 0.01–0.1g^?1 were reached in stage 3, and 0.001 g^?1 in stage 4.     

An improved linearization strategy for zero-one quadratic programming problems

We present a new linearized model for the zero-one quadratic programming problem, whose size is linear in terms of the number of variables in the original nonlinear problem. Our derivation yields three alternative reformulations, each varying in model size and tightness. We show that our models are at least as tight as the one recently proposed in [7], and examine the theoretical relationship of our models to a standard linearization of the zero-one quadratic programming problem. Finally, we demonstrate the efficacy of solving each of these models on a set of randomly generated test instances.     

Oxygen inhibition in thiol–acrylate photopolymerizations

The overall effects of oxygen on thiol–acrylate photopolymerizations were characterized. Specially, the choice of thiol monomer chemistry, functionality, and concentration on the extent of oxygen inhibition were considered. As thiol concentration was increased, the degree of oxygen inhibition was greatly reduced because of chain transfer from the peroxy radical to the thiol. When comparing the copolymerization of 1,6‐hexanediol diacrylate with the alkane‐based thiol (1,6‐hexane dithiol) to the copolymerization with the propionate thiol (glycol dimercaptopropionate), it was found that the propionate system was much more reactive and polymerized to a greater extent in the presence of oxygen. In addition, the functionality was considered where the glycol dimercaptopropionate was compared to a tetrafunctional propionate of similar chemistry (pentaerythritol tetrakis(mercaptopropionate)). Given the same thiol concentration, the higher functionality thiol imparted a faster polymerization rate, due to the increased polymer system viscosity, which limited oxygen diffusion and decreased the extent of overall oxygen inhibition. Thus, preliminary insight is provided into how thiol monomer choice affects the extent of oxygen inhibition in thiol–acrylate photopolymerization. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 2007–2014, 2006     

Synthesis and polymerization of a new nitrogen‐containing bis‐ortho‐diynylarene monomer

This study focuses on the preparation, characterization, and optical properties of new bis(3,4‐diphenylethynylphenyl)phenylamine. This is the first nitrogen‐containing bis‐ortho‐diynylarene (BODA) monomer having a nitrogen atom as the spacer group. BODA monomers are usually prepared from common bisphenols, thereby providing great synthetic versatility and the opportunity to develop a wide array of novel polyarylene thermosets by varying the aromatic spacer group. The new bis(3,4‐bisphenylethynylphenyl)phenylamine was synthesized in five steps. This compound emits an intense blue color (λ = 438 nm) upon irradiation by UV light and may be suitable for use as an emitting layer in electroluminescent devices. Bis‐(3,4‐bisphenylethynylphenyl)phenylamine and its polymer have photoluminescence quantum yields 34 and 38%, respectively, and long excited‐state lifetimes of 3.2 and 3.6 ns, respectively. The structure of the monomer and its polymer were characterized using spectroscopic techniques including Ultraviolet–visible Spectrophotometer, Photoluminescence Spectrophotometer, Fourier Transform infrared spectroscopy, and Gel Permeation Chromatography. The polymerizations were studied by Differential Scanning Calorimeter. The amount of weight loss and the thermostability of the nitrogen‐containing polymer were determined from thermogravimetric analysis. The electrical conductivity of neat HCl‐doped BODA‐derived polymer film was measured according to the standard four‐point probe technique. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 6988–6996, 2006