Modeling the effect of intercalators on the high-force stretching behavior of DNA

DNA is structurally and mechanically altered by the binding of intercalator molecules. Intercalation strongly affects the force-extension behavior of DNA, in particular the overstretching transition. We present a statistical model that captures all relevant findings of recent force-extension experiments. Two predictions from our model are presented. The first suggests the existence of a novel hyper-stretching regime in the presence of intercalators and the second, a linear dependence of the overstretching force on intercalator concentration, is verified by re-analyzing available experimental data. Our model pins down the physical principles that govern intercalated DNA mechanics, providing a predictive understanding of its limitations and possibilities.Comment: 5 pages, 4 figure

Determination of Absolute Gravity at BPRC/US Polar Rock Repository

We determined absolute gravity at a base station located in the north-east corner of the U.S. Polar Rock Repository based on two field surveys conducted in summer 2005. We used a CG-5 Scintrex Autograv System for our measurements. The meter can measure relative gravity to a precision of 0.001 mGal. To find the absolute gravity we visited three tie-point sites, one located at the OSU Main Library, one in downtown Columbus and one south-west of town near Bolton Airfield. The sites were set up by the NOAA and NGS and absolute gravity was determined using a relative gravimeter (Lacoste-Romberg) which in turn was tied back to a site of known gravity. An absolute gravity measurement was conducted by NOAA-NGS in summer 2005 at OSU, in Mendenhall Laboratory. At each of the sites, we recorded a series of gravity measurements. These were subsequently used to calculate absolute gravity at the rock repository base station where measurements were taken at the start and end of the survey. We found the absolute gravity at the base station to be 980082.070 mGal with an error of about 0.035 mGal. This report is a summary of this investigation

Fluctuating Nonlinear Spring Model of Mechanical Deformation of Biological Particles

We present a new theory for modeling forced indentation spectral lineshapes of biological particles, which considers non-linear Hertzian deformation due to an indenter-particle physical contact and bending deformations of curved beams modeling the particle structure. The bending of beams beyond the critical point triggers the particle dynamic transition to the collapsed state, an extreme event leading to the catastrophic force drop as observed in the force (F)-deformation (X) spectra. The theory interprets fine features of the spectra: the slope of the FX curves and the position of force-peak signal, in terms of mechanical characteristics --- the Young's moduli for Hertzian and bending deformations E_H and E_b, and the probability distribution of the maximum strength with the strength of the strongest beam F_b^* and the beams' failure rate m. The theory is applied to successfully characterize the $FX$ curves for spherical virus particles --- CCMV, TrV, and AdV

Generating Negatively Supercoiled DNA Using Dual-Trap Optical Tweezers

Many genomic processes lead to the formation of underwound (negatively supercoiled) or overwound (positively supercoiled) DNA. These DNA topological changes regulate the interactions of DNA-binding proteins, including transcription factors, architectural proteins and topoisomerases. In order to advance our understanding of the structure and interactions of supercoiled DNA, we recently developed a single-molecule approach called Optical DNA Supercoiling (ODS). This method enables rapid generation of negatively supercoiled DNA (with between <5% and 70% lower helical twist than nonsupercoiled DNA) using a standard dual-trap optical tweezers instrument. ODS is advantageous as it allows for combined force spectroscopy, fluorescence imaging, and spatial control of the supercoiled substrate, which is difficult to achieve with most other approaches. Here, we describe how to generate negatively supercoiled DNA using dual-trap optical tweezers. To this end, we provide detailed instructions on the design and preparation of suitable DNA substrates, as well as a step-by-step guide for how to control and calibrate the supercoiling density produced

Modelling of carbon nanotubes and carbon nanotube-reinforced polymers with applications to composite structures.

Thesis (M.Sc.Eng.)-University of KwaZulu-Natal, 2006.Owing to their exceptional mechanical and physical properties, carbon nanotubes seem t