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

Optical trap stiffness in the presence and absence of spherical aberrations

Optical traps are commonly constructed with high-numerical-aperture objectives. Oil-immersion objectives suffer from spherical aberrations when used for imaging in aqueous solutions. The effect of spherical aberrations on trapping strength has been modeled by approximation, and only a few experimental results are available in the case of micrometer-sized particles. We present an experimental study of the dependence of lateral and axial optical-trap stiffness on focusing depth for polystyrene and silica beads of 2 μm diameter by using oil- and water-immersion objectives. We demonstrate a strong depth dependence of trap stiffness with the oil-immersion objective, whereas no depth dependence was observed with the water-immersion objective. © 2006 Optical Society of America

Revealing the Competition between Peeled-Ssdna, Melting Bubbles and S-DNA during DNA Overstretching using Fluorescence Microscopy

Understanding the structural changes occurring in double-stranded (ds)DNA during mechanical strain is essential to build a quantitative picture of how proteins interact and modify DNA. However, the elastic response of dsDNA to tension is only well-understood for forces < 65 pN. Above this force, torsionally unconstrained dsDNA gains ∼70% of its contour length, a process known as overstretching. The structure of overstretched DNA has proved elusive, resulting in a rich and controversial debate in recent years. At the centre of the debate is the question of whether overstretching yields a base-paired elongated structure, known as S-DNA, or instead forms single-stranded (ss)DNA via base-pair cleavage. Here, we show clearly, using a combination of fluorescence microscopy and optical tweezers, that both S-DNA and base-pair melted structures can exist, often concurrently, during overstretching. The balance between the two models is affected strongly by temperature and ionic strength. Moreover, we reveal, for the first time, that base-pair melting can proceed via two entirely different processes: progressive strand unpeeling from a free end in the backbone, or by the formation of ‘bubbles' of ssDNA, nucleating initially in AT-rich regions. We demonstrate that the mechanism of base-pair melting is governed by DNA topology: strand unpeeling is favored when there are free ends in the DNA backbone. Our studies settle a long running debate, and unite the contradictory dogmas of DNA overstretching. These findings have important implications for both medical and biological sciences. Force-induced melting transitions (yielding either peeled-ssDNA or melting bubbles) may play active roles in DNA replication and damage repair. Further, the ability to switch easily from DNA containing melting bubbles to S-DNA may be particularly advantageous in the cell, for instance during the formation of RNA within transcription bubbles. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved

Calving cycle of the Brunt Ice Shelf, Antarctica, driven by changes in ice-shelf geometry

Despite the potentially detrimental impact of large-scale calving events on the geometry and ice flow of the Antarctic Ice Sheet, little is known about the processes that drive rift formation prior to calving, or what controls the timing of these events. The Brunt Ice Shelf in East Antarctica presents a rare natural laboratory to study these processes, following the recent formation of two rifts, each now exceeding 50 km in length. Here we use a unique 50-years' time series of in-situ and remote sensing observations, together with numerical modelling, to reveal how slow changes in ice shelf geometry over time caused build-up of mechanical tension far upstream of the ice front, and culminated in rift formation and a significant speed-up of the ice shelf. These internal feedbacks, whereby ice shelves generate the very conditions that lead to their own (partial) disintegration are currently missing from ice flow models, which severely limits their ability to accurately predict future sea level rise

Feature-Based Textures

This paper introduces feature-based textures, a new image representation that combines features and texture samples for high-quality texture mapping. Features identify boundaries within a texture where samples change discontinuously. They can be extracted from vector graphics representations, or explicity added to raster images to improve sharpness. Texture lookups are then interpolated from samples while respecting these boundaries. We present results from a software implementation of this technique demonstrating quality, efficiency and low memory overhead