Dynamics of a bubble formed in double stranded DNA

We study the fluctuational dynamics of a tagged base-pair in double stranded DNA. We calculate the drift force which acts on the tagged base-pair using a potential model that describes interactions at base pairs level and use it to construct a Fokker-Planck equation.The calculated displacement autocorrelation function is found to be in very good agreement with the experimental result of Altan-Bonnet {\it et. al.} Phys. Rev. Lett. {\bf 90}, 138101 (2003) over the entire time range of measurement. We calculate the most probable displacements which predominately contribute to the autocorrelation function and the half-time history of these displacements.Comment: 11 pages, 4 figures. submitted to Phys. Rev. Let

Effect of shear force on the separation of double stranded DNA

Using the Langevin Dynamics simulation, we have studied the effects of the shear force on the rupture of short double stranded DNA at different temperatures. We show that the rupture force increases linearly with the chain length and approaches to the asymptotic value in accordance with the experiment. The qualitative nature of these curves almost remains same for different temperatures but with a shift in the force. We observe three different regimes in the extension of covalent bonds (back bone) under the shear force.Comment: 4 pages, 4 figure

Numerical estimation of Carbonate properties using a digital rock physics workflow

Digital rock physics combines modern imaging with advanced numerical simulations to analyze the physical properties of rocks -- In this paper we suggest a special segmentation procedure which is applied to a carbonate rock from Switzerland -- Starting point is a CTscan of a specimen of Hauptmuschelkalk -- The first step applied to the raw image data is a nonlocal mean filter -- We then apply different thresholds to identify pores and solid phases -- Because we are aware of a nonneglectable amount of unresolved microporosity we also define intermediate phases -- Based on this segmentation determine porositydependent values for the pwave velocity and for the permeability -- The porosity measured in the laboratory is then used to compare our numerical data with experimental data -- We observe a good agreement -- Future work includes an analytic validation to the numerical results of the pwave velocity upper bound, employing different filters for the image segmentation and using data with higher resolutio

Fracture Unclogging: A Numerical Study of Seismically Induced Viscous Shear Stresses in Fluid‐Saturated Fractured Rocks

Dynamic shaking imposed by passing seismic waves is able to promote various hydrological processes in fractured reservoirs. This is often associated with seismically‐induced fracture unclogging due to mobilization of deposited colloids in the fracture network which, in turn, affects permeability at the reservoir scale. Numerous laboratory and field studies pointed out that fracture unclogging can be initiated when viscous shear stresses in the fracture fluid are in the range of 0.1‐1 Pascals. In this numerical study, we compute viscous shear stress in a fluid‐saturated fractured medium due to the action of passing P‐ and S‐waves. We perform a sensitivity analysis in terms of fluid, fracture, and host rock physical properties as well as seismic wave characteristics. Our results show that seismically‐induced viscous shearing increases with frequency and seismic strain and can be in the order of those initiating fracture unclogging for typical seismic strains and frequencies. S‐waves tend to produce viscous shearing approximately two times larger than P‐waves and, for anisotropic distribution of fractures, it is extremely dependent on the direction of wave propagation. Moreover, larger viscous shearing is expected for more viscous fluids and stiffer host rocks. Regarding the fracture network distribution, for the same fracture density, the presence of longer fractures drastically increases the potential of fracture unclogging at seismic frequencies. The fracture aperture distribution, on the other hand, can also affect the development of viscous shearing. Fractures with correlated distributions of contact areas exhibit an order of magnitude larger viscous shearing than uncorrelated ones

Thermomechanics of DNA

A theory for thermomechanical behavior of homogeneous DNA at thermal equilibrium predicts critical temperatures for denaturation under torque and stretch, phase diagrams for stable B--DNA, supercoiling, optimally stable torque, and the overstretching transition as force-induced DNA melting. Agreement with available single molecule manipulation experiments is excellent.Comment: 4 pages, 5 figures. Lette

Experimental and theoretical studies of sequence effects on the fluctuation and melting of short DNA molecules

Understanding the melting of short DNA sequences probes DNA at the scale of the genetic code and raises questions which are very different from those posed by very long sequences, which have been extensively studied. We investigate this problem by combining experiments and theory. A new experimental method allows us to make a mapping of the opening of the guanines along the sequence as a function of temperature. The results indicate that non-local effects may be important in DNA because an AT-rich region is able to influence the opening of a base pair which is about 10 base pairs away. An earlier mesoscopic model of DNA is modified to correctly describe the time scales associated to the opening of individual base pairs well below melting, and to properly take into account the sequence. Using this model to analyze some characteristic sequences for which detailed experimental data on the melting is available [Montrichok et al. 2003 Europhys. Lett. {\bf 62} 452], we show that we have to introduce non-local effects of AT-rich regions to get acceptable results. This brings a second indication that the influence of these highly fluctuating regions of DNA on their neighborhood can extend to some distance.Comment: To be published in J. Phys. Condensed Matte

Digital carbonate rock physics

Modern estimation of rock properties combines imaging with advanced numerical simulations, an approach known as digital rock physics (DRP). In this paper we suggest a specific segmentation procedure of X-ray micro-computed tomography data with two different resolutions in the µm range for two sets of carbonate rock samples. These carbonates were already characterized in detail in a previous laboratory study which we complement with nanoindentation experiments (for local elastic properties). In a first step a non-local mean filter is applied to the raw image data. We then apply different thresholds to identify pores and solid phases. Because of a non-neglectable amount of unresolved microporosity (micritic phase) we also define intermediate threshold values for distinct phases. Based on this segmentation we determine porosity-dependent values for effective P- and S-wave velocities as well as for the intrinsic permeability. For effective velocities we confirm an observed two-phase trend reported in another study using a different carbonate data set. As an upscaling approach we use this two-phase trend as an effective medium approach to estimate the porosity-dependent elastic properties of the micritic phase for the low-resolution images. The porosity measured in the laboratory is then used to predict the effective rock properties from the observed trends for a comparison with experimental data.The two-phase trend can be regarded as an upper bound for elastic properties; the use of the two-phase trend for low-resolution images led to a good estimate for a lower bound of effective elastic properties. Anisotropy is observed for some of the considered subvolumes, but seems to be insignificant for the analysed rocks at the DRP scale. Because of the complexity of carbonates we suggest using DRP as a complementary tool for rock characterization in addition to classical experimental methods

Regional climate variability in the western subtropical North Atlantic during the past two millennia

Author Posting. © American Geophysical Union, 2011. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Paleoceanography 26 (2011): PA2206, doi:10.1029/2010PA002038.Western subtropical North Atlantic oceanic and atmospheric circulations connect tropical and subpolar climates. Variations in these circulations can generate regional climate anomalies that are not reflected in Northern Hemisphere averages. Assessing the significance of anthropogenic climate change at regional scales requires proxy records that allow recent trends to be interpreted in the context of long-term regional variability. We present reconstructions of Gulf Stream sea surface temperature (SST) and hydrographic variability during the past two millennia based on the magnesium/calcium ratio and oxygen isotopic composition of planktic foraminifera preserved in two western subtropical North Atlantic sediment cores. Reconstructed SST suggests low-frequency variability of ∼1°C during an interval that includes the Medieval Climate Anomaly (MCA) and the Little Ice Age (LIA). A warm interval near 1250 A.D. is distinct from regional and hemispheric temperature, possibly reflecting regional variations in ocean-atmosphere heat flux associated with changes in atmospheric circulation (e.g., the North Atlantic Oscillation) or the Atlantic Meridional Overturning Circulation. Seawater δ 18O, which is marked by a fresher MCA and a more saline LIA, covaries with meridional migrations of the Atlantic Intertropical Convergence Zone. The northward advection of tropical salinity anomalies by mean surface currents provides a plausible mechanism linking Carolina Slope and tropical Atlantic hydrology.This study was supported by the Woods Hole Oceanographic Institution’s Ocean and Climate Change Institute (OCCI) and by the National Science Foundation

Bubble generation in a twisted and bent DNA-like model

The DNA molecule is modeled by a parabola embedded chain with long-range interactions between twisted base pair dipoles. A mechanism for bubble generation is presented and investigated in two different configurations. Using random normally distributed initial conditions to simulate thermal fluctuations, a relationship between bubble generation, twist and curvature is established. An analytical approach supports the numerical results.Comment: 7 pages, 8 figures. Accepted for Phys. Rev. E (in press