Adsorption of mono- and multivalent cat- and anions on DNA molecules

Adsorption of monovalent and multivalent cat- and anions on a deoxyribose nucleic acid (DNA) molecule from a salt solution is investigated by computer simulation. The ions are modelled as charged hard spheres, the DNA molecule as a point charge pattern following the double-helical phosphate strands. The geometrical shape of the DNA molecules is modelled on different levels ranging from a simple cylindrical shape to structured models which include the major and minor grooves between the phosphate strands. The densities of the ions adsorbed on the phosphate strands, in the major and in the minor grooves are calculated. First, we find that the adsorption pattern on the DNA surface depends strongly on its geometrical shape: counterions adsorb preferentially along the phosphate strands for a cylindrical model shape, but in the minor groove for a geometrically structured model. Second, we find that an addition of monovalent salt ions results in an increase of the charge density in the minor groove while the total charge density of ions adsorbed in the major groove stays unchanged. The adsorbed ion densities are highly structured along the minor groove while they are almost smeared along the major groove. Furthermore, for a fixed amount of added salt, the major groove cationic charge is independent on the counterion valency. For increasing salt concentration the major groove is neutralized while the total charge adsorbed in the minor groove is constant. DNA overcharging is detected for multivalent salt. Simulations for a larger ion radii, which mimic the effect of the ion hydration, indicate an increased adsorbtion of cations in the major groove.Comment: 34 pages with 14 figure

Algebraic Operations on PQ Trees and Modular Decomposition Trees

Partitive set families are families of sets that can be quite large, but have a compact, recursive representation in the form of a tree. This tree is a common generalization of PQ trees, the modular decomposition of graphs, certain decompositions of boolean functions, and decompositions that arise on a variety of other combinatorial structures. We describe natural operators on partitive set families, give algebraic identities for manipulating them, and describe efficient algorithms for evaluating them. We use these results to obtain new time bounds for finding the common intervals of a set of permutations, finding the modular decomposition of an edge-colored graphs (also known as a two-structure), finding the PQ tree of a matrix when a consecutive-ones arrangement is given, and finding the modular decomposition of a permutation graph when its permutation realizer is given

Greenland Ice Sheet Mass Balance Reconstruction. Part I: Net Snow Accumulation (1600–2009)

Ice core data are combined with Regional Atmospheric Climate Model version 2 (RACMO2) output (1958–2010) to develop a reconstruction of Greenland ice sheet net snow accumulation rate, ^At(G), spanning the years 1600–2009. Regression parameters from regional climate model (RCM) output regressed on 86 ice cores are used with available cores in a given year resulting in the reconstructed values. Each core site’s residual variance is used to inversely weight the cores’ respective contributions. The interannual amplitude of the reconstructed accumulation rate is damped by the regressions and is thus calibrated to match that of the RCM data. Uncertainty and significance of changes is measured using statistical models. A 12% or 86 Gt yr21 increase in ice sheet accumulation rate is found from the end of the Little Ice Age in ;1840 to the last decade of the reconstruction. This 1840–1996 trend is 30% higher than that of 1600–2009, suggesting an accelerating accumulation rate. The correlation of ^A t(G) with the average surface air temperature in the Northern Hemisphere (SATNHt) remains positive through time, while the correlation of ^A t(G) with local near-surface air temperatures or North Atlantic sea surface temperatures is inconsistent, suggesting a hemispheric-scale climate connection. An annual sensitivity of ^At(G) to SATNHt of 6.8%K21 or 51 Gt K21 is found. The reconstuction, ^At(G), correlates consistently highly with the North Atlantic Oscillation index. However, at the 11-yr time scale, the sign of this correlation flips four times in the 1870–2005 period

Greenland Ice Sheet Mass Balance Reconstruction. Part I: Net Snow Accumulation (1600–2009)

Ice core data are combined with Regional Atmospheric Climate Model version 2 (RACMO2) output (1958–2010) to develop a reconstruction of Greenland ice sheet net snow accumulation rate, ^At(G), spanning the years 1600–2009. Regression parameters from regional climate model (RCM) output regressed on 86 ice cores are used with available cores in a given year resulting in the reconstructed values. Each core site’s residual variance is used to inversely weight the cores’ respective contributions. The interannual amplitude of the reconstructed accumulation rate is damped by the regressions and is thus calibrated to match that of the RCM data. Uncertainty and significance of changes is measured using statistical models. A 12% or 86 Gt yr21 increase in ice sheet accumulation rate is found from the end of the Little Ice Age in ;1840 to the last decade of the reconstruction. This 1840–1996 trend is 30% higher than that of 1600–2009, suggesting an accelerating accumulation rate. The correlation of ^A t(G) with the average surface air temperature in the Northern Hemisphere (SATNHt) remains positive through time, while the correlation of ^A t(G) with local near-surface air temperatures or North Atlantic sea surface temperatures is inconsistent, suggesting a hemispheric-scale climate connection. An annual sensitivity of ^At(G) to SATNHt of 6.8%K21 or 51 Gt K21 is found. The reconstuction, ^At(G), correlates consistently highly with the North Atlantic Oscillation index. However, at the 11-yr time scale, the sign of this correlation flips four times in the 1870–2005 period