From Ribbons to Networks: Hierarchical Organization of DNA-Grafted Supramolecular Polymers

DNA-grafted supramolecular polymers (SPs) allow the programmed organization of DNA in a highly regular, one-dimensional array. Oligonucleotides are arranged along the edges of pyrene-based helical polymers. Addition of complementary oligonucleotides triggers the assembly of individual nanoribbons resulting in the development of extended supramolecular networks. Network formation is enabled by cooperative coaxial stacking interactions of terminal GC base pairs. The process is accompanied by structural changes in the pyrene polymer core that can be followed spectroscopically. Network formation is reversible, and disassembly into individual ribbons is realized either via thermal denaturation or by addition of a DNA separator strand.

Advance P. Chem. Problems (I) Populations, Partition Functions, Particle in Box, Harmonic Oscillators, Angular Momentum and Rigid Rotor

This is a set of P. Chem. problems posed at slightly higher than the normal text book level, for students who are continuing in the study of this subject.

Robust effect sizes and their confidence intervals for group difference between trajectories in hierarchical linear growth model

Hierarchical linear growth model (HLGM), as a flexible and powerful analytic method, has played an increased important role in psychology, public health and medical sciences in recent decades. Mostly, researchers who conduct HLGM are interested in the treatment effect on individual trajectories, which can be indicated by the cross-level interaction effects. However, the statistical hypothesis test for the effect of cross-level interaction in HLGM only show us whether there is a significant group difference in the average rate of change, rate of acceleration or higher polynomial effect; it fails to convey information about the magnitude of the difference between the group trajectories at specific time point. Thus, reporting and interpreting effect sizes have been increased emphases in HLGM in recent years, due to the limitations and increased criticisms for statistical hypothesis testing. However, most researchers fail to report these model-implied effect sizes for group trajectories comparison and their corresponding confidence intervals in HLGM analysis, since lack of appropriate and standard functions to estimate effect sizes associated with the model-implied difference between grouping trajectories in HLGM, and also lack of computing packages in the popular statistical software to automatically calculate them. ^ The present project is the first to establish the appropriate computing functions to assess the standard difference between grouping trajectories in HLGM. We proposed the two functions to estimate effect sizes on model-based grouping trajectories difference at specific time, we also suggested the robust effect sizes to reduce the bias of estimated effect sizes. Then, we applied the proposed functions to estimate the population effect sizes (d ) and robust effect sizes (du) on the cross-level interaction in HLGM by using the three simulated datasets, and also we compared the three methods of constructing confidence intervals around d and du recommended the best one for application. At the end, we constructed 95% confidence intervals with the suitable method for the effect sizes what we obtained with the three simulated datasets. ^ The effect sizes between grouping trajectories for the three simulated longitudinal datasets indicated that even though the statistical hypothesis test shows no significant difference between grouping trajectories, effect sizes between these grouping trajectories can still be large at some time points. Therefore, effect sizes between grouping trajectories in HLGM analysis provide us additional and meaningful information to assess group effect on individual trajectories. In addition, we also compared the three methods to construct 95% confident intervals around corresponding effect sizes in this project, which handled with the uncertainty of effect sizes to population parameter. We suggested the noncentral t-distribution based method when the assumptions held, and the bootstrap bias-corrected and accelerated method when the assumptions are not met.^

Phosphorus partition and acumulation rates in sediments of ODP Legs 130 and 138

Understanding phosphorus (P) geochemistry and burial in oceanic sediments is important because of the role of P for modulating oceanic productivity on long timescales. We investigated P geochemistry in seven equatorial Pacific sites over the last 53 Ma, using a sequential extraction technique to elucidate sedimentary P composition and P diagenesis within the sediments. The dominant P-bearing component in these sediments is authigenic P (61-86% of total P), followed in order of relative dominance by iron-bound P (7-17%), organic P (3-12%), adsorbed P (2-9%), and detrital P (0-1%). Clear temporal trends in P component composition exist. Organic P decreases rapidly in younger sediments in the eastern Pacific (the only sites with high sample resolution in the younger intervals), from a mean concentration of 2.3 µmol P/g sediment in the 0-1 Ma interval to 0.4 µmol/g in the 5- 6 Ma interval. Over this same time interval, decreases are also observed for iron-bound P (from 2.1 to 1.1 µmol P/g) and adsorbed P (from 1.5 to 0.7 µmol P/g). These decreases are in contrast to increases in authigenic P (from 6.0-9.6 µmol P/g) and no significant changes in detrital P (0.1 µmol P/g) and total P (12 µmol P/g). These temporal trends in P geochemistry suggest that (1) organic matter, the principal shuttle of P to the seafloor, is regenerated in sediments and releases associated P to interstitial waters, (2) P associated with iron-rich oxyhydroxides is released to interstitial waters upon microbial iron reduction, (3) the decrease in adsorbed P with age and depth probably indicates a similar decrease in interstitial water P concentrations, and (4) carbonate fluorapatite (CFA), or another authigenic P-bearing phase, precipitates due to the release of P from organic matter and iron oxyhydroxides and becomes an increasingly significant P sink with age and depth. The reorganization of P between various sedimentary pools, and its eventual incorporation in CFA, has been recognized in a variety of continental margin environments, but this is the first time these processes have been revealed in deep-sea sediments. Phosphorus accumulation rate data from this study and others indicates that the global pre-anthropogenic input rate of P to the ocean (20x10**10 mol P/yr) is about a factor of four times higher than previously thought, supporting recent suggestions that the residence time of P in the oceans may be as short as 10000-20000 years.

Sulphur contents and partition of iron in ODP Leg 112 sediments

Porewaters in site 680 Peru Margin sediments contain dissolved sulfide over a depth of approximately 70 m which, at a sedimentation rate of 0.005 cm/yr, gives a sediment exposure time to dissolved sulfide of about 1.4 Myr. Reactions with dissolved sulfide cause the site 680 sediments to show a progressive decrease in a poorly-reactive silicate iron fraction, defined as the difference between iron extracted by dithionite (FeD) at room temperature and that extracted by boiling concentrated HCl (FeH), normalised to the total iron content (FeT). Straight line plots are obtained for ln[(FeH - FeD)/FeT] against time of burial, from which a first order rate constant of 0.29 1/Myr (equivalent to a half-life of 2.4 Myr) can be derived for the sulfidation of this silicate iron. Comparable half-lives are also found for the same poorly-reactive iron fraction in the nearby site 681 and 684 sediments. This silicate Fe fraction comprises 0.8-1.0% Fe, only 30-60% of which reacts even with 1.5-3 million years exposure to dissolved sulfide. Diagenetic models based on porewater concentrations of sulfate and sulfide, and solid phase iron contents, at site 680 are consistent in indicating that this poorly-reactive iron fraction is only sulfidized on a million year time scale. Silicate iron not extracted by HCl can be regarded as unreactive towards dissolved sulfide on the time scales encountered in marine sediments.

Contents, partition, and isotopic composition of sulphur in sediments from ODP Sites 680 and 686

We have determined (1) the abundance and isotopic composition of pyrite, monosulphide, elemental sulphur, organically bound sulphur, and dissolved sulphide; (2) the partition of ferric and ferrous iron; (3) the organic carbon contents of sediments recovered at two sites drilled on the Peru Margin during Leg 112 of the Ocean Drilling Program. Sediments at both sites are characterised by high levels of organically bound sulphur (OBS). OBS comprises up to 50% of total sedimentary sulphur and up to 1% of bulk sediment. The weight ratio of S to C in organic matter varies from 0.03 to 0.15 (mean = 0.10). Such ratios are like those measured in lithologically similar, but more deeply buried petroleum source rocks of the Monterey and Sisquoc formations in California. The sulphur content of organic matter is not limited by the availability of porewater sulphide. Isotopic data suggest that sulphur is incorporated into organic matter within a metre of the sediment surface, at least partly by reaction with polysulphides. Most inorganic Sulphur occurs as pyrite. Pyrite formation occurred within surface sediments and was limited by the availability of reactive iron. But despite highly reducing sulphidic conditions, only 35-65% of the total iron was converted to sulphide; 10-30% of the total iron still occurs as Fe(III). In surface sediments, the isotopic composition of pyrite is similar to that of both iron monosulphide and dissolved sulphide. Either pyrite, like monosulphide, formed by direct reaction between dissolved sulphide and detrital iron, and/or the sulphur species responsible for converting FeS to FeS2 is isotopically similar to dissolved sulphide. Likely stoichiometries for the reaction between ferric iron and excess sulphide imply a maximum resulting FeS2:FeS ratio of 1:1. Where pyrite dominates the pool of iron sulphides, at least some pyrite must have formed by reaction between monosulphide and elemental sulphur and/or polysulphide. Elemental sulphur (S°) is most abundant in surface sediments and probably formed by oxidation of sulphide diffusing across the sediment-water interface. In surface sediments, S° is isotopically heavier than dissolved sulphide, FeS and FeS2 and is unlikely to have been involved in the conversion of FeS to FeS2. Polysulphides are thus implicated as the link between FeS and FeS2.