Back Accumulation of Diffusive Gradients in Thin-Films Devices with a Stack of Resin Discs To Assess Availability of Metal Cations to Biota in Natural Waters.

Determining species, concentrations, and physicochemical parameters in natural waters is key to improve our understanding of the functioning of these ecosystems. Diffusive Gradients in Thin-films (DGT) devices with different thicknesses of the resin or of the diffusive disc can be used to collect independent information on relevant parameters. In particular, DGT devices with a stack of two resin discs offer a simple way to determine dissociation rate constants of metal complexes from the accumulation of the target metal in the back resin disc. In this work, simple approximate expressions for the determination of the dissociation rate constant are reported and applied to a model Ni nitrilotriacetic complex as well as to Zn complexes in the Mediterranean Osor stream. Once the physicochemical parameters are known, one can plot the labile fraction of the metal complexes in terms of the thickness of the diffusion domain. These plots reveal a strong dependence on the nature of complexes as well as on the characteristics of the diffusion domain, and they are of high interest as predictors of availability to biota whose uptake is limited by diffusion.

Optimization of parallel implementation of UNRES package for coarse-grained simulations to treat large proteins.

We report major algorithmic improvements of the UNRES package for physics-based coarse-grained simulations of proteins. These include (i) introduction of interaction lists to optimize computations, (ii) transforming the inertia matrix to a pentadiagonal form to reduce computing and memory requirements, (iii) removing explicit angles and dihedral angles from energy expressions and recoding the most time-consuming energy/force terms to minimize the number of operations and to improve numerical stability, (iv) using OpenMP to parallelize those sections of the code for which distributed-memory parallelization involves unfavorable computing/communication time ratio, and (v) careful memory management to minimize simultaneous access of distant memory sections. The new code enables us to run molecular dynamics simulations of protein systems with size exceeding 100,000 amino-acid residues, reaching over 1 ns/day (1 µs/day in all-atom timescale) with 24 cores for proteins of this size. Parallel performance of the code and comparison of its performance with that of AMBER, GROMACS and MARTINI 3 is presented.

Effective concentration signature of Zn in a natural water derived from various speciation techniques.

The uptake of nutrients or toxicants by different organisms in aquatic systems is known to correlate with different fractions of the nutrient's or toxicant's total concentration. These fractions can be provided by different analytical techniques, from which the better correlation is expected to be found for those with a characteristic length comparable to that in the considered organism uptake. An effective concentration signature can be built up with the concentration values associated to the availability (i.e. fluxes in dynamic techniques) of the nutrient or toxicant measured by various analytical techniques with different characteristic lengths. Here, this new representation was obtained for the pool of Zn complexes in the Mediterranean stream Riera d'Osor (Girona, Catalonia, Spain) with a suite of four analytical techniques. Absence of Gradients and Nernstian Equilibrium Stripping (AGNES) and Polymer Inclusion Membrane (PIM) devices provided the free Zn concentration. Linear Anodic Stripping Voltammetry provided a labile fraction (defined here as cLASV, higher than the free concentration), related to the diffusion layer scale. Diffusion Gradients in Thin-films provided higher labile fractions (known as DGT concentrations, cDGT) connected to the different characteristic lengths of different configurations (e.g. one or two resin discs) longer, in any case, than that corresponding to LASV. The combination of the information retrieved by the techniques allowed to quantify lability degrees of the pool of Zn complexes and to build up the effective concentration signature for this water.

Availability of metals to DGT devices with different configurations. The case of sequential Ni complexation.

The analytical technique DGT (Diffusive Gradients in Thin-films) is able to gain access to a wealth of information by carefully interpreting accumulation data from passive samplers with different configurations (i.e. different thicknesses of its constituent layers). A set of DGT devices were simultaneously deployed in solutions of Ni and nitrilotriacetic acid (NTA) of different concentrations to measure the availability of Ni in these solutions. Accumulations indicate that the availability of Ni depends on both the thickness of the resin and the thickness of the diffusive gel. In both cases, the lability degree increases as the thickness increases. As the formation of successive complexes (such as Ni(NTA)2) proceeds, the availability of the metal decreases, which is quantitatively explained by reducing the formulation to a case with only one complex, but with an effective dissociation rate constant that decreases as the concentration of NTA increases. Simple analytical expressions are reported to quantify the lability degree in the different DGT configurations. These results indicate that a set of different DGT devices can characterize the availability of a cation in a natural sample with uptake processes at different spatial or time scales. Alternatively, and from a more fundamental point of view, information on speciation, mobilities and labilities of the species present in natural samples can be obtained with a set of DGT configurations.