Distance-based kriging relying on proxy simulations for inverse conditioning

Let us consider a large set of candidate parameter fields, such as hydraulic conductivity maps, on which we can run an accurate forward flow and transport simulation. We address the issue of rapidly identifying a subset of candidates whose response best match a reference response curve. In order to keep the number of calls to the accurate flow simulator computationally tractable, a recent distance-based approach relying on fast proxy simulations is revisited, and turned into a non-stationary kriging method where the covariance kernel is obtained by combining a classical kernel with the proxy. Once the accurate simulator has been run for an initial subset of parameter fields and a kriging metamodel has been inferred, the predictive distributions of misfits for the remaining parameter fields can be used as a guide to select candidate parameter fields in a sequential way. The proposed algorithm, Proxy-based Kriging for Sequential Inversion (ProKSI), relies on a variant of the Expected Improvement, a popular criterion for kriging-based global optimization. A statistical benchmark of ProKSI’s performances illustrates the efficiency and the robustness of the approach when using different kinds of proxies.

Combined effect of heterogeneity, anisotropy and saturation on steady state flow and transport: Structure recognition and numerical simulation

1 Natural soil profiles may be interpreted as an arrangement of parts which are characterized by properties like hydraulic conductivity and water retention function. These parts form a complicated structure. Characterizing the soil structure is fundamental in subsurface hydrology because it has a crucial influence on flow and transport and defines the patterns of many ecological processes. We applied an image analysis method for recognition and classification of visual soil attributes in order to model flow and transport through a man-made soil profile. Modeled and measured saturation-dependent effective parameters were compared. We found that characterizing and describing conductivity patterns in soils with sharp conductivity contrasts is feasible. Differently, solving flow and transport on the basis of these conductivity maps is difficult and, in general, requires special care for representation of small-scale processes.

Real-time simulation of nonequilibrium transport of magnetization in large open quantum spin systems driven by dissipation

Using quantum Monte Carlo, we study the nonequilibrium transport of magnetization in large open strongly correlated quantum spin-12 systems driven by purely dissipative processes that conserve the uniform or staggered magnetization, disregarding unitary Hamiltonian dynamics. We prepare both a low-temperature Heisenberg ferromagnet and an antiferromagnet in two parts of the system that are initially isolated from each other. We then bring the two subsystems in contact and study their real-time dissipative dynamics for different geometries. The flow of the uniform or staggered magnetization from one part of the system to the other is described by a diffusion equation that can be derived analytically.

Transport model of the human Na+-coupled L-ascorbic acid (vitamin C) transporter SVCT1

Vitamin C (L-ascorbic acid) is an essential micronutrient that serves as an antioxidant and as a cofactor in many enzymatic reactions. Intestinal absorption and renal reabsorption of the vitamin is mediated by the epithelial apical L-ascorbic acid cotransporter SVCT1 (SLC23A1). We explored the molecular mechanisms of SVCT1-mediated L-ascorbic acid transport using radiotracer and voltage-clamp techniques in RNA-injected Xenopus oocytes. L-ascorbic acid transport was saturable (K(0.5) approximately 70 microM), temperature dependent (Q(10) approximately 5), and energized by the Na(+) electrochemical potential gradient. We obtained a Na(+)-L-ascorbic acid coupling ratio of 2:1 from simultaneous measurement of currents and fluxes. L-ascorbic acid and Na(+) saturation kinetics as a function of cosubstrate concentrations revealed a simultaneous transport mechanism in which binding is ordered Na(+), L-ascorbic acid, Na(+). In the absence of L-ascorbic acid, SVCT1 mediated pre-steady-state currents that decayed with time constants 3-15 ms. Transients were described by single Boltzmann distributions. At 100 mM Na(+), maximal charge translocation (Q(max)) was approximately 25 nC, around a midpoint (V(0.5)) at -9 mV, and with apparent valence approximately -1. Q(max) was conserved upon progressive removal of Na(+), whereas V(0.5) shifted to more hyperpolarized potentials. Model simulation predicted that the pre-steady-state current predominantly results from an ion-well effect on binding of the first Na(+) partway within the membrane electric field. We present a transport model for SVCT1 that will provide a framework for investigating the impact of specific mutations and polymorphisms in SLC23A1 and help us better understand the contribution of SVCT1 to vitamin C metabolism in health and disease.

High-resolution computer simulation of electrophoretic mobilization in isoelectric focusing

Cationic and anionic electrophoretic mobilization for focusing of hemoglobins (Hb's) in the presence of 100 carrier ampholytes covering a pI range of 6.00-7.98 was studied by computer simulation at a constant current density of 300 A/m(2). Electropherograms that would be produced by whole column imaging and by single detectors placed at different locations along the focusing column are presented. Upon mobilization, peak heights of the Hb zones decrease, but the zones retain a relatively sharp constant profile and are migrating at a constant velocity. A further peak decrease occurs during readjustment at the locations of the original buffer/column interfaces, indicating that detection sensitivity is the lowest at these locations. An anionic carrier ampholyte mobility smaller than that of its cationic species produces a cathodic drift which is smaller than the transport rate used for electrophoretic mobilization. Compared to the case with equal mobilities of carrier ampholyte species, a small increase (decrease) is predicted for the cationic (anionic) mobilization rate within the focusing column. Simulation data suggest that electrophoretic mobilization after focusing and focusing with concurrent electrophoretic mobilization are comparable isotachophoretic processes that occur when there is an uninterrupted flux of an ion through the focusing column. Cathodic drift caused by unequal mobilities of the species of carrier ampholytes, electrophoretic mobilization, and decomposition occurring at the pH gradient edges are related electrophoretic processes.

Multi-scale micro-structure generation strategy for up-scaling transport in clays

Clays and claystones are used as backfill and barrier materials in the design of waste repositories, because they act as hydraulic barriers and retain contaminants. Transport through such barriers occurs mainly by molecular diffusion. There is thus an interest to relate the diffusion properties of clays to their structural properties. In previous work, we have developed a concept for up-scaling pore-scale molecular diffusion coefficients using a grid-based model for the sample pore structure. Here we present an operational algorithm which can generate such model pore structures of polymineral materials. The obtained pore maps match the rock’s mineralogical components and its macroscopic properties such as porosity, grain and pore size distributions. Representative ensembles of grains in 2D or 3D are created by a lattice Monte Carlo (MC) method, which minimizes the interfacial energy of grains starting from an initial grain distribution. Pores are generated at grain boundaries and/or within grains. The method is general and allows to generate anisotropic structures with grains of approximately predetermined shapes, or with mixtures of different grain types. A specific focus of this study was on the simulation of clay-like materials. The generated clay pore maps were then used to derive upscaled effective diffusion coefficients for non-sorbing tracers using a homogenization technique. The large number of generated maps allowed to check the relations between micro-structural features of clays and their effective transport parameters, as is required to explain and extrapolate experimental diffusion results. As examples, we present a set of 2D and 3D simulations and investigated the effects of nanopores within particles (interlayer pores) and micropores between particles. Archie’s simple power law is followed in systems with only micropores. When nanopores are present, additional parameters are required; the data reveal that effective diffusion coefficients could be described by a sum of two power functions, related to the micro- and nanoporosity. We further used the model to investigate the relationships between particle orientation and effective transport properties of the sample.

Reconstruction of a flash flood with large wood transport and its influence on hazard patterns in an ungauged mountain basin

The reconstruction of past flash floods in ungauged basins leads to a high level of uncertainty, which increases if other processes are involved such as the transport of large wood material. An important flash flood occurred in 1997 in Venero Claro (Central Spain), causing significant economic losses. The wood material clogged bridge sections, raising the water level upstream. The aim of this study was to reconstruct this event, analysing the influence of woody debris transport on the flood hazard pattern. Because the reach in question was affected by backwater effects due to bridge clogging, using only high water mark or palaeostage indicators may overestimate discharges, and so other methods are required to estimate peak flows. Therefore, the peak discharge was estimated (123 ± 18 m3 s–1) using indirect methods, but one-dimensional hydraulic simulation was also used to validate these indirect estimates through an iterative process (127 ± 33 m3 s–1) and reconstruct the bridge obstruction to obtain the blockage ratio during the 1997 event (~48%) and the bridge clogging curves. Rainfall–Runoff modelling with stochastic simulation of different rainfall field configurations also helped to confirm that a peak discharge greater than 150 m3 s–1 is very unlikely to occur and that the estimated discharge range is consistent with the estimated rainfall amount (233 ± 27 mm). It was observed that the backwater effect due to the obstruction (water level ~7 m) made the 1997 flood (~35-year return period) equivalent to the 50-year flood. This allowed the equivalent return period to be defined as the recurrence interval of an event of specified magnitude, which, where large woody debris is present, is equivalent in water depth and extent of flooded area to a more extreme event of greater magnitude. These results highlight the need to include obstruction phenomena in flood hazard analysis.

Forest dynamics during the transition from the Oldest Dryas to the Bølling–Allerød at Gerzensee—a simulation study

The aim of this study was to explore potential causes and mechanisms for the sequence and temporal pattern of tree taxa, specifically for the shift from shrub-tundra to birch–juniper woodland during and after the transition from the Oldest Dryas to the Bølling–Allerød in the region surrounding the lake Gerzensee in southern Central Europe. We tested the influence of climate, forest dynamics, community dynamics compared to other causes for delays. For this aim temperature reconstructed from a δ18O-record was used as input driving the multi-species forest-landscape model TreeMig. In a stepwise scenario analysis, population dynamics along with pollen production and transport were simulated and compared with pollen-influx data, according to scenarios of different δ18O/temperature sensitivities, different precipitation levels, with/without inter-specific competition, and with/without prescribed arrival of species. In the best-fitting scenarios, the effects on competitive relationships, pollen production, spatial forest structure, albedo, and surface roughness were examined in more detail. The appearance of most taxa in the data could only be explained by the coldest temperature scenario with a sensitivity of 0.3‰/°C, corresponding to an anomaly of − 15 °C. Once the taxa were present, their temporal pattern was shaped by competition. The later arrival of Pinus could not be explained even by the coldest temperatures, and its timing had to be prescribed by first observations in the pollen record. After the arrival into the simulation area, the expansion of Pinus was further influenced by competitors and minor climate oscillations. The rapid change in the simulated species composition went along with a drastic change in forest structure, leaf area, albedo, and surface roughness. Pollen increased only shortly after biomass. Based on our simulations, two alternative potential scenarios for the pollen pattern can be given: either very cold climate suppressed most species in the Oldest Dryas, or they were delayed by soil formation or migration. One taxon, Pinus, was delayed by migration and then additionally hindered by competition. Community dynamics affected the pattern in two ways: potentially by facilitation, i.e. by nitrogen-fixing pioneer species at the onset, whereas the later pattern was clearly shaped by competition. The simulated structural changes illustrate how vegetation on a larger scale could feed back to the climate system. For a better understanding, a more integrated simulation approach covering also the immigration from refugia would be necessary, for this combines climate-driven population dynamics, migration, individual pollen production and transport, soil dynamics, and physiology of individual pollen production.

Dynamic high-resolution computer simulation of electrophoretic enantiomer separations with neutral cyclodextrins as chiral selectors.

GENTRANS, a comprehensive one-dimensional dynamic simulator for electrophoretic separations and transport, was extended for handling electrokinetic chiral separations with a neutral ligand. The code can be employed to study the 1:1 interaction of monovalent weak and strong acids and bases with a single monovalent weak or strong acid or base additive, including a neutral cyclodextrin, under real experimental conditions. It is a tool to investigate the dynamics of chiral separations and to provide insight into the buffer systems used in chiral capillary zone electrophoresis (CZE) and chiral isotachophoresis. Analyte stacking across conductivity and buffer additive gradients, changes of additive concentration, buffer component concentration, pH, and conductivity across migrating sample zones and peaks, and the formation and migration of system peaks can thereby be investigated in a hitherto inaccessible way. For model systems with charged weak bases and neutral modified β-cyclodextrins at acidic pH, for which complexation constants, ionic mobilities, and mobilities of selector-analyte complexes have been determined by CZE, simulated and experimentally determined electropherograms and isotachopherograms are shown to be in good agreement. Simulation data reveal that CZE separations of cationic enantiomers performed in phosphate buffers at low pH occur behind a fast cationic migrating system peak that has a small impact on the buffer composition under which enantiomeric separation takes place.

Dynamic computer simulation of electrophoretic enantiomer migration order and separation in presence of a neutral cyclodextrin

One-dimensional dynamic computer simulation was employed to investigate the separation and migration order change of ketoconazole enantiomers at low pH in presence of increasing amounts of (2-hydroxypropyl)-β-cyclodextrin (OHP-β-CD). The 1:1 interaction of ketoconazole with the neutral cyclodextrin was simulated under real experimental conditions and by varying input parameters for complex mobilities and complexation constants. Simulation results obtained with experimentally determined apparent ionic mobilities, complex mobilities, and complexation constants were found to compare well with the calculated separation selectivity and experimental data. Simulation data revealed that the migration order of the ketoconazole enantiomers at low (OHP-β-CD) concentrations (i.e. below migration order inversion) is essentially determined by the difference in complexation constants and at high (OHP-β-CD) concentrations (i.e. above migration order inversion) by the difference in complex mobilities. Furthermore, simulations with complex mobilities set to zero provided data that mimic migration order and separation with the chiral selector being immobilized. For the studied CEC configuration, no migration order inversion is predicted and separations are shown to be quicker and electrophoretic transport reduced in comparison to migration in free solution. The presented data illustrate that dynamic computer simulation is a valuable tool to study electrokinetic migration and separations of enantiomers in presence of a complexing agent.

Benchmarking the simulation of Cr isotope fractionation

A benchmark problem set consisting of four problem levels was developed for the simulation of Cr isotope fractionation in 1D and 2D domains. The benchmark is based on a recent field study where Cr(VI) reduction and accompanying Cr isotope fractionation occurs abiotically by an aqueous reaction with dissolved Fe 2+ (Wanner et al., 2012., Appl. Geochem., 27, 644–662). The problem set includes simulation of the major processes affecting the Cr isotopic composition such as the dissolution of various Cr(VI) bearing minerals, fractionation during abiotic aqueous Cr(VI) reduction, and non-fractionating precipitation of Cr(III) as sparingly soluble Cr-hydroxide. Accuracy of the presented solutions was ensured by running the problems with four well-established reactive transport modeling codes: TOUGHREACT, MIN3P, CRUNCHFLOW, and FLOTRAN. Results were also compared with an analytical Rayleigh-type fractionation model. An additional constraint on the correctness of the results was obtained by comparing output from the problem levels simulating Cr isotope fractionation with the corresponding ones only simulating bulk concentrations. For all problem levels, model to model comparisons showed excellent agreement, suggesting that for the tested geochemical processes any code is capable of accurately simulating the fate of individual Cr isotopes.

Transport and Distribution of Hydroxyl Radicals and Oxygen Atoms from H2O Photodissociation in the Inner Coma of Comet 67P/Churyumov-Gerasimenko

With a combination of the Direct Simulation Monte Carlo (DSMC) calculation and test particle computation, the ballistic transport process of the hydroxyl radicals and oxygen atoms produced by photodissociation of water molecules in the coma of comet 67P/Churyumov-Gerasimenko is modelled. We discuss the key elements and essential features of such simulations which results can be compared with the remote-sensing and in situ measurements of cometary gas coma from the Rosetta mission at different orbital phases of this comet.