Direct Experimental Techniques Research Articles

Evaluating the role of soil properties on volumetric shrinkage characteristics of marine and inland clays

ABSTRACT Clayey soils that exhibit swelling and shrinkage behaviour have paved the way for various engineering problems such as foundation failure, slope stability issues, failure of earthen dams, cracking of clay liners, etc. The shrinkage behaviour of soil is often quantified by employing various direct and indirect experimental techniques to establish the Soil Shrinkage Curve (SSC), a relationship between soil volume change and moisture content. However, SSC can reveal only the overall volume change and does not exclusively comprehend the variation of volumetric shrinkage in linear and radial directions. Hence, a series of desiccation tests were performed on marine and inland clayey soils of different consistencies to evaluate the contribution of volumetric shrinkage in these orientations. From this study, it has been observed that the linear component of volumetric shrinkage was higher for soil samples with a consistency state between 1.0 and 1.5 times the liquid limit. However, the radial component of volumetric shrinkage was found to be higher at the end of the desiccation test for soils with an initial moisture content at or below the liquid limit. Furthermore, the results obtained from the present study have been utilised to establish the influence of soil properties on radial, linear, and total volumetric shrinkage.

Pore-scale hydrodynamics of non-Newtonian power-law fluids across a partially blocked porous medium in a confined channel

Transport of non-Newtonian fluids in porous media is pervasive in many natural and industrial applications. However, capturing the rheological behaviors of fluids by direct experimental techniques is challenging at the pore-scale. This paper outlines the pore-scale hydrodynamic interactions of non-Newtonian power-law fluids across a partially blocked porous medium in the laminar flow regime by computational fluid dynamics. The porous medium consists of an array of uniformly arranged square pillars. We explore the complex interplay of power-law rheology and Reynolds number on the microscopic flow field at the pore-scale. We capture the momentum transfer at the permeable interface between the porous and non-porous regions through stream-wise and span-wise velocity components and average volumetric flow rates at each pore-throat. Our results unveil a significant augmentation in stream-wise momentum by shear-thinning behavior and a diminution in momentum by shear-thickening behavior of the fluid through the porous medium. Further, the flow-leakage at the top interface purely depends on the combined effects of Reynolds number and power-law index. The channel pressure drop between the windward and leeward faces of the porous medium increases with the power-law index at low Reynolds number, while it decreases at high Reynolds number. Moreover, we provide a simple numerical framework to comprehend how the power-law behavior of the fluid dynamically regulates the flow field at the pore-scale.

Investigating Theoretical Frameworks: Comprehending the Relationship between σ, n, and μ in MnO2 Dispersed Films.

Solid polymer electrolytes (SPEs) made from a polymer-salt matrix show great potential for use in various applications, such as batteries, fuel cells, supercapacitors, solar cells, and electrochromic devices. Research on various theoretical and experimental aspects of these SPEs is highly pursued worldwide. However, due to the lack of direct experimental techniques for the measurement of the number of charge carriers (n) and their mobility (μ), reports on their correlation with conductivity (σ) and their exact theoretical justification are rare in literature studies. This paper is an attempt toward the search for the well-established theoretical formulation for n and μ that can justify the experimental results. In a previous attempt, it could only be demonstrated that the available theoretical bases show different values, but we could not come to any concrete conclusion. This research involves the use of three theoretical models, namely, the Rice and Roth model, the Trukhan model, and the Schutt and Gerdes model. The purpose of this study is to analyze the varying conductivity levels by calculating the concentration and mobility of charge carriers. To obtain the required parameters, impedance spectroscopy data were used. The Trukhan model was used to determine the precise value of the diffusion coefficient. By utilizing the dielectric tangent loss, the concentration of charge carriers and ion mobility were calculated. The Schutt and Gerdes (S&G) model was also used; this model is based on the dielectric constant and the relaxation frequency, which were derived from the EIS data. Finally, the Rice and Roth model was also employed, which is known for the ion transport in "super" ionic conductors. This was employed on the temperature-dependent impedance data for three different compositions of the films. A correlation is established between n and μ with σ using all three models. However, the Trukhan model is the most suitable for explaining the behavior of our system.

Computational mutation prediction to enhance or recover enzymatic activity.

Atomistic computational simulations have become a useful tool for biomolecular research. These tools are now becoming sufficiently accurate to predict single point mutations that can enhance or recover enzymatic activity. In this talk I will present the use of computational approaches to perform these predictions, and examples coupled with experimental validation. Two examples of applications of these methods to DNA transaction enzymes will be discussed. The first example involves an enzyme from the APOBEC3 family, which are host restriction factors that inhibit lentiviruses, such as HIV-1. For APOBEC3C (A3C), the chimpanzee and gorilla orthologues are more active than human A3C, and the Old World Monkey A3C from rhesus macaque (rh) is not active against HIV-1. Using a combination of molecular dynamics (MD), direct coupling analysis (DCA) and experimental techniques we have investigated the key residues for antivirala ctivities. Overall, our results determine the basis for why rhA3C is less active than human A3C and establish the amino acid network for dimerization and increased activity. The second example involves the methyltransferase (MTase) from Mycoplasma penetrans, which has recently been shown to synthesize the modified nucleotide 5-carboxymethylcytosine (5cxmC), formed as a trace byproduct of cytidine methylation by M.MpeI with the secondary metabolite carboxy-S-adenosyl-L-methionine (CxSAM) in place of the normal reaction cofactor, SAM. The use of computational simulations to investigate this new selectivity and predict additional mutations to enhance this new function, and experimental confirmation of these predictions will be presented and discussed.

Determination of bacterial surface charge density via saturation of adsorbed ions

Bacterial surface charge is a critical characteristic of the cell’s interfacial physiology that influences how the cell interacts with the local environment. A direct, sensitive, and accurate experimental technique capable of quantifying bacterial surface charge is needed to better understand molecular adaptations in interfacial physiology in response to environmental changes. We introduce here the method of second-harmonic light scattering (SHS), which is capable of detecting the number of molecular ions adsorbed as counter charges on the exterior bacterial surface, thereby providing a measure of the surface charge. In this first demonstration, we detect the small molecular cation, malachite green, electrostatically adsorbed on the surface of representative strains of Gram-positive and Gram-negative bacteria. Surprisingly, the SHS-deduced molecular transport rates through the different cellular ultrastructures are revealed to be nearly identical. However, the adsorption saturation densities on the exterior surfaces of the two bacteria were shown to be characteristically distinct. The negative charge density of the lipopolysaccharide coated outer surface of Gram-negative Escherichia coli (6.6 ± 1.3 nm−2) was deduced to be seven times larger than that of the protein surface layer of Gram-positive Lactobacillus rhamnosus (1.0 ± 0.2 nm−2). The feasibility of SHS-deduced bacterial surface charge density for Gram-type differentiation is presented.

Transesterification in Vitrimer Polymers Using Bifunctional Catalysts: Modeled with Solution-Phase Experimental Rates and Theoretical Analysis of Efficiency and Mechanisms.

Recently, thermoset vitrimer polymers have shown significant promise for structural applications because of their ability to be reshaped and remolded due to their covalent adaptive network (CAN). In these vitrimers, the transesterification reaction is responsible for the CAN, where the efficiency of the reaction is controlled either by organic or by organometallic catalysts. Understanding the mechanism of the transesterification reaction in the bulk phase using direct experimental techniques is extremely difficult due to the highly cross-linked complex structure of thermosetting vitrimers. Therefore, we use solution-phase experiments to investigate the catalytic efficiency and to guide density functional theory (DFT) simulations of the transesterification reaction mechanism with catalysts triazabicyclodecene (TBD), zinc acetate (Zn(OAc)2), 1-methylimidazole (1-MI), and dibutyltin oxide (DBTO). The estimated catalytic efficiency from the detailed DFT reaction path calculations follows the order TBD ≳ DBTO ≳ Zn(OAc)2 > 1-MI, which agrees with the experimental results. In addition to reaction path modeling, the mechanism and the relative rates of the transesterification reaction are analyzed with the assistance of Fukui indices as a measure of electrophilicity and nucleophilicity of atomic sites and with partial charges. It was found that the sum of the nucleophilicity index of the base and the electrophilicity index of the acid of the bifunctional catalysts correlates with the SN2 transition state and tetrahedral intermediate energies, which are related to the barrier of the rate-limiting step. This correlation provides a hypothesis for computational prescreening of potentially better catalysts that have an index in a range of values. These results provide a basis for understanding an important part of the mechanism of transesterification in vitrimer systems and may assist with designing new catalysts.

Nitrite oxidation exceeds reduction and fixed nitrogen loss in anoxic Pacific waters

The diversity of nitrogen-based dissimilatory metabolisms in anoxic waters continues to increase with additional studies to the marine oxygen deficient zones (ODZs). Although the microbial oxidation of nitrite (NO2–) has been known for over a century, studies of the pathways and microbes involved have generally proceeded under the assumption that nitrite oxidation to nitrate requires dioxygen (O2). Anaerobic NO2– oxidation until now has been conclusively shown only for anammox bacteria, albeit only as a limited sink for NO2– in their metabolism compared to the NO2– reduced to N2. Here, using direct experimental techniques optimized for replicating in situ anoxic conditions, we show that NO2– oxidation is substantial, widespread, and consistent across the ODZs of the eastern tropical Pacific Ocean. Regardless of the specific oxidant, NO2– oxidation rates are up to an order of magnitude larger than simultaneous N2 production rates for which these zones are known, and cannot be explained by anammox rates alone. Higher rates of NO2– oxidation over reduction in anoxic waters are paradoxical but help to explain how anammox rates can be enhanced over denitrification in shallow anoxic waters (σθ < 26.4) at the edge of the ODZs but not within the ODZ core. Furthermore, nitrite oxidation may be the key to reconciliation of the perceived imbalance of the global fixed nitrogen loss budget.

Comparison of Experimental and Predictive Approaches for Determination of Water Retention Curves of Intact Samples of Quaternary Soils

Retention curves were measured for intact samples of Quaternary soils, frequently involved in rainfall-triggered landslides. A full characterization of the retention curves required combined use of several direct and indirect experimental techniques. Experimental data was compared with predictive methods based on grain size distribution and in situ relative density ratio, namely a simple capillary tube prediction model, and the modified Kovacs method which also takes into account adhesive forces. Predicted drying curves captured the trend of the experimental curves, but generally lay below the experimental curves. Retention curve hysteresis was well predicted, particularly with the “Universal Mualem” method. Quick desaturation of the soils for suction above air entry value qualitatively explains why steep natural slopes with intermediate Quaternary sediments remain stable, except during intense short-term rainfall. Deviation between predicted and experimental curves in the low-suction range will affect infiltration analyses. The low-suction range of the retention curve should therefore preferably be measured for studies of rainfall triggering of landslides.

Impact of nucleon matrix element uncertainties on the interpretation of direct and indirect dark matter search results

We study in detail the impact of the current uncertainty in nucleon matrix elements on the sensitivity of direct and indirect experimental techniques for dark matter detection. We perform two scans in the framework of the cMSSM: one using recent values of the pion-sigma term obtained from Lattice QCD, and the other using values derived from experimental measurements. The two choices correspond to extreme values quoted in the literature and reflect the current tension between different ways of obtaining information about the structure of the nucleon. All other inputs in the scans, astrophysical and from particle physics, are kept unchanged. We use two experiments, XENON100 and IceCube, as benchmark cases to illustrate our case. We find that the interpretation of dark matter search results from direct detection experiments is more sensitive to the choice of the central values of the hadronic inputs than the results of indirect search experiments. The allowed regions of cMSSM parameter space after including XENON100 constraints strongly differ depending on the assumptions on the hadronic matrix elements used. On the other hand, the constraining potential of IceCube is almost independent of the choice of these values.

Functional Divergence and Convergent Evolution in the Plastid-Targeted Glyceraldehyde-3-Phosphate Dehydrogenases of Diverse Eukaryotic Algae

BackgroundGlyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a key enzyme of the glycolytic pathway, reversibly catalyzing the sixth step of glycolysis and concurrently reducing the coenzyme NAD+ to NADH. In photosynthetic organisms a GAPDH paralog (Gap2 in Cyanobacteria, GapA in most photosynthetic eukaryotes) functions in the Calvin cycle, performing the reverse of the glycolytic reaction and using the coenzyme NADPH preferentially. In a number of photosynthetic eukaryotes that acquired their plastid by the secondary endosymbiosis of a eukaryotic red alga (Alveolates, haptophytes, cryptomonads and stramenopiles) GapA has been apparently replaced with a paralog of the host’s own cytosolic GAPDH (GapC1). Plastid GapC1 and GapA therefore represent two independent cases of functional divergence and adaptations to the Calvin cycle entailing a shift in subcellular targeting and a shift in binding preference from NAD+ to NADPH.MethodsWe used the programs FunDi, GroupSim, and Difference Evolutionary-Trace to detect sites involved in the functional divergence of these two groups of GAPDH sequences and to identify potential cases of convergent evolution in the Calvin-cycle adapted GapA and GapC1 families. Sites identified as being functionally divergent by all or some of these programs were then investigated with respect to their possible roles in the structure and function of both glycolytic and plastid-targeted GAPDH isoforms.ConclusionsIn this work we found substantial evidence for convergent evolution in GapA/B and GapC1. In many cases sites in GAPDHs of these groups converged on identical amino acid residues in specific positions of the protein known to play a role in the function and regulation of plastid-functioning enzymes relative to their cytosolic counterparts. In addition, we demonstrate that bioinformatic software like FunDi are important tools for the generation of meaningful biological hypotheses that can then be tested with direct experimental techniques.

Facile non-hydrolytic synthesis of highly water dispersible, surfactant free nanoparticles of synthetic MFe2O4 (M–Mn2+, Fe2+, Co2+, Ni2+) ferrite spinel by a modified Bradley reaction

A series of the highly crystalline MFe2O4 ferrite spinel nanoparticles were synthesized via a modified Bradley reaction using microwave stimulation. Particle size was estimated using theoretical calculations from the X-ray data (Scherrer and Rietveld methods) as well as by direct experimental techniques such as TEM, DLS and NTA. The calculated average grain size for dry powders is in the range 10 to 23 nm. Hydrodynamic size was measured using DLS on non-modified, surfactant free particles of the whole MFe2O4 series. Raman spectra used for additional verification of the structure features of the produced spinel phases showed strong asymmetric behavior of the A1g mode, which was deconvoluted revealing additional components. Among all the products the lowest site inversion was found for the manganese ferrite (MnFe2O4). The oxidation of Fe3O4 leading to the formation of the Fe2O3 hematite phase induced by laser irradiation was observed. Magnetic characterization of the MFe2O4 family was carried out, showing that superparamagnetic blocking temperatures and calculated anisotropy constants K are in good agreement with the data for similar fine-particle systems.

Structure and interactions in fluids of prolate colloidal ellipsoids: Comparison between experiment, theory, and simulation

The microscopic structure of fluids of simple spheres is well known. However, the constituents of most real-life fluids are non-spherical, leading to a coupling between the rotational and translational degrees of freedom. The structure of simple dense fluids of spheroids - ellipsoids of revolution - was only recently determined by direct experimental techniques [A. P. Cohen, E. Janai, E. Mogilko, A. B. Schofield, and E. Sloutskin, Phys. Rev. Lett. 107, 238301 (2011)]. Using confocal microscopy, it was demonstrated that the structure of these simple fluids cannot be described by hard particle models based on the widely used Percus-Yevick approximation. In this paper, we describe a new protocol for determining the shape of the experimental spheroids, which allows us to expand our previous microscopy measurements of these fluids. To avoid the approximations in the theoretical approach, we have also used molecular dynamics simulations to reproduce the experimental radial distribution functions g(r) and estimate the contribution of charge effects to the interactions. Accounting for these charge effects within the Percus-Yevick framework leads to similar agreement with the experiment.

Inverse identification of intensity distributions from multiple flux maps in concentrating solar applications

Radiative flux measurements at the focal plane of solar concentrators are typically performed using digital cameras in conjunction with Lambertian targets. To accurately predict flux distributions on arbitrary receiver geometries directional information about the radiation is required. Currently, the directional characteristics of solar concentrating systems are predicted via ray tracing simulations. No direct experimental technique to determine intensities of concentrating solar systems is available. In the current paper, multiple parallel flux measurements at varying distances from the focal plane together with a linear inverse method and Tikhonov regularization are used to identify the directional and spatial intensity distribution at the solution plane. The directional binning feature of an in-house Monte Carlo ray tracing program is used to provide a reference solution. The method has been successfully applied to two-dimensional concentrators, namely parabolic troughs and elliptical troughs using forward Monte Carlo ray tracing simulations that provide the flux maps as well as consistent, associated intensity distribution for validation. In the two-dimensional case, intensity distributions obtained from the inverse method approach the Monte Carlo forward solution. In contrast, the method has not been successful for three dimensional and circular symmetric concentrator geometries.

Evaluation of adhesive and elastic properties of materials by depth-sensing indentation of spheres

Work of adhesion is the crucial material parameter for application of theories of adhesive contact. It is usually determined by experimental techniques based on the direct measurements of pull-off force of a sphere. These measurements are unstable due to instability of the load-displacement diagrams at tension, and they can be greatly affected by roughness of contacting solids. We show how the values of work of adhesion and elastic contact modulus of materials may be quantified using a new indirect approach (the Borodich–Galanov (BG) method) based on an inverse analysis of a stable region of the force-displacements curve obtained from the depth-sensing indentation of a sphere into an elastic sample. Using numerical simulations it is shown that the BG method is simple and robust. The crucial difference between the proposed method and the standard direct experimental techniques is that the BG method may be applied only to compressive parts of the force-displacements curves. Finally, the work of adhesion and the elastic modulus of soft polymer (polyvinylsiloxane) samples are extracted from experimental load-displacement diagrams.

Investigation of Pore-Scale Mixed Wettability

Summary The efficiency of secondary and tertiary-recovery processes can be improved by properly taking into account the reservoir's true wettability state. Most reservoirs are assumed to be mixed-wet, based on core-scale indices such as Amott-Harvey and USBM. Oil/brine/ mineral contact-angle measurements on smooth substrates offer some molecular-scale input and estimates for network modeling. However, direct experimental techniques to characterize wettability and validate the mixed-wet model at the pore scale in real or model rocks remain elusive. One promising avenue is the use of microtomography (µ-CT) to map the pore-scale distribution of multiple phases in miniplugs. A second, complementary approach involves the study of model rocks based on bead packs to probe the surface chemistry of the minerals exposed to crude oil and brine in pore confinement. Integrating the two approaches described in the current study provides a promising means of explaining the observed multiphase-fluid occupancy in pores by combining the detailed knowledge of the 3D pore structure and information on the surface chemistry of its walls.

How Is Charge Transport Different in Ionic Liquids and Electrolyte Solutions?

In this article we show that, analyzed in a barycentric reference frame, the deviation in conductivity measured directly from impedance experiments with respect to that estimated indirectly from NMR diffusion experiments has different origins in electrolyte solutions and pure salts. In the case of electrolyte solutions, the momentum conservation law is satisfied by solvent + ions. Instead, in a molten salt or ionic liquid momentum conservation must be satisfied solely by the ions. This has significant implications. While positively correlated motion of ions of opposite charge is a well justified explanation for the reduction in impedance conductivity in the case of electrolyte solutions, it is not so in the case of ionic liquids and molten salts. This work presents a set of equations that in the case of ionic liquids and molten salts can be used to obtain from direct measurements of impedance and NMR the distinct part of the diffusion coefficient matrix in the barycentric reference frame. In other words, by using experimentally measurable quantities, these equations allow us to access the motional coupling between ions for which there is no single direct experimental measurement technique. While equations of this type have been proposed before, the ones presented here can be easily derived from the momentum conservation law and linear response theory. Our results indicate that the decrease in the impedance conductivity with respect to NMR conductivity in ionic liquids and molten salts is due to anticorrelated motion of ions of same charge. This scenario is different in electrolyte solutions, where the positively correlated motion of ions of opposite charge makes a significant contribution to the decrease in the impedance conductivity. In contrast, in a system comprising a single binary salt (a room temperature ionic liquid or a molten salt), the cation-anion distinct diffusion coefficient is negative definite and opposes the contribution from the cation-cation and anion-anion distinct diffusion coefficients. This property of the cation-anion distinct diffusion coefficient in systems comprising just two ion-constituents holds true not just in the barycentric reference frame but also in any of the internal reference frames of nonequilibrium thermodynamics.

Direct measurements of cross section of astrophysical interest

New direct experimental methods and techniques, combined with the development of new theoretical tools have opened new avenues to explore nuclear reactions of significance for nucleosynthesis at or near the actual temperatures of stellar burning. The main difficulty of direct measurements is determined by the background, which, together with the low cross sections, set a limit on the energy range that can be investigated with a simple setup on the earth's surface. Essentially there are three sources of background, cosmic rays, environmental radioactivity and beam-target induced nuclear reactions. Each of these sources produces background of a different nature and energy, so that each reaction studied needs special care to suppress the relevant background component. I will show different experimental approaches that have been used to study processes of astrophysical interest. In particular, I will focus my attention on underground experiments and the recoil mass separator approach.

NMR Cross-Correlated Relaxation Rates Reveal Ion Coordination Sites in DNA

In this work, a novel NMR method for the identification of preferential coordination sites between physiologically relevant counterions and nucleic acid bases is demonstrated. In this approach, the NMR cross-correlated relaxation rates between the aromatic carbon chemical shift anisotropy and the proton-carbon dipolar interaction are monitored as a function of increasing Na(+), K(+), and Mg(2+) concentrations. Increasing the counterion concentration modulates the residence times of the counterions at specific sites around the nucleic acid bases. It is demonstrated that the modulation of the counterion concentration leads to sizable variations of the cross-correlated relaxation rates, which can be used to probe the site-specific counterion coordination. In parallel, the very same measurements report on the rotational tumbling of DNA, which, as shown here, depends on the nature of the ion and its concentration. This methodology is highly sensitive and easily implemented. The method can be used to cross-validate and/or complement direct but artifact-prone experimental techniques such as X-ray diffraction, NMR analysis with substitutionary ions, and molecular dynamics simulations. The feasibility of this technique is demonstrated on the extraordinarily stable DNA mini-hairpin d(GCGAAGC).

An Inverse Method to Obtain Porosity, Fibre Diameter and Density of Fibrous Sound Absorbing Materials

Characterization of sound absorbing materials is essential to predict its acoustic behaviour. The most commonly used models to do so consider the flow resistiv- ity, porosity, and average fibre diameter as parameters to determine the acoustic impedance and sound absorbing coefficient. Besides direct experimental techniques, numerical approaches appear to be an alternative to estimate the material’s pa- rameters. In this work an inverse numerical method to obtain some parameters of a fibrous material is presented. Using measurements of the normal incidence sound absorption coefficient and then using the model proposed by Voronina, subsequent application of basic minimization techniques allows one to obtain the porosity, aver- age fibre diameter and density of a sound absorbing material. The numerical results agree fairly well with the experimental data.

An inverse method to characterize fibrous sound absorbing materials.

Characterization of sound absorbing materials is needed to predict its behavior. The most commonly used models to do so consider the flow resistivity, porosity, and average fiber diameter as parameters to determine the acoustic impedance and sound absorbing coefficient. Besides direct experimental techniques, numerical approaches appear to be an alternative to estimate the material’s parameters. In this work an inverse numerical method to obtain the porosity, the fiber density, and the fiber average diameter of a fibrous material is described. Using normal incidence measurements of the sound absorption coefficient and then using the model proposed by Voronina, subsequent application of basic optimization techniques allows one to characterize a sound absorbing material. The numerical results agree fairly well with the experimental data.