Factor analytical approaches for evaluating groundwater trace element chemistry data

The multivariate statistical techniques principal component analysis (PCA), Q-mode factor analysis (QFA), and correspondence analysis (CA) were applied to a dataset containing trace element concentrations in groundwater samples collected from a number of wells located downgradient from the potential nuclear waste repository at Yucca Mountain, Nevada. PCA results reflect the similarities in the concentrations of trace elements in the water samples resulting from different geochemical processes. QFA results reflect similarities in the trace element compositions, whereas CA reflects similarities in the trace elements that are dominant in the waters relative to all other groundwater samples included in the dataset. These differences are mainly due to the ways in which data are preprocessed by each of the three methods.

The highly concentrated, and thus possibly more mature (i.e. older), groundwaters are separated from the more dilute waters using principal component 1 (PC 1). PC 2, as well as dimension 1 of the CA results, describe differences in the trace element chemistry of the groundwaters resulting from the different aquifer materials through which they have flowed. Groundwaters thought to be representative of those flowing through an aquifer composed dominantly of volcanic rocks are characterized by elevated concentrations of Li, Be, Ge, Rb, Cs, and Ba, whereas those associated with an aquifer dominated by carbonate rocks exhibit greater concentrations of Ti, Ni, Sr, Rh, and Bi. PC 3, and to a lesser extent dimension 2 of the CA results, show a strong monotonic relationship with the percentage of As(III) in the groundwater suggesting that these multivariate statistical results reflect, in a qualitative sense, the oxidizing/reducing conditions within the groundwater. Groundwaters that are relatively more reducing exhibit greater concentrations of Mn, Cs, Co, Ba, Rb, and Be, and those that are more oxidizing are characterized by greater concentrations of V, Cr, Ga, As, W, and U.     

Equilibrium free energy estimates based on nonequilibrium work relations and extended dynamics

Jarzynski's relation and the fluctuation theorem have established important connections between nonequilibrium statistical mechanics and equilibrium thermodynamics. In particular, an exact relationship between the equilibrium free energy and the nonequilibrium work is useful for computer simulations. In this paper, we exploit the fact that the free energy is a state function, independent of the pathway taken to change the equilibrium ensemble. We show that a generalized expression is advantageous for computer simulations of free energy differences. Several methods based on this idea are proposed. The accuracy and efficiency of the proposed methods are evaluated with a model problem.     

Different approaches for fabrication of low-cost electrochemical sensors

Electrochemistry combined with economical and sustainable platforms (such as paper) provides portable, affordable, robust, and user-friendly devices. In general, techniques, such as photolithography and sputtering, are excellent alternatives for producing these platforms. However, owing to the requirement of expensive and sophisticated instrumentation, as well as cleanroom facilities, these techniques have limited access. Thus, the search for easy to use and produce approaches have been reported, using consumables, including adhesives, carbon ink, graphite, pencil, office paper, paperboard, among others. In this sense, in this mini-review, we discuss various strategies explored to fabricate low-cost electrochemical sensors, including its main applications. Different manufacturing methods, such as screen and stencil printing, laser-scribing, and pencil drawing, will be discussed here, emphasizing the performance of the obtained devices, in addition to their advantages and disadvantages.     

Combining the lattice-sum and reaction-field approaches for evaluating long-range electrostatic interactions in molecular simulations

A new scheme, the lattice-sum-emulated reaction-field (LSERF) method, is presented that combines the lattice-sum (LS) and reaction-field (RF) approaches for evaluating electrostatic interactions in molecular simulations. More precisely, the LSERF scheme emulates a RF calculation (based on an atomic cutoff) via the LS machinery. This is achieved by changing the form of the electrostatic interactions in a standard LS calculation (Coulombic) to the form corresponding to RF electrostatics (Coulombic plus quadratic reaction-field correction term, truncated at the cutoff distance). It is shown (both analytically and numerically) that in the limit of infinite reciprocal-space accuracy, (i) the LSERF scheme with a finite reaction-field cutoff and a given reaction-field permittivity is identical to the RF scheme with the same parameters (and an atomic cutoff), and (ii) the LSERF scheme is identical to the LS scheme in the limit of an infinite reaction-field cutoff, irrespective of the reaction-field permittivity. This new scheme offers two key advantages: (i) from a conceptual point of view, it shows that there is a continuity between the RF and LS schemes and unifies them into a common framework; (ii) from a practical point of view, it allows us to perform RF calculations with arbitrarily large reaction-field cutoff distances for the same computational costs as a corresponding LS calculation. The optimal choice for the cutoff will be the one that achieves the best compromise between artifacts arising from the dielectric heterogeneity of the system (short cutoff) and its artificial periodicity (long cutoff). The implementation of the LSERF method is extremely easy, requiring only very limited modifications of any standard LS code. For practical applications to biomolecular systems, the use of the LSERF scheme with large reaction-field cutoff distances is expected to represent a significant improvement over the current RF simulations involving comparatively much shorter cutoffs.     

Fluctuation theorem for nonequilibrium reactions

A fluctuation theorem is derived for stochastic nonequilibrium reactions ruled by the chemical master equation. The theorem is expressed in terms of the generating and large-deviation functions characterizing the fluctuations of a quantity which measures the loss of detailed balance out of thermodynamic equilibrium. The relationship to entropy production is established and discussed. The fluctuation theorem is verified in the Schl?gl model of far-from-equilibrium bistability.     

Umbrella sampling for nonequilibrium processes

The authors introduce an algorithm for determining the steady-state probability distribution of an ergodic system arbitrarily far from equilibrium. By enforcing equal sampling of different regions of phase space, as in umbrella sampling simulations of systems at equilibrium, low probability regions are explored to a much greater extent than in physically weighted simulations. The algorithm can be used to accumulate joint statistics for an arbitrary number of order parameters for a system governed by any stochastic dynamics. They demonstrate the efficiency of the algorithm by applying it to a model of a genetic toggle switch which evolves irreversibly according to a continuous time Monte Carlo procedure.     

Validity and accuracy in evaluating surface tension of solids by additive approaches

The validity and the accuracy of both the Owens and Wendt and the Lifshitz-van der Waals/acid-base (LW/AB) methods for the determination of surface tensions of solids have been examined for a wide variety of situations. In each case, the allowed range of contact angles that result in positive values of all the square roots of the surface tension components of the solid has first been determined. Then the maximum relative errors in the surface tensions of solids that result from errors in contact angle measurements have been calculated within the allowed range. For both methods, it has been found that the maximum relative errors are minimal if one of the liquids is apolar. In the case of the LW/AB method, minimal errors are obtained if, in addition, the other two liquids are monopolar with different polarities. However, the more similar are the properties of the liquids, the narrower is the allowed range, and the larger are the maximum relative errors.     

Linear scaling approaches to quantum macromolecular similarity: evaluating the similarity function

The evaluation of the electron density based similarity function scales quadratically with respect to the size of the molecules for simplified, atomic shell densities. Due to the exponential decay of the function's atom-atom terms most interatomic contributions are numerically negligible on large systems. An improved algorithm for the evaluation of the Quantum Molecular Similarity function is presented. This procedure identifies all non-negligible terms without computing unnecessary interatomic squared distances, thus effectively turning to linear scaling the similarity evaluation. Presented also is a minimalist dynamic electron density model. Approximate, single shell densities together with the proposed algorithm facilitate fast electron density based alignments on macromolecules.     

Kramers problem for nonequilibrium current-induced chemical reactions

We discuss the use of tunneling electron current to control and catalyze chemical reactions. Assuming the separation of time scales for electronic and nuclear dynamics we employ Langevin equation for a reaction coordinate. The Langevin equation contains nonconservative current-induced forces and gives nonequilibrium, effective potential energy surface for current-carrying molecular systems. The current-induced forces are computed via Keldysh nonequilibrium Green's functions. Once a nonequilibrium, current-depended potential energy surface is defined, the chemical reaction is modeled as an escape of a Brownian particle from the potential well. We demonstrate that the barrier between the reactant and the product states can be controlled by the bias voltage. When the molecule is asymmetrically coupled to the electrodes, the reaction can be catalyzed or stopped depending on the polarity of the tunneling current.     

Different approaches to proximate analysis by thermogravimetry analysis

The experimental optimization by the simplex method of the proximate analysis of coal and biomass by thermogravimetry analysis (TGA) is reported. Heating rate, final temperature, holding time, Ar flow rate and sample size were the control variables. The response function used was chosen to minimize the difference in percentage of volatile matter with the ASTM characterization. The relative accuracy of the method was demonstrated by determination of the volatile matter contents of a number of coals in parallel with the ASTM certified method. The method is successfully used with biomass samples.     

A three-phase nonequilibrium model for catalytic distillation

Nonequilibrium model for steady state simulation of catalytic distillation is presented. Mathematical model takes into account both mass and heat transfers across the gas liquid interface and through the liquid-solid (catalyst) interface. Equations describing the mentioned phenomena are based on the effective diffusivity approach. The resulting system of nonlinear algebraic equations was implemented in the FORTRAN programming language and solved by the BUNLSI (Ferraris & Tronconi, 1986) solver. The described model was verified using the experimental data obtained from a continuous distillation column equipped with catalytic packing. As an experimental model system, synthesis of propyl propionate from propan-1-ol and propionic acid was chosen. Comparison of experimental and simulation data is presented, and appropriateness of the developed model for other types of catalytic distillation processes is discussed. Presented at the 35th International Conference of the Slovak Society of Chemical Engineering, Tatranské Matliare, 26–30 May 2008.     

Formal relations connecting different approaches to calculate relativistic effects on molecular magnetic properties

In the present work a set of formal relations connecting different approaches to calculate relativistic effects on magnetic molecular properties are proven. The linear response (LR) within the elimination of the small component (ESC), Breit Pauli, and minimal-coupling approaches are compared. To this end, the leading order ESC reduction of operators within the minimal-coupling four-component approach is carried out. The equivalence of all three approaches within the ESC approximation is proven. It is numerically verified for the NMR nuclear-magnetic shielding tensor taking HX and CH3X (X=Br,I) as model compounds. Formal relations proving the gauge origin invariance of the full relativistic effect on the NMR nuclear-magnetic shielding tensor within the LR-ESC approach are presented.     

Near-infrared mass median particle size determination of lactose monohydrate, evaluating several chemometric approaches

The influence of particle size on near-infra red (NIR) spectra is typically considered a 'nuisance factor' which many scatter correction methods attempt to eliminate, e.g., multiplicative scatter correction. However, particle size is a key issue in the formulation of many pharmaceutical products and has a profound effect on the behaviour of both raw materials and drug substances during formulation. NIR has already been demonstrated as a potential alternative particle sizing technique to current accepted methodology. This investigation assessed several chemometric approaches that model this information, using lactose monohydrate as the raw material. A variety of modelling techniques were applied to both zero order and second derivative spectra namely multiple linear regression, partial least squares, principal component regression and artificial neural networks. One further data transformation evaluated was polar coordinates, although no statistical data were generated. Typically, cross-validation root mean square errors of calibration and cross-validation root mean square errors of prediction of approximately 5 microns were calculated for all of the modelling techniques. These values are comparable to those associated with the reference technique (laser diffractometry). Correlation coefficients of approximately 0.98 for all techniques were also calculated. The predictive abilities for models generated using second derivative spectra were found to be comparable to those obtained using zero order spectra.     

Different approaches to multivariate calibration of nonlinear sensor data

In this study, different approaches to the multivariate calibration of the vapors of two refrigerants are reported. As the relationships between the time-resolved sensor signals and the concentrations of the analytes are nonlinear, the widely used partial least-squares regression (PLS) fails. Therefore, different methods are used, which are known to be able to deal with nonlinearities present in data. First, the Box–Cox transformation, which transforms the dependent variables nonlinearly, was applied. The second approach, the implicit nonlinear PLS regression, tries to account for nonlinearities by introducing squared terms of the independent variables to the original independent variables. The third approach, quadratic PLS (QPLS), uses a nonlinear quadratic inner relationship for the model instead of a linear relationship such as PLS. Tree algorithms are also used, which split a nonlinear problem into smaller subproblems, which are modeled using linear methods or discrete values. Finally, neural networks are applied, which are able to model any relationship. Different special implementations, like genetic algorithms with neural networks and growing neural networks, are also used to prevent an overfitting. Among the fast and simpler algorithms, QPLS shows good results. Different implementations of neural networks show excellent results. Among the different implementations, the most sophisticated and computing-intensive algorithms (growing neural networks) show the best results. Thus, the optimal method for the data set presented is a compromise between quality of calibration and complexity of the algorithm.Electronic Supplementary Material Supplementary material is available for this article at     

A temperature control technique for nonequilibrium molecular simulation

We describe a dynamical approach to thermal regulation in molecular dynamics. Temperature is moderated by a control law and an additional variable, as in Nose dynamics, but whose influence on the system decreases as the system approaches equilibrium. This device enables approximation of microcanonical averages and autocorrelation functions consistent with a given target temperature. Moreover, we demonstrate that the suggested technique is effective for the control of heat dissipation in a nonequilibrium setting, first by showing that the temperature control correctly regulates heat introduced by a rapid change to the system, and then by studying the slow relaxation of vibrational degrees of freedom (e.g., due to bonded atoms) in a solvent bath.     

Different approaches to the study of chelating agents for iron and aluminium overload pathologies

Our objective is to illustrate the activity of the groups operating in Italy involved in identification and study of new chelating agents, mainly intended for treatment of human pathology correlated with metal overload. The objective of “chelation therapy” is removal of toxic metal ions from the human body or attenuation of their toxicity by transforming them into less toxic compounds or by dislocating them from the site at which they exert a toxic action. Because most of this research activity is related to chelating agents for iron and aluminium, diseases related to these two metal ions are briefly treated. Iron overload is the most common metal toxicity disease worldwide. The toxicity of aluminium in dialysis patients was a serious problem for haemodialysis units in the seventies and eighties of the last century. In particular, this review focuses on research performed by the group at Cagliari and Ferrara, and by that at Padova. The former is studying, above all, bisphosphonate and kojic acid derivatives, and the latter is investigating 3,4-hydroxypyridinecarboxylic acids with differently substituted pyridinic rings.

Continuous medium theory for nonequilibrium solvation: I. How to correctly evaluate solvation free energy of nonequilibrium

Considering the influences of electrostatic potential Phi upon the change of solute charge distribution deltarho and rho upon the change deltaPhi at the same time, a more reasonable integral formula of dG = (1/2) integral (V) (rhodeltaPhi + Phideltarho)dV is used to calculate the change of the electrostatic free energy in charging the solute-solvent system to a nonequilibrium state, instead of the one of dG = integral (V) PhideltarhodV used before. This modification improves the expressions of electrostatic free energy and solvation free energy, in which no quantity of the intermediate equilibrium state is explicitly involved. Detailed investigation reveals that the solvation free energy of nonequilibrium only contains the interaction energy between the field due to the solute charge in vacuum, and the dielectric polarization at the nonequilibrium state. The solvent reorganization energies of forward and backward electron transfer reactions have been redefined because the derivations lead to a remarkable feature that these quantities are direction-dependent, unlike the theoretical models developed before. The deductions are given in the electric field-displacement form. Relevant discussions on the reliability of theoretical models suggested in this work have also been presented.     

Different approaches for estimating the deposition of radiocaesium on mountain pasture in southern Norway.

Different approaches to the estimation of radiocaesium deposition on different types of indigenous mountain pastures have been examined. In situ gamma spectrometric measurements performed using a portable multi-channel analyser (3 x 3 in Nal detector) with the detector placed on the ground, on a tripod at a height of 100 cm above the ground or fastened to a rucksack frame 90 cm above the ground were compared with conventional soil sampling. Field gamma-ray measurements in connection with soil sampling appear to be a promising tool for estimates of deposition on mineral soils in areas with different topography and vegetation.     

Different approaches in thin-layer chromatography for enantioresolution of acebutolol using colistin sulfate as chiral selector

JPC – Journal of Planar Chromatography – Modern TLC - This work reports the enantioresolution of (RS)-acebutolol (ACB) by a thin-layer chromatographic method involving colistin sulfate...     

An idealized model for nonequilibrium dynamics in molecular systems

The nonequilibrium dynamics of highly nonlinear and multidimensional systems can give rise to emergent chemical behavior which can often be tracked using low-dimensional order parameters such as a reaction path. Such behavior cannot be readily surmised by stationary projected stochastic representations such as those described by the Langevin equation or the generalized Langevin equation (GLE). The irreversible generalized Langevin equation (iGLE) contains a nonstationary friction kernel that in certain limits reduces to the GLE with space-dependent friction. For more general forms of the friction kernel, the iGLE was previously shown to be the projection of a mechanical system with a time-dependent Hamiltonian [R. Hernandez, J. Chem. Phys. 110, 7701 (1999)]. In the present work, the corresponding open Hamiltonian system is shown to be amenable to numerical integration despite the presence of a nonlocal term. Simulations of this mechanical system further confirm that the time dependence of the observed total energy and the correlations of the solvent force are in precise agreement with the projected iGLE. This extended nonstationary Hamiltonian is thus amenable to the study of nonequilibrium bounds and fluctuation theorems.