Chemical and isotopic tracers combined with mixing models for tracking nitrate contamination in the Pampa de Pocho aquifer, Argentina.

In recent years, it has become evident that human activities have significantly disrupted the nitrogen cycle surpassing acceptable environmental thresholds. In this study, chemical and isotopic tracers were combined with a mathematical mass balance model (EMMA), PHREEQC inverse mixing model, and statistical analyses to evaluate groundwater quality, across an area experiencing substantial human activities, with a specific focus on tracing the origin of nitrate (NO3-) with potential water mixing processes. This multi-technique approach was applied to an unconfined aquifer underlying an agricultural area setting in an inter-mountain depression (i.e., the "Pampa de Pocho Plain" in Argentina). Here, the primary identified geochemical processes occurring in the investigated groundwater system include the dissolution of carbonate salts, cation exchange, and hydrolysis of alumino-silicates along with incorporating ions from precipitation. It was observed that the chemistry of groundwater, predominantly of sodium bicarbonate with sulfate water types, is controlled by the area's geology, recharge from precipitation, and stream water infiltration originating from the surrounding hills. Chemical results reveal that 60% of groundwater samples have NO3- concentrations exceeding the regional natural background level, confirming the impact of human activities on groundwater quality. The dual plot of δ15NNO3 versus δ18ONO3 values indicates that groundwater is affected by NO3- sources overlapping manure/sewage with organic-rich soil. The mathematical EMMA model and PHREEQC inverse modeling, suggest organic-rich soil as an important source of nitrogen in the aquifer. Here, 64 % of samples exhibit a main mixture of organic-rich soil with manure, whereas 36 % of samples are affected mainly by a mixture of manure and fertilizer. This study demonstrates the utility of combining isotope tracers with mathematical modeling and statistical analyses for a better understanding of groundwater quality deterioration in situations where isotopic signatures of contamination sources overlap.

Effects of the concentration of seeds, finite time-dependent supersaturations, and viscosity on the crystallization kinetics of monosodium urate monohydrate.

CONTEXT: Although the crystallization of monosodium urate monohydrate (MSUM) has a crucial role in the occurrence of gout, which is an inflammatory arthritis disease, theoretical models have not been able to describe all features observed in its seeded growth kinetics. In contrast to previous modeling approaches, we show that our model can reproduce qualitative features typically observed in experiments. In particular, our results show that the higher the initial supersaturation and the lower the viscosity, the faster the crystallization kinetics, and they also indicate that there are distinct growth regimes for low and high concentrations of seeds. METHODS: In this work, we introduce an alternative approach based on a master equation that allows us to incorporate hypotheses for the seeded growth crystallization of MSUM in a more transparent way. Such an approach includes not only effects that are related to the finite time-dependent supersaturation and concentration of seeds, but it can also be used to determine how the viscosity of the solution can affect the crystallization kinetics of MSUM molecules.

Diclofenac sodium adsorption on activated carbon: experimental, modeling and bayesian statistics.

The present study modeled the adsorption process of the drug diclofenac sodium on activated charcoal. For this purpose, a mass balance-based model was used considering a fixed bed column. The mass transfer rate in the solid phase was represented by a driving force model proposed in this study, and a gamma exponent with a range of 0 > γ ≤ 2 was assigned to the model. Different isotherms were adopted to represent the equilibrium at the solid/liquid interface: the Langmuir, Freundlich, Sips and Redlich-Peterson isotherms. The modeling was approached from the perspective of Bayesian statistics, and the Markov chain Monte Carlo method was used for parameter estimation. Model validation was performed with experimental data obtained under different operating conditions of initial concentration ($C_{0.

Using the reactive/transport dispersive models to simulate a monolithic anion exchanger: Experimental parameter determination, simultaneous model evaluation, and validation.

Selecting an adequate model to represent the mass transfer mechanisms occurring in a chromatographic process is generally complicated, which is one of the reasons why monolithic chromatography is scarcely simulated. In this study, the chromatographic separation of model proteins bovine serum albumin (BSA), ß-lactoglobulin-A, and ß-lactoglobulin-B on an anion exchange monolith was simulated based on experimental parameter determination, simultaneous model testing, and validation under three statistical criteria: retention time, dispersion accuracies, and Pearson correlation coefficient. Experimental characterization of morphologic, physicochemical, and kinetic parameters was performed through volume balances, pressure drop analysis, breakthrough curve analysis, and batch adsorptions. Free Gibbs energy indicated a spontaneous adsorption process for proteins and counterions. Dimensionless numbers were estimated based on height equivalent to a theoretical plate analysis, finding that pore diffusion controlled ß-lactoglobulin separation, whereas adsorption/desorption kinetics was the dominant mechanism for BSA. The elution profiles were modeled using the transport dispersive model and the reactive dispersive model coupled with steric mass action (SMA) isotherms because these models allowed to consider most of the mass transport mechanisms that have been described. RDM-SMA presented the most accurate simulations at pH 6.0 and at low (250 mM) and high (400 mM) NaCl concentrations. This simulation will be used as reference to forecast the purification of these proteins from bovine whey waste and to extrapolate this methodology to other monolith-based separations using these three statistical criteria that have not been used previously for this purpose.

Development of a sustainability-oriented university laboratory: Insight into adsorption kinetics models for the removal of pollutants from aqueous solution.

The aim of the present research is to show the development of a sustainability-oriented lab that teaches adsorption concepts in a virtual environment based on the premise "learning-through-play". Kinetic results in the virtual environment are contrasted to those obtained experimentally when diverse adsorbents prepared from Agave Bagasse (Raw Fibers, Hydrothermal Fibers, and Activated Fibers) were synthesized. Comparison between virtual and real-life experiments involving removal of methylene blue in solution showed that a pseudo-first-order model could describe adsorption kinetics satisfactorily. The study is complemented with a characterization of the adsorbents through SEM, nitrogen adsorption isotherms, FTIR and Raman. In addition, the environmental impact of the synthesis of adsorbents was evaluated through well-known methodologies (GAPI, NEMI, and Eco-Scale), which agree that raw fibers are the most eco-friendly material. This research provides an exciting opportunity to advance our knowledge on developing new technologies for teaching in engineering and to compliment real-life practices that consider environmental impacts with virtual experiments.

Multistationarity questions in reduced versus extended biochemical networks.

We address several questions in reduced versus extended networks via the elimination or addition of intermediate complexes in the framework of chemical reaction networks with mass-action kinetics. We clarify and extend advances in the literature concerning multistationarity in this context, mainly from Feliu and Wiuf (J R Soc Interface 10:20130484, 2013), Sadeghimanesh and Feliu (Bull Math Biol 81:2428-2462, 2019), Pérez Millán and Dickenstein (SIAM J Appl Dyn Syst 17(2):1650-1682, 2018), Dickenstein et al. (Bull Math Biol 81:1527-1581, 2019). We establish general results about MESSI systems, which we use to compute the circuits of multistationarity for significant biochemical networks.

Assessment of Embedding Schemes in a Hybrid Machine Learning/Classical Potentials (ML/MM) Approach.

Machine learning (ML) methods have reached high accuracy levels for the prediction of in vacuo molecular properties. However, the simulation of large systems solely through ML methods (such as those based on neural network potentials) is still a challenge. In this context, one of the most promising frameworks for integrating ML schemes in the simulation of complex molecular systems are the so-called ML/MM methods. These multiscale approaches combine ML methods with classical force fields (MM), in the same spirit as the successful hybrid quantum mechanics-molecular mechanics methods (QM/MM). The key issue for such ML/MM methods is an adequate description of the coupling between the region of the system described by ML and the region described at the MM level. In the context of QM/MM schemes, the main ingredient of the interaction is electrostatic, and the state of the art is the so-called electrostatic-embedding. In this study, we analyze the quality of simpler mechanical embedding-based approaches, specifically focusing on their application within a ML/MM framework utilizing atomic partial charges derived in vacuo. Taking as reference electrostatic embedding calculations performed at a QM(DFT)/MM level, we explore different atomic charges schemes, as well as a polarization correction computed using atomic polarizabilites. Our benchmark data set comprises a set of about 80k small organic structures from the ANI-1x and ANI-2x databases, solvated in water. The results suggest that the minimal basis iterative stockholder (MBIS) atomic charges yield the best agreement with the reference coupling energy. Remarkable enhancements are achieved by including a simple polarization correction.

Kinetic modeling and optimization of the mono- and diglycerides synthesis mediated by the lipase Lipozyme® TL 100 L immobilized on clayey support.

Mono- and diglycerides play a crucial role in the food industry as multifunctional food additives and emulsifiers. Their importance stems from their unique properties, which allow them to improve the quality, texture, and stability of various food products. Here, results of the kinetic modeling of the mono- and diglycerides synthesis mediated by the lipase Lipozyme® TL 100 L immobilized on the clayey support Spectrogel® type C are reported. The support was characterized by TEM, SEM, and FTIR. Firstly, the influence of pH and lipase load on the immobilization process was analyzed, resulting in an enzymatic activity of 93.2 ± 0.7 U g-1 under optimized conditions (170.9 U g-1 of lipase and pH of 7.1). Afterward, the effects of reaction temperature and concentration of immobilized biocatalyst in the feedstock conversion were evaluated. At optimized parameters, a triglycerides conversion of 97% was obtained at 36.5 °C, 7.9 vol.% of enzyme, a glycerol to feedstock molar ratio of 2:1, and 2 h. The optimized conditions were used to determine the kinetic constants of the elementary reactions involved in the glycerolysis, where a fit superior to 0.99 was achieved between experimental values and predicted data.

The Impact of Interdisciplinary, Gender and Geographic Distributions on the Citation Patterns of the Journal of Chemical Information and Modeling.

There has been a growing recognition of the need for diversity and inclusion in scientific fields. This trend is reflected in the Journal of Chemical Information and Modeling (JCIM), where there has been a gradual increase in the number of papers that embrace this diversity. In this viewpoint, we analyze the evolution of the profile of papers published in JCIM from 1996 to 2022 addressing three diversity criteria, namely interdisciplinarity, geographic and gender distributions, and their impact on citation patterns. We used natural language processing tools for the classification of main areas and gender, as well as metadata, to analyze a total of 7384 articles published in the categories of research articles, reviews, and brief reports. Our analyses reveal that the relative number of articles and citation patterns are similar across the main areas within the scope of JCIM, and international collaboration and publications encompassing two to three research areas attract more citations. The percentage of female authors has increased from 1996 (less than 20%) to 2022 (more than 32%), indicating a positive trend toward gender diversity in almost all geographic regions, although the percentage of publications by single female authors remains lower than 20%. Most JCIM citations come from Europe and the Americas, with a tendency for JCIM papers to cite articles from the same continent. Furthermore, there is a correlation between the gender of the authors, as JCIM manuscripts authored by females are more likely to be cited by other JCIM manuscripts authored by females.

Mitochondrial dysfunction, oxidative stress, ER stress and mitochondria-ER crosstalk alterations in a chemical rat model of Huntington's disease: Potential benefits of bezafibrate.

Redox homeostasis, mitochondrial functions, and mitochondria-endoplasmic reticulum (ER) communication were evaluated in the striatum of rats after 3-nitropropionic acid (3-NP) administration, a recognized chemical model of Huntington's disease (HD). 3-NP impaired redox homeostasis by increasing malondialdehyde levels at 28 days, decreasing glutathione (GSH) concentrations at 21 and 28 days, and the activities of glutathione peroxidase (GPx), superoxide dismutase (SOD) and glutathione S-transferase at 7, 21, and 28 days, catalase at 21 days, and glutathione reductase at 21 and 28 days. Impairment of mitochondrial respiration at 7 and 28 days after 3-NP administration was also observed, as well as reduced activities of succinate dehydrogenase (SDH) and respiratory chain complexes. 3-NP also impaired mitochondrial dynamics and the interactions between ER and mitochondria and induced ER-stress by increasing the levels of mitofusin-1, and of DRP1, VDAC1, Grp75 and Grp78. Synaptophysin levels were augmented at 7 days but reduced at 28 days after 3-NP injection. Finally, bezafibrate prevented 3-NP-induced alterations of the activities of SOD, GPx, SDH and respiratory chain complexes, DCFH oxidation and on the levels of GSH, VDAC1 and synaptophysin. Mitochondrial dysfunction and synaptic disruption may contribute to the pathophysiology of HD and bezafibrate may be considered as an adjuvant therapy for this disorder.

Predicting octanol/water partition coefficients and pKa for the SAMPL7 challenge using the SM12, SM8 and SMD solvation models.

Blind predictions of octanol/water partition coefficients and pKa at 298.15 K for 22 drug-like compounds were made for the SAMPL7 challenge. Octanol/water partition coefficients were predicted from solvation free energies computed using electronic structure calculations with the SM12, SM8 and SMD solvation models. Within these calculations we compared the use of gas- and solution-phase optimized geometries of the solute. Based on these calculations we found that in general the use of solution phase-optimized geometries increases the affinity of the solutes for water as compared to octanol, with the use of gas-phase optimized geometries resulting in the better agreement with experiment. The pKa is computed using the direct approach, scaled solvent-accessible surface model, and the inclusion of an explicit water molecule, where the latter two methods have previously been shown to offer improved predictions as compared to the direct approach. We find that the use of an explicit water molecule provides superior predictions, and that the predicted macroscopic pKa is sensitive to the employed microstates.

Theoretical study about the hydrogen abstraction reactions on methyl acetate on combustion conditions.

Methyl acetate is considered a prototype molecule to study biodiesel ignition and combustion and is seen as a possible fuel or fuel additive. For this reason, methyl acetate decomposition paths have been investigated in recent years. In the present study, hydrogen abstraction reactions on methyl acetate by OH(2Π), HO2(2A'), H(2Σg), O(3P), and O2(3Σg) were conducted, and the effect of methodology and anharmonic corrections on the rate coefficients were evaluated. The M06-2X and B3LYP-D3 functionals with the cc-pVDZ, cc-pVTZ, aug-cc-pVDZ, and aug-cc-pVTZ basis set were used for methodology evaluation and the CCSD(T)/cc-pVTZ//M06-2X/aug-cc-pVTZ for the rate coefficients calculation and literature comparisons. The rate coefficients were calculated in the range of 250-3500 K, including tunneling corrections, methyl-hindered rotations, and anharmonic effects calculated by the VPT2 method. The methodology analysis showed that the B3LYP-D3 functional leads to lower activation energies for all elementary reactions studied, and the double-zeta basis is insufficient to calculate precise rate coefficients. The inclusion of anharmonic corrections consistently lowered the rate coefficients of all elementary reactions studied and changed the Arrhenius plot profile with the temperature. Significant anharmonic effects were observed at higher temperatures, being the reaction with O2(3Σg) the most affected by this correction. Differences superior to 105 cm3 molec-1 s-1 in the rate coefficients were observed in some cases.

Evolution and folding of repeat proteins.

Repeat proteins are made with tandem copies of similar amino acid stretches that fold into elongated architectures. These proteins constitute excellent model systems to investigate how evolution relates to structure, folding, and function. Here, we propose a scheme to map evolutionary information at the sequence level to a coarse-grained model for repeat-protein folding and use it to investigate the folding of thousands of repeat proteins. We model the energetics by a combination of an inverse Potts-model scheme with an explicit mechanistic model of duplications and deletions of repeats to calculate the evolutionary parameters of the system at the single-residue level. These parameters are used to inform an Ising-like model that allows for the generation of folding curves, apparent domain emergence, and occupation of intermediate states that are highly compatible with experimental data in specific case studies. We analyzed the folding of thousands of natural Ankyrin repeat proteins and found that a multiplicity of folding mechanisms are possible. Fully cooperative all-or-none transitions are obtained for arrays with enough sequence-similar elements and strong interactions between them, while noncooperative element-by-element intermittent folding arose if the elements are dissimilar and the interactions between them are energetically weak. Additionally, we characterized nucleation-propagation and multidomain folding mechanisms. We show that the global stability and cooperativity of the repeating arrays can be predicted from simple sequence scores.

Stoichiometric network analysis in reaction networks yielding spontaneous mirror symmetry breaking in a prebiotic atmosphere.

The generation of amino acid homochirality under prebiotic atmosphere conditions is a relevant issue in the study of the origin of life. This research is based on the production of amino acids via Strecker synthesis and how it is adjusted to the Kondepudi-Nelson autocatalytic model. The spontaneous mirror symmetry breaking (SMSB) of the new Kondepudi-Nelson-Strecker model, subject to two modifications (with Limited Enantioselective and Cross Inhibition), and also their combination were studied using the stoichiometric network analysis (SNA). In the calculations, the values obtained from the literature for alanine were considered. A total production of alanine of 7.56 × 109 mol year-1 was determined under prebiotic atmosphere conditions and starting from that value, the reaction rates for the models studied were estimated. Only the model with cross inhibition or achiral dimer formation is driven by stochastic fluctuations during SMSB. The stochastic fluctuation was estimated for a value of 2.619 × 10-15 mol L-1. This perturbation was sufficient to trigger SMSB. Finally, the results of SMSB were used to calculate the entropy production for the cross inhibition model.

Morphogenesis in Synthetic Chemical Cells.

We present an efficient model for describing morphogenesis and the emergence of spatiotemporal structures in synthetic chemical cells. This work is motivated by an experimental setup used for testing Turing's theory of morphogenesis. The model developed is based on the general theory of chemically active droplets, which combines the classical theory of phase separation with reaction-diffusion systems. Through the 2D calculations, we find the six spatiotemporal structures predicted by Turing in 1952 and experimentally observed, in a 1D array of droplets. Moreover, under Turing instability, with a determined chemical wavelength, the system undergoes morphogenesis. This theoretical approach provides a useful tool for understanding the physical differentiation through the direct calculation of the osmotic pressure in each cell as the chemical reaction occurs.

Residue interactions affecting the deprotonation of internal guanine moieties in oligodeoxyribonucleotides, calculated by FMO methods.

The effect of vicinal molecular groups on the intrinsic acidity of a central guanine residue in short single-stranded DNA models and the potentials exerted by the backbone and the nucleobases on the leaving proton were determined by the fragment molecular orbital (FMO) method, in terms of quantum descriptors (QDs) and pair interaction interfragment decomposition analysis (PIEDA). The acidity of the central guanine moiety decreased with increasing oligonucleotide length, in response to changes by less than 1 eV in the ionization potential, global softness, electrophilicity index, and electronegativity descriptors. The differences in these descriptors were majorly interpreted in terms of the electrostatic influence of the negative charges residing on the backbone of the molecule. Additionally, this electric-field effect was determined explicitly for the displacement of the test hydronium ion to a distance of 250 Å from its original position, resulting in good agreement with calculations of the variation in Gibbs free energies, obtained from physical experiments conducted on the identical oligonucleotide sequences. The reported results are useful for biophysical applications of deoxyriboligonucleotides containing guanine residues in order to induce local negative charges at specific positions in the DNA chain.

Influence of design and material characteristics on 3D printed flow-cells for heat transfer-based analytical devices.

Redesigning 3D-printed flow cells is reported used for heat transfer based detection of biomolecules from a flow-through system to an addition-type measurement cell. The aim of this study is to assess the performance of this new measurement design and critically analyse the influence of material properties and 3D printing approach on thermal analysis. Particular attention is paid to reduce the time to stabilisation, the sample volume in order to make the technique suitable for clinical applications, and improving the sensitivity of the platform by decreasing the noise and interference of air bubbles. The three different approaches that were studied included a filament polylactic acid cell using only fused filament fabrication (FFF), a resin cell printed using stereolitography (SLA), and finally a design made of copper, which was manufactured by combining metal injection moulding (MIM) with fused filament fabrication (FFF). Computational fluid dynamic (CFD) modelling was undertaken using ANSYS Fluent V18.1 to provide insight into the flow of heat within the measurement cell, facilitating optimisation of the system and theoretical response speed.It was shown that the measurement cells using SLA had the lowest noise (~ 0.6%) and shortest measurement time (15 min), whereas measurement cells produced using other approaches had lower specificity or suffered from voiding issues. Finally, we assessed the potential of these new designs for detection of biomolecules and amoxicillin, a commonly used beta lactam antibiotic, to demonstrate the proof of concept. It can be concluded that the resin addition-type measurement cells produced with SLA are an interesting affordable alternative, which were able to detect amoxicillin with high sensitivity and have great promise for clinical applications due to the disposable nature of the measurement cells in addition to small sample volumes.

Homodimeric and Heterodimeric Interactions among Vertebrate Basic Helix-Loop-Helix Transcription Factors.

The basic helix-loop-helix transcription factor (bHLH TF) family is involved in tissue development, cell differentiation, and disease. These factors have transcriptionally positive, negative, and inactive functions by combining dimeric interactions among family members. The best known bHLH TFs are the E-protein homodimers and heterodimers with the tissue-specific TFs or ID proteins. These cooperative and dynamic interactions result in a complex transcriptional network that helps define the cell's fate. Here, the reported dimeric interactions of 67 vertebrate bHLH TFs with other family members are summarized in tables, including specifications of the experimental techniques that defined the dimers. The compilation of these extensive data underscores homodimers of tissue-specific bHLH TFs as a central part of the bHLH regulatory network, with relevant positive and negative transcriptional regulatory roles. Furthermore, some sequence-specific TFs can also form transcriptionally inactive heterodimers with each other. The function, classification, and developmental role for all vertebrate bHLH TFs in four major classes are detailed.

Ab initio simulations of black and blue phosphorene functionalised with chemical groups for biomolecule anchoring.

Black and blue phosphorene (2D-dimensional allotropes of phosphorus) have shown fascinating electronic, optical, and magnetic properties, with promising technological applications. In this work, we studied the adsorption of amine, hydroxyl, amide, and carboxyl groups onto both black and blue phosphorenes, in order to analyse the effects of biomolecule anchoring on the structural and electronic properties of phosphenes, using density functional simulations. Analyses were carried out of six different configurations for each chemical group functionalised on black and blue phosphorene. We observed that the radicals interacted via a chemisorption regime with the nanostructures, with binding energies that varied from 1.42 to 3.78 eV. The electronic properties showed that the presence of the chemical groups altered the energy gaps for both black and blue phosphorenes, due to a presence of a half-filled level when a single radical was adsorbed. We were able to observe that functionalised two-dimensional phosphorene showed promising characteristics in terms of anchoring molecules, and particularly those of biological interest, due to its high surface area, strong coupling between phosphorene and chemical groups, and the possibility of chemically manipulating radicals.

Physicochemical and biological characterization of a xanthan gum-polyvinylpyrrolidone hydrogel obtained by gamma irradiation.

Xanthan gum (XG) and polyvinylpyrrolidone (PVP) are two polymers with low toxicity, high biocompatibility, biodegradability, and high hydrophilicity, making them promising candidates for multiple medical aspects. The present work aimed to synthesize a hydrogel from a mixture of XG and PVP and crosslinked by gamma irradiation. We assessed the hydrogel through a series of physicochemical (FT-IR, TGA, SEM, and percentage of swelling) and biological (stability of the hydrogel in cell culture medium) methods that allowed to determine its applicability. The structural evaluation by infrared spectrum demonstrated that a crosslinked hydrogel was obtained from the combination of polymers. The calorimetric test and swelling percentage confirmed the formation of the bonds responsible for the crosslinked structure. The calorimetric test evidenced that the hydrogel was resistant to decomposition in contrast to non- irradiated material. The determination of the swelling degree showed constant behavior over time, indicating a structure resistant to hydrolysis. This phenomenon also occurred during the test of stability in a cell culture medium. Additionally, microscopic analysis of the sample revealed an amorphous matrix with the presence of porosity. Thus, the findings reveal the synthesis of a novel material that has desirable attributes for its potential application in pharmaceutical and biomedical areas.