Probing defects and correlations in the hydrogen-bond network of ab initio water

The hydrogen-bond network of water is characterized by the presence of coordination defects relative to the ideal tetrahedral network of ice, whose fluctuations determine the static and time-dependent properties of the liquid. Because of topological constraints, such defects do not come alone, but are highly correlated coming in a plethora of different pairs. Here we discuss in detail such correlations in the case of ab initio water models and show that they have interesting similarities to regular and defective solid phases of water. Although defect correlations involve deviations from idealized tetrahedrality, they can still be regarded as weaker hydrogen bonds that retain a high degree of directionality. We also investigate how the structure and population of coordination defects is affected by approximations to the inter-atomic potential, finding that in most cases, the qualitative features of the hydrogen bond network are remarkably robust

Thermal transport at a nanoparticle-water interface: A molecular dynamics and continuum modeling study

Heat transfer between a silver nanoparticle and surrounding water has been studied using molecular dynamics (MD) simulations. The thermal conductance (Kapitza conductance) at the interface between a nanoparticle and surrounding water has been calculated using four different approaches: transient with/without temperature gradient (internal thermal resistance) in the nanoparticle, steady-state non-equilibrium and finally equilibrium simulations. The results of steady-state non-equilibrium and equilibrium are in agreement but differ from the transient approach results. MD simulations results also reveal that in the quenching process of a hot silver nanoparticle, heat dissipates into the solvent over a length-scale of ~ 2nm and over a timescale of less than 5ps. By introducing a continuum solid-like model and considering a heat conduction mechanism in water, it is observed that the results of the temperature distribution for water shells around the nanoparticle agree well with MD results. It is also found that the local water thermal conductivity around the nanoparticle is greater by about 50 percent than that of bulk water. These results have important implications for understanding heat transfer mechanisms in nanofluids systems and also for cancer photothermal therapy, wherein an accurate local description of heat transfer in an aqueous environment is crucial.Comment: 22 pages, 7 figures

Evaluating potential of borage (Borago officinalis L.) in bioremediation of saline soil

Bioremediation is an efficient, economical and environmentally acceptable strategy used for coping with the salinization of agricultural soils. In this study, borage has been proposed as possible candidate for bioremediation of Na+ and Cl−. In this order, the borage (Borago officinalis L.) seeds were sown under four levels of salinity (non-saline as control, 5, 10 and 15 dSm-1). Bioremediation and production potentials of borage were evaluated at three growth stages: seedling or early growth, vegetative and flowering stages. This study has been conducted using factorial experiment in randomized complete block design with three replications. The saline ions accumulation in company with changes in growth and chemical composition of borage was studied. The results indicated that the contents of Na+ and Cl− in plants increased as salinity levels of growth medium were enhanced. The noticeable contents of Na+ and Cl− (9.096 and 5.665%, respectively) were accumulated in borage aerial parts at the highest level of salinity (EC of 15 dSm-1), whereas minimum values, 2.029 and 1.520%, occurred at non-saline condition. Although, borage growth decreased with increasing salinity, its survival/or noticeable growth indicated that this plant could tolerate salinity up to EC of 15 dSm-1. The salinity had a significant effect on the total phenol, alkaloids and tannins and their contents increased with increasing salinity. In contrast, mucilage content and swelling index significantly decreased with increasing salinity. Therefore, borage had noticeable quality and quantity yield up to salinity level of 15 dSm-1 and could cumulatively remove considerable amounts of salt from the soil. In addition, if borage can be cultivated as an inter-crop all year round at saline soil with EC up to 15 dSm-1, it can remedy saline soil in respect to Na+ and Cl−.Keywords: Borago officinalis L., bioremediation, growth stage, salinity, salt toleranc

Learning the Hydrophilic, Hydrophobic and Aromatic Character of Amino Acids from their Interfacial Thermal Conductance in Water

In this study, the thermal relaxation of the 20 naturally occurring amino-acids in water is investigated using transient non-equilibrium molecular-dynamics simulations. By modeling the thermal relaxation process, the relaxation times of the amino-acids in water occurs over a timescale covering 2-5 ps. For the hydrophobic amino acids, the relaxation time is controlled by the size of the hydrocarbon side chain, while for hydrophilic amino acids, the number of hydrogen bonds do not significantly affect the timescales of the heat dissipation. Our results show that the interfacial thermal conductance at the amino-acid water interface is in the range of~40-80 MWm$^{-2}$K$^{-1}$. Hydrophobic and aromatic amino acids tend to have a lower interfacial thermal conductance. Notably, we reveal that amino acids can be classified, in terms of their thermal relaxation times and molar masses, into simply connected phases with the same hydrophilicity, hydrophibicity and aromaticity.Comment: 19 pages, 6 figure

Do Machine-Learning Atomic Descriptors and Order Parameters Tell the Same Story? The Case of Liquid Water

Machine-learning (ML) has become a key workhorse in molecular simulations. Building an ML model in this context, involves encoding the information of chemical environments using local atomic descriptors. In this work, we focus on the Smooth Overlap of Atomic Positions (SOAP) and their application in studying the properties of liquid water both in the bulk and at the hydrophobic air-water interface. By using a statistical test aimed at assessing the relative information content of different distance measures defined on the same data space, we investigate if these descriptors provide the same information as some of the common order parameters that are used to characterize local water structure such as hydrogen bonding, density or tetrahedrality to name a few. Our analysis suggests that the ML description and the standard order parameters of local water structure are not equivalent. In particular, a combination of these order parameters probing local water environments can predict SOAP similarity only approximately, and viceversa, the environments that are similar according to SOAP are not necessarily similar according to the standard order parameters. We also elucidate the role of some of the metaparameters entering in the SOAP definition in encoding chemical information

A novel sorting method topsis-sort: an applicaiton for tehran environmental quality evaluation

Many real-life problems are multi-objective by nature that requires evaluation of more than one criterion, therefore MCDM has become an important issue. In recent years, many MCDM methods have been developed; the existing approaches have been improved and extended. Multi criteria decision analysis has been regarded as a suitable set of methods to perform sustainability evaluations. Among numerous MCDM methods developed to solve real-life decision problems, Technique for Order Preference by Similarity to Ideal Solution (TOPSIS) continues to work satisfactorily in diverse application areas. In this paper, a novel sorting method (TOPSIS-Sort) based on the classic TOPSIS method is presented. In the TOPSIS-Sort approach an outranking relation is used for sorting purposes. The proposed approach uses characteristic profiles for defining the classes and outranking relation as the preference model. Application of the proposed approach is demonstrated by classifying 22 districts of Tehran into five classes (but none of the districts fits into Classes 4 and 5), representing areas with different levels of environmental quality. An analysis and assessment of the environmental conditions in Tehran helps to identify the districts with the poor environmental quality. Priority should be given to these areas to maintain and improve the quality of environment. The results obtained by the TOPSIS-Sort give credence to its success, because the results of sorting con firm our and specialists’ evaluation of the districts. This research provides appropriate results with respect to the development of sorting models in the form of outranking relations. The model, proposed by this study, is applicable to the other outranking methods such as ELECTRE, PROMETHEE, etc