By-passing the Kohn-Sham equations with machine learning

Last year, at least 30,000 scientific papers used the Kohn-Sham scheme of density functional theory to solve electronic structure problems in a wide variety of scientific fields, ranging from materials science to biochemistry to astrophysics. Machine learning holds the promise of learning the kinetic energy functional via examples, by-passing the need to solve the Kohn-Sham equations. This should yield substantial savings in computer time, allowing either larger systems or longer time-scales to be tackled, but attempts to machine-learn this functional have been limited by the need to find its derivative. The present work overcomes this difficulty by directly learning the density-potential and energy-density maps for test systems and various molecules. Both improved accuracy and lower computational cost with this method are demonstrated by reproducing DFT energies for a range of molecular geometries generated during molecular dynamics simulations. Moreover, the methodology could be applied directly to quantum chemical calculations, allowing construction of density functionals of quantum-chemical accuracy

Protective effect of (-) α-bisabolol on markers of oxidative stress in erythrocytes subjected to oxidative insult

(-)-α-bisabolol is a sesquiterpene alcohol found as a major component of essential oil of chamomile (Matricaria recutita L., Chamomilla recutita L., Matricaria chamomilla L.; Family Asteraceae). Chamomile, one of the most ancient and widely recognized herbs to mankind, has been used traditionally for centuries as an anti-inflammatory, antispasmodic, carminative, mild astringent and healing medicine. It is also known to be very helpful as an external agent for encouraging the rapid healing of ulcers and burns without infection, as well as persistent skin problems such as eczema and psoriasis. Since clinical trials and human studies are limited, we have investigated the effect of (-)-α-bisabolol on markers of oxidative stress in human erythrocytes by incubating with hydrogen peroxide (2mM) and tert-butyl hydroperoxide (10 µM). Subjecting erythrocyte to oxidative stress caused a significant alteration in reduced glutathione GSH), malondialdehyde (MDA) concentration as well as superoxide dismutase and catalase activity compare to control. Presence of (-)-α-bisabolol as low as 0.1µM in incubation medium protected the erythrocytes from oxidative stress and helps to maintain the basal level of GSH and MDA. The activity of superoxide dismutase and catalase were also restored in a concentration-dependent manner (0.01-100µM). The effect was also compared with L-Ascorbic acid, quercetin and BHT. Our findings provide evidence for the protection of oxidative stress in erythrocytes by (-)-α-bisabolol that could be considered for further studies

Estimating Local Function Complexity via Mixture of Gaussian Processes

Real world data often exhibit inhomogeneity, e.g., the noise level, the sampling distribution or the complexity of the target function may change over the input space. In this paper, we try to isolate local function complexity in a practical, robust way. This is achieved by first estimating the locally optimal kernel bandwidth as a functional relationship. Specifically, we propose Spatially Adaptive Bandwidth Estimation in Regression (SABER), which employs the mixture of experts consisting of multinomial kernel logistic regression as a gate and Gaussian process regression models as experts. Using the locally optimal kernel bandwidths, we deduce an estimate to the local function complexity by drawing parallels to the theory of locally linear smoothing. We demonstrate the usefulness of local function complexity for model interpretation and active learning in quantum chemistry experiments and fluid dynamics simulations.Comment: 19 pages, 16 figure

Nimesulide limits kainate-induced oxidative damage in the rat hippocampus

Kainate induces a marked expression of cyclooxygenase-2 after its systemic administration. Because cyclooxygenase-2 activity is associated to the production of reactive oxygen species, we investigated the effects of nimesulide, a selective cyclooxygenase-2 inhibitor, on kainate-induced in vivo oxidative damage in the rat hippocampus. A clinically relevant dose of nimesulide (6 mg/kg, i.p. ) was administered three times following kainate application (9 mg/kg, i.p.). After 24 h of kainate administration, the drastic decrease in hippocampal glutathione content and the significant increase in lipid peroxidation were attenuated in nimesulide-treated rats, suggesting that the induction of cyclooxygenase-2 is involved in kainate-mediated free radicals formation

Effect of carboxymethyl cellulose-based coatings incorporated with Zataria multiflora Boiss. essential oil and grape seed extract on the shelf life of rainbow trout fillets

To prolong the shelf life of seafood products, lipid oxidation and growth of microorganisms should be retarded. The objective of the current study was evaluating the potential application of carboxymethyl cellulose (CMC) coatings incorporated with Zataria multiflora Boiss. essential oil (ZMEO) and grape seed extract (GSE) on chemical (thiobarbituric acid reactive substances (TBARS) and total volatile basic nitrogen (TVB-N)), microbial (total viable count, lactic acid bacteria and Pseudomonas spp.) and organoleptic attributes of rainbow trout fillets during refrigerated storage for twenty days. GCeMS analysis showed that ZMEO is rich in monoterpene phenols such as thymol and carvacrol. The following results were obtained after 20 days of storage: The minimum level of TVB-N was measured in the fillets coated with CMC + 2 v/v ZMEO + 0.5 v/v GSE. The minimum number of total viable bacteria, lactic acid bacteria and Pseudomonas spp. were determined in the fillets coated with CMC + 2 v/v ZMEO + 1 v/v GSE. The fillets coated with CMC + 1 v/v ZMEO + 1 v/v GSE showed the best organoleptic properties. Our results revealed that CMC-based coatings incorporated with ZMEO and GSE could improve chemical, microbial and sensorial characteristics of rainbow trout fillets during cold storage. © 2015 Elsevier Ltd

Symmetry of Hydrogen Bonds in Two Enols in Solution.

The enols of 4-cyano-2,2,6,6-tetramethyl-3,5-heptanedione and of nitromalonamide were prepared as statistical mixtures of 18O n ( n = 0, 1, 2) isotopologues. The symmetries of their hydrogen bonds were probed by isotopic perturbation of their 13CO NMR signals. The former mixture shows a total of four signals, due to both intrinsic and perturbation isotope shifts. Therefore, that enol is a mixture of tautomers with an asymmetric hydrogen bond. In contrast, the mixture of isotopologues of nitromalonamide enol shows only two signals, due to an intrinsic isotope shift. Therefore, this is the first case, to be compared with the FHF- anion, of a neutral species with a single symmetric structure in solution and with a centered hydrogen

An efficient Monte Carlo method for calculating ab initio transition state theory reaction rates in solution

In this article, we propose an efficient method for sampling the relevant state space in condensed phase reactions. In the present method, the reaction is described by solving the electronic Schr\"{o}dinger equation for the solute atoms in the presence of explicit solvent molecules. The sampling algorithm uses a molecular mechanics guiding potential in combination with simulated tempering ideas and allows thorough exploration of the solvent state space in the context of an ab initio calculation even when the dielectric relaxation time of the solvent is long. The method is applied to the study of the double proton transfer reaction that takes place between a molecule of acetic acid and a molecule of methanol in tetrahydrofuran. It is demonstrated that calculations of rates of chemical transformations occurring in solvents of medium polarity can be performed with an increase in the cpu time of factors ranging from 4 to 15 with respect to gas-phase calculations.Comment: 15 pages, 9 figures. To appear in J. Chem. Phy