Metabolomic Profiling Reveals the Anti-Herbivore Mechanisms of Rice (Oryza sativa).

The use of secondary metabolites of rice to control pests has become a research hotspot, but little is known about the mechanism of rice self-resistance. In this study, metabolomics analysis was performed on two groups of rice (T1, with insect pests; T2, without pests), indicating that fatty acids, alkaloids, and phenolic acids were significantly up-regulated in T1. The up-regulated metabolites (p-value < 0.1) were enriched in linoleic acid metabolism, terpene, piperidine, and pyridine alkaloid biosynthesis, α-linolenic acid metabolism, and tryptophan metabolism. Six significantly up-regulated differential metabolites in T1 were screened out: N-trans-feruloyl-3-methoxytyramine (1), N-trans-feruloyltyramine (2), N-trans-p-coumaroyltyramine (3), N-cis-feruloyltyramine (4), N-phenylacetyl-L-glutamine (5), and benzamide (6). The insect growth inhibitory activities of these six different metabolites were determined, and the results show that compound 1 had the highest activity, which significantly inhibited the growth of Chilo suppressalis by 59.63%. Compounds 2-4 also showed a good inhibitory effect on the growth of Chilo suppressalis, while the other compounds had no significant effect. RNA-seq analyses showed that larval exposure to compound 1 up-regulated the genes that were significantly enriched in ribosome biogenesis in eukaryotes, the cell cycle, ribosomes, and other pathways. The down-regulated genes were significantly enriched in metabolic pathways, oxidative phosphorylation, the citrate cycle (TCA cycle), and other pathways. Eighteen up-regulated genes and fifteen down-regulated genes from the above significantly enriched pathways were screened out and verified by real-time quantitative PCR. The activities of detoxification enzymes (glutathione S-transferase (GST); UDP-glucuronosyltransferase (UGT); and carboxylesterase (CarE)) under larval exposure to compound 1 were measured, which indicated that the activity of GST was significantly inhibited by compound 1, while the activities of the UGT and CarE enzymes did not significantly change. As determined by UPLC-MS, the contents of compound 1 in the T1 and T2 groups were 8.55 ng/g and 0.53 ng/g, respectively, which indicated that pest insects significantly induced the synthesis of compound 1. Compound 1 may enhance rice insect resistance by inhibiting the detoxification enzyme activity and metabolism of Chilo suppressalis, as well as promoting cell proliferation to affect its normal growth and development process. The chemical-ecological mechanism of the insect resistance of rice is preliminarily clarified in this paper.

The diffusion of a Ga atom on GaAs(001)ß2(2 × 4): Local superbasin kinetic Monte Carlo.

We use first-principles density-functional theory to characterize the binding sites and diffusion mechanisms for a Ga adatom on the GaAs(001)ß2(2 × 4) surface. Diffusion in this system is a complex process involving eleven unique binding sites and sixteen different hops between neighboring binding sites. Among the binding sites, we can identify four different superbasins such that the motion between binding sites within a superbasin is much faster than hops exiting the superbasin. To describe diffusion, we use a recently developed local superbasin kinetic Monte Carlo (LSKMC) method, which accelerates a conventional kinetic Monte Carlo (KMC) simulation by describing the superbasins as absorbing Markov chains. We find that LSKMC is up to 4300 times faster than KMC for the conditions probed in this study. We characterize the distribution of exit times from the superbasins and find that these are sometimes, but not always, exponential and we characterize the conditions under which the superbasin exit-time distribution should be exponential. We demonstrate that LSKMC simulations assuming an exponential superbasin exit-time distribution yield the same diffusion coefficients as conventional KMC.

A local superbasin kinetic Monte Carlo method.

We present a local superbasin kinetic Monte Carlo (LSKMC) method that efficiently treats multiple-time-scale problems in kinetic Monte Carlo (KMC). The method is designed to solve the small-barrier problem created by groups of recurrent free-energy minima connected by low free-energy barriers and separated from the full phase space of the system by high barriers. We propose an algorithm to detect, on the fly, groups of recurrent free-energy minima connected by low free-energy barriers and to consolidate them into "superbasins," which we treat with rate equations and/or absorbing Markov chains. We discuss various issues involved with implementing LSKMC simulations that contain local superbasins and non-superbasin events concurrently. These issues include the time distribution of superbasin escapes and interactions between superbasin and non-superbasin states. The LSKMC method is exact, as it introduces no new approximations into conventional KMC simulations. We demonstrate various aspects of LSKMC in several examples, which indicate that significant increases in computational efficiency can be achieved using this method.

A stand-alone mesoporous crystal structure model from in situ X-ray diffraction: nitrogen adsorption on 3D cagelike mesoporous silica SBA-16.

We present a modeling scheme to analyze cagelike silica mesoporous crystals based on in situ X-ray diffraction (XRD) data collected during gas adsorption-desorption (physisorption) processes. Nitrogen physisorption on a silica mesoporous crystal of SBA-16 was directly monitored by using synchrotron in situ powder XRD measurements conducted at SPring-8. SBA-16 is a well-ordered mesoporous silica in which three-dimensional interconnected cagelike primary mesopores are located at the body-centered cubic lattice points. In addition, the surrounding silica matrix contains random microporous and mesoporous intrawall porosities that are significantly influential to the diffusion properties, and thus important to be quantified for this media. The in situ XRD data exhibits seven Bragg reflections throughout the measurements, and the present method allows one to obtain the maximal and stand-alone information about the pore structure (for example, the mesopore size, the matrix density, the intrawall porosity, and pore surface roughness) together with the nitrogen film evolution in the primary mesopores and the intrawall pore-filling in the silica matrix. We furthermore observe a macroscopic amount of nitrogen adsorbed assuming the density of the fluid, and confirm that the XRD "isotherm" recalculated from the analysis result is consistent with the conventional nitrogen isotherm on a semi-quantitative level; however, these results suggest that the intrawall pores would have a greater contribution to the adsorption than considered based on the conventional isotherm analyses. The present method is readily extendable to any ordered mesopores wrapped by the wall matrix containing a certain intrawall porosity.

Diverse ruthenium nitrides stabilized under pressure: a theoretical prediction.

First-principles calculations were performed to understand the structural stability, synthesis routes, mechanical and electronic properties of diverse ruthenium nitrides. RuN with a new I-4m2 symmetry stabilized by pressure is found to be energetically preferred over the experimental NaCl-type and ZnS-type ones. The Pnnm-RuN2 is found to be stable above 1.1 GPa, in agreement with the experimental results. Specifically, new stoichiometries like RuN3 and RuN4 are proposed firstly to be thermodynamically stable, and the dynamical and mechanical stabilities of the newly predicted structures have been verified by checking their phonon spectra and elastic constants. A phase transition from P4/mmm-RuN4 to C2/c-RuN4 is also uncovered at 23.0 GPa. Drawn from bonding and band structure analysis, P4/mmm-RuN4 exhibits semi-metal-like behavior and becomes a semiconductor for the high-pressure C2/c-RuN4 phase. Meanwhile the P21/c-RuN3 shows metallic feature. Highly directional covalent N-N and Ru-N bonds are formed and dominating in N-enriched Ru nitrides, making them promising hard materials.

Study on osmotic pressures for aqueous lysozyme and alpha-chymotrypsin-electrolyte solutions with two Yukawa potentials.

The equation of state (EOS) of Duh and Mier-y-Terán for one Yukawa potential is expanded to two Yukawa potentials to describe the nonidealities of the charged lysozyme and alpha-chymotrypsin solutions. Instead of the classical DLVO theory, the attractive dispersion and double-layer repulsion interactions are represented by two Yukawa potentials, respectively. For the aqueous lysozyme solutions, the only adjustable dispersion energy parameter epsilon/k is regressed and the average deviation is 1.76%. For the aqueous alpha-chymotrypsin solutions, two adjustable parameters (the molecular weight and dispersion energy parameter) are regressed and the average deviation is 7.62%. Some correlation and prediction results are discussed.

Solvation forces between molecularly rough surfaces.

Surface heterogeneity affects significantly wetting and adhesion properties. However, most of the theories and simulation methods of calculating solid-fluid interactions assume a standard thermodynamic model of the Gibbs' dividing solid-fluid interface, which is molecularly smooth. This assumption gives rise to a layering of the fluid phase near the surface that is displayed in oscillating density profiles in any theories and simulation models, which account for the hard core intermolecular repulsion. This layering brings about oscillations of the solvation (or disjoining) pressure as a function of the gap distance, which are rarely observed in experiments, except for ideal monocrystal surfaces. We present a detailed study of the effects of surface roughness on the solvation pressure of Lennard-Jones (LJ) fluids confined by LJ walls based on the quenched solid density functional theory (QSDFT). In QSDFT, the surface roughness is quantified by the roughness parameter, which represents the thickness of the surface "corona" - the region of varying solid density. We show that the surface roughness of the amplitude comparable with the fluid molecular diameter effectively damps the oscillations of solvation pressure that would be observed for molecularly smooth surfaces. The calculations were done for the LJ model of nitrogen sorption at 74.4 K in slit-shaped carbon nanopores to provide an opportunity of comparing with standard adsorption experiments. In addition to a better understanding of the fundamentals of fluid adsorption on heterogeneous surfaces and inter-particle interactions, an important practical outcome is envisioned in modeling of adsorption-induced deformation of compliant porous substrates.

First-order mean spherical approximation for attractive, repulsive, and multi-Yukawa potentials.

The first-order mean spherical approximation (FMSA) theory proposed by Tang et al. [Fluid Phase Equilib., 134, 21(1997)] is applied for studying several typical Yukawa fluids, including attractive, repulsive, and multi-Yukawa cases. The FMSA study is particularly advantageous in providing thermodynamics and structure information in a simple, analytical, and consistent manner. Comparisons with the latest reported computer simulation data for compressibility factor, internal energy, and radial distribution function show that FMSA performs very well and the performance is very close to the full MSA and to several other theories, developed individually for the above-mentioned cases or properties. The present study provides solid evidence to support FMSA applications to more complex fluids.

Correlation and Prediction of Osmotic Pressures for Aqueous Bovine Serum Albumin-NaCl Solutions Based on Two Yukawa Potentials.

A new equation of state is proposed to correlate and predict the osmotic pressure data for aqueous bovine serum albumin (BSA) solutions with different NaCl concentrations and pH values with only one adjustable parameter. The Carnahan-Starling equation represents the contribution of the hard sphere repulsion to the osmotic pressure. The attractive dispersion and double-layer repulsion interactions are represented by two Yukawa potentials, respectively. The equation of state of Duh and Mier-Y-Teran for one Yukawa potential is expanded to two Yukawa potentials to describe the nonidealities of the charged BSA-aqueous NaCl solution, instead of the classical DLVO theory. The average relative deviation of correlation of the osmotic pressure in 0.15 M NaCl solution is 18%. The average relative deviation of prediction in 1-5 M NaCl solutions is 20.33%. A comparison with other models and the limitations of our model are discussed. Copyright 2001 Academic Press.