Self-assembly mechanism of PEG-b-PCL and PEG-b-PBO-b-PCL amphiphilic copolymer micelles in aqueous solution from coarse grain modeling

We followed the self-assembly of high-molecular weight MePEG- b -PCL (poly(methyl ethylene glycol)-block-poly(ε-caprolactone)) diblock and MePEG- b -PBO- b -PCL (poly(methyl ethylene glycol)-block-poly(1,2-butylene oxide)-block-poly(ε-caprolactone)) into micelles using molecular dynamics simulation with a coarse grain (CG) force field based on quantum mechanics (CGq FF). The triblock polymer included a short poly(1,2-butylene oxide) (PBO) at the hydrophilic-hydrophobic interface of these systems. Keeping the hydrophilic length fixed (MePEG₄₅), we considered 250 chains in which the hydrophobic length changed from PCL₄₄ or PBO₆- b -PCL₄₃ to PCL₆₂ or PBO₉- b -PCL₆₁. The polymers were solvated in explicit water for 2 μs of simulations at 310.15 K. We found that the longer diblock system undergoes a morphological transition from an intermediate rod-like micelle to a prolate-sphere, while the micelle formed from the longer triblock system is a stable rod-like micelle. The two shorter diblock and triblock systems show similar self-assembly processes, both resulting in slightly prolate-spheres. The dynamics of the self-assembly is quantified in terms of chain radius of gyration, shape anisotropy, and hydration of the micelle cores. The final micelle structures are analyzed in terms of the local density components. We conclude that the CG model accurately describes the molecular mechanisms of self-assembly and the equilibrium micellar structures of hydrophilic and hydrophobic chains, including the quantity of solvent trapped inside the micellar core.     

Melting thermodynamics of oligonucleic acids conjugated with relatively solvophobic linear polymers: A coarse‐grained molecular simulation study

Oligonucleic acids (ONAs), such as DNA and RNA, are used in various biotechnology and nanotechnology applications due to their ability to form a double helix that is stable at low temperature and melts at high temperatures. The melting temperature (T_m) of ONA duplexes can be tuned by the ONA composition, sequence, length and concentration, solvent quality, and salt concentration and by conjugation to other macromolecules. In this article, we use coarse‐grained (CG) molecular simulations to study ONAs conjugated with linear homopolymers that are relatively more solvophobic than the ONA. We study charged and stiff 8‐mer ONAs (e.g., DNA) and neutral and flexible 8‐mer ONAs (e.g., peptide nucleic acids or PNA), and vary the composition (or G‐C content) and sequence of ONA, conjugated homopolymer lengths and solvent quality for the polymer. For neutral and flexible ONAs, as the solvent quality worsens for the polymer, the ONA melting temperature increases from that of unconjugated ONA. The melting curves broaden with polymer length and worsening solvent quality, especially for ONAs with higher G‐C content. For charged and stiff ONAs, as the solvent quality worsens, the ONA melting temperature decreases compared to unconjugated ONA while the width of the melting curve remains the same. © 2019 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2019 , 57, 1196–1208     

基于SVM的固化土无侧限抗压强度模型

为实现较少试验次数下固化土无侧限抗压强度(qu)的准确预测, 提出了基于支持向量机(SVM)的固化土qu的预测模型. 以固化剂各组分掺入比、龄期、初始含水量、固化剂掺量等因素为输入量, 固化土的qu作为输出量, 以径向基为核函数, 采用网格搜索法和交叉验证法进行参数优化, 建立了基于SVM的固化土qu的预测模型. 算例分析表明: 该模型适用于任意条件下固化土qu的精确预测, 且在较小试验成本下实现与响应面法相当的预测精度.     

Influence of Earthworms on the Sulfur Turnover in the Soil

Abstract

The effects of earthworm activity on the concentration and isotopic composition of total sulfur in soils was investigated using batch experiments. Two ecologically different lumbricid species, the anecic Lumbricus terrestris and the endogeic Aporrectodea caliginosa, were used. The earthworms were fed birch leaves, beech leaves, cattle manure or mixed plant litter. All food sources differed isotopically (δ³⁴S) from the soil (Parabraunerde). As a reference, one experiment was carried out without additional food.

The experimental results show, that both earthworm species influence the total S-content and the δ³⁴S-values in the soil by digestion of the different food sources. The differences in the total S-content of the earthworm tissues and in the S-isotopic composition of the casts can be attributed to the ecological differences between the earthworm species.     

15N-Traceruntersuchungen zum Mechanismus der N2O-Bildung in Böden

Nitrous oxide is a potential environmental hazard responsible for the green house effect and the destruction of the ozone layer in the lower stratosphere. Biological denitrification under anaerobic conditions in soils results in the formation of both N₂O and N₂, whereby highly nitrogen-fertilized agricultural soils contribute to a considerable extent of the N₂O emission. Latest results in the literature indicate that nitrous oxide can also be formed as a byproduct of the microbial nitrification. This is of importance for soils in central Germany because of the non-existence of typical denitrification conditions in a semiaride climate.

This study was conducted to measure the path of N₂O formation in Haplic Phaeozen: using [¹⁵N] ammonium and [¹⁵N] nitrat and a GC-MS aided incubation system. The kinetic isotope method was used to evaluate the experimental data. The results are:

- Under anaerobic conditions (～ 90% of the water holding capacity = WHC) N₂O originates mainly from the nitrate pool by denitrification.

- As expected, the N₂O formation is low under aerobic conditions (～ 80% WHC) but the gas originates directly from the ammonium and not from the nitrate pool, probably as a byproduct of the nitrification process.     

Calibration Curve with Improved Limit of Detection for Cadmium in Soil: An Approach to Minimize the Matrix Effect in Laser-Induced Breakdown Spectroscopic Analysis

The present article describes a working or combined calibration curve in laser-induced breakdown spectroscopic analysis, which is the cumulative result of the calibration curves obtained from neutral and singly ionized atomic emission spectral lines. This working calibration curve reduces the effect of change in matrix between different zone soils and certified soil samples because it includes both the species' (neutral and singly ionized) concentration of the element of interest. The limit of detection using a working calibration curve is found better as compared to its constituent calibration curves (i.e., individual calibration curves). The quantitative results obtained using the working calibration curve is in better agreement with the result of inductively coupled plasma–atomic emission spectroscopy as compared to the result obtained using its constituent calibration curves.     

超声辅助提取/离子色谱法测定铬污染土壤中的六价铬

建立了超声辅助提取/离子色谱法测定铬污染场地中铬（Ⅵ）的方法。选用0.3 mol/L的KCl溶液作提取剂,对12组土壤样品中的铬（Ⅵ）进行超声辅助提取20 min。采用Metrosep A Supp 4-250（250 mm×4.0mm）型阴离子分离柱,以4 mmol/L Na₂CO₃-1 mmol/L NaHCO₃混合溶液为淋洗液对样品进行分离分析。铬（Ⅵ）在0.01²0 mg/L浓度范围有较好的线性关系,相关系数（r²）为0.999 8;该方法的检出限为0.003 mg/L,加标回收率为96.4%¹06.8%,相对标准偏差（RSD,n=3）为0.56%。该方法具有简便、快速、准确等优点,适用于铬污染场地的监测与调查。     

Characterization and Three-dimensional Structural Modeling of Humic Acid via Molecular Mechanics and Molecular Dynamic Simulation

The humic acid（HA） sample obtained from the alluvial soil was characterized by elemental composition, pyrolysis gas chromatography-mass spectrometry（Py-GC-MS） and solid-state 13C nuclear magnetic resonance （13C NMR） spectroscopy. There is high fat content and a few nitrogen-containing functional groups in HA. Py-GC-MS demonstrates the characterization and structural identification of HA. One long list of identified pyrolysis products was proposed for the construction of conceptual model of HA. Solid-state 13C NMR data indicate there are higher values of alkyl-C, O-alkyl-C and aryl-C in HA. The elemental composition, structural carbon distribution and L3C NMR spectroscopy of simulated HA are consistent with those of experimental HA. HyperChem was used to simulate the three-dimensional molecular structure of the monomer, which was optimized by the molecular mechanics of the optimized potential for liquid simulations（OPLS） force field and molecular dynamics simulation to get the stable and balanced conformation. The deprotonation process study depicts that the degree of ionization of HA gets deeper, while the electronegativity of HA and the energy of van der Waals（vdW） increase. Moreover, the 3D structure of humic acid with -4 charges is the most stable. The deprotonation process is an endothermic process.     

High–quality protein backbone reconstruction from alpha carbons using Gaussian mixture models

Coarse‐grained protein structure models offer increased efficiency in structural modeling, but these must be coupled with fast and accurate methods to revert to a full‐atom structure. Here, we present a novel algorithm to reconstruct mainchain models from C traces. This has been parameterized by fitting Gaussian mixture models (GMMs) to short backbone fragments centered on idealized peptide bonds. The method we have developed is statistically significantly more accurate than several competing methods, both in terms of RMSD values and dihedral angle differences. The method produced Ramachandran dihedral angle distributions that are closer to that observed in real proteins and better Phaser molecular replacement log‐likelihood gains. Amino acid residue sidechain reconstruction accuracy using SCWRL4 was found to be statistically significantly correlated to backbone reconstruction accuracy. Finally, the PD2 method was found to produce significantly lower energy full‐atom models using Rosetta which has implications for multiscale protein modeling using coarse‐grained models. A webserver and C++ source code is freely available for noncommercial use from: http://www.sbg.bio.ic.ac.uk/phyre2/PD2_ca2main/ . © 2013 Wiley Periodicals, Inc.     

A New Organophosphorus Insecticides Removal Process Using Fly ASH

Abstract

Fly ash and soil mixtures with a range of fly ash content from 1 to 100% were used to study adsorption and desorption of four organophosphorus insecticides, ethyl parathion, methyl parathion, fenitrothion and fenthion, in batch experiments. The object of the study was to develop a treatment process using fly ash as sorbent material to isolate/immobilize organic contaminants from aqueous solutions. The adsorption isotherms fit the Freundlich equation x/m=K_dC^1/n. The K_d values increase with the increase of the fly ash content. The isotherms seem to fit the S type, in mixtures of soil with a fly ash content from 0 to 10%, which implies that adsorption becomes easier as the concentration in the liquid phase increases. In mixtures of soil with a fly ash content from 25 to 50% the isotherms become L type and correspond to a decrease of site availability as the solution concentration increases. Finally in mixtures of soil with a fly ash content over 50%, C type adsorption was observed which correspond to a constant partition of the insecticides between the bulk solution and the adsorbent. Mass balance estimations show that the mean percent amounts of insecticides for a range of concentration 0.5–15 mg/l, removed by adsorption in the soil sample are 81.56 % for ethyl parathion, 48.97 % for methyl parathion, 67.06 % for fenitrothion and 86.65 % for fenthion. The adsorption increases as the fly ash content increased and reach the 100% in the “pure” fly ash. The adsorbed amounts of insecticides in mixtures of soils with >50% fly ash content, are up to 99%. In contrast, the amounts of desorption in water decrease as the fly ash content increase.

The results of this research demonstrate that the fly ash shows a significant capacity for adsorption of organophosphorus compounds from aqueous solution and can be used for pesticide removal process.