A benchmark of optimally folded protein structures using integer programming and the 3D-HP-SC model

The Protein Structure Prediction (PSP) problem comprises, among other issues, forecasting the three-dimensional native structure of proteins using only their primary structure information. Most computational studies in this area use synthetic data instead of real biological data. However, the closer to the real-world, the more the impact of results and their applicability. This work presents 17 real protein sequences extracted from the Protein Data Bank for a benchmark to the PSP problem using the tri-dimensional Hydrophobic-Polar with Side-Chains model (3D-HP-SC). The native structure of these proteins was found by maximizing the number of hydrophobic contacts between the side-chains of amino acids. The problem was treated as an optimization problem and solved by means of an Integer Programming approach. Although the method optimally solves the problem, the processing time has an exponential trend. Therefore, due to computational limitations, the method is a proof-of-concept and it is not applicable to large sequences. For unknown sequences, an upper bound of the number of hydrophobic contacts (using this model) can be found, due to a linear relationship with the number of hydrophobic residues. The comparison between the predicted and the biological structures showed that the highest similarity between them was found with distance thresholds around 5.2–8.2 Å. Both the dataset and the programs developed will be freely available to foster further research in the area.     

大数据背景下水厂自动投矾模型研究

根据某市自来水有限责任公司第二水厂的历史矾耗数据，建立矾耗流量关于原水浊度、温度等的动态矾耗模型. 通过对数据进行处理得到10900个合格且净水效果高效的数据，将筛选出的数据分为训练样本集和测试样本集. 在回归拟合中，通过拟合R2的大小将原水浊度划分为“低浊”“中浊”“高浊”3个区间，利用泰勒展开公式的非线性变量代换分别对3个区间建立不同的多项式回归模型，得到预测正确率约为72%，总的矾耗流量值约减少了9.6%的结果；在随机森林模型中，使用10900个合格数据，利用训练样本集，以“原水浊度”“pH值”“原水流量”和“水温”为输入变量，建立包含2000棵决策树的随机森林模型，得到预测正确率约为44. 21%，总的矾耗流量值增加了0.04%的结果. 从模型对合格数据的拟合优度看，随机森林模型比非线性回归模型效果更好；在平均绝对误差、平均绝对偏差百分比等评价指标上，前者均优于后者；但从历史数据检验的结果，模型的可解读性，模型的操作难度和推广角度看，分段二元非线性回归模型的优势更为突出.     

一带一路背景下企业地域影响力发展的规划研究

面对一个分布在新地理区域的新市场,合理规划区域服务影响力的发展战略对企业至关重要。本文假设企业的服务影响力在地理区域上的发展可以用其地理上分布的立足点来表示。单个立足点覆盖有限范围内的地理区域,并且在一个特定时刻用所有立足点所覆盖地理区域的总和来表示企业该时刻的发展状态。由于资源限制,企业对经济发展迅速的区域的覆盖必须在一定时间内逐步完成。因此,在发展时期内如何确定立足点的位置并使其位于知名城市中,是企业管理者亟待解决的问题。针对这个问题,本文首先基于时间序列预测方法建立了区域经济指标评估模型;然后使用集合覆盖理论提出了以成本和满意度为目标的选址优化模型并使用分支定界算法求解该模型;最后,使用从“一带一路”地区收集的数据对模型进行了检验。结果表明,该方法对有相关问题的企业具有较大的参考价值。     

Fabricating Dual-Atom Iron Catalysts for Efficient Oxygen Evolution Reaction: A Heteroatom Modulator Approach

Understanding the thermal aggregation behavior of metal atoms is important for the synthesis of supported metal clusters. Here, derived from a metal–organic framework encapsulating a trinuclear Fe^III₂Fe^II complex (denoted as Fe₃) within the channels, a well-defined nitrogen-doped carbon layer is fabricated as an ideal support for stabilizing the generated iron nanoclusters. Atomic replacement of Fe^II by other metal(II) ions (e.g., Zn^II/Co^II) via synthesizing isostructural trinuclear-complex precursors (Fe₂Zn/Fe₂Co), namely the “heteroatom modulator approach”, is inhibiting the aggregation of Fe atoms toward nanoclusters with formation of a stable iron dimer in an optimal metal–nitrogen moiety, clearly identified by direct transmission electron microscopy and X-ray absorption fine structure analysis. The supported iron dimer, serving as cooperative metal–metal site, acts as efficient oxygen evolution catalyst. Our findings offer an atomic insight to guide the future design of ultrasmall metal clusters bearing outstanding catalytic capabilities.     

Synthesis and characterization of dimeric μ-oxidovanadium complexes as the functional model of vanadium bromoperoxidase

Two vanadium (IV) complexes [V^IVO(Haeae-sal)(MeOH)]⁺ ( 1 ) and [V^IVO(Haeae-hyap)(MeOH)]⁺ ( 2 ) were prepared by reacting [VO(acac)₂] with ligands [H₂aeae-sal] ( I ) and [H₂aeae-hyap] ( II ) respectively. Condensation of 2-(2-aminoethylamino)ethanol with salicylaldehyde and 2-hydroxyacetophenone produces the ligands ( I ) and ( II ) respectively. Both vanadium complexes 1 and 2 are sensitive towards aerial oxygen in solution and rapidly convert into vanadium(V) dioxido species. Vanadium(V) dioxido species crystalizes as the dimeric form in the solid-state. Single-crystal XRD analysis suggests octahedral geometry around each vanadium center in the solid-state. To access the benefits of heterogeneous catalysis, vanadium(V) dioxido complexes were anchored into the polymeric chain of chloromethylated polystyrene. All the synthesized neat and supported vanadium complexes have been studied by a number of techniques to confirm their structural and functional properties. Bromoperoxidase activity of the synthesized vanadium(V) dioxido complexes 3 and 4 was examined by carrying out oxidative bromination of salicylaldehyde and oxidation of thioanisole. In the presence of hydrogen peroxide, 3 shows 94.4% conversion ( TOF value of 2.739 × 10² h⁻¹) and 4 exhibits 79.0% conversion (TOF value of 2.403 × 10² h⁻¹) for the oxidative bromination of salicylaldehyde where 5-bromosalicylaldehyde appears as the major product. Catalysts 3 and 4 also efficiently catalyze the oxidation of thioanisole in the presence of hydrogen peroxide where sulfoxide is observed as the major product. Covalent attachment of neat catalysts 3 and 4 into the polymer chain enhances substrate conversion (%) and their catalytic efficiency increases many folds, both in the oxidative bromination and oxidation of thioether. Polymer supported catalysts 5 displayed 98.8% conversion with a TOF value of 1.127 × 10⁴ h⁻¹ whereas catalyst 6 showed 95.7% conversion with a TOF value of 4.675 × 10³ h⁻¹ for the oxidative bromination of salicylaldehyde. These TOF values are the highest among the supported vanadium catalysts available in the literature for the oxidative bromination of salicylaldehyde.     

Single crystal X-ray of 1-[(1,2,4-triazole-4-yl)imino]diacetyl monoxime (L) as a novel triazole and the characterization and biological studies of its chelates of Co2+, Pd2+, and Fe3+

A novel and efficient synthesis of 1-[(1,2,4-triazole-4-yl)imino]diacetyl monoxime ( L ) is described. The advantages of this method are that it is inexpensive, the starting reactants are readily available, and it has good yield and short reaction times. The hull of the product was suggested by elemental analyses, spectral and single crystal X-ray. Novel Co ²⁺ , Pd²⁺, and Fe ³⁺ chelates derived from L were characterized by Fourier transform infrared spectroscopy, suggesting that L acts as bidentate via the two azomethine groups. Tetrahedral geometry for Fe³⁺ and Co²⁺ and square-planar geometry around the Pd²⁺ chelate were suggested depending on the spectral and magnetic data. The results of density functional theory were applied to illustrate the geometry of L towards the metal ions. Coats–Redfern and Horowitz–Metzger methods were applied to investigate the kinetic and thermodynamic parameters of the chelates. Cyclic voltammetry was carried out to study the stability of the Co²⁺ and Fe³⁺ chelates. L and its complexes were tested against three types of cancer cells, antibacterial and antifungal.     

A DNA Switch for Detecting Single Nucleotide Polymorphism within a Long DNA Sequence Under Denaturing Conditions

DNA detection is usually conducted under nondenaturing conditions to favor the formation of Watson–Crick base-paring interactions. However, although such a setting is excellent for distinguishing a single-nucleotide polymorphism (SNP) within short DNA sequences (15–25 nucleotides), it does not offer a good solution to SNP detection within much longer sequences. Here we report on a new detection method capable of detecting SNP in a DNA sequence containing 35–90 nucleotides. This is achieved through incorporating into the recognition DNA sequence a previously discovered DNA molecule that forms a stable G-quadruplex in the presence of 7 molar urea, a known condition for denaturing DNA structures. The systems are configured to produce both colorimetric and fluorescent signals upon target binding.