Genes Identification,Molecular Docking and Dynamics Simulation Analysis of Laccases from Amylostereum areolatum Provides Molecular Basis of Laccase Bound to Lignin

An obligate mutualistic relationship exists between the fungus Amylostereum areolatum and woodwasp Sirex noctilio. The fungus digests lignin in the host pine, providing essential nutrients for the growing woodwasp larvae. However, the functional properties of this symbiosis are poorly described. In this study, we identified, cloned, and characterized 14 laccase genes from A. areolatum. These genes encoded proteins of 508 to 529 amino acids and contained three typical copper-oxidase domains, necessary to confer laccase activity. Besides, we performed molecular docking and dynamics simulation of the laccase proteins in complex with lignin compounds (monomers, dimers, trimers, and tetramers). AaLac2, AaLac3, AaLac6, AaLac8, and AaLac10 were found that had low binding energies with all lignin model compounds tested and three of them could maintain stability when binding to these compounds. Among these complexes, amino acid residues ALA, GLN, LEU, PHE, PRO, and SER were commonly present. Our study reveals the molecular basis of A. areolatum laccases interacting with lignin, which is essential for understanding how the fungus provides nutrients to S. noctilio. These findings might also provide guidance for the control of S. noctilio by informing the design of enzyme mutants that could reduce the efficiency of lignin degradation.     

Sequence-Dependent Nanofiber Structures of Phenylalanine and Isoleucine Tripeptides

The molecular design of short peptides to achieve a tailor-made functional architecture has attracted attention during the past decade but remains challenging as a result of insufficient understanding of the relationship between peptide sequence and assembled supramolecular structures. We report a hybrid-resolution model to computationally explore the sequence–structure relationship of self-assembly for tripeptides containing only phenylalanine and isoleucine. We found that all these tripeptides have a tendency to assemble into nanofibers composed of laterally associated filaments. Molecular arrangements within the assemblies are diverse and vary depending on the sequences. This structural diversity originates from (1) distinct conformations of peptide building blocks that lead to different surface geometries of the filaments and (2) unique sidechain arrangements at the filament interfaces for each sequence. Many conformations are available for tripeptides in solution, but only an extended β-strand and another resembling a right-handed turn are observed in assemblies. It was found that the sequence dependence of these conformations and the packing of resulting filaments are determined by multiple competing noncovalent forces, with hydrophobic interactions involving Phe being particularly important. The sequence pattern for each type of assembly conformation and packing has been identified. These results highlight the importance of the interplay between conformation, molecular packing, and sequences for determining detailed nanostructures of peptides and provide a detailed insight to support a more precise design of peptide-based nanomaterials.     

基于VOF模型的层叠器流动过程分析及流道结构优化

基于FLUENT软件的流体体积(VOF)模型研究了不同壁面滑移程度以及不同流道结构参数下4层等厚熔体通过层叠器倍增为8层熔体时,流道中熔体的分层情况变化。结果表明,壁面滑移程度的降低会促使熔体在上下壁面聚集,进而导致上下壁面处熔体层厚增加;汇流段与出口段间圆角半径、汇流段扩压角和平衡段长度这3个结构参数则只会影响熔体在左右壁面的聚集,进而影响各层熔体的尺寸精度,且其中扩压角的影响程度最大,平衡段长度次之,圆角半径的影响较小。     

金属配合物与核酸作用机理的理论计算

通过计算机模拟金属配合物与核酸作用机理,对其理论模型能量计算和结构优化。在不同的化学环境条件下得到不同的实验模拟结果,对真实的化学反应过程有重要的指导意义和参考意义。通过Gaussian03,Gauss View等软件的结合应用,分别应用于优化计算和理论建模,熟悉了对化学软件操作应用。     

超深溜井爆破一次成井技术实践

为解决溜井掘进效率低、安全性差等问题，以柿竹园多金属矿掘进出矿溜井为例，提出了爆破一次成井技术，根据矿山具体爆破条件，设计了布孔参数、装药结构和起爆顺序等。实践表明，爆破一次成井技术施工天井效果良好，溜井贯穿上下2个分段，与设计相符，相较于普通法施工天井，节约成本30.7%，节约时间58.3%，经济效益显著，施工周期短，且安全性好，值得在其他类似矿山推广应用。     

采油树平板闸阀柔性密封圈结构优化设计

为了提高采油树平板闸阀密封圈的密封性能,在泛塞封的基础上,设计一种密封圈本体唇边开有锯齿状凸起的新型柔性密封结构;运用有限元分析方法模拟密封圈的工作状况,分析柔性密封结构特性参数对密封圈密封性能的影响,获得不同柔性密封圈结构参数下密封面间接触应力分布规律,并对新型密封结构进行优化。结果表明:密封面间最大接触应力随唇边锯齿数量、唇边夹角度数的增大而增大,随唇谷夹角度数的增大而减小;新型密封结构选择锯齿数量为3、唇边夹角为20°、唇谷夹角为30°的特性参数时,其最大接触应力比常规Y形密封圈提高了15倍;新型柔性密封结构的密封圈与阀杆、阀盖壁面间接触应力比常规Y形密封圈有显著提高,提高了密封圈的密封性能。     

Methods and Applications of In Silico Aptamer Design and Modeling

Aptamers are nucleic acid analogues of antibodies with high affinity to different targets, such as cells, viruses, proteins, inorganic materials, and coenzymes. Empirical approaches allow the design of in vitro aptamers that bind particularly to a target molecule with high affinity and selectivity. Theoretical methods allow significant expansion of the possibilities of aptamer design. In this study, we review theoretical and joint theoretical-experimental studies dedicated to aptamer design and modeling. We consider aptamers with different targets, such as proteins, antibiotics, organophosphates, nucleobases, amino acids, and drugs. During nucleic acid modeling and in silico design, a full set of in silico methods can be applied, such as docking, molecular dynamics (MD), and statistical analysis. The typical modeling workflow starts with structure prediction. Then, docking of target and aptamer is performed. Next, MD simulations are performed, which allows for an evaluation of the stability of aptamer/ligand complexes and determination of the binding energies with higher accuracy. Then, aptamer/ligand interactions are analyzed, and mutations of studied aptamers made. Subsequently, the whole procedure of molecular modeling can be reiterated. Thus, the interactions between aptamers and their ligands are complex and difficult to understand using only experimental approaches. Docking and MD are irreplaceable when aptamers are studied in silico.     

The origin of the modulated structure in Sr2CuO3+δ (δ = 0.4): [CuO2] in-plane oxygen vacancy or apical oxygen vacancy?

We propose the question of the modulated structures of copper oxide is caused by the [CuO₂] in-plane oxygen vacancy or apical oxygen vacancy. Sr₂CuO_3+δ single-crystal samples were prepared using high-temperature and high-pressure methods. The major phase of Sr₂CuO_3+δ (δ = 0.4) single-crystal system is found to be constituted by the 5 a modulated structure with the Fmmm space group, which originates from the [CuO₂] in-plane oxygen vacancy appearing in octahedral Cu-O. Besides, the presence of the [CuO₂] in-plane oxygen vacancy may obliterate the superconductivity of the system. Experimental results deduce that the oxygen vacancy may appear in the apical oxygen sites in high-temperature copper oxide superconductors.     

Bilayer-mediated assembly of cationic nanoparticles adsorbed to lipid bilayers: Insights from molecular simulations

Understanding interactions between functionalized gold nanoparticles (NPs) and lipid bilayers is essential for biomedical applications. Experiments have shown that NPs that are stable in solution can assemble into clusters when adsorbed to a lipid bilayer, suggesting that bilayer-mediated interactions facilitate assembly. In this work, we use coarse-grained molecular dynamics simulations to study bilayer-mediated interactions between NPs adsorbed to single- and multicomponent lipid bilayers. We perform unbiased simulations and umbrella sampling calculations using an implicit solvent force field to determine the thermodynamic contributions to assembly. We show that bilayer-mediated interactions drive the assembly of NPs into linear aggregates on liquid-disordered bilayers, which we attribute to a reduction in bilayer curvature. Similar bilayer-mediated interactions induce the alignment of NP clusters with phase boundaries in phase-separated bilayers. Together, these simulation results provide new physical insight into the balance of forces that dictate the assembly of charged NPs at multicomponent lipid bilayer interfaces.     

Influences of magnetic fields on current–voltage characteristics of gold-DNA-gold structure with variable gaps

Achieving highly sensitive magnetic sensors by means of Metal-DNA-Metal (MDM) structure is a key issue. DNA, being a genetic information carrier in living cells reveals tunable semiconducting response in the presence of external electric and magnetic fields, which is promising for molecular electronics. The influence of magnetic fields up to 1200 mT on the current–voltage (I–V) behavior of Gold-DNA-Gold (GDG) structure having variable gap sizes from 20–50 μm are reported in this work. These structures were fabricated using UV lithography, DC magnetron sputtering and thermal evaporation techniques. DNA strands were extracted from Boesenbergia rotunda plant via standard protocol. The acquired I–V characteristics display the semiconducting diode nature of DNA in GDG structures. The potential barrier for all the structures exhibit an increasing trend with the increase of externally imposed magnetic field irrespective of variable gap sizes. Furthermore, the potential barrier in GDG junction at higher magnetic field strengths (>1000 mT) is found to be considerably enhanced. This enhancement in the junction barrier height at elevated magnetic fields is attributed to the reduction of carrier mobility and augmentation of resistance. The achieved admirable features of magnetic sensitivity suggest the viability of using these GDG sandwiches as a prospective magnetic sensor.