Sofosbuvir Selects for Drug-Resistant Amino Acid Variants in the Zika Virus RNA-Dependent RNA-Polymerase Complex In Vitro

The nucleotide analog sofosbuvir, licensed for the treatment of hepatitis C, recently revealed activity against the Zika virus (ZIKV) in vitro and in animal models. However, the ZIKV genetic barrier to sofosbuvir has not yet been characterized. In this study, in vitro selection experiments were performed in infected human hepatoma cell lines. Increasing drug pressure significantly delayed viral breakthrough (p = 0.029). A double mutant in the NS5 gene (V360L/V607I) emerged in 3 independent experiments at 40–80 µM sofosbuvir resulting in a 3.9 ± 0.9-fold half- maximal inhibitory concentration (IC₅₀) shift with respect to the wild type (WT) virus. A triple mutant (C269Y/V360L/V607I), detected in one experiment at 80 µM, conferred a 6.8-fold IC₅₀ shift with respect to the WT. Molecular dynamics simulations confirmed that the double mutant V360L/V607I impacts the binding mode of sofosbuvir, supporting its role in sofosbuvir resistance. Due to the distance from the catalytic site and to the lack of reliable structural data, the contribution of C269Y was not investigated in silico. By a combination of sequence analysis, phenotypic susceptibility testing, and molecular modeling, we characterized a double ZIKV NS5 mutant with decreased sofosbuvir susceptibility. These data add important information to the profile of sofosbuvir as a possible lead for anti-ZIKV drug development.     

CFD Modeling of Active Volume Creation in a Non‐Newtonian Fluid Agitated by Submerged Recirculating Jets

Computational fluid dynamics (CFD) models were employed to investigate flow conditions inside a model reactor in which yield stress non‐Newtonian liquid is mobilized using submerged recirculating jets. The simulation results agree well with the experimental results of active volume in the reactor obtained using flow visualization by the authors in a previous study. The models developed are capable of predicting a critical jet velocity (v_c) that determines the extent of active volume obtained due to jet mixing. The v_c values are influenced both by the rheological properties of the liquid and the nozzle orientation. The liquid with higher effective viscosity leads to higher v_c for a downward facing injection nozzle. However, an upward facing injection nozzle along with a downward facing suction nozzle generates enhanced complementary flow fields which overcome the rheological constraints of the liquid and lead to lower v_c.     

Soret and Dufour effects between two rectangular plane walls with heat source/sink

This study addresses the thermo‐diffusion and the diffusion‐thermo phenomena in a semi‐infinite absorbent channel whose walls are contracting/expanding, with heat source/sink effects. The governing partial differential equations with suitable boundary conditions are transformed to a system of dimensionless ordinary differential equations. An analytic solution of the problem has been found using a technique called homotopy analysis method (HAM). HAM gives consistently valid answers to the problem over an extensive variety of parameters and also provides better accuracy. To validate the analytical results, a comparison has been presented with a numerical solution calculated by using the parallel shooting method. The effects of dimensionless parameters, that is, deformation parameter, Reynolds number, Soret and Dufour numbers, and heat source/sink parameter on the expressions of velocity, temperature, and concentration profiles are analyzed graphically to understand the physics of the deformable channel. It has been noted that the velocity across the channel is higher for the expanding channel, as compared to that for the contracting channel. Also the Soret and Dufour number increases the temperature of the fluid, and decreases the concentration. The temperature profile has an increasing behavior in the case of heat source, and a decreasing behavior in the case of heat sink.     

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.     

Grain size dependence of hardness in nanocrystalline silicon carbide

The response of nanocrystalline silicon carbide (nc-SiC) to nanoindentation is investigated using molecular dynamics (MD) simulation. It is found that the hardness of the nc-SiC decreases with decreasing grain size, showing an inverse Hall-Petch relationship. The behavior is primarily attributed to the reduced number of intact covalent bonds with grain refinement. Dislocation nucleation and growth in nc-SiC are strongly suppressed by the grain boundaries (GBs). In addition to the dislocation region in the grains, the indentation-induced amorphization of nanograins proceeds preferentially from the GBs, leading to grain shrinkage until the grains are fully amorphized. The results provide an improved understanding of the mechanical properties in nc-SiC and other nanostructured covalent materials.     

PDC钻头水力结构优化设计研究

在PDC钻头工作过程中，钻井液对钻头体表面的冲洗、冷却和润滑是保证钻头正常工作的一个非常重要的条件。对PDC钻头而言，水力结构（主要是中心水眼和冠部水道）设计的重要性尤其突出。以前,对钻头水力系统研究只能通过实验的方法进行,研究周期长、成本高、结构调整不方便，而数值模拟的方法在几年前还不成熟，甚至静态的复杂结构流场问题基本无法解决。为此，在提出PDC钻头水力结构优化设计原则的基础上，对PDC钻头的三维流场进行了数值模拟。模拟中考虑了钻头的喷嘴布置位置、直径、数量以及切削齿对流场的影响。计算结果表明，原设计在喷嘴布置位置和喷射角度上存在不足，以此为基础进行了水力结构的优化设计。文中的研究成果成功地应用在新型钻头水力结构的设计中，研究方法为PDC钻头水力结构优化分析奠定了理论基础。     

泥页岩井壁稳定研究及在临盘地区的应用

从岩石力学和物理化学两个主要因素简要分析了井壁失稳的机理，指出泥页岩井壁失稳是由力学与化学两方面因素共同作用的结果。钻井液与泥页岩存在化学势差，并改变了井壁附近的孔隙压力，降低岩石强度。借助于井壁处有效应力的变化,将泥页岩与钻井液相互作用时页岩水化所产生的力学效应与纯力学效应结合起来，计算出任意井斜方位井眼围岩应力状态，利用测井资料求出有关岩石力学参数和Mohr Couloumb准则，计算得出防塌的临界钻井液密度。     

川东北飞仙关组碳酸盐岩气藏产能影响因素及压裂酸化新技术探讨

川东北地区飞仙关组碳酸盐岩气藏的储集层条件起好，不论直井还是水平井均可获高产工业气流，投产前的解堵酸化均可实现大幅度增产。在分析介绍该地区气藏地质特征的基础上，全面剖析了影响产能的主要因素，并对多功能深部酸化技术方案和稠化酸加砂压裂技术方案进行了具体探讨。     

湘中海相浅层湘冷1井酸压工艺研究及应用

湘冷1井具有气层埋藏浅（400m-500m）、纵向上裂隙发育的特点，属低孔、低渗的含泥质灰岩致密储层。大量室内实验和研究采用“前置液酸压＋闭合酸化”工艺技术，并优选了相应降阻酸和闭合酸配方。通过酸压实现了该井工业油气流的突破，取得了明显的增产效果，为新区海相浅层气的开发探索出了一套成熟的改造增产措施。