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71.
Andrey A. Buglak Alexey V. Samokhvalov Anatoly V. Zherdev Boris B. Dzantiev 《International journal of molecular sciences》2020,21(22)
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. 相似文献
72.
《Journal of the European Ceramic Society》2020,40(13):4396-4402
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. 相似文献
73.
The solvent-dependent polymorphism of the active pharmaceutical ingredient (API) carbamazepine is interpreted from calculations of the solid-state and API-solvent intermolecular interactions. These simulations suggested that apolar solute-solute interactions could be disrupted by apolar solvents. In contrast, the polar solute-solute interactions were found to be easily disrupted by polar and protic solvents. This is consistent with experimental observations that the crystallization of the metastable form II is more dominant in apolar solvents. The Mercury program remains the gold standard in terms of usability; however, further expansion into more complex simulation techniques could make this package of even greater use in pharmaceutical manufacturing workflows. 相似文献
74.
75.
Kinetic,thermodynamic parameters and in vitro digestion of tannase from Aspergillus tamarii URM 7115
Amanda Reges de Sena Tonny Cley Campos Leite Talita Camila Evaristo da Silva Nascimento Anna Carolina da Silva Catiane S. Souza Antônio Fernando de Mello Vaz 《Chemical Engineering Communications》2018,205(10):1415-1431
Tannase is an enzyme used in various industries and produced by a large number of microorganisms. The aim of this study was to evaluate tannase production to determine the biochemical, kinetic, and thermodynamic properties and to simulate tannase in vitro digestion. The tannase-producing fungal strain was isolated from “jamun” leaves and identified as Aspergillus tamarii. Temperature at 26°C for 67?h was the best combination for maximum tannase activity (6.35-fold; initial activity in Plackett–Burman design—15.53?U/mL and average final activity in Doehlert design—98.68?U/mL). The crude extract of tannase was optimally active at 40°C, pH 5.5 and 6.5. Moreover, tannase was stimulated by Na+, Ca2+, Mg2+, and Mn2+. The half-life at 40°C lasted 247.55?min. The free energy of Gibbs, enthalpy, and entropy, at 40°C, was 81.47, 16.85, and ?0.21?kJ/mol?·?K, respectively. After total digestion, 123.95% of the original activity was retained. Results suggested that tannase from A. tamarii URM 7115 is an enzyme of interest for industrial applications, such as gallic acid production, additive for feed industry, and for beverage manufacturing, due to its catalytic and thermodynamic properties. 相似文献
76.
77.
张峰水库溢洪道体型优化设计 总被引:1,自引:0,他引:1
本文对已设计的张峰水库溢洪道进行了模型试验,根据对试验结果分析,认为原方案设计存在一些问题,并针对问题进行了优化设计。通过对修改方案模型试验结果分析,得出修改方案改进了原方案中存在的不足,优化合理,是可以采用的。 相似文献
78.
Defects are often present in rolled products, such as wire rod. The market demand for wire rod without any defects has increased. In the final wire rod products, defects originating from steel making, casting, pre‐rolling of billets and during wire rod rolling can appear. In this work, artificial V‐shaped longitudinal surface cracks have been analysed experimentally and by means of FEM. The results indicate that the experiments and FEM calculations show the same tendency except in two cases, where instability due to fairly “round” false round bars disturbed the experiment. FE studies in combination with practical experiments are necessary in order to understand the behaviour of the material flows in the groove and to explain whether the crack will open up as a V‐shape or if it will be closed as an I‐shape. 相似文献
79.
PDC钻头水力结构优化设计研究 总被引:9,自引:0,他引:9
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。 相似文献
80.