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81.
82.
Fast folding and comparison of RNA secondary structures 总被引:40,自引:0,他引:40
I. L. Hofacker W. Fontana P. F. Stadler L. S. Bonhoeffer M. Tacker P. Schuster 《Monatshefte für Chemie / Chemical Monthly》1994,125(2):167-188
Summary Computer codes for computation and comparison of RNA secondary structures, the Vienna RNA package, are presented, that are based on dynamic programming algorithms and aim at predictions of structures with minimum free energies as well as at computations of the equilibrium partition functions and base pairing probabilities.An efficient heuristic for the inverse folding problem of RNA is introduced. In addition we present compact and efficient programs for the comparison of RNA secondary structures based on tree editing and alignment.All computer codes are written in ANSI C. They include implementations of modified algorithms on parallel computers with distributed memory. Performance analysis carried out on an Intel Hypercube shows that parallel computing becomes gradually more and more efficient the longer the sequences are.
Schnelle Faltung und Vergleich von Sekundärstrukturen von RNA
Zusammenfassung Die im Vienna RNA package enthaltenen Computer Programme für die Berechnung und den Vergleich von RNA Sekundärstrukturen werden präsentiert. Ihren Kern bilden Algorithmen zur Vorhersage von Strukturen minimaler Energie sowie zur Berechnung von Zustandssumme und Basenpaarungswahrscheinlichkeiten mittels dynamischer Programmierung.Ein effizienter heuristischer Algorithmus für das inverse Faltungsproblem wird vorgestellt. Darüberhinaus präsentieren wir kompakte und effiziente Programme zum Vergleich von RNA Sekundärstrukturen durch Baum-Editierung und Alignierung.Alle Programme sind in ANSI C geschrieben, darunter auch eine Implementation des Faltungs-algorithmus für Parallelrechner mit verteiltem Speicher. Wie Tests auf einem Intel Hypercube zeigen, wird das Parallelrechnen umso effizienter je länger die Sequenzen sind.相似文献
83.
The reaction of electroreduction of platinum(II) aquachloride complexes on a negatively charged dropping mercury electrode is used to determine specific features of interpretation of experimental data in the case of parallel conversion of several forms of a reactant, connected with the manner of introducing a correction for the concentration polarization. The difference in the charges of species undergoing simultaneous reduction gives rise to ambiguity when analyzing kinetic data on the dependence of current on the supporting-electrolyte concentration at constant electrode charge. A new self-consistent technique for deducing model parameters (ratio between reactant discharge rate constants) is proposed. 相似文献
84.
Using a probabilistic approach, the deterministic and the stochastic parallel dynamics of aQ-Ising neural network are studied at finiteQ and in the limitQ. Exact evolution equations are presented for the first time-step. These formulas constitute recursion relations for the parallel dynamics of the extremely diluted asymmetric versions of these networks. An explicit analysis of the retrieval properties is carried out in terms of the gain parameter, the loading capacity, and the temperature. The results for theQ network are compared with those for theQ=3 andQ=4 models. Possible chaotic microscopic behavior is studied using the time evolution of the distance between two network configurations. For arbitrary finiteQ the retrieval regime is always chaotic. In the limitQ the network exhibits a dynamical transition toward chaos. 相似文献
85.
Prospecting for oil and gas resources poses the problem of determining the geological structure of the earth's crust from indirect measurements. Seismic migration is an acoustic image reconstruction technique based on the inversion of the scalar wave equation. Extensive computation is necessary before reliable information can be extracted from large sets of recorded data. In this paper a collection of industrial migration techniques, each giving rise to a data parallel algorithm, is outlined. Computer simulations on synthetic seismic data illustrate the problem and the approach. 相似文献
86.
Emanuele Galligani 《Numerical Algorithms》1993,5(11):549-555
Givenn pairwise distinct and arbitrarily spaced pointsP
i in a domainD of thex–y plane andn real numbersf
i, consider the problem of computing a bivariate functionf(x, y) of classC
1 inD whose values inP
i are exactlyf
i,i=1,,n, and whose first or second order partial derivatives satisfy appropriate equality and inequality constraints on a given set ofp pointsQ
l inD.In this paper we present a method for solving the above problem, which is designed for extremely large data sets. A step of this method requires the solution of a large scale quadratic programming (QP) problem.The main purpose of this work is to analyse an iterative method for determining the solution of this QP problem: such a method is very efficient and well suited for parallel implementation on a multiprocessor system.Work supported by MURST Project of Computational Mathematics, Italy. 相似文献
87.
综述了近8年来液相平行合成和组合合成中应用的不同技术, 包括可溶性载体、氟合成技术、离子液体、固相试剂树脂以及低聚乙烯二醇(OEG)衍生物的应用等几方面内容. 论述了它们的基本原理以及相关的应用实例, 并着重强调了目标化合物的分离纯化方法. 相似文献
88.
介绍废弃线路板中有回收价值元素和有害物质分析的采样、制样及检测技术。样品经过分类采样、剪切破碎和高温灰化制样,采用样品全分析或副批混合样分析。通过提高称样量、多次测定求平均值的办法,火试金富集-重量法测定贵金属金、银。湿法王水溶解样品,碘量法测定主体元素铜。电感耦合等离子体发射光谱(ICP-AES)法测定其它杂质元素,被测元素质量浓度在0~10μg/mL范围内与光谱强度呈良好线性关系,相关系数均大于0.9998。测定结果的相对标准偏差小于10%(n=5),加标回收率为97.0%~102.5%。该方法简单、快速,有效地解决了线路板样品不均匀而难采样,以及硬度、韧性强制样难,金属易包裹难分解的技术瓶颈,测定结果准确,具有代表性。该方法适用于废弃线路板化学成分分析,其它废弃电子产品检测可参考此方法。 相似文献
89.
The electrical interaction between two long, parallel cylinders each is covered by an ion-penetrable charged membrane immersed in an oil/water interface is investigated. The effects of contact angle, radius of cylinder, and membrane thickness on the electrical interaction force are examined. The results of numerical simulation reveal that the following conditions lead to a greater electrical interaction force: (i) a larger contact angle, i.e. a larger fraction of a cylinder in the oil phase; (ii) a larger cylinder radius; and (iii) a thinner membrane. For a fixed ionic strength, the electrical interaction force is insensible to the type of electrolytes in the water phase, in general. However, if two cylinders are close enough, then the higher the valence of counterions the greater the electrical interaction force. 相似文献
90.
Main characteristics are described of the PRIRODA quantum-chemical program suite designed for the study of complex molecular systems by the density functional theory, at the MP2, MP3, and MP4 levels of multiparticle perturbation theory, and by the coupled-cluster single and double excitations method (CCSD) with the application of parallel computing. A number of examples of calculations are presented.__________Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 3, pp. 804–810, March, 2005. 相似文献