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31.
32.
We present new generalized-ensemble molecular dynamics simulation algorithms, which we refer to as the multibaric-multithermal molecular dynamics. We describe three algorithms based on (1) the Nosé thermostat and the Andersen barostat, (2) the Nosé-Poincaré thermostat and the Andersen barostat, and (3) the Gaussian thermostat and the Andersen barostat. The multibaric-multithermal simulations perform random walks widely both in the potential-energy space and in the volume space. Therefore, one can calculate isobaric-isothermal ensemble averages in wide ranges of temperature and pressure from only one simulation run. We test the effectiveness of the multibaric-multithermal algorithm by applying it to a Lennard-Jones 12-6 potential system. 相似文献
33.
35.
Isolating Reactions at the Picoliter Scale: Parallel Control of Reaction Kinetics at the Liquid–Liquid Interface
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Gia Chuong Phan‐Quang Hiang Kwee Lee Prof. Xing Yi Ling 《Angewandte Chemie (International ed. in English)》2016,55(29):8304-8308
Miniaturized liquid–liquid interfacial reactors offer enhanced surface area and rapid confinement of compounds of opposite solubility, yet they are unable to provide in situ reaction monitoring at a molecular level at the interface. A picoreactor operative at the liquid–liquid interface is described, comprising plasmonic colloidosomes containing Ag octahedra strategically assembled at the water‐in‐decane emulsion interface. The plasmonic colloidosomes isolate ultrasmall amounts of solutions (<200 pL), allowing parallel monitoring of multiple reactions simultaneously. Using the surface‐enhanced Raman spectroscopy (SERS) technique, in situ monitoring of the interfacial protonation of dimethyl yellow (p‐dimethylaminoazobenzene (DY)) is performed, revealing an apparent rate constant of 0.09 min?1 for the first‐order reaction. The presence of isomeric products with similar physical properties is resolved, which would otherwise be indiscernible by other analytical methods. 相似文献
36.
The possibility of simultaneous application of an electron capture (ECD) and a flame ionization detector (FID) connected to a glass capillary column for analyzing polynuclear aromatic hydrocarbons (PNA) has been investigated. The ECD/FID ratio is determined for 46 PNA compounds. The ratios vary from 0.02 to 117 with relative standard deviations better than 20 percent determined from 10 replicate analyses. The results suggest that the method may be used for obtaining additional evidence in identifying PNA in environmental samples. Impurities and transformation products in the standard were identified by computerized glass capillary gas chromatography/mass spectrometry. Quinones and diones are responsible for the high EC-response determined in some trace components in the standard. An application of the method is shown for PNA from particulates in urban atmospheres. 相似文献
37.
Marián Slodička 《Applications of Mathematics》2003,48(1):49-66
In this paper, we consider a 2nd order semilinear parabolic initial boundary value problem (IBVP) on a bounded domain N, with nonstandard boundary conditions (BCs). More precisely, at some part of the boundary we impose a Neumann BC containing an unknown additive space-constant (t), accompanied with a nonlocal (integral) Dirichlet side condition.We design a numerical scheme for the approximation of a weak solution to the IBVP and derive error estimates for the approximation of the solution u and also of the unknown function . 相似文献
38.
A new scheme, called "list of nonredundant bonds", is presented to record the number of bonds and their positions for the atoms involved in Kekulé valence structures of (poly)cyclic conjugated systems. Based on this scheme, a recursive algorithm for generating Kekulé valence structures has been developed and implemented. The method is general and applicable for all kinds of (poly)cyclic conjugated systems including fullerenes. The application of the algorithm in generating Valence Bond (VB) wave functions, in terms of Kekulé valence structures, is discussed and illustrated in actual VB calculations. Two types of VBSCF calculations, one involving Kekulé valence structures only and the second one involving all covalent VB structures, were performed for benzene, pentalene, benzocyclobutadiene, and naphthalene. Both strictly local and delocalised p-orbitals were used in these calculations. Our results show that, when the orbitals are restricted to their own atoms, other VB structures (Dewar structures) also have a significant contribution in the VB wave function. When removing this restriction, the other VB structures (Dewar and also the ionic structures) are accommodated in the Kekulé valence structures, automatically. Therefore, at VBSCF delocal level, the ground states of these systems can be described almost quantitatively by considering Kekulé valence structures only at a considerable saving of time. 相似文献
39.
Medvedev NN Voloshin VP Luchnikov VA Gavrilova ML 《Journal of computational chemistry》2006,27(14):1676-1692
The paper presents an algorithm for calculating the three-dimensional Voronoi-Delaunay tessellation for an ensemble of spheres of different radii (additively-weighted Voronoi diagram). Data structure and output of the algorithm is oriented toward the exploration of the voids between the spheres. The main geometric construct that we develop is the Voronoi S-network (the network of vertices and edges of the Voronoi regions determined in relation to the surfaces of the spheres). General scheme of the algorithm and the key points of its realization are discussed. The principle of the algorithm is that for each determined site of the network we find its neighbor sites. Thus, starting from a known site of the network, we sequentially find the whole network. The starting site of the network is easily determined based on certain considerations. Geometric properties of ensembles of spheres of different radii are discussed, the conditions of applicability and limitations of the algorithm are indicated. The algorithm is capable of working with a wide variety of physical models, which may be represented as sets of spheres, including computer models of complex molecular systems. Emphasis was placed on the issue of increasing the efficiency of algorithm to work with large models (tens of thousands of atoms). It was demonstrated that the experimental CPU time increases linearly with the number of atoms in the system, O(n). 相似文献
40.
The concept of crystalline module, that is, an unambiguously isolated, repeated quasi-molecular element, is introduced. This concept is more general than the concept of crystal lattice. The generalized modular approach allows extension of the methods and principles of crystallography to quasi-crystals, clusters, amorphous solids, and periodic biological structures. Principles of construction of aperiodic, nonequilibrium regular modular structures are formulated. Limitations on the size of icosahedral clusters are due to the presence of spherical shells with non-Euclidean tetrahedral tiling in their structure. A parametric relationship between the structures of icosahedral fullerenes and metal clusters of the Chini series was found. 相似文献