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41.
Thomas Huber Andrew E. Torda Wilfred F. van Gunsteren 《Journal of computer-aided molecular design》1994,8(6):695-708
Summary The concept of memory has been introduced into a molecular dynamics algorithm. This was done so as to persuade a molecular system to visit new areas of conformational space rather than be confined to a small number of low-energy regions. The method is demonstrated on a simple model system and the 11-residue cyclic peptide cyclosporin A. For comparison, calculations were also performed using simulated temperature annealing and a potential energy annealing scheme. Although the method can only be applied to systems with a small number of degrees of freedom, it offers the chance to generate a multitude of different low-energy structures, where other methods only give a single one or few. This is clearly important in problems such as drug design, where one is interested in the conformational spread of a system. 相似文献
42.
Slow pyrolysis of walnut shell which is a cheap and abundantly available solid waste was carried out using thermogravimetric
analysis. The effects of raw material heating rate on the pyrolysis properties and kinetic parameters were investigated. A
two-step consecutive reaction model were used to simulate the pyrolysis process. The kinetic parameters were established by
using the pattern search method. Comparison between experimental data and the model prediction indicated that the two-step
consecutive reaction model can better describe the slow pyrolysis of walnut shell as the formation of an intermediate during
the pyrolysis process was taken into account. 相似文献
43.
The basic primary and scatter dose-spread kernels used for convolution methods are usually produced by Monte Carlo simulations with the interaction point forced to the center of a large water phantom. However, it is still not clear whether such Monte Carlo based kernels allow accurate dose calculations with a wide range of field sizes and depths, especially in thorax phantoms. Using the differential primary and scatter concept, this paper proposes another type of basic kernel, with which perfectly accurate primary and scatter absorbed dose calculations can be performed under conditions that the beam is parallel, the incident beam intensity is uniform within and zero outside the field, and the primary beam attenuation coefficient along raylines is not a function of depth and off-axis distance. 相似文献
44.
Ioannis?Z.?EmirisEmail author Theodoros?G.?Nikitopoulos 《Journal of mathematical chemistry》2005,37(3):233-253
Three-dimensional molecular structure is fundamental in chemical function identification and computer-aided drug design. The enumeration of a small number of feasible conformations provides a rigorous way to determine the optimal or a few acceptable conformations. Our contribution concerns a heuristic enhancement of a method based on distance geometry, typically in relation with experiments of the NMR type. Distance geometry has been approached by different viewpoints; ours is expected to help in several subtasks arising in the process that determines 3D structure from distance information. More precisely, the input to our algorithm consists of a set of approximate distances of varying precision; some are specified by the covalent structure and others by Nuclear Magnetic Resonance (NMR) experiments (or X-ray crystallography which, however, requires crystallization). The output is a valid tertiary structure in a specified neighborhood of the input. Our approach should help in detecting outliers of the NMR experiments, and handles inputs with partial information. Moreover, our technique is able to bound the number of degrees of freedom of the conformation manifold. We have used numerical linear algebra algorithms for reasons of speed, and because they are well-implemented, fully documented and widely available. Our main tools include, besides distance matrices, structure-preserving matrix perturbations for minimizing singular values. Our MATLAB (or SCILAB) implementation is described and illustrated.AMS subject Classification: 92E10 Molecular structure, 92C40 Biochemistry, molecular biology, 65F15 Eigenvalues, eigenvectors, 15A18 Eigenvalues, singular values, and eigenvectors 相似文献
45.
J. A. Hageman R. Wehrens H. A. van Sprang L. M. C. Buydens 《Analytica chimica acta》2003,490(1-2):211-222
Constructing multilayer optical coatings (MOCs) is a difficult large-scale optimisation problem due to the enormous size of the search space. In the present paper, a new approach for designing MOCs is presented using genetic algorithms (GAs) and tabu search (TS). In this approach, it is not necessary to specify how many layers will be present in a design, only a maximum needs to be defined. As it is generally recognised that the existence of specific repeating blocks is beneficial for a design, a specific GA representation of a design is used which promotes the occurrence of repeating blocks. Solutions found by GAs are improved by a new refinement method, based on TS, a global optimisation method which is loosely based on artificial intelligence. The improvements are demonstrated by creating a visible transmitting/infrared reflecting filter with a wide variety of materials. 相似文献
46.
Summary A set of algorithms designed to enhance the display of protein binding cavities is presented. These algorithms, collectively entitled CAVITY SEARCH, allow the user to isolate and fully define the extent of a particular cavity. Solid modeling techniques are employed to produce a detailed cast of the active site region, which can then be color-coded to show electrostatic and steric interactions between the protein cavity and a bound ligand. 相似文献
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We present a series of conformational search calculations on the aggregation of short peptide fragments that form fibrils similar to those seen in many protein mis-folding diseases. The proteins were represented by a face-centered cubic lattice model with the conformational energies calculated using the Miyazawa-Jernigan potential. The searches were performed using algorithms based on the Metropolis Monte Carlo method, including simulated annealing and replica exchange. We also present the results of searches using the tabu search method, an algorithm that has been used for many optimization problems, but has rarely been used in protein conformational searches. The replica exchange algorithm consistently found more stable structures then the other algorithms, and was particularly effective for the octamers and larger systems. 相似文献