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1.
We have developed a two‐dimensional replica‐exchange method for the prediction of protein–ligand binding structures. The first dimension is the umbrella sampling along the reaction coordinate, which is the distance between a protein binding pocket and a ligand. The second dimension is the solute tempering, in which the interaction between a ligand and a protein and water is weakened. The second dimension is introduced to make a ligand follow the umbrella potential more easily and enhance the binding events, which should improve the sampling efficiency. As test cases, we applied our method to two protein‐ligand complex systems (MDM2 and HSP 90‐alpha). Starting from the configuration in which the protein and the ligand are far away from each other in each system, our method predicted the ligand binding structures in excellent agreement with the experimental data from Protein Data Bank much faster with the improved sampling efficiency than the replica‐exchange umbrella sampling method that we have previously developed. © 2013 Wiley Periodicals, Inc.  相似文献   
2.
Multiple conformations separated by high‐energy barriers represent a challenging problem in free‐energy calculations due to the difficulties in achieving adequate sampling. We present an application of thermodynamic integration (TI) in conjunction with the local elevation umbrella sampling (LE/US) method to improve convergence in alchemical free‐energy calculations. TI‐LE/US was applied to the guanosine triphosphate (GTP) to 8‐Br‐GTP perturbation, molecules that present high‐energy barriers between the anti and syn states and that have inverted preferences for those states. The convergence and reliability of TI‐LE/US was assessed by comparing with previous results using the enhanced‐sampling one‐step perturbation (OSP) method. A linear interpolation of the end‐state biasing potentials was sufficient to dramatically improve sampling along the chosen reaction coordinate. Conformational free‐energy differences were also computed for the syn and anti states and compared to experimental and theoretical results. Additionally, a coupled OSP with LE/US was carried out, allowing the calculation of conformational and alchemical free energies of GTP and 8‐substituted GTP analogs. © 2013 Wiley Periodicals, Inc.  相似文献   
3.
The accurate prediction of protein–ligand binding is of great importance for rational drug design. We present herein a novel docking algorithm called as FIPSDock, which implements a variant of the Fully Informed Particle Swarm (FIPS) optimization method and adopts the newly developed energy function of AutoDock 4.20 suite for solving flexible protein–ligand docking problems. The search ability and docking accuracy of FIPSDock were first evaluated by multiple cognate docking experiments. In a benchmarking test for 77 protein/ligand complex structures derived from GOLD benchmark set, FIPSDock has obtained a successful predicting rate of 93.5% and outperformed a few docking programs including particle swarm optimization (PSO)@AutoDock, SODOCK, AutoDock, DOCK, Glide, GOLD, FlexX, Surflex, and MolDock. More importantly, FIPSDock was evaluated against PSO@AutoDock, SODOCK, and AutoDock 4.20 suite by cross‐docking experiments of 74 protein–ligand complexes among eight protein targets (CDK2, ESR1, F2, MAPK14, MMP8, MMP13, PDE4B, and PDE5A) derived from Sutherland‐crossdock‐set. Remarkably, FIPSDock is superior to PSO@AutoDock, SODOCK, and AutoDock in seven out of eight cross‐docking experiments. The results reveal that FIPS algorithm might be more suitable than the conventional genetic algorithm‐based algorithms in dealing with highly flexible docking problems. © 2012 Wiley Periodicals, Inc.  相似文献   
4.
A valence‐universal multireference coupled cluster (VUMRCC) theory, realized via the eigenvalue independent partitioning (EIP) route, has been implemented with full inclusion of triples excitations for computing and analyzing the entire main and several satellite peaks in the ionization potential spectra of several molecules. The EIP‐VUMRCC method, unlike the traditional VUMRCC theory, allows divergence‐free homing‐in to satellite roots which would otherwise have been plagued by intruders, and is thus numerically more robust to obtain more efficient and dependable computational schemes allowing more extensive use of the approach. The computed ionization potentials (IPs) as a result of truncation of the (N−1) electron basis manifold involving virtual functions such as 2h‐p and 3h‐2p by different energy thresholds varying from 5 to 15 a.u. with 1 a.u. intervals as well as thresholds such as 20, 25, and 30 a.u. have been carefully looked into. Cutoff at around 25 a.u. turns out to be an optimal threshold. Molecules such as C2H4 and C2H2 (X = D,T), and N2 and CO (X = D,T,Q) with Dunning's cc‐pVXZ bases have been investigated to determine all main and 2h‐p shake‐up and 3h‐2p double shake‐up satellite IPs. We believe that the present work will pave the way to a wider application of the method by providing main and satellite IPs for some problematic N‐electron closed shell systems. © 2013 Wiley Periodicals, Inc.  相似文献   
5.
In mine planning problems, cutoff grade optimization defines a threshold at every time period such that material above this value is processed, and the rest is considered waste. In orebodies with multiple minerals, which occur in practice, the natural extension is to consider a cutoff surface. We show that in two dimensions the optimal solution is a line, and in n dimensions it is a hyperplane.  相似文献   
6.
Abstract

The following analytical method has been used to identify some odorous compounds in the air of the water treatment plant Werdholzli, Zurich: sampling of contaminated air with the help of activated carbon, desorption by the solvents carbon disulphide and methylene chloride, separation of the carbon disulfide extract into a polar and a nonpolar fraction by adsorption column chromatography on silica. Hereafter gaschromatographic analysis of the polar fraction on glass capillary column (Ucon HB 5100); detection and identification were achieved by flame ionisation, thermoionic nitrogen selective detector and computerized mass spectrometry (Finnigan 3200 F, data system 6110).

The results show the presence of sulfur compounds: thiophenes, thiazoles; nitrogen compounds: pyrazines; oxygen compounds: phenols, alcohols and some unsatured hydrocarbons. The malodorous compounds were sulfur and nitrogen compounds in the range of 0.01-0.1 ppm.  相似文献   
7.
This work concentrates on extending the utilization of multiple dual mode (MDM) counter‐current chromatography in chiral separations. Two aromatic acids, 2‐(6‐methoxy‐2‐naphthyl)propionic acid (NAP) and 2‐phenylpropionic acid (2‐PPA), were enantioseparated by MDM counter‐current chromatography using hydroxypropyl‐β‐cyclodextrin (HP‐β‐CD) as chiral selector. The two‐phase solvent systems consisting of n‐hexane/ethyl acetate 0.1 mol/L phosphate buffer pH 2.67 containing 0.1 mol/L HP‐β‐CD (7.5:2.5:10 for NAP and 7:3:10 for 2‐PPA, v/v/v) were used. Conventional MDM and modified MDM were compared according to peak resolution under current separation mechanism. The influence of elution time after the first‐phase inversion and number of cycles for MDM were investigated. Peak resolution of NAP and 2‐PPA increased from 0.62 to 1.05 and 0.72 to 0.84, respectively, using optimized MDM conditions. Being an alternative elution method for counter‐current chromatography, MDM elution greatly improved peak resolution in chiral separations.  相似文献   
8.
In this work, we study the multiplicity of solutions for a stationary nonhomogeneous problem associated to the nonlinear one-dimensional Klein-Gordon Equation. We prove that the existence of positive solutions is equivalent to the solvability of a scalar equation 2F(M) = 1, where F is a real function depending on V. Moreover, we prove some existence and multiplicity results for the Dirichlet problem in the superlinear case.  相似文献   
9.
Abstract

Reliable and comprehensive sampling methods are required to obtain accurate data for VOC concentrations in air samples. The major drawback of the adsorption tube sampling method, widely employed in environmental studies, is the fact that C2 compounds are usually not trapped quantitatively.

The focus of this work was thus to improve sampling based on adsorption tubes packed with Molsieve and Carbosieve. To improve the sampling efficiency for the C2 compounds, a cooling device, based on Peltier cooling was constructed, which could be operated at a temperature down to ?30°C.

Experiments under laboratory and field conditions were carried out to study the influence of the sampling temperatuie on the recovery of ethane and ethene as the most volatile VOCs. The results clearly demonstrate the need for a cooled sampling device for the analysis of C2 compounds in air. Under the investigated conditions, the recoveries with ambient temperature sampling were only in the range of 38–46% for ethane and 33–59% for ethene respectively, in comparison to the cooled sampling device. These findings are only valid for the described conditions and can change significantly with temperature and concentration. A generalisation of the recovery is thus very difficult to give.

The use of the sampling device for a field study is reported, where samples were collected simultaneously at three different altitudes in a diurnal profile on the slope of the Schulterberg mountain in Tyrol (Austria).  相似文献   
10.
Abstract

A new coating procedure for different diffusion controlled preconcentration methods (tubular denuder, annular denuder, diffusion screen) is described for the determination of nitric acid in air. In this study, a silanization reaction is applied to obtain a chemically fixed coating with an end placed functional NH2-group, which can be used as a sink to collect acidic compounds from air. This coating must be carried out only once and can be used for a long time. The denuders, coated with this procedures, were compared with conventionally coated NaF denuders.  相似文献   
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