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91.
Physicochemical and Graph Theoretical Descriptors in Developmental Toxicity SAR: A Comparative Study
O. T. Macina N. B. Sussman H. G. Claycamp S. G. Grant 《SAR and QSAR in environmental research》2013,24(5-6):345-362
Abstract Chemical insults to the developing fetus can lead to growth retardation, malformation, death, and functional deficits. The present study seeks to determine if physicochemical and/or graph theoretical parameters can be used to determine a structure-activity relationship (SAR) for developmental toxicity, and if consistency is observed among the selected features. The biological data utilized consists of a diverse series of compounds evaluated within the Chernoff-Kavlock in vivo mouse assay. Physicochemical parameters calculated correspond to electronic, steric, and transport properties. Graph theoretical parameters calculated include the simple, valence, and kappa indices. Both sets of parameters were independently applied to derive SARs in order to compare the quality of the respective models. Multiple random sampling, without replacement, was utilized to obtain ten training/test partitions. Models were built by linear discriminant analysis, decision trees, and neural networks respectively. Comparisons on identical sets of data were carried out to determine if any of the model building procedures had a significant advantage in terms of predictive performance. Furthermore, comparison of the features selected within and across the model building processes led to the determination of model consistency. Our results indicate that consistent features related to developmental toxicity are observed and that both physicochemical and graph theoretical parameters have equal utility. 相似文献
92.
J. Sarah Caygill Stuart D. Collyer Joanne L. Holmes Frank Davis Séamus P. J. Higson 《Electroanalysis》2013,25(11):2445-2452
We describe the use of cobalt phthalocyanine as a mediator to improve the sensitivity for the electrochemical detection of TNT. Commercial screen‐printed electrodes containing cobalt phthalocyanine were employed for determination of TNT. Improved sensitivities compared to screen‐printed carbon electrodes without phthalocyanine were observed, current response for cyclic voltammetric measurements at modified electrodes being at least double that of unmodified electrodes. A synergistic effect between oxygen and TNT reduction was also observed. Correlation between TNT concentrations and sensor output was observed between 0–200 µM TNT. Initial proof‐of‐concept experiments combining electrochemical determinations, with the use of an air‐sampling cyclone, are also reported. 相似文献
93.
《高分子科学杂志,C辑:聚合物评论》2013,53(2):99-124
Thermally stimulated recovery (TSR) is a non‐conventional mechanical spectroscopy technique that allows to analyse in detail the relaxation processes of polymeric systems in the low frequency region. This work reviews the main aspects and potentialities of this technique. The different kinds of TSR experiments that can be performed, global and thermal sampling (TS) experiments, are described and illustrated with several examples. Also, the different methods for the determination of the thermokinetic parameters (activation energy and pre‐exponential factor) of the thermal sampling (TS) procedure are explained and compared. In this context, the compensation phenomenon, which always appears in TSR results when the studies are performed in the glass transition region of a given system, is discussed. Examples of the application of this technique to different polymeric systems during the last 20 years are provided. An emphasis will be made on the analysis of the effect of crystallinity degree and crosslink density on the TSR response. A comparison between the results (characteristic times and activation energies) obtained by different techniques, namely TSR, dynamic mechanical analysis (DMA), and differential scanning calorimetry (DSC), is made. 相似文献
94.
Barbara Bojko Krzysztof Gorynski German Augusto Gomez-Rios Jan Matthias Knaak Tiago Machuca Vinzent Nikolaus Spetzler Erasmus Cudjoe Michael Hsin Marcelo Cypel Markus Selzner Mingyao Liu Shaf Keshavjee Janusz Pawliszyn 《Analytica chimica acta》2013
Metabolomics and biomarkers discovery are an integral part of bioanalysis. However, untargeted tissue analysis remains as the bottleneck of such studies due to the invasiveness of sample collection, as well as the laborious and time-consuming sample preparation protocols. In the current study, technology integrating in vivo sampling, sample preparation and global extraction of metabolites – solid phase microextraction was presented and evaluated during liver and lung transplantation in pig model. Sampling approaches, including selection of the probe, transportation, storage conditions and analyte coverage were discussed. The applicability of the method for metabolomics studies was demonstrated during lung transplantation experiments. 相似文献
95.
Yaxiao Guo Feifei Xu Lei Meng Wei Tang Yan Xia Yangjie Wu Shusheng Zhang 《Electrophoresis》2013,34(9-10):1312-1318
A new trimethylamine amination polychloromethyl styrene nanolatex (TMAPL) and TMAPL coated capillary column (ccc‐TMAPL) were successfully prepared. The TMAPL coating was characterized with reversed steady EOF values of ca. ?16.8 × 10?5 cm2 V?1 s?1. It was applied to establish open‐tubular (OT) CEC and field‐amplified sample stacking (FASS) OT‐CEC methods for the determination of bromate in tap water. Compared to OT‐CEC, the LOD with FASS‐OT‐CEC was improved from 80 to 8 ng/mL. The developed FASS‐OT‐CEC method was practically used for the analysis of bromate in tap water samples with recoveries ranging from 93.6 to 103.5%. 相似文献
96.
Yu Liu Lei Zhao Wentao Li Dongyu Zhao Miao Song Yongliang Yang 《Journal of computational chemistry》2013,34(1):67-75
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
97.
Hironori Kokubo Toshimasa Tanaka Yuko Okamoto 《Journal of computational chemistry》2013,34(30):2601-2614
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
98.
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
99.
B. W. Bailey J. M. Rankin R. Weinbloom 《International journal of environmental analytical chemistry》2013,93(1):3-9
The use of ternary complexes in the determination of anionic surfactants has been investigated and an analytical method using linear alkyl sulfonates as a test substance has been developed. The method involves the formation of the chloroform-extractable bisphenanthroline Cu(II)-linear alkyl sulfonate (LAS) complex and the subsequent equilibration of the extract with erythrosine to form the extractable bisphenanthroline Cu(II)-erythrosine complex. In the equilibration step erythrosine displaces LAS quantitatively, allowing the determination of the LAS originally present by measuring the absorbance of the extracted bisphenanthroline-Cu(II)-erythrosine complex. Results are reported of studies made to determine the optimum analytical conditions, the sensitivity, and the precision for the method described. 相似文献
100.
A. De Kok M. Van Opstal T. De Jong B. Hoogcarspel R. B. Geerdink R. W. Frei 《International journal of environmental analytical chemistry》2013,93(1-2):101-123
Abstract In earlier work, various strategies have been developed for the trace-level determination of phenylurea herbicides and the anilines which are their main degradation products. They include catalytic hydrolysis of the phenylureas on silica, liquid chromatographic fractionation of complex mixtures of herbicides and anilines, derivatization of anilines and herbicides with electron-capture-sensitive reagents, and final analysis by means of capillary gas chromatography. In the present paper, the application of these principles to trace-level analysis of surface water, soil and crop samples is demonstrated. 相似文献