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101.
Pieter Van Renterghem Pierre-Edouard Sottas Martial Saugy Peter Van Eenoo 《Analytica chimica acta》2013
Due to their performance enhancing properties, use of anabolic steroids (e.g. testosterone, nandrolone, etc.) is banned in elite sports. Therefore, doping control laboratories accredited by the World Anti-Doping Agency (WADA) screen among others for these prohibited substances in urine. It is particularly challenging to detect misuse with naturally occurring anabolic steroids such as testosterone (T), which is a popular ergogenic agent in sports and society. 相似文献
102.
Chuan Li Marharyta Petukh Lin Li Emil Alexov 《Journal of computational chemistry》2013,34(22):1949-1960
Due to the enormous importance of electrostatics in molecular biology, calculating the electrostatic potential and corresponding energies has become a standard computational approach for the study of biomolecules and nano‐objects immersed in water and salt phase or other media. However, the electrostatics of large macromolecules and macromolecular complexes, including nano‐objects, may not be obtainable via explicit methods and even the standard continuum electrostatics methods may not be applicable due to high computational time and memory requirements. Here, we report further development of the parallelization scheme reported in our previous work (Li, et al., J. Comput. Chem. 2012, 33, 1960) to include parallelization of the molecular surface and energy calculations components of the algorithm. The parallelization scheme utilizes different approaches such as space domain parallelization, algorithmic parallelization, multithreading, and task scheduling, depending on the quantity being calculated. This allows for efficient use of the computing resources of the corresponding computer cluster. The parallelization scheme is implemented in the popular software DelPhi and results in speedup of several folds. As a demonstration of the efficiency and capability of this methodology, the electrostatic potential, and electric field distributions are calculated for the bovine mitochondrial supercomplex illustrating their complex topology, which cannot be obtained by modeling the supercomplex components alone. © 2013 Wiley Periodicals, Inc. 相似文献
103.
Nicholas F. Chilton Russell P. Anderson Lincoln D. Turner Alessandro Soncini Keith S. Murray 《Journal of computational chemistry》2013,34(13):1164-1175
A new program, PHI, with the ability to calculate the magnetic properties of large spin systems and complex orbitally degenerate systems, such as clusters of d‐block and f‐block ions, is presented. The program can intuitively fit experimental data from multiple sources, such as magnetic and spectroscopic data, simultaneously. PHI is extensively parallelized and can operate under the symmetric multiprocessing, single process multiple data, or GPU paradigms using a threaded, MPI or GPU model, respectively. For a given problem PHI is been shown to be almost 12 times faster than the well‐known program MAGPACK, limited only by available hardware. © 2013 Wiley Periodicals, Inc. 相似文献
104.
本文对抛物型方程的Du Fort-Frankel(DFF)格式以及基于该格式构造的并行差分格式(DFF-I)进行了稳定性分析。采用矩阵分析方法, 证明了其无条件(LR)稳定性, 给出了DFF格式的稳定性系数的最小值的上界估计, 结果表明其与网格比有关, 从而DFF格式并非绝对稳定。本文改进了并行差分格式(DFF-I)的稳定性分析结果, 证明了其增长矩阵的谱半径严格小于1, 从而具有长时间稳定性。数值算例验证了DFF-I格式具有空间二阶精度, 且有很好的稳定性。 相似文献
105.
106.
Bruce M. Allen Paul K. Predecki Maciej Kumosa 《Journal of computational chemistry》2014,35(9):756-764
Three open‐source applications, NanoEngineer‐1, packmol, and mis2lmp are integrated using an open‐source file format to quickly create molecular dynamics (MD) cells for simulation. The three software applications collectively make up the open‐source software (OSS) suite known as MD Studio (MDS). The software is validated through software engineering practices and is verified through simulation of the diglycidyl ether of bisphenol‐a and isophorone diamine (DGEBA/IPD) system. Multiple simulations are run using the MDS software to create MD cells, and the data generated are used to calculate density, bulk modulus, and glass transition temperature of the DGEBA/IPD system. Simulation results compare well with published experimental and numerical results. The MDS software prototype confirms that OSS applications can be analyzed against real‐world research requirements and integrated to create a new capability. © 2014 Wiley Periodicals, Inc. 相似文献
107.
On the induced‐fit mechanism of substrate‐enzyme binding structures of nylon‐oligomer hydrolase
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Takeshi Baba Ryuhei Harada Masayoshi Nakano Yasuteru Shigeta 《Journal of computational chemistry》2014,35(16):1240-1247
We present a detailed computational investigation of the induced‐fit motion in a nylon‐oligomer hydrolase (NylB) upon substrate binding. To this aim, we resort on the recently introduced parallel cascade selection molecular dynamics approach, allowing for an accelerated access to the set of conformational changes from an open‐ to a closed‐state structure to form the enzyme‐substrate complex in a specific induce‐fit mechanism. The structural investigation is quantitatively complemented by free energy analyses within the umbrella sampling algorithm accompanied by weighted histogram analysis. We find that the stabilization free energy is about 1.4 kcal/mol, whereas the highest free energy barrier to be overcome is about 2.3 kcal/mol. Conversely, the energetic contribution for the substrate binding is about 20 kcal/mol, as estimated from Generalized Born/Surface Area. This means that the open‐close induced‐fit motion could occur frequently once the substrate binds to the open state of NylB. © 2014 Wiley Periodicals, Inc. 相似文献
108.
Irena Zupanič Pajnič Carlo Previderè Tomaž Zupanc Martina Zanon Paolo Fattorini 《Electrophoresis》2022,43(13-14):1521-1530
The recent introduction of polymerase chain reaction (PCR)-massively parallel sequencing (MPS) technologies in forensics has changed the approach to allelic short tandem repeat (STR) typing because sequencing cloned PCR fragments enables alleles with identical molecular weights to be distinguished based on their nucleotide sequences. Therefore, because PCR fidelity mainly depends on template integrity, new technical issues could arise in the interpretation of the results obtained from the degraded samples. In this work, a set of DNA samples degraded in vitro was used to investigate whether PCR-MPS could generate “isometric drop-ins” (IDIs; i.e., molecular products having the same length as the original allele but with a different nucleotide sequence within the repeated units). The Precision ID GlobalFiler NGS STR panel kit was used to analyze 0.5 and 1 ng of mock samples in duplicate tests (for a total of 16 PCR-MPS analyses). As expected, several well-known PCR artifacts (such as allelic dropout, stutters above the threshold) were scored; 95 IDIs with an average occurrence of 5.9 IDIs per test (min: 1, max: 11) were scored as well. In total, IDIs represented one of the most frequent artifacts. The coverage of these IDIs reached up to 981 reads (median: 239 reads), and the ratios with the coverage of the original allele ranged from 0.069 to 7.285 (median: 0.221). In addition, approximately 5.2% of the IDIs showed coverage higher than that of the original allele. Molecular analysis of these artifacts showed that they were generated in 96.8% of cases through a single nucleotide change event, with the C > T transition being the most frequent (85.7%). Thus, in a forensic evaluation of evidence, IDIs may represent an actual issue, particularly when DNA mixtures need to be interpreted because they could mislead the operator regarding the number of contributors. Overall, the molecular features of the IDIs described in this work, as well as the performance of duplicate tests, may be useful tools for managing this new class of artifacts otherwise not detected by capillary electrophoresis technology. 相似文献
109.
110.
Mubashir Hussain Zhen Chen Mu Lv Jingyi Xu Xiaohan Dong Jingzhou Zhao Song Li Yan Deng Nongyue He Zhiyang Li Bin Liu 《中国化学快报》2021,31(12):3163-3167
The rapid identification of pathogens is crucial in controlling the food quality and safety. The proposed system for the rapid and label-free identification of pathogens is based on the principle of laser scattering from the bacterial microbes. The clinical prototype consists of three parts: the laser beam, photodetectors, and the data acquisition system. The bacterial testing sample was mixed with 10 mL distilled water and placed inside the machine chamber. When the bacterial microbes pass by the laser beam, the scattering of light occurs due to variation in size, shape, and morphology. Due to this reason, different types of pathogens show their unique light scattering patterns. The photo-detectors were arranged at the surroundings of the sample at different angles to collect the scattered light. The photodetectors convert the scattered light intensity into a voltage waveform. The waveform features were acquired by using the power spectral characteristics, and the dimensionality of extracted features was reduced by applying minimal-redundancy-maximal-relevance criterion (mRMR). A support vector machine (SVM) classifier was developed by training the selected power spectral features for the classification of three different bacterial microbes. The resulting average identification accuracies of E. faecalis,E. coli and S. aureus were 99%, 87%, and 94%, respectively. The overall experimental results yield a higher accuracy of 93.6%, indicating that the proposed device has the potential for label-free identification of pathogens with simplicity, rapidity, and cost-effectiveness. 相似文献