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1.
Dr. Jeffery M. Tharp Dr. Omer Ad Dr. Kazuaki Amikura Fred R. Ward Emma M. Garcia Prof. Dr. Jamie H. D. Cate Prof. Dr. Alanna Schepartz Prof. Dr. Dieter Söll 《Angewandte Chemie (Weinheim an der Bergstrasse, Germany)》2020,132(8):3146-3150
By transplanting identity elements into E. coli tRNAfMet, we have engineered an orthogonal initiator tRNA (itRNATy2) that is a substrate for Methanocaldococcus jannaschii TyrRS. We demonstrate that itRNATy2 can initiate translation in vivo with aromatic non-canonical amino acids (ncAAs) bearing diverse sidechains. Although the initial system suffered from low yields, deleting redundant copies of tRNAfMet from the genome afforded an E. coli strain in which the efficiency of non-canonical initiation equals elongation. With this improved system we produced a protein containing two distinct ncAAs at the first and second positions, an initial step towards producing completely unnatural polypeptides in vivo. This work provides a valuable tool to synthetic biology and demonstrates remarkable versatility of the E. coli translational machinery for initiation with ncAAs in vivo. 相似文献
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Robert Lindner Xinghua Lou Jochen Reinstein Robert L Shoeman Fred A Hamprecht Andreas Winkler 《Journal of the American Society for Mass Spectrometry》2014,25(6):1018-1028
Hydrogen–deuterium exchange (HDX) experiments analyzed by mass spectrometry (MS) provide information about the dynamics and the solvent accessibility of protein backbone amide hydrogen atoms. Continuous improvement of MS instrumentation has contributed to the increasing popularity of this method; however, comprehensive automated data analysis is only beginning to mature. We present Hexicon 2, an automated pipeline for data analysis and visualization based on the previously published program Hexicon (Lou et al. 2010). Hexicon 2 employs the sensitive NITPICK peak detection algorithm of its predecessor in a divide-and-conquer strategy and adds new features, such as chromatogram alignment and improved peptide sequence assignment. The unique feature of deuteration distribution estimation was retained in Hexicon 2 and improved using an iterative deconvolution algorithm that is robust even to noisy data. In addition, Hexicon 2 provides a data browser that facilitates quality control and provides convenient access to common data visualization tasks. Analysis of a benchmark dataset demonstrates superior performance of Hexicon 2 compared with its predecessor in terms of deuteration centroid recovery and deuteration distribution estimation. Hexicon 2 greatly reduces data analysis time compared with manual analysis, whereas the increased number of peptides provides redundant coverage of the entire protein sequence. Hexicon 2 is a standalone application available free of charge under http://hx2.mpimf-heidelberg.mpg.de. Figure
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The linear stability analysis of vertical throughflow of power law fluid for double-diffusive convection with Soret effect in a porous channel is investigated in this study. The upper and lower boundaries are assumed to be permeable, isothermal and isosolutal. The linear stability of vertical through flow is influenced by the interactions among the non-Newtonian Rayleigh number (Ra), Buoyancy ratio (N), Lewis number (Le), Péclet number (Pe), Soret parameter (Sr) and power law index (n). The results indicate that the Soret parameter has a significant influence on convective instability of power law fluid. It has also been noticed that buoyancy ratio has a dual effect on the instability of fluid flow. Further, it is noticed that the basic temperature and concentration profiles have singularities at \(Pe = 0\) and \(Le = 1\), the convective instability is looked into for the limiting case of \(Pe\rightarrow 0\) and \(Le \rightarrow 1\). For the case of pure thermal convection with no vertical throughflow, the present numerical results coincide with the solution of standard Horton–Rogers–Lapwood problem. The present results for critical Rayleigh number obtained using bvp4c and two-term Galerkin approximation are compared with those available in the literature and are tabulated. 相似文献
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Jeffery M. Tharp Omer Ad Kazuaki Amikura Fred R. Ward Emma M. Garcia Jamie H. D. Cate Alanna Schepartz Dieter Sll 《Angewandte Chemie (International ed. in English)》2020,59(8):3122-3126
By transplanting identity elements into E. coli tRNAfMet, we have engineered an orthogonal initiator tRNA (itRNATy2) that is a substrate for Methanocaldococcus jannaschii TyrRS. We demonstrate that itRNATy2 can initiate translation in vivo with aromatic non‐canonical amino acids (ncAAs) bearing diverse sidechains. Although the initial system suffered from low yields, deleting redundant copies of tRNAfMet from the genome afforded an E. coli strain in which the efficiency of non‐canonical initiation equals elongation. With this improved system we produced a protein containing two distinct ncAAs at the first and second positions, an initial step towards producing completely unnatural polypeptides in vivo. This work provides a valuable tool to synthetic biology and demonstrates remarkable versatility of the E. coli translational machinery for initiation with ncAAs in vivo. 相似文献
8.
From the N‐Heterocyclic Carbene‐Catalyzed Conjugate Addition of Alcohols to the Controlled Polymerization of (Meth)acrylates 下载免费PDF全文
Winnie Nzahou Ottou Damien Bourichon Dr. Joan Vignolle Anne‐Laure Wirotius Dr. Fredéric Robert Prof. Yannick Landais Dr. Jean‐Marc Sotiropoulos Dr. Karinne Miqueu Prof. Daniel Taton 《Chemistry (Weinheim an der Bergstrasse, Germany)》2015,21(26):9447-9453
Among various N‐heterocyclic carbenes (NHCs) tested, only 1,3‐bis(tert‐butyl)imidazol‐2‐ylidene (NHCtBu) proved to selectively promote the catalytic conjugate addition of alcohols onto (meth)acrylate substrates. This rather rare example of NHC‐catalyzed 1,4‐addition of alcohols was investigated as a simple means to trigger the polymerization of both methyl methacrylate and methyl acrylate (MMA and MA, respectively). Well‐defined α‐alkoxy poly(methyl (meth)acrylate) (PM(M)A) chains, the molar masses of which could be controlled by the initial [(meth)acrylate]0/[ROH]0 molar ratio, were ultimately obtained in N,N‐dimethylformamide at 25 °C. A hydroxyl‐terminated poly(ethylene oxide) (PEO‐OH) macro‐initiator was also employed to directly access PEO‐b‐PMMA amphiphilic block copolymers. Investigations into the reaction mechanism by DFT calculations revealed the occurrence of two competitive concerted pathways, involving either the activation of the alcohol or that of the monomer by NHCtBu. 相似文献
9.
Carlos García-Martínez Fred Glover Francisco J. Rodriguez Manuel Lozano Rafael Martí 《Computational Optimization and Applications》2014,58(1):161-185
The quadratic multiple knapsack problem (QMKP) consists in assigning a set of objects, which interact through paired profit values, exclusively to different capacity-constrained knapsacks with the aim of maximising total profit. Its many applications include the assignment of workmen to different tasks when their ability to cooperate may affect the results. Strategic oscillation (SO) is a search strategy that operates in relation to a critical boundary associated with important solution features (such as feasibility). Originally proposed in the context of tabu search, it has become widely applied as an efficient memory-based methodology. We apply strategic oscillation to the quadratic multiple knapsack problem, disclosing that SO effectively exploits domain-specific knowledge, and obtains solutions of particularly high quality compared to those obtained by current state-of-the-art algorithms. 相似文献
10.
Cyclodimerization versus Polymerization of Methyl Methacrylate Induced by N‐Heterocyclic Carbenes: A Combined Experimental and Theoretical Study 下载免费PDF全文
Winnie Nzahou Ottou Damien Bourichon Dr. Joan Vignolle Anne‐Laure Wirotius Dr. Fredéric Robert Prof. Yannick Landais Dr. Jean‐Marc Sotiropoulos Dr. Karinne Miqueu Prof. Daniel Taton 《Chemistry (Weinheim an der Bergstrasse, Germany)》2014,20(14):3989-3997
The activation behavior of two N‐heterocyclic carbenes (NHCs), namely, 1,3‐bis(isopropyl)imidazol‐2‐ylidene(NHCiPr) and 1,3‐bis(tert‐butyl) imidazol‐2‐ylidene (NHCtBu), as organic nucleophiles in the reaction with methyl methacrylate (MMA) is described. NHCtBu allows the polymerization of MMA in DMF at room temperature and in toluene at 50 °C, whereas NHCiPr reacts with two molecules of MMA, forming an unprecedented imidazolium–enolate cyclodimer (NHCiPr/MMA=1:2). It is proposed that the reaction mechanism occurs by initial 1,4‐nucleophilic addition of NHCiPr to MMA, generating a zwitterionic enolate 2 , followed by addition of 2 to a second MMA molecule, forming a linear imidazolium–enolate 3 (NHCiPr/MMA=1:2). Proton transfer, generating intermediate 5 , followed by cyclization and release of methanol yielded the aforementioned zwitterionic cyclodimer 1:2 adduct 7 , the molecular structure of which has been established by NMR spectroscopy, X‐ray diffraction, and mass spectrometry. This unexpected difference between NHCtBu and NHCiPr in the reaction with MMA (polymerization and cyclodimerization, respectively) can be rationalized by using DFT calculations. In particular, the nature of the NHC strongly influences the cyclodimerization pathway, the cyclization of 5 and the release of methanol are the discriminating step and limiting step, respectively. In the case of NHCtBu, both steps are strongly disfavoured compared with that of NHCiPr (energetic difference of around 14 and 9 kcal mol?1, respectively), preventing the cyclization mechanism from a kinetic viewpoint. Moreover, addition of a third molecule of MMA in the polymerization pathway results in a lower activation barrier than that of the limiting step in the cyclodimerization pathway (difference of around 14 kcal mol?1), in agreement with the formation of polymethyl methacrylate (PMMA) by using NHCtBu as nucleophile. 相似文献