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21.
Sindbert S Kalinin S Nguyen H Kienzler A Clima L Bannwarth W Appel B Müller S Seidel CA 《Journal of the American Chemical Society》2011,133(8):2463-2480
In Fo?rster resonance energy transfer (FRET) experiments, the donor (D) and acceptor (A) fluorophores are usually attached to the macromolecule of interest via long flexible linkers of up to 15 ? in length. This causes significant uncertainties in quantitative distance measurements and prevents experiments with short distances between the attachment points of the dyes due to possible dye-dye interactions. We present two approaches to overcome the above problems as demonstrated by FRET measurements for a series of dsDNA and dsRNA internally labeled with Alexa488 and Cy5 as D and A dye, respectively. First, we characterize the influence of linker length and flexibility on FRET for different dye linker types (long, intermediate, short) by analyzing fluorescence lifetime and anisotropy decays. For long linkers, we describe a straightforward procedure that allows for very high accuracy of FRET-based structure determination through proper consideration of the position distribution of the dye and of linker dynamics. The position distribution can be quickly calculated with geometric accessible volume (AV) simulations, provided that the local structure of RNA or DNA in the proximity of the dye is known and that the dye diffuses freely in the sterically allowed space. The AV approach provides results similar to molecular dynamics simulations (MD) and is fully consistent with experimental FRET data. In a benchmark study for ds A-RNA, an rmsd value of 1.3 ? is achieved. Considering the case of undefined dye environments or very short DA distances, we introduce short linkers with a propargyl or alkenyl unit for internal labeling of nucleic acids to minimize position uncertainties. Studies by ensemble time correlated single photon counting and single-molecule detection show that the nature of the linker strongly affects the radius of the dye's accessible volume (6-16 ?). For short propargyl linkers, heterogeneous dye environments are observed on the millisecond time scale. A detailed analysis of possible orientation effects (κ(2) problem) indicates that, for short linkers and unknown local environments, additional κ(2)-related uncertainties are clearly outweighed by better defined dye positions. 相似文献
22.
Maximilian Zieringer Abel Garcia‐Bernabé Dr. Burkhard Costisella Prof. Dr. Heiko Glatz Dr. Willi Bannwarth Prof. Dr. Rainer Haag Prof. Dr. 《Chemphyschem》2010,11(12):2617-2622
This paper describes the behavior of various generations of polyglycerol dendrimers that contain a perfluorinated shell. The aggregation in organic solvents is based on supramolecular fluorous–fluorous interactions, which can be described by means of 19F NMR spectroscopy. In order to study the interaction and aggregation phenomena of dendrimers with perfluorinated shell and perfluoro‐tagged guest molecules we investigated [G3.5]‐dendrimer with a perfluorinated shell in the presence of perfluoro‐tagged disperse red. Noteworthy, the interaction intensities varied in an unexpected manner depending on the equivalents of perfluoro‐tagged guest molecules added to the dendrimers in solution which then formed supramolecular complexes based on fluorous–fluorous interactions. We found that these complexes aggregated around residual air in the solvent to form stable micron‐sized bubbles. Their sizes correlated with the interaction intensities measured for certain dendrimer–guest molecule ratios. Degassing of the solutions led to a quasi phase separation between organic and fluorous phase, whereby the dendrimers formed the fluorous phases. Regassing the sample with air afforded bubbles of the initial size again. 相似文献
23.
Haiping Qi Manfred Gröning Tyler B. Coplen Bryan Buck Stanley J. Mroczkowski Willi A. Brand Heike Geilmann Matthias Gehre 《Rapid communications in mass spectrometry : RCM》2010,24(13):1821-1827
A new method to seal water in silver tubes for use in a TC/EA (thermal conversion/elemental analyzer) reduction unit using a semi‐automated sealing apparatus can yield reproducibilities (1 standard deviation) of δ2H and δ18O measurements of 1.0‰ and 0.06‰, respectively. These silver tubes containing reference waters may be preferred for the calibration of H‐ and O‐bearing materials analyzed with a TC/EA reduction unit. The new sealing apparatus employs a computer‐controlled stepping motor to produce silver tubes identical in length. The reproducibility of the mass of water sealed in tubes (in a range of 200–400 µg) can be as good as 1%. Approximately 99% of the sealed silver tubes are satisfactory (leak free). Although silver tubes sealed with reference waters are robust and can be shaken or heated to 110°C with no loss of integrity, they should not be frozen because the expansion during the phase transition of water to ice will break the cold seals and all the water will be lost. The tubes should be shipped in insulated containers. This new method eliminates air inclusions and isotopic fractionation of water associated with the loading of water into capsules using a syringe. The method is also more than an order of magnitude faster than preparing water samples in ordinary Ag capsules. Nevertheless, some laboratories may prefer loading water into silver capsules because expensive equipment is not needed, but users of this method are cautioned to apply the necessary corrections for evaporation, back exchange with laboratory atmospheric moisture, and blanks. Copyright © 2010 John Wiley & Sons, Ltd. 相似文献
24.
25.
Auwärter W Klappenberger F Weber-Bargioni A Schiffrin A Strunskus T Wöll C Pennec Y Riemann A Barth JV 《Journal of the American Chemical Society》2007,129(36):11279-11285
We present a combined low-temperature scanning tunneling microscopy and near-edge X-ray adsorption fine structure study on the interaction of tetrapyridyl-porphyrin (TPyP) molecules with a Cu(111) surface. A novel approach using data from complementary experimental techniques and charge density calculations allows us to determine the adsorption geometry of TPyP on Cu(111). The molecules are centered on "bridge" sites of the substrate lattice and exhibit a strong deformation involving a saddle-shaped macrocycle distortion as well as considerable rotation and tilting of the meso-substituents. We propose a bonding mechanism based on the pyridyl-surface interaction, which mediates the molecular deformation upon adsorption. Accordingly, a functionalization by pyridyl groups opens up pathways to control the anchoring of large organic molecules on metal surfaces and tune their conformational state. Furthermore, we demonstrate that the affinity of the terminal groups for metal centers permits the selective capture of individual iron atoms at low temperature. 相似文献
26.
MNDO-PM3 calculations, carried out on an experimentally determined structure of an intermediate in the cycloaddition of an electrophilic azide and a nucleophilic 1,3-dipolarophile, show that the semiempirical MO scheme models this structure closely. Transition structures for formation of the intermediate and ring closure of the latter are described. 相似文献
27.
Willi R. Berg Dr. Jonathan F. Berengut Changzhuang Bai Dr. Laura Wimberger Prof. Lawrence K. Lee Dr. Felix J. Rizzuto 《Angewandte Chemie (International ed. in English)》2023,62(51):e202314458
Hierarchical DNA nanostructures offer programmable functions at scale, but making these structures dynamic, while keeping individual components intact, is challenging. Here we show that the DNA A-motif—protonated, self-complementary poly(adenine) sequences—can propagate DNA origami into one-dimensional, micron-length fibrils. When coupled to a small molecule pH regulator, visible light can activate the hierarchical assembly of our DNA origami into dissipative fibrils. This system is recyclable and does not require DNA modification. By employing a modular and waste-free strategy to assemble and disassemble hierarchical structures built from DNA origami, we offer a facile and accessible route to developing well-defined, dynamic, and large DNA assemblies with temporal control. As a general tool, we envision that coupling the A-motif to cycles of dissipative protonation will allow the transient construction of diverse DNA nanostructures, finding broad applications in dynamic and non-equilibrium nanotechnology. 相似文献
28.
Parabolic initial boundary-value problems coupled (via the boundary condition) with ordinary differential equations whose right-hand side contains the Preisach hysteresis operator are considered. In particular, these problems model thermocontrol processes in chemical reactors, climate-control systems, biological cells, etc. For the Preisach operator with and without time delay, solvability, periodicity of solutions, and global B-attractors are studied. 相似文献
29.
Summary The convergence of semi-discrete and discrete linear approximation schemes is analysed for nonlinear degenerate parabolic systems of porous medium type. The enthalpy formulation and variational technique are used. The semi-discretization used reduces the original parabolic P.D.E. to linear elliptic P.D.E. The algebraic correction arising from nonlinearities is treated by Newton-like iterations in finite steps. Some numerical experiments are discussed and compared with the analytical solutions.Supported by the Alexander von Humboldt-Foundation in 1989, and by SFB 123, University Heidelberg 相似文献
30.
Maria Neuss-Radu Stephan Ludwig Willi Jäger 《Nonlinear Analysis: Real World Applications》2010,11(6):4572-4585
This paper considers a transmission problem for partial differential equations obtained in the recent paper [M. Neuss-Radu, W. Jäger, Effective transmission conditions for reaction-diffusion processes in domains separated by an interface, SIAM J. Math. Anal. 39 (2007) 687–720] as the effective system modeling a reaction–diffusion process in two domains separated by a membrane. For the analysis of this problem an appropriate function space, which includes the coupling conditions for the concentrations on the interface, is introduced. The transmission conditions for the flux are included in the variational formulation with respect to this function space.The solution of the transmission problem is approximated by using the Galerkin method. Numerically the problem is reduced to a system of ordinary differential equations, where the coupling of the micro- and macro-variables leads to a special structure, distinguishing the variables relevant for the transmission. Results of numerical simulations are illustrating the effect of the microscopic process in the membrane on the macroscopic reaction–diffusion process in the bulk domains. 相似文献