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11.
Multiple time step (MTS) algorithms present an effective integration approach to reduce the computational cost of dynamics simulations. By using force splitting to allow larger time steps for the more slowly varying force components, computational savings can be realized. The Particle-Mesh-Ewald (PME) method has been independently devised to provide an effective and efficient treatment of the long-range electrostatics interactions. Here we examine the performance of a combined MTS/PME algorithm previously developed for AMBER on a large polymerase beta/DNA complex containing 40,673 atoms. Our goal is to carefully combine the robust features of the Langevin/MTS (LN) methodology implemented in CHARMM-which uses position rather than velocity Verlet with stochasticity to make possible outer time steps of 150 fs-with the PME formulation. The developed MTS/PME integrator removes fast terms from the reciprocal-space Ewald component by using switch functions. We analyze the advantages and limitations of the resulting scheme by comparing performance to the single time step leapfrog Verlet integrator currently used in AMBER by evaluating different time-step protocols using three assessors for accuracy, speedup, and stability, all applied to long (i.e., nanosecond) simulations to ensure proper energy conservation. We also examine the performance of the algorithm on a parallel, distributed shared-memory computer (SGI Origin 2000 with 8 300-MHz R12000 processors). Good energy conservation and stability behavior can be demonstrated, for Newtonian protocols with outer time steps of up to 8 fs and Langevin protocols with outer time steps of up to 16 fs. Still, we emphasize the inherent limitations imposed by the incorporation of MTS methods into the PME formulation that may not be widely appreciated. Namely, the limiting factor on the largest outer time-step size, and hence speedup, is an intramolecular cancellation error inherent to PME. This error stems from the excluded-nonbonded correction term contained in the reciprocal-space component. This cancellation error varies in time and introduces artificial frequencies to the governing dynamics motion. Unfortunately, we find that this numerical PME error cannot be easily eliminated by refining the PME parameters (grid resolution and/or order of interpolating polynomial). We suggest that methods other than PME for fast electrostatics may allow users to reap the full advantages from MTS algorithms. 相似文献
12.
An interlaboratory study was performed on behalf of the UK Food Standards Agency to evaluate the effectiveness of an immunoaffinity column cleanup liquid chromatographic (LC) method for the determination of deoxynivalenol in a variety of cereals and cereal products at proposed European regulatory limits. The test portion was extracted with water. The sample extract was filtered a applied to an immunoaffinity column. After being washed with water, the deoxynivalenol was eluted with acetonitrile or methanol. Deoxynivalenol was quantitated by reversed-phase LC with UV determination. Samples of artificially contaminated wheat-flour, rice flour, oat flour, polenta, and wheat based breakfast cereal, naturally contaminated wheat flour, and blank (very low level) samples of each matrix were sent to 13 collaborators in 7 European countries. Participants were asked to spike test portions of all samples at a range of deoxynivalenol concentrations equivalent to 200-2000 ng/g deoxynivalenol. Average recoveries ranged from 78 to 87%. Based on results for 6 artificially contaminated samples (blind duplicates), the relative standard deviation for repeatability (RSDr) ranged from 3.1 to 14.1%, and the relative standard deviation for reproducibility (RSDR) ranged from 11.5 to 26.3%. The method showed acceptable within-laboratory and between-laboratory precision for all 5 matrixes, as evidenced by HorRat values < 1.3. 相似文献
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Danny L. Yeager Hosung Sun Karl F. Freed Michael F. Herman 《Chemical physics letters》1978,57(4):490-495
The n = 2 effective valence shell hamiltonian, v, of carbon is evaluated through second order using 3P Hartree—Fock orbitals (5s4p) with added d functions to provide results within a few percent of the spd convergence limits. The calculated v is employed to evaluate the n = 2 valence states of C, C?, C+, C2+ and C3+ with an average deviation of the 21 excitation energies, ionization potentials and electron affinity from experimental values of 0.32 eV. Three-electron parts of v contribute substantially to a number of these excitation energies. 相似文献
14.
Campos LM Dang H Ng D Yang Z Martinez HL Garcia-Garibay MA 《The Journal of organic chemistry》2002,67(11):3749-3754
A detailed thermochemical analysis of the alpha-cleavage and decarbonylation reactions of acetone and several ketodiesters was carried out with the B3LYP/6-31G* density functional method. The heats of formation of several ground-state ketones and radicals were calculated at 298 K to determine bond dissociation energies (BDE) and radical stabilization energies (RSE) as a function of substituents. Results show that the radical-stabilizing abilities of the ketone substituents play a very important role on the thermodynamics of the alpha-cleavage and decarbonylation steps. An excellent correlation between calculated values and previous experimental observations suggests that photochemical alpha-cleavage and decarbonylation in crystals should be predictable from knowledge of excitation energies and the RSE of the substituent. 相似文献
15.
Rudolph A. Abramovitch Suchet S. Mathur Daniel W. Saunders Danny P. Vanderpool 《Tetrahedron letters》1980,21(8):705-708
Pyridinium -toluenesulfonylmethylide serves as a formyl anion equivalent and, in the presence of an alcohol, undergoes 1,4-addition to -substituted maleimides to give alkoxy- (or aryloxy)-methylene-succinimides. The protected aldehyde group can be liberated readily. 相似文献
16.
Danny K. Long Wolfgang Bangerth Derek R. Handwerk Christopher B. Whitehead Patrick D. Shipman Richard G. Finke 《Journal of computational chemistry》2022,43(1):43-56
In order to quantitatively predict nano- as well as other particle-size distributions, one needs to have both a mathematical model and estimates of the parameters that appear in these models. Here, we show how one can use Bayesian inversion to obtain statistical estimates for the parameters that appear in recently derived mechanism-enabled population balance models (ME-PBM) of nanoparticle growth. The Bayesian approach addresses the question of “how well do we know our parameters, along with their uncertainties?.” The results reveal that Bayesian inversion statistical analysis on an example, prototype nanoparticle formation system allows one to estimate not just the most likely rate constants and other parameter values, but also their SDs, confidence intervals, and other statistical information. Moreover, knowing the reliability of the mechanistic model's parameters in turn helps inform one about the reliability of the proposed mechanism, as well as the reliability of its predictions. The paper can also be seen as a tutorial with the additional goal of achieving a “Gold Standard” Bayesian inversion ME-PBM benchmark that others can use as a control to check their own use of this methodology for other systems of interest throughout nature. Overall, the results provide strong support for the hypothesis that there is substantial value in using a Bayesian inversion methodology for parameter estimation in particle formation systems. 相似文献
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Danny Mortimer Matthew Whiting Joseph P.A. Harrity Simon Jones Iain Coldham 《Tetrahedron letters》2014
Lewis acid mediated intramolecular Mannich reaction between an azocinone and a 3-formylindole was investigated as part of a study towards the synthesis of actinophyllic acid. The intramolecular Mannich reaction resulted in a single diastereomer of the 1-azabicyclo[4.2.1]nonan-5-one core framework, although single crystal X-ray structure analysis revealed that this had the undesired stereochemistry in comparison with the natural product. 相似文献