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61.
Molecular dynamics-based free energy calculations allow the determination of a variety of thermodynamic quantities from computer simulations of small molecules. Thermodynamic integration (TI) calculations can suffer from instabilities during the creation or annihilation of particles. This "singularity" problem can be addressed with "soft-core" potential functions which keep pairwise interaction energies finite for all configurations and provide smooth free energy curves. "One-step" transformations, in which electrostatic and van der Waals forces are simultaneously modified, can be simpler and less expensive than "two-step" transformations in which these properties are changed in separate calculations. Here, we study solvation free energies for molecules of different hydrophobicity using both models. We provide recommended values for the two parameters α(LJ) and β(C) controlling the behavior of the soft-core Lennard-Jones and Coulomb potentials and compare one- and two-step transformations with regard to their suitability for numerical integration. For many types of transformations, the one-step procedure offers a convenient and accurate approach to free energy estimates. 相似文献
62.
63.
Daeha Joung Luona Anjia Hiroshi Matsui Saiful I. Khondaker 《Applied Physics A: Materials Science & Processing》2013,112(2):305-310
We investigate the room temperature electronic transport properties of a zinc oxide (ZnO) coated peptide nanotube contacted with Au electrodes. Current–voltage (I–V) characteristics show asymmetric negative differential resistance (NDR) behavior along with current rectification. The NDR phenomenon is observed in both negative and positive voltage sweep scans, and found to be dependent on the scan rate and humidity. Our results suggest that the NDR is due to protonic conduction arising from water molecule redox reaction on the surface of ZnO coated peptide nanotubes rather than the conventional resonant tunneling mechanism. 相似文献
64.
65.
In this study, the sequential dispersion of multi-walled carbon nanotubes (CNTs) in PDMS/PB (polydimethylsiloxane/polybutene) blends and the change of blend morphology by the dispersion of CNTs were investigated by rheological and morphological observations. The dispersion of CNTs into PDMS/PB blend was accomplished by the dilution of the CNT master (2?wt.% CNT in PDMS) in PDMS/PB blend using an extensional mixer. The morphological study shows that under the extensional flow, CNTs in the dispersed CNT master phase are mainly broken up by tip-streaming and the continuous pinching-off of PDMS drops during morphology evolution enhances the dispersion of CNT. It has been shown that CNTs can be disentangled as in the case of dispersing CNTs in a Boger fluid. Rheological data and TEM observations show that it is not simply a mixing of two phases and the CNTs in the master phase can be dispersed in the single CNT level. 相似文献
66.
Clinton G. Joung 《Rheologica Acta》2006,46(1):143-152
A new simulation framework was created for modeling the dynamics of arbitrarily shaped particles dispersed in Newtonian fluid.
Theoretical complexity usually restricts suspension simulations to those for spheroids. This new simulation is loosely based
on the Stokesian Dynamics method including long range hydrodynamic interaction and uses spheres as building components for
greater particulates of arbitrary shape. This approach is capable of accurately reproducing the dynamics of an isolated arbitrarily
shaped particle. As verification, the simulated results are compared against known results for a rod-like particle. An elongated
rod-shaped structure made from linked spheres is shown to reproduce the well-known elongated ellipsoidal particle dynamics
described by [Jeffrey Proc R Soc Lond A 102:161–179, 1923]. The predicted orbital period and spin rates for a fiber in shear are reproduced and compare well with theoretical prediction
over a wide aspect ratio range. Predicted particle dynamics for other shaped particles are then demonstrated. 相似文献
67.
Baik J Kim M Park CY Kim Y Ahn JR An KS 《Journal of the American Chemical Society》2006,128(26):8370-8371
We first found experimentally a cycloaddition reaction of a molecule on a symmetry Si pair, 1,3-butadiene on the Si adatom pair of Si(111)7x7, while up to now only asymmetric Si pairs were reported to be involved in cycloaddition reactions on Si surfaces. As the symmetry of a Si pair is expected to influence significantly a cycloaddition product and a reaction pathway, the [4+2]-like cycloaddition product of 1,3-butadiene on the Si adatom pair is suggested to form through a concerted reaction pathway in comparison to a stepwise reaction pathway, which is favorable in the formation of the [4+2]-like cycloaddition product on the asymmetric Si pair (the Si adatom-restatom pair). 相似文献
68.
Jeong MS Kim E Kang HJ Choi EJ Cho AR Chung SJ Park SB 《Chemical communications (Cambridge, England)》2012,48(52):6553-6555
We report a Seoul-Fluor-based bioprobe, SfBP, for selective monitoring of protein tyrosine phosphatases (PTPs). A rational design based on the structures at the active site of dual-specific PTPs can enable SfBP to selectively monitor the activity of these PTPs with a 93-fold change in brightness. Moreover, screening results of SfBP against 30 classical PTPs and 35 dual-specific PTPs show that it is selective toward vaccinia H1-related (VHR) phosphatase, a dual-specific PTP (DUSP-3). 相似文献
69.
Jun Feng Zhang Young Hoon Lee Joung Hae Lee Jong Seung Kim 《Tetrahedron letters》2010,51(29):3719-3723
Two calix[4]arene derivatives with modified bipyridine as binding sites have been designed and synthesized. Compounds 1 and 2 are the first 2,2′-bipyridine-modified calix[4]arene-based sensors that can detect Zn2+ selectively with respect to ratiometric fluorescent changes and red shift. A binuclear complex structure has been demonstrated in the binding modes of 1-Zn2+ and 2-Zn2+ complexes. 相似文献
70.
A novel 1,3,5-substituted triethylbenzene derivative with a 2-aminobenzimidazole moiety as a binding and signaling subunit was synthesized. The sensor was tested in a buffered CH(3)CN/H(2)O (99:1, v/v) solution and found to be selective for iodide as demonstrated by the photophysical properties obtained through UV-vis absorption and fluorescence spectroscopy analyses. 相似文献