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111.
Declan Williams Suzanne Ackloo Peihong Zhu Peter Bowden Kenneth R. Evans Christina L. Addison Chris Lock John G. Marshall 《Analytical and bioanalytical chemistry》2010,396(3):1223-1247
The endogenous peptides of human serum may have regulatory functions, have been associated with physiological states, and
their modifications may reveal some mechanisms of disease. In order to correlate levels of specific peptides with disease
alongside internal standards, the polypeptides must first be reliably extracted and identified. Endogenous blood peptides
can be effectively enriched by precipitation of the serum with organic solvents followed by selective extraction of peptides
using aqueous solutions modified with organic solvents. Polypeptides on filter paper were assayed with Coomasie brilliant
blue binding. The polypeptides were resolved by detergent tricine polyacrylamide electrophoresis and visualized by diamine
silver staining. Peptides in the extracts were collected by C18 and analyzed by matrix-assisted laser desorption/ionization
and liquid chromatography–electrospray ionization–tandem mass spectrometry (MS/MS) quadrupole time-of-flight MS/MS. Peptides
were resolved as multiple isotopic peaks in MS mode with mass deviation of 0.1 Da or less and similar accuracy for fragments.
The sensitivity of MS and MS/MS analysis was estimated to be in the picomolar range or less. The peptide composition of the
extracts was dependent on solvent formulation. Multiple peptides from apolipoproteins, complement proteins, coagulation factors,
and many others were identified by X!Tandem with high mass accuracy of peptide ions and fragments from collision-induced dissociation.
Many previously unreported posttranslational modifications of peptides including phosphorylations, oxidations, glycosylations,
and others were detected with high mass accuracy and may be of clinical importance. About 4,630 redundant peptides were identified
with 99% confidence separately, and together some 1,251 distinct proteins were identified with 99% confidence or greater using
the Paragon algorithm. 相似文献
112.
Sasa Kazazic Hui-Min Zhang Tanner M. Schaub Mark R. Emmett Christopher L. Hendrickson Gregory T. Blakney Alan G. Marshall 《Journal of the American Society for Mass Spectrometry》2010,21(4):550-558
Mass analysis of proteolytic fragment peptides following hydrogen/deuterium exchange offers a general measure of solvent accessibility/hydrogen
bonding (and thus conformation) of solution-phase proteins and their complexes. The primary problem in such mass analyses
is reliable and rapid assignment of mass spectral peaks to the correct charge state and degree of deuteration of each fragment
peptide, in the presence of substantial overlap between isotopic distributions of target peptides, autolysis products, and
other interferant species. Here, we show that at sufficiently high mass resolving power (m/Δm50% ≥ 100,000), it becomes possible to resolve enough of those overlaps so that automated data reduction becomes possible, based
on the actual elemental composition of each peptide without the need to deconvolve isotopic distributions. We demonstrate
automated, rapid, reliable assignment of peptide masses from H/D exchange experiments, based on electrospray ionization FT-ICR
mass spectra from H/D exchange of solution-phase myoglobin. Combined with previously demonstrated automated data acquisition
for such experiments, the present data reduction algorithm enhances automation (and thus expands generality and applicability)
for high-resolution mass spectrometry-based analysis of H/D exchange of solution-phase proteins. 相似文献
113.
SKATE is a docking prototype that decouples systematic sampling from scoring. This novel approach removes any interdependence between sampling and scoring functions to achieve better sampling and, thus, improves docking accuracy. SKATE systematically samples a ligand's conformational, rotational and translational degrees of freedom, as constrained by a receptor pocket, to find sterically allowed poses. Efficient systematic sampling is achieved by pruning the combinatorial tree using aggregate assembly, discriminant analysis, adaptive sampling, radial sampling, and clustering. Because systematic sampling is decoupled from scoring, the poses generated by SKATE can be ranked by any published, or in‐house, scoring function. To test the performance of SKATE, ligands from the Asetex/CDCC set, the Surflex set, and the Vertex set, a total of 266 complexes, were redocked to their respective receptors. The results show that SKATE was able to sample poses within 2 Å RMSD of the native structure for 98, 95, and 98% of the cases in the Astex/CDCC, Surflex, and Vertex sets, respectively. Cross‐docking accuracy of SKATE was also assessed by docking 10 ligands to thymidine kinase and 73 ligands to cyclin‐dependent kinase. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010 相似文献
114.
We investigate the dynamical behavior of finite rings of classical spin vectors interacting via nearest-neighbor isotropic exchange in an external magnetic field. Our approach is to utilize the solutions of a continuum version of the discrete spin equations of motion (EOM) which we derive by assuming continuous modulations of spin wave solutions of the EOM for discrete spins. This continuum EOM reduces to the Landau-Lifshitz equation in a particular limiting regime. The usefulness of the continuum EOM is demonstrated by the fact that the time-evolved numerical solutions of the discrete spin EOM closely track the corresponding time-evolved solutions of the continuum equation. It is of special interest that our continuum EOM possesses soliton solutions, and we find that these characteristics are also exhibited by the corresponding solutions of the discrete EOM. The robustness of solitons is demonstrated by considering cases where initial states are truncated versions of soliton states and by numerical simulations of the discrete EOM equations when the spins are coupled to a heat bath at finite temperatures. 相似文献
115.
Xiong C Monat C Clark AS Grillet C Marshall GD Steel MJ Li J O'Faolain L Krauss TF Rarity JG Eggleton BJ 《Optics letters》2011,36(17):3413-3415
We report the generation of correlated photon pairs in the telecom C-band at room temperature from a dispersion-engineered silicon photonic crystal waveguide. The spontaneous four-wave mixing process producing the photon pairs is enhanced by slow-light propagation enabling an active device length of less than 100?μm. With a coincidence to accidental ratio of 12.8 at a pair generation rate of 0.006 per pulse, this ultracompact photon pair source paves the way toward scalable quantum information processing realized on-chip. 相似文献
116.
Noah J. Tremblay Alon A. Gorodetsky Dr. Marshall P. Cox Theanne Schiros Dr. Bumjung Kim Rachel Steiner Zachary Bullard Aaron Sattler Woo‐Young So Dr. Yoshimitsu Itoh Dr. Michael F. Toney Dr. Hirohito Ogasawara Dr. Arthur P. Ramirez Prof. Ioannis Kymissis Dr. Michael L. Steigerwald Dr. Colin Nuckolls Prof. 《Chemphyschem》2010,11(4):742-742
117.
Ian Marshall 《Letters in Mathematical Physics》2017,107(4):619-642
Presentation of a method for generating Lax pairs for systems obtained by means of Hamiltonian reduction. 相似文献
118.
Douglas S. Burns Marshall G. Cory Joseph L. Vasey 《International Journal for Ion Mobility Spectrometry》2010,13(2):73-82
Low level ab initio Quantum Chemistry (QC) is shown to be a promising technique for predicting the relative ordering of a wide variety of potential
analyte, dopant, and interferent molecules, by their proton affinities (PA). Computed PAs, using a single level of chemical
theory, are summarized for 53 compounds and when compared to literature reference data have a mean unsigned error of ∼9.5 kJ/mol.
Where applicable, multiple conformations of the protonated species were explored. In these cases, the Boltzmann weighted PA
is reported. Finally, examples are shown in which QC modeling is used to predict potential fragmentation products initiated
by the positive mode ionization. 相似文献
119.
120.
When a negative high voltage pulse is applied to a target material immersed in a plasma, a boundary layer (sheath) forms
around the target and the motion of cold ions in the plasma is governed by the Euler-Poisson system. In this paper, by simplifying
the Euler-Poisson system on suitable physical regimes, we present a theory for the existence and dynamics of time-dependent
sheaths with planar, cylindrical and spherical symmetry. For the construction of ion-sheaths, we employ the method of characteristics
and study the dynamic behavior of a plasma-sheath edge based on ODEs which are formally derived from the Euler-Poisson system.
Received: 9 December 2002 / Accepted: 16 January 2003
Published online: 28 May 2003
Communicated by P. Constantin 相似文献