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1.
We report systematic quantum mechanics‐only (QM‐only) and QM/molecular mechanics (MM) calculations on an enzyme‐catalyzed reaction to assess the convergence behavior of QM‐only and QM/MM energies with respect to the size of the chosen QM region. The QM and MM parts are described by density functional theory (typically B3LYP/def2‐SVP) and the CHARMM force field, respectively. Extending our previous work on acetylene hydratase with QM regions up to 157 atoms (Liao and Thiel, J. Chem. Theory Comput. 2012, 8, 3793), we performed QM/MM geometry optimizations with a QM region M4 composed of 408 atoms, as well as further QM/MM single‐point calculations with even larger QM regions up to 657 atoms. A charge deletion analysis was conducted for the previously used QM/MM model ( M3a , with a QM region of 157 atoms) to identify all MM residues with strong electrostatic contributions to the reaction energetics (typically more than 2 kcal/mol), which were then included in M4 . QM/MM calculations with this large QM region M4 lead to the same overall mechanism as the previous QM/MM calculations with M3a , but there are some variations in the relative energies of the stationary points, with a mean absolute deviation (MAD) of 2.7 kcal/mol. The energies of the two relevant transition states are close to each other at all levels applied (typically within 2 kcal/mol), with the first (second) one being rate‐limiting in the QM/MM calculations with M3a ( M4 ). QM‐only gas‐phase calculations give a very similar energy profile for QM region M4 (MAD of 1.7 kcal/mol), contrary to the situation for M3a where we had previously found significant discrepancies between the QM‐only and QM/MM results (MAD of 7.9 kcal/mol). Extension of the QM region beyond M4 up to M7 (657 atoms) leads to only rather small variations in the relative energies from single‐point QM‐only and QM/MM calculations (MAD typically about 1–2 kcal/mol). In the case of acetylene hydratase, a model with 408 QM atoms thus seems sufficient to achieve convergence in the computed relative energies to within 1–2 kcal/mol.Copyright © 2013 Wiley Periodicals, Inc.  相似文献   
2.
We present a spectral algorithm based on the convex combination of two modified spectral coefficients for solving systems of nonlinear equations. The proposed algorithm does not require the exact or approximated directional derivative for its implementation. By employing a derivative-free line search, the global convergence of the sequence generated by the algorithm is supported. Numerical experiments are given to demonstrate the performance of the algorithm compared with a similar algorithm in the literature for solving nonlinear equations problems.  相似文献   
3.
In this paper, we consider the three dimensional Cauchy problem of the compressible micropolar viscous flows. We prove the existence of unique global classical solution for smooth initial data with small initial energy but possibly large oscillations and the initial density may allowed to contain the interior and far field vacuum states. Furthermore, the large time behavior of the solution is obtained as well.  相似文献   
4.
This research study deals with the numerical solutions of linear and nonlinear time-fractional subdiffusion equations of distributed order. The main aim of our approach is based on the hybrid of block-pulse functions and shifted Legendre polynomials. We produce a novel and exact operational vector for the fractional Riemann–Liouville integral and use it via the Gauss–Legendre quadrature formula and collocation method. Consequently, we reduce the proposed equations to systems of equations. The convergence and error bounds for the new method are investigated. Six problems are tested to confirm the accuracy of the proposed approach. Comparisons between the obtained numerical results and other existing methods are provided. Numerical experiments illustrate the reliability, applicability, and efficiency of the proposed method.  相似文献   
5.
In this paper, we are interested in the existence and bifurcation of positive solutions for Kirchhoff-type eigenvalue problems involving the fractional p $$ p $$-Laplacian. First, we investigate the properties of the first eigenvalue for fractional p $$ p $$-Laplacian equations with weighted functions. Furthermore, by using fixed-point argument and modified global bifurcation theorem of Rabinowitz, together with topological degree theory, we obtain the existence of unbounded continuum of positive weak solutions to Kirchhoff-type equations with subcritical and critical nonlinearities, where the bifurcation emanates from (0,0) $$ \left(0,0\right) $$. It is worth mentioning that our main results fill in some gaps of the available results.  相似文献   
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7.
Fisher linear discriminant analysis is a well-known technique for dimensionality reduction and classification. The method was first formulated in 1936 by Fisher. In this paper we concentrate on three different formulations of the multi-dimensional problem. We provide a mathematical explanation why two of the formulations are equivalent and prove that this equivalency can be extended to a broader class of objective functions. The second contribution is a rate of convergence of a fixed point method for solving the third model.  相似文献   
8.
Using the theory of negative association for measures and the notion of unimodularity for random weak limits of sparse graphs, we establish the validity of the cavity method for counting spanning subgraphs subject to local constraints in asymptotically tree‐like graphs. Specifically, the normalized logarithm of the associated partition function (free energy) is shown to converge along any sequence of graphs whose random weak limit is a tree, and the limit is directly expressed in terms of the unique solution to a limiting cavity equation. On a Galton–Watson tree, the latter simplifies into a recursive distributional equation which can be solved explicitly. As an illustration, we provide a new asymptotic formula for the maximum size of a b‐matching in the Erd?s–Rényi random graph with fixed average degree and diverging size, for any $b\in\mathbb{N}Using the theory of negative association for measures and the notion of unimodularity for random weak limits of sparse graphs, we establish the validity of the cavity method for counting spanning subgraphs subject to local constraints in asymptotically tree‐like graphs. Specifically, the normalized logarithm of the associated partition function (free energy) is shown to converge along any sequence of graphs whose random weak limit is a tree, and the limit is directly expressed in terms of the unique solution to a limiting cavity equation. On a Galton–Watson tree, the latter simplifies into a recursive distributional equation which can be solved explicitly. As an illustration, we provide a new asymptotic formula for the maximum size of a b‐matching in the Erd?s–Rényi random graph with fixed average degree and diverging size, for any $b\in\mathbb{N}$. To the best of our knowledge, this is the first time that correlation inequalities and unimodularity are combined together to yield a general proof of uniqueness of Gibbs measures on infinite trees. We believe that a similar argument is applicable to other Gibbs measures than those over spanning subgraphs considered here. © 2012 Wiley Periodicals, Inc. Random Struct. Alg., 2013  相似文献   
9.
Abstract. Ensuring drought resilience for farmers is an important policy concern. Yet, a quantitative treatment of the concept of drought resilience has been lacking in the literature. This paper designs a mathematical model of drought resilience to assess farmers’ survival strategies when faced with the prospect of repeated droughts. A key distinction is being made here between consecutive droughts and one‐off droughts, as it is the former, which is of most concern to farmers as well as policy makers. The mathematical model is generalized to incorporate the possibility of more than one set of a certain number of consecutive droughts occurring in the future. Findings indicate varying implications for groundwater sustainability when resilience outcomes are directly linked to the length of a farmer's drought planning horizon as well as to the planned minimum consumption during drought years.  相似文献   
10.
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