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41.
Prof. Shingo Saito Toshiki Sakamoto Naoki Tanaka Ryo Watanabe Takuya Kamimura Kazuki Ota Kathryn R. Riley Keitaro Yoshimoto Yuiko Tasaki-Handa Masami Shibukawa 《Chemistry (Weinheim an der Bergstrasse, Germany)》2021,27(39):10058-10067
In DNA aptamer selection, existing methods do not discriminate aptamer sequences based on their binding affinity and function and the reproducibility of the selection is often poor, even for the selection of well-known aptamers like those that bind the commonly used model protein thrombin. In the present study, a novel single-round selection method (SR-CE selection) was developed by combining capillary electrophoresis (CE) with next generation sequencing. Using SR-CE selection, a successful semi-quantitative and semi-comprehensive aptamer selection for thrombin was demonstrated with high reproducibility for the first time. Selection rules based on dissociation equilibria and kinetics were devised to obtain families of analogous sequences. Selected sequences of the same family were shown to bind thrombin with high affinity. Furthermore, data acquired from SR-CE selection was mined by creating sub-libraries that were categorized by the functionality of the aptamers (e. g., pre-organized aptamers versus structure-induced aptamers). Using this approach, a novel fluorescent molecular recognition sensor for thrombin with nanomolar detection limits was discovered. Thus, in this proof-of-concept report, we have demonstrated the potential of a “DNA Aptaomics” approach to systematically design functional aptamers as well as to obtain high affinity aptamers. 相似文献
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Murray Riley Chandrasekaran Venkat Wierman Adam 《Foundations of Computational Mathematics》2021,21(6):1703-1737
Foundations of Computational Mathematics - Certifying function nonnegativity is a ubiquitous problem in computational mathematics, with especially notable applications in optimization. We study the... 相似文献
44.
Andrew M. Riley Stephen J. Mills Barry V. L. Potter 《Phosphorus, sulfur, and silicon and the related elements》2013,188(1-4)
Abstract Data are presented on the magnitudes of 5 J pp and 6 J PP spin-spin coupling constants in the 31P NMR spectra of a variety of novel polyphosphite triesters. 相似文献
45.
Modelling of the proline (1) catalyzed aldol reaction (with acetone 2) in the presence of an explicit molecule of dimethyl sulfoxide (DMSO) (3) has showed that 3 is a major player in the aldol reaction as it plays a double role. Through strong interactions with 1 and acetone 2, it leads to a significant increase of energy barriers at transition states (TS) for the lowest energy conformer 1a of proline. Just the opposite holds for the higher energy conformer 1b. Both the ‘inhibitor’ and ‘catalyst’ mode of activity of DMSO eliminates 1a as a catalyst at the very beginning of the process and promotes the chemical reactivity, hence catalytic ability of 1b. Modelling using a Molecular-Wide and Electron Density-based concept of Chemical Bonding (MOWED-CB) and the Reaction Energy Profile–Fragment Attributed Molecular System Energy Change (REP-FAMSEC) protocol has shown that, due to strong intermolecular interactions, the HN-C-COOH (of 1), CO (of 2), and SO (of 3) fragments drive a chemical change throughout the catalytic reaction. We strongly advocate exploring the pre-organization of molecules from initially formed complexes, through local minima to the best structures suited for a catalytic process. In this regard, a unique combination of MOWED-CB with REP-FAMSEC provides an invaluable insight on the potential success of a catalytic process, or reaction mechanism in general. The protocol reported herein is suitable for explaining classical reaction energy profiles computed for many synthetic processes. 相似文献
46.
Chong Saehwa Riley Brian J. Nienhuis Emily T. Lee Dongjin McCloy John S. 《Journal of chemical crystallography》2021,51(3):293-300
Journal of Chemical Crystallography - Four different rare-earth oxyapatites of Ca2RE8(SiO4)6O2 (RE?=?Pr, Tb, Ho, Tm) were synthesized using a solution-based method followed by drying,... 相似文献
47.
Enzymes can be used in nonpolar reaction media to modify waterinsoluble substrates. A variety of pretreatments, applied to
the enzyme prior to introduction to the nonpolar media, can improve enzyme activity. However, the various pretreatments have
not been studied using directly comparable conditions, nor have they been applied simultaneously to test for interactive effects.
This work evaluates pretreatment of lipase with various classes of additives. The pretreated lipase is used to catalyze esterification
between citronellol and acetic acid in a medium of n-hexane. The effectiveness of a particular pretreatment is presented in terms of relative performance (RP), which is equal
to the number of times faster the pretreated lipase catalyzes the reaction relative to untreated lipase. The individual and
interactive effects of the pretreatment factors were studied and compared. Buffer salts had a much stronger performance-enhancing
effect than nonbuffer salts; pretreatment with 90% (w/w) sodium phosphate yielded lipase with an RP of approx 64. A strong
interaction was found between the treatments with sodium phosphate and pH adjustment. These treatments may mitigate the inhibitory
effect of acetic acid. Activating effects of phase interfaces and active-site protectants are shown to be complementary to
other treatments, demonstrating that they likely act by distinct mechanisms. 相似文献
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We study the filling length function for a finite presentation of a group , and interpret this function as an optimal bound on the length of the boundary loop as a van Kampen diagram is collapsed to the basepoint using a combinatorial notion of a null-homotopy. We prove that filling length is well behaved under change of presentation of . We look at 'AD-pairs' (f,g) for a finite presentation
: that is, an isoperimetric function f and an isodiametric function g that can be realised simultaneously. We prove that the filling length admits a bound of the form [g+1][log (f+1)+1] whenever (f,g) is an AD-pair for
. Further we show that (up to multiplicative constants) if
is an isoperimetric function (
) for a finite presentation then (
) is an AD-pair. Also we prove that for all finite presentations filling length is bounded by an exponential of an isodiametric function.Partially supported by NSF grant DMS-9800158Supported by EPSRC Award No. 98001683 and Corpus Christi College, Oxford. 相似文献