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Electronic Structures and Spectra of the Bases and Base Pairs of Nucleic Acids 被引量:1
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作者 WANG Zhi-zhong and BAI Ya-wen (Institute of Theoretical Chemistry, Jilin University, Changchun, 130023) 《Chemical Research in Chinese Universities》 SCIE CAS CSCD 1992年第2期89-95,共7页
The present paper covers electronic structures and spectra of the bases and the base pairs of nucleic acids calculated by using the INDO/S method. For free bases we give the energy levels of ground states and transiti... The present paper covers electronic structures and spectra of the bases and the base pairs of nucleic acids calculated by using the INDO/S method. For free bases we give the energy levels of ground states and transition energies of low-lying excited states and discuss the band characters. The results indicate that the calculated spectra are in good agreement with experimental values. On the other hand, our calculations for A-T and G-C pairs are very beneficial to understanding hydrogen bond properties of these pairs. 展开更多
关键词 bases and base pairs of nucleic acid Electronic structures and spectra INDO/S
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Pt(Ⅱ), Pd(Ⅱ) and Ni(Ⅱ) Complexes Binding to the N(7) Position of Guanine: Influence on the Guanine and Watson-crick GC Base Pair
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作者 章志强 周立新 +1 位作者 和芹 赵亚英 《Chinese Journal of Structural Chemistry》 SCIE CAS CSCD 北大核心 2005年第1期114-120,共7页
Comprehensive ab initio calculations were performed on the coordination of Pt(II), Pd(II) and Ni(II) adducts to the N(7) of guanine and guanine-cytosine (GC) base pair at the DFT level. The fully optimized geometrie... Comprehensive ab initio calculations were performed on the coordination of Pt(II), Pd(II) and Ni(II) adducts to the N(7) of guanine and guanine-cytosine (GC) base pair at the DFT level. The fully optimized geometries of the metal complexes were obtained and the stabilization energies of the interaction between metal adducts and nucleobase were calculated with B3LYP method by using 6-31* basis set for the light atom. While the effective core potential (ECP) is used for metal cation. The results show that both cispalladium and cisnickel cause similar geometric changes of the base pair as cisplatin. For the coordination of metal adducts to guanine, platinum adduct possesses the highest stabilization energy; but the interaction between metal-guanine and cytosine for nickel is larger than that for platinum and palladium. It is worthy to note that hydrolysis effect can also cause significant changes in H-bonds. 展开更多
关键词 cis-platin (palladium nickel) GC base pair hydrogen bond ab initio nature bond orbital (NBO)
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Formation and dissociation of protonated cytosine–cytosine base pairs in i-motifs by ab initio quantum chemical calculations
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作者 张小虎 黎明 +1 位作者 王延颋 欧阳钟灿 《Chinese Physics B》 SCIE EI CAS CSCD 2014年第2期189-192,共4页
Formation and dissociation mechanisms of C-C+ base pairs in acidic and alkaline environments are investigated, employing ab initio quantum chemical calculations. Our calculations suggest that, in an acidic environmen... Formation and dissociation mechanisms of C-C+ base pairs in acidic and alkaline environments are investigated, employing ab initio quantum chemical calculations. Our calculations suggest that, in an acidic environment, a cytosine monomer is first protonated and then dimerized with an unprotonated cytosine monomer to form a C-C+ base pair; in an alkaline environment, a protonated cytosine dimer is first unprotonated and then dissociated into two cytosine monomers. In addition, the force for detaching a C-C+ base pair was found to be inversely proportional to the distance between the two cytosine monomers. These results provide a microscopic mechanism to qualitatively explain the experimentally observed reversible formation and dissociation of i-motifs. 展开更多
关键词 ab initio quantum chemical calculation I-MOTIF protonated cytosine-cytosine base pair
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Cis Watson-Crick/Watson-Crick Base Pairs in DNA: A Density Functional Theory(DFT) Study
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作者 金能智 张志斐 +3 位作者 张其斌 者建武 李葆光 孙一桐 《Chinese Journal of Structural Chemistry》 SCIE CAS CSCD 2017年第8期1251-1263,共13页
The four nucleic acid DNA bases(adenine, thymine, guanine, cytosine) and ten cis Watson-Crick/Watson-Crick(cis WC/WC) DNA base pairs were investigated by density functional theory(DFT) quantum chemical calculati... The four nucleic acid DNA bases(adenine, thymine, guanine, cytosine) and ten cis Watson-Crick/Watson-Crick(cis WC/WC) DNA base pairs were investigated by density functional theory(DFT) quantum chemical calculations. Geometry optimizations were carried out on the four bases and ten base pairs at the B3LYP level with 6-31G^(**) basis set. All the optimizations were performed within Cs symmetry. The optimum structures for the four bases and seven cis WC/WC base pairs were obtained, and Natural Bond Orbital analysis(NBO) was based on these structures. The possibilities of matches between any two of the four bases through their Watson-Crick(WC) edges were discussed. The structures of seven cis WC/WC base pairs change to a certain extent relative to these of the four bases due to the formation of hydrogen bonds. These base pairs existing in DNA have an important influence on the structural stability of the double helix. The analysis of the electronic structures and molecular orbitals for seven cis WC/WC base pairs can provide significant information about the relationship between charge transfer along the hydrogen bond and the Frontier orbitals of these base pairs. 展开更多
关键词 cis Watson-Crick/Watson-Crick(cis WC/WC) base pairs hydrogen bond
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DFT Study on Reaction Mechanism of DNA Base Pair with Hydroxyl Radical
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作者 Eisuke Shimizu Ryota Hoshino +2 位作者 Kazuya Nomura Victor I. Danilov Noriyuki Kurita 《Journal of Modern Physics》 2013年第3期442-451,共10页
In order to elucidate the indirect effect by radiation on DNA base pairs, we investigate the mechanism for the attacking reaction of a hydroxyl radical (·OH-radical) to the G-C and A-T base pairs, by the density ... In order to elucidate the indirect effect by radiation on DNA base pairs, we investigate the mechanism for the attacking reaction of a hydroxyl radical (·OH-radical) to the G-C and A-T base pairs, by the density functional theory (DFT) calculations. The effect of solvation on the mechanism is also revealed by performing the same DFT calculations under the continuum solvation approximation. We find the stable structures for the dehydrogenated G-C and A-T base pairs, in which the hydrogen atom of NH2 group of G or A base is abstracted by the ·OH-radical. The solvation around the base pairs stabilizes the dehydrogenated structures significantly, indicating the acceleration of the attacking reaction by ·OH-radical to the base pairs in water. Therefore, we conclude that the hydrogen atom of the NH2 group of G or A base in the G-C and A-T base pairs is the most preferably abstracted by the ·OH-radical in living cells. 展开更多
关键词 Density Functional Theory DNA HYDROXYL RADICAL base pair Reaction Mechanism DEHYDROGENATION
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Anharmonic vibrations of nucleobases: Structural basis of one-and two-dimensional infrared spectra for canonical and mismatched base pairs
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作者 WANG GuiXiu ZHAO Juan WANG JianPing 《Science China Chemistry》 SCIE EI CAS 2011年第10期1590-1606,共17页
Canonical Watson-Crick base pairs and four representative mismatched base pairs have been studied by quantum chemical computations. Detailed anharmonic vibrational analysis was carried out to reveal some vibrational s... Canonical Watson-Crick base pairs and four representative mismatched base pairs have been studied by quantum chemical computations. Detailed anharmonic vibrational analysis was carried out to reveal some vibrational signatures characteristic of structural aspects of the base monomers and dimers, which were well manifested in simulated 1D IR and 2D IR spectra. The degree of delocalization of the selected normal modes, represented by the potential energy distribution, was found to vary sig-nificantly from isolated bases to H-bonded dimers, and was accompanied by changes in anharmonicities of these modes. Examples are given for the generally accepted carbonyl stretching mode of base pairs appearing in the 6-m wavelength region of IR spectra. 展开更多
关键词 quantum chemical computation canonical Watson–Crick base pair mismatched base pair anharmonic vibration infrared
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Stabilization and Multiple-Responsive Recognition of Natural Base Pairs in Water by a Cationic Cage 被引量:3
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作者 Lin Cheng Ping Tian +2 位作者 Qingfang Li Anyang Li Liping Cao 《CCS Chemistry》 CAS 2022年第9期2914-2920,共7页
The hydrogen-bonded(H-bonded)base pairs,double H-bonded A•T and triple H-bonded G•C in DNA,are important units for storing,encoding,and expressing genetic information.Owing to the interference from water,however,the f... The hydrogen-bonded(H-bonded)base pairs,double H-bonded A•T and triple H-bonded G•C in DNA,are important units for storing,encoding,and expressing genetic information.Owing to the interference from water,however,the formation of H-bonded base pairs from short deoxynucleotide fragments such as mono-or di-deoxynucleotide are not easily achieved in aqueous solutions. 展开更多
关键词 host–vip chemistry chiral recognition adaptive chirality tetraphenylethene-based cationic cage base pair
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Effect of Base Pairing Property in Three Stems of Hammerhead Ribozyme on Its Catalytic Activity
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作者 陆长德 庄旻 祁国荣 《Chinese Science Bulletin》 SCIE EI CAS 1994年第23期1998-2003,共6页
As is well known, the hammerhead ribozyme has a shorter chain length and is easy to design.The ribozyme that we designed against fragment of polyhedron mRNA of Autographa californica Nuclear Polyhedrosis Virus (AcNPV)... As is well known, the hammerhead ribozyme has a shorter chain length and is easy to design.The ribozyme that we designed against fragment of polyhedron mRNA of Autographa californica Nuclear Polyhedrosis Virus (AcNPV) was proved to be effective by cleavage experiments in vitro.Using this model, 展开更多
关键词 RIBOZYME PROPERTY of base pairING CONFORMATION of stem optimal temperature CLEAVAGE efficiency.
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DFT Calculations on the Effect of Solvation on the Tautomeric Reactions for Wobble Gua-Thy and Canonical Gua-Cyt Base-Pairs
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作者 Kazuya Nomura Ryota Hoshino +3 位作者 Eisuke Shimizu Yasuhiro Hoshiba Victor I. Danilov Noriyuki Kurita 《Journal of Modern Physics》 2013年第3期422-431,共10页
To elucidate the reaction mechanism from wobble Guanine-Thymine (wG-T) to tautomeric G-T base-pairs, we investigate its transition state (TS) by density functional theory (DFT) calculations, in vacuum and in water app... To elucidate the reaction mechanism from wobble Guanine-Thymine (wG-T) to tautomeric G-T base-pairs, we investigate its transition state (TS) by density functional theory (DFT) calculations, in vacuum and in water approximated by continuum solvation model. From the comparison of these results, we attempt to elucidate the effect of solvation on the tautomeric reaction for wG-T. In addition, the same DFT calculations are performed for the canonical G-C base-pair, in order to reveal the difference in the activation energy for the reactions involving wG-T and G-C. The obtained TS structures between wG-T and G*-T/G-T* (asterisk is an enol-form of base) are almost the same in vacuum and in water. However, the activation energy is 16.6 and 19.1 kcal/mol in vacuum and in water, respectively, indicating that the effect of solvation enlarges the energy barrier for the reactions from wG-T to G-T*/G*-T. The activation energy for the tautomeric reaction from G-C to G*-C* is also evaluated to be 15.8 and 12.9 kcal/mol in vacuum and in water, respectively. Therefore, it is expected that the tautomeric reaction from wG-T to G*-T/G-T* can occur in vacuum with a similar probability as that from G-C to G*-C*. We furthermore investigate the TS structure for wG-BrU to reveal the effect of the BrU introduction into wG-T. The activation energy is 14.5 and 16.7 kcal/mol in vacuum and in water, respectively. Accordingly, the BrU introduction is found to increase the probability of the tautomeric reaction producing the enol-form G* and T* bases. Because G* prefers to bind to T rather than to C, and T* to G not A, our calculated results reveal that the spontaneous mutation from C to T or from A to G bases is accelerated by the introduction of wG-BrU base-pair. 展开更多
关键词 DFT Wobble base pair base pair TAUTOMERIZATION Transition State Activation Energy SOLVATION
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Spin fluctuations and unconventional superconducting pairing in iron-based superconductors
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作者 于顺利 李建新 《Chinese Physics B》 SCIE EI CAS CSCD 2013年第8期146-161,共16页
In this article, we review the recent theoretical works on the spin fluctuations and superconductivity in iron-based superconductors. Using the fluctuation exchange approximation and multi-orbital tight-binding models... In this article, we review the recent theoretical works on the spin fluctuations and superconductivity in iron-based superconductors. Using the fluctuation exchange approximation and multi-orbital tight-binding models, we study the char- acteristics of the spin fluctuations and the symmetries of the superconducting gaps for different iron-based superconductors. We explore the systems with both electron-like and hole-like Fermi surfaces (FS) and the systems with only the electron-like FS. We argue that the spin-fluctuation theories are successful in explaining at least the essential part of the problems, indicating that the spin fluctuation is the common origin of superconductivity in iron-based superconductors. 展开更多
关键词 iron-base superconductors spin fluctuations pairing symmetry
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Authenticated Privacy Preserving Pairing-Based Scheme for Remote Health Monitoring Systems
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作者 Kambombo Mtonga Eun Jun Yoon Hyun Sung Kim 《Journal of Information Security》 2017年第1期75-90,共16页
The digitization of patient health information has brought many benefits and challenges for both the patients and physicians. However, security and privacy preservation have remained important challenges for remote he... The digitization of patient health information has brought many benefits and challenges for both the patients and physicians. However, security and privacy preservation have remained important challenges for remote health monitoring systems. Since a patient’s health information is sensitive and the communication channel (i.e. the Internet) is insecure, it is important to protect them against unauthorized entities. Otherwise, failure to do so will not only lead to compromise of a patient’s privacy, but will also put his/her life at risk. How to provide for confidentiality, patient anonymity and un-traceability, access control to a patient’s health information and even key exchange between a patient and her physician are critical issues that need to be addressed if a wider adoption of remote health monitoring systems is to be realized. This paper proposes an authenticated privacy preserving pairing-based scheme for remote health monitoring systems. The scheme is based on the concepts of bilinear paring, identity-based cryptography and non-interactive identity-based key agreement protocol. The scheme also incorporates an efficient batch signature verification scheme to reduce computation cost during multiple simultaneous signature verifications. 展开更多
关键词 Remote Healthcare BILINEAR pairING Privacy PRESERVATION Mutual Authentication ID-baseD CRYPTOGRAPHY
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Dtrie-allpair:高效的集合T-覆盖连接算法 被引量:2
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作者 贾连印 奚建清 +3 位作者 李孟娟 游进国 刘勇 苗德成 《华南理工大学学报(自然科学版)》 EI CAS CSCD 北大核心 2012年第6期109-117,共9页
传统的T-覆盖连接算法会因生成的候选集庞大而导致系统性能降低,为此,文中提出了一种基于trie的动态索引结构——DTI结构,并构建了基于该结构的相似度连接算法——Dtrie-allpair算法.通过该算法可以直接得到allpair连接的结果,不产生任... 传统的T-覆盖连接算法会因生成的候选集庞大而导致系统性能降低,为此,文中提出了一种基于trie的动态索引结构——DTI结构,并构建了基于该结构的相似度连接算法——Dtrie-allpair算法.通过该算法可以直接得到allpair连接的结果,不产生任何候选集,有效解决了高候选集产生的问题,克服了传统算法因生成并验证候选集而带来的开销.文中还研究了数据库中记录的顺序及记录中元素顺序对Dtrie-allpair算法性能的影响,并在msweb、msnbc两个数据集下对Dtrie-allpair算法与All-pair、PPJoin算法进行对比.结果表明:Dtrie-allpair算法具有明显的优势,覆盖阈值较小时优势更明显;对msweb数据集,阈值为2时,Dtrie-allpair算法的效率相对于All-pair、PPJoin算法提高近两个数量级;通过对数据集进行频率降序和长度升序组合预处理可大幅降低Dtrie-allpair算法访问的trie结点数量,从而显著提升性能. 展开更多
关键词 集合相似度 T-覆盖连接 覆盖阈值 基于trie的动态索引 All-pair算法 PP-Join算法 频率降序 长度升序
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关于frustrated Lewis pair的中文名 被引量:5
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作者 彭斌 聂永 《中国科技术语》 2010年第6期44-44,49,共2页
frustrated Lewis pair(FLP)是一个最近出现的新名词,指分子内或混合体系中同时具有路易斯酸和路易斯碱两个位点,由于空间位阻较大而使得这两个位点不能结合形成路易斯酸碱加合物,从而具有独特的反应活性。建议译为"受阻路易斯酸碱... frustrated Lewis pair(FLP)是一个最近出现的新名词,指分子内或混合体系中同时具有路易斯酸和路易斯碱两个位点,由于空间位阻较大而使得这两个位点不能结合形成路易斯酸碱加合物,从而具有独特的反应活性。建议译为"受阻路易斯酸碱对"。 展开更多
关键词 frustrated LEWIS pair 路易斯酸碱加合物 空间位阻
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Efficient ID-Based Proxy Blind Signature Scheme 被引量:2
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作者 ZHANG Qing WEN Qiaoyan CHEN Gengli 《Wuhan University Journal of Natural Sciences》 CAS 2007年第1期105-108,共4页
In a proxy blind signature scheme, the proxy signer is allowed to generate a blind signature on behalf of the original signer. The proxy blind signature scheme is useful in several applications such as e-voting and e-... In a proxy blind signature scheme, the proxy signer is allowed to generate a blind signature on behalf of the original signer. The proxy blind signature scheme is useful in several applications such as e-voting and e-payment. In this paper, we propose an identity-based proxy blind signature scheme which combines the advantages of proxy signature and of blind signature. Our scheme fulfills peffecdy the security requirements of a proxy blind signature. Comparing the previous scheme, our scheme needs less computational overhead and is more efficient. 展开更多
关键词 proxy signature blind signature IDENTITY-baseD bilinear pairings
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An Identity-Based Strong Designated Verifier Proxy Signature Scheme 被引量:3
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作者 WANG Qin CAO Zhenfu 《Wuhan University Journal of Natural Sciences》 CAS 2006年第6期1633-1635,共3页
In a strong designated verifier proxy signature scheme, a proxy signer can generate proxy signature on behalf of an original signer, but only the designated verifier can verify the validity of the proxy signature. In ... In a strong designated verifier proxy signature scheme, a proxy signer can generate proxy signature on behalf of an original signer, but only the designated verifier can verify the validity of the proxy signature. In this paper, we first define the security requirements for strong designated verifier proxy signature schemes. And then we construct an identity-based strong designated verifier proxy signature scheme. We argue that the proposed scheme satisfies all of the security requirements. 展开更多
关键词 strong designated verifier signature proxy signature identity-based cryptosystem bilinear pairing
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An Efficient Identity-Based Anonymous Signcryption Scheme 被引量:4
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作者 YU Yong LI Fagen XU Chunxiang SUN Ying 《Wuhan University Journal of Natural Sciences》 CAS 2008年第6期670-674,共5页
Signcryption is a cryptographic primitive that performs encryption and signature in a single logical step more efficiently than sign-then-encrypt approach. Till now, various kinds of signcryption schemes have been pro... Signcryption is a cryptographic primitive that performs encryption and signature in a single logical step more efficiently than sign-then-encrypt approach. Till now, various kinds of signcryption schemes have been proposed. Among them, the requirement of signcrypter's privacy protection is needful in some practical applications. In this paper, a new identity-based anonymous signcryption scheme from hilinear pairings, which is the organic combination of identity-based ring signature and encryption scheme, is proposed. The proposed scheme is indistinguishable against the chosen ciphertext attack under the Decisional Bilinear Diffie-Hellman assumption in the random oracle model. Its unforgeability relies on the computational Diffieellman problem. Compared with the previous schemes, the new scheme is more efficient in computation. 展开更多
关键词 IDENTITY-baseD ring signature anonynaous signcryption bilinear pairing
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New Constructions of Identity-Based Threshold Decryption 被引量:1
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作者 ZHANG Leyou HU Yupu +1 位作者 TIAN Xu'an YANG Yang 《Wuhan University Journal of Natural Sciences》 CAS 2010年第3期222-226,共5页
In this paper, based on the verifiable pair and identity-based threshold cryptography, a novel identity-based (ID-based) threshold decryption scheme (IDTDS) is proposed, which is provably secure against adaptive c... In this paper, based on the verifiable pair and identity-based threshold cryptography, a novel identity-based (ID-based) threshold decryption scheme (IDTDS) is proposed, which is provably secure against adaptive chosen cipbertext attack under the computational bilinear Diffie-Hellman (CBDH) problem assumption in the random oracle. The pubic cheekability of ciphertext in the IDTDS is given by simply creating a signed E1Gamal encryption instead of a noninteractive zero-knowledge proof. Furthermore, we introduce a modified verifiable pairing to ensure all decryption shares are consistent. Our scheme is more efficient in verification than the schemes considered previously. 展开更多
关键词 ID-based threshold decryption verifiable pair computational bilinear Diffie-Hellman (CBDH) problem provable security
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Improvement of Identity-Based Threshold Proxy Signature Scheme with Known Signers
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作者 LI Fagen HU Yupu CHEN Jie 《Wuhan University Journal of Natural Sciences》 CAS 2006年第6期1653-1656,共4页
In 2006, Bao et al proposed an identlty-based threshold proxy signature scheme with known signers. In this paper, we show that Bao et al's scheme is vulnerable to the forgery attack. An adversary can forge a valid th... In 2006, Bao et al proposed an identlty-based threshold proxy signature scheme with known signers. In this paper, we show that Bao et al's scheme is vulnerable to the forgery attack. An adversary can forge a valid threshold proxy signature for any message with knowing a previously valid threshold proxy signature. In addition, their scheme also suffers from the weakness that the proxy signers might change the threshold value. That is, the proxy signers can arbitrarily modify the threshold strategy without being detected by the original signer or verifiers, which might violate the original signer's intent. Furthermore, we propose an improved scheme that remedies the weaknesses of Bao et al's scheme. The improved scheme satisfies all secure requirements for threshold proxy signature. 展开更多
关键词 identity-based cryptography threshold proxy signature bilinear pairings
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Competitions of magnetism and superconductivity in FeAs-based materials
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作者 杨硕 尤文龙 +1 位作者 顾世建 林海青 《Chinese Physics B》 SCIE EI CAS CSCD 2009年第6期2545-2550,共6页
Using the numerical unrestricted Hartree-Fock approach, we study the ground state of a two-orbital model describing newly discovered FeAs-based superconductors. We observe the competition of a (0, π) mode spin-dens... Using the numerical unrestricted Hartree-Fock approach, we study the ground state of a two-orbital model describing newly discovered FeAs-based superconductors. We observe the competition of a (0, π) mode spin-density wave and the superconductivity as the doping concentration changes. side where the magnetism and superconductivity coexist. The orbital even, and coexisting sxy +dx^2-y^2 wave (even parity). There might be a small region in the electron-doping superconducting pairing is found to be spin singlet, 展开更多
关键词 FeAs-based superconductors MAGNETISM Hartree-Fock approach pairing symmetry
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Construction and Implementation of a Privacy-Preserving Identity-Based Encryption Architecture
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作者 David Bissessar Carlisle Adams 《Journal of Information Security》 2023年第4期304-329,共26页
A recent proposal by Adams integrates the digital credentials (DC) technology of Brands with the identity-based encryption (IBE) technology of Boneh and Franklin to create an IBE scheme that demonstrably enhances priv... A recent proposal by Adams integrates the digital credentials (DC) technology of Brands with the identity-based encryption (IBE) technology of Boneh and Franklin to create an IBE scheme that demonstrably enhances privacy for users. We refer to this scheme as a privacy-preserving identity-based encryption (PP-IBE) construction. In this paper, we discuss the concrete implementation considerations for PP-IBE and provide a detailed instantiation (based on q-torsion groups in supersingular elliptic curves) that may be useful both for proof-of-concept purposes and for pedagogical purposes. 展开更多
关键词 Identity-based Encryption (IBE) Digital Credentials (DC) PRIVACY pairing-based Cryptography Supersingular Elliptic Curve q-Torsion Group
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