小牛胸腺DNA与天青I相互作用研究

应用循环伏安法和紫外光谱技术，分别研究了在天青I或小牛胸腺DNA吸附修饰的玻碳电极上小牛胸腺DNA与天青I的相互作用。由天青I与小牛胸腺DNA作用的电化学及光谱特征数据表明，天青I和小牛胸腺DNA之间存在镶嵌、静电作用。在PBS缓冲液中天青I—DNA的表观结合常数为5．1×10^-4L／mol。     

HCIO致DNA碱基dG氧化损伤的密度泛函研究

HClO与碱基dG的反应是致DNA突变的重要原因之一,应用密度泛函理论研究HCIO致DNA碱基dG氧化损伤的的反应机理,在DFT(BLYP/GGA)水平上将反应过程中主要反应物、产物的几何构型全优化,确认中间体和过渡态,计算了反应路径的能量.尤其详细分析致癌氧化物1-oxo-dG→dS的转变过程,找到了转变机制.     

富勒烯D_(3h)-C_(74)与氟原子相互作用的密度泛函理论研究

在密度泛函B3LYP/3-21G(d)水平下研究了D_(3h)-C_(74)与氟原子之间的自由基反应,在笼外一定距离扫描得到了氟原子与C_(74)笼相互作用的势能面,优化代表区中关键点的结构和能量得到了可能的自由基异构体,结果显示D_(34)-C_(74)F有9种自由基异构体。另外,探寻了各自由基异构体之间的过渡态和氟原子在不同关键点之间转化的反应机理,反应路径分析表明在两两异构体之间有且只有一个过渡态,即它们之间的反应是一步反应。除此之外,分析了9种自由基异构体的自旋密度并预测了第二个氟原子进攻的首选位置,同时采用密度泛函理论进一步讨论了由最稳定的自由基异构体加成得到的双氟衍生物C_(74)F_2的稳定性,结果表明第二个自由基氟原子和C_(74)F发生加成反应时主要以1,4-加成为主。     

HClO致DNA碱基dG氧化损伤的密度泛函研究

HClO与碱基dG的反应是致DNA突变的重要原因之一,应用密度泛函理论研究HClO致DNA碱基dG氧化损伤的的反应机理,在DFT(BLYP/GGA)水平上将反应过程中主要反应物、产物的几何构型全优化,确认中间体和过渡态,计算了反应路径的能量。尤其详细分析致癌氧化物1-oxo-dG→dS的转变过程,找到了转变机制。     

t-ZrO_2晶体中Cr~(3+)和La~(3+)的杂质取代效应(英文)

利用分子模拟技术评价了含Cr3+和La3+杂质的t-ZrO2晶体缺陷的性质.在推导、拟合和验证计算模型的势能参数,以及建立合适的体系模型后,研究了t-ZrO2晶体的内在缺陷和外来缺陷的性质,预测出:La3+较Cr3+容易掺入t-ZrO2晶体中;在本研究范围内缺陷簇[La'a·V o·La'zr]x最容易生成;La3+掺杂到t-ZrO2晶体后将阻止Cr3+的进入.     

DNA与小分子药物相互作用研究进展

现代医学中,抗肿瘤,抗病毒药物与DNA之间的反应研究对疾病治疗有着重要意义.该文讨论抗癌药物及小分子与DNA之间的反应,综述小分子与DNA之间的反应的研究方法.     

环状氮杂Cu(II)配合物与DNA的相互作用研究

电分析方法是研究金属配合物与DNA作用非常有效的方法，本文研究了六氮杂环状过渡金属配合物与DNA的作用，推导了峰电流（ipc)与代表DNA浓度的核苷酸磷酸浓度[NP]的关系工，并利用最小二乘法对实验数据进行非线性拟合，以此估计金属配合物与DNA作用的参数：金属配合物与DNA结合的稳定常数K，键合位点数s，与DNA结合和未结合的金属离子的扩散系数Db和Df，为进一步研究金属配合物与DNA作用提供了有用信息。     

(Ni_(1-y)~(2+)Co_y~(2+))(Co_(2-x)~(3+)Fe_x~(3+))O_4系NTC热敏半导瓷新材料的研究

本文报导一种低温NTC热敏电阻的新材料——(Ni_(1-y)~(2+)Co_y~(2+))(Co_(2-x)~(3+)Fe_x~(3+))O_4系半导体陶瓷,该材料系尖晶石结构。当Ni~(2+)和Co~(2+)、Co~(3+)和Fe~(3+)按适当摩尔比共存于尖晶石相时,NTC热敏电阻器阻温特性的线性度得到改善,而且线性测温区域可向低温方向扩展。实验发现,当x=1.25,y=0.5时,线性测温区域为-70～200℃,若再加入适量的RuO_2,则线性测温区域可扩展为-90～200℃之间。 本文对热敏半导瓷的微观结构和导电机理也进行了研究。     

模拟3种有机膦系阻垢剂与方解石(104)面的相互作用

通过pH曲线实验研究了乙二胺四亚甲基膦酸(EDTMP),己二胺四亚甲基膦酸(HDTMP)和二乙烯三胺五亚甲基膦酸(DTPMP)对碳酸钙垢的阻垢性能,在相同的加药浓度下阻垢性能强弱顺序为:DTPMPEDTMPHDTPM。同时采用周期性边界条件下的分子动力学方法,模拟研究了在水分子存在条件下各阻垢剂与方解石(104)面的相互作用,得到了相应的结合能和原子间距离等参数。结果表明:阻垢分子膦酸基团中的双键氧与碳酸钙中的Ca~(2+)形成的强静电相互作用力对吸附起了主导作用,同时膦酸基团中的氢与晶面中的氧形成了氢键,加强了吸附效果。综合考虑各分子在晶面(104)上的吸附效果,其结果与实验相符合;从分子中膦酸基团作用个数也可看出,HDTMP只有一个膦酸基团靠近晶面,因此作用力也是最弱的。     

直链酸与水相互作用的理论研究

采用量子化学方法中的密度泛函理论B3LYP方法,在B3LYP/6-311++G(d,p)基组水平上,对直链酸(甲酸至庚酸)与单分子水形成的体系进行结构优化和频率计算,从分子水平上研究了体系的相关的结构参数、电荷分布以及结合能,运用AIM理论分析了体系的电了密度拓扑。结果表明:直链酸与水形成两个氢键,其中羧基中氢原子作为质子供体的氢键1的键能强于水的氢作为质子供体的氢键2的键能。氢键1对体系的结合能影响起主导作用。稳定构型为六元环构型。直链酸与水结合能不随碳链增长呈明显变化,在(38.7-39.7)kJ/mol之间。     

Quantum mechanical description of the interactions between DNA and water

In recent years, a lot of attention has been focused on the electronic properties of DNA. With recent advances in linear scaling quantum mechanics there are now new tools available to enhance our understanding of the electronic properties of DNA among other biomolecules. Using both explicit solvent models and implicit (continuum) solvent models, the electronic characteristics of a dodecamer duplex DNA have been fully studied using both divide and conquer (D&C), semi-empirical quantum mechanics and non-D&C semi-empirical quantum mechanics. According to the AM1 Hamiltonian, 3.5 electrons (0.3 electron/base pair) are transferred from the duplex to the solvent. According to the density of state (DOS) analysis, in vacuo DNA has a band gap of 1 eV showing that in the absence of solvent, the DNA may exhibit similar properties to those of a semiconductor. Upon increasing solvation (2.5–5.5 Å), the band gap ranges from 3 eV to 6 eV. For the implicit solvent model, the band gap continues this widening trend to 7 eV. Therefore, upon solvation and in the absence of dopants, the DNA should begin to loose its conductive properties. Finally, when one considers the energy and localization of the frontier orbitals (HOMO and LUMO), solvent has a stabilizing effect on the DNA system. The energy of the HOMO drops from 15 eV in vacuo to 2 eV for 5.5 Å of water to −8 eV for the implicit solvent model. Similarly, the LUMO drops from 16 eV for in vacuo to 9 eV for 5.5 Å of water to −1 eV for the implicit model. Beyond the importance of the computed results on the materials properties of DNA, the present work also shows that the behavior of intercalators will be affected by the electronic properties of DNA. This could have an impact on our understanding of how DNA based drugs interact with DNA and on the design of new DNA based small molecule drugs.     

Quantum mechanical description of the interactions between DNA and water

In recent years, a lot of attention has been focused on the electronic properties of DNA. With recent advances in linear scaling quantum mechanics there are now new tools available to enhance our understanding of the electronic properties of DNA among other biomolecules. Using both explicit solvent models and implicit (continuum) solvent models, the electronic characteristics of a dodecamer duplex DNA have been fully studied using both divide and conquer (D&C), semi-empirical quantum mechanics and non-D&C semi-empirical quantum mechanics. According to the AM1 Hamiltonian, ∼3.5 electrons (∼0.3 electron/base pair) are transferred from the duplex to the solvent. According to the density of state (DOS) analysis, in vacuo DNA has a band gap of ∼1 eV showing that in the absence of solvent, the DNA may exhibit similar properties to those of a semiconductor. Upon increasing solvation (2.5–5.5 Å), the band gap ranges from ∼3 eV to ∼6 eV. For the implicit solvent model, the band gap continues this widening trend to ∼7 eV. Therefore, upon solvation and in the absence of dopants, the DNA should begin to loose its conductive properties. Finally, when one considers the energy and localization of the frontier orbitals (HOMO and LUMO), solvent has a stabilizing effect on the DNA system. The energy of the HOMO drops from ∼15 eV in vacuo to ∼2 eV for 5.5 Å of water to ∼−8 eV for the implicit solvent model. Similarly, the LUMO drops from ∼16 eV for in vacuo to ∼9 eV for 5.5 Å of water to ∼−1 eV for the implicit model. Beyond the importance of the computed results on the materials properties of DNA, the present work also shows that the behavior of intercalators will be affected by the electronic properties of DNA. This could have an impact on our understanding of how DNA based drugs interact with DNA and on the design of new DNA based small molecule drugs.     

Specifying relations between research and the design of human-computer interactions

This paper argues the need for more effective: human-computer interactions; design of such interactions; and research to support such design. More effective research for design would result in more effective human-computer interactions. One contribution to more effective research would be the specification of relations between research and the design of human-computer interactions. The aim of this paper is to propose such a specification. Frameworks for specifying relations are proposed for: disciplines; the human-computer interaction (HCI) general design problem; and validation. The frameworks are used to model, and so to specify, the relations: between HCI research and the HCI general design problem; and within the particular scope of HCI, to support HCI research. Together, the models specify the relations between HCI research and the design of human-computer interactions. Meeting these specifications renders HCI knowledge coherent, complete and “fit-for-design-purpose”. An illustration of the relations, thus specified, is provided by a model of the planning and control of multiple task work in medical reception and its hypothetical application. The same frameworks are also used to specify the relations between Cognitive Science and the understanding of natural and artificial forms of intelligence. Lastly, they are further used to identify the relations not specified between Cognitive Science and the design of human-computer interactions. The absence of such relations renders Cognitive Science knowledge not coherent, complete nor “fit-for-design-purpose” (as opposed to “fit-for-understanding-purpose”). It is proposed how the relations specified for HCI and Cognitive Science might be used in the assessment of relations between other research and the design of human-computer interactions. Finally, the paper recommends that such an assessment should be undertaken by any discipline, such as Cognitive Science, which claims a relation between its research and the design of human-computer interactions. Such an assessment would establish whether or not such relations are, or can be, specified. The paper concludes that specification of relations is required for more effective research support for the design of human-computer interactions.     

基于微博交互关系算法的敏感舆情研究

传统的敏感舆情模型中,不论是基于文本或是数据挖掘的分析方法都是直接处理网络舆情,未结合网络传播特性分析.针对上述问题,研究并采用基于微博交互关系算法:通过量化微博的敏感程度,分析用户的交互关系来构建微博敏感舆论传播模型.实验基于新浪微博,搜索到一定数量的敏感用户,对用户的交互行为进行分析,得到未来有发表敏感舆论倾向的用户并进行监控.实验结果证明,与传统的舆情模型相比,该方法可行且有效,开拓了舆情分析思路,适用于当前网络舆情研究.     

Insight into the interaction between DNA bases and defective graphenes: Covalent or non-covalent

Although some metal clusters and molecules were found to more significantly bind to defective graphenes than to pristine graphenes, exhibiting chemisorptions on defective graphenes, the present investigation shows that the adsorption of DNA bases on mono- and di-vacant defective graphenes does not show much difference from that on pristine graphene, and is still dominantly driven by noncovalent interactions. In the present study the adsorptions of the nucleobases, adenine (A), cytosine (C), guanine, (G), and thymine (T) on pristine and defective graphenes, are fully optimized using a hybrid-meta GGA density functional theory (DFT), M06-2X/6-31G*, and the adsorption energies are then refined with both M06-2X and B97-D/6-311++G**. Graphene is modeled as nano-clusters of C₇₂H₂₄, C₇₁H₂₄, and C₇₀H₂₄ for pristine, mono- and di-vacant defective graphenes, respectively, supplemented by a few larger ones. The result shows that guanine has the maximum adsorption energy in all of the three adsorption systems; and the sequence of the adsorption strength is G > A > T > C on the pristine and di-vacant graphene and G > T > A > C on the mono-vacant graphene. In addition, the binding energies of the DNA bases with the pristine graphene are less than the corresponding ones with di-vacant defective graphene; however, they are greater than those of mono-vacant graphene with guanine and adenine, while it is dramatic that the binding energies of mono-vacant graphene with thymine and cytosine appear larger than those of pristine graphene.     

DNA computation simulator based on abstract bases

 We developed a simulator to aid those who design algorithms and protocols for DNA computing. In this simulator, abstract sequences instead of real DNA sequences are used to represent molecules in order to increase efficiency of simulations. Two approaches for simulation are available: threshold and stochastic. The simulator consists of two main parts, one for finding reactions among existing molecules and generating new ones, and the other for numerically solving differential equations to calculate the concentration of each molecule. The two parts rely on each other. In particular for the threshold approach, the former avoids a combinatorial explosion by setting a threshold on concentrations of molecules that can take part in reactions. In addition, the stochastic approach is also available for simulations which are hard by the threshold approach. Some simulation results by the approaches are also presented: computation of Boolean circuits, whiplash PCR, formation of DNA tiles and polymerase chain reaction (PCR). We also integrate simulating DNA computation and fitting parameters by the genetic algorithm (GA), where simulation results are used as evaluation functions for the genetic algorithm. The integration is applied to find good protocols for PCR amplification. A trial to refine the reaction model for hybridization is also described before the final discussion on the simulator.     

Theoretical studies on the interactions of XIAP-BIR3 domain with bicyclic and tricyclic core monovalent Smac mimetics

X-linked IAP can bind caspase-9 and inhibit its activity. Mitochondrial protein Smac/DIABLO can also interact with XIAP and relieve the inhibition on caspase-9 to induce apoptosis. A series of artificial Smac mimetics have been used to mimic the Smac N-terminal tetrapeptide AVPI to bind to XIAP-BIR3, but these structural diverse mimetics exhibited distinct binding affinities. To get an insight into the binding nature and optimize the structures, molecular docking and dynamics simulations were used to study the binding of XIAP-BIR3 with three groups of Smac mimetics. The docking results reveal that these Smac mimetics anchored on the surface groove of XIAP-BIR3 and superimposed well with AVPI. The modifications on the seven-membered ring of bicyclic core segment do not strengthen the binding affinity, while a benzyl introduced to the five-membered ring is favorable to the binding. Molecular dynamics simulations on three typical systems show that these complexes are very stable. Hydrogen bonds between the bicyclic core segment and Thr308 play critical roles in maintaining the stability of complex. The binding free energies calculated by MM_PBSA method are consistent with the experimental results.     

SPR传感芯片的理论与实验研究

针对光纤SPR(表面等离子体共振)传感器制作工艺复杂的问题,提出了一种光纤先固定后部分镀膜的SPR传感芯片的制作方法.依据电磁场和射线理论,分析并讨论了此种波长调制部分镀膜SPR传感芯片的工作原理,采用MEMS制作工艺对探测光纤进行封装固定以后,再对光纤进行部分镀膜,其结构简单,工艺性好,易于实现批量化.最后,搭建了一套基、于波长检测的光纤SPR测试系统对其进行测试.实验结果表明:在折射率范围为1.33～1.36时,共振波长同折射率具有良好的线性关系,光谱仪分辨率为0.1 m时,其分辨率可达到3×10-5折射率单位.     

Bukn还原型硫辛酸抗氧化活性的理论研究

硫辛酸是一种强抗氧化剂,本文运用量子化学计算,模拟了还原型硫辛酸即二氢硫辛酸(DHLA)和谷胱甘肽(GSH)在真空、水和四氯化碳3种溶剂环境中发生氧化反应的过程,来研究它们在这3种溶剂条件下的抗氧化活性。以GSH作对比,分析得出DHLA上的巯基抗氧化活性较强,且其作用机理为2个S-H键同时发生断裂。此外,通过对比分析真空和溶剂环境中的键解离焓、质子解离焓和HOMO、LUMO能级差值,发现溶剂环境极性越大,越容易发生电子转移反应:极性越小,越易发生自由基反应。