本文選題：分子動力學(xué)模擬 + DNA-AuNPs��； 參考：《電子科技大學(xué)》2015年碩士論文

【摘要】：在DNA納米技術(shù)中,利用DNA良好的編碼性,結(jié)合納米粒子進(jìn)行生物納米制造具有很大前景,同時也具有巨大挑戰(zhàn)。在科學(xué)實(shí)驗(yàn)中,利用DNA和金納米粒子(Au NPs)得到了完美晶體,制造出了納米器械,這給DNA-Au NPs自組裝研究帶來了更多積極的啟示。近期在DNA-Au NPs自組裝的實(shí)驗(yàn)研究中,發(fā)現(xiàn)無化學(xué)官能團(tuán)修飾的DNA和Au NPs具有吸附現(xiàn)象,能自組裝成DNA-Au NPs結(jié)構(gòu)單元,打破了傳統(tǒng)的DNA和Au NPs的連接。隨著計算機(jī)技術(shù)的高速發(fā)展,先進(jìn)的計算機(jī)技術(shù)被廣泛應(yīng)用到DNA-Au NPs自組裝的研究中,特別是分子動力學(xué)模擬技術(shù)的發(fā)展,加快了DNA-Au NPs自組裝研究的腳步。本文基于分子動力學(xué)原理,應(yīng)用Materials Studio分子模擬軟件,對無化學(xué)官能團(tuán)修飾的DNA和金納米粒子(Au NPs)進(jìn)行自組裝模擬分析。體系建模采用全原子建模方式,能清楚的觀察到模型的化學(xué)元素組成及其結(jié)構(gòu)變化。目標(biāo)體系由生物分子DNA、Au NPs和溶劑分子組成,其中DNA模型是從3D-DART模型生成器中得到的B-DNA骨架結(jié)構(gòu),包含10個腺嘌呤脫氧核苷酸,然后根據(jù)DNA的化學(xué)結(jié)構(gòu),利用Materials Studio軟件補(bǔ)全DNA骨架結(jié)構(gòu)中缺失的原子和化學(xué)鍵,得到完善的DNA全原子結(jié)構(gòu);Au NPs是金的晶體結(jié)構(gòu)模型,由Materials Studio軟件建模得到,由201個金原子組成;溶劑是由水分子組成。整個體系用分子力場中的COMPASS全原子模型力場進(jìn)行描述。本文首先用分子動力學(xué)模擬的方法模擬實(shí)現(xiàn)了無化學(xué)官能團(tuán)修飾的DNA和Au NPs自組裝吸附的過程,分析了體系的能量變化,并發(fā)現(xiàn)靜電相互作用力是DNA和Au NPs發(fā)生自主裝吸附現(xiàn)象的主導(dǎo)因素。為了分析對DNA和Au Nps自組裝吸附情況的影響因素,本文從平衡時間、均方根偏差(RMSD)、吸附能等方面研究水溶液和溫度對吸附的影響。我們發(fā)現(xiàn),水溶液對DNA-Au NPs自組裝體系具有“奴役”作用,相對于真空體系,水溶液中的DNA的動力學(xué)特征和吸附作用更弱。另外,在DNA的活性范圍內(nèi),溫度對DNA-Au NPs自組裝體系影響較大,在280K到360K的模擬溫度下,我們發(fā)現(xiàn),當(dāng)體系溫度為340K時,DNA和Au NPs的吸附作用最強(qiáng),穩(wěn)定性最好。
[Abstract]:In DNA nanotechnology, it has great prospect and great challenge to use DNA to code well and combine nanoparticles to fabricate biological nanocrystals. In scientific experiments, the perfect crystal was obtained by using DNA and gold nanoparticles au NPs, and the nanoscale instruments were manufactured, which brought more positive enlightenment to the study of DNA-Au NPs self-assembly. Recently, in the experimental study of DNA-Au NPs self-assembly, it was found that DNA and au NPs without chemical functional group were adsorbed and could self-assemble into DNA-Au NPs structure unit, which broke the connection between DNA and au NPs. With the rapid development of computer technology, advanced computer technology is widely used in the research of DNA-Au NPs self-assembly, especially the development of molecular dynamics simulation technology, which speeds up the research of DNA-Au NPs self-assembly. Based on the principle of molecular dynamics, Materials Studio molecular simulation software was used to simulate the self-assembly of DNA and au nanoparticles modified with no chemical functional groups. The chemical element composition and structure change of the model can be clearly observed by using the whole atomic modeling method. The target system is composed of NPs and solvent molecules, in which the DNA model is a B-DNA skeleton structure obtained from the 3D-DART model generator, containing 10 adenine deoxynucleotides, and then according to the chemical structure of DNA. By using Materials Studio software to complement the missing atoms and chemical bonds in the DNA skeleton structure, a perfect DNA all-atomic structure au NPs is obtained, which is a crystal structure model of gold, which is modeled by Materials Studio software and composed of 201 gold atoms, and the solvent is composed of water molecules. The whole system is described by the force field of the COMPASS model in the molecular force field. In this paper, the adsorption process of DNA and au NPs without chemical functional group modification was simulated by molecular dynamics simulation, and the energy change of the system was analyzed. It is also found that electrostatic interaction force is the dominant factor of DNA and au NPs self-loading adsorption phenomenon. In order to analyze the factors affecting the adsorption of DNA and au Nps, the effects of aqueous solution and temperature on adsorption were studied from the aspects of equilibrium time, RMSD deviation and adsorption energy. We found that aqueous solution has "enslavement" effect on DNA-Au NPs self-assembly system, and the kinetic characteristics and adsorption of DNA in aqueous solution are weaker than that in vacuum system. In addition, in the range of DNA activity, the temperature has a great influence on the DNA-Au NPs self-assembly system. At the simulated temperature of 280K to 360K, we find that the adsorption of DNA-Au NPs and au NPs is the strongest and the best when the system temperature is 340 K.
【學(xué)位授予單位】：電子科技大學(xué)
【學(xué)位級別】：碩士
【學(xué)位授予年份】：2015
【分類號】：Q523;TB383.1
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本文編號：1822895