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Parallel synthesis method of the electronic structures for proteins/nucleic acids and the development of the analytic system of their structures and functions

蛋白质/核酸电子结构的并行合成方法及其结构与功能分析体系的建立

基本信息

批准号：
14340185
负责人：
AOKI Yuriko
金额：
$ 8.9万
依托单位：
KYUSHU UNIVERSITY (2004-2005)Hiroshima University (2002-2003)
依托单位国家：
日本
项目类别：
Grant-in-Aid for Scientific Research (B)
财政年份：
2002
资助国家：
日本
起止时间：
2002 至 2005
项目状态：
已结题

项目摘要

In this work, some new improvements of the elongation method will be addressed. The elongation calculations are demonstrated to be much more efficient compared to the conventional one with high accuracy. The elongation CPU time is shown as linear or sub-linear scaling for quasi-one-dimensional systems. Parallel calculations were also succeeded in our systems.In the elongation method, after we obtain the electronic structure of the starting cluster, we localize the canonical molecular orbitals into regional localized molecular orbitals so that any polymer chain can be built up by adding a monomer unit to this starting cluster step by step. By this fashion, any random polymer can be theoretically synthesized by the elongation method using parallel CPUs.One can see from our publications that the elongation method can reproduce very high accuracy in total energy with much of CPU time savings compared to the conventional one. The model systems cover non-bonded water chain, weakly bonded system (polyethylene), and very delocalized polymer (polyacetylene). It can be seen that all these models, the elongation method can provide chemical accuracy for the energy compared to the conventional one. The differences can be given to be less than 10^<-8>Hartree/atom.The advantages of the elongation method are also highlighted for larger conducting polymers like polyparaphenylene, polydiacetylene, polythiophene and their substituted systems as well as polypeptides like collagen triple helix. As this system is very large for any conventional treatment and the elongation treatment guarantees the accuracy and also gains much CPU time saving.

在这项工作中，一些新的改进的伸长方法将被解决。伸长率计算被证明是更有效的相比，传统的高精度。对于准一维系统，伸长CPU时间显示为线性或次线性标度。在伸长方法中，我们在得到起始团簇的电子结构后，将正则分子轨道局域化到区域局域化的分子轨道上，这样，任何聚合物链都可以通过在起始团簇上逐步加入单体单元来构建。通过这种方式，理论上可以通过使用并行CPU的延伸方法合成任何无规聚合物。从我们的出版物中可以看出，与传统方法相比，延伸方法可以再现非常高的总能量准确度，并且节省了大量的CPU时间。模型体系包括非键合水链、弱键合体系（聚乙烯）和离域性很强的聚合物（聚乙炔）。可以看出，所有这些模型中，与常规方法相比，伸长方法可以提供能量的化学准确性。对于<-8>较大的导电聚合物如聚对苯撑、聚丁二炔、聚噻吩及其取代的系统以及多肽如胶原三螺旋，也突出了延伸方法的优点。由于该系统对于任何常规处理来说都是非常大的，并且延伸处理保证了精度，并且还节省了大量的CPU时间。