从完全基因组出发建立原核生物亲缘关系和分类系统时遇到的数学问题

我们课题组近10年所发展的组分矢量(CVTree)方法,已经成为从完全基因组出发而不使用序列联配来构建细菌亲缘关系的有效手段.在整个生物分类学日益后继乏人的背景下,组分矢量(CVTree)方法伴随着基因组时代的发展,成为人人可以方便使用的微生物分类的定义性工具.本综述不讨论CVTree的生物学结果,而着重从非线性科学的角度,介绍我们在研究过程中所提出和解决的数学问题.这将涉及组合学、图论、形式语言学等离散数学的篇章.我们特别希望,本文所列举的一些尚未解决的数学问题能引发新的研究工作,使CVTree方法的理论基础更为坚实.     

Folding Behaviour for Proteins BBL and E3BD with Go-like Models

Folding behaviour of protein BBL and its homologue domain E3BD are studied by using an off-lattice Go-like model. It is found that the folding behaviours of these two proteins are different. Protein BBL folds in a downhill manner, which is consistent with experiments. In contrast, protein E3BD folds cooperatively and has a bimodal distribution of the Q values (the similarity to the native state). By analysing the native structures of the two proteins, it is found that the difference in folding behaviours can be attributed to the different structural features described by the number of nonlocal contacts per residue.     

Water Transport through Multinanopores Membranes

We investigate the influence of correlation between water molecules transport through the neighbouring nanopores, whose centres are at a distance of only 6.2A, using the molecular dynamics simulations. Water molecule distribution in nanopore and average water flow are obtained. It is found that the average water molecule number and water flow are slightly different between a system made of the neighbouring nanopores and a system of a single pore. This indicates that transport of water chains in neighbouring pores do no show significant influence each other. These findings should be helpful in designing efficient artificial membrane made of nanopores and providing an insight into effects of the biological channel structure on the water permeation.     

Protein Folding under Mediation of Ordering Water： an Off-Lattice Goe-Like Model Study

Water plays an important role in the structure and function of biomolecules. Water confined at the nanoscale usually exhibits phenomena not seen in bulk water, including the ice-like ordering structure on the surfaces of many substrates. We investigate the behaviour of protein folding in which the proteins are assumed in an environment with ordering water by using of an off-lattice GO-like model, It is found that in the physiological temperature, both the folding rate and the thermodynamic stability of the protein are greatly promoted by the existence of ordering of water.