Complex Systems Discussion Group

 Forgot Password
 Register now

QQ登录

只需一步,快速开始

Search
View: 11101|Reply: 9

[KnowledgeExchange] 求建模指导

[Copy Link]

3

Threads

27

Posts

107

Credits

Registered member


IP  162.105.248.165

Posted at 2013-9-21 13:28:17 | All floors |Read mode
最近有个idea,想写篇理论文章,才发现数学功底实在堪忧,特来求教

求推荐数学建模方面基础教材或者网络公开课最好,本科时候的工程数学基本都就饭吃了,所以越基础越好


问题具体点是要估算膜脂与膜蛋白的作用力,主要是疏水作用部分,粗查了下文献好像这方面学界尚未有共识,不知道通过建模估算是否有戏?

至于exchange,我自己本来也是生物领域新人,实在没啥拿的出手的东西,如果有健身或者格斗方面兴趣可以一起探讨吧……






1

Threads

16

Posts

84

Credits

Registered member


IP  27.21.28.113

Posted at 2013-9-22 07:28:50 | All floors
如果是对具体的体系的分子水平模型的话,膜蛋白+膜的Molecular dynamics或者是Coarse-grained dynamics已经挺成熟了;就算是想做唯相的模型,应该也有好些前人工作可以采纳。不过你说的实在太模糊了,不知道到底是要做怎样的建模呢。。

3

Threads

27

Posts

107

Credits

Registered member


IP  162.105.248.165

 Author| Posted at 2013-9-22 14:12:19 | All floors
嗯,是想做MD,但读了些文献发现MD的基础还是静电力啥的,但我觉得疏水作用才是膜和膜蛋白作用的主要部分,不知道怎么能把这部分算出来

0

Threads

2

Posts

6

Credits

Newbie Member


IP  162.105.160.225

Posted at 2013-9-24 08:26:37 | All floors
力场没问题的话, 计算的结果会显示出疏水效果的

1

Threads

16

Posts

84

Credits

Registered member


IP  162.105.160.163

Posted at 2013-9-24 11:47:55 | All floors
恩 同意ls裴老师的话,不要小看静电力。。应该说所有的化学都是静电力造成的= =

3

Threads

27

Posts

107

Credits

Registered member


IP  162.105.248.165

 Author| Posted at 2013-9-25 08:22:12 | All floors
俄……这就是外行的问题,都问不到点子上

那就请推荐下MD方面的学习资料吧,多谢

3

Threads

27

Posts

107

Credits

Registered member


IP  162.105.248.165

 Author| Posted at 2013-9-26 13:33:12 | All floors
jfpei Posted at 2013-9-24 08:26
力场没问题的话, 计算的结果会显示出疏水效果的

再请问下,即使膜脂和膜蛋白间的作用可以显示,但膜蛋白与膜脂的紧密作用的力场来源应该是膜脂两侧的水分子,这种在MD模型中可以计算么
目前还只能看懂wiki,引用下,Limitations of the method are related mostly to underlying molecular mechanics force fields. A single run of MD simulation optimizes potential energy, rather than free energy of the protein. It means that all entropic contributionsto stability of protein structure are neglected. Neglected contributions include conformational entropy of polypeptide chain, main factor that destabilizes protein structure, and hydrophobic interactions that are known as main driving force of protein folding.


说法正确么

1

Threads

16

Posts

84

Credits

Registered member


IP  162.105.160.24

Posted at 2013-9-26 17:53:41 | All floors
Fleo Posted at 2013-9-25 08:22
俄……这就是外行的问题,都问不到点子上

那就请推荐下MD方面的学习资料吧,多谢

MD从学习上手到能做出点像样的东西来,还真不是短时间的事情。。我是能推荐一些我都不太熟悉的资料,不过我感觉还是找合适的实验室合作比较好,中心这边有刘志荣老师和来老师实验室,再就是BIOPIC那边高毅勤老师。

1

Threads

16

Posts

84

Credits

Registered member


IP  162.105.160.24

Posted at 2013-9-26 17:58:43 | All floors
Fleo Posted at 2013-9-26 13:33
再请问下,即使膜脂和膜蛋白间的作用可以显示,但膜蛋白与膜脂的紧密作用的力场来源应该是膜脂两侧的水分 ...

这个是没有问题的,你在一堆水分子里放俩油性分子(比如最简单的甲烷?)跑足够长的MD,俩分子是会总喜欢黏在一起的。通过跑MD来观察所谓水分子的冰山结构什么的来解释疏水效应成因的文章一抓一大把啦。就算是隐式水模型(连续介质),也会有相应的考虑疏水效应的方式。
You need to log in before you can reply Login | Register now

This forum Credits Rules

Mobile ver.|Darkroom|Complex Systems Discussion Group

GMT+8, 2019-5-22 06:58 , Processed in 0.078394 second(s), 21 queries .

Powered by Discuz! X3 English ver.

© 2001-2013 Comsenz Inc.

Quick Reply Back to top Back to list