User talk:Feng2016

Business

 * 1) My Bestbuy Citi credit card: it will be automatically closed if there is no activities within 24 months, no annual fee at all, keep it for next black Friday; balance 0$.
 * 2) Chase Disney premier credit card (visa): balance 0$; cancelled and cut two cards already. All the rewards and credit have moved to freedom credit card, so now the freedom card has total credit of 5900$.
 * 3) Priceline rewards credit card: it will be automatically closed if there is no activities within 24 months, no annual fee at all, and it can be used outside of US, so keep it, too.
 * 4) American express, Delta Skymiles credit card has no payments required at the moment. Set to autopayment on 23rd every month.
 * 5) SDGE automatically payment Bill Account # *****71366 (8795GILMAN): Your online automatic payment is automatically scheduled to take place on 03/12/2017 for $66.27. This is only for Jan, seems we have to pay another month for Feb.
 * 6) 当当网：QQ登录，微信支付；
 * 7) 国家公派留学管理信息平台：旧账号：fengzhang1978；密码：nxx-xxxx-xxxx; 新账号：zfimau, nxx-xxxx-xxxx

Private

 * 1) EES (nanomedicine Nbm) nxx-xxxx-xxxx-$ Feng2016 (talk) 23:24, 17 December 2017 (UTC)
 * 2) 岳钊：BLE（Bluetooth low energy）只要加上几十到几百即可从电信号到手机接收（40 m）；
 * 3) 张懋：可以用他的新农村建设项目做个模型，在内蒙得个大奖后，让他的专利被利用.
 * 4) 张益：谈基金，目前的瓶颈与自己的技术问题结合；多肽折纸术概念弱化.
 * 5) 张和平：包裹可以继续，重点抓一个方向益生菌如何治疗胃溃疡——幽门螺旋杆菌（内蒙医院消化科主任他认识，可以直接上人体做实验；我想的是特格喜白音——一起搞项目）.
 * 6) 李永胜、张永明：红细胞膜提取.
 * 7) cell antenna, biological antenna
 * 8) open access book chapter for peptide: fengzhang1978@imau.edu.cn, nxx-xxxx-xxxx

Techniques

 * 1) 路由器：移动的光猫只有Lan1口可以通讯（拨号）；直接把Lan1口与PC网线相连接后，PC检测不到链接；两个路由器的配置问题：主路由pppeo拨号上网，关闭WiFi信号（DD2016），只用有线连接书房的PC；DHPC的地址段默认即可（100-199）；副路由改变Lan口地址为192.168.1.2；在DHPC中改变地址段为10-99，网关设为192.168.1.1 （主路由的lan口地址），DNS设为主路由检测到的移动网商所提供的地址；SSID为JN1401. 打印机设置为自动获取地址即可. 这样可以保证大家都在统一网段互访.

Useful Tools

 * 1) Fedex Track

Colleagues/Friends
潘佳奎 解码DNA

中国相关组
武汉病毒所 崔宗强 苏州纳米所 王强斌

PNA
赛百盛

GFP Mice
赛百盛

Phage Display
睿智化学

AFM Tips
Nanoworld

Mica and Glass
Novascan Technologies

Phage Library
[Creative Biolab]

DNA labelling

 * 1) 上海基康
 * 2) Biosune
 * 3) 赛百盛
 * 4) 上海生工
 * 5) 三博远志
 * 6) 广州欧谱生物

Used Equipments

 * 1) 上海智岩

Synthetic Chemicals

 * 1) Sigma for Nucleotide Derivatives

Mica Modification

 * 1) JPK

Crosslinkers

 * 1) Thermofisher Selection Tools

Labeling/Modification

 * 1) Amine Labelled DNA

Biophotonics at UCSD Fall 2016

 * 1) Jesse Jokerst
 * 2) Michael W. Berns

Modeling of NanoEngineering Systems NANO 110 at UCSD Fall 2016

 * 1) Gavrav Arya

NANO 156 - Nanomaterials at UCSD Fall 2016

 * 1) Sheng Xu

NANO 102: Foundations of NanoEngineering A: Chemical Principles (4 units) Fall 2016

 * 1) Andrea Tao

Nano 201: Intro to NanoEngineering at UCSD Fall 2016

 * 1) Chen Yi

Need Inspirations

 * 1) 3D -printing @ Harvard

Bull Guys

 * 1) Bob Langer at MIT Bob Langer @ MIT
 * 2) Whitesides @ Harvard
 * 3) Helmuth Möhwald @ Max planck Institute of Colloid and Interface

DNA Origami
Importantly, there is a long list of people who do work on DNA nanotechnology. Among them the inventor of DNA nanotechnology Ned Seeman at NYU, William Shih at Harvard, Milan Stojanovic and Darko Stefanovic at Columbia and UNM, Hao Yan at Arizona State University, Thom LaBean at Duke, Andrew Turberfield at Oxford, Hiroshi Sugiyama and Masayuki Endo at Kyoto University, Bernie Yurke and others in the Nanoscale Materials and Devices Lab at Boise State University, Hendrik Dietz, Fritz Simmel , and Tim Liedl with their three groups in Munich, and many others.
 * 1) Seeman @ NYU
 * 2) Paul W. K. Rothemund @ Caltech
 * 3) Peng Yin @ Harvard
 * 4) Yonggang Ke @ Georgia Tech
 * 5) Liedl @ LMU

Flexible Sensors

 * 1) Rogers @ UIUC

SAMs

 * 1) Ralph G. Nuzzo @ University of Illinois

Chemistry Tree

 * 1) Gu Hongwei @ Suchou Uni

Peptide Nanotech/Self-assembly/Origami

 * 1) Maxim G Ryadnov @ National Physical Lab UK
 * 2) Baker @ UW
 * 3) Protein Design Institute @ UW
 * 4) Woolfson @ Bristol
 * 5) DiMaio @ UW
 * 6) Gu @ UW
 * 7) Akif Tezcan @ UCSD
 * 8) Granja - Montenegro
 * 9) Ghadiri Lab
 * 10) Sebastien Perrier
 * 11) Bing Xu @ Brandeis University
 * 12) Rein Ulijn @ CUNY
 * 13) Ehud Gazit @ Tel Aviv University
 * 14) Tell Tuttle @ University of Strathclyde
 * 15) Peter Nielsen @ Uni of Copenhagen
 * 16) Erkki Ruoslahti @ SBP
 * 17) Seung-Wuk Lee @ Berkeley
 * 18) Angela Belcher @ MIT
 * 19) Serpell @ Sussex
 * 20) Anna @ University of Florence
 * 21) Vincent @ Emory Uni
 * 22) Liu Chong @ Shanghai OI
 * 23) David Sisenberg @ UCLA
 * 24) DANIEL OTZEN @ iNano
 * 25) KURT VESTERAGER GOTHELF @ iNano
 * 26) He Dong @ Clarkson

Succeeding transferring from peptider to nanomediciner

 * 1) Steven @ Imperial College London

Still struggling as peptider

 * 1) Daniel Aili @ Linköping University
 * 2) Raffaele Mezzenga @ ETH

国内相关实验室

 * 1) Junbai Li @ Ins of Chemistry, CAS
 * 2) Xuehai Yan @ Ins of process engineering, CAS
 * 3) Yinlin Sha @ Peking Uni
 * 4) Guangya Zhang @ Huaqiao Uni
 * 5) Wei Wang @ Nanjing Uni

Self-Replication
BBC Interviewing with Graham Cairns-Smith

Nearly every culture on earth has an origins story, a legend explaining its existence. We humans seem to have a deep need for an explanation of how we ended up here, on this small planet spinning through a vast universe. Scientists, too, have long searched for our origins story, trying to discern how, on a molecular scale, the earth shifted from a mess of inorganic molecules to an ordered system of life. The question is impossible to answer for certain -- there's no fossil record, and no eyewitnesses. But that hasn't stopped scientists from trying.

Over the past 150 years, our shifting understanding of the origins of life has mirrored the emergence and development of the fields of organic chemistry and molecular biology. That is, increased understanding of the role that nucleotides, proteins and genes play in shaping our living world today has also gradually improved our ability to peer into their mysterious past.

The identification of DNA as the hereditary material common to all life, and the discovery that DNA coded for RNA, which coded for proteins, provided fresh insight into the molecular basis for life. But it also forced origins of life researchers to answer a challenging question: how could this complicated molecular machinery have started? DNA is a complex molecule, requiring a coordinated team of enzymes and proteins to replicate itself. Its spontaneous emergence seemed improbable.

Graham Cairns-Smith, for instance, has argued since the 1960s that the earliest gene-like structures were not based on nucleic acids, but on imperfect crystals that emerged from clay. The defects in the crystals, he believed, stored information that could be replicated and passed from one crystal to another. His idea, while intriguing, is not widely accepted today.

At a later stage, Cairns-Smith reasoned, biological molecules like DNA began to associate with the crystals. This helped the replication process. Eventually, a "genetic takeover" happened: the biological molecules developed the ability to replicate by themselves, and left the crystals behind.


 * Introduction
 * News
 * Polymers


 * 1) Joyce Laboratory @ Scripps
 * 2) Donna Blackmond @ Scripps
 * 3) Jack W. Szostak @ Harvard
 * 4) John Sutherland @ MRC
 * 5) Sergei Maslov @ UIUC Research ID
 * 6) Alexe V. Tkachenko @ Brookhaven National Laboratory

AFM Groups

 * 1) Simon Scheuring
 * 2) Iwan A. T. Schaap @ Eindingburg
 * 3) Simon Scheuring @ Cornell Uni
 * 4) Thomas Perkins @ University of Colorado
 * 5) Media AFM @ MIT
 * 6) Zhou Feimeng @ California State University, LA
 * 7) Utah Nanofab Lab
 * 8) Julio M. Fernandez @ Columbia University
 * 9) Jane Clarke @ Cambrigde
 * 10) Flemming Besenbacher @ iNano
 * 11) Dong Mingdong @ iNano

20160501

 * 1) VMD can measure the distance between residues of proteins [image: VMD-distance.jpg]

分子模拟
不同软件的详细列表在这里：https://en.wikipedia.org/wiki/Comparison_of_software_for_molecular_mechanics_modeling#opennewwindow

扯点自己看法. 比较主流的几个软件是AMBER, CHARMM, gromacs, LAMMPS, DL_POLY, NAMD, TINKER, Desmond, cp2k, material studio也算，但因为源代码不开放，专业人士用的不多.

免费的几个是gromacs, LAMMPS, DL_POLY, NAMD, TINKER, cp2k, Desmond（仅对学术界）.

理论上来讲，只要是平衡态的MD模拟，任何软件都可以做. 但每个软件在各自的发展过程中，开发者往里面添加了适合一些特定体系模拟和分析的功能以方便后人，所以每个软件都有自己的特长. 仅根据我个人的了解，AMBER, CHARMM, NAMD用来模拟生物体系是极其强大的，LAMMPS有很多功能适合研究传热和材料力学性质，DL_POLY适合界面体系，TINKER里面自带极化力场，cp2k适合ab initio MD.

就速度而言，gromacs和NAMD应该是相当快的，如果考虑GPU加速，NAMD，AMBER和gromacs的GPU优化做得是非常好的.

就上手容易程度而言，很多人觉得gromacs最容易上手. 以上只是我个人一点了解，你在网上搜索MD软件的对比应该可以获得更多信息.

我了解的分子动力学软件是分2种，基于力场和基于第一性原理的

第一性原理的限制比较少，只要你服务器配置够好，不嫌弃速度慢

基于力场的很多，forcite，discover，gulp，lammps等

大多数情况都是挑基于力场的，因为计算速度快，至于选哪种看软件支持力场的情况，比如算合金类的一般挑gulp或者lammps，因为支持eam势函数

Other Profs

 * 1) Zang Ling @ Utah
 * 2) Daneil Anderson @ MIT, Chen Yi's Postdoc Boss