User:Feng2016

20190404
refractive index, ATP-dependent bioreaction efficiency: after tried several strategies for measuring efficiency of ATP-dependent bioreactions in artificial micro-confined departments, we found it is not only difficult to construct such micro-confined spaces, but also is not easy to measure the readout signal. So a transfering idea comes out: creat the micro confined space by crowding degree, which may be the truth for life to confine a fixed number of molecules into a cellular space to maintain the refractive index, and therefore the number changes of cellular molecules will change the refractive index of cell, and further change the efficiency of bioreactions inside cells, and finally leads to cell death and disorders such as protein-aggregation diseases, in this case, though the number of protein molecules does not change, the distance among molecules changes thus the confined space among molecules changes which finally results in the efficiency of bioreactions changes. In this sense, we can construct such conditions with same molecule/material of different number confined in a certain volume to check out this theory.

However, most of cells are only 4 micrometer, how could this make sense?

20171218
Peptide particles-->Synthetic Virus

After reading the news and relevant reports of synthetic organisms, I started thinking of one idea: if we got "VLP" particles just by peptide self-assembly (even by coincidence, like Ruibo found her antibacterial peptides all aggregated into particles with even diameters), since the homopeptides can do this, why not retrieve their genetic code, DNA, to develop a simple virus? In this way, what's aim of virus? They may just a simple "SELEX" product by coincidence? And if we could really get a DNA which can be translated into peptide and self-assembled into a "virus", whether they could lead to a disease of some organisms? Or raise a disaster of Human Beings?

Sep 2016
06：

melanin 黑色素，  melatonin 褪黑素

choroid 脉络膜

macular degeneration 黄斑变性

breach = break

angiogenesis 血管生成

Aug 2016
Aug 1:
 * 1) A molecular-imprint nanosensor for ultrasensitive detection of proteins
 * 2) Instant adhesive [pdf] mechanism
 * 3) Ultrasensitive detection of proteins and sugars at single-cell level
 * 4) Thio-NADH has the absorbance at 400 nm (11900 M¡1cm¡1). The other cofactors of 3a-HSD, such as thio-NAD, NAD, and NADH, have the absorbance maxi-mums under 340 nm.

Aug 5:
 * 1) what is the driving force for cell life ... what can make a molecule move... eventually the origin is electron spin ... write a book ... is molecular motor is the smallest unit with mobility? circadian rythem of life, how about longer periods like 7 days for wound curing, 28 days for women period, 10 month for preganant, 1 year for tree year-rotation, in this sense, cell circle, animal development like buterfly changes from one form to another one, even the life/death can be a period, so it is rational to doubt whether all of these phenomena are controlled by genes?


 * 1) self-assembly of molecules, just play or beautiful? that's because the molecules are too short to be functional, how about making the self-assembly by some biomacromolecules? like enzymes, to make it not only self-moving but also self-functional? eventually, how to self replicate? division?


 * 1) modifying AP with thoil groups to do the ligand exchange of citrate AuNP. how about poly-cysteine or GSH?


 * 1) thinking is much more important than doing regarding to the level or phylosphy aspect, that is why Hawking and Einstein different from others. keeping thinking, like Qigong or christion, in some sense, whether the thinking could make mutation, too? for examples, self shape-changing, functionality on/off, gene express inhibition. eventually, brain study will explore all of this, especially memory, how can I mimic this by molecule self-assembly? all of these question worthy of writing a book for several years, and build up a long-term project for research interest.

Jun 2016
Jun 13:


 * 1) Ratnesh talking about the Haigeli Company, whether they could afford 1 million $? and how long could we apply our technology into market? I said at most 2 years.
 * 2) BSA protected JPs can be used for Cell, and with different geography (TEM)--> how BSA/PVA influence the hydrophobic NP'd distribution in emulsion-based JPs?

Simulation

 * 1) Finish all training (Molecular Modeling in the Curriculum) by Troy Messina, which is a very good tutorial for a new user like me. Find my laptop is not fast enough for the simulation, maybe i7 cpu better. Feng2016 (talk) 19:26, 10 May 2016 (UTC)
 * 2) The FDTD solutions can be free for 30 days trial, which has been used for surface plasmonic charge simulation as used by {Jiang, 2016 #43216}.Feng2016 (talk) 17:50, 12 May 2016 (UTC)

Nanostructure from biomolecules and in return for Sensing

 * 1) Why not using calmodulin to synthesize AuNCs or AgNCs because of its well known acidic properties? It can bind to Ca++ ions. Calmodulin has been proved its robust function even binding to CaF2 NP. {Astegno, 2014 #41215} Calcium binding can quench the intrisinc fluorescence of tryptophan residue in proteins. {Cameron, 1998 #41216} Could this be developped into ion sensors? Click here to see how calmodulin, calcium and ca2+ depedent binding peptide M13 cooperate together.

Janus Nanostructure

 * 1) How about make Janus NPs for Janus C-dots? Yuanming? 76.88.54.96 (talk) 06:13, 7 May 2016 (UTC)
 * 2) Our BSA-AP-AuNPs are also Janus NPs with patchy and different functional regions like carboxyllic groups and amine/carboxylic/thiol mixed region, so why not extend/amplify them to bigger/more visible particles?
 * 3) Is that possible to use our BSA-AP-AuNPs for bigger Janus NP preparation by using Pickering emulsion approaches? Inspired by {He, 2007 #19932}.
 * 4) Many papers made best use of the curvatural contact between spheres/balls/particles for conjugating single molecule per partice {Worden, 2004 #10221;Xu, 2006 #10845;DeVries, 2007 #11261}, and there are also masking approaches to realize this end, too. However, I haven't seen any paper making use of magnetic attraction method to first mask face/point, then modify the rest surface and then remove the magnetic field to expose the unmodified face to do something else (e.g. asymmetric functionalization). Can we do it with nanocubes?
 * 5) Inspired by a PS-b-PAA capsulated dimmer citrated AuNP for growing ZnO nanowires {Wang, 2008 #14030}, why not using Janus PVA-AuNP-PS-b-PAA NPs for ZnO nanowire bundles growth?
 * {Lu, 2003 #41347}, uCP nanofilm water nanocube to Januc nanocube? expitaxial growth after increasing the humidity? Feng2016 (talk) 08:47, 10 May 2016 (UTC)

Template Assisted Growth

 * 1) Since the peptide alpha-helix can template helix gold nanofibers {Chen, 2008 #28004}, why not expand this idea to PS-DNA and other peptide nanostructure and other metal NPs (like silver)?

Controlled Assembly

 * 1) Inspired by CMC of polymer {Chen, 2008 #41344}, why not try our AP or other polymer like PVA, PS-b-PAA (seems only highly asymmetric copolymers work well) and polyelectrolytes (like PSS and PAH, DNA and haperin) for encapsulating single or dimmer/trimmer NPs? This paper told us only the short hydrophilic block with long hydrophobic block polymer works well, which recall the polyA binding to AuNP, so why not directly use such kinds of polymer to in situ synthesize AuNPs due to the protection role?
 * 2) Why not encapsulate MNP, QD and AuNP inside PS-b-PAA by the same method of {Wang, 2008 #14030}? The keypoint is how to get a comparable molar concentration of different NPs, so why not apply our discrete BSA-AP-NP to get this number (coefficient), this can even deduce those of their hydrophobic NPs.
 * 3) Inspired by this paper {Wang, 2008 #17681}, we can try peptide self-assembly/aggregation in emulsion-based micelles. The advantage is to increase the peptide's concentration by slowly evaporating the water/oil solution, and after getting a solid peptide aggregated ball/particle, and then put into nanofilm water to see whether they can grow into some star-like fiber morphology.
 * 4) If GAV-9 or Pep11 contain nnAA with azide/alkyne groups, what will happen for their self-assembly?2607:F720:F00:4041:6457:B35:EB96:85C5 (talk) 19:35, 12 May 2016 (UTC)

Bioconjugation

 * 1) Since the closer distance can surely help the conjugation between functional groups, so how about the controlled aggregation's role in the biochemical conjugation?
 * 2) To link Graphene and Aptamer, using 1-pyrenebutanoic acid succinimidyl ester referring to the SI of {Ohno, 2010 #41217}.

Sensing

 * 1) By using FET-based method, protein's adsorption can be studied and the thermodynamic parameters (like dissociation constant, Kd) can be obtained by plotting Drain-current change against the concentration of protein, and then fit the curve to a Langmuir adsorption isotherm (with the equation shown) {Ohno, 2010 #41217}. There is a webpage to explain Langmuir adsorption equation ,but still presents errors in equation deduction processes.
 * 2) The conventional CNT-FETs have been shown to exhibit p-type characteristics in air and electrolytes,4,7-10 but they can detect only positively charged species in electrolytes due to their band structure. But this disadvantage can be made up by graphene-FET {Ohno, 2009 #41218}.
 * 3) Why not combine AFM with FET? Because FET can monitor the kinetics and thermodynamics of reaction/interaction on the surface, and AFM can tell the morphological changes occuring on the surface, too. What a nice combination after the TIRF-AFM and SERS-AFM! However, this might be only realized in nonconductive media like air or oil solution?

Delivery

 * 1) Since our AP-AuNP-BSA are robust, and BSA can carry hodrophobic drugs as well, so why not using AP-MNP-BSA or with other protein's combinations to deliver drugs?

Thinking

 * 1) Material Letter IF: 2.489, supporting open access http://www.journals.elsevier.com/materials-letters. This may be a good choice for IMAU lecturers.
 * 2) There is specific DNA sequence to enhance the emission of AgNCs which is originally not fluorescent (Fig 2 of {Obliosca, 2013 #41221}), and combined with AIE (aggregation induced emission), GFP/GYP, and recently the fluorescent dipeptide NPs, how about the next combination/complex?
 * 3) After they created the paper-based assay, Whitesides group again developed a paper-based synthesizing DNA on site {Glavan, 2016 #41223}, what's the next? Another paper from this group used thread and steel pin to build up electrochemical assay with the embossed-silicalized paper (again paper), simple paper, also low impacted journal, but big open mind, fitting for my style {Glavan, 2016 #39067}.
 * 4) Mingjun Zhang's Nat Nanotech 2016, 11, 389 paper: trp-phe dipeptide NP show a 420 nm emission；all other demonstrations are very simple；just an aggregation induced fluorescence shift with help of Zn2+ chelating effects by Trp; how about other peptide? de novo design a core for other proteins with genetic method? move the PL more to IR region? what about antibody?
 * 5) Inspired by Soh JACS 2009, 131, 15311 paper: bring the triple-stem DNA probe on AuNPs (to replace the Au substrate), in which the MB (methylene blue) can be replaced by a fluorophore; with the help of NSET, the PL can be the signal readout; in this way we transfer the electrochemical sensor to a chemoluminescent sensor. how to add more cascades? in cell activities?
 * 6) For Micheal's PNAS paper with the FET of graphene, applied a dynamic study of peptide self-assembly? A new method to kinetically study template-assisted assembly of peptide/DNA/starch?
 * 7) Why not make use of BSA-AuNCs(fluorescent) for Thiolated DNA (or phosphorthoiate DNA, PS DNA) conjugation? further for complicated DNA-BSA nanostructure design for drug delivery? In another paper the BSA-AuNC-SH-DNA can be also used for graphene-based FET sensing of DNA or other molecules (Micheal PNAS paper continued?)

Ideas Recorded by Date
From today, I think it might be better to directly use the topic for the "edit title" and use signature for the ending, in this way I both have date and a whole logic for my mind.

2016-05-06 Fri

 * 1) How about make Janus NPs for Janus C-dots? Yuanming?

2016-05-05 Thu

 * 1) Our BSA-AP-AuNPs are also Janus NPs with patchy and different functional regions like carboxyllic groups and amine/carboxylic/thiol mixed region, so why not extend/amplify them to bigger/more visible particles?
 * 2) Is that possible to use our BSA-AP-AuNPs for bigger Janus NP preparation by using Pickering emulsion approaches? Inspired by {He, 2007 #19932}.

2016-05-04 Wed

 * 1) Since the peptide alpha-helix can template helix gold nanofibers {Chen, 2008 #28004}, why not expand this idea to PS-DNA and other peptide nanostructure and other metal NPs (like silver)?
 * 2) Inspired by CMC of polymer {Chen, 2008 #41344}, why not try our AP or other polymer like PVA, PS-b-PAA (seems only highly asymmetric copolymers work well) and polyelectrolytes (like PSS and PAH, DNA and haperin) for encapsulating single or dimmer/trimmer NPs? This paper told us only the short hydrophilic block with long hydrophobic block polymer works well, which recall the polyA binding to AuNP, so why not directly use such kinds of polymer to in situ synthesize AuNPs due to the protection role?
 * 3) Inspired by this paper {Wang, 2008 #17681}, we can try peptide self-assembly/aggregation in emulsion-based micelles. The advantage is to increase the peptide's concentration by slowly evaporating the water/oil solution, and after getting a solid peptide aggregated ball/particle, and then put into nanofilm water to see whether they can grow into some star-like fiber morphology.
 * 4) Many papers made best use of the curvatural contact between spheres/balls/particles for conjugating single molecule per partice {Worden, 2004 #10221;Xu, 2006 #10845;DeVries, 2007 #11261}, and there are also masking approaches to realize this end, too. However, I haven't seen any paper making use of magnetic attraction method to first mask face/point, then modify the rest surface and then remove the magnetic field to expose the unmodified face to do something else (e.g. asymmetric functionalization). Can we do it with nanocubes?

2016-05-03 Tue

 * 1) Since the closer distance can surely help the conjugation between functional groups, so how about the controlled aggregation's role in the biochemical conjugation?
 * 2) Inspired by a PS-b-PAA capsulated dimmer citrated AuNP for growing ZnO nanowires {Wang, 2008 #14030}, why not using Janus PVA-AuNP-PS-b-PAA NPs for ZnO nanowire bundles growth?
 * 3) Why not encapsulate MNP, QD and AuNP inside PS-b-PAA by the same method of {Wang, 2008 #14030}? The keypoint is how to get a comparable molar concentration of different NPs, so why not apply our discrete BSA-AP-NP to get this number (coefficient), this can even deduce those of their hydrophobic NPs.

2016-05-02 Mon

 * 1) Since our AP-AuNP-BSA are robust, and BSA can carry hodrophobic drugs as well, so why not using AP-MNP-BSA or with other protein's combinations to deliver drugs?

2016-04-30 Sat

 * 1) Why not using calmodulin to synthesize AuNCs or AgNCs because of its well known acidic properties? It can bind to Ca++ ions. Calmodulin has been proved its robust function even binding to CaF2 NP. {Astegno, 2014 #41215} Calcium binding can quench the intrisinc fluorescence of tryptophan residue in proteins. {Cameron, 1998 #41216} Could this be developped into ion sensors? Click here to see how calmodulin, calcium and ca2+ depedent binding peptide M13 cooperate together.
 * 2) By using FET-based method, protein's adsorption can be studied and the thermodynamic parameters (like dissociation constant, Kd) can be obtained by plotting Drain-current change against the concentration of protein, and then fit the curve to a Langmuir adsorption isotherm (with the equation shown) {Ohno, 2010 #41217}. There is a webpage to explain Langmuir adsorption equation ,but still presents errors in equation deduction processes.
 * 3) To link Graphene and Aptamer, using 1-pyrenebutanoic acid succinimidyl ester referring to the SI of {Ohno, 2010 #41217}.
 * 4) The conventional CNT-FETs have been shown to exhibit p-type characteristics in air and electrolytes,4,7-10 but they can detect only positively charged species in electrolytes due to their band structure. But this disadvantage can be made up by graphene-FET {Ohno, 2009 #41218}.
 * 5) Why not combine AFM with FET? Because FET can monitor the kinetics and thermodynamics of reaction/interaction on the surface, and AFM can tell the morphological changes occuring on the surface, too. What a nice combination after the TIRF-AFM and SERS-AFM! However, this might be only realized in nonconductive media like air or oil solution?
 * 6) Material Letter IF: 2.489, supporting open access http://www.journals.elsevier.com/materials-letters. This may be a good choice for IMAU lecturers.
 * 7) There is specific DNA sequence to enhance the emission of AgNCs which is originally not fluorescent (Fig 2 of {Obliosca, 2013 #41221}), and combined with AIE (aggregation induced emission), GFP/GYP, and recently the fluorescent dipeptide NPs, how about the next combination/complex?
 * 8) After they created the paper-based assay, Whitesides group again developed a paper-based synthesizing DNA on site {Glavan, 2016 #41223}, what's the next? Another paper from this group used thread and steel pin to build up electrochemical assay with the embossed-silicalized paper (again paper), simple paper, also low impacted journal, but big open mind, fitting for my style {Glavan, 2016 #39067}.

2016-04-28 Thu

 * 1) Mingjun Zhang's Nat Nanotech 2016, 11, 389 paper: trp-phe dipeptide NP show a 420 nm emission；all other demonstrations are very simple；just an aggregation induced fluorescence shift with help of Zn2+ chelating effects by Trp; how about other peptide? de novo design a core for other proteins with genetic method? move the PL more to IR region? what about antibody?
 * 2) Inspired by Soh JACS 2009, 131, 15311 paper: bring the triple-stem DNA probe on AuNPs (to replace the Au substrate), in which the MB (methylene blue) can be replaced by a fluorophore; with the help of NSET, the PL can be the signal readout; in this way we transfer the electrochemical sensor to a chemoluminescent sensor. how to add more cascades? in cell activities?
 * 3) For Micheal's PNAS paper with the FET of graphene, applied a dynamic study of peptide self-assembly? A new method to kinetically study template-assisted assembly of peptide/DNA/starch?
 * 4) Why not make use of BSA-AuNCs(fluorescent) for Thiolated DNA (or phosphorthoiate DNA, PS DNA) conjugation? further for complicated DNA-BSA nanostructure design for drug delivery? In another paper the BSA-AuNC-SH-DNA can be also used for graphene-based FET sensing of DNA or other molecules (Micheal PNAS paper continued?)

Links
Ratnesh Lal grouppage

Discrete Bands

 * 1) A paper showed discrete bands of streptavidin conjugated QD on agarose gel {Howarth, 2008 #41255}; and even protein-DNA origami complex can also show discrete bands on agarose gel {Duckworth, 2007 #42243}. What a nice agarose!Feng2016 (talk) 01:15, 5 May 2016 (UTC) Another paper for protein-polymerization also showed dimmer, trimer to tetramer of protein on gels for the discrete bands {Albayrak, 2014 #42276}. Feng2016 (talk) 22:41, 11 May 2016 (UTC) Protein's crosslinking by formadehyde also showed discrete bands on gel {Payne, 1973 #42277} Feng2016 (talk) 05:44, 12 May 2016 (UTC)

Practice

 * 1) Go through the VMD with youtube courses, PDB, PSF, Mutation, but there is an issue for save the PSF files in the right file folder? Is that true we need to load the TK console firstly and enter into the right file folder before doing the PSF and mutation work? Feng2016 (talk) 06:23, 5 May 2016 (UTC)

link title==Remember==
 * 1) apple ID：fengzhang1978@hotmail.com/icloud.com, ZhXXXXXXXXX, mengmian/chengdu/beyond;
 * 2) Facebook: fengzhang1978@hotmail.com, nbmXXXXXXXX
 * 3) Put my dissertation to 金琅出版社；没有录入银行账号，完成了稿件上传并编辑了封面；接受了条款. https://www.goldenlight-publishing.com//content/login 您的登陆数据：用户名: fengzhang1978@hotmail.com 密码: nbmXXXXXXXX (@2016-04-29 Fri)
 * 4) Baidu cloud acount：13347159923/nbm2012imau, or by QQ log in: 42793985, zhfeng

Private

 * 1) Starbuck Coffee make my stomack sick!!!
 * 2) Facebook: fengzhang1978@hotmail.com, nbmXXXXXXXX
 * 3) My Chase Credit maximum credit is only 295$ and I have asked to extend it Feng2016 (talk) 02:16, 5 May 2016 (UTC)