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miniproject-report

https://github.com/eximius8/miniproject-report

Science Score: 44.0%

This score indicates how likely this project is to be science-related based on various indicators:

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    CITATION.cff file
    Found CITATION.cff file
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    DOI references
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    Academic publication links
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    Low similarity (9.9%) to scientific vocabulary

Scientific Fields

Materials Science Physical Sciences - 40% confidence
Last synced: 4 months ago · JSON representation ·

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  • Host: GitHub
  • Owner: eximius8
  • Language: TeX
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Created 5 months ago · Last pushed 5 months ago
Metadata Files
Readme Citation

README.md

Self-Assembly of Core-Shell nanoparticles

Miniproject report written by me in 2017. Everything left as is - even my comments in code. The project was migrated from overleaf here since the report has too many tikz images and overleaf doesn't compile it for free. Compile pdf with github actions in this repo, or here is the compiled PDF

Grade and feedback

To not include Prof. Engel's signature in this report, I didn't add the page with feedback in the report. However, I got 1.0 - highest grade, and here is Prof. Engel's feedback:

The miniproject of Mikhail Trunov simulated structure formation in nanoparticles consisting of a solid core and a soft shell. Past work focused on 2d and the aim now was to extend to 3d using a provided event-driven simulation code. The tasks consist of generating scripts, performing simulations, and analysing the data. As the 2d case is already difficult (published in Nature in 2014), this was a challenging problem that required significant computational resources and some ingenuity on how to use them efficiently. Mr Trunov succeed to set up an efficient computing environment and infrastructure involving multiple computers and computer pools.

Not only was much data collected (four phase diagrams) but also exciting results produced. Although the report does not show it directly, there was a bit of searching in parameter space involved, which demonstrates tenacity on part of Mikhail Trunov. The report is well structured and of good enough quality that it could with some additional effort be converted into a publication. Overall, the project was highly successful and leaves nothing to be desired. In fact, as a next step a new Miniproject student is taking over and, in collaboration with Mikhail Trunov, we aim to completely wrap up this work within the next semester.

Owner

  • Name: Mikhail Trunov
  • Login: eximius8
  • Kind: user
  • Location: Russia

Citation (citations.bib) 

@article{qcexper,
  title={Supramolecular dendritic liquid quasicrystals},
  author={Zeng, Xiangbing and Ungar, Goran and Liu, Yongsong and Percec, Virgil and Dulcey, Andr\'{e}s and Hobbs, Jamie K.},
  journal={Nature},
  volume={428},
  number={6979},
  pages={157},
  year={2004},
  publisher={Nature Publishing Group}
}

@article{hardspherepack,
author = {Tang, Jiawei and Zhou, Xufeng and Zhao, Dongyuan and Lu, Gao Qing and Zou, Jin and Yu, Chengzhong},
title = {Hard-Sphere Packing and Icosahedral Assembly in the Formation of Mesoporous Materials},
journal = {Journal of the American Chemical Society},
volume = {129},
number = {29},
pages = {9044-9048},
year = {2007},
doi = {10.1021/ja070999r},
note ={PMID: 17595080},
URL = {http://dx.doi.org/10.1021/ja070999r},
eprint = {http://dx.doi.org/10.1021/ja070999r}
}


@book{edmd,
  title={Computational granular dynamics: models and algorithms},
  author={P{\"o}schel, Thorsten and Schwager, Thomas},
  year={2005},
  publisher={Springer Science \& Business Media}
}
  	
@article{compareicos,
  author={Pablo F Damasceno and Sharon C Glotzer and Michael Engel},
  title={Non-close-packed three-dimensional quasicrystals},
  journal={Journal of Physics: Condensed Matter},
  volume={29},
  number={23},
  pages={234005},
  url={http://stacks.iop.org/0953-8984/29/i=23/a=234005},
  year={2017},
  abstract={Quasicrystals are frequently encountered in condensed matter. They are important candidates for equilibrium phases from the atomic scale to the nanoscale. Here, we investigate the computational self-assembly of four quasicrystals in a single model system of identical particles interacting with a tunable isotropic pair potential. We reproduce a known icosahedral quasicrystal and report a decagonal quasicrystal, a dodecagonal quasicrystal, and an octagonal quasicrystal. The quasicrystals have low coordination number or occur in systems with mesoscale density variations. We also report a network gel phase.}
}
	

@article{reviewstart,
author = {Boles, Michael A. and Engel, Michael and Talapin, Dmitri V.},
title = {Self-Assembly of Colloidal Nanocrystals: From Intricate Structures to Functional Materials},
journal = {Chemical Reviews},
volume = {116},
number = {18},
pages = {11220-11289},
year = {2016},
doi = {10.1021/acs.chemrev.6b00196},
note ={PMID: 27552640},
URL = {http://dx.doi.org/10.1021/acs.chemrev.6b00196},
eprint = {http://dx.doi.org/10.1021/acs.chemrev.6b00196}
}


@article{shapes,
title = "Synthesis and applications of noble metal nanocrystals with high-energy facets",
journal = "Nano Today",
volume = "7",
number = "6",
pages = "586 - 605",
year = "2012",
issn = "1748-0132",
doi = "https://doi.org/10.1016/j.nantod.2012.10.005",
url = "http://www.sciencedirect.com/science/article/pii/S1748013212001211",
author = "Ling Zhang and Wenxin Niu and Guobao Xu",
keywords = "Metal nanocrystals",
keywords = "High-energy facets",
keywords = "Crystal growth",
keywords = "Growth mechanisms",
keywords = "Application"
}

@article {engelscience,
	author = {Damasceno, Pablo F. and Engel, Michael and Glotzer, Sharon C.},
	title = {Predictive Self-Assembly of Polyhedra into Complex Structures},
	volume = {337},
	number = {6093},
	pages = {453--457},
	year = {2012},
	doi = {10.1126/science.1220869},
	publisher = {American Association for the Advancement of Science},
	abstract = {Predicting structure from the attributes of a material{\textquoteright}s building blocks remains a challenge and central goal for materials science. Isolating the role of building block shape for self-assembly provides insight into the ordering of molecules and the crystallization of colloids, nanoparticles, proteins, and viruses. We investigated 145 convex polyhedra whose assembly arises solely from their anisotropic shape. Our results demonstrate a remarkably high propensity for thermodynamic self-assembly and structural diversity. We show that from simple measures of particle shape and local order in the fluid, the assembly of a given shape into a liquid crystal, plastic crystal, or crystal can be predicted.},
	issn = {0036-8075},
	URL = {http://science.sciencemag.org/content/337/6093/453},
	eprint = {http://science.sciencemag.org/content/337/6093/453.full.pdf},
	journal = {Science}
}

@article{ligandsexample,
author = {Hui, Chin Ming and Pietrasik, Joanna and Schmitt, Michael and Mahoney, Clare and Choi, Jihoon and Bockstaller, Michael R. and Matyjaszewski, Krzysztof},
title = {Surface-Initiated Polymerization as an Enabling Tool for Multifunctional (Nano-)Engineered Hybrid Materials},
journal = {Chemistry of Materials},
volume = {26},
number = {1},
pages = {745-762},
year = {2014},
doi = {10.1021/cm4023634},
URL = {http://dx.doi.org/10.1021/cm4023634},
eprint = {http://dx.doi.org/10.1021/cm4023634}
}


@article{qctalap,
  title={Quasicrystalline order in self-assembled binary nanoparticle superlattices},
  author={Talapin, Dmitri V and Shevchenko, Elena V and Bodnarchuk, Maryna I and Ye, Xingchen and Chen, Jun and Murray, Christopher B},
  journal={Nature},
  volume={461},
  number={7266},
  pages={964},
  year={2009},
  publisher={Nature Publishing Group}
}

@Article{coreshell1,
author ="Schoberth, Heiko G. and Emmerich, Heike and Holzinger, Markus and Dulle, Martin and Forster, Stephan and Gruhn, Thomas",
title  ="Molecular dynamics study of colloidal quasicrystals",
journal  ="Soft Matter",
year  ="2016",
volume  ="12",
issue  ="36",
pages  ="7644-7654",
publisher  ="The Royal Society of Chemistry",
ddoi  ="10.1039/C6SM01454B",
url  ="http://dx.doi.org/10.1039/C6SM01454B"
}

@article{qcmetal,
author = {Young Kyun Kim and Won Tae Kim and Do Hyang Kim},
title = {Quasicrystal-reinforced Mg alloys},
journal = {Science and Technology of Advanced Materials},
volume = {15},
number = {2},
pages = {024801},
year  = {2014},
publisher = {Taylor & Francis},
doi = {10.1088/1468-6996/15/2/024801},
URL = {http://dx.doi.org/10.1088/1468-6996/15/2/024801}
}




@article{tabulatedpot,
  title={Non-close-packed three-dimensional quasicrystals},
  author={Damasceno, Pablo F and Glotzer, Sharon C and Engel, Michael},
  journal={Journal of Physics: Condensed Matter},
  volume={29},
  number={23},
  pages={234005},
  year={2017},
  publisher={IOP Publishing}
}

@article{morzepot,
  title={Quasicrystalline nanocrystal superlattice with partial matching rules},
  author={Ye, Xingchen and Chen, Jun and Irrgang, M Eric and Engel, Michael and Dong, Angang and Glotzer, Sharon C and Murray, Christopher B},
  journal={Nature materials},
  volume={16},
  number={2},
  pages={214--219},
  year={2017},
  publisher={Nature Research}
}

@article{dzugutpote,
  title={Universal self-assembly of one-component three-dimensional dodecagonal quasicrystals},
  author={Ryltsev, Roman and Chtchelkatchev, Nikolay},
  journal={Soft Matter},
  year={2017},
  publisher={Royal Society of Chemistry}
}


@article{opticalex,
author={Kuzyk, Anton
and Schreiber, Robert
and Fan, Zhiyuan
and Pardatscher, Gunther
and Roller, Eva-Maria
and Hogele, Alexander
and Simmel, Friedrich C.
and Govorov, Alexander O.
and Liedl, Tim},
title={DNA-based self-assembly of chiral plasmonic nanostructures with tailored optical response},
journal={Nature},
year={2012},
month={Mar},
day={15},
publisher={Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
volume={483},
number={7389},
pages={311-314},
issn={0028-0836},
doi={10.1038/nature10889},
url={http://dx.doi.org/10.1038/nature10889}
}

@article{dotera2014mosaic,
  title={Mosaic two-lengthscale quasicrystals},
  author={Dotera, T and Oshiro, T and Ziherl, Primo{\v{z}}},
  journal={Nature},
  volume={506},
  number={7487},
  pages={208},
  year={2014},
  publisher={Nature Publishing Group}
}

@article{catalitprop,
author = {Miao, Xiaoming and Cao, Wei and Zheng, Wenting and Wang, Jingyu and Zhang, Xiaoli and Gao, Jie and Yang, Chengbiao and Kong, Deling and Xu, Huaping and Wang, Ling and Yang, Zhimou},
title = {Switchable Catalytic Activity: Selenium-Containing Peptides with Redox-Controllable Self-Assembly Properties},
journal = {Angewandte Chemie International Edition},
volume = {52},
number = {30},
publisher = {WILEY-VCH Verlag},
url = {http://dx.doi.org/10.1002/anie.201303199},
ddoi = {10.1002/anie.201303199},
pages = {7781--7785},
year = {2013}
}

@article{drugappl,
  title={Polymerization-Induced Self-Assembly (PISA)--control over the morphology of nanoparticles for drug delivery applications},
  author={Karagoz, Bunyamin and Esser, Lars and Duong, Hien T and Basuki, Johan S and Boyer, Cyrille and Davis, Thomas P},
  journal={Polymer Chemistry},
  volume={5},
  number={2},
  pages={350--355},
  year={2014},
  publisher={Royal Society of Chemistry}
}

@article{optappl,
author = {Sun, Hang and Li, Wen and Wu, Lixin},
title = {Honeycomb-Patterned Films Fabricated by Self-Organization of DNA-Surfactant Complexes},
journal = {Langmuir},
volume = {25},
number = {18},
pages = {10466-10472},
year = {2009},
ddoi = {10.1021/la900322d},
URL = {http://dx.doi.org/10.1021/la900322d}
}


@article{stability,
  title={On the stability of a quasicrystal and its crystalline approximant in a system of hard disks with a soft corona},
  author={Pattabhiraman, Harini and Gantapara, Anjan P and Dijkstra, Marjolein},
  journal={The Journal of chemical physics},
  volume={143},
  number={16},
  pages={164905},
  year={2015},
  publisher={AIP Publishing}
}


@article{stability2,
author = {Harini Pattabhiraman and Marjolein Dijkstra},
title = {Phase behaviour of quasicrystal forming systems of core-corona           particles},
journal = {The Journal of Chemical Physics},
volume = {146},
number = {11},
pages = {114901},
year = {2017},
ddoi = {10.1063/1.4977934},
URL = {http://dx.doi.org/10.1063/1.4977934}
}

@article{frenkel2015order,
  title={Order through entropy},
  author={Frenkel, Daan},
  journal={Nature materials},
  volume={14},
  number={1},
  pages={9--12},
  year={2015},
  publisher={Nature Research}
}

@article {sadef,
	author = {Whitesides, George M. and Grzybowski, Bartosz},
	title = {Self-Assembly at All Scales},
	volume = {295},
	number = {5564},
	pages = {2418--2421},
	year = {2002},
	ddoi = {10.1126/science.1070821},
	publisher = {American Association for the Advancement of Science},
	URL = {http://science.sciencemag.org/content/295/5564/2418},	
	journal = {Science}
}

@article{methods,
  title={Computational self-assembly of a one-component icosahedral quasicrystal},
  author={Engel, Michael and Damasceno, Pablo F and Phillips, Carolyn L and Glotzer, Sharon C},
  journal={Nature materials},
  volume={14},
  number={1},
  pages={109},
  year={2015},
  publisher={Nature Publishing Group}
}

@Article{notindlvo,
author="Grasso, D.
and Subramaniam, K.
and Butkus, M.
and Strevett, K.
and Bergendahl, J.",
title="A review of non-{DLVO} interactions in environmental colloidal systems",
journal="Reviews in Environmental Science and Biotechnology",
year="2002",
month="Mar",
day="01",
volume="1",
number="1",
pages="17--38",
ddoi="10.1023/A:1015146710500",
url="https://doi.org/10.1023/A:1015146710500"
}

@article {saterm1,
author = {Halley, Julianne. D. and Winkler, David A.},
title = {Consistent concepts of self-organization and self-assembly},
journal = {Complexity},
volume = {14},
number = {2},
publisher = {Wiley Subscription Services, Inc., A Wiley Company},
url = {http://dx.doi.org/10.1002/cplx.20235},
ddoi = {10.1002/cplx.20235},
pages = {10--17},
year = {2008},
}

@article{saterm2, 
title={Directed block copolymer self-assembly for nanoelectronics fabrication}, volume={26}, 
DdOI={10.1557/jmr.2010.74}, 
number={2}, 
journal={Journal of Materials Research}, 
publisher={Cambridge University Press}, 
author={Herr, Daniel J.C.}, 
year={2011}, 
pages={122–139}}

@article{mirkin1996dna,
  title={A DNA-based method for rationally assembling nanoparticles into macroscopic materials},
  author={Mirkin, Chad A and Letsinger, Robert L and Mucic, Robert C and Storhoff, James J},
  journal={Nature},
  volume={382},
  number={6592},
  pages={607--609},
  year={1996},
  publisher={Springer}
}

@article{dnaunit1,
author = {Wilner, Ofer I. and Willner, Itamar},
title = {Functionalized DNA Nanostructures},
journal = {Chemical Reviews},
volume = {112},
number = {4},
pages = {2528-2556},
year = {2012},
ddoi = {10.1021/cr200104q},
URL = {http://dx.doi.org/10.1021/cr200104q}
}

@article {dnaunit,
author = {Sacc\'{a}, Barbara and Niemeyer, Christof M.},
title = {DNA Origami: The Art of Folding DNA},
journal = {Angewandte Chemie International Edition},
volume = {51},
number = {1},
publisher = {WILEY-VCH Verlag},
issn = {1521-3773},
url = {http://dx.doi.org/10.1002/anie.201105846},
ddoi = {10.1002/anie.201105846},
pages = {58--66},
year = {2012},
}


@article{molecunit,
author ="Hamley, I. W.",
title  ="Self-assembly of amphiphilic peptides",
journal  ="Soft Matter",
year  ="2011",
volume  ="7",
issue  ="9",
pages  ="4122-4138",
publisher  ="The Royal Society of Chemistry",
ddoi  ="10.1039/C0SM01218A",
url  ="http://dx.doi.org/10.1039/C0SM01218A"
}


@Article{blockcpunit,
author ="Mai, Yiyong and Eisenberg, Adi",
title  ="Self-assembly of block copolymers",
journal  ="Chemical Society Reviews",
year  ="2012",
volume  ="41",
issue  ="18",
pages  ="5969-5985",
publisher  ="The Royal Society of Chemistry",
ddoi  ="10.1039/C2CS35115C",
url  ="http://dx.doi.org/10.1039/C2CS35115C",
}


@article{nanopartunit,
author = {Grzelczak, Marek and Vermant, Jan and Furst, Eric M. and Liz-Marzán, Luis M.},
title = {Directed Self-Assembly of Nanoparticles},
journal = {ACS Nano},
volume = {4},
number = {7},
pages = {3591-3605},
year = {2010},
ddoi = {10.1021/nn100869j},
URL = {http://dx.doi.org/10.1021/nn100869j}
}

@article{nanpartun1,
  title={Properties and emerging applications of self-assembled structures made from inorganic nanoparticles},
  author={Nie, Zhihong and Petukhova, Alla and Kumacheva, Eugenia},
  journal={Nature nanotechnology},
  volume={5},
  number={1},
  pages={15--25},
  year={2010},
  publisher={Nature Publishing Group}
}

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