Computational Chemistry A Whole New Virtual World

COMPUTATIONAL CHEMISTRY A WHOLE NEW VIRTUAL WORLD

#UNIT FESTIVAL 2016 | CONNECTING UNICORNSJovan DrageljFreie Universitt Berlin jovandragelj@gmail.comhttp://de.linkedin.com/in/jdrageljhttps://www.facebook.com/jovandragelj

BerlinApril 16, 2016

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Have you heard of any famous gay scientists?2

Have you heard of any famous gay scientists?This is not enough, we need more!

Alan Turing

David K. Smith3

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Have you heard of any famous gay scientists?

Science, Technology, Engineering and Mathematicshttps://twitter.com/lgbtstemhttps://lgbtstem.wordpress.com/

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What is Computational Chemistry?5

What is Computational Chemistry?

Computer simulations and calculationsSolving chemical and biological problems

in vivo or in vitroin sillico6

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MOLECULAR MODELLING &MOLECULARDYNAMICS

QUANTUM MECHANICSCHEMINFORMATICS

What is Computational Chemistry?7

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How do we create our virtual reality?8

How do we create our virtual reality?

Insulin

Database of coordinates

3Dstructure9

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WaterboxMolecular Dynamics simulationVirtual reality in all dimensions

Applied forceRules: Force fieldHow do we create our virtual reality?10

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ICE MELTING12

What now?13

What now?

Very large amount of data to be understoodMore calculationsEnergyPhysical propertiesChemical propertiesPrograming

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Software?15

Software?Over 100 commercially available software packagesCHARMM (Molecular modelling & Molecular Dynamics)

Gaussian(Quantum mechanics)

16www.charmm.org

www.gaussian.com

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Computer power ?17

Computer power ?

CPUSupercomputers and computer clusters

GPU (CUDA)simulations

simple calculations

ANTONSmartphones18High end gear

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How is this useful?19

How is this useful?

FUNDAMENTAL RESEARCH many more like nanotechnology, material science, education etc. GAMES

PHARMACY AND MEDICINE

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Fundamental research21

Fundamental researchHow do chemical and biological systems work?What can we use this knowledge for?What happens with oxygen when we breathe?

Fuel for all our cells22

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H2O

H2OO=OO

EnergyHow does it work?If it does not work, the cell is dying!Improve its efficiencyCure diseases like cardiomyopathy, anemia etc. and even deadly Leigh syndromeMake a nanomachine that does the same jobFundamental research Molecular dynamics simulationsCytochrome c oxidase24

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Pharmacy and Medicine25

Pharmacy and MedicineMOST OF THE DISEASES HAVE REASONS HIDDEN DEEP ON THE LEVEL OF MOLECULESIdentify mechanism and cause of some disease to the very detail (huge advances in mechanism of cancer research for example )

Major role in discovery of new drugs - Drug Design

Identify reasons for drug resistance26

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DRUG DESIGN

Molecular modellingCheminformaticssaves time for new drug discoveries in yearssaves money costs in millions of eurosHuge databases of moleculesPharmacy and Medicine27

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Games28

Proteins fold into unique 3D structure and only then they can do their job

Center for Game Science, University of Washington UW Department of BiochemistryGAME WITH PROTEINShttps://fold.it/portal/GamesGOALSfold proteins for which we dont known 3D structure make new ones

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ContestsTeamsChallengesScientific publicationsFoldIt players have discovered the structure of a protein that can fight retroviruses (HIV belongs here)Games30

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Referenceshttp://3dprint.nih.gov/discover/3dpx-000479http://www.nature.com/polopoly_fs/7.19844.1410784494!/image/LGBT1.jpg_gen/derivatives/landscape_630/LGBT1.jpghttp://images.wisegeek.com/red-haired-woman-in-lab-coat-and-blue-gloves-with-beakers-and-chemistry-equipment.jpghttp://www.pqs-chem.com/https://kpwu.wordpress.com/tag/pymol/page/2/http://www.gesundheit-adhoc.de/files/1403853398_423ef88a.jpghttp://1.bp.blogspot.com/-BsPZyaB4vnA/Toy2zNJ4qUI/AAAAAAAAALE/z6goyqrJHwk/s1600/Nanomaterials_for_Environmental_Remediation_1.jpghttp://www.ks.uiuc.edu/Research/HIV/img/cosb_methods.jpghttps://upload.wikimedia.org/wikipedia/commons/6/66/Blausen_0580_Insulin_Syringe%26Pen.pnghttp://www.nature.com/nrd/journal/v1/n10/extref/nrd917-s3.gifhttp://biochemistry.wur.nl/motion/box1start.gifhttp://27.109.7.67:1111/econtent/images/water-9.JPGhttp://www.nyu.edu/classes/tuckerman/pchem/extras/ice_melt.gifhttp://www.thecommunitymedia.com/wp-content/uploads/2015/06/3d-white-solution.jpghttp://old.icnanotox.org/files/2009/01/program_ad.gifhttps://blog4students.files.wordpress.com/2010/05/busy-bax-student1.jpghttp://www.soibio.org/sites/default/files/WebFM/uploaded-files/NobelPrize2013-small.pnghttps://s-media-cache-ak0.pinimg.com/736x/f4/b4/97/f4b497b4a54ae99999f98420ecc2ffba.jpghttp://i1-news.softpedia-static.com/images/news2/First-Germanium-Circuits-Open-Doors-for-Non-Silicon-CPUs-468005-2.jpghttps://www.techpowerup.com/gpudb/images/2621.jpghttps://www.theguardian.com/science/2014/feb/14/gay-prejudice-coming-out-scientist-lgbthttp://www.ks.uiuc.edu/

32https://upload.wikimedia.org/wikipedia/commons/b/b1/Anton_supercomputer.jpghttp://img5a.flixcart.com/image/mobile/h/s/q/apple-iphone-5s-400x400-imadpppcxjauphdg.jpeghttp://imgur.com/twNglpYhttp://www.pnas.org/content/107/50/21470/F1.large.jpghttps://fold.it/portal/http://www.petpoisonhelpline.com/wp-content/uploads/2011/09/Diuretic.jpghttp://www.buildhealthybody.com/wp-content/uploads/2015/03/Top-10-Most-Dangerous-Diseases-in-World.jpghttp://www.massagetoday.com/mpacms/mt/article.php?id=14973http://d6igaq6njxgjh.cloudfront.net/content/physrev/95/1/219/F1.large.jpghttps://upload.wikimedia.org/wikipedia/commons/f/f5/Hexokinase_induced_fit.svghttp://www.riken.jp/zhangiru/en_research_3.htmlhttps://inst.eecs.berkeley.edu/~ee127a/book/login/Images/protein_folding1.pnghttp://inspirationalquotes.club/wp-content/uploads/2015/04/InspirationalQuotes.Club-science-present-technology-future-inspirational-intelligent-Edward-Teller.jpghttp://www.gaia3d.co.uk/wp-content/uploads/2010/11/Coordinates-579.jpghttp://www.rcsb.org/pdb/home/home.dohttps://upload.wikimedia.org/wikipedia/commons/thumb/e/ea/Thats_all_folks.svg/2000px-Thats_all_folks.svg.pngKaila, Ville RI, Michael I. Verkhovsky, and Mrten Wikstrom. "Proton-coupled electron transfer in cytochrome oxidase."Chemical Reviews110.12 (2010): 7062-7081.Khatib, Firas, et al. "Crystal structure of a monomeric retroviral protease solved by protein folding game players."Nature structural & molecular biology18.10 (2011): 1175-1177.Woelke, Anna Lena, et al. "Exploring the Possible Role of Glu286 in C c O by Electrostatic Energy Computations Combined with Molecular Dynamics."The Journal of Physical Chemistry B117.41 (2013): 12432-12441.Woelke, Anna Lena, Gegham Galstyan, and Ernst-Walter Knapp. "Lysine 362 in cytochrome c oxidase regulates opening of the K-channel via changes in pK A and conformation."Biochimica et Biophysica Acta (BBA)-Bioenergetics1837.12 (2014): 1998-2003

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AG Knapp33

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