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Dimensions in Silicon and in Biology

m. 10 -10. 10 -9. 10 -8. 10 -7. 10 -6. 10 -5. 10 -4. 10 -3. 10 -2. Dimensions in Silicon and in Biology. red blood cell ~5 m (SEM). diatom 30 m. DNA proteins nm. Simple molecules <1nm . bacteria 1 m. SOI transistor width 0.12 m. semiconductor nanocrystal (CdSe)

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Dimensions in Silicon and in Biology

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  1. m 10-10 10-9 10-8 10-7 10-6 10-5 10-4 10-3 10-2 Dimensions in Silicon and in Biology red blood cell ~5 m (SEM) diatom 30 m DNA proteins nm Simple molecules <1nm bacteria 1 m SOI transistor width 0.12m semiconductor nanocrystal (CdSe) 5nm Circuit design Copper wiring width 0.2m Nanometer memory element (Lieber) 1012 bits/cm2 (1Tbit/cm2) IBM PowerPC 750TM Microprocessor 7.56mm×8.799mm 6.35×106 transistors • control biological machines

  2. Biological machines • Compute (DNA) • Input/Output • Energetically efficient • High data density • Error correction • Self replication • Fabrication (synthesis) and breakdown • All processes highly efficient • How to take advantage of Nature’s engineering?

  3. Goals: Control biological activity external reversible on molecular scale (selective) direct in vitro/ in vivo universal Controlling Biology Inside E.Coli M. Hoppert et al, American Scientist, 2001

  4. biomolecule RFMF active site Au nanocrystal “1” “0” Interfacing to biology • metal nanocrystal as antennas • inductively heat the nanocrystal to heat biomolecule • induce conformational change • Universality: • Biomolecules denature with heat • Structure: function correlation

  5. Alternating magnetic field induces alternating eddy currents in metal samples For nm particles: f=1GHz (radiofrequency 109/s): Radiofrequency magnetic field: RFMF Magnetic field alternating current i frequency f Induced current in metal Metal piece Ameritherm, Inc. Induction Heating Inductively heat solution of gold nanocrystals

  6. Controlled systems Molecular Machines group Hamad-Schifferli, et al DNA double stranded DNA single stranded + Zhang group Shi, et al Protein assembled: active Protein disassembled into subunits: inactive

  7. Biomolecular Machines • Manufacturing and assembly: Polymerases, ligases, synthetases, ribosomes, ATP synthase, RNA ribozymes, telomerases, • Breakdown: Proteases, nucleases, hydrolases, glycosidases, protesome, ATPases, ribozymes, DNAzymes. • Conversion: Isomerases, dehydrogenases, protein kinases, phosphatases, transposases, oxidases, reductases, splicesome, chaperonin, transferases, deaminases. • Transport: Hemoglobin, ion and amino acid transport proteins, nuclear receptors. • Signal transmission: G-proteins, membrane ion channels, NMDA and other neurotransmitter receptors. • Structural Organization: Histones/nucleosomes, collagens, keratins, actin, tubulin filaments, neurofilaments, dentin and other matrix proteins. • Binding receptors: Antibodies,repressors, activators and other ion binding proteins.

  8. no protein transcription translation DNA RNA protein polymerase ribosome ribosome mRNA AUG AUG Control of expression: antisense protein antisense strand with Au AUG protein no protein RFMF antisense strand (DNA 15-20mer) + protein

  9. 1.) Transfection: Electroporate Chemically induced peptide mediated 2.) RFMF 3.) detection: GFP (Green Fluorescent Protein) Antisense in cells antisense GFP Protein expressed Protein not expressed RFMF Protein expressed

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