MIT Molecular Machines ( Jacobson ) Group 3.9.13

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Fabricational Complexity. MIT Molecular Machines ( Jacobson ) Group 3.9.13. What Drives T he C ost of Placing A toms W here W e W ant T hem ? What are The F undamental L imits ?. Si Wafer with Area sufficient for 2 Billion Transistors Cost: ~$0.50. - PowerPoint PPT Presentation

Transcript of MIT Molecular Machines ( Jacobson ) Group 3.9.13

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MIT Molecular Machines (Jacobson) Group

Fabricational Complexity


Itanium Quad TukwilaTransistor Count: 2BCost: ~$50

Si Wafer with Area sufficient for2 Billion TransistorsCost: ~$0.50

Flash MemoryTransistor Count: 2BCost: ~$3SmartPhoneCost: ~$200Sand (Chips and Screen)Cost: ~$0

Plastic Resin / Metal OreCost: ~$4

What Drives The Cost of Placing Atoms Where We Want Them? What are The Fundamental Limits?

Fabricational Complexity

Fabricational Complexity Per Unit Cost

N BLOCKSFabricational Complexity for N Blocks or M Types =

Fabricational Cost for N Blocks =

Where is the Yield Per Fabricational Step

Complexity Per Unit CostComplexity Per Unit Time*EnergyAGCTTCTGCACGAGCT3

Complexity Per Unit Cost

Printed Electronics~Minutes ~ 3Weeks of 7x24 Processing

LithographyPrinted Electronics+

Liquid InorganicSemiconductors[1][1] Ridley et al., Science, 286, 746 (1999)Science 297,416 (2000)Printing

Towards $10 Tablets & E Books

5Why does a lapto cost more than a newspaper?Chip takes 2 weeks x 7 days a week x 24 hrs to make. Made in a $2 Billion dollar fab.

Maximally interesting world - as many people as possible involved in the inventive process.Fabricational Complexity

Fabricational Complexity Per Unit Cost

N BLOCKSFabricational Complexity for N Blocks or M Types =

Fabricational Cost for N Blocks w/ Error Correction =

Where is the Yield Per Fabricational Step

Complexity Per Unit CostComplexity Per Unit Time*EnergyAGCTTCTGCACGAGCT6N DevicesYielding N Devices with Error Correction(Why A Small Amount of Error Correction Has A Very Large Effect)

Fraction of Chips with M or More Perfect Devices (i.e. N-M or Fewer Errors).0.750.970.9970.99980.50.850.970.990.250.600.840.950.10.330.600.800. 1. Yields as a function of the number of repaired errors.

J. Jacobson 02/12/09

Error Correcting Fabrication - TFT

Moores Law Without Moores 2nd Law

Moores LawError Correcting ManufacturingSuper Geometric ScalingError Corrected TFTError Corrected CMOSError Corrected DNA SynthesisExponential Resource -> Exponential GainLinear Resource-> Exponential Gain

DNA SynthesisChemical Synthesis (Open Loop Protection Group)Biological Synthesis (Error Correcting Polymerase)Error Rate: 1:102Throughput: 300 S per Base Addition Error Rate Product Differential: ~108

template dependant 5'-3' primer extension5'-3' error-correcting exonuclease3'-5' proofreading exonucleaseExample: [A] Synthesize 1500 Nucleotide Base Gene. Error Rate = 0.99(0.99)1500 ~ 10-7. [B] 3000 Nucleotide Base Gene. (0.99)3000 ~ 10-13.

Error Rate: 1:106Throughput: 10 mS per Base AdditionBeese et al. (1993), Science, 260, 352-355.

Error Correcting Gene SynthesisNucleic Acids Research 2004 32(20):e162

Lamers et al. Nature 407:711 (2000)XXX

Nucleic Acids Research 2004 32(20):e162Error Rate 1:10411

Nature Biotechnology 18, 85-90 (January 2000) Deinococcus radiodurans (3.2 Mb, 4-10 Copies of Genome )D. radiodurans: 1.7 Million Rads (17kGy) 200 DS breaksE. coli:25 Thousand Rads 2 or 3 DS breaks

photos provided by David Schwartz (University of Wisconsin, Madison)]

D. radiodurans 1.75 million rads, 0 hD. radiodurans 1.75 million rads, 24 h

Atoms: ~ 20 [C,N,O]Complexion: W~ 320 x = 32Product: C = 4 statesx = 2x[Product / Parts] =~ .0625 Complexity (uProcessor/program):x ~ 1K byte = 8000Product: C = 4 statesx = 2x[Product / Parts] =~ .00025

DNA PolymeraseNucleotides: ~ 1000Complexion: W~41000 x = 2000 = 2KbProduct: 107 Nucleotidesx = 2x107x[Product / Parts] =104x >1 Product has sufficient complexity to encode for parts / assemblerSynthetic Complexities of Various Systems

Threshold for LifeWhat is the Threshold for Self Replicating Systems?Measurement Theory Correcting Exonuclease(Ruler)DNANumber of NucleotidesProbability of Self Replication

Watson Crick .18 nmHow Well Can N Molecules Measure Distance?

/ length: 1541 bp for 50% yield. 379 bp for 10-6 yield.

Threshold for LifeWhat is the Threshold for Self Replicating Systems?Measurement TheoryNumber of Nucleotides m Per Building BlockMinimum Machine Size N To be Self-Replicating

Threshold for assembling blocks of m mers (monomer, dimer , trimer etc.)The longer the block the greater the binding energy. mN for 50% YieldNumber of Build Steps1 (A,G,T,C)154115412 (AA,AG,AT )13816913 (AAA,AAG)128642910994100505641210033641232452Yield___ 50%___ 10%___ 1%___ 1E-6Threshold Machine Complexity N for Self-ReplicationNOTESSheet1Fabricational ComplexitySemi-conductor Chip[1]TFT[2]Brain (Man)[5]Genome (Natural)[3]Gene(Chemical Linear Synthesis)[3]Gene(Chemical Parallel Synthesis)[4]Organism (Man)[4]Printed Page (Web Offset)[9]Printed Page (Ink Jet)[10]LaserPrinter[10b]777-200 Aircraft[11]Atom by atom Assembly[12]Allowed by Physics[13]Pocket Watch (1800)BuildingNeed notion of connected complexity - must be difference between fully yielded via chain and printed unconnected dots.Design Rule Smallest Dimension (microns)0.1220.0003Number of Types of Elements8824442672132500100Dimemsion x of SOA (yielded) Artifact(cm)30.4810049.E+01Dimemsion y of SOA Artifact(cm)30.4812043.00E-08Dimemsion z of SOA Artifact(cm)1.00E-051.00E-0543.00E-08Volume of SOA Artifact (Cubic Microns)7.29E+091.20E+11640000000000000.081Number of Elements in SOA Artifact7.E+123.E+115.E+113.E+091.E+041.E+043.E+209.E+095.E+09520200003.E+066.E+23Numer of Elements in SOA ArtifactVolume Per Element(Cubic Microns)Volume Per Element(Cubic Microns)1.E-034.E-011.E+023.E-114.E-114.E-114.E-111.E+011.E+012.E+021.E-12Fabrication Time(seconds)9.E+047.E+022.E+074.E+033.E+062.E+042.E+076.E-021.E+024.E-013.E+07use evaporator velocitiesTime Per Element (Seconds)1.E-082.E-095.E-051.E-063.E+023.E+021.E-02Fabrication Cost for SOA Artifact($)1.E+022.E+034.E+021.E-015.E-021.E+08Cost Per Element2.E-116.E-097.E-10Energy Per Element (Joules/Element)Complexity2.E+136.E+113.E+114.E+091.E+041.E+042.E+202.E+101.E+104.E+074.E+073.E+24Complexity Per Unit Volume of SOA(um^3)2.E+035.E+005.E-035.E+100.E+000.E+008.E+062.E-012.E-014.E-032.E-135.E+12Complexity Per Unit Time2.E+089.E+081.E+041.E+065.E-039.E-011.E+133.E+119.E+078.E+071.E+00Complexity Per Unit Cost1.E+113.E+082.E+112.E+114.E-01Error rateVolume(Cubic Microns)7.E+091.E+00*****3.E+139.E+105.E+109.E+092.E+206.E+11Area Per Element(Sq. Microns)1.E-024.E+00NANANANANA1.E+021.E+022.E+031.E-08Notes1] Semiconductor Chip. 0.1 um, 12 inch wafer process. Numbers are for single mask layer. 24 hours per mask layer2]TFT Processs: 40 steps * 90 seconds per step. PECVD 20 sheets per hour. Gen V 5 masks Numbers are for single mask layer3]4]5]6]7]8]9] 24 page, .5 meters per page10] StylusPro 270010b]]]Atom by atom assembly13]


Sheet5Fabricational Complexity - Error RateGenome (Natural)[1]Gene SynthesizerSemi-conductor ChipTFTDVD-5Design Rule Smallest Dimension (microns)0.00030.00030.120.5Number of Types of Elements44882Error Rate1.E-081.E-021.E-092.E-071.E-09Volume of SOA Artifact (Cubic Microns)6.E+01NA7.E+091.E+117.E+12Fabrication Time(seconds)4.E+033.E+049.E+047.E+023Fabrication Cost ($)1.E-073.E+011.E+001.E+013.E-02Complexity1.E+081.E+022.E+091.E+077.E+08Complexity Per Unit Volume of SOA(um^3)2.E+06NA3.E-011.E-041.E-04Complexity Per Unit Time4.E+045.E-032.E+041.E+042.E+08Complexity Per Unit Cost1.E+155.E+002.E+099.E+052.E+10

Sheet6Genome (Natural)Chemical SynthesisSemi-conductor ChipHigh Speed Offset WebTFTDVD-6Liquid EmbossingDesign Rule Smallest Dimension (microns)0.00030.00030.11020.250.2Number of Types of Elements4486824Area of SOA Artifact (Sq. Microns)NA7.E+087.E+102.E+121.E+121.E+108.E+09Volume of SOA Artifact (Cubic Microns)6.E+015.E+067.E+092.E+121.E+117.E+128.E+08Number of Elements in SOA Artifact3.E+097.E+047.E+122.E+103.E+112.E+112.E+11Volume Per Element(Cubic Microns)2.E-088.E+011.E-031.E+024.E-014.E+014.E-03Fabrication Time(seconds)4.E+032.E+049.E+041.E-017.E+0236.E+01Time Per Element (Seconds)1.E-063.E+021.E-087.E-122.E-092.E-113.E-10Fabrication Cost for SOA Artifact($)1.E-071.E+021.E+021.E-012.E+033.E-022.E-01Cost Per Element3.E-172.E-032.E-116.E-126.E-092.E-131.E-12Complexity4.E+099.E+042.E+134.E+106.E+111.E+113.E+11Complexity Per Unit Volume of SOA(um^3)7.E+072.E-022.E+032.E-025.E+002.E-023.E+02Complexity Per Unit Time1.E+066.E+002.E+083.E+119.E+084.E+105.E+09Complexity Per Unit Cost4.E+169.E+021.E+113.E+113.E+084.E+121.E+12Cost Per AreaNA2.E-072.E-096.E-142.E-093.E-123.E-11

Sheet4Fabricational Complexity - ShortGenome (Natural)[1]Gene Chip (Chemical Parallel Synthesis)Semi-conductor ChipHigh Speed Offset WebTFTDVD-5Liquid Embo