Motivation Operations on DNA Solution to Knapsack Problem Perspectives In-vitro Molecular Computing Based on DNA Strands An unconventional computing concept inspired by nature PD Dr. Thomas Hinze Brandenburg University of Technology Cottbus – Senftenberg Institute of Computer Science and Information and Media Technology thomas.hinze@b-tu.de In-vitro Molecular Computing Based on DNA Strands Thomas Hinze
Motivation Operations on DNA Solution to Knapsack Problem Perspectives DNA as an Excellent Data Storage Medium high storage density up to 1 bit / nm 3 L.M. Adleman. Molecular Computation of Solutions to Combinatorial Problems. Science 266:1021-1024, 1994 In-vitro Molecular Computing Based on DNA Strands Thomas Hinze
Motivation Operations on DNA Solution to Knapsack Problem Perspectives DNA as an Excellent Data Storage Medium 2 bit per nucleotide or per high storage base pair in strand of density up to deoxyribonucleic acid (DNA) 1 bit / nm 3 T A C G 00 01 10 11 L.M. Adleman. Molecular Computation of Solutions to Combinatorial Problems. Science 266:1021-1024, 1994 In-vitro Molecular Computing Based on DNA Strands Thomas Hinze
Motivation Operations on DNA Solution to Knapsack Problem Perspectives DNA as an Excellent Data Storage Medium 2 bit per nucleotide or per high storage base pair in strand of density up to deoxyribonucleic acid (DNA) 1 bit / nm 3 T A C G 3’ 00 01 10 11 5’ A T G C 2 nm 3 / base pair A T T A A T C G G C T A 5’ 3’ L.M. Adleman. Molecular Computation of Solutions to Combinatorial Problems. Science 266:1021-1024, 1994 In-vitro Molecular Computing Based on DNA Strands Thomas Hinze
Motivation Operations on DNA Solution to Knapsack Problem Perspectives DNA as an Excellent Data Storage Medium 2 bit per nucleotide or per high storage base pair in strand of density up to deoxyribonucleic acid (DNA) 1 bit / nm 3 T A C G 3’ 00 01 10 11 5’ A T G C 2 nm 3 / base pair A T T A electronic flash memory card A T C G 128 Gbit / 146 qmm G C corresponds to T A 5’ 3’ 3 0.001 bit / nm L.M. Adleman. Molecular Computation of Solutions to Combinatorial Problems. Science 266:1021-1024, 1994 In-vitro Molecular Computing Based on DNA Strands Thomas Hinze
Motivation Operations on DNA Solution to Knapsack Problem Perspectives DNA as an Excellent Data Storage Medium high storage persistence up to several thousand years W. Miller et al. Sequencing the nuclear genome of the extinct woolly mammoth. Nature 456:387-391, 2008 In-vitro Molecular Computing Based on DNA Strands Thomas Hinze
Motivation Operations on DNA Solution to Knapsack Problem Perspectives DNA as an Excellent Data Storage Medium high storage persistence up to several thousand years under optimal environmental conditions W. Miller et al. Sequencing the nuclear genome of the extinct woolly mammoth. Nature 456:387-391, 2008 In-vitro Molecular Computing Based on DNA Strands Thomas Hinze
Motivation Operations on DNA Solution to Knapsack Problem Perspectives DNA as an Excellent Data Storage Medium high storage persistence up to several thousand years under optimal environmental conditions www.zmescience.com approx. 80% of genome reconstructed from >20,000 years old mammoth W. Miller et al. Sequencing the nuclear genome of the extinct woolly mammoth. Nature 456:387-391, 2008 In-vitro Molecular Computing Based on DNA Strands Thomas Hinze
Motivation Operations on DNA Solution to Knapsack Problem Perspectives DNA as an Excellent Data Storage Medium high storage persistence up to several thousand years under optimal environmental conditions www.zmescience.com approx. 80% of genome reconstructed from >20,000 years old mammoth floppy disk: hard disk: DVD (expected): 5 ... 10 years 10 ... 15 years 30 ... 50 years W. Miller et al. Sequencing the nuclear genome of the extinct woolly mammoth. Nature 456:387-391, 2008 In-vitro Molecular Computing Based on DNA Strands Thomas Hinze
Motivation Operations on DNA Solution to Knapsack Problem Perspectives DNA as an Excellent Data Storage Medium highly efficient chemical processing by low energy consumption L. Kari. Arrival of biological mathematics. The Mathematical Intelligencer 19(2):9-22, 1997 In-vitro Molecular Computing Based on DNA Strands Thomas Hinze
Motivation Operations on DNA Solution to Knapsack Problem Perspectives DNA as an Excellent Data Storage Medium highly efficient chemical processing A G by low energy consumption A G A G T C T C T C CH 3 3’ Thymine OH O C H up to 10 18 CH CH C C 2 H H 2’ 3’ N N N CH 1’ 4’ CH O Adenine elementary operations H C O C N 5’ CH O P O 2 C N O O (break or form CH N C H C CH CH CH H C C 2 2’ 3’ 5’ N N internucleotide OH CH 2 N N CH 1’ 4’ CH 5’ O O 5’ C Cytosine O CH 4’ 1’ CH N C H CH OH chemical bond) 5’ 2 C N O 3’ 2’ CH CH 2 CH per Joule C C H O N N N Guanine O P O CH 2 O 5’ H O : covalent bond CH 4’ 1’ CH : hydrogen bond 3’ 2’ CH CH 2 3’ OH L. Kari. Arrival of biological mathematics. The Mathematical Intelligencer 19(2):9-22, 1997 In-vitro Molecular Computing Based on DNA Strands Thomas Hinze
Motivation Operations on DNA Solution to Knapsack Problem Perspectives DNA as an Excellent Data Storage Medium highly efficient chemical processing A G by low energy consumption A G A G T C T C T C CH 3 3’ Thymine OH O C H up to 10 18 CH CH C C 2 H H 2’ 3’ N N N CH 1’ 4’ CH O Adenine elementary operations H C O C N 5’ CH O P O 2 C N O O (break or form CH N C H C CH CH CH H C C 2 2’ 3’ 5’ N N internucleotide OH CH 2 N N CH 1’ 4’ CH 5’ O O 5’ C Cytosine O CH 4’ 1’ CH N C H CH OH chemical bond) 5’ 2 C N O 3’ 2’ CH CH 2 CH per Joule C C H O N N N Guanine O P O CH 2 O 5’ H O : covalent bond CH 4’ 1’ CH : hydrogen bond bit set 3’ 2’ CH CH 10 16 2 0 1 3’ OH or reset electronically L. Kari. Arrival of biological mathematics. The Mathematical Intelligencer 19(2):9-22, 1997 In-vitro Molecular Computing Based on DNA Strands Thomas Hinze
Motivation Operations on DNA Solution to Knapsack Problem Perspectives DNA as an Excellent Data Storage Medium massive data parallelism L.M. Adleman. Molecular Computation of Solutions to Combinatorial Problems. Science 266:1021-1024, 1994 In-vitro Molecular Computing Based on DNA Strands Thomas Hinze
Motivation Operations on DNA Solution to Knapsack Problem Perspectives DNA as an Excellent Data Storage Medium massive data parallelism up to 10 15 DNA strands per test tube (2ml) simultaneous DNA and other and autonomous molecules molecular interactions without central control L.M. Adleman. Molecular Computation of Solutions to Combinatorial Problems. Science 266:1021-1024, 1994 In-vitro Molecular Computing Based on DNA Strands Thomas Hinze
Motivation Operations on DNA Solution to Knapsack Problem Perspectives 2. Operations on DNA In-vitro Molecular Computing Based on DNA Strands Thomas Hinze
Motivation Operations on DNA Solution to Knapsack Problem Perspectives Operations on DNA (Selection) Gaining DNA strands • Synthesis (oligos) 5’−ACGGAAC−3’ A C G G A A C • Isolation (like plasmids or genomic DNA from organisms) In-vitro Molecular Computing Based on DNA Strands Thomas Hinze
Motivation Operations on DNA Solution to Knapsack Problem Perspectives Operations on DNA (Selection) Gaining DNA strands • Synthesis (oligos) 5’−ACGGAAC−3’ A C G G A A C • Isolation (like plasmids or genomic DNA from organisms) Handling DNA solutions • Union (merge) • Split (aliquot) In-vitro Molecular Computing Based on DNA Strands Thomas Hinze
Motivation Operations on DNA Solution to Knapsack Problem Perspectives Operations on DNA (Selection) Gaining DNA strands • Synthesis (oligos) 5’−ACGGAAC−3’ A C G G A A C • Isolation (like plasmids or genomic DNA from organisms) Handling DNA solutions • Union (merge) • Split (aliquot) Forming and breaking hydrogen bonds A C G G A A C • Annealing (hybridisation) A C G G A A C T T G C C T T T T G C C T T A C G G A A C A C G G A A C • Melting (denaturation) T T G C C T T T T G C C T T In-vitro Molecular Computing Based on DNA Strands Thomas Hinze
Motivation Operations on DNA Solution to Knapsack Problem Perspectives Operations on DNA (Selection) Enzymatically catalysed reactions T C G P T A T T C G T A T • Ligation (concatenation)................ A G C A T A A G C A T A P A G C G C A 5’ 3’ A G P C G C A G C G C 3’ C G C G 5’ • Digestion (cleavage)..................... T C G C G T T C G C G T P HinP1 I A G C G C A P A G C G C A • Labelling (strand end modification) T C G C G T T C G C G T + 5’−Phosphat P A G C G C A A G C G • Polymerisation (completion).......... G C T C G C • PCR (polymerase chain reaction)... ........ duplicate strands In-vitro Molecular Computing Based on DNA Strands Thomas Hinze
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