DNA Computers Applications:

Cryptography

Constanza Lampasona

Innovative Computer Architectures and Concepts

Computer Architecture Department - University of Stuttgart
 Motivation
• Silicon technologies have limits

• Research intends to deal with “silicon” disadvantages

• DNA computing -> inherent parallelism

• Cryptographic problem requires vast parallelism

Let’s solve the cryptographic problem using a molecular computer!!!

June 2002 DNA Computers Applications: Cr 2
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Outline
1. Introduction

2. Cryptography

3. DNA Computing

4. Breaking DES using a molecular computer

5. Conclusions

June 2002 DNA Computers Applications: Cr 3

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Introduction
 Encoding data “as in nature”

Input Recombination Output

algorithm

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Introduction
 Cryptography

Secret writing

Gjoejoh uif lfz Shift by one Finding the key

Data Encryptation Standard: approved cryptographic algorithm as

required by FIPS 140-1 (Federal Information Processing Standards)

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Outline
1. Introduction

2. Cryptography

3. DNA Computing

4. Breaking DES using a molecular computer

5. Conclusions

June 2002 DNA Computers Applications: Cr 6

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 Cryptography
From the Greek: crypto-, hidden + -graphy,
-graphy writing

“The art of writing with a secret key or in an enigmatic way”

Let’s look at history...

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Cryptography
 Encryption

Protecting information

Data Transformation Unreadable form

Ensure privacy

Keep the information hidden

June 2002 DNA Computers Applications: Cr 8
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 Cryptography
 Decryption

Reverse of Encryption

Encrypted data Transformation Intelligible form

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Cryptography

Encryption Decryption

Secret KEY

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 Cryptography
Encrypted data (cipher-text): Khoor zruog

Secret KEY: shift by 3

a b c d e f g h i j k l m n o p q r s t u v w x y z

d e f g h i j k l m n o p q r s t u v w x y z a b c

Decrypted data (plain-text): Hello world

June 2002 DNA Computers Applications: Cr 11

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Cryptography
 Data Encryption Standard (DES)
• Crytographic algorithm (National Bureau of Standards).

• Enciphering and Deciphering.

Deciphering

• 64-bit key.

• Data depends on key’s security.

• Unique key for encryting and decryting.

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 Cryptography
 DES’ Data Encryption Algorithm
Enciphering

Initial Inverse initial

Input Computation Output
permutation permutation
IP IP -1

June 2002 DNA Computers Applications: Cr 13

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 Cryptography
Initial Inverse initial
Input Computation Output
permutation permutation
IP IP -1

IP
58 50 42 34 26 18 10 2
60 52 44 36 28 20 12 4
62 54 46 38 30 22 14 6
64 56 48 40 32 24 16 8
57 49 41 33 25 17 9 1
59 51 43 35 27 19 11 3
61 53 45 37 29 21 13 5
63 55 47 39 31 23 15 7

June 2002 DNA Computers Applications: Cr 14

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 Cryptography
Initial Inverse initial
Input Computation Output
permutation permutation
IP IP -1

• Uses the permuted input block as input.

• Produces a pre-output block.

• 16 iterations.

June 2002 DNA Computers Applications: Cr 15

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 Cryptography
Initial Inverse initial
Input Computation Output
permutation permutation
IP IP -1

IP-1
40 8 48 16 56 24 64 32
39 7 47 15 55 23 63 31
Plain-text
38 6 46 14 54 22 Cipher-text
62 30
37 5 45 13 53 21 61 29
36 4 44 12
Key 52 20 60 28
35 3 43 11 51 19 59 27
34 2 42 10 50 18 58 26
33 1 41 9 49 17 57 25

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Outline
1. Introduction

2. Cryptography

3. DNA Computing

4. Breaking DES using a molecular computer

5. Conclusions

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 DNA Computing
 DNA

DNA Genetic information “memory”

(Deoxyribonucleic acid)
Nucleotides strung into
polymer chains (DNA Strands)

Four classes of nucleotides:

Adenine, Guanine, Cytosine, Thymine (A,C,G,T)

June 2002 DNA Computers Applications: Cr 18

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DNA Computing
• The Structure of DNA

The double helix structure discovered by Watson and Crick

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 DNA Computing
DNA
DNA
Computer:
Computer:
• Based on Adleman’s work (1994) DNAStrands
Strands
DNA
• Solve huge problems by parallel search
++
• Much faster than a conventional computer Combinations
Combinations
• More hardware vs. more DNA
==

“Solution”
“Solution”

June 2002 DNA Computers Applications: Cr 20

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Outline
1. Introduction

2. Cryptography

3. DNA Computing

4. Breaking DES using a molecular computer

5. Conclusions

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Breaking DES
• The Idea

 Finding a key given one pair (plain-text, cipher-text).

 Pre-processing + one day of work = recover the key.

 First example of a real problem solved using DNA.

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Breaking DES
• Massive parallel DNA computing approach:

• Generate all possible solutions in parallel

• Remove wrong solutions

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Breaking DES

 Representing binary strings

 Plan of DES attack

 Prepare the DNA solution
 Extract desired patterns
 Read the result

 Break DES!!!

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 Breaking DES
• Summary of the experiment
 DES(M0,k) encoding plain-text with all possible 256 keys
 4 months
 Extract DES(M0,k)=E0, (plaintext, cipher-text)
 Read k
 1 day
DNAComputer:
DNA Computer:
DNAStrands
DNA Strands
++
Combinations
Combinations
==
“Solution”
“Solution”
June 2002 DNA Computers Applications: Cr 25
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Outline
1. Introduction

2. Cryptography

3. DNA Computing

4. Breaking DES using a molecular computer

5. Conclusions

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Conclusions
 DNA computing with a concrete application,
Cryptography

 Very general attack on DES, using 64-bit key

 Cryptosystems with 64-bit key are insecure

 Future of molecular computers: Unclear

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Summary

 Cryptography

 DES

 DNA Computing >>> Parallelism

 Breaking DES

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http://www.ra.informatik.uni-stuttgart.de/~virazela/Seminar/Material/Presentation8/

June 2002 DNA Computers Applications: Cr 29

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