CS252

Graduate Computer Architecture

Lecture 28

Esoteric Computer Architecture

DNA Computing & Quantum Computing

Prof John D. Kubiatowicz

http://www.cs.berkeley.edu/~kubitron/cs252
 DNA Computing
• Can we use DNA to do massive
computations?
– Organisms do it
– DNA has very high information
density:
» 4 different base pairs:
• Adenine/Thymine
• Guanine/Cytosine
» Always paired on opposite
strands  Energetically
favorable
– Active operations:
» Copy: Split strands of DNA apart
in solution, gain 2 copies
» Concatenate: eg:
GTAATCCT will combine
XXXXXCATT with AGGAYYYYY
» Polymerase Chain Reaction (PCR):
amplifies region of molecule ©1999 Access Excellence
between two marker molecules @ the National Health Museum
5/11/2009 cs252-S09, Lecture 28 2
 DNA Computing and Hamiltonian Path
• Given a set of cities and costs
between them (possibly directed
paths):
– Find shortest path to all cities
– Simpler: find single path that
visits all cities
• DNA Computing example is latter version:
– Every city represented by unique 20 base-pair strand
– Every path between cities represented by complementary pairs:
10 pairs from source city, 10 pairs from destination
– Shorter example: AAGT for city 1, TTCG for city 2
Path 1->2: CAAA
Will build: AAGTTTCG
..CAAA..
– Dump “city molecules” and “path molecules” into testtube.
Select and amplify paths of right length. Analyze for result.
– Been done for 6 cities! (Adleman, ~1998!)

5/11/2009 cs252-S09, Lecture 28 3

 Even more promising uses of DNA

• Self-assembly of components
– DNA serves as substrate
– Attach active elements in middle of components.
– Final step – metal deposited over DNA

Active Region

Bonding
DNA
Active Region
• Other interesting structures could be built

5/11/2009 cs252-S09, Lecture 28 4

 Use Quantum Mechanics to Compute?
• Weird but useful properties of quantum mechanics:
– Quantization: Only certain values or orbits are good
» Remember orbitals from chemistry???
– Superposition: Schizophrenic physical elements don’t quite know
whether they are one thing or another
• All existing digital abstractions try to eliminate QM
– Transistors/Gates designed with classical behavior
– Binary abstraction: a “1” is a “1” and a “0” is a “0”
• Quantum Computing:
Use of Quantization and Superposition to compute.
• Interesting results:
– Shor’s algorithm: factors in polynomial time!
– Grover’s algorithm: Finds items in unsorted database in time
proportional to square-root of n.
– Materials simulation: exponential classically, linear-time QM

5/11/2009 cs252-S09, Lecture 28 5

 Quantization: Use of “Spin”
North

Spin ½ particle: Representation:

(Proton/Electron) |0> or |1>

South
• Particles like Protons have an intrinsic “Spin”
when defined with respect to an external
magnetic field
• Quantum effect gives “1” and “0”:
– Either spin is “UP” or “DOWN” nothing between

5/11/2009 cs252-S09, Lecture 28 6

 Kane Proposal II
(First one didn’t quite work)

Single Spin
Control Gates

Inter-bit
Control Gates
Phosphorus
Impurity Atoms

• Bits Represented by combination of proton/electron spin

• Operations performed by manipulating control gates
– Complex sequences of pulses perform NMR-like operations
• Temperature < 1° Kelvin!
5/11/2009 cs252-S09, Lecture 28 7
 Now add Superposition!
• The bit can be in a combination of “1” and “0”:
– Written as: = C0|0> + C1|1>
– The C’s are complex numbers!
– Important Constraint: |C0|2 + |C1|2 =1
• If measure bit to see what looks like,
– With probability |C0|2 we will find |0> (say “UP”)
– With probability |C1|2 we will find |1> (say “DOWN”)
• Is this a real effect? Options:
– This is just statistical – given a large number of protons, a
fraction of them (|C0|2 ) are “UP” and the rest are down.
– This is a real effect, and the proton is really both things until you
try to look at it
• Reality: second choice!
– There are experiments to prove it!

5/11/2009 cs252-S09, Lecture 28 8

 A register can have many values!
• Implications of superposition:
– An n-bit register can have 2n values simultaneously!
– 3-bit example:
= C000|000>+ C001|001>+ C010|010>+ C011|011>+
C100|100>+ C101|101>+ C110|110>+ C111|111>
• Probabilities of measuring all bits are set by coefficients:
– So, prob of getting |000> is |C000|2, etc.
– Suppose we measure only one bit (first):
» We get “0” with probability: P0=|C000|2+ |C001|2+ |C010|2+ |C011|2
Result: = (C000|000>+ C001|001>+ C010|010>+ C011|011>)
» We get “1” with probability: P1=|C100|2+ |C101|2+ |C110|2+ |C111|2
Result: = (C100|100>+ C101|101>+ C110|110>+ C111|111>)
• Problem: Don’t want environment to measure
before ready!
– Solution: Quantum Error Correction Codes!

5/11/2009 cs252-S09, Lecture 28 9

 Spooky action at a distance
• Consider the following simple 2-bit state:
= C00|00>+ C11|11>
– Called an “EPR” pair for “Einstein, Podolsky, Rosen”
• Now, separate the two bits:

Light-Years?

• If we measure one of them, it instantaneously sets other one!

– Einstein called this a “spooky action at a distance”
– In particular, if we measure a |0> at one side, we get a |0> at the other
(and vice versa)
• Teleportation
– Can “pre-transport” an EPR pair (say bits X and Y)
– Later to transport bit A from one side to the other we:
» Perform operation between A and X, yielding two classical bits
» Send the two bits to the other side
» Use the two bits to operate on Y
» Poof! State of bit A appears in place of Y
5/11/2009 cs252-S09, Lecture 28 10
 Model:
Operations on coefficients + measurements
Input Output
Unitary
Complex Measure Classical
Transformations
State Answer
• Basic Computing Paradigm:
– Input is a register with superposition of many values
» Possibly all 2n inputs equally probable!
– Unitary transformations compute on coefficients
» Must maintain probability property (sum of squares = 1)
» Looks like doing computation on all 2n inputs simultaneously!
– Output is one result attained by measurement
• If do this poorly, just like probabilistic computation:
– If 2n inputs equally probable, may be 2n outputs equally probable.
– After measure, like picked random input to classical function!
– All interesting results have some form of “fourier transform” computation being
done in unitary transformation

5/11/2009 cs252-S09, Lecture 28 11

 Security of Factoring
• The Security of RSA Public-key cryptosystems
depends on the difficult of factoring a number N=pq
(product of two primes)
– Classical computer: sub-exponential time factoring
– Quantum computer: polynomial time factoring
• Shor’s Factoring Algorithm (for a quantum computer)
Easy 1) Choose random x : 2  x  N-1.
Easy 2) If gcd(x,N)  1, Bingo!
Hard 3) Find smallest integer r : xr  1 (mod N)
Easy 4) If r is odd, GOTO 1
Easy 5) If r is even, a  x r/2 (mod N)  (a-1)(a+1) = kN
Easy 6) If a = N-1 GOTO 1
Easy 7) ELSE gcd(a ± 1,N) is a non trivial factor of N.

5/11/2009 cs252-S09, Lecture 28 12

 Finding r with xr  1 (mod N)

 \ 1\  \ k\
k/ / k/ x /
k r 1 k
\ w\
 w 
r y/ x /
r 1 w  0 y
Quantum ( ) w\
x/
Fourier w0
Transform 0 1 k
r r r
• Finally: Perform measurement
– Find out r with high probability
– Get |y>|aw’> where y is of form k/r and w’ is related
5/11/2009 cs252-S09, Lecture 28 13
 ION Trap Quantum Computer:
Promising technology
Top
Cross-
Sectional
View

• IONS of Be+ trapped in

oscillating quadrature field
– Internal electronic modes of IONS
used for quantum bits
– MEMs technology
– Target? 50,000 ions
– ROOM Temperature!
• Ions moved to interaction regions
– Ions interactions with one another Top View
moderated by lasers
Proposal: NIST Group
5/11/2009 cs252-S09, Lecture 28 14
 Ion Trap Quantum Computer

Two-Qubit Gate
• Major Components
- Data = an ion
- Gate = a location
Q1
• Ballistic Movement
- Apply pulse sequences to electrodes
- Electrostatic forces move ion
- Intersections similar, but more
complicated pulse sequences

Q2

5/11/2009 cs252-S09, Lecture 28 15

 Ballistic Movement Network
One-Qubit Two-Qubit
Gate Gate
Q2
R R Q3

One-Qubit R Two-Qubit
Gate R Gate

Q4 Q5

Memory Cell Interconnection Memory Cell

Network
Q1

• Problem: Noise accumulation!

5/11/2009 cs252-S09, Lecture 28 16

 Noise Accumulation from Movement
1.0E-02

1.0E-03
Qubit Error

1.0E-04 1.0E-4 inital error

1.0E-5 inital error
1.0E-05
1.0E-6 inital error
1.0E-06 1.0E-7 inital error
1.0E-8 inital error
1.0E-07

1.0E-08
0 16 32 48 64
Distance Moved in Gates

• Noise may increase error by factor of 100

5/11/2009 cs252-S09, Lecture 28 17
 Movement Option 2: Teleportation
Source Location 3. Transmit two Target Location
classical bits
2. Local
D Entanglement 4. Local Ops
Ops E1 E2 D?
D

1. Generate EPR pair

• Goal: Transfer the state, not the data ion

• Problem: EPR pairs become noisy
• Teleportation Benefits
- Error Correction of data (arbitrary state): ~100 ms
Purification of EPR pair (known state): ~120 µs
- Pre-distribution of EPR pairs
5/11/2009 cs252-S09, Lecture 28 18
 EPR Pair Distribution Network

One-Qubit Two-Qubit
Gate Gate
Q2 Q3
R EPRR Pair
One-Qubit R Two-Qubit
Gate Generators Gate
R
Q4 Q5

Memory Cell Interconnection Memory Cell

Q1 Network

5/11/2009 cs252-S09, Lecture 28 19

 Setting Up a Teleportation Link
• Purification = Amplification of EPR pair link
- Two EPR pairs  One “purer” pair, one junk pair
- Chance of failure
• Need to send multiple pairs

STRONGER
EPR Qubits EntanglementEPR Qubits

P G P

Recycled Qubits Recycled Qubits

For Data Teleportation

5/11/2009 cs252-S09, Lecture 28 20
 Chained Teleportation
Teleportation Teleportation

T G T G T G T G T G T

P • Adjacent T nodes linked for teleportation P

• Positive Features
- T node linking not on critical path
- Pre-purification (Link Amplification): part of link setup

5/11/2009 cs252-S09, Lecture 28 21

 Quantum Network Architecture
T G T G T G T

P P P P
G G G G
Gate Gate Gate Gate

T G T G T G T

P P P P
Gate Gate Gate Gate

• Grid of T nodes , linked by G nodes

• Packet-switched network
- Dimension-order routing
• Each qubit has associated message
5/11/2009 cs252-S09, Lecture 28 22
 Classical Control
• Quantum Datapath Layer
- T Nodes and G Nodes (P Nodes and Gates not shown)
• Classical Control Layers
- Messages Associated with Qubits
- Teleportation and Purification Bits

5/11/2009 cs252-S09, Lecture 28 23

 Running a Quantum Circuit
• Simple gates (transversal)
• More complex gates (non-transversal)
– Exist in any universal set
• Quantum Error Correction (QEC)
– 10-8 to 10-6 error rates from gates, movement and idleness
– Data must be encoded and periodically error corrected
• Ancilla (helper) qubits
– Necessary for complex gates and for QEC
– Computation with ancilla qubits > 90% of quantum program

Q0 H QEC QEC QEC QEC T T QEC QEC

C
X
Q1 T T QEC QEC QEC QEC H QEC QEC

time Serial Circuit Latency

5/11/2009 cs252-S09, Lecture 28 24
 Running a Quantum Circuit
• Ancilla qubits are independent of data
– Preparation may be pulled offline
– Ancilla qubits should be ready just in time to avoid noise from
idleness

Q0 H QEC QEC T QEC

C
X
Q1 T QEC QEC H QEC

Parallel Circuit Latency

5/11/2009 cs252-S09, Lecture 28 25
 Running at The Speed of Data

• Ideally, execution time determined solely by data

Operations
hardware involving
data qubits

time

Ancilla encoding

5/11/2009 cs252-S09, Lecture 28 26

 Limited Ancilla Bandwidth
900000
800000
Execution Time of a
32-Bit QCLA (μs)

700000
600000
500000
400000
300000
200000
100000
0
1 10 100 1000
Encoded Ancilla Bandwidth Available (Ancillae per ms)

• 32-bit Quantum Carry-Lookahead Adder

– Varying rate at which encoded zero ancillae are provided for QEC
– Conclusion: design architecture with “ancilla factories”
5/11/2009 cs252-S09, Lecture 28 27
 Ancilla Factory Design I
• “In-place” ancilla preparation 0 Prep ?
QEC QEC
Cat Prep
Verify Bit
Correct
0 Prep ?
Verify Phase
Cat Prep
Correct
0 Prep ?
Verify
Cat Prep
Ancilla Generation Circuit
Encoded Ancilla Verification Qubits

• Ancilla factory consists of many of these

– Encoded ancilla prepared
in many places, then In-place In-place
Prep Prep
moved to output port
– Movement is costly!

In-place In-place
Prep Prep
5/11/2009 cs252-S09, Lecture 28 28
 Idealized Qalypso Architecture
• Dense data region
– Data qubits only
– Local communication
• Shared Ancilla Factories
– Distributed to data as needed
– Fully multiplexed to all data
– Output ports ( ): close to data
– Input ports ( ): may be far from
data, since recycled qubits have
irrelevant state
• Goals
– Design ancilla factories
– Answer Question: How much hardware is needed for ancilla
generation to run at the speed of data?

5/11/2009 cs252-S09, Lecture 28 29

 Discussion of ISCA 2009 paper
• “A Fault Tolerant, Area Efficient Architecture for Shor’s
Factoring Algorithm”
– Mark Whitney, Nemanja Isailovic, Yatish Patel, and John Kubiatowicz
– ISCA 2009
• How to compare layouts? (what is good)?
– Probabilistic circuits  need metric that includes probability of failure
– ADCR = Probabilistic version of area-delay product
Area  Latencysingle
ADCR 
Psuccess
– Lower is better
• What to optimize?
– Many different “datapath organizations”
– Far too much error correction

5/11/2009 cs252-S09, Lecture 28 30

 Datapath Organizations

• QLA: “Quantum Logic Array”

– Every compute region has space for 2 bits and ancilla generation
for 2 bits (to correct after every operation
• CQLA: “Compressed Quantum Logic Array”
– Same compute regions as QLA, but ability to have less ancilla
generation/bit for memory (idle bits less prone to error)
• Qalypso
– Matching ancilla generation to needs

5/11/2009 cs252-S09, Lecture 28 31

 Error Correction Optimization

• Selectively error correction placement

– Standard techniques: correct after every error
– Instead – only correct bits that are particularly “dirty”
• Error correction modeled after retiming optimization
– Only place correction when approximate “EDist” parameter reaches threshold
– Then, perform full mapping
– Choose EDist by optimizing ADCR
• Very successful at reducing area/latency
• Even improves probability of success in some cases!
– Why? Because error correction involves operations which can introduce error

5/11/2009 cs252-S09, Lecture 28 32

 Shor’s Factoring Circuit

• Most of time spent in modular exponentiation

– QFT is much smaller fraction of time
– Easiest way to build modular exponentiation: with adders
» Build multiplier instead? Not studied yet – would be very large
• Paper result: can factor in 7659 mm2
– Previous result was 0.9 m2
5/11/2009 cs252-S09, Lecture 28 33
 Conclusion
• Computing can be done in a variety of ways
– Normal silicon gates not required
• DNA Computing
– Limited use “demonstration of concept”
– Form of massive parallelism
– Interesting consequences: self assembly
• Quantum Computing:
– Computing using superposition and quantization
– Ion Traps: a particularly promising technology
• CAD Tools for Quantum Computing
– Can actually optimize circuits – just like classical case
– ADCR = probabilistic version of Area-Delay product

5/11/2009 cs252-S09, Lecture 28 34