Class 

Date 

Topics 

Primary

Lecture

Notes 

Secondary

Lecture

Notes 

Primary

Readings 

Secondary

Readings 

Handouts 

Jan 14

Overview of Course Topics

Introduction & Foundations:

- Church Turing Hypothesis

- Conventional Computing Models

-Overview of Types of Alternative Computing Models

Jan 19

Introduction & Foundations:

Thermodynamics of Computation:

- Maxwell’s demon,

- Landauer’s principle

Reversible Computation:

Toffoli Universal Gates

-Billiard ball computers

- Brownian Computers

-Reversible Turing Machines

-Reversible Simulation of Determinist Computation

[Preskill Ch1Sec 1.1 only

[Preskill Ch6 Sec 6.1 only

Thermodynamics of Computation: [Bennett] 

 Landauer Principle of Nonreversible Computation:

[Landauer]

[Bennett]

Reversible Computation: [Bennett]

Fredkin and Toffoli’s Ballistic (Billiard Ball) Computer:

[Fredkin] [LiVitanyi]

Physical Computation:  [Margolus]

Jan 21

Quantum Computation:

- Introduction to Quantum Mechanics: - - Hilbert Space, Qubits, Tenor Products

- Unitary Operations & Projections

- Quantum Circuits

- Example of Quantum Teleportation

[Vazirani]

[Vazirani]

[Vazirani]

[Vazirani]

[Arora]

[AB, Ch 21]

[Mermin Ch1]

[Mermin Ch2]

[Preskill Ch2]

Teleportation:

[Preskill Ch4 Sec 4.4]

Handbook of Quantum Information

Jan 26

Quantum Computation:

- Quantum Complexity Classes

- Simulating Classical Computations

- Errors in Quantum Gates

- Universal Quantum Gates

- Quantum Hadamard Transform & Simon’s Algorithm

- QMA-Completeness

[Spielman]

[Spielman] 

[Vazirani]

[Vazirani]

QMA-Completeness

Vazirani]

[Vazirani]

[

Quantum Algorithm Zoo

[AB, Ch 21]

[Preskill Ch6 Sec 6.1 – 6.3]

Jan 28

Quantum Computation:

- Quantum Fourier Transform

- Quantum Factoring

Quantum Fourier Transform:

[Vazirani]

Schor Factoring Algorithm:

[Vazirani]

Kitaev Phase Estimation Algorithm:

[Arora]

[Vazirani]

Quantum Fctorization

[Spielman]

[Vazirani]

[Vazirani]

[Mosca] Chapter 4

[AB, Ch 21]

[Preskill Ch6 Sec 6.8]

[Mermin Ch3]

Handbook of Quantum Information

Handbook of Quantum Information: Shor's factoring algorithm

Feb 4

Quantum Computation:

- Quantum Sensing: Quantum Zeno Effect,

- Quantum Search: Grover’s Algorithm

- Quantum Random Walk for Search

Grover’s Algorithm:

[Vazirani]

[Vazirani]

[Arora]

Quantum Walks:

[Vazirani]

[Mosca] Chapter 5

Grover's Quantum Algorithm for NP Search

Quantum Walk Papers:

[Szegedy]

[Szegedy]

[AB, Ch 21]

[Preskill Ch6 Sec 6.4 – 6.6]

[Mermin Ch4]

Handbook of Quantum Information: Grover's Search algorithm

Feb 9

Quantum Computation:

- Quantum Quantum Phase Sampling

–

Simulating Sparse Hamiltonians

- Quantum Solution of Linear Systems

Quantum Solution of Linear Systems:

[Lloyd] [Lloyd]

Quantum Phase Sampling: Quantum Algorithms Revisited:

Simulating sparse Hamiltonians

Feb 11

Quantum Computation:

-Quantum Error Correction

Quantum Error Correction:

[Vazirani]

[Vazirani]

[Gottesman]

Quantum Error Correction: [Mermin Ch5]

[Preskill Ch7]

Handbook of Quantum Information: Quantum Error Correction

Feb 18

Quantum Information Theory:

-- Von Neumann Entropy

-Holevo’s Thm

-Quantum Compression:

[Nielsen]

Von Neumann Entropy:

[Vazirani]

Quantum Communication & Coding:

[Vazirani]

Efficient Quantum Data Compression:

[Reif]

Universal Quantum Data Compression:[Jozsa]

Handbook of Quantum Information: Quantum Information Theory

Feb 23

Quantum Computation:

-Adiabatic Quantum Computation

-Hamiltonian Quantum Computation

Adiabatic Quantum Computation

[Mosca] Chapter 4, 7 & 9

Lower bounds on Speed of Adiabatic Quantum:

[Altshuler]

Adiabatic=Quantum:

[Aharonov]

Simulation of Quantum Mechanical Systems

[Mosca] Chapter 6

Adiabatic Quantum Computation

[Vazirani]

Lower bounds on Speed of Adiabatic Quantum:

[Vazirani]

Adiabatic=Quantum:

[AdiabaticSimQuantum]

Feb 25

Quantum Computation:

- Quantum Algorithm for NonAbelian Hidden Subgroup Algorithm

Abelian Hidden Subgroup Algorithm

[Vazirani]

NonAbelian Hidden Subgroup Algorithm

[Vazirani]

[Vazirani]

[Mosca] Chapter 7

Overview paper on Hidden Subgroup Algorithm

[Vazirani]

March 2

Quantum Computation:

- Quantum Cryptography

Quantum Crytography

Overview:

[Bartlett]

Experiments & Attacks:

[Kim]

[Hutter]

[Lydersen]

Quantum Teleportation:

[Safronova]

[Polzik]

[Mermin Ch6]

also:

[Preskill Ch4 Sec 4.5]

March 4

Quantum Computation:

- Quantum Games,

- Quantum Interactive Protocols = PSPACE

Quantum Games:

[Carmeli]

[Tame]

Quantum Complexity

[Zhang]

[Voufo]

Quantum Interactive Protocols = PSPACE

[QIP = PSPACE]

March 9, 11

No Class - SPRING BREAK

March 16

DNA Overview

Overview of DNA structure, hybridization and DNA nanostructures

-DNA Structure Transitions

-DNA Mechanics

-DNA Systems Modeling

-DNA Nanostructures

DNA Overview

-Overview of DNA structure, hybridization and DNA nanostructures

[DNA Structure: Lavery]

[DNAstucture: pharmacy.umn]

DNA Structure Transitions:

[DuplexTriplexTransition: Mao]

[B-Z.Transition: Mao]

DNA Mechanics:

[MechanicsofDNA:Bustamante]

DNA Systems Modeling:

[DNAModeller: Sudheer]

DNA Nanostructures

[DNA Nanostructures: Reif]

March 18

Tiling Assembly, Intro

- Wang tiling

- Tiles via DNA Nanostructures

-Tiling Computability

-Tile Complexity Assembled Squares

-Randomized Assembly

- Wang tiling

- Tiles via DNA Nanostructures

[DNA Nanostructures: Reif]

-Tiling Computability

[Undecidability Tiling: Robinson]

[Complexity Assembly: Winfree]

-Deterministic Tile Complexity Assembled Squares

[Tile Complexity Assembled Squares: Rothemund]

[Tile Complexity Assembled Squares: Adleman]

[Models Self-assembly: Aggarwal]

-Randomized Assembly

[Randomized Assembly Exact Shapes: Schellerr]

[Randomized Assembly Approx Shapes: Schellerr]

March 25

Tiling Assembly, Cont

- Temp Programmed Assembly

-Staged Assembly

-Assembling Shapes

- Temp Programmed Assembly

[Temp Programmed Assembly: Kao]

-Staged Assembly

[Reif]

[Staged Assembly O(1) glues: Demaine]

-Assembling Shapes

[Complexity Assembled Shapes: Winfree]

[Assembling Shapes: Becker]

March 30

Tiling Assembly, Cont

- Kinetic Model of Assembly:

- Assembly Error-Correction

- Kinetic Model of Assembly:

[Simulations of Tiling Assembly: Winfree]

- Assembly Error-Correction via Proofreading:

[Proofreading Tile Sets: Winfree]

[Compact Proofreading: Zhang Winfree]

- Compact Assembly Error-Correction:

[Compact Error Resilient Assembliy: Reif]

[Limits to Errorcorrection: Sahu]

April 1

Assembly Error-Correction, cont

 Assembly Error-Correction:

Reducing Facet Nucleation

PPT: [Error Correction Assembly: Goel PPT]

Snaked Proofreading:

[Error Correction Assembly: Goel]

[Reducing Facet Nucleation Assembly Errors: Winfree]

Tiles with State Changes:

[Error Suppression Self-assembly: Fujibayashi]

Self-Healing:

[Self-HealingTilings: Winfree]

[Invadable Self-Assembly: Chen]

[Reversible Selfrepair: Majumder]

April 8

Intro to DNA Robotics: Natural & Re-Engineered Protein Molecular Motors

-Molecular Robotics Principals

--Molecular Ratchets: Myosin & Kinesin

-Quantum Ratchets

-Polymerase & Kinesin

DNA Robotics via External State Changes:

Yurke-Tuberfield DNA Tweezers

-DNA Nanostructure Actuation using DNA B-Z transitions

-DNA Walkers using external state changes

Intro to DNA Robotics: Natural Protein Molecular Motors

-Molecular Ratchets:

[Brownian Ratchet Motors: Elmer]

[Feynman Notes V1 Ch46: Ratchet & Pawl]

[Overviews of Brownian Ratchets]

[Biophysics of Brownian Ratchets: PPT]

[More Slides on Brownian Ratchets]

Examples: Myosin & Kinesin

[Examples of Molecular Ratchets]

[Mechanics Kinesin: Cross]

-Quantum Ratchets

[Quantum Ratchets]

Surveys:

[Synthetic Molecular Motors Survey: Zerbetto]

[DNA Walkers Survey: Kelly]

DNA Robotics via External State Changes:

-DNA Nanostructure Actuation using DNA B-Z transitions

[PX Nanomechanical Devi: Seeman & Yan]

Duplex to Triplex Transitions

[DuplexTriplexTransition: Mao]

Yurke-Turberfield DNA Tweezers

[DNA Tweezer: Yurke & Tuberfield]

[DNA Tweezer: Step 1]

[DNA Tweezer: Step 2]

[DNA Tweezer: Step 3]

-DNA Walkers using external state changes

[DNA Biped Walking Device: Sherman&Seeman]

[DNA Walker: Pierce]

April 13

DNA Computation & Robotics using Enzymes:

DNA Computation & Robotics using Polymerase:

- Autonomous DNA  Computation via Polymerase Reactions: Whiplash PCR

-- DNA  Robotics via Polymerase

DNA Autonomous Computation & Robotics using Restriction Enzymes:

- Autonomous DNA  Computation via Restriction Enzyme Reactions

- Autonomous Molecular Robotics using Restriction Enzyme Reactions  

DNA Computation & Robotics using DNAzymes:

- Autonomous Molecular Computation via DNAzyme  Reactions

- Spiders: Autonomous Molecular Robotics using DNAzyme 

DNA Computation & Robotics using Enzymes:

DNA Computation & Robotics using Polymerase:

- Autonomous DNA  Computation via Polymerase Reactions: Whiplash PCR

[Whiplash PCR: Winfree]

[Simulating Whiplash PCR: Hagiya]

[Isothermal Whiplash PCR: Reif]

[Isothermal Whiplash PCR: Reif PPT]

-- DNA  Robotics via Polymerase

[Polymerase DNA Transport: Sahu]

DNA Autonomous Computation & Robotics using Restriction Enzymes:

- Autonomous DNA  Computation via Restriction Enzyme Reactions

[FSA Computation: Shapiro Nature 2001]

[More FSA Computation: Shapiro PNAS 2003]

[DNA Doctor: Shapiro Nature 2004]

[Stochastic FSA Computation: Shapiro PNAS 2004]

- Autonomous Molecular Robotics using Restriction Enzyme Reactions 

Yin  Reif Restriction Enzyme DNA Walker:

[Restriction Enzyme DNA Walker Design: Yin]

[Restriction Enzyme DNA Walker Experiments: Yin]

[Restriction Enzyme DNA Walker Paper: Yin]

[Restriction Enzyme DNA Walker Turing Computation: Yin]

Further Restriction Enzyme DNA Walkers

[Restriction Enzyme DNA Walker: Turberfield]

[Restriction Enzyme DNA Walker: Yamamura]

DNA Computation & Robotics using DNAzymes:

- Autonomous Molecular Computation via DNAzyme  Reactions

[DNAzyme Computation: Stojanovic]

[DNAzyme Nanomotor: Mao]

[Improved DNAzyme Motor: Klavins]

[DNAzyme Walker: Mao]

[DNAzyme Computation: Reif]

[DNAzyme Computation: Reif PPT]

- Spiders: Autonomous Molecular Robotics using DNAzyme 

[DNAzyme Spiders: Stojanovic]

[DNAzyme Spiders: Stojanovic PPT]

April 14

Makeup lecture

Molecular Computation via DNA hybridization:

-Autocatalytic Hybridization Reactions

DNA Robotics via DNA Hybridization:

- Autonomous

Molecular Walkers using DNA hybridization

DNA Robotics via DNA Hybridization:

- Autonomous

Molecular Motors & Walkers using Hybridization Reactions

[DNA motor: Pierce]

[Autonomous DNA Walker: Turberfield]

[Piped Walker: Seeman Slides]

[Piped Walker: Seeman]

Molecular Gears

[Molecular Gears: Mao]

April 15

Molecular Computation via DNA hybridization:

-Autocatalytic Hybridization Reactions

Molecular Computation via DNA Hybridization:

Autocatalytic Hybridization Reactions for Detection:

[Hybridization Chain Reaction: Pierce]

DNA Hairpins Fueling Autocatalytic Reactions:

[Catalyzed Metastable DNA Fuel: Seelig]

[DNA Hairpin Fueling Devices: Turberfield]

[DNA Hairpin Hybridization Circuits: Winfree]

DNA Reaction Networks Fueled by Strand Displacement:

[Seesaw Gates: Winfree]

[DNA Catalytic Cascades: Yurke Slides]

[DNA Reaction Networks: Zhang

[Allosteric DNA Catalytic Reactions: Zhang]

[DNA Chemical Kinetics: Soloveichik]

[DNA Catalytic Reactions: Zhang]

DNA Strand Algebra:

[DNA Strand Algebra: Cardelli]

Computational Complexity Chemical Reaction Networks:

[Complexity Chemical Reaction Networks: Bruck]

[Complexity Stochastic Chemical Reaction Networks: Bruck

April 25

FINAL PROJECTS DUE APRIL 25