COMPSCI 590d: Molecular Assembly and Computation

Department of Computer Science

Duke University

John H. Reif
 Spring Semester, 2024

Room LSRC A156

 

 

 

Textbooks:

·      [Douglas]: Kenneth Douglas, DNA Nanoscience: From Prebiotic Origins to Emerging Nanotechnology, CRC Press, Edition 1, (2016) ISBN 9781498750127

 

·      [Seeman]: Nadrian Seeman, Structural DNA Nanotechnology, Cambridge University Press, Edition 1, (2016), ISBN 9780521764483

 

SCHEDULE 

 

 

Class 

Date 

Topics 

& Primary

Lecture

Notes

Required Reading

 

Secondary Lecture

Notes

Lecture 1

Jan 11

 

Overview of DNA structure

- DNA Overview

- dsDNA secondary and tertiary structure

- DNA Hairpins

- Base Stacking

- DNA Hybridization & Duplex DNA

- dsDNA Mechanical Properties

DNA Thermodynamics

- Dependence on temperature, salinity, magnesium

- Steric hindrance

-Nonstandard DNA confirmations &  DNA Structure Transitions:

-B, A, and Z form DNA

- DNA Structure Transitions: DNA B-Z transitions

- DNA Triplex Conformations

- G Quadra-Complexes

Overview of DNA Structure:

Introduction to DNA Structure [PDF] [PPT]

 

Video of DNA Structure

 

 

 

 

Required Reading:

[Douglas] Chapters 1 & 2

 

 

 

 [DNA Structure: Lavery]

[DNAstucture: pharmacy.umn]

 

 

 

 

 

Lecture 2

Jan 16

 

 

Coarse-Grain Modeling of DNA Nanostructures and Reactions: Graph & Cartoon Models

- Cartoon models of DNA

- Dot Bracket Notation For RNA & DNA nanostructures

 

Dot Bracket Notation For DNA nanostructures [PDF][PPT]

Required Reading:

[Douglas] Chapters 1 & 2

 

Extra Reading:

Programming Biomolecular Selfassembly Pathways [PDF] [PPT]

Programming Biomolecular Selfassembly Pathways

 Modeling DNA Nanodevices Using Graph Rewrite Systems [PDF] [PPTX]

Restriction enzymes

Helicase enzyme

Lecture 3

 

Jan 17

DNA Enzyme reactions:

- Ligation,

- Restriction enzymes

- Helicase enzymes

- Polymerization & Strand-displacing polymerases

 

- Kinetic Models of DNA Enzymic Reactions]

Enzyme Reactions on DNA [PDF] [PPTX]

 

Required Reading:

[Douglas] Chapters 1 & 2

 

 

 

Lecture 4

 

 

 

 

Jan 18

Adleman’s first demonstration of DNA Computation: [PDF]

 

 

 

Adleman’s first demonstration of DNA Computation: [PDF]

 

 

 

 

  Extra Reading:

 

DNA Computation (Adleman)

 

 

 

Lecture 5

 

 

 

 

 

 

 

Jan 23

Homework #1 Assigned 

 

 

DNA Computation using Restriction Enzymes

Enzymic Molecular Finite State Automata (Shapiro)

Molecular Doctor using  Enzymic Molecular Finite State Automata

 

DNA Autonomous Computation using Restriction Enzymes:

- Autonomous DNA Computation via Restriction Enzyme Reactions

 

Enzymic Molecular Finite State Automata (Shapiro) [PPTX] [PDF]

 

 

Extra Reading:

 

DNA Autonomous Computation using Restriction Enzymes:

 

[FSA Computation: Shapiro Nature 2001 PPT]

 

[More FSA Computation: Shapiro PNAS 2003 PPT]

 

 [Stochastic FSA Computation: Shapiro PNAS 2004]

 

[DNA Doctor: Shapiro Nature 2004]

Lecture 6

 

Jan 24

 

 

The PCR DNA amplification protocol

Bracketed PCR

Isothermal DNA Amplification Protocols:

- Rolling Circle PCR

- Strand-Displacement PCR

- RT-LAMP

 

The PCR DNA amplification protocol [PDF] [PPTX]

 

Peng Yin’s Autonomous Proximity Protocol

 

 

 

 

Lecture 7

Jan 25

 

 

DNA Computation via Polymerase Reactions:

 

- Whiplash PCR

- Autonomous Whiplash PCR

DNA Computation by Whiplash PCR [PPT] [PDF]

 

 

 

 

[Simulating Whiplash PCR: Hagiya]

 

Winfree’s use of Whiplash PCR for Branching Programs [PPT] [PDF]

Paper: [Whiplash PCR: Winfree]

 

 

Lecture 8

 

Feb 6

 

1 page Project Abstract Due

 

Intro to Molecular Robotics:

 

Natural & Re-Engineered Protein Molecular Motors

- Molecular Robotics Principals

- Brownian Ratchets & Quantum Ratchets

- Natural Protein Molecular Motors: Polymerase, Myosin, Kinesin, Polymerase

 

 

 

Overview of Natural Protein Motors

[PDF][PPTX]

 

 

Molecular Ratchets for Protein Molecular Motors

Overview: [PDF] [PPTX]

 

 

 

 

 

 

 

 

 

 

 

 

Optional Reading:

More on Natural Protein Motors [PPT] [PPT]

 

Molecular Ratchets:

Molecular Ratchets for Protein Molecular Motors (Mokhtar)

Details: [PDF]

 

[Brownian Ratchet Motors: Elmer]

[Feynman Notes V1 Ch46: Ratchet & Pawl]

[Overviews of Brownian Ratchets]

[Biophysics of Brownian Ratchets: PPT]

 

More on Molecular Ratchets:

[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]

Lecture 9

Feb 7

 

Non-Autonomous Molecular Robots:

Molecular  DNA Robotics & Walkers via External State Changes:

- DNA Nanostructure Actuation using DNA B-Z transitions

- PX Nanomechanical Devices

- DNA Robotics

using Duplex to Triplex Transitions

Non-Autonomous DNA Robotics via External State Changes:

[PDF][PPTX]

 

 

Required Reading:

 

[Douglas] Chapter 9

 

[Seeman] Chapter 8

 

DNA Structure Transitions:

[DuplexTriplexTransition: Mao]

[B-Z.Transition: Mao]

 

DNA Mechanics:

[MechanicsofDNA:Bustamante]

 

Papers on DNA Walkers using external state changes:

 

[DNA Biped Walking Device: Sherman&Seeman]

 

[DNA Walker: Pierce]

 

[DNA Walkers Survey: Kelly]

 

 

 

DNA Nanostructure Actuation using DNA B-Z transitions

[PX Nanomechanical Device: Seeman & Yan]

Duplex to Triplex Transitions:[DuplexTriplexTransition: Mao]

 

 

 

 

 

 

 

 

Lecture 10

 

 

 

 

 

 

 

Feb 8

 

Autonomous DNA Robotics:

 

 

Autonomous DNA Robotics using Enzymes:

 

Autonomous DNA Computation via Restriction Enzyme Reactions

 

- Autonomous Molecular Robotics using Restriction Enzyme Reactions 

 

-       DNA Robotics using Polymerase

 

-Mao’s Molecular Gears

 

Autonomous DNA Robotics via DNA Hybridization:

- Turberfield's Autonomous DNA Walker

- Seeman's Piped Walker

 

 

 

 

Autonomous DNA Robotics and Walkers [PDF][PPTX]

 

 

Autonomous Restriction Enzyme DNA Walker  by Yin Reif:

[Restriction Enzyme DNA Walker Design: Yin]

 

Autonomous Robot using Polymerase Sahu & Reif:

[Polymerase DNA Transport: Sahu]

 

Autonomous Molecular Robotics using Restriction Enzyme Reactions 

Yin Reif Restriction Enzyme DNA Walker:

[Restriction Enzyme DNA Walker Experiments: Yin]

[Restriction Enzyme DNA Walker Paper: Yin]

[Restriction Enzyme DNA Walker Turing Computation: Yin]

 

Papers on Autonomous Robot Restriction Enzyme DNA Walkers

[Restriction Enzyme DNA Walker: Turberfield]

[Restriction Enzyme DNA Walker: Yamamura]

 

 

 

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]

 

[Douglas] Chapter 9

 

[Seeman] Chapter 8

 

 

 

 

 

 

 

 

 

 

 

 

 

Lecture 11

 

 

 

 

 

 

 

 

 

Feb 13

 

DNA Robotic Devices & Applications:

 

 

- Seeman’s Molecular Assembly Lines and Reaction Factories

 

- Quan’s Cargo Sorting via Random DNA Walkers

 

- Yan & Reif’s Social DNA Nanorobots

Autonomous DNA Robotics and Walkers [PDF][PPTX]

 

 

 

 

 

Molecular Gears

[Molecular Gears: Mao]

 

Quan’s Cargo Sorting via Random DNA Walkers

 

 

Yan & Reif’s Social DNA Nanorobots

 

 

 

Lecture 12

 

 

 

Feb 14

 

 

DNA Nanostructures

DNA Tiles

- DNA crossovers junctions: Holliday junctions

- T-junctions

- DNA DX, TX tiles

- Crossover (4 x 4 and Mao's) and Double Decker Tiles

- Hexagonal Tiles

- other novel tile types: Hao's Grid-tiles

2D DNA Lattices & Tubes

- 2D DNA lattices

- corrugation methods to flatten assembly

- DNA Tubes

3D DNA Lattices

Seeman's tensegrity tiles & lattices

DNA Tiles [PDF][PPTX]

 

 

 

Required Reading:

 

[Douglas] Chapter 6 & 7

 

[Seeman] Chapters 1-7

 

 

Lecture 13

 

 

 

Feb 14

 

 

DNA Nanostructures, Cont

3D DNA Bricks

 

2D & 3D DNA  Lattices

[PDF][PPTX]

 

 

DNA Bricks [PDF] [PPTX]

 

Required Reading:

 

[Douglas] Chapter 6 & 7

 

[Seeman] Chapters 1-7

 

 

 

 

 

 

 

 

 

Lecture 14

 

 

 

 

 

 

 

Feb 15

 

2D DNA Origami

- 2D DNA Origami

- Origami design software

-CADnano

- other software

3D DNA Origami

Shi’s Curved and 3D DNA Origami

Han’s Curved and Circular DNA shapes

Modeling the Self-Assembly of DNA Origami

2D DNA Origami [PDF] [PPTX]

3D DNA Origami

[PDF] [PPTX]

 

Required Reading:

 

DNA Origami Primer [PDF]

 

[Douglas] Chapter 8

 

[Seeman] Chapter 9

 

Review of  DNA Origami:

Fan Hong, Fei Zhang, Yan Liu, and Hao Yan, DNA Origami: Scaffolds for Creating Higher Order Structures, Chem. Rev., 2017, 117 (20), pp 12584–12640 DOI: 10.1021/acs.chemrev.6b00825

 

3D DNA Origami Gridion - Han

DNA Origami Rothemund Supplemental

 

 

caDNAno Design Software for DNA Origami - Shi

 

Cadnano Tool Design DNA Origami [PDF]

 

DNA Nanotube induced alignment of membrane proteins for NMR structure determination(Shi)

 

 

 

 

 

 

 

 

 

 

 

 

Lecture 15

 

 

 

 

 

 

 

 

Feb 20

Homework #1  Due

 

Homework #2  Assigned

 

 

 

Aptimers & DNAzmes

In vivo Evolution of Aptimers & DNAzmes

DNA Robotics using DNAzymes:

- Spiders: Autonomous Molecular Robotics using DNAzyme 

DNA Robotics and Computation using DNAzymes

In-vivo Evolution & SELECT Protocols

For

-DNA&RNA Aptamers

-DNA enzymes (DNAzymes)

-RNA enzymes (Ribozymes)

 [PPTX] [PDF]

 

Molecular Robotics and Computation using DNAzymes

DNAzyme Computation & Robotics (Stojanovic): [PPT, PDF]

DNAzyme Computation & Robotics (Reif): [PPT, PDF]

Required reading:

 

DNAzymes:

 

A general purpose RNA-cleaving DNA enzyme (Joyce)

 

Mechanism and utility of an RNA-cleaving DNA enzyme(Joyce)

 

DNARobotics using DNAzymes:

 [DNAzyme Nanomotor: Mao]

[Improved DNAzyme Motor: Klavins]

[DNAzyme Walker: Mao]

 

- Spiders: Autonomous Molecular Robotics using DNAzymes

[DNAzyme Spiders: Stojanovic]

[DNAzyme Spiders: Stojanovic PPT]

Further Reading on In vitro Selection of Aptamers &DNAzymes:

In vitro selection of RNA molecules that bind specific ligands

 

Systematic evolution of ligands by exponential enrichment

 

Directed Evolution of an RNA Enzyme

 

Nucleic Acid Enzymes (Ribozymes and Deoxyribozymes): In Vitro Selection and Application

 

Further Reading on DNAzyme Devices:

An Autonomous DNA Nanomotor Powered by a DNA Enzyme[Mao]

Molecular devices—a DNAzyme that walks processively and autonomously along a one-dimensional track[Mao]

An improved autonomous DNA nanomotor [Klavins]

 

 

 

 

 

 

 

 

 

 

 

Lecture 16

 

 

 

 

 

 

 

 

 

Feb 21

 

 

DNA Reaction Networks Fueled by Strand Displacement

Catalytic Gates & Cascades:

- Winfree's Seesaw Gates

- Yurke's DNA Catalytic Cascades

- Zhang's DNA Reaction Networks and Allosteric DNA Catalytic Reactions

- Soloveichi's DNA Chemical Kinetics

 

 

 

 

DNA Hybridization Reactions

Strand Invasion [PPTX][PDF]

Invention of Toehold binding & Strand displacement: Yurke-Turberfield DNA Tweezers

[DNA Tweezer: Yurke & Tuberfield]

[DNA Tweezer: Step 1]

[DNA Tweezer: Step 2]

[DNA Tweezer: Step 3]

 

DNA Reaction Networks Fueled by Strand Displacement [PPTX][PDF]

 

 

 

 

Required Reading:

 

Example of Toehold binding & Strand displacement: Yurke-Turberfield DNA Tweezers [DNA Tweezer: Yurke & Tuberfield]

 

 

[Douglas] page 166

 

[Seeman] Chapter 8

 

 

DNA Reaction Networks Fueled by Strand Displacement:

(1) [Seesaw Gates: Winfree]

[DNA Catalytic Cascades: Yurke Slides]

 

(1) [Catalyzed Metastable DNA Fuel: Seelig]

 

(2) [DNA Reaction Networks: Zhang]

 

(3) [DNA Catalytic Reactions: Zhang]

 

 

(4) [Allosteric DNA Catalytic Reactions: Zhang]

 

(5) [DNA Chemical Kinetics: Soloveichik]

 

 

Intro:

DNA Computing (Reif)

 

 

Analysis:

Cardelli ‘s DNA Strand Algebra

 [PDF] Paper:[PDF]

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Lecture 17

 

 

 

 

 

 

 

 

 

 

Feb 21

 

Kinetics Modeling

- Introduction to Kinetics

- Stochastic Chemical Reaction Networks

 

DNA Hybridization Kinetics

Primary Chemical Reaction Kinetics Lecture:

Kinetics Overview: [PDF] [PPT]

 

 

 DNA Hybridization Kinetics [PDF][PPTX]

DNA Seesaw Gate Kinetics [PDF][PPTX]

 

 

 

 

 

 

 

 

Optional Chemical Reaction Kinetics Lectures:

Bookstaver: [PDF] [PPT]

Chieh: [PDF] [PPT]

Reid: [PDF] [PPT]

 

Optional Chemical Reaction Kinetics Lectures Applied to Biochemical Networks:

Schnell: [PDF] [PPT]

El-Samad: [PDF] [PPT]

 

Detailed Reading on Kinetics:

Vallance: [PDF]

 

Extra Reading:

Introducing Improved Structural Properties and Salt Dependence into a Coarse-Grained Model of DNA

 

 DNA hybridization kinetics: zippering, internal displacement and sequence dependence

 

On the biophysics and kinetics of toehold-mediated DNA strand displacement

 

Stochastic Simulation of the Kinetics of Multiple Interacting Nucleic Acid Strands

 

 

 

 

 

 

 

 

 

 

Lecture 18

 

 

 

 

 

 

 

Feb 22

 

 

 

Kinetic Software for Simulation of DNA Hybridization Reactions

- Probabilistic Model Checking & PRISM software

 

Kinetic Simulation of DNA Nanostructures:

- coarse-grained models of DNA,

- other model and simulation techniques,

- the biophysical basis of toehold-mediated strand displacement

Multistrand (Caltech) [PPTX] [PDF]

Visual DSD (Cambridge Microsoft) [PPTX] [PDF]

 

Visual DSD Modeling Leaks in DNA Strand Displacement Circuits & Shadow Cancelation [PPTX][PDF]

 

In Class Activities:  Design and Simulate a Simple DNA Strand Displacement Reaction Network [PDF]

Solution to in-class exercises [PDF]

Required Reading:

 

Multistrand(Caltech)

Schaeffer Master Thesis: Stochastic Simulation of the Kinetics of Multiple Interacting DNA Strands

 

Visual DSD (Microsoft Cambridge UK)

Visual DSD: a design and analysis tool for DNA strand displacement systems

 

Design and analysis of DNA strand displacement devices using probabilistic model checking

 

 

Extending Visual DSD Modeling Leaks in DNA Strand Displacement Circuits:

Automated Leak Analysis of Nucleic Acid Circuits(Zarubiieva&Philips,ACS Synth. Biol. 2022)

 

Shadow Cancelation:

Improving the Performance of DNA Strand Displacement Circuits by Shadow Cancellation (SongACSNano2018)

 

Extra Reading:

Introducing Improved Structural Properties and Salt Dependence into a Coarse-Grained Model of DNA

 

 DNA hybridization kinetics: zippering, internal displacement and sequence dependence

 

On the biophysics and kinetics of toehold-mediated DNA strand displacement

 

Stochastic Simulation of the Kinetics of Multiple Interacting Nucleic Acid Strands

 

DNA Systems Modeling:

[DNAModeller: Sudheer]

 

 

 

 

 

 

 

Lecture 19

 

 

 

 

 

March 5

 

 

Thermodynamics and Kinetic Simulation of DNA Nanostructures

 

- Kinetics simulation methods

 

OxDNA: Coarse-graining DNA for simulations of DNA nanotechnology

A Primer on the oxDNA Software Simulation Model of DNA [PPT] [PDF]

 

OxDNA

Coarse-graining DNA for simulations of DNA nanotechnology

 

Reference Papers:

Reference Papers on DNA Thermodynamics & Kinetics 

Other Suggested Text Books on Kinetics

P. W. Atkins, Physical Chemistry

 

M. J. Pilling and P. W. Seakins, Reaction Kinetics,

 

K. J. Laidler, Chemical Kinetics

 

B. G. Cox, Modern Liquid Phase Kinetics

 

 

 

 

Lecture 20

 

 

 

March 6

DNA Hybridization Reactions using DNA Hairpins:

(1) Pierce's Hybridization Chain Reaction

(2) Turberfield's DNA Hairpin Fueling Devices

(3) Winfree's DNA Hairpin Hybridization

 

DNA Hybridization Reactions using DNA Hairpins:

Solution-Based DNA Hairpin Hybridization Reactions: [PPTX][PDF]

(1) Hybridization Chain Reaction: Pierce

(2) Turberfield's DNA Hairpin Fueling Devices

(3) Winfree's DNA Hairpin Hybridization

Required Reading:

 

 

[Douglas] page 166

 

 

Papers on DNA Hybridization Reactions using DNA Hairpins:

 

Catalytic Hybridization Reactions

 (1) [Hybridization Chain Reaction: Pierce]

 

 

(2) [Catalyzed Metastable DNA Fuel: Seelig]

 

(2) [DNA Hairpin Fueling Devices: Turberfield]

 

(3) [DNA Hairpin Hybridization Circuits: Winfree]

On the biophysics and kinetics of toehold-mediated strand-displacement (Sudhanshu)

 

Catalytic Hybridization Reactions for Detection:

[Hybridization Chain Reaction: Pierce]

 

Niranjan Srinivas PHD Thesis:

Programming chemical kinetics: engineering dynamic reaction networks with DNA strand displacement

 

 

 

Lecture 21

 

 

 

March 7

Homework #2  Due

 

Homework #3 Assigned

 

 

 

Localized Hybridization Reactions

 

- on Nanotracks

 

- on DNA origami

- on cell membranes

 

 

Localized DNA Hybridization Reactions  using Hairpins: [PPTX][PDF]

- On 1D DNA Nanostructures (Nanotracks)

 

-  On DNA Origami

 

-  On Cancer Cell Membranes

Localized DNA Hybridization Reactions on Cell Membranes: [PPTX][PDF]

 

 

Required Reading:

 

 

Probabilistic Analysis of Localized DNA Hybridization Circuits

 

Local Hybridization Chain-Reactions on the Surface of DNA Origami

 

 

Extra Reading:

Protection of DNA from Degradation in Serum and the Cell:

DNA nanotechnology from the test tube to the cell(Seelig, 2015)

DNA topology influences molecular machine lifetime in human serum

Circularized synthetic oligodeoxynucleotides serve as promoter less RNA polymerase III templates for small RNA generation in human cells

Modified deoxyoligonucleotides stable to exonuclease degradation in serum

 

 

Week of March 11

No Class - Spring BREAK

 

 

 

 

 

 

 

 

Lecture 22

 

 

March 20

Homework #1 Due Feb ?

 

Homework #2 Assigned Due March ?

 

 

3 Page Project Summary Due Feb ?

 

DNA Photonics

- Fluorescent labels

- Fluorescence resonance energy transfer (FRET)

- Quantum dots

Plasmonics

-Plasmonics of Metallic Nanoparticles

-Optically-induced cutting of DNA

Fluorescence & Plasmonics Study Guide [PDF]

DNA Photonics [PPTX] [PDF]

Plasmonics [PDF]

 

 

 

 

 

 

 

 

 

Lecture 23

 

 

 

March 21

 

 

 

 

Super Resolution Imaging

Original Super Resolution Techniques

DNA paint used for Super Resolution Imaging

-Exchange DNA paint

-Strand Displacement DNA paint

Imaging in Cells via DNA Nanotechnology  

Super Resolution imaging [PPTX] [PDF]

Imaging in Cells via DNA Nanotechnology  [PPTX][PDF]

 

-

 

 

 

 

   

Extra readings

 

Molecular Imaging and Quantification

Gel Electrophoresis

AFM Imaging

SEM Imaging

STM Imaging

Molecular Imaging and Quantification

-AFM Imaging [PPT(Grutter)]

-SEM & TEM Imaging [SEM&TEM]

-STM Imaging [PPT(Grutter)]

 

 

[Seeman] Chapter 5

 

 

 

 

 

-AFM Imaging PDF(Kronenberger)]

Basic Intro to AFM Video

-STM Imaging [PPT(Grutter)]

Basic Intro to SEM Video

 

 

Extra readings

 

- Gel Electrophoresis [Agarose gel electrophoresis of DNA (Michael E. Clark)]

[Agarose gel electrophoresis of DNA (Michael E. Clark)]

 

 

 

 

 

 

Lecture 24

 

   

 

March 26

 

 

Tile Complexity of Deterministic Assembled Shapes

- Tile Complexity of Assembled Squares

- Exact Squares

- Approx Square

-Linear Structures

Tile Complexity of General Shapes

 

 

Tile Complexity of Randomized Assembly

- Exact Shapes

- Approx Shape

-Linear Structure

 

 Tile Complexity of Assembly of Squares and Linear Structures [PPTX] [PDF]

 

 

 

Required Reading:

 

-Deterministic Tile Complexity Assembled Squares

[Tile Complexity Assembled Squares: Rothemund]

 

-

Deterministic Tile Complexity of Assembling Shapes:

 

[Complexity Assembled Shapes: Winfree]

[Assembling Shapes: Becker]

 

 

 -Deterministic Tile Complexity Assembled Squares

[Tile Complexity Assembled Squares: Rothemund]

 

Exact Det. Tile Complexity of Squares: [Tile Complexity Assembled Squares: Adleman]

 

 - Approximate Squares [Assembly of Approx Square Tilings Chandran]

 

 -Randomized 1D Assembly

[Tile Complexity of Linear Assemblies: Chandran] [PPT] [PDF]

 

 

-Randomized Tile Complexity of Assembling Shapes:

[Randomized Assembly Exact Shapes: Doty]

 

[Randomized Assembly Approx Shapes: Schellerr]

 

 

March 27

 

 

 

 

 

Lecture 25   

 

 

 

 

 

March 28

 

 

 

Preliminary Project Draft Due

 

Assembly Error-Correction

- Assembly Error-Correction via Proofreading

- Compact Assembly Error-Correction:

- Error-Correction Lower Bounds