John
H. Reif
Spring Semester, 2020
Classes: Tuesday, Thursday 11:45AM – 1:00 PM at LSRC A155
(also when scheduled: Wednesday 4:30PM-5:45pm at LSRC A155)
SCHEDULE
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, CRC Press, Edition 1, (2016),
ISBN 9780521764483
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Class |
Date |
Topics |
& Primary Lecture Notes |
Required Reading
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Secondary Lecture Notes |
|
LSRC A155 |
Thurs Jan 9 |
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 |
Overview of DNA Structure: Introduction to DNA
Structure
[PDF] [PPT]
|
Required Reading: [Douglas] Chapters 1 & 2 |
|
|
LSRC A155 |
Tues Jan 14 |
Overview of DNA Structure, Cont: -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 Coarse-Grain Modeling of DNA Nanostructures
and Reactions: Graph & Cartoon Models - Cartoon
models of DNA - Dot Bracket Notation For RNA & DNA nanostructures |
Overview of DNA Structure: Introduction to DNA
Structure
[PDF] [PPT] Dot Bracket Notation For RNA & 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] |
|
LSRC A155 |
Wed Jan 15 |
DNA Enzyme reactions: - Ligation, - Restriction enzymes - Helicase enzymes - Polymerization & Strand-displacing polymerases - Kinetic Models of DNA Enzymic Reactions Adleman’s first demonstration of DNA Computation: [PDF] |
Enzyme Reactions on DNA [PDF] [PPTX] Adleman’s first demonstration of DNA Computation: [PDF] |
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Extra Reading: |
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LSRC A155 |
Thurs Jan 16 |
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) [PPT] [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] |
|
LSRC A155 |
Tues Jan 21 |
The PCR DNA amplification
protocol Bracketed PCR Isothermal PCR
protocols: - Rolling Circle PCR - Strand-Displacement PCR DNA
Computation by Whiplash PCR Autonomous Whiplash PCR |
The PCR DNA amplification protocol [PDF] [PPTX] DNA Computation by Whiplash PCR [PPT] [PDF] |
DNA Computation s using Polymerase: - Autonomous DNA Computation via Polymerase Reactions:
Whiplash PCR [Simulating Whiplash PCR: Hagiya] [Isothermal Whiplash PCR: Reif] [PPT] [PDF] |
|
|
LSRC A155 |
Wed Jan 22 |
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 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 |
Overview of
Natural Protein Motors Molecular
Ratchets for Protein Molecular Motors Non-Autonomous
DNA Robotics via External State Changes: |
Required Reading: [Douglas] Chapter 9 [Seeman] Chapter 8
DNA Structure Transitions: [DuplexTriplexTransition: Mao]
DNA Mechanics: Papers on DNA
Walkers using external state changes: [DNA Biped Walking Device:
Sherman&Seeman] |
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] -Quantum Ratchets
Surveys: [Synthetic Molecular Motors
Survey: Zerbetto] DNA
Nanostructure Actuation using DNA B-Z transitions [PX Nanomechanical Device: Seeman & Yan] Duplex to Triplex Transitions:[DuplexTriplexTransition: Mao] |
|
LSRC A155 |
Thurs Jan 23 |
Autonomous
DNA Robotics & Computation using
Enzymes: Autonomous DNA Computation via
Restriction Enzyme Reactions - Autonomous Molecular Robotics
using Restriction Enzyme Reactions DNA Computation & Robotics
using Polymerase |
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] |
|
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LSRC A155 |
Tues Jan 28 Homework
%1 Assigned |
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 |
DNA Tiles: in DNA Tiles & Lattices [PDF][PPTX] |
Required Reading: [Douglas] Chapter 6 & 7 [Seeman] Chapters 1-7 |
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LSRC A155 |
Wed Jan 29 |
DNA Nanostructures, Continued 2D DNA Lattices & Tubes - 2D DNA lattices - corrugation methods to flatten assembly - DNA Tubes |
2D DNA Lattices in DNA Tiles & Lattices [PDF][PPTX] |
Required Reading: [Douglas] Chapter 6 & 7 [Seeman] Chapters 1-7 |
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LSRC A155
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Thurs Jan 30 Project
Abstract Due |
DNA Nanostructures, Continued 3D DNA
Lattices Seeman's tensegrity tiles & lattices 3D DNA Bricks |
3D DNA Lattices In DNA Tiles
& Lattices [PDF][PPTX] DNA Bricks [PDF] [PPTX] |
Required Reading: [Douglas] Chapter 6 & 7 [Seeman] Chapters 1-7 |
|
|
LSRC A155 |
*Tues Feb 4 |
2D DNA Origami - 2D DNA Origami - Origami
design software -CADnano - other software |
Overview of 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 |
DNA Origami Rothemund
Supplemental caDNAno Design Software for DNA Origami - Shi Cadnano Tool Design DNA Origami [PDF] |
|
LSRC A155 |
*Thurs Feb 6 |
3D DNA Origami Shi’s Curved and 3D DNA Origami Han’s Curved and Circular DNA
shapes |
Overview of DNA Origami, Cont [PDF] [PPTX] 3D DNA Origami |
DNA Nanotube induced alignment of membrane
proteins for NMR structure determination(Shi) |
|
|
LSRC A155 |
Tues Feb 11 |
Aptimers & DNAzmes In vivo Evolution of Aptimers & DNAzmes |
In-vivo
Evolution & SELECT Protocols For -DNA&RNA
Aptamers -DNA
enzymes (DNAzymes) -RNA
enzymes (Ribozymes) |
Required
reading: DNAzymes: A general purpose
RNA-cleaving DNA enzyme (Joyce) Mechanism and utility of an RNA-cleaving DNA
enzyme(Joyce) |
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 |
|
LSRC A155 |
Wed Feb 12 |
Aptimers & DNAzmes, Continued DNA Robotics using DNAzymes: - Spiders: Autonomous Molecular Robotics using DNAzyme DNA Robotics and Computation using DNAzymes |
Molecular Robotics and Computation using DNAzyme |
Required
reading: DNARobotics using DNAzymes: [Improved DNAzyme Motor: Klavins] - Spiders:
Autonomous Molecular Robotics using DNAzymes: |
Further Reading
on DNAzyme Devices: An Autonomous DNA
Nanomotor Powered by a DNA Enzyme[Mao] An improved autonomous
DNA nanomotor [Klavins] |
|
LSRC A155 |
Thurs Feb 13 |
DNA Reaction Networks Fueled by Strand Displacement,
Continued 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 - Cardelli's DNA Strand Algebra |
DNA Hybridization Reactions Invention of Toehold
binding & Strand displacement:
Yurke-Turberfield DNA Tweezers [DNA Tweezer: Yurke & Tuberfield] 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: Analysis: Cardelli ‘s DNA
Strand Algebra |
|
LSRC A155 |
*Tues Feb 18 |
Kinetics Modeling - Introduction to Kinetics - Stochastic Chemical Reaction Networks |
Primary Chemical Reaction Kinetics Lecture: Kinetics Overview: [PDF] [PPT]
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|
Optional Chemical Reaction Kinetics Lectures:
Optional Chemical Reaction Kinetics Lectures Applied to Biochemical Networks:
Detailed Reading on Kinetics: Vallance: [PDF] |
|
LSRC A155 |
*Thurs Feb 20 |
- Kinetic Models of DNA Hybridization Reactions Thermodynamics and Kinetic Simulation of DNA
Nanostructures - Kinetics simulation methods -
Probabilistic Model Checking & PRISM software |
DNA Hybridization Kinetics [PDF][PPTX] 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] OxDNA
(Oxford Univ): Coarse-graining DNA for simulations of DNA nanotechnology [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 OxDNA
Coarse-graining
DNA for simulations of DNA nanotechnology |
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 Reference Papers: Reference Papers on DNA Thermodynamics & Kinetics DNA Systems Modeling: 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 |
|
LSRC A155 |
Tues Feb 25 |
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: 1st
part of [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] |
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 |
|
LSRC A155 |
Wed Feb 26 |
Localized
Hybridization Reactions - on Nanotracks - on DNA origami - on cell membranes DNA Computing
in Serum and in the Cell |
Localized DNA Hairpin Hybridization Reactions: 2nd
part of [PPTX][PDF] Localized Localized Hybridization Reactions using Hairpins [PPTX] [PDF] - On 1D DNA
Nanostructures (Nanotracks) - On DNA Origami - On Cancer Cell Membranes DNA
Computations on and Inside Cells and Protection of DNA in Serum and in the
Cell: |
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 Modified
deoxyoligonucleotides stable to exonuclease degradation in serum |
|
LSRC A155 |
Thurs Feb 27 Homework
%1 Due Homework
%2 Assigned 3
Page Project Summary Due |
DNA Robotics via DNA Hybridization: - Autonomous Molecular Walkers using DNA hybridization
- Turberfield's Autonomous DNA Walker: - Seeman's Piped Walker DNA Robotic
Devices & Applications: -Molecular Gears - Molecular Assembly Lines and Reaction Factories - Cargo Sorting via Random DNA Walkers |
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[Douglas] Chapter 9 [Seeman] Chapter 8 DNA Robotics via DNA Hybridization: - Autonomous Molecular Motors & Walkers using Hybridization Reactions [Autonomous DNA Walker: Turberfield] Molecular Gears |
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LSRC A155 |
*Tues March 3 x |
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] Plasmonics [PDF] |
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LSRC A155 |
*Thurs March 5 |
Super Resolution Imaging -DNA paint -Temporal DNA paint |
DNA paint: Multiplexed 3D Cellular
Super-Resolution Imaging with DNA-PAINT and Exchange-PAINT Fluorescence
microscopy and super-resolution imaging [PPTX] [PDF] More on Super Resolution Imaging [PDF] |
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Tues March 10 & Thurs March 12 |
No Class - Spring BREAK |
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Zoom Steaming |
Tues March 17 |
Overview
of Theoretical Tile Assembly Models: Wang
tiling Abstract
tile assembly model (TAM) Reversible
tile assembly model Kinetic
tile assembly model (KTAM) Alternative Models of Tiling Assembly - Staged tile assembly: Step-wise
tile assembly model - Hierarchical tile assembly model Temperature
Programmed Tiling The
q-tile tile assembly model - Modified
Glue Models for Tiling Assembly: - The flexible glue tile assembly model - Time-dependent glue tile assembly model Tiles with
State Changes |
Intro to Tile
Assembly [PDF][PPT] |
Required
Reading: [Seeman] Chapter 7 [Complexity of Tiling
Assembly: Winfree] Survey of Tile Assembly Models (Patitz) [PDF]
|
Other Overviews of Tiling Assembly Intro to Tile Assembly (Goel) [PDF] [PPT] Intro to Tile Assembly (Chen) [PDF] [PPT] Self-Assembled Circuit Patterns [PDF] [PPTX] Overview of Tile Assembly Models (Tianqi Song)
[PDF] [PPTX] Wang tiling Undecidability Tiling Assembly Models Undecidability Wang tiling [Undecidability Tiling: Robinson] NP completeness of tiling on N x N square [Garey, Johnson, Papadimitrou, 1977] Undecidability aTAM [Complexity Assembly:
Winfree] - Kinetic Model of Assembly: [Simulations of Tiling Assembly: Winfree] -Modified Glue Models for Tiling Assembly: [Models Self Assembly:
Aggarwal] Self-Assembly
Model of Time-Dependent Glue Strength Sahi [PPT] -Staged Assembly [Reif] [Staged Assembly O(1) glues: Demaine] - Temp Programmed Assembly [Temp Programmed Assembly: Kao] Alternative Tile Assembly Models (Tianqi Song)
[PDF] [PPTX] Tiles with State Changes: [Error Suppression
Self-assembly: Fujibayashi] Activatable
Tiles for Compact Error-Resilient Directional Assembly [Harish et al] |
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Zoom Steaming |
Wed March 18 |
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 [PPT] [PDF] |
Required Reading: -Deterministic Tile Complexity Assembled Squares [Tile Complexity Assembled
Squares: Rothemund] - Deterministic Tile Complexity of Assembling Shapes: [Complexity Assembled Shapes: Winfree]
|
-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] |
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Zoom Steaming |
Thurs March 19 |
Assembly Error-Correction - Assembly Error-Correction
via Proofreading - Compact
Assembly Error-Correction: -
Error-Correction Lower Bounds - Self-Healing - Invadable Self-Assembly - Reversible Self-repair |
Tile Assembly Error-Correction: via Proofreading, Snaking & Redundancy [PDF] [PPTX] |
Required Reading: Assembly
Error-Correction via Proofreading: [Proofreading Tile Sets:
Winfree] - Compact
Assembly Error-Correction: [Compact Error Resilient
Assembliy: Reif] Reducing Facet
Nucleation Via Snaked Proofreading: [Error Correction Assembly:
Goel] |
- Assembly Error-Correction via Proofreading: [Proofreading Tile Sets:
Winfree] [Compact Proofreading:
Zhang Winfree] - Compact
Assembly Error-Correction: [Compact Error Resilient
Assembliy: Reif] Talk: [PDF] [PPT] [Limits to Errorcorrection:
Sahu] Assembly
Error-Correction: Reducing Facet
Nucleation Via Snaked Proofreading: [Error Correction Assembly:
Goel] PPT: [Error Correction Assembly:
Goel PPT] [Reducing Facet Nucleation
Assembly Errors: Winfree] Self-Healing: [Self-HealingTilings:
Winfree] |
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Zoom Steaming |
*Tues March 24 |
Chemical Reaction Networks (CRNs)
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Tuitorial on CRNs(Anderson):[PDF] Software for Simulations of CRNs Introduction to Theory of CRNs [PDF] [PPT] |
Required Reading: Papers on Theory of CRNs: Deterministic Function Computation with Chemical Reaction Networks Computation with finite
stochastic chemical reaction networks
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Secondary Readings: Shin Master Thesis: Compiling and Verifying DNA-Based Chemical Reaction Network Implementations Programmability of Chemical Reaction Networks DNA as a universal substrate for chemical kinetics
Computational Complexity Chemical Reaction Networks: |
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Zoom Steaming |
*Thurs March 26 |
Analog CRN & DNA Computations - reaction
giving exponential signals - arithmetic
operations -
log-transforms -
Analog-to-digital and digital-to-analog transformations |
Analog CRN
& DNA Computations [PDF] [PPTX] CRNs Using
Strand-Displacing Polymerase [PDF] [PPTX]
|
Required
Reading: CRN
Computations Computing Algebraic Functions with Biochemical
Reaction Networks(ArtificialLife2009) CRN
Computations using DNA strand-displacement Reactions DNA as a universal substrate for chemical
kinetics(WinfreePNAS2010) |
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Zoom Steaming |
Tues March 31 Homework
%2 Due Homework
%3 Assigned Preliminary
Project Draft Due |
Molecular Reactions Generating Sinusoidal Signals - DNA
enzymatic reactions giving sinusoidal signals - DNA
hybridization reactions giving sinusoidal signals |
DNA Oscillator Reactions [PDF] [PPTX] |
Required Reading: DNA Oscillator Reactions Programming an in vitro DNA oscillator using a molecular networking
strategy(RondelezMolSyBio2010) Synthetic in vitro transcriptional oscillators
(WinfreeMolSysBio2010) |
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Zoom Steaming |
Thurs April 2 |
DNA Feedback Control Circuits |
DNA Feedback Control Circuits |
Required
Reading: Biomolecular implementation of linear I/O
systems(Klavins, SynBio2010) Programmable chemical controllers made from
DNA(Seelig, NatureBio2013) Computational Design of Nucleic Acid Feedback Control
Circuits (Phillips, ACS Syn Bio 2015) |
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Zoom Steaming |
Tues April 7 |
DNA Reaction Diffusion Systems |
DNA Reaction
Diffusion Systems [PPTX] [PDF] |
Pattern Formation
by Reaction Diffusion [PPT] [PDF] Required
Reading: Synthesis of Programmable
Reaction Diffusion Fronts Using DNA Catalyzers (Estevez-Torres) Designing modular reaction-diffusion programs for complex pattern formation (Schulman) Stable DNAbased Reaction
Diffusion Patterns (Schulman) Emulating cellular
automata in chemical reaction–diffusion networks(Schulman) Modeling scalable pattern
generation in DNA reaction networks
(Ellington) Pattern transformation with DNA
circuits (Chen) |
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Zoom Steaming |
Thurs April 9 |
Molecular Imaging and Quantification Gel Electrophoresis AFM Imaging SEM Imaging STM Imaging |
Molecular Imaging and Quantification - Gel Electrophoresis [Agarose gel electrophoresis of DNA (Michael E. Clark)] [Agarose gel electrophoresis of DNA (Michael E. Clark)] -AFM Imaging [PPT(Grutter)] -SEM & TEM Imaging [SEM&TEM] -STM Imaging [PPT(Grutter)] |
[Seeman] Chapter 5 |
-AFM Imaging PDF(Kronenberger)] -STM Imaging [PPT(Grutter)] |
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Zoom Steaming |
Thursday April 12 |
Biotechnology for Detecting COVID-19 and Discussion of
student’s final projects |
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April
24 Homework
#3 Due Final
Project Paper Due |
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