Advanced Topics: BioNanoTechnology (CPS296.04)



EVOLVING LECTURE SCHEDULE

W.Jan.7 Class Introduction and Overview
F.Jan.9 Overview of Nanotechnology, Feynman, Drexler, Smalley vs Drexler Debate STM mechanical chemistry.
M.Jan.12 Intro. NanoTechnology, Overview of BioNanoTech, Overview of Self-assembly, Rothemund Mesoscale Self-assembly.
W.Jan.14 NanoStructured Materials (Intro): Carbon Nanotubes, NanoParticles, NanoParticle Arrays, NanoWires.
F.Jan.16 Biomolecular Structure (DNA, RNA, Proteins), mage
M.Jan.19 MLK, Jr. Holiday (no meeting)
W.Jan.21 Biomolecular Structure (DNA, RNA, Proteins), mage
F.Jan.23 Methods. Tools. Instrumentation: STM, Scanning Probe Microscopies.
M.Jan.26 Methods. Tools. Instrumentation: TEM EDXS, EM EELS.
W.Jan.28 NanoStructured Materials: Carbon nanotube transistor, Carbon nanotube devices, Carbon nanotube circuits, CNT targeted deposition, SWCNT surface patterning, CNT bibliography
F.Jan.30 Topics: Carbon nanotubes (continued), Carbon nanotube biosensors, DNA and SWCNT, DNA bond SWCNT for separation.
M.Feb.2 Topics: , DNA Templating: DNA templating for nanoelectronics, DNA Templated Ag Nanowire, DNA molecular lithography, DNA/Au + CNT FET, 4x4 tube templates, TAO tube templates, DNA templated nanowires of: palladium, platinum, gold, copper.
W.Feb.4 No Class Meeting
F.Feb.6 Topics: Nanoparticles. NanoParticles, NanoParticle DNA Conjugates, DNA & Protein directed NanoParticle Assembly, TAE tile linear assembler.
M.Feb.9 Talk about homework (Interaction of nanoparticles with EM and ionizing radiation), Finish Nanoparticles, Remote control DNA hybridization
W.Feb.11 DNA Self-Assembly: Seeman's views of DNA-based Nanofabrication 1999, 2001, 2003, DNA-based Computing and Nanofabrication, Early Seeman Lab work.
F.Feb.13 DNA Self-Assembly: 2D DNA crystals (DX), TX Lattice, TX Tubes and Wires, 4x4 Lattice & Tubes
M.Feb.16 DNA Self-Assembly: Barcode Lattice, Parallelogram tiles,
W.Feb.18 DNA Self-Assembly: TAE linear arrays, Random DNA Networks, Cloned octahedron
F.Feb.20 DNA-Based Nanofabrication - Actuators & Robotics, DNA fueled DNA machine, DNA Nanoactuator, Motor Lattice, BZ device, PX-JX device,
M.Feb.23 Dip-Pen Nanolithography Demonstration, DipPen paper,
W.Feb.25 Protein and Peptide Engineering and Design: Evidence of folding in arbitrary sequence proteins. De novo design: Alpha-4, designed hydrophobic cores ,
F.Feb.27 Protein and Peptide Engineering and Design: FELIX, Folding sequences from binary patterned combinatorial library , Stable designed protein Top7, Re-engineered function ,
M.Mar.1 (Snow day)
W.Mar.3 Tour of SMiF, AFM, TEM, SEM
F.Mar.5 (Canceled)
M.Mar.8 SPRING BREAK (no meeting)
W.Mar.10 SPRING BREAK (no meeting)
F.Mar.12 SPRING BREAK (no meeting)
M.Mar.15 DNA-based Computing: Adleman's original experiment, Landweber Review, 20 Variable 3-SAT,Hairpin DNA computer, RNA computer, Surface computer I, Surface computer II
W.Mar.17 DNA-based Computing: DNA Algorithmic Assembly XOR self-assembly, Parallel string tile XOR,
F.Mar.19 DNA-based Computing, Autonomous computing machine I, Autonomous computing machine II, DNA molecular logic gates , Tictactoe DNA automaton , Tictactoe news & views , DNA Steganography,
M.Mar.22 RNA In vitro Evolution: Tuerk & Gold, Ellington & Szostak, Bartel & Szostak, NA selection review, Neutral path,
W.Mar.24 Protein In vitro Evolution: M13 Phage display, Peptide ligands by library methods , Sexual PCR, Gene shuffling, Stemmer review,
F.Mar.26 Guest lecture: Chris Dwyer - DNA Templated Nanoelectronics
M.Mar.29 Protein BioNano. S-layers, Nucleoprotein Assemblies Review, self-assembled protein networks, Peptide templates for nanowires, Chaperonin organized nanoparticles, Designed fusion protein assemblies,
W.Mar.31 Protein and Peptide BioNano. Switchable Protein Surfaces , Review , Protein/CNT Biosensor, others
F.Apr.2 Biomineralization. Ceramics & semiconductors , On peptide templates , Biocatalytically formed silica, Diatoms (1), Diatoms (2) , Biopeptides for silica templating 1, 2.
M Apr 5 Protein molecular motors. Kinesin 1, 2. ATP Synthase 1, 2. Other: Flagellum .
W.Apr.7 BioNanoTech with Cells and Viruses: Filamentous phage and semiconductors, and Quantum dot assembly, as nanotool box , Icosohedral phage: 1,
F.Apr.9 Moletronics. Phil Ball NanoComputing Review, Molecular electronics overview, ME Reed-Tour. Sci Am., Molecular switches, Better molecular switches , Tunable Quantum Dots, Templated nanowire patterning, Directed Assembly of NW Arrays.
M.Apr.12 Project presentations. Hieu Nhan. Woo Lee.
W.Apr.14 Project presentations. Scott Kennedy. Dave Sebba. Will Palmeri.
F.Apr.16 Project presentations. Alice De Bellis. Gwangrog Lee. Dong Woo Lim.
Other Useful Things Periodic Table of Elements
Other Things to Cover Given Time Review of Molecular Electronics, Silicon nanowire synthesis,Silicon nanowire contacts, Silicon nanowire doping, SiNW devices, SiNW circuits. Quantum Cellular Automata: Quantum CA Review, Tie-ins, etc. Electrically assembled microwires from nanoparticles, sequence specific DNA helix angles,



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