New motifs in DNA nanotechnology (2008)

Foundations of Nanoscience, April 21-24, 2009     Back to Projects

Quick Reference Guide to Current Research

conference website, short agenda, detailed agenda, conference summary

NOTE: Includes presented talks only, not posters


A. Taxonomy of nanoscience tracks

1. Processes

3. Nanostructures

5. Fundamentals

Top-down meets bottom-up

Molecular motors/machines

Principles and theory

Surface chemistry

Virus platforms

Computational tools

Biomedical nanotechnology

DNA nanostructures





2. Components

4. Materials


Computer circuit & system architectures

Nanoplasmonics & nanophotovoltaics


Self-assembly across scales

Protein & peptide design



Carbon-based nanostructures




B. Quick reference summary of nanoscience tracks and talks


Track: Top-down meets Bottom-up (April 22, 2009) Back to Top

Theme: Mix of organic and inorganic techniques to create functional nanomaterials and substrates

1. “Top-down Meets Bottom-up: Rational Approach towards SERS Engineering” Zhiyong Li, HP Labs

Approach: SERS (surface-enhanced raman scattering); rational engineering of SERS physics; a fundamental understanding of “enhancement effect”

Result: Possibility of fabricating a large-area SERS (surface-enhanced raman scattering) substrate with uniform and quantifiable enhancement factors

2. “Polymer Self Assembly in Semiconductor Microelectronics” Charles T. Black, Brookhaven National Laboratory

Approach: Use block copolymer self-assembly (a biological bottoms-up method) as an alternative to traditional lithography

Result: Sub-50 nm semiconductor microelectronics patterning/circuit etching as a next-generation lithography technique for extending Moore’s Law

3. “Bio-inspired Assembly of Functional Nanomaterials” Song Jin, University of Wisconsin-Madison

Approach: Mimic biomineralization process; controlled assembly of organic materials from solution; generate surface carboxylic groups, block copolymer

Result: Create functional nanomaterials; nucleate nanoscale crystalline inorganic materials

4. “Lithographically patterned colloids as cell surface mimics” T. Andrew Taton, University of Minnesota

Approach: Make synthetic versions of protein patterns found on cell surfaces; protein-functionalized, lithographically-fabricated colloids, T-cells that react as with natural proteins

Result: Engineered immune response simulators


Track: Self-Assembled Surface Chemistry (April 23, 2009) Back to Top

Theme: Integrate top-down inorganic and bottom-up organic methods for new applications

1. “Harnessing Nature's Powerful DNA Sequencing Engine: Single Molecule Real Time Sequencing-by-Synthesis” Stephen W. Turner, Pacific Biosciences

Approach: SMRT (single molecule real-time) DNA sequencing; eavesdropping on template-directed synthesis by DNA polymerase in real-time via 1) phospholinked nucleotides and 2) zero-mode waveguide confinement technique

Result: $100, 1 hour whole human genome sequencing expected in 2011; 30,000-fold improvement on the current method

2. “Surface Bio-Engineering Using Peptides for Enhanced Cell Adhesion and Proliferation” Mustafa Gungormus, University of Washington

Approach: Use GEPI (genetically-engineered peptides) to regulate cell behavior at interfaces by modifying surface chemistry; immobilize bioactive molecules causing infection

Result: Improved binding at bio-inorganic interfaces; potential use in biomedical implants (reduce infection) and scaffolds (improved nanodevice construction)

3. “Lithography and DNA Synthesis: Integration at the Nanoscale” Franco Cerrina, Boston University

Approach: Test a wide variety of existing lithography and DNA synthesis methods together in different configurations

Result: Integrate top-down and bottom-up methods, assemble DNA nanostructures on lithographically-patterned templates

4. “Cell-free Protein Translation” Brian Fox, University of Wisconsin-Madison

Approach: Use an enriched preparation of ribosomes for cell-free protein translation, especially wheat-germ cell-free translation

Result: De novo protein synthesis; more efficient protein synthesis


Track: Biomedical Nanotechnology (April 24, 2009) Back to Top

Theme: Deeper understanding of biological mechanisms and the construction of targeting nanostructures

1. “Self Assembly of the Ribosome Protein Synthesis Machine” James Williamson, The Scripps Research Institute

Approach: Develop an isotope pulse-chase assay using quantitative mass spec. Develop a two photon excitation three-color fluorescence correlation spectroscopy to monitor assembly reactions involving labeled ribosomal proteins

Result: Characterization of the assembly mechanism of the 30S ribosomal subunit (responsible for mRNA decoding)

2. “Viral Nanoparticles (VNPs) as platforms for biomedicine: Targeting VNPs to sites of disease in vivo” Nicole F. Steinmetz, The

Scripps Research Institute

Approach: Design and test (via assay) multivalent display of endothelial targeting CPMV (cowpea mosaic virus) peptides

Result: In vivo targeting of CPMV (cowpea mosaic virus) particles to tumor endothelium and cancer cells

3. “Targeting Nanoparticles to Tumors Using Adenoviral Vectors” Maaike Everts, University of Alabama-Birmingham

Approach: Coupled gold nanoparticles and quantum dots to adenoviral vectors

Result: Demonstrated the feasibility of coupling metal (e.g.; gold) nanoparticles and quantum dots to targeted adenoviral vectors; however a higher number of nanoparticles would need to be attached to the adenoviral vector for therapeutic use

4. “Nanodiamond-Based Therapeutic Delivery Agents for Cancer, Inflammation, and Wound Healing” Dean Ho, Northwestern University

Approach: Functionalize nanodiamonds with a wide variety of therapeutics for drug delivery

Result: Therapeutic delivery agents for cancer inflammation and wound healing, specifically nanodiamond-based

microfilm device formation for localized chemotherapy

5. “Molecular Biomimetics – Coupling Peptides and Nanoparticles for Nanotechnology and Medicine” Candan Tamerler, University of Washington

Approach: Couple peptides and nanoparticles into biocomposites; genetically select and/or design peptides with specific binding to functional solids, tailor their binding and assembly characteristics, develop bifunctional peptide/protein genetic constructs with both material binding and biological activity, and utilize these as molecular-synthesizers, erectors, and assemblers

Result: Solid-binding peptides as novel molecular agents coupling bio- and nanotechnology


Track: Self-assembled Computer Circuit and System Architectures (April 21, 2009) Back to Top

Theme: use DNA self-assembly to manufacture nanoscale devices; extend/replace CMOS with traditional and novel methods

1. “Nanoscale Integrated Sensing and Processing: Architectures for a New Computational Domain” Constantin Pistol, Duke University

Approach: Use DNA self-assembly (nanostructure grids) to place chromophores a few nm apart to generate Resonance Energy Transfer (RET) for molecular sensing and pass gate creation

Result: Make an nSP (nanoscale sensor processor) by integrating both molecular probe sensing and computation

2. “A simple DNA gate motif for synthesizing large-scale circuits” Lulu Qian, Caltech

Approach: Use toe-hold mediated DNA strand replacement as a gate motif

Result: Scale up circuit assembly, large-scale circuit synthesis

3. “Self-Assembly of Carbon Nanotube Devices Directed by 2D DNA Nanostructures” Si-ping Han, Caltech

Approach: Use 2D DNA origami nanostructures

Result: Direct assembly of cross-junction CNTs

4. “Finding the Missing Memristor” Stanley Williams, HP Labs

Approach: Use traditional methods - imprint lithography

Result: Make a memristor to make smaller digital switches as a means of extending Moore’s Law

5. “Magnetic Logic Based on Field-Coupled Nanomagnets: Clocking Structures and Power Analysis” Wolfgang Porod, Notre Dame

Approach: Use room-temperature nanomagnets/magnetic QCA (quantum dot cellular automata) (vs. molecular QCA)

Result: Build a nanoscale device/system with more atomically correct gates/circuits


Track: Self-Assembly Across Scales (April 23, 2009) Back to Top

Theme: Make electronic components or proto-components with organic and inorganic mechanisms

1. “Quilt Packaging – a Quasi-Monolithic Way to Merge Size Scales” Gary Bernstein, Notre Dame

Approach: Use MEMs to protrude from the sides of the die (vs. TSVs (through silicon vias) across the full surface of the chip for direct metal-to-metal interconnects over short distances; use a 2D approach to increase the density and speed of interconnects

Result: Shift focus from smaller chips to complete electronic systems (system improvement, not IC improvement), maximize space efficiency with 3D packaging/chip stacking

2. “Shape-Selective Assembly in Deformable Systems using Templated Assembly by Selective Removal” Gunjan Agarwal, MIT

Approach: Selectively assemble deformable polymer microspheres on rigid assembly templates using TASR (templated assembly by selective removal)

Result: Selected assembly of deformable polymer microspheres on patterned silicon templates

3. “Towards Self-Replicating Materials of DNA Functionalized Colloidal Particles” Mirjam Leunissen, NYU

Approach: Use colloidal particles functionalized with complementary single-stranded DNA ‘sticky ends’

Result: Develop a new class of non-biological materials that can self-replicate/grow indefinitely; colloidal building blocks

4. “Magnetic Self-Assembly of Multiple Component Types: Simultaneous and Sequential Sorting of a Heterogeneous Mixture” Sheetal Shetye, University of Florida

Approach: Simultaneous and sequential heterogeneous assembly; free floating components from a heterogeneous mixture self-assemble onto pre-defined receptor sites on a fixed substrate using magnetic forces between permanent magnets integrated onto the component surfaces

Result: Fabricate a micromagnet; magnetically-directed self-assembly for low-cost, high–throughput parallel assembly of multi-chip modules, etc.

5. “Three Dimensional Nanostructures using Dielectrophoretic Assembly” Mehmet Dokmeci, Northeastern University

Approach: Use DEP (dielectrophoretic) assembly to manipulate CNTs in aqueous solution

Result: Self-assembly of 3D nanostructures; 3D nanomaterial-based interconnects, sensors and active devices; 3D vertically-integrated CNT and gold nanoparticle-based devices


Track: Molecular Motors (April 21, 2009) Back to Top

Theme: Replicate and extend naturally occurring motor functions with designed organic and inorganic processes

1. “Mapping molecular landscapes inside cells by cryoelectron tomography” Wolfgang Baumeister, Max-Planck-Institute of Biochemistry

Approach: Use cryoelectron tomography to elucidate 3D cell architecture and allow automated and unperturbed data collection

Result: Map intracellular macromolecule spatial relationships, molecular mapping of the whole cell

2. “A Unidirectional Autonomous Bipedal DNA Nanorobot with Coordinated Legs” Tosan Omabegho, Harvard University

Approach: Construct a directed autonomous bipedal walker coordinating two parts of the motor powered by a DNA fuel strand/catalysis strand

Result: In the future, use DNA walkers as sensors, to pull cargo, to synthesize waste products and develop artificial ribosomes/polymerases. DNA plus movement could generate a self-organizing system

3. “Rotary molecular motion at the nanoscale: Motors, propellers, wheels” Petr Kral, University of Illinois at Chicago

Approach: Use the naturally occurring rotary mechanism in molecular nanomachines to create molecular propellers, nanoscopic wheels rolling on water, molecular motors

Result: Deliver nanomaterials (molecules, nanoparticles, other nanoscale componentry) for use in building molecular electronics

4. “Maximum force obtainable from a molecular photoactuator” Roman Boulatov, University of Illinois

Approach: Use small molecules to replace AFM (atomic force microscope) laser traps in nanoscale microscopy. Translate objects by the structural change in reacting macromolecules (molecular propulsion)

Result: Improved nanoscale microscopy technique, taking into account different propulsion dynamics at the nanoscale

5. “Nanocrystal molecules with applications in single molecule biological imaging” Paul Alivisatos, UC Berkeley and Lawrence Berkeley National Laboratory 

Approach: Use two approaches: DNA/plasmonic coupling and DNA-inspired inorganic synthesis of nanoparticles/electronic coupling

Result: Build coupled inorganic nanocrystals for single molecule biological imaging (groups of nanocrystals exhibit distinct properties)

6. “Molecular Motors: Contractile fluctuations and stiffening of motor-activated gels” F. C. MacKintosh, Vrije Universiteit

Approach: Construct a three-component filamentous protein in vitro model system consisting of myosin II, actin filaments, and cross-linkers to quantify the effects of motor activity non-equilibrium stresses, and showing a 100-fold stiffening of the cytoskeleton

Result: Use microtubule models as endogenous probes of motor-activated dynamics in living cell cytoplasm


Track: Viral Self-Assembly (April 23, 2009) Back to Top

Theme: Use unique properties of viruses, especially from a physics perspective to develop nanostructures

1. “Physics of Virus-inspired Self-Assembly” Bogdan Dragnea, Indiana Nanoscience Institute

Approach: Use abiotic nanotemplates and self-assembling viral proteins. Model viruses as thermodynamic systems. Integrate optics, viruses and nanoparticles together in one system using thermodynamics/charge neutralization

Result: Build particle supramolecular assemblies

2. “Assembly of multilayered viral nanoparticles: a new approach for vaccine design” Anette Schneemann, The Scripps Research Institute

Approach: Make VLPs (virus-like-particles; recombinantly expressed viruses without the viral genome). Making chimeric nanoparticles, protein domains containing more than 150 amino acids displayed on a VLP

Result: Nanoparticle platforms to make better vaccines (e.g.; for anthrax)

3. “Stability and Dynamics of Protein Cages” Brian Bothner, Montana State University

Approach: Use virus nanoparticles, protein cages and other biophysical techniques

Result: Scaffolds for nanomaterials; characterize the stability and dynamics (e.g.; thermal) of protein cages and virus particles in solution


Track: Self-Assembled DNA Nanostructures (April 22, 2009) Back to Top

Theme: Refine assembly techniques, processes and mechanisms to achieve build more complex nanodevices

1. “A route to DNA polyhedra and cages” Chengde Mao, Purdue University

Approach: Use branched DNA star motifs

Result: Systematically self-assemble regular [structurally strong/desirable] polyhedra (examples: spherical virus capsid/protein shell; C60 buckyball)

2. “Bringing the Full Strength of Branched DNA Nanostructures to the Scaffolding of Nanoparticles” William Sherman, Brookhaven National Laboratory

Approach: Use self-assembled branched DNA nanostructures; build a Mao Tensegrity Triangle structure and cover gold nanoparticles with DNA and zwitterions

Result: Scaffolding of nanoparticles; allow aggregation-resistance sequence-specific binding of nanoparticles to DNA scaffolds

3. “Two- and threedimensional prestressed DNA Tensegrity structures” Tim Liedl, Dana-Farber Cancer Institute and Harvard Medical School

Approach: Explore traditional examples of tensegrity structures (mechanical stability from continuous tension and local compression distributed over the entire structure) and define their use in the nanoscale realm

Result: A structure for building stronger and more structurally sound nanomaterials

4. “DNA nanostructures made of monomolecular G-Wires” Sébastien Lyonnais, Muséum National d’Histoire Naturelle, Paris

Approach: Use G-wires (long mono-molecular 1D structures that are self-folded long poly(dG) strands where guanines interact through G-Quartets motifs and form superwires with

a continuous backbone)

Result: Use the G-wire specific properties to assemble rigid nanowires potentially usable as structural and functional components, connectors and scaffolds for nanodevice assembly

5. “Self-assembly of a nano-scale DNA box with a controllable lid” Ebbe Andersen, Aarhus University

Approach: Nanoscale box (42 × 36 × 36 nm) with controllable lid; “key” sequence signal binds to the lock toehold to open; a Cy3-Cy5 FRET system detects the lid opening

Result: More sophisticated object for drug delivery and other complicated activities vs. small molecules


Track: Nanoplasmonics & Nanophotovoltaics (April 21, 2009) Back to Top

Theme: Apply optics and bottom-up techniques to produce nanomaterials for improved photovoltaics

1. “Amorphous Si and CuIn(Ga)Se2 Nanowire Solar Cell” Yi Cui, Stanford University

Approach: Use inorganic nanowires (a-Si:H  and CuIn(Ga)Se2) to deliver enhanced absorption

Result: Improved solar cells and batteries

2. “Self-Assembled Plasmonic Crystals” Andrea Tao, UC Berkeley

Approach: Use silver nanocrystals (bottom-up method; lithography substitute) to focus light to sub-wavelength volumes through surface plasmon excitation

Result: Colloidal plasmonic crystals to be used as fabrication materials for nanoscale imaging, near-field photonics and optical spectroscopy

3. “Vacuum Rabi splitting and strong coupling dynamics for surface plasmon polaritons and organic molecules” Päivi Törmä, Helsinki University of Technology

Approach: Realize strong coupling with waveguided plasmons propagating through a controllable-length molecular area

Result: Ability to better manipulate and work with SPPs (surface plasmon polaritons) to achieve sub-wavelength light

4. “Periodic Plasmonic Nanostructures for Biosensing and Photovoltaics” Sang-Hyun Oh, University of Minnesota

Approach: Use the EOT (extraordinary optical transmission) effect for real-time label-free biosensing in nanostructured metallic substrates

Result: Build a new generation of biosensors and thin-film photovoltaic cells


Track: Protein and Peptide Design and Assembly (April 22, 2009) Back to Top

Theme: Use molecular materials (proteins, peptides, etc.) to generate useful nanoconstruction materials

1. “Designing and assembling repeat proteins with novel structures and properties” Lynne Regan, Yale University

Approach: Use the modular architecture of designed repeat proteins vs. globular proteins, specifically TPR (tetratricopeptide repeat), whose basic motif is a 34 amino acid helix-turn-helix. Also redesign TPR module binding specificity

Result: Make novel materials for protein engineering; create smart nanogels with controllable and reversible assembly properties

2. “Extremely Thin Crystalline Sheet Assembly from Periodic Amphiphilic Peptoid Polymers” Ronald N. Zuckermann, Molecular Foundry, Lawrence Berkeley National Laboratory

Approach: Use peptoids (bio-inspired material) for the improved-property/lower-cost synthesis of protein-like (structure and function) materials

Result: Ability to design precisely-structured nanomaterials; achiral (e.g.; greater planarity) thin (3 nm thick x 100 microns) crystalline sheets

3. “Collagen Peptide-Based Biomaterials: Designing 3-D Structures through Metal Chelation” Jean Chmielewski, Purdue University

Approach: Use collagen peptide-based biomaterials (vs. natural collagen) to deliver enhanced function

Result: Generate better scaffolds for tissue engineering from synthetic collagen metal-ligand assembly, unique collagen assemblies include florettes, fibers, meshes, disks

4. “Progress in the Design of Protein Shells, Layers” Todd O. Yeates, UCLA

Approach: Use bacterial carboxysome shell proteins

Result: Novel knotted topologies of folded proteins to lead to standardized construction of 3D synthesized proteins. Design of protein shells, layers, filaments and knotted materials.


Track: Carbon-based Nanostructures (April 24, 2009) Back to Top

Theme: Improved techniques for higher quality manufacture of carbon-based nanostructures

1. “Ultrathin Films of Single Walled Carbon Nanotubes for Analog RF and Digital Electronics” John Rogers, University of Illinois

Approach: Use ultrathin films of SWNTs as a method for growing aligned CNTs

Result: Better quality CNTs for analog RF and digital electronics, not semiconductors (because would require too much change to the current manufacturing process)

2. “Order-disorder transitions in nano-clusters and implications in their catalytic activity” Stefano Curtarolo, Duke University

Approach: Use a thermodynamic model to evaluate the solubility of C in Fe nanoclusters and the behavior of phases competing for stability

Result: Determine the effects of Mo (Molybdenum) concentration on growth capability and the attainment of stable phases

3. “Large area, Few Layer Graphene Films on Insulating Substrates” Alfonso Reina, MIT

Approach: Synthesize large-area few-layer grapheme films with ambient pressure CVD

Result: Reliable low-cost fabrication method of graphene-based structures

4. “Toroidal Fullerenes with the Cayley Graphs Structures” Ming-Hsuan Kang, Pennsylvania State University

Approach: Use Cayley graphs and structures to measure the excitability of a molecule (HOMO-LUMO gap)

Result: Understanding of how to realize toroidal fullerenes in 3D space

5. “Selective growth of well aligned semiconducting single-walled carbon nanotubes” Jie Liu, Duke University

Approach: Use a CVD method to allow selective growth of high-density arrays of well-aligned SWNTs to produce almost exclusively (95%) semiconducting SWNTs

Result: Better control and alignment in the construction of SWNTs; a method to produce well-aligned arrays of pure semiconducting nanotubes for large-scale fabrication of nanotube FETs


Track: Principles and Theory of Self-Assembly (April 22, 2009) Back to Top

Theme: Theoretical development of frameworks and extensions for nanoscience

1. “Programmable Chemical Kinetics” David Soloveichik, Caltech

Approach: Derive new molecules and reactions from the math that describes chemical systems. Information-bearing polymers like nucleic acids can be more easily programmed for reactions with mathematical models

Result: Use math to design complex behaviors with nucleic acids like motors, logic gates, catalysts

2. “Non-Biological Sequence Replication and Evolution Using DNA Crystals” Rebecca Schulman, UC Berkeley

Approach: Experiment with programmable DNA crystals

Result: Deepen understanding of how replication in clays, crystal systems is possible

3. “Global-to-Local Programming and Theory for Spatial Multi-Agent Systems” Radhika Nagpal, Harvard University

Approach: Use programmable self-organization to design local interaction rules for global outcomes; design spatial

computer programs in a principled way, for the case of pattern formation problems in asynchronous 1D cellular automata

Result: Build novel spatial computers, a global-to-local compiler

4. “Directing colloidal self-assembly using roughness-controlled depletion attractions” Thomas Mason, UCLA

Approach: Use predictive calculation and Janus platelets (different surface roughness on opposite faces) to direct

thermodynamic self-assembly of a pure dimer phase

Result: Insight into directing the self-assembly of colloidal particles through purely entropic interactions. Calculations for Janus particles predict the dimer phase and also a new type of configuration of columnar phase that has not yet been seen experimentally


Track: Computational Tools for Self-assembly (April 23, 2009) Back to Top

Theme: Computer models as an increasingly integral step in design and simulation of biologically-directed behavior

1. “Rapid prototyping of three-dimensional DNA-origami shapes with caDNAno” Shawn Douglas, Harvard Medical School

Approach: Open-source rapid prototyping CAD software for DNA

Result: Design of DNA sequences for folding into 3D honey-comb pleated shapes

2. “Simulation of Self-Assembly in the Abstract Tile Assembly Model with ISU TAS” Matthew J. Patitz, Iowa State University

Approach: ISU TAS (Iowa State University tile assembly model), a graphical simulator and tile set editor

Result: Design and build 2D and 3D tile assembly systems and simulate their self-assembly, an extension of Erik Winfree’s 1998 aTAM (abstract tile assembly model)

3. “Foldit: Scientific Discovery through Computer Games” Adrien Treuille, Carnegie Mellon University

Approach: Take advantage of human skills in visualizing 3D space, abstractions and spatial macromanipulations in a 3D abstract reasoning computer game

Result: Human-computer cooperative model for problem solving; solve the molecular chemistry problem of getting a protein folded to its final minimal energy state