California NanoSystems Institute
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March 28, 2003

David Leigh
University of Edinburgh
Tooling up for Nanoworld: Hydrogen Bond-Assembled Molecular Machines

March 11, 2003

Mark Welland
University of Cambridge
Controlling Physical Properties by Nanoscale Patterning

March 04, 2003

Erik Winfree
Biomolecular Computing with DNA

What is a molecular algorithm? Is biochemistry a Turing-universal model of computation? If so, can we hope to reliably implement arbitrary algorithms by proper design of molecules and reactions? Both answers appear to be "yes". I will describe research in our lab on two models, algorithmic DNA self-assembly and RNAP transcriptional networks, and discuss the current state of experimental implementation, challenges, and prospects.


(1) Design and self-assembly of two-dimensional DNA crystals. Nature 394, 539-544 (1998), Erik Winfree, Furong Liu, Lisa Wenzler, Nadrian C. Seeman.

(2) The Program-Size Complexity of Self-Assembled Squares. (STOC 2000) Paul W. K. Rothemund, Erik Winfree.

February 25, 2003

Steve Chu
Stanford University
What We Can Learn from Looking at Biological Processes, One Molecule at a Time

Virtually all knowledge of chemical and biochemical processes has been deduced from studies of a large number of molecules. The ability to look at individual molecules has given us new insights into biological processes. As an example, our polymer studies using DNA have altered our thinking of polymer dynamics by showing that identical molecules placed under identical conditions take several distinct paths to a new equilibrium state.

We have been applying sensitive fluorescence microscopy to study the behavior of individual biomolecules. Using energy transfer between two dye molecules, a change in relative fluorescence from the two dyes can be used to measure the distance between two locations of a bio-macromolecule. This technique has proven to be particularly powerful in linking molecular structural information with biological activity measured with molecular biology methods.

Examples of how this work is allowing us to test mechanistic models of how biological systems function will be given. This talk will emphasize our study of how fluorescence techniques are enabling us to see the motion of tRNA as they traverse through the ribosme during the manufacture of the amino acid chain that folds into a protein. Also a progress report of our work on neural vesicle fusion that occurs in at the synapse between neurons will also be given.


Initiation and re-initiation of DNA unwinding by the Escherichia coli Repheli case, Taekjip Ha, Ivan Rasnik, Wei Cheng, Hazen P. Babcock, George Gauss, Timothy M. Lohman and Steven Chu, Nature 419, 638-641 (2002).

Channels in the Folding Landscape of a Structured RNA, Rick Russell, Xiaowei Zhuang, Hazen P. Babcock, Ian S. Millett, Sebastian Doniach, Steven Chu, and Daniel Herschlag, PNAS 99, 155-160 (2002).

The Relationship between Structural Dynamics and Function of a RNA enzyme - A Single Molecule Study of the Hairpin Ribozyme, Xiaowei Zhuang, Harold Kim, Miguel Pereira, Hazen P. Babcock, Nils Walter, Steven Chu, Science 296, 1473-1476 (2002).

February 18, 2003

Colin Nuckolls
Columbia University
Creating Nanostructured Materials Trhough Self-Assembly

This presentation discusses new molecular systems, and the self-assembly of these systems into novel materials. One of the systems discussed utilizes hydrogen bonds to enforce stacking between hexasubstituted aromatic rings forming one-dimensional nanostructures possessing a dipole moment that sums as the molecules stack. In bulk, these columns further self-assemble into two-dimensional arrays. In films with submonolayer coverage, some derivatives of these structures form self-assembled stacks that are isolated from each other—only one molecule wide. The structure of these stacks can be probed down to atomic resolution with atomic force microscopy, electrostatic force microscopy, and scanning tunneling microscopy. Other derivatives adopt the opposite orientation in thin films and possess polar order. Ongoing efforts to measure the electrical properties and to direct the self-assembly process will also be presented.


T.Q. Nguyen, M.L. Bushey, L.E. Brus, and C. Nuckolls, Tuning Intermolecular Attraction to Create Polar Order and One Dimensional Nanostructures on Surfaces, Journal of American Chemical Society, 124, 15051-15054 (2002).

M.L. Bushey, A. Hwant, P.W. Stephens, and C. Nuckolls, The Consequences of Chirality in Crowded Arenas-Macromolecular Helicity, Hierarchical Ordering, and Directed Assembly, Agnew. Chem. Int. Ed, 41, 2828-2831 (2002).

February 11, 2003

Mark Reed
Yale University
The Physics of Atomic and Molecular Scale Electronic Transport

Charge transport at the atomic and molecular scale is an intriguing and experimentally challenging area of physics. This talk presents measurements in this regime in a variety of systems, spanning semiconductor, metallic, and organic embodiments.

Metallic systems present the simplest case, where ideal Landauer conductance quantization can be observed. A novel inherently stable microfabricated atomic junction, with a mechanical stability of approximately 3pm, will be discussed.

In semiconductor systems, an ultimate quantum dot [1] is created by a single impurity in a heterostructure quantum well. Zeeman splitting of a single atom is demonstrated. The magnitude of the effective magnetic spin splitting factor g* and electron tunneling rates through potential barriers are measured.

In organic systems, electronic transport in a variety of stable self-assembled conjugated oligomers is demonstrated. The electronic properties of single and/or few molecule systems will be discussed, including the electrical transport properties of a single molecule [2], systematic measurements of the barriers and transport mechanisms of these molecules, and potential device applications.


1. M.R. Deshpande et al, Phys. Rev. Lett. 76, 1328 (1996).
2. M. A. Reed et al., Science 278, 252 (1997).

February 04, 2003

George Gruner
Chemical and Bio-Sensing at the Nanoscale: From Basic Science to Product Development

G.Gruner* Nanomix Inc. Emeryville, CA

With the relentless reduction of electronic device dimensions comes increased sensitivity to the environment. This opens up opportunities in diverse areas, ranging from chemical and bio sensing to opto-electronics.

We have fabricated electronic devices with carbon nanotubes as active elements, and combined these with recognition molecules and recognition layers that are sensitive to specific analytes. Charge rearrangements, driven by chemistry and biology, and also by electronics connect these different areas at the nanoscale, and open up the opportunity of electronic detection of chemical and biological species with extreme sensitivity and specificity. The architecture allows potentially single molecule and also quantum limited detection.

We have made initial steps to fabricate sensors that can be regarded the basic elements of an electronic sensory system, elements of an artificial nose, tongue and eye. Biosensors that detect antibody-antigen binding have also been fabricated with the single protein sensitivity.

I will also discuss large-scale fabrication issues, together with strategic decisions facing a venture-capital funded company with focus on nanotechnology.

* On sabbatical leave from Department of Physics UCLA

January 28, 2003

Chad Mirkin
Northwestern University
Massively Parallel Dip Pen Nanolithography: Towards Combinatorial Nanotechnology

Dip-Pen Nanolithography (DPN) is a scanning-probe technique that permits the chemical functionalization of surfaces with nanoscale precision. Based upon a conventional Atomic Force Microscope, DPN combines ambient operation and resolutions superior to those of e-beam lithography, and allows one to create combinatorial libraries of soft matter nanostructures that can be used in fundamental surface science studies, biological diagnostics, and organic nanoelectronics. This talk will describe the fundamental capabilities of DPN and its use to generate and study a wide variety of nanostructures using materials ranging from oligonucleotides to proteins to conjugated polymers.


Lee, K.-B.; Park, S.-J.; Mirkin, C. A.; Smith, J. C.; Mrksich, M. "Protein Nanoarrays Generated by Dip-Pen Nanolithography," Science, 2002, 295(5560), 1702-1705.

Holliday, B. J.; Mirkin C. A. "Strategies for the Construction of Supramolecular Compounds through Coordination Chemistry," Angew. Chem., Int. Ed., 2001, 40, 2022-2043.

January 21, 2003

Marc Madou
UC Irvine
Nanotechnology: Icarus Revisited?

The combination of natural polymers such as proteins and nucleic acids with MEMS and NEMS promises the advent of a totally new class of devices such as sensors and actuators with applications in diagnostics, responsive drug delivery, biocompatibility, self-assembly etc. Proteins and nucleic acid are information rich molecules with structural and electrical properties making their incorporation in the human manufacturing arsenal an attractive proposition. This combination has become possible as today both top-down traditional manufacturing (e.g., MEMS and NEMS) and novel bottom-up manufacturing can realize components overlapping in size. Examples to illustrate the tremendous potential of merging top-down and bottom-up manufacturing techniques will be presented. These examples are culled from the fields of molecular diagnostics, responsive drug delivery systems, protein and DNA structural elements and sensors and actuators and molecular self-assembly. In molecular diagnostics we conclude that an important avenue to success is the merging of DNA arrays with microfluidics to achieve sample to answer systems. Widespread introduction of molecular diagnostics is not about if but when. Future responsive drug delivery systems are seen as a culmination of results from genomics and proteomics coupled with implantable telemetric devices. This and other developments will cause a renewed interest in in-vivo diagnostics. Natural polymers will become part of our manufacturing arsenal and when using building blocs in the nanometer range a fundamental understanding and the use of molecular self-assembly is a must for future progress. While biomimetics in the macrodomain often has led to failure in the past (airplanes do not flap their wings as birds do, see Icarus legend), we believe that biomimetics in the nanodomain will succeed. Nature indeed has worked much longer on arriving at a biological cell than it did at making birds, trees or humans: nature excels at engineering in the nanodomain. While top-down manufacturing approaches will continue to prevail over the next two decades we will start seeing hybrid solutions, such as the use of flexible materials (e.g., hydrogels) rather than stiff building materials (e.g., steel and Si). There will be more emphasis on non-Si . modular and “beyond batch” techniques such as pick and place, drop delivery, lamination , etc. The next big breakthrough will be continuous manufacturing, perhaps rendered possible through molecular self-assembly (continuous fabrication rather than batch fabrication!).

January 14, 2003

Mokoto Fujita
University of Tokyo
Nano-Manipulation Through Molecular Self-Assembly

In this lecture, we will show the principle and the power of self-assembly for nanoscopic manipulation of molecular components. In contrast to physical manipulation of molecules that requires molecule-by-molecule operation, the chemical manipulation through molecular self-assembly is furnished by the spontaneous organization of components themselves into well-defined functional systems quite efficiently even in a mol-scale. We will show that the simple combination of metals and organic molecules induces the spontaneous, quantitative formation of highly ordered, nano-sized organic frameworks such as macrocycles, cages, capsules, tubes, and interlocked molecules.


(1) A nanometre-sized hexahedral coordination capsule assembled from 24 components N. Takeda, K. Umemoto, K.Yamaguchi, M. Fujita

(2) Spontaneous assembling of ten small components into a three-dimensionally interlocked compound consisting of the same two cage frameworks M. Fujita, N. Fujita, K. Ogura, K. Yamaguchi, Nature, 400, 52 (1999).
January 07, 2003

Ned Seeman
New York University
Structural DNA Nanotechnology

DNA nanotechnology uses reciprocal exchange between DNA double helices or hairpins to produce branched DNA motifs or related structures, such as double crossover (DX), triple crossover (TX), paranemic crossover (PX) and parallelogram motifs. We combine DNA motifs to produce specific structures by using sticky-ended cohesion, or, more recently, forms of paranemic and edge-sharing cohesion. From simple branched junctions, we have constructed DNA stick-polyhedra, knots and Borromean rings. We have used two DX molecules to construct a DNA nanomechanical device by linking them with a segment that can be switched between left-handed Z-DNA with right-handed B-DNA. PX DNA has been used to produce a robust sequence-dependent device; sequence-dependent devices can provide the diversity of structures necessary for nanorobotics.

A central goal of DNA nanotechnology is the self-assembly of periodic matter. We have constructed micron-sized 2-dimensional DNA arrays from DX, TX and parallelogram motifs. We can produce specific designed patterns visible in the AFM from DX and TX molecules. We can change the patterns by changing the components, and by modification after assembly. In addition, we have generated 2D arrays from DNA parallelograms. These arrays contain cavities whose sizes can be tuned by design. In studies complementary to specific periodic self-assembly, we have performed algorithmic constructions, corresponding to XOR operations.


N.C. Seeman, DNA Engineering and its Application to Nanotechnology, Trends in Biotechnology 17, 437-443 (1999).

H. Yan, X. Zhang, Z. Shen and N.C. Seeman, A Robust DNA Mechanical Device Controlled by Hybridization Topology, Nature 415, 62-65 (2002).