NSF Annual Report
CCR-0122419
2004

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Activities and Findings


  1. Describe the major research and education activities of the project.

    The Center for Bits and Atoms is studying two core complementary questions: how can a logical description be embodied in, and abstracted from, a physical form? These are old questions, dating back to the origins of modern manufacturing, and before that to the birth of the natural sciences, but they are profoundly changed by the recognition of the computational universality of nature.

    CBA comprises 15 research groups from across MIT's campus, including physicists, chemists, biologists, mathematicians, computer scientists, and electrical and mechanical engineers. All are working at the boundary between logical and physical descriptions of information, an essential interface that has historically been divided between hardware and software, and between physical science and computer science. Their work is supported by a unique experimental resource enabling input and output across these discipline boundaries, from nanometers to meters.

    A focal event over the last year was a workshop CBA hosted on "Avogadro-Scale Engineering", gathering collaborators on campus and from around the world to explore the need for, and prospects for, engineering practice in a limit of thermodynamic complexity. Two key ideas from this meeting are at the heart of CBA's research program:
    • Form: the use of error-correcting tools to assemble perfect systems from imperfect components. This promises to have the same impact on fabrication as digital threshold theorems have had on communications and computation.
    • Function: the use of physical realizations of mathematical programs as an architecture for organizing physical resources to solve computational problems, from devices to circuits to systems.
    These are connected by investigation of transduction at the interface between physical form and logical function.

    CBA's activities are complemented on-campus by a growing sequence of classes providing training in these interdisciplinary technical research areas, and collaborations on applications of CBA's infrastructure. Beyond MIT, CBA is deploying a network of field "fab labs" around the world, providing access in non-traditional communities to prototype tools for personal fabrication. And CBA's research is transferred to industry through joint development projects, including the Internet 0 (I0) initiative.

  2. Describe the major findings resulting from these activities.

    A central focus that emerged over the last year is the role of error correction in fabrication. Macroscopically, this was studied through the development of mechanical and electromechanical finite-state machines for programmed assembly:

    [Griffith, 2004]. These have been used to demonstrate linear extrusion of a space-filling curve, mechanical assembly of a self-reproducing string, and error-corrected growth of a crystal:

        

    (images linked to videos).

    There are CBA projects seeking comparable control over programmed assembly across the range of systems and length scales represented. At molecular scales, new materials are being developed based on molecular self-assembly [Zhang, 2003], and error-corrected assembly is being applied to de novo fabrication of large DNA molecules with a goal of being able to synthesize an entire genome. In support of this a "green screen" GFP assay was developed to quantitate successful gene syntheses through simple colony counts:



    This rapid metric has already enabled the improvement of gene synthesis protocols to reach an error rate of 0.001 per base synthesized. While this is better than anything in the current literature, ongoing work is investigating error-correcting enzymes and genetic circuits for asymptotic scaling [Carr, to be published].

    To provide external control over molecular function, an earlier report described a CBA project functionalizing proteins with nanocrystal antennas to electromagnetically control their conformation [Hamad-Schifferli et al., 2002; Hamad-Schifferli, 2004]. Because this mechanism is poorly understood, self-assembled monolayers on gold nanoparticles have been used to adsorb DNA oligonucleotides in a radial configuration in order to monitor the local heat distribution. A change was observed in the hydrodynamic radius through analysis of gel electrophoresis following treatment with mercaptohexanol (MCH) [Park, 2004].

    Reversing roles, instead of using a nanoparticle to control a protein, L-lysine (Lys) monofunctionalized gold nanoparticles were synthesized by a solid-phase reaction using 4-hydroxymethylphenoxyacetyl (HMPA) -- polyethylene glycolacrylamide copolymer (PEGA) resin:



    [Sung et al., 2004]. This allows the assembly of functional nanoparticles to be coded for by the attached ligand. The monofunctionalization was confirmed by HRTEM observation of dimerization of the nanoparticles:


    For larger-scale patterning of functional nanoparticles to assemble active systems, earlier work reported used CBA's beam tools to direct-write nanostructures [Griffith et al., 2002]. This year, an offset liquid embossing process was developed for printing three-dimensional structures with nanoparticles:



    [Wilhelm and Jacobson, 2004]. This process was used to fabricate an array of electrostatically-actuated mirrors, imaged here with CBA's confocal microscope and linked to a video taken with its ESEM:



    A printing process was also developed for patterning networks of neurons and glia cells:


    [Fuller, 2003].

    Finally, on the largest length scales, geometries were developed to encode the global structure of a building in the local constraints of it components, shown assembling a dome:



    [Seely and Sass, to be pubished]. The state of the art in modern architecture uses NC tools in fabrication but still relies on conventional blueprints for construction; this approach promises to extend the computational description of a design all the way from conception to construction.

    Taken together, the preceeding results provide a framework for the development of a "logical" manufacturing practice that builds with intelligence that is internal to the materials rather than contained in an external controller. The second broad area of CBA activities is exploring mechanisms and architectural principles to organize such materials to solve problems.

    Two projects considered electromagnetic properties. The first, reported last year, constructed an artificial "metamaterial" with a negative index of refraction [Houck et al., 2003]. This was picked by Science magazine as one of the top 10 scientific highlights of 2003. This year, the internal and external foci predicted for a rectangule slab of a negative index material were observed:



    [Brock, Houck, and Chuang, to be published]. And the second project used CBA's laser micromachining tool to create a slot antenna in a microstripline:



    [Maguire, 2004]. This creates an impedance-matched discontinuity locally converting RF energy to a strong homogeneous magnetic field, and has shown the best reported sensitivity for a planar spin-resonance probe. Here is a two-dimensional spectra obtained from a picomolar sample of an acetyl-amide peptide:

    This project grew out of CBA research seeking to improve the scaling of molecular quantum computing, but is likely to have significant implications for molecular biology by making structural measurements possible on much smaller samples. Another spinoff from that effort comes from the pulse sequences that have been developed for experiments such as last year's report of the first implementation of an adiabatic algorithm [Steffen et al., 2003]. These composite pulses have been found to be much more broadly applicable in controlling coherent quantum information, including restricting a three-level Josephson junction to a two-dimensional qubit Hilbert space [Steffen, Martinis, and Chuang, 2003].

    CBA's program for providing macroscopic molecular interfaces has progressed with the development of two new MEMS structures. Last year we reported electronic readout of DNA hybridization with single-base selectivity [Fritz et al., 2002]. This year, a suspended microchannel resonant mass sensor was developed for specific biomolecular detection in a sub-nanoliter fluid volume. This measures shifts in the resonance frequency of a suspended microfluidic channel upon accumulation of molecules on the inside walls of the device, enabling direct integration with conventional microfluidic systems, significantly increasing sensitivity by reducing ambient damping and viscous drag, and allowing the resonator to be actuated by electrostatic forces. This mechanism has been demonstrated by measuring the specific binding between avidin and biotinylated Bovine Serum Albumin (bBSA):


    [Burg and Manalis, 2003; Shusteff, 2003; Levy-Tzedek, 2004]. These measurements are expected to reach changes in surface mass loading order of 10-19 g/um2. A related result builds on last year's report of peptide nanotubes [Santoso et al., 2002], to design peptide surfactant detergents that can solubilize, stabilize and crystallize membrane proteins:


    [Yang, 2004]. Because all 5 of our senses are based on membrane proteins, this significantly enlarges the class of candidate molecular sensors. And for controlling fluids at molecular scales, a capacitative readout was developed for a flexural valve with nanometer displacement and resolution:

    [Ma et al., 2003 (won a student paper award)].

    The digital interface to analog electrical signals was improved by the development of an A/D converter using a new successive approximation algorithm for temporal rather than voltage or current degrees of freedom. This has a conversion time that grows linearly with the precision of the converter, and is expected to scale to sub-uW power consumption:



    [Heemin and Sarpeshkar, to be published]. Along with the analog storage cell reported last year [O'Halloran and R. Sarpeshkar, 2004], this is part of a growing family of mixed-signal components using continuous device degrees of freedom. Two theses in the last year explored circuit architectures for such devices. One grew out of the study of fault tolerance in quantum computation, finding that classical fault-tolerant constructions can improve the reliability and efficiency of conventional circuits as they approach fundamental scaling limits [Impens, 2004]. And a second applied message-passing algorithms to circuit design, rolling up a state estimation trellis to obtain a "Noise-Locked Loop" that acquires a spread-spectrum code using an analog logic representation of bit probabilities:


    [Vigoda, 2003]. The messages passed in this circuit can be understood as dynamically solving a mathematical program; current work is extending this insight to organize large-scale distributed systems. CBA support contributed to the development of a prototype 1000 node "paintable" computer that is programmed by propagating mobile code:



    [W. Butera, to be published].

    The relationship between physical dynamics and algorithm dynamics is also being explored in the context of mechanical control; a passive dynamical walker was developed that is controlled by an onboard online reinforcement learning algorithm:



    [Tedrake et al., 2004], and a synthetic skin is being developed as a distributed physical interface [Stiehl et al., 2004].

  3. Describe the opportunities for training and development provided by your project.

    CBA has directly supported about 50 students and indirectly contributed to about 150 students, working with a unique experimental resource developed to provide input and output across 9 orders of magnitude:


    A popular rapid-prototyping class was developed to provide instruction in its integrated use, MAS.863: How To Make (almost) Anything. This has led to student research projects such as the production of photonic band-gap materials:



    [J. Walish, to be published].

    Rapid-prototyping of microstructures is being taught in 6.151: Semiconductor Devices Project Laboratory. The class project this year made a significant research contribution in developing a microfluidic device with integrated DNA amplification and detection:



    Hands-on training in quantum computing is provided by a project developed for
    8.13: Experimental Physics:


    Other classes that CBA has directly or indirectly contributed to include:

       4.206: Introduction to Computing
       4.212: Design Fabrication
       4.173: Design Fabrication Workshop
       6.971: Engineering Simple Biological Systems
       7.86, BE.481, MAS.866: Fundamental Limits of Biological Measurement
       8.371J, MAS.865J: Quantum Information Science
       BE.442: Molecular Structure of Biological Materials
       MAS.862: The Physics of Information Technology
       MAS.864: The Nature of Mathematical Modeling
       MAS.961: How To Make Something That Makes (almost) Anything

  4. Describe outreach activities your project has undertaken.

     The focus of CBA's outreach activities has been its field "fab lab" program. This is bringing prototype versions of the on-campus infrastructure beyond campus, to explore their implications and applications in non-traditional communities. Capabilities currently being deployed include laser cutting of three-dimensional structures, sign cutting of interconnect and electromagnetics, precision machining of circuit boards, and programming of embedded RISC microcontroller signal chains. Together, these provide access to engineering in space and time down to microns and microseconds. Fab labs have been opened so far in inner-city Boston, rural India, northern Norway, Costa Rica, and Ghana:



    (here an 11-year-old girl is successfully learning to stuff a surface-mount circuit board in the Boston lab). Emerging lessons from the fab lab project include the recognition that beyond the digital divide there are instrumentation and fabrication divides, and that these can be addressed by bringing IT development rather than just IT to the masses. These themes are being explored with a growing group of institutional partners including the National Academies, the Indian Department of Science and Technology, and the Africa-America Institute. A related project to produce eyeglasses in the field led to a CBA-funded student, Saul Griffith, winning the Lemelson Foundation Student Prize for inventiveness:


    CBA is participating in a number of joint development projects with industry for technology transfer; one with broad economic and social implications is the "Internet 0" (I0) effort. This grew out of the need to develop embedded IP processors for interfacing distributed devices:



    and led to the recognition that for low data-rate devices a near-field time-domain encoding can be used that is the same across physical transports:


    This picture of an I0 packet looks the same whether it is scanned optically, capacitatively coupled through a powerline, clicked acoustically, or sent electromagnetically. Just as the IP protocol first enabled internetworking across heterogeneous networks, I0 is extending that insight to "interdevice internetworking" as an alternative to the proliferation of standards for different devices [Gershenfeld et al., 2004]. An industry initiative is developing around this project, driven by embedded networking applications including construction and energy efficiency, healthcare monitoring, and distributed user interfaces. Current development work is building on related CBA activities including the use of physical mechanisms for security [Pappu et al., 2002], and study of scaling and heterogeneity in large-scale networks [K. Sollins, to be published].

Publications and Products
  1. What have you published as a result of this work?

    Journal publications

    T. Burg and S.R. Manalis, Suspended microchannel resonators for biomolecular detection, Applied Physics Letters (83), 2698 (2003)

    J. Fritz, E.B. Cooper, S. Gaudet, P.K. Sorger, and S.R. Manalis, Electronic detection of DNA by its intrinsic molecular charge, Proceedings of the National Academy of Sciences (99), 14142-14146 (2002)

    N. Gershenfeld, R. Krikorian, and D. Cohen, Internet 0: Interdevice Internetworking, Scientific American, to appear (2004)

    Saul Griffith, Mark Mondol, David S. Kong, and Joseph M. Jacobson, Nanostructure fabrication by direct electron-beam writing of nanoparticles, J. Vac. Sci. Technol. (B 20), 2768-2772 (2002)

    A.A. Houck, J.B. Brock, I.L. Chuang, Experimental Observations of a Left-Handed Material That Obeys Snell's Law, Phys. Rev. Lett. (90), 137401/1-4 (2003)

    K. Hamad-Schifferli, J.J. Schwartz, A.T. Santos, S.G. Zhang, and J.M. Jacobson, Remote Electronic Control of DNA Hybridization Through Inductive Coupling to an Attached Metal Nanocrystal Antenna, Nature (415), 152-155, (2002)

    Ma, H., White, J., Paradiso, J., and Slocum, A., Sub-nanometer Displacement Sensing for the Nanogate, In the Proceedings of the 2003 IEEE International Conference on Sensors, October 21-24, Toronto Canada, pp. 46-51 (2003)

    M. O'Halloran and R. Sarpeshkar, A 10nW 12-bit Accurate Analog Storage Cell with 10aA Leakage, IEEE Journal of Solid State Circuits, to appear (2004)

    R. Pappu, B. Recht, J. Taylor, N. Gershenfeld Physical One-Way Functions, Science (297), 2026-2030 (2002)

    S. Santoso, W. Hwang, H. Hartman, S. Zhang, Self-Assembly of Surfactant-Like Peptides with Variable Glycine Tails to Form Nanotubes and Nanovesicles, NanoLetters (2), 687-691 (2002)

    M. Steffen, J. Martinis, I. Chuang, Accurate control of Josephson phase qubits, Physical Review B, vol 68, num 224518/1-9, 2003

    M. Steffen, W. van Dam, T. Hogg, G. Breyta, and I. Chuang, Experimental Implementation of an Adiabatic Quantum Optimization Algorithm, Phys. Rev. Lett. (90), 067903/1-4 (2003)

    Kie-Moon Sung, David W. Mosley, Beau R. Peelle, Shuguang Zhang, and Joseph M. Jacobson, Synthesis of Monofunctionalized Gold Nanoparticles by Fmoc Solid-Phase Reactions, J. Am. Chem. Soc (126), 5064-5065 (2004)

    Russ Tedrake, Teresa Weirui Zhang, Ming-fai Fong, and H. Sebastian Seung, Actuating a Simple 3D Passive Dynamic Walker, IEEE International Conference on Robotics and Automation (ICRA 2004)

    David W. Mosley, Mark A. Sellmyer, Erin J. Daida, and Joseph M. Jacobson., Polymerization of Diacetylenes by Hydrogen Bond Templated Adlayer, Formation, J. Amer. Chem. Soc. (125), 10532-33 (2003)

    Eric J. Wilhelm and Joseph M. Jacobson, Direct printing of nanoparticles and spin-on-glasses by offset liquid embossing, Appl. Phys. Lett. (84), 3507 (2004)

    Zhang, S., Fabrication of novel materials through molecular self-assembly, Nature Biotechnology (21), 1171-1178 (2003)


    Books or other non-periodical, one-time publications

    S.B. Fuller, A Fast Flexible Ink-Jet Printing Method for Patterning Networks of Neurons in Culture, M.S. thesis, MIT (2003)

    Saul Griffith, Growing Machines, Ph.D. thesis, MIT (2004)

    K. Hamad-Schifferli, DNA Hybridization, Electronic Control, in Encyclopedia of Nanoscience and Nanotechnology, edited by J. A. Schwarz, C. Contescu and K. Putyera (Marcel Dekker, New York, 2004).

    F. Impens, Fine-Grained Fault-Tolerance: Reliability as a Fungible Resource, M.S. thesis, MIT (2004)

    S. Levy-Tzedek, Biological Detection by means of Mass Reduction in a Suspended Microchannel Resonator, M.S. thesis, MIT (2004)

    Yael Maguire, Scalable Electromagnetic Microstructure Instrumentation, Ph.D. thesis, MIT (2004)

    Sunho Park, Control of Oligonucleotide Conformation on Nanoparticle Surfaces for Nanoscale Heat Transfer Study, M.S. thesis, MIT (2004).

    Maxim Shusteff, A Microfabricated Hollow Cantilever Sensor for Sub-nanoliter Thermal Measurements, M.S. thesis, MIT (2003).

    W.D. Stiehl, L. Lalla, and C. Breazeal, A Somatic Alphabet Approach to Sensitive Skin, Proceedings of the ICRA (2004)

    Kie-Moon Sung, David W. Mosley, Beau R. Peelle, Shuguang Zhang and Joseph M. Jacobson, Nanopearls: A New Synthetic Approach Towards Creating Monofunctionalized Building Blocks for Programmable Biochemical Nanocrystal Linear Sequences, in Proceedings Foundations of Nanoscience, Snowbird, UT, April 21-23, p. 105 (2004).

    B. Vigoda, Analog Logic: Continuous-Time Analog Circuits for Statistical Signal Processing, Ph.D. thesis, MIT (2003)

    Steve Yang, Self-Assembly of Surfactant-like Amphiphilic Peptides made of Natural Amino Acids, Ph.D. thesis, MIT (2004)

    Oren Zuckerman, System Blocks: Learning about Dynamic Behavior through Hands-on Modeling and Simulation, M.S. thesis, MIT (2004)

  2. What Web site or other Internet site have you created?

    The primary CBA site is http://cba.mit.edu, containing archives of publications and videos from events including the weekly Colloquia, http://cba.mit.edu/presentations/, and the Avogadro-Scale Engineering meeting, http://cba.mit.edu/events/03.11.ASE/. CBA's fab classes and fab labs on and off of campus are run from http://fab.cba.mit.edu. CBA has also helped support http://www.thinkcycle.org for open collaborative design.

  3. What other specific products (databases, physical collections, educational aids, software, instruments, or the like) have you developed?

    CBA's progress both at MIT and in the field fab labs has been constrained by the limitations of available CAM software, including restrictive assumptions about possible workflows, unreliable algorithms, steep learning curves, and expensive licenses. This led to the development of a single CAM environment to connect all of CBA's tools, cam.py:



    It can currently read 2D DXF and SVG drawings, 3D DXF shapes, JPG and TIFF images, Gerber PCBs, and Excellon drill holes, and can write G codes and RML for NC machining, EPI and UNI for laser cutting, ORD for waterjet cutting, CAMM for knife cutting, and JPG for beam rasters, with more formats being added.

    A second limitation has been the need for collaborative Web site development across the field fab labs in order to share projects, instructions, and files. For this a site authoring tool was written, site.py:



    that exposes a command shell within a Web page.

    For teaching kids about core concepts in systems dynamics, "System Blocks" were developed that let dynamic systems be assembled from computationally-enhanced blocks:



    [Zuckerman, 2004].