DNA integrated circuit/proposal import 2007

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A DNA integrated circuit is a integrated circuit semiconductor system incorporating or interacting with deoxyribonucleic acids or other molecules. The interaction of molecules with the IC system may be due to the adsorption of the molecules on the IC, or the electromagnetic or mechanical interaction of the IC with molecules.

Depending on the attachment methodology, the molecules incorporated into a dIC may be other than deoxyribonucleic acid.

25142.070113235749.djvu

proposes one way to attach molecules to CMOS integrated circuits.

\title{Aluminum Anodization for DNA Integrated Circuits}

\textbf{Proposal in response to DARPA BAA04-12}

\begin{flushleft} \textbf{Title:} Aluminum Anodization for DNA Integrated Circuits\\ \textbf{Technical area:} New Materials, Materials Concepts, Materials Processing and Devices (Smart Materials) \\

\begin{large} Executive Summary \end{large} \end{center}

\bigskip


Published research has indicated that DNA molecules can be adsorbed on the surface of aluminum electrodes in an electrochemical reaction. Exploitation of this phenomenon with aluminum structures in standard integrated circuits may enable fundamentally new microscale and nanoscale systems for the warfighter and other integrated circuit users. This proposal outlines an effort, highly focused on deliverables and commercial relevance, to demonstrate and characterize this process using a CMOS microsystem, to be fabricated using the MOSIS service, and low-cost DNA printing equipment.


\pagebreak


\section{Introduction}

Molecular self-assembly is increasingly viewed as a critical enabling technology for the development of nanosystems expected to provide significant new capabilities for the Department of Defense and the individual warfighter. The pervasive use of integrated circuit technology in current-day DoD operations, and in society at large, provides motivation for the fullest possible exploitation of standard IC processes for the development of molecular self-assembly and molecular nanotechnology in general. Specifically, this preeminence of IC technology, and complementary metal-oxide-semiconductor ICs in particular, justifies a detailed characterization and thorough understanding of molecular adsorption processes on materials present in CMOS integrated circuits, as molecular adsorption on solid surfaces is a fundamental process in the integration of molecules and molecular systems with solid-state technology.

Aluminum alloy is the primary material used to conduct electricity in CMOS integrated circuits. It is well known that aluminum can be coated with an oxide film, in an electrochemical process called anodization, to alter its appearance or mechanical properties, although this coating is usually performed on macroscopic aluminum objects. From the standpoint of micro- and nanofabrication, the anodic aluminum oxide film itself has been the primary focus of contemporary research, as it forms an ordered nanoporous structure under a wide range of processing conditions\cite{osaka98,gosele98}.

When aluminum is anodized in an aqueous solution containing acids such as phosphoric, sulfuric, or carboxylic acid, the molecular acids are incorporated into the film, forming an electrochemical bond with the oxidized aluminum atoms. This incorporation of molecules present in the anodizing bath is key to the modification of the appearance, and other properties, of anodized aluminum. While anodization of aluminum by small-molecule acids is a routine process, the use of macromolecular acids for aluminum anodization is largely unexplored.

Deoxyribonucleic acid is perhaps the most important example of a macromolecular acid. In the course of experiments on the manipulation of DNA molecules by time-varying electric fields generated by aluminum microelectrodes, one group has demonstrated DNA adsorption on aluminum\cite{washizu99b}. Their research has provided support for the hypothesis that, by applying a voltage to an aluminum microelectrode, one end of a DNA molecule can be anchored to the aluminum surface, with the other end extending from the surface. Despite the fact that this research has largely been ignored in the years since it was first published, it is best perceived as a tantalizing glimpse of opportunity.

The unique molecular properties of DNA, in addition to its obvious ubiquity, make DNA molecules a natural component of molecular self-assembly processes. The incorporation of DNA molecules into CMOS integrated circuits, using aluminum anodization, potentially presents the opportunity to use standard IC technology as the foundation for complex self-assembled nanosystems.

In the following, we propose an effort to characterize DNA adsorption on aluminum microelectrodes. The proposed research is focused on the design, fabrication, operation, and physical analysis of a CMOS microsystem for performing anodization and controlling hybridization with microelectrode arrays.

After a more detailed description of the evidence for DNA adsorption on aluminum, we provide further motivation for the proposed research by describing several potential applications of DNA hybridization on standard integrated circuits. This is followed by a description of the CMOS microsystem to be created for the performance of the proposed research, along with a description of the fluidic system necessary for performing electrochemical processing, using DNA solutions, on the surface of the proposed CMOS microsystem. The goals for the research, along with some of the accompanying risks, are presented, and a timeline for performance of the research is outlined. We conclude with a description of the resources, human and material, to be devoted to the proposed research.

\section{Prior Work and Future Possibilities}

\subsection{DNA manipulation by Al microelectrodes}

One early effort to manipulate cells and molecules using microfabricated electrodes\cite{washizu90}, called the fluidic integrated circuit by its creators, used aluminum evaporated onto glass and patterned to form electrodes, which created an electric field when a voltage was applied to the opposing electrodes (see Figure \ref{early_electrodes}). In the presence of a spatially nonuniform electric field, polarizable cells and molecules experience a force in the direction of increasing electric field magnitude, a phenomenon called dielectrophoresis\cite{pohl78}. During experiments to characterize the response of DNA molecules, 48.5kbp (kilo base pairs) in length, to intense (approximately 1MV/m) AC (1MHz) electric fields\cite{washizu94,washizu95}, it was discovered that DNA molecules, which have a random coil conformation in solution, are stretched straight along the field lines. It was also observed that the stretched DNA molecules rapidly migrated to the region of highest field strength by dielectrophoresis, until one end of the stretched molecule contacted the surface of the aluminum electrode. Using fluorescent DNA labels, it was determined that, while one end was anchored at the surface of the electrode, the rest of the molecule extended into the solution. Later investigations used atomic force microscopy to confirm that DNA molecules were adsorbed on the surface of the electrodes\cite{washizu99a}.

\begin{figure}[h] \begin{center}

\includegraphics{early_electrodes.eps}

\end{center} \caption{Early demonstration of DNA-aluminum adsorption: Aluminum

 electrodes evaporated onto a glass cover slip, with an interelectrode
 spacing of 80 microns.  When a 1MHz AC voltage is applied to the
 electrodes to create an electric field of approximately 1MV/m, DNA
 molecules (solid lines between electrodes) rapidly migrate to the
 highest-field region and attach to the electrode surfaces. }

\label{early_electrodes} \end{figure}


While these investigations were important in understanding the interaction of DNA with aluminum, they did not address several questions relevant to the practical application of DNA adsorption on aluminum. Specifically: \begin{itemize} \item{how does the process depend on the applied voltage and

 frequency?  In previous studies, a peak-to-peak voltage of 80V was
 applied to electrodes spaced 80$\mu$m apart, for an electric field
 of 1MV/m.  Not addressed was the effect of smaller electrode
 separation or smaller applied voltage.  Similarly, the applied
 frequency was 1MHz for all of the experiments performed.  The effect
 on adsorption of varying the electric field frequency was not
 addressed.}

\item{how does the process depend on the length of DNA molecule used?

 The only molecule used for these studies was $\lambda$-phage DNA,
 with a length of 48.5 kbp.  Many applications use DNA molecules
 significantly smaller than this, such as cDNA microarrays in which
 the molecular lengths are on the order of several thousand bp or
 fewer, and oligonucleotide arrays which are on the order of tens of
 base pairs.  Previous studies of thiolated DNA adsorption on
 gold\cite{tarlov2000} have shown that surface coverage is affected
 by DNA sequence length.}

\item{what is the long-term stability of adsorbed DNA on aluminum?

 The long-term stability of aluminum interconnect in integrated
 circuits is an important concern\cite{dunn92}, and device
 applications of DNA adsorption must address this issue.}

\item{what is the microstructure of the interaction between the

 adsorbed DNA molecules and the aluminum surface?}

\end{itemize}


\subsection{Future Possibilities} \label{fantasies}

An obvious application for adsorbed DNA molecules on the surface of an integrated circuit is micropositioning of objects for heterogeneous integration\cite{heller98}. In this process, a surface used as the platform for integration has single stranded DNA molecules adsorbed at one or more locations, and the objects to be placed on the surface have complementary single stranded DNA molecules attached. By controlling the placement and sequence of DNA molecules on the surface and on the objects to be placed, it is possible to use the hybridization of complementary DNA molecules to self-assemble the components into the desired finished product.

One of the most important applications of heterogeneous integration is the Smart Dust project\cite{pister01}. Smart Dust motes are projected to be systems, on the order of 1 cubic millimeter in size, with self-contained sensing, computation, and communication capabilities. A key component of Smart Dust systems is CMOS integrated circuits, along with microfabricated optical and mechanical components. The use of DNA-based self-assembly to manufacture Smart Dust motes may contribute to large-scale, low-cost production processes that enable Smart Dust to reach its full potential. The economical incorporation of DNA-based systems for biological assays also may enable new applications for detection of environmental pathogens by Smart Dust motes.

Another important phenomenon that may be demonstrated with DNA adsorbed to aluminum is electronic control of DNA hybridization\cite{heller97pnas,heller97nar}. This process, illustrated in Figure \ref{electronic_dna_hybridization}, occurs when a double stranded DNA molecule is exposed to an electric field and a single strand of the molecule is attached to a surface (generally the surface of the electrode generating the electric field). By controlling the applied electric field, the single stranded DNA not adsorbed to the surface can be dissociated from the complementary adsorbed ssDNA. The magnitude of the electric field necessary to cause two ssDNA molecules to dissociate can also indicate whether there are base pair mismatches between the molecules, a fact that is relevant to the diagnosis of genetic disorders.

\begin{figure}[h] \begin{center}

\includegraphics{electronic_dna_hybridization.eps}

\end{center} \caption{Electronic control of DNA hybridization: (\textbf{A})

 Complementary single-stranded DNA molecules form a double-stranded
 DNA molecule, with one of the strands adsorbed on the surface of an
 electrode.  (\textbf{B}) By applying a voltage to the electrode, an
 electric field is created, which forces the negatively charged
 non-adsorbed ssDNA from the electrode.}

\label{electronic_dna_hybridization} \end{figure}


From the perspective of micro- and nanosystems, electronic control of DNA hybridization may enable the dynamic control of mechanical associations between discrete objects. One potential application is the mechanical association of multiple Smart Dust motes to form a microscale multiple independent reconnaissance vehicle system, or ``microMIRV (see Figure \ref{microMIRV}). The envisioned system could potentially take the form of a bullet, containing a three-dimensional arrangement of multiple Smart Dust motes, launched using standard propellants and rifles or pistols as launch systems. Firing a microMIRV skyward would deploy multiple Smart Dust motes, which would dissociate at the peak of the composite vehicle trajectory, for aerial surveillance, data networking, and other functions. Assuming that the economic trends of the microelectronics industry continue, several such systems may be available for use by any individual soldier, enabling even dismounted and isolated soldiers to have decisive battlefield awareness in a wide variety of scenarios.


\begin{figure}[h] \begin{center}

\includegraphics{microMIRV_sm.eps}

\end{center} \caption{Dynamic control of mechanical association between Smart Dust

 motes: (\textbf{A}) A cross-section view of several SD motes
 connected by hybridized complementary DNA molecules.  (\textbf{B})
 Using electronic signals, SD motes disrupt hybridization and
 dissociate.  }

\label{microMIRV} \end{figure}


\section{Research Plan}


The goal of the proposed research is the demonstration, characterization, and optimization of DNA adsorption on aluminum, in order to effectively utilize this phenomenon in DoD and commercial integrated circuit systems. In order to accomplish this, it may be necessary to conduct a large number of experiments with varying parameters (voltage, frequency, temperature, solution composition, etc.). Because the experiments, if successful, entail surface modifications to the aluminum microelectrodes to be used, it will be necessary to have a large number of the microelectrodes for one-time experiments and subsequent analysis.

The need for large numbers of test structures, and the imperative to apply this research to commercial systems, indicates that the use of CMOS technology to fabricate the microsystem, instead of custom microfabrication processes, is warranted. The feature sizes achievable with CMOS are smaller than those achievable by all but the most specialized and expensive custom microfabrication processes. The availability of active circuitry and transducers in CMOS processes creates the opportunity to integrate a wide variety of capabilities on the finished chip. As well, the use of foundry CMOS increases the relevance of the proposed research to contemporary integrated circuit manufacturing, enhancing the likelihood that this research will be adopted for use in DoD and commercial systems.

\subsection{CMOS microsystem}

For specific discussion of the CMOS process to be used, we refer to the Taiwan Semiconductor Manufacturing Corporation TSMC35\_P2 process\cite{tsmc35p2-www}, available from MOSIS. This process has two polysilicon layers and up to four metal layers available, with a minimum transistor length of .35 microns. In this process, chemical-mechanical planarization is used to create flat surfaces for deposition and patterning of thin film layers.

For the creation of the proposed microsystem, the fundamental structure is the aluminum microelectrode. In order to exploit the small feature size possible with CMOS fabrication, the exposed surface of the electrode is 1 micron square. Directly underneath the square electrode is a ``via, connecting the top layer of metal (metal-4) with the lower level of metal (metal-3). Sixteen microelectrodes are arranged on the perimeter of a square $9 \mu$m on each side to form an electrode array, with the individual microelectrodes separated by $.6 \mu$m (Figure \ref{electrode_array}). While there is generally a thick ``overglass layer present on the surface of a CMOS integrated circuit to protect the circuitry from mechanical damage, the need to have the microelectrodes exposed will require the overglass layer to be removed from the vicinity of the microelectrode array\cite{warneke2000}.

\begin{figure}[h] \begin{center} \includegraphics{electrode_array_cross_section_2.eps} \end{center} \caption{Diagram of the microelectrode array: (\textbf{A}) Plan view

 of microelectrode array, showing 1 $\mu$m square microelectrodes,
 with centered vias, arranged about the perimeter of a 9 micron
 square.  (\textbf{B}) A cross-section view from the dotted line in
 \textbf{A} with labeled dimensions.  A: 1$\mu$m wide metal-4.  B:
 .6$\mu$m interelectrode spacing.  C: .5$\mu$m via width.  D:
 .9$\mu$m metal-3 width.  E: .7$\mu$m separation between metal-3
 interconnect. }

\label{electrode_array} \end{figure}

Conceptually, the simplest scenario for performing anodization on the surface of this microelectrode array is, while the surface is exposed to an aqueous solution containing DNA molecules, to set 15 of the microelectrodes to the ground voltage, and set the microelectrode to be anodized (the so-called ``working electrode) at the positive supply voltage, referred to as $V_{DD}$. Given the variation of DNA dynamics with frequency in an AC electric field\cite{washizu90}, it may be necessary to cycle the working electrode between $V_{DD}$ and ground at an appropriate frequency. Controlling the voltages applied to the microelectrodes in the array can easily be accomplished with CMOS digital circuits incorporated into the microsystem.

Determining the $V_{DD}$ necessary for effecting anodization is a critical goal of the proposed research. The standard reduction potential for the conversion of Al to Al$^{3+}$ is -1.676V\cite{al-webelements-www}. This indicates that, in order to effect the electrochemical reaction of anodization, the applied interelectrode voltage must be greater than 1.676V. The magnitude of the necessary additional voltage is determined by the current flow in the solution, and the associated Ohmic voltage drop.

The most straightforward way to adjust the voltage used for anodization is to adjust $V_{DD}$. While the maximum voltage that can be used in this TSMC process with standard design techniques is 5.0V, and the preferable maximum voltage is 3.3V, it is possible to design circuits that will operate correctly at lower supply voltages. When electronically controlling DNA hybridization on the surface of the microsystem, it is important to avoid electrochemical reactions at the aluminum surface. Because scaling $V_{DD}$ is expected to be the most economical way to achieve low voltages for hybridization, the circuits used to control the microelectrode array will be engineered to function consistently at supply voltages between 1.0V and 3.3V. Achieving this objective will require low-voltage CMOS circuit design techniques\cite{piguet97} that are critical to the design of portable and power-sensitive systems for DoD and commercial customers.

The size of the microelectrode array, including the circuitry necessary to control an individual array, is anticipated to be less than (250$\mu$m)$^2$. This will make it possible to integrate a sizable number of microelectrode arrays in the CMOS microsystem, in an array-of-arrays system. To effectively utilize the arrayed microelectrodes, it will be necessary to integrate control circuitry into the microsystem to enable input signals to be directed to the appropriate microelectrode array for anodization or hybridization. To simplify this task, a hierarchical approach to system design will be taken. Specifications will be prepared outlining the performance requirements for the array-level circuitry, system control circuitry, and input/output circuitry, as well as the interfaces between each level. Proceeding from this system specification, the system will be designed and thoroughly simulated to ensure correct operation.

\subsection{Integrated processing system}

The CMOS microsystem is the primary platform for the proposed research, but it is only one component of the system necessary to perform anodization. Development of a system to coordinate microelectrode voltages with fluid deposition and removal will be essential to the success of the proposed research. At the same time, it is important to minimize the complexity of the processing system in order to successfully complete the initial research proposed here.

The deposition system needed for the proposed research has many features in common with systems for DNA microarray fabrication\cite{heller2002}. An important difference, however, is the requirement in this case to remove nonspecifically adsorbed DNA molecules before each deposition step. While it is not necessary to remove nonadsorbed DNA molecules if the goal is to simply demonstrate DNA adsorption on aluminum, for applications of this process it may be necessary to carefully control the DNA molecules present at each microelectrode.

Due to the vulnerability of the exposed microelectrodes to mechanical damage, only noncontact deposition methods are practical in this case. The most cost-effective deposition system in this case is likely to be an inkjet printing system, adapted to use solutions containing DNA molecules instead of conventional inks\cite{gonzalez2000,yamamoto2000}.

A long-term goal for the proposed system is to have a controllable number of DNA molecules of specific sequence on each microelectrode, fabricated in a process that is as rapid as possible. The objective of the current work will be the development of an economical system that balances the short-term need to quickly and inexpensively perform a large number of experiments with the anticipated long-term need for a specialized and powerful system for large-scale manufacturing.

\subsection{Microsystem physical analysis}

Atomic force microscopy is expected to be the primary tool for determining the effects of the electrochemical processes at the aluminum electrodes. Due to the extremely small size of the microelectrodes, other techniques for surface analysis, such as surface plasmon resonance and X-ray spectroscopy, are not likely to be applicable to the analysis of individual microelectrodes. Fluorescence microscopy will be used to analyze the hybridization of DNA molecules. Other optical techniques may be applicable to the study of the processed microsystem.


\section{Research Goals}

The overriding goal of the proposed research is the successful demonstration of electric field-directed DNA adsorption on the surface of a CMOS integrated circuit, and the characterization of this process. Several accomplishments will be necessary to achieve this goal: \begin{itemize} \item{design and fabrication of the CMOS microsystem.} \item{design of a fluidic system for deposition of DNA solution.} \item{development of supporting hardware and software to combine the microsystem and fluidic system into a computer-controlled integrated system.} \item{performance and analysis of anodization on the microsystem.} \item{performance and analysis of DNA hybridization control on the microsystem.} \end{itemize} A preliminary estimate of the project schedule is presented in Table 1.

\begin{table}[h] \begin{center} \begin{tabular}{|l|c|c|} \hline \hspace{20pt} Milestone & Work & Scheduled completion \\

&               (weeks)        & (weeks after project start)\\

\hline \textbf{Microsystem Design} & \textbf{11} & \textbf{11} \\ \hspace{4pt} Microsystem specification & 2 & 2 \\ \hspace{4pt} Microsystem implementation & 9 & 11 \\ \textbf{CMOS Fabrication} & \textbf{7} & \textbf{18} \\ \textbf{Processing System Development} & \textbf{13} & \textbf{15} \\ \hspace{4pt} Processing system specification & 3 & 5 \\ \hspace{4pt} Processing system implementation & 10 & 15 \\ \textbf{Microsystem Anodization} & \textbf{6} & \textbf{24} \\ \textbf{Microsystem Analysis} & \textbf{6} & \textbf{30} \\ \textbf{Electrically Controlled Hybridization} & \textbf{12} & \textbf{30} \\ \hline

\hline \end{tabular} \end{center} \label{schedule_table} \caption{Estimated project schedule.} \end{table}


It is anticipated that the bulk of the integrated circuit design for the CMOS microsystem will be performed by a subcontractor yet to be selected. Within two weeks (10 working days) of the project commencement, the primary contractor will prepare specifications for the CMOS microsystem. This specification will be used to direct the efforts of the subcontractor designing the CMOS integrated circuitry. It is expected that this design process, including verification, will take another 9 weeks. The milestone of CMOS design completion (``tapeout) is expected 11 weeks after the start of the project. The fabrication of the integrated circuit design is expected to take 6-7 weeks\cite{tsmc35p2-www}, for estimated delivery of the CMOS microsystems 18 weeks after project start.


Development of the processing system to be used to print DNA solutions onto the surface of the CMOS microsystem in coordination with electronic control of the arrayed microelectrodes, will also largely be conducted by a subcontractor yet to be selected. Beginning two weeks after the start of the project, specifications for the fluid processing system will be developed, to be finished within 3 weeks. Proceeding on the basis of this specification, the system to process the CMOS microsystem will be developed within 10 weeks, or 15 weeks after project start. Due to the potentially complex nature of the system, and the uncertain partition of effort between the primary contractor and the selected subcontractor, it is not possible at this time to further subdivide this effort into specific goals.

Once the CMOS fabrication is complete and the processing system has been designed and developed, experiments will be performed to demonstrate anodization on the surface of the CMOS microsystem. While it is expected that, given the extremely large number of microelectrodes on each of the 40 microsystems to be fabricated, there will be opportunities for experiments over an indefinite and extended period of time, the first processed microsystems will be prepared for analysis within 6 weeks, or approximately 24 weeks after project start. These processed microsystems will be analyzed by subcontractors providing materials analysis services, in order to characterize the modifications at the surface of the microsystems. The first results from the physical analysis of the anodized microelectrodes are expected to be available within 6 weeks of initial preparation, or 30 weeks after project start.

For experiments analyzing electrically controlled hybridization, it is anticipated, again, that the opportunities created by the CMOS microsystem will enable numerous experiments to be conducted. However, focused efforts to demonstrate controlled hybridization on the surface of the microelectrode arrays are expected to be successfully completed within 12 weeks after delivery of the CMOS microsystems, or 30 weeks after project start.

In addition to the specific goals listed, it is expected that monthly progress reports will be prepared, describing the project research activities and developments. A final report presenting the project research accomplishments will be prepared at the conclusion of the project, ten months after the start of the project. All information products of the research will be furnished to the Government with unlimited rights.

This schedule is relatively ambitious, and the overall time span of the proposed project relatively short. This proposal, while intended to open inquiry into a new system for materials research, is also intended to be focused as much as possible on short-term results for DoD and commercial customers. It is anticipated that, if the proposed research is successful, opportunities will be available for further research, with an emphasis on commercialization as soon as is practical.


%% milestones clearly and quantitatively described %% CMOS tapeout %% specifications %% interfaces between design levels %% array <--> control %% control <--> external inputs %% I/O for built-in self-test? %% outputs for on-chip sensors in future microsystems %% integrated processing system design / development %% first step toward future dnajet manufacturing systems? %% exploiting COTS inkjet systems for deposition %% subcontract for hardware integration %% clean room not necessary %% anodization demonstrated %% processing %% physical analysis %% electronic hybridization control demonstrated


%% specification, design, simulation, design, sim., etc.

%% %% Proposers must demonstrate that their proposal is innovative and %% %% unique, that the technical approach is sound, that they have an %% %% understanding of critical technical issues and risk and that they have %% %% a plan for mitigation of those risks. A significant improvement in %% %% capability or understanding above the state of the art must be %% %% demonstrated. All milestones must be clearly and quantitatively %% %% described.


%% goal / milestone breakdown

%% detailed understanding of array electrochemistry %% electric field simulation %% approximate calculation of necessary cell overpotential

%% cmos microsystem design %% array level %% AoA control system %% physical and logical simulation

\subsection{Risks and Their Mitigation}

The primary technical risk inherent in this proposal arises from the complex nature of the electrochemical environment in the vicinity of the aluminum microelectrodes. Due to the intense electric fields and accompanying ionic separation, extremely acidic and basic environments will be present in the anodizing solution during the operation of the microelectrode array. This may cause unwanted reactions, including etching of the aluminum or degradation of the DNA molecules. It is known that the buffer composition affects electronically-controlled hybridization at microfabricated electrodes\cite{heller97nar}, and the composition and pH of the buffer will be controlled to minimize unwanted effects and maximize anodization and hybridization efficiency.

The uncertainty in the schedule and cost estimates for design of the CMOS microsystem and the processing system introduce a certain amount of project risk. Systems for efficient collaboration between the prime contractor and subcontractors, as well as an emphasis on the use of commercial-off-the-shelf technologies and components, will be used to mitigate this risk, but a certain amount of risk in this area must be acknowledged.

\section{Facilities and Personnel}

In order to maximize the value provided to DoD, a ``virtual research laboratory strategy will be pursued to complete the proposed research. The team designing the CMOS microsystem will collaborate over the Internet, and, to the greatest extent possible, utilize open-source design tools for layout and simulation of the integrated circuit. Space and materials for operating the microsystem to anodize the microelectrodes will be procured on a ``just-in-time basis, so as to minimize overall expense and maximize flexibility. Materials analysis services will be procured by subcontract as necessary, most likely from university laboratories, with a focus on minimizing costs to DoD and maximizing research productivity.

It is expected that support from DoD for this proposal will be used to accomplish the necessary first steps in pursuing this unconventional research. Achieving the ambitious goals described above in \ref{fantasies} will require significant long-term contributions from the semiconductor industry, and it is anticipated that support from DoD will be used to leverage further efforts toward developing and commercializing integrated circuits incorporating DNA and other macromolecules.

The principal investigator for the proposed research is J. Patrick Bedell, the chief executive officer of DNAputer Research, Incorporated. In addition to a bachelor's degree in physics from the University of California at Santa Cruz, Mr. Bedell has an intense desire to contribute to the national security of the United States.


%% technical risks

%% standard CMOS voltage not sufficient for anodization %% utilize high-voltage CMOS structures - only if necessary %% solution conductivity / counterions / buffer

%% nonspecific adsorption %% control pH of deposited solution %% washing system


%% long-term stability of alumina film %% alumina is hygroscopic

\bibliography{dso_dic2003_proposal_technical}

\pagebreak


\begin{center} \begin{Large} \textbf{Cost Volume} \end{Large} \end{center}

\thispagestyle{empty} \begin{flushleft}

\textbf{BAA Number:} BAA04-12\\ \textbf{Technical area:} New Materials, Materials Concepts, Materials Processing and Devices (Smart Materials) \\ \textbf{Proposal title:} Aluminum Anodization for DNA Integrated Circuits \\

\textbf{Award instrument requested:} Cost contract - no fee.\\ \textbf{Places and periods of performance:} The United States in the years 2004-2005. \\ \textbf{Total proposed cost:} \$170000 \\

%% material cost elements %% dna printer customization %% processing system components %% reagents


%% subcontracts %% cmos design services %% dna printer development %% materials analysis %% use of facilities for performing processing / experiments

%% equipment purchase %% CMOS microsystem - TSMC, via MOSIS %% DNA printer - TBD



%% \$25000 for CMOS design %% \$25000 for CMOS fabrication %% \$25000 for DNA printing system %% \$10000 for necessary customization of DNA printing system %% \$10000 for experimental overhead

\begin{table}[h] \begin{center} \begin{tabular}{|c|c|} \hline Equipment purchases & \$65000 \\ Subcontracts & \$55000 \\ Direct labor & \$30000 \\ Materials & \$10000 \\ Overhead charges & \$10000 \\ \hline Total estimated cost & \$170000 \\ \hline \end{tabular} \end{center} \caption{Total estimated project cost.} \end{table}


\begin{table}[h] \begin{center} \begin{tabular}{|c|c|} \hline Equipment & Cost \\ \hline CMOS microsystems (40) & \$25000 \\ DNA printer & \$25000 \\ Computer workstation (inc. software) & \$5000 \\ Probe station & \$10000 \\ \hline Total equipment cost & \$65000\\ \hline \end{tabular} \end{center} \caption{Equipment purchases and estimated costs.} \end{table}

\begin{table}[h] \begin{center} \begin{tabular}{|c|c|} \hline Subcontract & Cost \\ \hline CMOS design verification & \$20000 \\ DNA printer customization & \$20000 \\ Materials analysis services & \$15000 \\ \hline Total subcontract cost & \$55000\\ \hline \end{tabular} \end{center} \caption{Subcontracts and estimated costs.} \end{table}

\pagebreak

\begin{table}[t] \begin{center} \begin{tabular}{|c|c|c|c|} \hline Employee & Hourly Wage & Hours & Total Cost \\ \hline John Smith & \$30.00 & 1000 & \$30000 \\ \hline Total cost & & & \$30000\\ \hline \end{tabular} \end{center} \caption{Direct labor costs.} \end{table}


The estimates presented here of project costs are preliminary, to say the least. It is hoped that, among other factors, cooperation between the DARPA program manager and the primary contractor will enable the project's goals to be achieved as economically as possible.


No existing or potential conflicts of interest are known to the offeror. The offeror has no existing contractual relationship with DARPA or any other unit of the US Government.

Today, we lack metrics

It is well known that molecules containing a thiol (-SH) group can form a self-assembled monolayer on gold surfaces, due to the interaction between the sulfur and the gold surface. This effect has been used with chemically modified DNA molecules to create DNA microarrays.


Controlling DNA hybridization with electric field generated by microelectrodes on the surface of a chip is a fundamental attraction of DNA adsorption on aluminum.


compare / contrast adsorption systems

 gold-thiol system (Figure)
 alumina less well-defined than SAMs 
 electric-field directed process provides for high spatial resolution
 economics of aluminum adsorption qualitatively different!
   unmodified DNA
   aluminum surface available in standard IC processes
   electrically-controlled hybridization possible on large scale with
  CMOS integration
 dna hybridization as component of micromechanical assembly systems
   precise positioning
   assembled microobject at bottom of potential well created by
  sequential dna hybridizations
   micro Fresnel lens as potential example 
 articulating relevance of DNA self-assembly to Smart Dust... long-term
   microMIRV
     

cmos microsystem for anodization / dna manipulation


primary feature of design is electrode array for anodization /

hybridization
 16 microelectrodes arranged around the perimeter of a square 
   why 16 electrodes?
     minimize size of array
   why perimeter?
     reduces dissimilarity of electrode configurations  
   why 1 square micron? want *small* electrodes, .9 micron the
  width to cover via in TSMC 2P4M


   1 square micron top-layer metal electrodes over via
   minimizing interelectrode capacitance
 temperature control using CMOS thermal elements

concept of operations for electrode array

 anodization
   pl volume of DNA solution deposited on array
   working electrode(s) cycled between VDD and GND at some frequency
   cathodes set at GND
   frequency determined by multiplexing, clock frequency, VDD
    magnitude
     DNA frequency-dependent conformation / orientation / dynamics
hybridization
controlled by electric field and temperature
demonstration of PCR on chip?
enzyme-friendly microenvironment?
pH variations due to electric field


control circuitry
per-array circuitry
single control input to array is demultiplexed to microelectrodes
electrode control circuitry must deal with electrochemical circuit
all ``analog functionality contained in array block
system control circuitry
address individual arrays
similar to load-only memory - no array sensors in first version


The central feature of the proposed microsystem is an electrode array (Figure \ref{electrode_array}). This array contains 16 microelectrodes arranged along the perimeter of a square $9 \mu$m on each side. The individual microelectrodes are composed of the top-layer metal in the CMOS process, and are $1 \mu$m square, with an interelectrode separation of $.6 \mu$m.

The two processes occurring at the electrode array are anodization of the exposed aluminum to form a film with adsorbed DNA molecules, and hybridization of DNA molecules complementary to the DNA molecules adsorbed on the anodized aluminum. To simplify the investigations proposed here, these processes initially should be considered and conducted separately.

The standard reduction potential for the conversion of Al to Al$^{3+}$ is -1.676V. This indicates that, in order to effect the electrochemical reaction of anodization, the applied interelectrode voltage must be greater than 1.676V.

current a function of applied voltage necessary voltage a function of current...

cmos voltage scaling allows for systematic variation in anodization voltage



The standard voltage for integrated circuitry in the selected process is 3.3V. While this voltage can be exceeded with careful design\cite{}, such nonstandard designs inevitably increase the development time and cost and should be avoided if possible.


The interelectrode current and the effective resistance of the solution through which the current flows determines, by Ohm's law $V = I R$, the overpotential necessary for the electrochemical reaction at the working electrode.


Conversely, if one wants to avoid electrochemical reactions at an aluminum electrode, the applied voltage must be less than 1.676V.

Accordingly, in the first phase of the research, anodization of the microelectrodes will be e


scaling VDD for anodization - analyze effects

 plurality of electrode arrays makes it possible to conduct numerous
  experiments with varied process parameters


scientific foundation for estimate of necessary anodization voltage?

 solution conductivity
   how does resistance scale with interelectrode distance - positive correlation
   back-of-the-envelope calculation for necessary cell overpotential


deposition system:

 must remove nonadsorbed dna molecules
 limited parallels to existing microarray deposition - removal of dna
  molecules also important in this case
 
 

technical concept of operations


clock to electrode array cycles input signal through set of microelectrodes

 inactive electrodes set at ground, active electrode(s) at VDD
 

how to provide voltages less than Al reduction potential using digital CMOS with a minimal transistor count? D/A for each electrode?

 preliminary answer: scale VDD for anodization vs. hybridization application
   voltage scaling for digital circuitry
     draws upon previous DARPA-funded research, relevant to smart dust
   1V for hybridization, more for anodization - how much more TBD

poly-Si heater


system-level diagram

 array of unit cells

unit cell

 16 microelectrode array
 polysilicon heater
 

how many pins?

 >100 pins easily available
 supporting board design, PC interface?
   USB-interfaced DNA chip? :)
     PC-interfaced personal DNA analysis / sequencing long-term goal
   initial systems must minimize complexity
   numerous ground, VDD pins


conops must include deposition system

 inkjet system
   control of droplet size, dna concentration, pH
   removal of excess fluid
    

metrology for ultramicroelectrodes?

 one or more orders of magnitude smaller than previous adsorption surfaces
 in-situ monitoring of anodization / hybridization
   labeled molecules for ellipsometry / fluorescence microscopy


GOALS

first CMOS implementation

 demonstration of DNA adsorption
 characterize process parameters for adsorption
 in-situ anodization metrology?
 hybridization control with electric field and integrated poly-Si heater

second CMOS system

 interelectrode hybridization
 hybridization-directed self-assembly

electric field simulation

DNA microdroplet deposition


RISKS

standard CMOS voltage not sufficient for anodization

 utilize high-voltage CMOS structures - only if necessary
 

nonspecific adsorption

 control pH of deposited solution
 washing system
 

long-term stability of alumina film

 alumina is hygroscopic
 


NOTES:

focus of microfabrication

 outsourced - foundry CMOS
   submicron metallization / structures (DD)
   micron-scale metallization
 university microfab facilities

advantages

 foundry CMOS 
   incorporate multiplexing circuits for anodization
   demonstrating / assessing anodization at CMOS voltages
 microlab - custom fab
   quicker turnaround time
   lower investment necessary 
   potentially lower cost

all-CMOS approach absolutely necessary for current proposal

 unconventional circumstances of proposer / proposal require that CMOS platform with minimal to high functionality be present
 all-CMOS guarantees relevance to contemporary fabrication processes
 only minimal voltage sources required + appropriate materials characterization facilities

materials characterization

 atomic force microscopy 
 ellipsometry (with refractive index label)
 FTIR microscopy?
 

CMOS circuits

 voltages for anodization
 interelectrode capacitance minimization
 detecting interelectrode hybridization
 compatibility of applying voltages for anodization and capacitance measurement
   MOSFET switches?


Much of the existing research on DNA adsorption on surfaces has been directed toward systems in which chemically modified DNA molecules form covalent bonds with the surface of interest. Perhaps most well-studied is the formation of self-assembled monolayers by thiolated molecules on gold (see Figure \ref{au_thiol_sam}).

To be cost-effective, these tools should be as automated as possible and be conducive to massive parallel processing.


alumina formation

 thin film amorphous solid
 porous alumina formation
 acid incorporation into alumina film
 long-term stability of alumina
 biocompatibility of alumina
 material analysis
   x-ray spectroscopy
   ellipsometry
   afm

dna adsorption on surfaces

 gold
 silicon
 silicon oxide
 mica

self-assembled monolayer formation

 alkylthiols on gold most studied system
 

the increased flexibility and economy afforded by use of technological progress


As we know, there are known knowns. There are things we know we know. We also know there are known unknowns. That is to say we know there are some things we do not know. But there are also unknown unknowns, the ones we don't know we don't know.

KK: cmos fabrication, dna structure

     KK the smallest group in this case? :)

KU: al microelectrochemistry, operation of deposition system, how to

 design IC system for anodization / hybridization, COSTS,
 organization of research effort

UU: unknown by definition, but likely to be interesting, useful, and difficult


In parallel with the development of the microsystem used for DNA adsorption is the development of a microfluidic system for deposition.

in order to make the system work, must address the complexity of the whole and not just idealize it as simply a microsystem design problem - failure is guaranteed if entire system not addressed as a whole

basic microfluidic operations -

 deposition
   inkjet - picoliter volumes necessary
     fantasy: on-line preparation of picodroplets containing homogeneous DNA
      solution from initial heterogeneous solution, i.e. cDNA
      isolation from PCR products - long-term, CEA one possibility
     initially, several inkjet wells sufficient
   dip pen risks mechanical damage to CMOS structures 
 removal
   simple milli-scale washing system sufficient initially 
   vacuum system
 solution hybridization 
   well-forming barrier on periphery of chip?  
   deposition of microliters of solution for hybridization
   not presently necessary to provide context for hybridization
    operations? 
 

Phase I microfluidic system

 inkjet printing with several wells (Canon bubblejet?)
   any COTS print head with buffered DNA solution?
 jury-rigged wash-in-place system compatible with circuitry
 hybridization performed in several microliters contained on surface
 of chip
 address cost of system - not necessarily high


Phase II microfluidic system

 current proposal not a microfluidics development proposal
 if it works, it's good enough!  


technology challenges for droplet deposition

 micropositioning - stationary surface or stationary print head?
 dna droplet physics - high viscosity for macromolecular solutions
   canon work indicates that at least 300bp molecules can be used in
  standard bubblejet systems
 time scale for specific anodization directly related to droplet
  size, positioning precision 


regardless of fluidic system design, microsystem can be specified

SIMPLIFY fluidic system not necessary for anodization demonstration fluidic system necessary for microarray production, product

manufacturing 

current proposal NOT a fluidic system development effort

several tens of microliters covering surface of chip for each

anodization step
 processing one electrode per array, all arrays at the same time, for
  each deposited solution
 16 deposition / removal steps
 noncontact processes essential