Robert L. Clark - US grants

9501470 Clark This CAREER award emphasizes research and educational activities related to attenuating acoustic response of enclosed sound fields such as the fuselage of an aircraft subjected to turbulent boundary layer excitations. A coupled model of the aeroelastic, structural acoustic system is developed for single-leaf and double-leaf partitions between compressible flow fields with a mean velocity and an enclosed sound field. Turbulent boundary layer noise models are used to generate the exogenous inputs to the system, and acoustic response is controlled through structural acoustic control methods. Wind tunnel tests are performed for model validation and alternate control strategy evaluation. Educational programs include the development of an electromechanical control system demonstration unit, outreach to a local science museum, design of a course on adaptive structures, and integration of latest computer software packages for dynamics and control in undergraduate mechanical engineering instructions.***

Robert L. Clark, Duke University
CMS-9908271
Industrial / University Collaboration for Research in Control of Sound and Vibration
The Adaptive Systems and Structures Laboratory of Duke University and the Millennium Technologies Group of the Lord Corporation have jointly identified critical technical research objectives regarding advancements in the control of sound and vibration. The programmatic objective is aimed at the successful integration of research efforts at the Lord Corporation and Duke University with regards to the control of sound and vibration. The program aims to facilitate the transfer of technology and ideas between the academic and industrial setting through an integrated and collaborative research program. The technical objective of the proposed program is focused on the advancement of transducer technologies and controller design methodologies required for structural control of sound and vibration.
The proposed program will have a significant impact within the field of applied control of sound and vibration. New methods will be developed for determining optimal positions of transducers based upon experimental system identification techniques. The method proposed will lead to a design methodology of value to the general community. Additionally, practical issues facing the integration of self-sensing transducers will be addressed to facilitate technology transfer and determine limits of performance for applications requiring induced strain transducers. For practical realization of multivariable control, self-tuning or adaptation is a necessity due to the variation in transducer dynamics, structural dynamics, and system parameters with each application. Thus, to provide practical design guidelines, adaptive control methodologies will also be explored with an emphasis on determining limits of performance and robust stability given a basic knowledge of the time-varying parameters of the system.

This award from the Instrumentation for Materials Research program supports the construction of a suite of four single-molecule force spectrometers for development, training and research to be shared by the Departments of Mechanical Engineering, Chemistry, and Biochemistry at Duke University. These instruments permit the measurement of very weak forces (tens of picoNewtons) on the spectrometer tip as a function of its distance from a surface (controlled to 0.3 nm), so that the properties of individual molecules can be studied. In-house construction of the instruments will provide the expertise necessary to modify and develop the facility to meet future educational and research needs. The presence of multiple instruments provides the resources necessary to allow concurrent development and training while still meeting the research needs of the users. Students from each of the represented disciplines will receive training in the development and/or use of single-molecule force spectrometry, an area of growing importance in fundamental research, biotechnology and materials science. No such general training opportunity presently exists on campus. The facility will be centrally located to encourage interactions and collaborations between users from all disciplines, and these interactions will be fostered through a course in macromolecular interactions to be taught and supervised by faculty from each department.

This award from the Instrumentation for Materials Research program supports the construction of a suite of four single-molecule force spectrometers for development, training and research to be shared by the Departments of Mechanical Engineering, Chemistry, and Biochemistry at Duke University. These instruments permit the measurement of very weak forces (tens of piconewtons) on the spectrometer tip as a function of its distance from a surface (controlled to a fraction of a nanometer), so that the properties of individual molecules can be studied. In-house construction of the instruments will provide the expertise necessary to modify and develop the facility to meet future educational and research needs. The presence of multiple instruments provides the resources necessary to allow concurrent development and training while still meeting the research needs of the users. Students from each of the represented disciplines will receive training in the development and/or use of single-molecule force spectrometry, an area of growing importance in fundamental research, biotechnology and materials science. No such general training opportunity presently exists on campus. The facility will be centrally located to encourage interactions and collaborations between users from all disciplines, and these interactions will be fostered through a course in macromolecular interactions to be taught and supervised by faculty from each department.

This four-year Nanoscale Interdisciplinary Research Team (NIRT) project at Duke University, with Professor Robert L. Clark as principal investigator, addresses both scientific and engineering aspects of nanopatterning of surfaces and in-situ nanofabrication that will directly impact biotechnology, biologically inspired engineering, transducers and electronics at nanoscale. Instrumentation based on scanning probe lithography and dip-pen lithography will be developed for use in specially designed nanolithography. New fabrication methods will be developed for nanometer length structures with biomolecules and stimulus-responsive macromolecules.

This project was received in response to Nanoscale Science and Engineering initiative, NSF 01-157, category NER. The purpose of this research is to develop the technology to deliver regulated torques to nanosystems; such torques would be on the order of piconewton-nanometers. Helicallv structured light possessing angular momentum will be used in an optical trapping arrangement to deliver angular momentum to trapped particles thereby applying a torque to the trapped object. Position and orientation of a trapped object will be achieved with a trapping beam constructed from the interference of a helical wave front and a plane wave. This research focuses on developing an optical trap using a conventional single-beam trap architecture; constructing the requisite helically-structured laser beam modes as Laguerre-Gaussian (LG) beam modes and constructing an interference pattern between LG beam modes and plane-wave beam modes. Torque spectroscopy experiments of biomolecules will be performed. Candidate molecules are coiled-coil proteins like myosin, modular matrix proteins like fibronectin and tenascin, and the DNA double helix.

This research program will have a broad impact in the advancement of knowledge, education, industry and technology. An optical torque-trap is an enabling technology for the comprehensive development of nanoscience and engineering, and will have wide application in nanotechnology from characterization to fabrication. In nanoscale biosystems it would be used to provide an understanding of the behavior of single molecules. For nanoscale structures, it would enable the characterization of novel nanoscale structures and phenomena which depend upon rotary motion . Finally for nanoscale manufacturing processes it would enable new nanofabrication processes which would depend upon the manipulation of particles in six-dimensions Other applications include measuring the torque and power output of rotary nanomotors, measuring the bending strength of molecules, measuring the drag on nanobearings, and driving nanosystems by photonic components. This program will also have impacts in new curriculum for graduate students, combining elements of engineering and physics for nanoscience and engineering; the study of nanosystems and nanobiosystems; training opportunities for undergraduate students in nanotechnology through participation in research projects; and industrial collaboration providing technology transfer and training opportunities for faculty, research associates, and students.

Engineering - Civil (54)
Our team at the Pratt School of Engineering at Duke University has previously developed and documented a prototype web-based instructional system for solid mechanics. Our basic goal has been to promote an inquiry-based style of modern engineering analysis, experimentation, and design into undergraduate solid and fluid mechanics courses. A central effort of our team's work has been the design and evaluation of a modular and portable framework so that faculty can create a diverse set of experiments based on our web- based model. To help guide faculty toward adoption of our model a workbook and accompanying CD-ROM is being published.

Through our project Web-based Educational Framework for Analysis, Visualization, and Experimentation (WEAVE) faculty will have the option of complimenting traditional labs with module-based projects designed to encourage students to compare, contrast, and improve models of actual physical experiments. An interactive web-based tutorial for each module will be developed in conjunction with Shodor, a non-profit educational research foundation based in Durham, N.C. The deployment of WEAVE across the engineering curriculum enables students to follow interactive tutorials, execute numerical simulations, and conduct physical experiments. In these self-paced labs, students explore concepts of fluid and solid mechanics through trial and error iterations by directly controlling and modifying the physical experiments and their associated numerical simulation. The dissemination of our materials and findings has been promoted on our campus, and at the state and national levels through oral presentations, publications in educational journals, and via the Internet. We also plan to present at the Frontiers in Education in 2003.

The vision of the Center for Biologically Inspired Materials and Material Systems research and educational program is to map traditional engineering onto biology. Through this approach, the IGERT project seeks to establish a new curriculum for graduate education in Biologically Inspired Materials and Materials Systems. The curriculum serves as an integration of natural science, life science, and engineering. This program will create a new graduate training program that uses biologically inspired approaches to bridge a gap in current biomedical and bioengineering programs. The Center's vision is to bring nature's engineering into the engineering curriculum and engineering principles into the study of materials, revolutionizing the way engineering and life sciences are taught at the graduate student level. Thus, this IGERT project will develop a new paradigm for education and research, using nature as an example for engineering, while explaining nature using engineering principles and rigor. This program focuses on three specific areas: (1) Bio-NanoScience and Engineering (single molecules and self-assembly), (2) Encapsulation, Coatings, and Surface Patterning (materials at the cellular scale where the lipid bilayer serves as the defining basis of all life), and (3) Hierarchical Systems (larger, more macroscopic, functional organisms). This focused approach will allow students and faculty to develop mapping concepts to the leading edge of knowledge and to explore the intellectual and practical aspects of creating a new curriculum at the interfaces of biology, medicine, engineering, and basic physical and chemical sciences. This is an initial step towards establishing a new paradigm in science and engineering education that explores life's mechanisms at the molecular level and translates these findings up through hierarchical scales of structure and organization to bring greater understanding of mechanism to the biological organism and unique designs to engineered devices.

IGERT is an NSF-wide program intended to meet the challenges of educating U.S. Ph.D. scientists and engineers with the multidisciplinary backgrounds and the technical, professional, and personal skills needed for the career demands of the future. The program is intended to catalyze a cultural change in graduate education by establishing innovative new models for graduate education and training in a fertile environment for collaborative research that transcends traditional disciplinary boundaries. In the fifth year of the program, awards are being made to twenty-one institutions for programs that collectively span the areas of science and engineering supported by NSF.

The purpose of this research is to further the understanding of DNA damage and repair by elucidating the relationship between these processes and DNA nanomechanics and by visualizing repair protein activities on DNA using atomic force microscopy techniques. The objectives are: 1) optimize the AFM platform for single-molecule DNA measurements 2) examine various lesions in individual DNA molecules and follow in the AFM their direct reversal by DNA repair enzymes 3) use AFM imaging and force spectroscopy to visualize the mismatch repair reaction of E. coli. To achieve these objectives the AFM platform needs to be optimized to reduce force errors to single piconewtons and to accelerate image acquisition by using the ultra-small cantilever technology. DNA repair proteins such as photolyases, endonucleases and ligases will be used as damage markers and will be imaged in complexes with DNA by AFM in order to locate and identify the damage sites. Force spectroscopy measurements will determine the mechanical fingerprints of various types of DNA damage caused by UV and gamma radiation and will directly follow damage reversal in the presence of the repair activities. This project will also examine and visualize the DNA mismatch repair reaction using E. coli repair activities and AFM imaging and force spectroscopy technologies. This project will provide an exciting education and research opportunity for three graduate students at the interface between engineering and biology and will likely develop new ultra sensitive assays for DNA damage detection that is of significance to many areas of biology.

The Ethics Education in Science and Engineering award to Duke University supports a team of five faculty led by Dr. Tod A. Laursen, Civil & Environmental Engineering Department, to conduct research and education on ethical issues which can have profoundly adverse impacts on society, such as those posed by unintended consequences of nanoscientific breakthroughs.
This combined research and educational project consists of a team of engineers, scientists,
ethicists, and educational specialists to collaboratively develop a new paradigm of ethical education of graduate-level researchers in emerging fields. The team includes researchers from several such interdisciplinary fields and benefits from its presence in a university that has already systematized the delivery of Responsible Conduct of Research (RCR) in all its Ph.D. programs. This project will build upon that base by developing, implementing, and assessing multiple modes of delivery for micro- and macroethical training and by working with doctoral and professional master's students to imbed these modes within their graduate experience. The project's collaborative approach to providing ethics education will involve multiple schools and centers within Duke as well as interactions and partnerships with NC Central University's Biomedical/Biotechnology Research Institute, NC State University's Graduate School and Research and Professional Ethics Program, and the UNC-Chapel Hill's Graduate School.
The proposal for this award was received in response to the Ethics Education in Science and Engineering announcement, NSF 05-532, and was funded by the Division of Engineering Education and Centers (EEC) in the Directorate for Engineering and by the Directorate for Social, Behavioral & Economic Sciences.

The objective of this Nanoscale Interdisciplinary Research Team (NIRT) project is to develop hierarchical manufacturing processes for parallel fabrication of biomolecular and polymer components on surfaces with nanometer resolution and to trigger their function by external signals. Deposition of these soft biological materials on surfaces of engineered materials with nanoscale precision and their externally triggered control will afford unprecedented opportunities to conduct basic research in the biological sciences, develop new diagnostic sensing devices for medical applications, and advance drug discovery. Research in this project will pursue two parallel, but complementary research pathways. The first path will focus on patterning surfaces with chemical features to position proteins and metal nanostructures on the surface with nanoscale precision and to develop the engineering hardware and software tools required to trigger the activity of these patterned components with an external signal, creating active nanostructures. The second research path will focus on the development of a massively parallel implementation of the surface patterning process to enable high-throughput manufacturing of nanoscale features through stamping.

The largest hurdle in the advancement of bionanomanufacturing is the development of nanofabrication processes that are compatible with water, enable mass production without the need for a clean-room, and are biocompatible. This project's activities address this issue through the integration and development of existing and new tools to enable hierarchical manufacturing that is directly relevant to the biotechnology industry. Specifically, new, innovative fabrication tools and strategies for the integration of nature's soft-wetCE materials and engineering's hard-dryCE materials at the nanoscale will be developed. This highly multidisciplinary research effort draws upon expertise in the biological sciences, chemistry, materials science, and engineering to fabricate hierarchical bionanostructures with functional relevance to automation of the biotechnology industry.

Scientific Goals: The long-term goal of this project is to define the cellular states that occur during root development in Arabidopsis when subjected to different stimuli. As a tractable approach to defining cellular state, transcriptional networks active in different cell types when grown under a variety of environmental conditions will be identified. To describe a first-order transcriptional network three types of data are needed: 1) transcriptional profiles at cell-type specific resolution under normal lab conditions and when subjected to external stimuli; 2) knowledge of transcription factor localization at cellular resolution and 3) information about the targets of transcription factors. For the first, a technique that involves sorting of fluorescently marked cell populations followed by microarray analysis of the RNA from the marked cells will be used. For the second, comparisons will be made of the expression patterns of constructs containing the promoter regions of transcription factors driving fluorescent reporter genes with constructs containing the same promoter regions driving the coding sequences of transcription factors fused to fluorescent reporter genes. For the third, yeast one-hybrid and two-hybrid methods will be used with libraries of tissue-specific transcription factors. Analyses will initially be performed on plants growing under standard laboratory conditions. To determine how expression is perturbed by external stimuli, plants will be systematically subjected to a variety of external stimuli and the effects on transcriptional profiles determined at cell-type specific resolution. To determine the effect of external stimuli on expression at high spatial and temporal resolution a novel technology called the "RootArray" will be developed. The combination of results, from these different approaches, will provide information concerning the function of the identified genes. Results from these studies will be posted on the Arabidopsis Gene Expression Database, at www.arexdb.org.


Broader Impact: To achieve continued improvement in plant traits while minimizing unwanted side effects will require a sophisticated understanding of the networks that control plant development and physiology. This research will provide a high-resolution dataset for the identification of transcriptional networks active during root development. It will also determine the effect on root transcriptional networks of stimuli relevant to plant growth in the field. Another outcome of the research will be detailed knowledge of the spatial and temporal expression patterns of large numbers of plant genes and the regulatory sequences able to confer specific expression patterns. These should be of immediate value in many plant research programs and are likely to be useful for agronomic purposes as well. Another important part of the project will be to train the next generation of plant scientists in Systems Biology, which integrates computational, engineering and experimental approaches. Postdoctoral fellows, graduate and undergraduate students will be trained in this research. The PIs also will participate actively in outreach efforts such as development of a Systems Biology curriculum at Duke. The research program will also leverage the currently funded NSF IGERT program in biologically inspired materials and material systems directed by Co-PI Clark. A significant focus of the IGERT program is placed upon recruitment and training of women and underrepresented minorities in engineering and the sciences.

Relevance to Arabidopsis 2010 goals: The research activities will contribute to all three of the primary goals of the Arabidopsis 2010 program. Enhancing the resolution of the root expression map under normal laboratory conditions and producing expression profiles at cell-type specific resolution in response to different stimuli will substantially aid in "Benchmarking Gene Function." Developing computational tools for cis-element identification and automated image analysis as well as developing the RootArray should provide "genome wide experimental approaches and tools for analyzing gene function and regulation." Perhaps most directly, the research has as its aim to identify the transcriptional networks acting in root development and physiology, thus "exploring exemplary networks and systems."

DESCRIPTION (provided by applicant): Cells respond to physical forces in their environment through a process called mechanotransduction. Mechanotransduction molecules on the cell surface recognize physical forces and transmit an internal biochemical signal that can affect cell growth, gene expression, etc. Endothelial cells (ECs), or the cells lining the blood vessels, can sense shear stress induced by the blood flow. In regions of high shear stress, the cells elongate and align with the direction of the flow. However, in regions of low shear stress or disturbed flow, the ECs do not have an elongated and oriented morphology. These regions of low or disturbed flow are susceptible to the formation of atherosclerotic lesions. Therefore the study of mechanotransduction in ECs will aid in our understanding of atherosclerosis and cardiovascular disease. Experiments with ECs exposed to fluid flow or stretched ECs have shown that cytoplasmic domain of platelet endothelial cell adhesion molecule-1 (PECAM-1) is phosphorylated by the protein kinase Fyn. SHP-2, a protein tyrosine phosphatase, propagates the signal along the ERK/MAPK biochemical pathway, eventually altering the EC growth and alignment. It is hypothesized that physical stretching of PECAM-1 unravels the cytoplasmic domain and exposes the region that is phosphorylated. The proposed research will build an understanding of how PECAM-1 responds to physical forces through three aims. In Aim 1, a construct consisting of the cytoplasmic domain of PECAM-1 will be produced through molecular biology and biotechnology techniques. In Aim 2, the physical characteristics of the construct will be measured using single molecule force spectroscopy techniques. To perform these measurements, the PECAM-1 construct will be elongated with an atomic force microscope (AFM), and the resultant forces will be measured. Finally, in Aim 3, the PECAM-1 construct will be stretched with the AFM while the signal propagation event will be measured in real time using fluorescence. This will allow the determination of the forces required to perform PECAM-1 mechanotransduction.

DESCRIPTION (provided by applicant): Single molecule force spectroscopy (SMFS) is used to study the fundamental forces that drive the biological activity of cells and proteins. Nearly al of these biophysical measurements are performed in vitro using purified biomolecules. When studying the function and mechanics of cells, this approach yields inherently incomplete results by failing to account for the influence of the intracellular environment. Therefore, the development of a force spectroscopy system capable of in vivo sensing will advance biophysical measurement capability and help clarify the origins of the interactions driving cellular function. Broadly, a more complete understanding of cellular processes will aid researchers in the discovery and development of treatments for various disorders including cancer. This proposal outlines the development of a novel instrument that combines the manipulation capabilities of optical and magnetic tweezers to facilitate high resolution positioning as well as the application of a relatively large range of forces inside a living cell. To realize an instrumen of this type, an optical tweezers system will be retrofitted with a magnetic apparatus capable of generating controllable rotating magnetic fields. Magnetically anisotropic Janus spheres, less than 200 nm in diameter, will be fabricated to serve as probes that can be optically trapped and magnetically actuated. Their size will facilitate cellular uptake via endocytosis. Once inside the cell infrared laser beams or ultrafast laser pulses combined with external magnetic actuation will enable probe motility and force application without compromising the health of the cell. Advanced servo control schemes will allow the accurate application of forces and measurement of intracellular mechanics. Initially probes will be inserted into live granulocytes to access instrument performance. Once parameters are optimized the in vivo force spectroscopy instrument will be made available to the general research community for the characterization of a myriad of cell lines.

DESCRIPTION (provided by applicant): The overall objective of the Molecular Atlas of Lung Development Program (LungMAP) is to develop a molecular atlas of the developing lung from human and mouse to serve as a unique reference resource for the research community. The objective of our application is to serve as the Data Coordinating Center (DCC) for the Molecular Atlas of Lung Development Program (LungMAP-DCC). We have taken several innovative and cost-effective approaches to build the LungMAP-DCC that will greatly benefit the research community and promote a greater understanding of molecular lung development. We have created a multi-disciplinary team of investigators from Duke Clinical Research Institute, RTI International, and Cincinnati Children's Hospital Medical Center to lead and operationalize the LungMAP-DCC. We are leveraging the strengths of two highly experienced investigators as multiple PIs (Drs. Palmer and Clark) and we will apply novel data management and bioinformatics approaches to create the Bioinformatics REsource ATlas for the Healthy lung (BREATH) database. The DCC will perform data collection, integration, and analysis; develop and maintain the LungMAP database and website; and coordinate research activities of the Human Tissue Core (HTC) and the Research Centers (RCs). We will complement these goals with the following Specific Aims that support the success of consortium: Specific Aim 1) Administrative Coordinating Infrastructure: The DCC will serve as the administrative infrastructure that facilitates collaboration among our multidisciplinary team, RC, and the HTC by 1) providing expertise in molecular lung development, clinical design, statistics, and bioinformatics; and 2) the creation of consortium-wide priorities and policies, communication plan, and resource catalog and Specific Aim 2) LungMAP Portal and BREATH (Bioinformatics REsource ATlas for the Healthy lung): The DCC will build the centralized data repository and public interface for LungMAP by creating and managing 1) BREATH; 2) LungMAP Website; 3) standard operating procedures for data management; 4) existing lung development results; 5) ontologies for lung development, structures, and cross species comparisons; 6) experimental data from RCs and biologic sample data from the HTC; and 7) novel tools to analyze the experimental data. This application leverages the complementary strengths of multi-disciplinary research teams with clinical pulmonary expertise, basic understanding of lung molecular development, successful leadership of multicenter research networks, and in-depth computer programing, database development, and bioinformatics skills that will create a highly functional, integrated, publically accessible platform that will facilitate analysis of data generated by the RCs and HTC to advance our understanding of molecular lung development. (End of Abstract)