Mechanical Engineering and Materials Science REU

The Department of Mechanical Engineering and Materials Science at Duke University will provide a research experience for undergraduate students (REU) and host undergraduates from around the country in its research laboratories. The REU students will work with a faculty member and their research group to tackle an innovative research project (see list of projects below). 

Stipend

Students admitted to the program will receive a competitive, monthly research stipend which includes:

  • Dates: Sunday, May 25, 2014, to Saturday, July 26, 2014
  • $4,200 stipend
  • Up to $400 towards travel costs
  • Housing provided
  • Food budget: $175

When to Apply

The application for 2014 is closed. Please check back in 2015 for next year's REU opportunities.

Selected students should expect to hear of their acceptance to the program by April 1.

Eligibility

All applicants must be United States citizens or permanent residents. The program is designed for student who are juniors during the internship period, but exceptional sophomores will also be considered. Students do not have to be majoring in mechanical engineering and materials science.

Research Opportunities for 2014

The following projects are available for the coming summer. Interested students are encouraged to apply. Questions about any of the projects or the REU program in general should be directed to Kathy Parrish (kparrish@duke.edu). To be considered for any project, students must apply online through the link above.

Energy Harvesting

A number of research projects are underway in our research group.  Each of these is concerned with some aspects of dynamics and usually involves the dynamic interaction of fluid and an elastic structure. This field of study is often termed fluid/structure interaction, i.e., fluid mechamics plus highly deformable elastic structures. Recent work has emphasized nonlinear aspects of the phenomena. Research in this field has often been motivated by aerospace applications such as the oscillations of aircraft wings, turbine blades in jet engines and the wind loading on missiles during their launch. However applications to biomedical engineering, e.g., blood flow through arteries or airflow through the mouth; civil engineering, e.g., wind loads on bridges and buildings; electrical engineering, e.g., wind induced oscillations of power lines and energy harvesting; and to many other aspects of engineering are also studied worldwide and are of interest to our group at Duke. Current projects involve an opportunity for either theoretical or experimental work. Students are welcome to suggest project ideas of their own and are encouraged to discuss those with Professor Dowell.

Current research projects underway include the following:

  • Dynamic response of highly deformable beam and plate structures due to self-excitation and external forces such as; high performance airfoils; delta wing platforms that deform as plates; long span, highly flexible wings typical of uninhabited air vehicles; and bluff bodies typical of bridges and skyscrapers
  • Control of such systems
  • Investigation of nonlinear effects such as freeplay, structural stiffness and damping changes due to large deflections, shock wave motion and viscous effects in the fluid flow
  • Energy harvesting from large mechanical oscillations caused by the interaction of a flowing fluid and a flexible, elastic structure

Many of the projects make use of our acoustic test chamber, active control test facilities, nonlinear dynamics laboratory and/or wind tunnel laboratory.

Undergraduates from Duke University during the academic year and from a wide range of universities including Rice, North Carolina State and North Carolina A&T during the summer have also pursued research in our group.

Dean Martha Absher is a nationally recognized mentor of students from underrepresented groups in Engineering and will partner with the PI in the recruitment and mentoring of these students. Please see her letter of support and endorsement.

Faculty contact: Professor Earl Dowell, earl.dowell@duke.edu

Vectorial Folding of Polypeptide Chains

The folding of proteins is one of the most important yet not completely understood topics in biology. The question “Can we predict how proteins will fold?” was listed in 2005 as one of the 125 most important unsolved problems in science by Science Magazine. Significant progress has been made toward understanding the protein folding through in vitro experiments and computer simulations, but much less is known about folding in vivo. During co-translational folding, the nascent polypeptide chain (NPC) is extruded sequentially in a vectorial manner from the ribosome exit tunnel and starts folding under severe conformational constraints. It is presently unknown how such 1D constraints affect the folding pathway.

The long-term objective of this proposal is to advance understanding of protein folding by:

a) studying the vectorial folding of single proteins under 1D constraints by Atomic Force Microscopy(AFM)-based single-molecule force spectroscopy (AFM-SMFS) and computer simulations using steered molecular dynamics (SMD) calculations.

b) directly examining the folding behavior of the nascent polypeptide chain emerging from the ribosome using AFM mechanical manipulations.

Atomic force microscopy is a novel form of (non-optical) microscopy that can be mastered easily by undergraduate students. Although some knowledge of biology as it relates to proteins and their “folding” problem would be desirable it is not a pre-requisite for participation.

Faculty contact: Piotr E. Marszalek, pemar@duke.edu

Construction of an Atomic Force Microscope for Combined Mechanical and Optical Measurements in Nanobiotechnology

The objective of this proposal is to provide hands-on experience to undergraduate students in the design and construction of a robust high-precision and very inexpensive research-grade atomic force microscope that can be operated on top of an inverted optical microscope for combined force and fluorescence measurements. Moreover, once constructed, this instrument will serve many other students, including future generations of Pratt Fellows and independent study students to get hands-on experience in the cutting edge nanobiotechnology research. The instrument will be designed in a modular fashion in such a way that its future modifications, improvements and expansions will be easy to implement and these perpetual improvements will provide yet another avenue of continuous research experience for future undergraduate students.

We note that a complete home-made AFM instrument was already designed, constructed and successfully used in the Marszalek laboratory by several undergraduate students who carried out a number of independent studies and Pratt Fellows projects using this instrument. Its design was published by Rabbi and Marszalek1, with Mahir Rabbi being a Pratt Fellow who designed and constructed this AFM. These previous projects demonstrate the feasibility of developing a research grade AFM instrument solely by engineering undergraduates.

This AFM instrument will require a complete design overhaul to be able to work on top of an inverted microscope. To capture the fluorescence from the molecule being stretched by the AFM, the microscope objective needs to be inserted into the AFM head and positioned right below the sample. It will occupy the space that in a traditional AFM is taken by a high precision piezoelectric stage that translates the sample in the z direction for the mechanical stretching of molecules. Therefore, in the new AFM, the Z-stage that moves the sample will need to be located outside of the AFM head (e.g., as in Z-sample stage). One of the main difficulties for the new AFM to operate successfully will be to keep the molecule stretched within the focal depth of the microscope objective. To achieve this goal, the whole AFM head will need to be also translated in the Z direction, relative to the sample. This can be achieved e.g. by attaching another high precision piezoelectric Z stage directly to the top of the AFM head and mounting it on the body of the optical microscope (e.g., as in AFM head Z-stage). This modification will force the relocation of the laser from the top of the head to a horizontal location inside the head.

This project will initially involve two undergraduate students who will work over the summer in Dr. Marszalek laboratory to design and construct such an instrument. This project will provide an extremely fulfilling experience for these undergraduate students in the planning and execution of their real-world engineering activities whose final product will be a sophisticated research-grade instrument. The students will directly get experience in designing and constructing an instrument which is composed of very precise mechanical, electrical, electronic and opto-electronic components, which need to be perfectly aligned and actuated/probed by digital to analog interfaces controlled by a computer. Thus, their practical experience will integrate many areas of engineering. Importantly, their product will be later used for real research activities done by their undergraduate peers. These activities will focus on simultaneous measurements of the elastic and optical properties of single molecules such as DNA and various proteins (force spectroscopy) that will be labeled with fluorescent probes. This project will directly leverage the Pratt Fellow Program by providing a unique research experience for undergraduate students in the area of nanotechnology and nanobioengineering.

Project Plan

To achieve our objective we will need to acquire components and materials for building the AFM instrument, whose simplified schematic is shown in Figure 1C. Additional funds are requested to support two graduate students over one summer (nine weeks). Thestudents will design and construct the AFM instrument and develop its electronic control unit. Both students will test and calibrate the instrument.

An AFM is composed of three main parts: (i) a detector head, which houses a quadrant position-sensitive photodiode (PSD), a diode laser and a force sensor (micro-cantilever) whose bending is monitored by the laser-PSD system, (ii) nanopositioning stages that control the position of the sample relative to the force sensor, (iii) a control unit for the piezoelectric actuator and a control unit for the AFM head including DA/AD interfaces, a PC computer and a Labview/Matlab program to operate the instrument and collect the data.

The students will start by closely inspecting our home-made AFM instrument and inverted microscope that are available in the Marszalek laboratory and will learn how to operate these instruments (one to two weeks). Later, they will propose their own design that needs to guarantee a high resolution of force and length measurements within the budgetary constrain for the instrument of~$20,000 (two weeks). After the approval of the initial design of the AFM by PIs, the students will order necessary parts/materials and will machine various parts, assemble the AFM head and integrate it with the optical microscope base, while simultaneously working on the development of a control unit that will control the instrument (~one month). Lastly, they will test the instrument, carry out its calibration and carry out combined force and light test measurements of the elasticity of modular proteins containing fluorescent domains (three weeks).

While we plan an extensive use of this instrument in dedicated research projects by undergraduate students during the regular academic year, the summer time should be an opportunity for some undergraduate students to carry on the effort to further improve this instrument and expand its capabilities. This could be done in stages over several summers.

In summary, this project will offer an excellent opportunity for many undergraduate students to engage in the design, construction and continuous development of a sophisticated instrument that they will be able to use by themselves to get a profound research experience at the forefront of engineering. Similar instruments can be later “cloned” in future projects to create a nanotechnology laboratory that could be integrated into the undergraduate curriculum.

References

1. Rabbi, M. & Marszalek, P. Probing Polysaccharide and Protein Mechanics by Atomic Force Microscopy. in Single-Molecule Techniques: A Laboratory Manual (eds. Selvin, P.R. & Ha, T.) 371-394 (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, 2008).

Faculty contact: Piotr E. Marszalek, pemar@duke.edu

Development of Self-Assembled Protein-Based Soft Materials with Tailored Mechanical Properties

The main goal of this research is to develop novel soft materials with unusual and programmable mechanical and viscoelastic properties, which will self-assemble from protein-based building blocks, and to understand the principles that relate the properties of these materials to the properties of their protein building blocks. The unusual properties of these materials will be a) extremely large stretch ratios of around 1000 percent, and b) programmable ratios of the storage modulus to the loss modulus. Large stretch ratios will be achieved by exploiting proteins whose folded length is on the order of 1/10th of the length of the polypeptide chain. Storage and loss moduli will be controlled by varying the percentage of protein domains that mechanically unfold and refold in near equilibrium, with minimal energy dissipation, such as ankyrin repeats (ANK)1,2, (Fig. 1) and mechanically strong protein domains that dissipate large amounts of energy when mechanically unfolded, such as immunoglobulin (Ig) domains (Fig. 1). Self-assembly of these protein building blocks into materials will be achieved by exploiting two novel approaches: a) using functionalized homo tetrameric proteins to serve as network nodes and b) using the newly-developed SpyTag-SpyCatcher technology3 to covalently connect protein building blocks to tetrameric hubs4. At low forces (up to ~100 pN/molecule) these materials should will display large stretch ratios and will stretch in a fully reversible fashion with minimal energy dissipation. At higher forces (>100 pN/molecule) these materials will display significant plasticity and will dissipate great amounts of energy, working as “shock absorbers” (Fig. 1) applications, e.g., as scaffolds for growing cells subjected to mechanical stimulations, or as highly stretchable fibers and membranes.

Figure 1
Figure 1
 

Key References

1. Lee, G. et al. Nanospring behaviour of ankyrin repeats. Nature 440, 246-9 (2006).

2. Lee, W. et al. Full Reconstruction of a Vectorial Protein Folding Pathway by Atomic Force Microscopy and Molecular Dynamics Simulations. Journal of Biological Chemistry 285, 38167-38172 (2010).

3. Zakeri, B. et al. Peptide tag forming a rapid covalent bond to a protein, through engineering a bacterial adhesin. Proceedings of the National Academy of Sciences 109, E690-E697 (2012).

4. Kim, M. et al. Nanomechanics of Streptavidin Hubs for Molecular Materials. Advanced Materials 23, 5684-5688 (2011).

Faculty contact: Piotr E. Marszalek, pemar@duke.edu

Self-Cleaning Materials

The objective of this project is to create self-cleaning materials that function regardless of external forces, including gravity. The project takes advantage of the jumping-drop discovery at Duke, where water condensate self-propels to jump away from superhydrophobic surfaces, carrying away contaminants in the condensate drop. The background is discussed in the magazine Scientific American (PDF). This project is primarily experimental but will also involve the development of scaling laws. The student will have the opportunity to use high-speed photography to the self-cleaning process at up to a million frames per second, and use the mechanistic understanding to guide the engineering of practical self-cleaning materials.

Faculty contact: Chuan-Hua Chen, chuanhua.chen@duke.edu, 919-660-5343

Surface Energy Harvesting

The objective of this project is to create an engineering device that harvests environmental energy, mimicking the ballistospore fungi which discharge spores by the so-called one-shot microengines powered by surface energy. This biological process has been reproduced at Duke: coalescing condensate droplets on a superhydrophobic surface release surface energy, which is eventually converted to kinetic energy propelling the droplets to jump. The background is discussed in a news item in the magazine Science (PDF). This project is primarily experimental but will also involve the development of scaling laws. The student will have the opportunity to use high-speed photography to capture surface energy conversion process of ballistospore discharge at one million frames-per-second, and use the mechanistic understanding to guide the design and development of an engineering prototype that mimics this energy harvesting process.

Faculty contact: Chuan-Hua Chen, chuanhua.chen@duke.edu, 919-660-5343

Developing an Automated Air Traffic Control System for Small Drones

There is increasing global interest in the use of small Unmanned Aerial Vehicles (UAVs, aka drones) for commercial and other non-military uses like humanitarian assistance and disaster relief (Figure 1). However, there has been very little research conducted in the changes that will have occur in the air traffic control system to handle the expected increase in volume of small unmanned aircraft, which typically operate at altitudes below that of commercial aircraft, but potentially in conflict with manned, general aviation aircraft. A new air traffic control paradigm is needed that contains substantially more automation to handle the increased volume of small, remotely guided drones, but still be flexible enough to handle inevitable contingencies.

Figure 1: An Amazon.com drone delivering a package (Credit: Amazon.com)
Figure 1: An Amazon.com drone delivering a package (Credit: Amazon.com)

This project will focus on adapting a previously-developed interface for goal-based control of multiple military UAVs by a single operator to that of the commercial drone world, and then conduct pilot testing on a small group of participants to determine the effectiveness of such an approach. This project may include travel to brief results to relevant organizations like the DoD, FAA, and NASA. Students are welcome to suggest derivative project ideas and are encouraged to discuss those with Professor Cummings.

This project is one of many examining human-machine interaction in one of Duke’s newest laboratories, the Humans and Autonomy Laboratory. Required skills include the ability to program in Java or a closely related language and the desire to learn to conduct human-in-the-loop experiments.

Faculty contact: Professor Mary (Missy) Cummings, m.cummings@duke.edu