Fellowship recipient Jorge Ramirez
1) Review the summer 2019 NURF project descriptions (below) and select a project of interest.
2) Complete the APPLICATION, and save the file with your last name and your first name as the first words in the file name. (Ex: Smith-Barb 2019 NURF Application)
3) Email your completed application and current resumé (saved with the same name convention -- Smith-Barb resumé) to the project’s faculty mentor(s) for consideration, and cc: Heidi Deethardt at email@example.com. NDnano faculty will follow-up with selected applicants directly. Award notifications will begin in early March.
Students are welcome to apply for more than one project. However, please list and prioritize on your application(s) all the projects for which you have applied.
For purposes of the NURF program, undergraduates are students who will not yet have completed their undergraduate studies at the start of their summer fellowship.
The University allows students to work a maximum of 40 hours per week during the summer (all campus jobs combined). This means that students cannot participate in the NURF program on a full-time basis and at the same time hold any other paid, on-campus, summer position. (Fellowships of less than 40 hours per week would be considered on a case-by-case basis.)
In addition, fellowship recipients who attend Notre Dame and have 2018-2019 on-campus, academic-year jobs may be prohibited from starting their NURF position before the last week of May; contact Heidi Deethardt for more details.
Project: Multilayer high contrast dielectric graded index lenses for millimeter wave antenna systems
Figure 1. Radially varying perforations across 2" silicon wafer; lattice close-ups and cross-sections.
The desire for low power antenna configurations is found in nearly every modern wireless application, from the well-established satellite communications industry to the burgeoning 5G mobile data standards. In these and other applications, the advancement of small mobile platforms places greater performance constraints on antenna systems; not only are smaller form factors required, but mobile antenna systems must also exhibit robust beam steering capabilities. To this end, phased array antenna configurations are becoming more commonplace, but even as they become smaller and more accessible, their power consumption makes them undesirable in small mobile cells. Rather, we’re investigating dielectric lenses as a low power, low cost alternative. As a completely passive device, a dielectric lens antenna consumes no power. Furthermore, if the lens material is constructed with spatially varying permittivity in three dimensions, the lens could occupy any form factor. The performance of the lens is then determined by its spatial permittivity profile. Lens designs that exhibit greater wavebending in smaller form factors require more extreme refractive-index gradients and a larger range of manufacturable permittivities. As a result, these GRaded-INdex (GRIN) profiles are primarily limited by the permittivity resolution of the fabrication process. In our microfabrication process, we use the Bosch Deep Reactive Ion Etching Process to etch hexagonal arrays through 280um thick silicon wafers; the perforations themselves vary in size from 30μm wide to 185μm wide. In prior work, we’ve demonstrated that this process yields silicon-air composite materials with dielectric constants ranging from 1.25 to 8. With subsequent process refinements, we can now fabricate a radial permittivity gradient across a full 2” diameter silicon wafer. Shown in Figure 1, the GRIN lens layer exhibits continuous radial variation in perforation size with 30μm perforations in the wafer center and 185μm perforations at the wafer edge; the close up images show the lattice, and cross-sections where the dark areas are the perforations and the light areas are silicon substrate. Projected dielectric constants range from 11.3 at the center to 2.5 at the edge. We are now at the exciting stage of fabricating full lenses for testing at millimeter wave frequencies and are looking for a motivated undergraduate researcher to assist with this latest stage of our work. The student will be involved in every step of the lens fabrication process:
- At the design stage, the student will use HFSS full-wave electromagnetic simulation software to analyze lens permittivity profiles. With these designs, the student will also design the photolithography masks using Python CAD automation and Cadence CAD software.
- At the fabrication stage, the student will work hands-on in our class 100 clean room to actually craft the effective permittivity samples and lenses. With training and practice, the student will become comfortable with general photolithographic processes (including fabricating their own mask designs), metal deposition, and deep reactive ion etching. The student will be trained in other processes on a need basis.
- Finally, post-fabrication the student will be involved with the antenna measurement process. The student will perform material parameter extraction and radiation pattern determination using our own antenna chamber and state-of-the-art 50GHz network analyzer.
- The student will work closely with a graduate student in the above activities. A rising junior or senior with electrical engineering background is expected but qualified candidates from all levels will be considered.
Project: Using piezoelectric and pyroelectric crystals to directly convert motion and heat into electrical plasmas
Professor David Go • Aerospace & Mechanical Engineering • 140G McCourtney Hall • 574-631-8394 • firstname.lastname@example.org
Professor Seong-kyun Im • Aerospace & Mechanical Engineering • 113A Hessaert Laboratory • 574-631-7264 • email@example.com
The technical objective of this National Science Foundation-sponsored project is to engineer devices and systems to harvest mechanical or thermal energy to directly produce an electric discharge or plasma. These plasmas can be used for applications such as water purification or pollution mitigation without the need for an electrical power supply. The key to this strategy is to utilize piezoelectric and pyroelectric crystals that can produce large voltages from vibrations or heat. The role of the student is to help design, build, and test both the mechanical and thermal harvesting systems. They will work closely with a graduate student who is focused more on the plasma generation science, and have the opportunity to do experimental work, data analysis, and potentially some computational modeling. Applicants from any science and engineering discipline are acceptable, although those with a background in electrical engineering and mechanical engineering are preferred. Students interested in continuing the research throughout the school year will be given priority.
Project: Polymer membranes with tunable microporosity for gas separations
Polymers with well-defined microporosity are highly desired for gas separation membranes, wherein high microporosity enables fast gas transport while the finely tuned pore size regulates selective transport via size sieving. Recently there have been markedly increasing research interests in developing microporous polymers for gas separation membranes, such as polymers with intrinsic microporosity (PIMs). However, the reportedly super high gas permeability of microporous polymers always accompanies with low selectivity, mainly due to the lack of precise control over pore size distribution in these polymers. Moreover, physical aging induced deterioration of permeability remains one of the biggest challenges for microporous polymer membranes. This project will focus on constructing highly rigid ladder-like polymers using a shape-persistent building block based on pentiptycene-containing structural units. The novelty of this new type of microporous polymers lies in the truly intrinsic microporosity defined configurationally by the shape of the pentiptycene units, which offers the unique opportunity to tailor the microcavity architecture in the membranes and simultaneously provide superior resistance towards physical aging by taking advantage of the rigid framework of pentiptycene moieties. The project will involve the synthesis of pentiptycene-based monomers with various bridgehead substituent groups, polymerization of tetra-functional pentiptycene monomers with commercial comonomers, membrane fabrication/characterization, and pure-gas permeation tests. A student in materials science, chemical engineering, or chemistry is preferred, and having previous experience in a chemical laboratory would be helpful.
Project: Nanostructured polysulfone polyelectrolyte copolymer membranes for fuel cells
Sulfonated polysulfone copolymers with controlled nanophase-separated morphology hold great potential as alternatives to benchmark Nafion® for polyelectrolyte membrane fuel cells (PEMFCs), due to their much better proton conductivity at low relative humidity (RH) levels and thermal stability. Previous research has shown that long hydrophilic (ionic) sequences or a high degree of sulfonation are needed to form well-connected proton conducting nanochannels that enables high proton conductivity at low RH. However, it invariably comes at the expense of high water uptake and excessive membrane swelling, resulting in deterioration of the dimensional stability and mechanical robustness. This project aims to exploit an innovative supramolecular strategy to address this water management challenge in PEM membranes via introducing triptycene-based building blocks into polymer backbones. It is expected that supramolecular interactions of chain threading and interlocking induced by triptycene units can effectively suppress water swelling while maintaining high water uptake, which is critical to provide high proton conductivity under low RH conditions. Specifically, both random and multiblock copolymers of systematically varied compositions will be developed in this project to investigate how supramolecular interactions of triptycene units govern the formation of proton-conducting nanochannels as well as proton transport properties. The project will start with the synthesis of triptycene diol monomer, which will be copolymerized with commercial sulfonated monomer to produce both random and multiblock copolymers. Comprehensive characterizations of the copolymers will be conducted to confirm the chemical structure (NMR and FTIR) and assess their thermal and mechanical properties (DSC, TGA, tensile test, etc.). Membrane fabrication and acidification will then follow to prepare free standing, defect-free films for water swelling measurement, morphology characterization (AFM, TEM) and proton conductivity measurements (impedance spectroscopy). A student in materials science, chemical engineering, or chemistry is preferred, and having previous experience in a chemical laboratory would be helpful.
Project: Engineering biomimetic materials to control stem cell morphogenesis
Blood and lymphatic vasculatures are two important components of the tumor microenvironments. Blood vessels supply nutrients important for tumor growth and serve as a conduit for hematogenous tumor spread, while the lymphatic vessels are used by the cancer cells to interact with the immune system as well as for lymphatic tumor metastasis. Consequently, the growth of blood and lymphatic vasculatures surrounding the tumor have been associated with tumor metastases and poor patient prognosis. The objective of this project is to understand what governs the formation of blood and lymphatic vessels from stem cells, how these processes are affected by the tumor microenvironment, and how we can use these insights to develop novel therapies. The student will synthesize and characterize biomaterials for in vitro evaluation using stem cell. The student is expected to maintain stem cell culture and study cell-materials interaction using microscopy and molecular biology techniques. Students with a background in mechanical engineering, chemical/bio-engineering, materials science, or biochemistry are encouraged to apply. Prior lab experience is preferred.
Project: Magneto-silica nanoparticles (MagSiNs) for combinatorial chemotherapeutics and gene delivery against metastatic cancers
Professor Paul Helquist • Chemistry & Biochemistry • 361 Stepan Hall • 574-631-7822 • firstname.lastname@example.org
Professor Prakash Nallathamby • Aerospace & Mechanical Engineering • 145 Multidisciplinary Research Bldg • 574-631-5735 • email@example.com
We intend to target non-targetable cancer cells by tuning the magnetic field induced force exerted by label-free magnetic nanomaterials at the cell membrane to selectively permeabilize the more compliant cancer cell membranes but not the stiff healthy cell membranes. Systemic delivery chemotherapeutics is toxic to all cells but more so to cancer cells due to the high metabolic rate of cancer cells. Targeted drug delivery using antibody tagged drug carriers reduces the dosage required to kill cancer cells and thereby mitigate the toxicity associated with systemic drug delivery. But the lack of unique targetable biomarkers on aggressive cancer cells such as 3º negative breast cancer makes the targeted drug delivery option a non-starter. But with the recent advances in biophysics, it is well documented that cancer cells have significantly different cell membrane stiffness in comparison to healthy cells. Cancer cell membranes are less stiff and more compliant, and the cells as a whole are easily deformable. The difference in membrane physical properties can be exploited by applying a force that is above the threshold required to permeabilize the cancer cells, but the force is still below the threshold required to permeabilize normal cells. While the cancer cell permeabilization and cancer cell-specific drug delivery have been validated in vitro, it is not known how effective such systems are in vivo. Studies that have tried to validate magnetic field directed drug delivery systems in vivo did so by sticking a permanent magnet on the tumor site before administering the nanocarriers intravenously or intratumorally. The requirement to know the tumor location beforehand to use magnetic targeting is the shortcoming of previous studies as such targeting modes offer no advantage over surgical re-sectioning, which is the current standard of care. Therefore, in this proposed study we will validate a label-free magnetic nanocarrier system (PEG-MagSiNs, PEG-Dox-MagSiNs) that will localize to cancer cells without the need for prior knowledge of the cancer cells location in vivo. We will exploit this property for selective drug delivery and gene delivery to cancer cells. In this project the students will get exposure to (a) the conjugation of multiple therapeutics to PEG-MagSiNs; (b) design multiple modes of drug delivery from the PEG-MagSiNs (ON-Demand, stimuli dependent, enzymatic release, etc.) and (c) execute in vitro cell and in vivo mouse studies that show selective targeting of PEG-MagSiNs to metastatic breast cancer cells and improved survivability in the sample group.
1. Chen Q1, Schweitzer D, Kane J, Davisson VJ, Helquist P. “Total synthesis of iejimalide B” J Org Chem. 2011 Jul 1;76(13):5157-69
2. Guduru, R.; Liang, P.; Runowicz, C.; Nair, M.; Atluri, V.; Khizroev, S., "Magneto-electric Nanoparticles to Enable Field-controlled High-Specificity Drug Delivery to Eradicate Ovarian Cancer Cells." Scientific Reports 2013, 3, 2953
3. Nallathamby, P. D.; Hopf, J.; Irimata, L. E.; McGinnity, T. L.; Roeder, R. K., "Preparation of fluorescent Au-SiO2 core-shell nanoparticles and nanorods with tunable silica shell thickness and surface modification for immunotargeting." Journal of Materials Chemistry B 2016, 4 (32), 5418-5428.
Project: Phononic nanoparticles for low-loss, tunable nanophotonics in the mid- and far-IR
Professor Anthony Hoffman • Electrical Engineering • 266 Cushing Hall • 574-631-4103 • firstname.lastname@example.org
Professor Ryan Roeder • Aerospace & Mechanical Engineering, Bioengineering Graduate Program • 148 Multidisciplinary Research Bldg • 574-631-7003 • email@example.com
Phononic nanoparticles are a new class of optical materials with untapped potential for realizing new mid- and far-infrared detection and sensing nanotechnologies that are functionally analogous to ultraviolet and near-infrared plasmonic nanotechnologies but with even greater sensitivity. Phononic nanotechnologies have potential application in analytical chemistry, biomedicine, environmental science, homeland security, astrophysics, and geology. However, basic scientific knowledge of the governing structure-property relationships for engineering the optical properties of phononic nanoparticles are not well understood or developed. Therefore, students on this project will investigate the optical properties of candidate phononic materials using both modeling and experimental characterization of synthesized nanoparticles. As such, this interdisciplinary research experience will cut across both materials science and optical science.
Project: Fabrication of ductile yet tough polymer nanocomposites
The purpose of this project is to create a polymer composite material with great ductility yet high tensile strength. It is uncommon for a material to exhibit both of these properties, as high strength is generally accompanied by a low ductility. However, the possible combination of these two properties is desirable as it would allow for a material to undergo significant strain without the risk of failure. This would be especially useful in the area of flexible electronics as it would allow for the development of reusable devices. Therefore, the focus of this project is to develop and optimize a procedure that would allow for the extreme flexibility of polymer film to be combined with the high tensile strength of molecularly aligned polyethylene nano films. Applicants studying engineering and with some lab experience are preferred.
Project: Therapeutic cell engineering with synthetic nanoparticles
Professor Prakash Nallathamby • Aerospace & Mechanical Engineering • 145 Multidisciplinary Research Bldg • 574-631-5735 • firstname.lastname@example.org
Professor Donny Hanjaya-Putra • Aerospace & Mechanical Engineering, Bioengineering Graduate Program • 141 Multidisciplinary Research Building • 574-631-2291 • email@example.com
Endothelial colony forming cells (ECFCs) are a population of rare stem cells identified from circulating adult and human cord blood. Due to their robust clonal proliferative potential and ability to form de novo blood vessel in vivo, ECFCs have been used in pre-clinical and clinical studies as a therapeutic candidate to treat peripheral artery disease (PAD) and critical limb ischemia (CLI). During the course of chronic diseases (e.g., cardiovascular diseases and diabetes) and aging, resident and circulating endothelial cells are subject to stress-induced premature dysfunction that limits their therapeutic use. The objective of this project is to utilize synthetic nanoparticle and surface cell engineering to improve the therapeutic potential of ECFCs. The student will synthesize and characterize nanoparticles, as well as quantify drug release. The student is expected to maintain stem cell cultures and study cell-material interaction using microscopy and molecular biology techniques. Students with a background in mechanical engineering, chemical/bio-engineering, materials science, or biochemistry are encouraged to apply. Prior lab experience is preferred.
Project: When shock-waves and nanoparticles collide
Professor Svetlana Neretina • Aerospace & Mechanical Engineering • 370 Fitzpatrick Hall • 574-631-6127 • firstname.lastname@example.org
Professor Karel Matous • Aerospace & Mechanical Engineering • 367 Fitzpatrick Hall • 574-631-1376 • email@example.com
When a bubble rapidly collapses in solution it gives rise to a shock wave that influences its local environment. This so-called cavitation process can be detrimental to nearby metal surfaces as the cyclic stress caused by the repeated exposure to imploding bubbles can cause fatigue-related defects and failures. These same defects, however, can be highly beneficial when occurring in a metal nanostructure. This project, therefore, aims to demonstrate cavitation as a simple and inexpensive means for positively impacting the properties of metal nanoparticles dispersed in solution as well those that are immobilized on solid surfaces. Various aspects of the project include the (i) design, construction, and validation of an apparatus capable of producing collapsing cavitation bubbles, (ii) simulations of the cavitation process and its expected influence on metal nanoparticles, (iii) synthesis of nanoparticles, and (iv) characterization of nanostructures before and after their exposure to cavitation using scanning electron microscopy and transmission electron microscopy. The student working on this project will carry out the experimental aspects of this project by working in close collaboration with members of the Nanomaterial Fabrication Research Lab (Prof. Neretina) while computational work will be carried out at the Center for Shock-Wave Processing of Advanced Reactive Materials (C-SWARM, Prof. Matous). Students with experience in design, computation, fluids, and materials are preferred.
Project: Designing an optical stage for the light-driven synthesis of nanomaterials
Schematic of an optical stage.
This research position will entail the design and implementation of research devices geared toward the development and improvement of nanomaterial manufacturing processes. We are currently pioneering light-driven chemical syntheses for manufacturing nanomaterial-based high-sensitivity chemical and light sensors. With recent successes, we are looking to build an optical stage to increase the capabilities of our process. The optical stage will include mounting options for a variety of optical filters, polarizers, and light sources. Additionally, it will include a spectrometer attachment to monitor the chemical growth process in real time. The objective over the course of the summer will be to design, machine, assemble, and test the device as an improvement to current lab equipment used for light-driven growth processes. The project will involve CAD design, material selection and analysis, and culminate in the machining of the device in the AME machine shop. The undergraduate responsible for this project will work closely with Ph.D. students in the lab. Students with experience in design, machining, and materials are preferred.
Project: Intermetallic hydrogen separation membranes: towards unprecedented permeability and stability
Figure 1. Ball model of ordered intermetallic compounds (left), with the different elements in well-defined positions within the lattice, and randomly disordered alloys (right), where the different elements are positioned randomly throughout the lattice.
Intermetallic compounds are solids composed of at least two metals that form an atomically ordered crystal structure with well-defined stoichiometry, in contrast to randomly disordered alloys (see Figure 1). The ordered crystal structure of intermetallic compounds results in some unique properties that have been exploited in several fields, including building materials and catalysis. One promising application of intermetallic compounds, which has received little attention thus far, is for hydrogen separation membranes. We hypothesize that intermetallic membranes will exhibit greater permeability and stability than the current state-of-the-art disordered alloy membranes. This is important because the biggest obstacle preventing commercialization of metal-alloy membranes for industrial hydrogen separation applications is their poor chemical stability in the presence of contaminating gases that are common in hydrogen-containing gas streams, such as CO, propylene, and H2S. The goals of this project are to determine whether intermetallic membranes are more stable than metal-alloy membranes in reactive gas mixtures, and to determine the underlying mechanisms that control their stability. To achieve these goals, the student will work closely with a graduate student to (1) prepare a series of palladium-based intermetallic membranes (PdCu, PdAu, PdRh, and PdIn) using electroless deposition, (2) measure hydrogen permeation rates across the membranes in pure hydrogen and in the presence of CO, propylene, and H2S in a membrane testing apparatus, and (3) characterize the used membranes using a variety of techniques, including temperature programmed oxidation, x-ray photoelectron spectroscopy, and scanning electron microscopy. When successful, this project will lead to new strategies for designing hydrogen separation membranes with unprecedented permeability and stability, which will reduce the costs and environmental impact of industrial chemical processes. Laboratory experience (e.g., gas chromatography, mass spectrometry) is preferred though not required.
Project: Molecular layer-by-layer thin film composite membranes for separations
Professor William Phillip • Chemical & Biomolecular Engineering • 205F McCourtney Hall • 574-631-2708 • firstname.lastname@example.org
Professor Jennifer Schaefer • Chemical & Biomolecular Engineering • 205G McCourtney Hall • 574-631-5114 • email@example.com
Next-generation polymer membranes are sought after for many applications including desalination, water purification, organic separations, and flow batteries. Thin film composite (TFC) membranes, wherein a nanometrically thin selective layer is backed with a porous support, have maintained a significant market share of commercial organic separation membranes for many years. The active layer in these TFC membranes is produced by conventional interfacial polymerization, and exact concentrations of monomers and other conditions can drastically impact the overall density of network crosslinks, defect density, and surface roughness. This variability makes fundamental structure-property studies difficult. In this project, the molecular layer-by-layer (mLbL) method will be adopted to create uniform and reproducible TFC membranes. In the mLbL approach, monomer solutions are successively coated onto the substrate and then excess rinsed away such that the active layer is densely grown in a layer-by-layer fashion. The student will be tasked with setting up equipment to perform automated mLbL in a reproducible fashion. Once the experimental setup is demonstrated, novel TFC membranes will be fabricated and characterized. The ideal candidate for this position would have a background in chemical engineering.
Project: Nanoparticle contrast agents for quantitative molecular imaging with CT
Molecular imaging with computed tomography (CT) could offer a single, low-cost and widely available modality for combined molecular and anatomic imaging at high spatiotemporal resolution. Nanoparticles (NPs) comprising high-Z metals, such as Au, have gained recent interest as X-ray contrast agents due to enabling the delivery of a greater mass payload compared with molecular contrast agents used clinically. Core-shell NPs are designed in our laboratory for strong X-ray contrast, biostability, multimodal/multi-agent imaging, and targeted delivery. Concomitant developments in photon-counting spectral CT are also transforming the capabilities of CT by providing quantitative multi-material decomposition. Applications include quantitative molecular imaging of multiple probe/tissue compositions, specific cancer cell populations (e.g., HER2+ breast cancer cells, cancer stem cells, etc.), tumors, associated pathologies (e.g., microcalcifications), drug delivery, and biomaterial degradation using both conventional CT and photon-counting spectral CT. Research opportunities are available for nanoparticle synthesis and characterization, image acquisition, image reconstruction and decomposition, and imaging applications using in vitro and in vivo models, depending on student interest and educational background.
Project: Polymers in next-generation rechargeable batteries
Advanced energy storage devices are sought after for use in electric vehicles and in conjunction with solar farms and wind farms for load leveling of the electric grid. To meet the cost and performance requirements of these applications, new battery chemistries are under development. Many of these battery designs incorporate functional organic components, such as polymer electrolytes, polymer coatings at the electrode-electrolyte interface, and polymer binders in the electrodes. In this project, the student will synthesize and characterize new organic materials for applications in rechargeable lithium, magnesium, or aluminum batteries. Multiple opportunities are available. Students with educational backgrounds in chemical engineering, chemistry, polymer science/engineering, or materials science/engineering are preferred.
1. H. O. Ford, L. C. Merrill, P. He, S. P. Upadhyay, and J. L. Schaefer, "Cross-Linked Ionomer Gel Separators for Polysulfide Shuttle Mitigation in Magnesium–Sulfur Batteries: Elucidation of Structure–Property Relationships," Macromolecules, 2018. (Cover) https://pubs.acs.org/doi/10.1021/acs.macromol.8b01717
2. C. T. Elmore, M. E. Seidler, H. O. Ford, L. C. Merrill, S. P. Upadhyay, W. F. Schneider, and J. L. Schaefer, "Ion Transport in Solvent-Free, Crosslinked, Single-Ion Conducting Polymer Electrolytes for Post-Lithium Ion Batteries," Batteries, 4(2), 28, 2018. (Special Issue: Recent Advances in Post-Lithium Ion Batteries) https://doi.org/10.3390/batteries4020028
Project: Artificial intelligence-aided nanoparticle design
Professor Geoffrey H. Siwo • Biological Sciences • 917 Flanner Hall • 574-631-9970 • firstname.lastname@example.org
Professor Prakash Nallathamby • Aerospace & Mechanical Engineering • 145 Multidisciplinary Research Bldg • 574-631-5735 • email@example.com
Previous studies on the anti-microbial activity of nanoparticles suggest that various properties of the nanoparticles such as size, shape, charge, roughness, and coating density influence anti-microbial activity. How these physical, chemical, and electrical properties of nanoparticles interact to influence anti-microbial activity is unknown. The aim of this project is to develop an artificial intelligence framework that leverages machine learning and deep-learning algorithms to i) predict anti-microbial activity of nanoparticles based on physical, chemical and electrostatic properties, ii) discover and extract nanoparticle features from images that correlate with anti-microbial activity and iii) automatically generate nanoparticle designs based on the identified features. The project will attempt to synthesize the nanoparticles generated by the AI algorithms using similar concentrations, shapes, sizes, and chemical properties of the silica core and Au nanoparticles. Students will acquire skills in various areas including exposure to machine learning algorithms, deep learning, nanoparticles assembly and synthesis. Applicants are expected to have a background in computer science and engineering or related areas such as electrical engineering.
Project: Sub-nanometer-diameter pores for sequencing beta-amyloid variants
Professor Gregory Timp • Electrical Engineering/Biological Sciences • 316 Stinson-Remick • 574-631-1272 • firstname.lastname@example.org
Dr. Eveline Rigo • Electrical Engineering • 230 Stinson-Remick • 574-631-2334 • email@example.com
It is now possible to read directly the sequence of amino acid residues (AAs) in a proteoform and discriminate post-translation modifications (PTMs) of it with single site specificity using a sub-nanometer-diameter pore through an ultra-thin (< 5 nm thick) amorphous silicon (a-Si) membrane. When a denatured proteoform immersed in electrolyte is impelled by an electric field through the pore, measurements of a blockade in the current revealed reproducible fluctuations that were highly correlated after dynamical time warping with the volume, hydropathy and mobility associated with either a single (k =1) or two (k = 2) residues in the pore waist. The PTMs and their site assignments could be identified this way with single residue resolution. As a crucible for testing, the AA sequence of beta-amyloid (BA), the main component comprising amyloid plaques found in the brains of Alzheimer’s patients, was called with k = 1 resolution and PTMs were discriminated. In this project, undergraduate students will measure blockades associated with BA translocating through a sub-nanopore and interpret the corresponding electrical signals. Applicants with prior experience with low noise electrical measurements, transmission electron microscopy, and MATLAB, C++ and/or LabVIEW coding are preferred.
Project: Modular assembly of metamaterials using light gradient
Professor Gregory Timp • Electrical Engineering/Biological Sciences • 316 Stinson-Remick • 574-631-1272 • firstname.lastname@example.org
Dr. Eveline Rigo • Electrical Engineering • 230 Stinson-Remick • 574-631-2334 • email@example.com
The use of light gradient forces to manipulate and organize nanometer-scale matter is a radically new strategy for manufacturing nanosystems. Light gradient forces are developed by focusing a laser using a high numerical aperture objective lens on a small (nanometer-diameter) particle. Although the force is weak (<100 pN), nanometer-scale objects have a miniscule mass so that light gradients can be effective for manipulation with nanometer-scale precision over a wide field. Using the light gradient forces produced by a tightly focused, one-dimensional standing wave optical trap (SWOT) that is time-multiplexed across a 2D lattice, pre-fabricated, monodispersed nanoparticles (NPs) can be assembled into a three-dimensional crystal on a hydrogel scaffold to form a voxel. Thousands of NPs can be manipulated concurrently into a complex heterogeneous voxel this way, and then the process can be repeated to stitch together voxels, registered to one another, to form nanosystems of any size, shape and constituency. In this project, undergraduate students will fabricate arrays of NPs to produce metamaterials and scatter llight from them. Applicants with prior experience in optics, wet labs, and MATLAB, C++ and/or LabVIEW coding are preferred.
Project: Synthesis and measurement of charge switching in mixed-valence molecules
Professor Emily Tsui • Chemistry and Biochemistry • 278 Stepan Hall • 574-631-0005 • firstname.lastname@example.org
Professor Gregory Snider • Electrical Engineering • 270/275 Fitzpatrick Hall • 574-631-4148 • email@example.com
Diagram of molecule to be used as electronic device.
In today’s high-density integrated circuits, the real limit to progress is the problem of power dissipation. Since microprocessors can stretch the limits of cooling by dissipating more than 100 W/cm2, design compromises, such as multi-core processors and dark silicon, must be made. Advances in fabrication technology have delivered more than a billion transistors per square centimeter, but they cannot all be fully utilized without melting the chip. Using molecules as electronic devices is attractive because molecules are small, have interesting functionalities, and operate at room temperature. Molecules make poor conductors, but are very good at localizing charge. The plan is to use an electron, localized on a “dot” within the molecule (see figure), that can be switched to the other dot by an electric field. This can be used to encode information and provide the basis for computation. In this interdisciplinary project that combines chemistry and electrical engineering, an undergraduate researcher will work with the research group to synthesize molecules and use them as electronic device elements. Direct electrical measurements will be made on the synthesized molecules to confirm, for the first time, the controlled switching of an electron within a single molecule. Students will work on the synthesis of molecules, as well as making precision low-noise electrical measurements. Chemistry, electrical engineering, and physics students are preferred.
Project: Control theory of ecosystems
Figure 1. Schematics of Evolutionary Control. Our goal is to develop a theory that will allow manipulating biosocial evolution by topological and parametric perturbations. The fundamental object we aim to control is not populations, but the structure of interactions.
Evolutionary control has a long history starting with agricultural domestication and culminating into contemporary genome editing technologies. However, this history is largely limited to controlling individual species. We view ecological and biosocial networks as the new circuit board, and evolution as a manufacturing process capable of fabricating eco-machines. Evolutionary control promises terraforming worlds, degrading pollution, and manufacturing astonishing compounds. This is a theoretical / computational project that aims to establish an analytical framework to steer the evolution of multiple populations that strongly interact with one other. Specifically, we wish to theoretically understand how to manipulate the connectivity of networks representing ecological or biosocial webs, which range from bacterial biofilms to rainforests. The project particularly focuses on ecological control under noisy or incomplete knowledge of the existing interactions and population levels of species. The project requires mathematical and computational dexterity. Applicants are expected to be familiar with MATLAB, differential equations / dynamic systems, and linear algebra.
Project: Targeting therapeutics through supramolecular affinity
We are motivated to advance the practice of therapeutic nanotechnology by capturing several of the benefits of antibody targeting while avoiding some known complications. Antibodies are used for targeting due to high affinity and biological tissue-specificity. There are, however, downsides to antibody use in nanomedicine that could present issues in application moving forward: (i) Antibodies are fundamentally opsonins, a bio-recognizable signal that promotes cell-mediated uptake and clearance of foreign particles (e.g., viruses) by the reticuloendothelial system. Can we use alternative high-affinity targeting groups that would not be subjected to active biological clearance? (ii) A typical therapeutic nanoparticle (diameter ~50-100 nm) endowed with antibodies (hydrodynamic diameter of ~10 nm) would be expected to have its surface properties and function altered by addition of this bulky appendage; furthermore, there is limited area on the nanoparticle surface to attach such a large targeting group. Can we design targeting based on minimal groups that have comparable affinity while limiting impact on the properties of the functional nanoparticle? Using ultra-high affinity supramolecular interactions as a type of “molecular Velcro” our group envisions a new therapeutic nanoparticle targeting axis built on minimal small molecule affinity motifs that serve as drivers of localization, in lieu of large targeting antibodies, while at the same time not sacrificing any affinity relative to an antibody-antigen interaction. An undergraduate working on this project will be expected to learn techniques for formulating synthetic nanoparticles to contain drugs and quantifying drug release using a combination of spectroscopy and chromatography. Additionally, this individual will be tasked with validating this mechanism for targeting in vitro through microscopy of fluorescent nanoparticles on cultured cells. Students studying chemistry, chemical engineering, materials science, or bioengineering are encouraged to apply. A minimum of some prior laboratory coursework is expected.
Project: Effects of acidity and salinity on polymer drug-delivery complexes
A host of interesting phenomena, both biological and technological, involve the complexation of charged polymers; these may be long polymers with well-defined secondary structure, such as proteins1, linear polyelectrolytes, or multi-branched species2. A particularly interesting phenomenon within polyelectrolyte solutions is coacervation3,4, a liquid-liquid phase separation where polymer-enriched liquid droplets are formed within a dilute phase5. Coacervation is an intriguing process where two primarily aqueous phases become immiscible6. Coacervates occur in many natural systems7,8, and have found application in microencapsulation9,10 and extraction11 processes, as their ultra-low surface tension allows them to readily assimilate nanoparticles or drug payloads within aqueous suspension. Complex coacervation, where two oppositely charged polymers make up the aggregate phase, is intimately related to the process of layer-by-layer deposition, where films up to micrometers in thickness are built by iterative surface adsorption of polyelectrolytes. Such films are of interest as solid electrolytes in lightweight batteries12,13, fuel-cell electrodes12,14, protective coatings14, and drug micro-encapsulation15. This topic inspires undergraduate projects involving characterization of coacervates through molecular dynamics simulation. These are focused on the use of complex coacervates in the delivery of therapeutic compounds to specific biological targets, as the highly charged, condensed environments they facilitate can act to stabilize and protect molecular and macromolecular species.
- Using a customized version of the LAMMPS open-source molecular simulation package16, the student will examine the role of pH in the complexation of long polyions in the presence of added salt. Of particular note are the connections between molecular structure and effective pKa in dilute and concentrated solutions, as this quantity determines the useful phase window for coacervates as a host material for drug delivery applications.
- A second project involves the influence of the highly charged environment provided by a complex coacervate in stabilizing drugs -- in particular protein based therapies -- against deactivation and degradation. The student will explicitly determine how these environments shift a model drug's pKa and how the native structure of therapeutic compounds is modified using either coarse-grained or fully atomistic models.
It is preferable (but not required) for students interested in this project to have prior experience with writing computer code (C++ preferred) and with scripting languages such as python and bash to facilitate running computations on the Whitmer group cluster and CRC machines.
Project: Predicting material elastic responses from molecular simulations
Elastic materials exhibit a restoring force which opposes applied stress, resulting from a perturbation away from thermodynamic equilibrium. Materials may exhibit different types of elasticity depending on their character.1 Each opposed deformation defines an elastic modulus; liquid crystals may have three or more elastic moduli characterizing their response to curvature deformations in their ordering field;2 solids, both crystalline and amorphous, also have several elastic moduli, such as the bulk modulus, shear modulus and Young's modulus. Each of these moduli may be related to derivatives of the system's free energy relative to a variable characterizing the extent of deformation. The Whitmer group has four potential projects related to measurements of elastic properties in silico, which build on recent formalisms3-5 utilizing free energy perturbation simulations to extract the elastic coefficients of liquid crystals into the domain of two dimensional membranes and three dimensional solids. We aim to characterize the typical elastic properties of each phase, and validate our data against previous simulations and theoretical models. In particular, the four projects are:
- Application of free-energy perturbations to coarse-grained and atomistic models of liquid crystals to predict elastic constants in silico, and contribute to development of a high throughput work flow for elastic property screening.
- The utilization of recently developed coarse-grained models of biological membranes to understand how the enthalpic interactions and entropic packing alter the elastic behavior of a membrane. This project also seeks to demonstrate the effectiveness of “flat-histogram" methods6 relative to fluctuation methods in determining surface tension and elasticity of membranes.
- Ionic liquid crystals, salt species which self-assemble into phases with charged and uncharged domains, have recently been of interest as novel battery electrolytes. Here we will examine the response behavior of self-assembled phases in the ionic liquid crystal [C16mim][PF6], to obtain structure-property relationships which will be useful in processing these materials.
- Coarse-grained modeling of chromonic liquid crystals, which stack into aggregates that form a liquid crystalline nematic phase. In particular, we are interested in the role of dopant molecules that create chiral stacks, and the influence this chirality has on the measured elastic coefficients.
The student will work intensively on molecular simulation models and learn techniques of advanced sampling, in particular at-histogram methods7 used for the measurement of free energies. The student will be expected to have some familiarity with writing computer codes, preferably in C++. Knowledge of undergraduate thermodynamics (any of the subjects engineering thermodynamics, physical chemistry, or statistical mechanics are good starting points). Beyond this, only general knowledge of physics and chemistry is required.
Project: Self-assembly of functional colloidal structures
Self-assembling systems are ubiquitous in nature. Using a simple palette of interactions, the world around us performs a complex and delicate dance connecting amino acids to nucleic acids, forming functional proteins and lipids, and making life possible.1,2 The level of complexity and extremely robust nature of self-assembly in biological systems has inspired scientists and engineers to mimic nature within the laboratory, with the goal of robust, scalable assembly of functional materials.3-7 The most successful approaches to robust materials assembly often derive directly from biology, either by simulating the underlying chemistry or by employing biomolecules in order to promote specificity in interactions. Though the rules of assembly are similar, biological adaptations have the advantage of millions of years of evolution relative to a few decades of focused self-assembly research. Hence, laboratory results are not always successful. It is common for systems to form partial aggregates, unintended assemblies, or disordered glassy configurations.8-10 We are interested in making the assembly of colloidal materials more robust, and take inspiration from the large array of beautiful and functional crystal structures available to metal-organic frameworks (MOFs). In this project, students will be working with coarse-grained models of anisotropic colloids to build colloidal lattices, and study their assembly and stability properties. This work serves as a fundamental study that can support the design of colloidal photonic crystals, and further serve as a model system in which to test ideas surrounding the assembly and stability of MOFs and other small molecule-derived crystals. The student will build molecular simulation models and learn techniques for statistically characterizing the properties of crystal lattices, in addition to thermodynamic integration and manifold reduction methods. The student will be expected to have some familiarity with writing computer codes, preferably in C++. Beyond this, only general knowledge of physics and chemistry is required. Prior courses in engineering thermodynamics, physical chemistry, or statistical mechanics are helpful, but not required.
Project: Physical mechanisms of Hofmeister effects
Many ionic solutions exhibit species-dependent properties, including surface tension and the salting out of proteins. These effects may be loosely quantified in terms of the Hofmeister series, first identified in the context of protein solubility. It is important for the accuracy of theoretical and computational modeling that a clear understanding of the mechanisms underlying the Hofmeister effects be developed. In this project, we focus on the use of a coarse-grained model for polar fluids known as the Stockmayer fluid, and its role in solvating molecular species. We will be interested in how strongly solvated ions within a liquid phase can be systematically altered to be surface adsorbers or desorbers based on ionic size, charge, structure, and polarization. The work will involve use of advanced algorithms for the computation of free energies in order to understand how ion solvation and local fluid configurations contribute to the preferred placement of ions in the liquid. The student will build molecular simulation models and learn techniques for statistically characterizing the properties of crystal lattices, in addition to thermodynamic integration and manifold reduction methods. The student will be expected to have some familiarity with writing computer codes, preferably in C++. Beyond this, only general knowledge of physics and chemistry is required. Prior courses in engineering thermodynamics, physical chemistry, or statistical mechanics are helpful, but not required.