Seed Research

Seed #1

Molecular Logic for Nanoelectronics

Fraser Stoddart, chemistry

Following the successful demonstration (Nature 2007, 445, 414–417) of a working defect-tolerant 160,000 bit molecular memory composed of a Langmuir-Blodgett (LB) derived monolayer of amphiphilic, bistable rotaxane molecules and fabrication in a crossbar architecture with nanowires (15 nm wide polysilicon underneath and 15 nm wide Ti/Al on top sandwiching approximately 200 molecules) at a density (10¹¹ bits cm^-2) not predicted, according to the 2005 International Technology Roadmap for Semiconductors (2005 ITRS), to be reached until 2020 at the earliest, the aim of this research project is to design and synthesize, by template-directed protocols that depend upon the operation of molecular recognition and self-assembly processes, bistable rotaxanes, which are amphiphilic or functionalized for carrying out Huisgen/Sharpless-style ‘click chemistry’ with matching electrode surfaces, and undego a change in their dipole moments in response to an electrochemical stimulus that causes relative mechanical motions to occur within the bistable rotaxane molecules. Monolayers of these molecules will then be assessed in a device setting which involves a two-terminal molecular switch tunnel junction (MSTJ) to establish whether or not they can be switched electrically between high and low capacitance states, and hence, in principle at least, can serve as active reconfigurable channels in logic circuits. The research objectives will be reached by controlling the nature and location of the charged components in these nanoelectromechanical systems (NEMS) where control of the dielectric properties of monolayers of these bistable molecules (see figure below) will be achieved through dipole induction and/or charge-storage processes. The compounds that are designed to address reconfigurable molecular logic will also feature a unique collection of recognition units which could be employed to expand the available chemical space for a much wider range of applications addressable by artificial molecular machinery.

The principal mode of operation for a new bistable [2]rotaxane designed for molecular logic. An electron-poor cationic station (blue) is encircled by an electron-rich macrocycle (purple). Reduction of the blue station to its neutral state (blue with orange stripes) causes the macrocycle to move to the secondary electron-poor station (red). Returning the system to zero bias reoxidizes the blue station, creating a high dipole, charge- separated metastable state.

Seed #2

Porous Ceramics for Energy Applications

Katherine Faber, materials science and engineering

Solid oxide fuel cells (SOFCs) are efficient devices for producing electricity from a variety of gaseous fuels, including hydrogen, methane, and propane through a clean solid-state reaction.  A typical SOFC consists of a porous nickel + yttria-stabilized zirconia (Ni-YSZ) support layer and anode, YSZ electrolyte, and lanthanum strontium manganate (LSM) cathode.  The efficiency of the SOFC depends in part on the morphology of the pore network, which serves as the conduit for fuel to reach the electrolyte and reaction products to escape, and the number of triple phase boundaries (TPBs) between pore, electrolyte, and anode phases.  In particular, the tortuosity of the pore network limits transport and should be minimized while the number of TPBs should be maximized.  Thermoreversible gelcasting (TRG) provides a convenient pathway to producing net-shaped, porous bodies such as SOFC supports.  The pore networks of SOFC supports produced with this technique are evaluated using mercury intrusion porosimetry and X-ray computed tomography in order to optimize pore size and pore network morphology and tortuosity.

Thermoelectric generators provide the ability to convert waste heat from industrial processes and transportation into electricity.  Oxide-based thermoelectric generators have advantages over their more common metal counterparts due to their better temperature and environmental stability.  Calcium cobaltite-based materials have high thermoelectric figures of merit at high temperatures.  Using TRG, the material can be aligned in a chosen direction during component processing, producing anisotropic properties that improve the thermoelectric figure of merit in that direction.

X-ray computed tomography image of fully interconnected pore network in gelcast material. Approx. 30% porosity.  450 x 450 x 450 micron³.

Seed #3

Shaping Plasmonic Nanomaterials by Chemical Synthesis

Jiaxing Huang, materials science and engineering

Metal nanoparticles (e.g., Au, Ag, Cu, Al) are essential components in the toolbox of plasmonic nanostructures. Bottom-up chemical synthesis offers the potential for scaling up the materials production, as well as tailoring optical properties by fine tuning size, shape and surface beyond the conventional photolithography limit. We aim to develop rational synthesis strategies for producing nanoparticles with desired morphologies, and for building up a knowledge base of shape-properties relationships. Some examples are shown in the following figures including chemically synthesized Au nanowires with single crystalline surface (Figure a, b), Au nanocubes (Figure c) and Au nano square cuboids (Figure d). Such nanoparticles can be used as the building blocks in many areas such as plasmonic circuits, surface enhanced Raman scattering (SERS), bioimaging and even cancer therapy.

Seed #4

Dynamics of Novel Self-Assembling Protein-Polymer Hydrogels

Igal Szleifer, biomedical engineering
Guillermo A. Ameer, biomedical engineering

Hydrogels are extensively used in medical applications and they are an important class of biomaterials that are under significant study for regenerative medicine applications. They are cross-linked, three-dimensional, hydrophilic polymer networks that can swell but not dissolve in water. Hydrogels derived from biological macromolecules such as proteins and polysaccharides are of great interest to the biomedical community as they can contain intrinsic biological information or serve as an extracellular matrix mimic. The study of the properties of functional and responsive hydrogels presents a fundamental challenge with important practical applications. What are the molecular factors that determine the structure of the gel? What is the activity of specific ligands within the gel? How do pH sensitive groups respond within the network structure? In order to study these complex systems we are carrying out a combined experimental and theoretical effort aimed at the fundamental understanding of the mechanism of formation and properties of hydrogels formed by mixtures of proteins and polymers.

We have developed a novel family of water-soluble poly(diol citrates) that can mediate the formation of a protein gel via complexation. Protein-polymer gels with water content of up to 90% have been fabricated with bovine and human serum albumin, fibrinogen, and hemoglobulin without covalently modifying the protein. The gels can form within 10 minutes, depending on the protein and temperature of the gelation and degrade within 4 to 8 weeks. The overall objectives of this project include the understanding at the fundamental level of the driving forces for the formation of this class of hydrogels, the mechanism of gel formation and the identification of design criteria that would allow the formation of the protein gels for tissue engineering applications. Toward this goal, we are using a combination of theoretical studies and experimental observations to investigate the formation and properties of the gels as well as the feasibility of using these protein gels for controlled release of proteins and cell encapsulation. The results of this research will lead to a new paradigm on the mechanism for protein gel formation and protein delivery.

Schematic representation of a polymer mediated cross linked gel based on BSA proteins.

Seed #5

Analysis and Design of Genetic and Metabolic Control Systems of Bacterial Cells

Adilson E. Motter, physics
John F. Marko, biochemistry, molecular biology & cell biology/physics (joint)

Molecular biology permits custom programming of cells to carry out specific tasks, such as synthesis of specific biomolecules or modification of molecules in the extracellular environment. Further examples include formation of multicellular structures or sending chemical or optical signals in response to detection of specific molecules.

The bacterium Escherichia coli, for which there exists a staggering array of genetic engineering methods and genomic data, is well suited for such tasks. Efforts at bioengineering of E. coli depend on understanding unresolved basic questions of the mechanisms underlying control of gene expression (i.e., modulation of which genes are expressed at any given time, largely through DNA-protein interactions on the chromosome) and metabolic processes (i.e., the biochemical reaction pathways through which the basic molecules of a cell are processed).

The overall objective of this joint project between the Motter and Marko labs is to biologically engineer bacterial cells, and design them to perform specific tasks and to produce specific materials. Two complementary projects focus on understanding mechanistic aspects of gene expression and metabolic processes in E. coli. Key strengths of the project are the complementary abilities of groups in the areas of theoretical study of metabolic and genetic networks of E. coli (Motter), study of information in genetic sequences (Motter), theoretical and experimental study of protein-DNA interactions at the single-molecule level (Marko), experimental study of chromosome structure and function (Marko), and theoretical and experimental study of soft materials including supramolecular assemblies of biomolecules (Marko).

Components of the genetic and metabolic system of the bacterium E.coli explored in this project. Cyan arrows highlight protein-gene interactions (D->c), protein-protein interactions (E<->F), and the enzymatic catalysis of metabolic reactions (B->R1, G->R5). In this example, A...G represent proteins encoded by genes a...g, respectively, and R1...R6 are enzyme-catalyzed metabolic reactions interconnected by metabolic compounds (red arrows).

Selected Research Highlights:

Network-based Design of Microbial Strains for the Production of Biomaterials

A.E. Motter, T. Nishikawa, N. Gulbahce , E. Almaas , and A.-L. Barabasi

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Moldable Supraspheres Made of Metal Nanoparticles

R. Klajn, K.J.M. Bishop, M. Fialkowski, M. Paszewski, C.J. Campbell, T.P. Gray, B.A. Grzybowski

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