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Research Experience for Undergraduates (REU)

Undergraduate Research at the Nano-Bio Interface

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The Nano/Bio Interface Center (NBIC) at the University of Pennsylvania seeks highly qualified and motivated undergraduate applicants for its Undergraduate Research at the Nano-Bio Interface program for summer 2015.

This 10-week program is designed to give undergraduate students the opportunity to work with scientists on the cutting-edge of nanoscale research. NBIC capitalizes on Penn's recognized strengths in design of molecular function and quantification of individual molecules, and has led interdisciplinary, internationally recognized research around the themes of biomolecular optoelectronic function and molecular motions.

Students in this summer research program will work with a mentor in an NBIC investigator's laboratory on a project appropriate for the duration of the program. Students will gain experience with substantial aspects of doing science: experimental design, data collection and communication of results. Important components of the program are the activities that complement the lab research: seminars, paper discussions, career sessions and skills workshops.

Student participants will earn a $5000 stipend (before taxes, paid in installments). Students will be housed within walking distance of the university. Students will need to pay for their own housing, which will be at a subsidized/reduced rate. Philadelphia is an exciting place to live for the summer, with many social and recreational activities.

Program at-a-glance

Focus: Nanoscale research opportunities across a wide range of disciplines from materials science, mechanical engineering, chemistry, physics, biology, bioengineering, physiology, chemical engineering and electrical engineering.

Dates: June 1 – August 7, 2015 (10 weeks)

Location: University of Pennsylvania, Nano-Bio Interface Center in Philadelphia, Pennsylvania

Eligibility: You must be an enrolled undergraduate student, who will not graduate before the summer program ends. Students attending a college or university other than Penn are invited to apply.* You must be a U.S. citizen or permanent resident to participate in this program.

The University of Pennsylvania values diversity and seeks talented students from diverse backgrounds. We strongly encourage women, underrepresented minorities, individuals with disabilities and veterans to apply. One of the program's goals is to have enough underrepresented minority participation in each cohort to explore diversity in STEM issues in meaningful and effective ways.  

*Penn students looking for summer research opportunities are encouraged to look at http://www.pathwaystoscience.org/.

Stipend: $5000 (before taxes, 9 AM – 5 PM full-time participation for the duration of the program is expected)

Application Components: a) online application form, b) personal statement (1-page), c) two letters of recommendation, d) transcript from your current school and from all colleges you have attended and e) resume (1-page). These components are described in the application form below.

For files with page limits (e.g., statement, resume), please respect the requested length limitations. Files longer than the limit will not be reviewed.

Application Deadline: 5 PM, Feb. 27, 2015 (applicants will be notified of the status of their application by April 1, 2015)

Apply: [ Online Application Form ]

Contact: Kristin Field, PhD, NBIC Director of Programs, kfield@seas.upenn.edu, 215-746-2488


 

click arrow CLICK to See Past REU Information
REU 2013
Class of 2014

 

CLASS of 2014
Student (click name for abstract) Home university Lab placement
Mary Frances Barr Eastern University Jorge Santiago (ESE)
Nupur Bhatt Cornell University Russell  Composto (MSE)
Christopher Caulfield New Jersey's Science & Tech University Bodhana Discher (Biochem/Biophysics)
Malgorzata Chwatko University of Connecticut David Issadore (BE)
Raymundo Moya Rice University Paul Ducheyne (BE)
Camri Robinson Louisiana Tech University Haim H. Bau (MEAM)
Rodrigo Rodriguez New Mexico State University A.T. Charlie Johnson (Physics)
Jerry Shih SUNY College of Nanoscale Science & Engineering Paulo E. Arratia (MEAM)
Luke Villermin Louisiana Tech University Robert Carpick (MEAM)
Daniel Wilson Clarion University Marija Drndic (Physics)

 

2014 Abstracts

Electropolymerization of Conducting Polymers for Pseudocapacitive Devices
Mary Frances Barr, Eastern University
Santiago-Avilés Group, Electrical and Systems Engineering

We report on the pseudocapacitive properties of the electrically conducting polymers: poly-pyrrole and poly-(3,4-propylenedioxythiophene) (ProDOT).  Due to their pseudocapactitance, electrically conducting polymers have intermediate energy density and power as compared to batteries and capacitors.  With these characteristics, electrically conducting polymers hold the potential of becoming a valuable energy storage material.  Each monomer was polymerized by electropolymerization individually.  A copolymer of pyrrole and ProDOT in a 1:1 ratio was electropolymerized to investigate the effects of monomer ratio and concentration on the capacitance of a pseudocapacitve device.

Measuring the nano-mechanical properties of pH responsive bilayer brushes using scanning probe microscopy
Nupur Bhatt, Cornell University
Composto Group, Materials Science and Engineering

The change in mechanical properties of polymer bilayers chitosan (top)-poly (acrylic acid) (bottom) and quaternary ammonium chitosan (top)-poly (acrylic acid) (bottom) at different pH was determined using colloidal probe atomic force microscopy. Polymer bilayers capable of reversible swelling such as these show promise as platforms for drug delivery. Monolayers of poly (acrylic acid) (PAA), chitosan (CH), and quaternary ammonium chitosan (CHQ) were also mechanically characterized to determine their individual influence on the bilayers. Force v. indentation curves were acquired to determine the adhesion and elastic modulus, and lateral friction loops were acquired to determine the friction force of each film. The adhesion of the bilayers was influenced by their top layer, while the elastic modulus and lateral stiffness was influenced by the underlying layer.

Quantification of Amphiphilic Protein Maquettes in Various Solutions using the Bradford Assay
Christopher Caulfield, New Jersey's Science & Tech University
Discher Group, Biochemistry and Biophysics

In experiments involving trans-membrane protein maquettes, quantification of these maquettes was achieved through the use of the Bradford Assay. Other protein assays were rejected for various reasons, including incompatibility with the solution and logistical concerns. It was found, as was theorized, that the relationship between the concentration of the protein and the ratio of absorbances at 595 nm and 466 nm was linear. It was also found that the surfactant (detergent) do-decyl maltoside (DDM) reacted undesirably with the assay, and that the detergent poly(ethylene glycol) octyl ether (octyl-POE) was much more compatible with the Bradford Assay, especially in the presence of membrane lipids. It was also discovered that a slightly higher concentration of octyl-POE (2% vs 0.5% by volume) was more conducive to the quantification process. And finally, it was proven that the observed changes in absorbance were indeed due to the protein maquette, and not any absorbance by the lipids, because the absorbance of a solution containing just lipids and no protein maquette was substantially lower than that of a solution which contained both the lipids and the maquettes.

Digital droplet-based isothermal quantification of DNA
Malgorzata Chwatko, University of Connecticut
Issadore Group, Bioengineering

The development of polymerase chain reaction (PCR) changed genetic analysis dramatically. The set up allows users to focus on one specific gene and amplify said gene in order to enhance the user's ability to study it. One current application of PCR is the identification of whether a certain gene is present in sufficient quantities to make an impact on an organism such as cancer. But even though various modifications and improvements were made to PCR, its use is still not popular in a clinical setting. This project attempts to combine the benefits of isothermal and droplet digital PCR by creating a device able to perform isothermal reactions in microliter sized droplets. This device is inexpensive, highly accurate, and easy to use, allowing for better adaptations of PCR in clinical settings.

Zwitterionic Sol-Gel Films to Prevent Bacterial Adhesion
Raymundo Moya, Rice University
Ducheyne Group, Bioengineering

Current research suggests that zwitterionic surfaces can prevent the adhesion of bacteria.  Herein, we functionalized sol-gel films with ionic moieties so as to impose a zwitterionic nature. The zwitterionic capacity was endowed to sol-gel film through two different routes: co-condensation (one-pot synthesis) and post-grafting. Silica precursor with charged moieties, including N-(trimethoxysilylpropyl) ethylenediaminetriacetate (TEM), (3-Aminopropyl)triethoxysilane (APTES) and carboxyethylsilanetriol (CES) was co-condensed with tetraethyl orthosilicate (TEOS) to form sol-gel films with zwitterionic groups. The post-grafting involved an addition step to modify the surface of TEOS derived silica film with aforementioned organosilanes. The bacteria attachment, contact angles, and degradation rate of the sol-gel films were evaluated. Results confirmed a decreasing bacterial adherence among the zwitterionic films compared to unmodified sol-gel film. However, the anti-fouling effect was strongly correlated to degradation rate of the films, suggesting improving stability of modified sol-gel film should be considered for future study.

Imaging Processes in Liquids with Nanoscale Resolution Using Graphene
Camri Robinson, Louisiana Tech University
Bau Group, Mechanical Engineering and Applied Mechanics

Imaging dynamic processes in their native liquid states in real time at the nanoscale has been a significant challenge in microscopy. Observing these processes in real time, particularly biological processes, could provide essential information and insight to structural details. Typically, to capture dynamic events in real time, one must freeze a sample at specific time intervals during a process and take snapshots at each time. Each static image shows a single stage in the dynamic process and are later merged together to create a dynamic video, much like a flipbook makes a series of pictures appear to be animated when flipped through rapidly. Although this method has been responsible for many advances in microscopy, it still does not guarantee that images are taken at the most significant moments. The nanoaquarium, developed by Joseph Grogan and Haim Bau at UPenn, allows for samples to be observed in their native liquid environments in real time using two silicon nitride membranes sandwiched together. We investigate the effects of using two graphene membranes in the fabrication of the nanoaquarium instead of the silicon nitride membranes to increase imaging resolution and contrast, leading to a better understanding of important dynamical processes.

[ Visit the Bau Lab web pages to watch Camri's final presentation of her summer research. ]

Graphene field effect transistors for breast cancer diagnosis
Rodrigo Rodriguez, New Mexico State University
Johnson Group, Physics and Astronomy

We report the manufacturing of a device to detect the cancer indicative biomarker HER2 (human epidermal growth factor receptor 2) protein. The genetically engineered single chain variable fragment (scFv) of the immunoglobulin of HER2 protein, with high selectivity towards the HER2 protein, was attached to graphene field effect transistors (GFETs) using pyrene-NHS as the linking molecule. Electron transport properties of the GFETs are measured before and after each chemical alteration. A shift in the current vs. gate voltage (I-Vg) curve is observed after the addition of the biomarker that is dependent upon the concentration used. Concentrations ranging from the pico to microgram could be successfully detected and differentiated. A model of the Hill-Langmuir modeling plot was then fit to the data to quantitatively track the response of the devices as a function of HER2 concentration.

Undulatory Swimming in Viscoelastic Fluids Under Confinement
Jerry Shih, SUNY College of Nanoscale Science & Engineering
Arratia Group, Mechanical Engineering and Applied Mechanics

The effects of confinement on the swimming behavior of model organism, Caenorhabditis elegans, in viscoelastic fluids is experimentally investigated by tracking the nematode's motion though channels of varying widths. We observed a direct relationship between channel width and swimming velocity. Compared to boundless conditions in viscoelastic fluids, introduction of channel walls can significantly decrease swimming speed.

Understanding the Effects of Colloidal Roughness on Atomic Force Microscopy Measurements of Hydrogel Mechanics
Luke Villermin, Louisiana Tech University
Carpick Group, Mechanical Engineering and Applied Mechanics

Micro- and nano-scale hydrogel structures pose much potential for developing intelligent drug delivery systems that can both sense and respond directly to patho-physiogical conditions of a patient.  To characterize the structural and mechanical properties of these systems (such as elastic modulus) at a small scale an accurate estimation of the contact area formed between the sample surface and a colloidal probe can be obtained using Atomic Force Microscopy (AFM).  However, when fitting these measurements with the commonly used Hertz Model, the effects of probe roughness on contact area are usually not considered.  Here we first show the contamination of colloids as received from the vendor and how the roughness of a colloidal probe can be varied with different cleaning procedures.  We then test the effects of colloidal surface roughness on elastic modulus measurements of Poly acrylamide hydrogels when fitting with the Hertz Model.  It is concluded that high surface roughness increases contact area against a deformed gel, thus lowering the modulus measurement.

Fabrication of Nanocolumns to Improve Solid-State Nanopore DNA Sequencing
Daniel Wilson, Clarion University
Drndic Group, Physics and Astronomy

Measuring changes in ionic current as molecules pass through a solid-state nanopore has recently enabled detection of nucleotide bases in short (30 base-pairs) ssDNA homopolymers (poly(dA), poly(dC), poly(dT)). Multiple problems stand in the way of sequencing genomic information, such as secondary structures in ssDNA, signal noise produced by capacitance, and resolution of individual bases. Here we address the problem of single stranded DNA's tendency to fold and form secondary structures that can interfere with the ionic signals at the nanopore. Secondary structures can be eliminated with heat (~90°C), but this increases the speed at which the DNA translocates through the pore, making it harder to resolve a readable signal. Nanocolumns have been shown to spatially confine DNA and force it into a single-stranded conformation. We fabricate nanocolumns on silicon nitride (SiN) using electron beam lithography. Nanocolumns are a promising method of eliminating secondary structures in solid-state nanopore sequencing.

 

REU 2013
Class of 2013

 

CLASS of 2013
Student (click name for abstract) Home university Lab placement
Roland Beard University of Pittsburgh Paul Ducheyne (BE)
Michael Cao Cornell University Shu Yang (MSE)
Christine Emery Swarthmore College Andrew Tsourkas (BE)
Audrey Green Rutgers University Arjun Yodh (Physics)
Alexa Kuenstler University of Rochester Karen Winey (MSE)
Brent Powell Morgan State University Jeffery Winkler (Chem)
Margaret Prendergast University of Maryland Virgil Percec (Chem)
Jaclyn Robustelli Iona College Jorge Santiago (ESE)
Charles Roco Virgina Tech Russell  Composto (MSE)

 

2013 Abstracts

Controlled Release of Antibiotics from Polymer-coated Mesoporous Silica Nanoparticles
Roland Beard, University of Pittsburgh
Ducheyne Group, Bioengineering

The purpose of this study is to determine the release kinetics of antibiotics by polymer coated mesoporous silica nanoparticles (MSNs). The desired release profile is characterized by a zero order release over an extended period of time. We synthesized MSNs with aldehyde surface functionalization in order to covalently bond the polymer layer. To maximize the amount of antibiotics absorbed, the pores of the functionalized MSNs were expanded by a hydrothermal treatment prior to drug loading. In vitro release studies of both chitosan and poly (ethylene glycol) (PEG) coated MSNs showed an initial burst followed by constant release for over 4 weeks. The in vitro release study of the uncoated functionalized MSNs showed a minor initial burst release followed by a linear release for over 4 weeks. We have shown the capability of non polymer coated MSNs to attain desirable release profiles. As for the polymer coated MSNs, further research is required to determine the reason for the lack of control of the release of the antibiotics.

 

Topologically Induced Square Lattice of Focal Conic Domains in Smectic Liquid Crystal
Michael Cao, Cornell University
Yang Group, Materials Science and Engineering

The formation of Focal Conic Domains (FCD) in smectic liquid crystals under contrasting homeotropic and planar anchoring is an interesting study due to its potential application in soft patterning.  By using two substrates with 1-D channels, a square lattice of FCD’s are formed with each domain’s hyperbola in the same direction.  Experiments show that domain size and the location of the point defect can be controlled by the angle and spacing of the substrates.  While the exact mechanism behind the formation of the FCD remains to be investigated, it has been shown that using 1-D substrates is a viable way to control patterned FCD formation.

 

Synthesis and Liposome Encapsulation of Hydrophilic Iron Oxide Nanoparticles for Combined Magneto-thermal Therapy and MRI Imaging
Christine Emery, Swarthmore College
Tsourkas Group, Bioengineering

Superparamagnetic iron oxide nanoparticles for drug delivery and magnetic resonance imaging (MRI) must be hydrophilic for successful transport into the body. This study focuses on coating hydrophobic SPIONs with hydrophilic compounds to generate water soluble nanoparticles that can subsequently be encapsulated in liposome. Three different hydrophilic compounds were tested: dopamine hydrochloride, dimercaptosuccinic acid (DMSA), and zwitterionic dopamine sulfonate (ZDS). Only the ZDS-coated SPIONs were water soluble and exhibited stability with regard to size, magnetic sensitivity, and time. While liposome formation using a thermo-responsive lipid (DPPC) in the presence of ZDS-coated SPIONs was possible, successful encapsulation of nanoparticles was not achieved.

 

Improving Accuracy of Diffuse Correlation Spectroscopy Instrumentation: Measuring Cerebral Blood Flow
Audrey Green, Rutgers University
Yodh Group, Physics

Diffuse Correlation Spectroscopy (DCS) is a medical instrumentation pioneered at University of Pennsylvania that measures cerebral blood flow (rCBF).  DCS has been applied in a clinical setting to neonates born with congenital heart defects in a joint study between the University of Pennsylvania and the Children’s Hospital of Philadelphia in order to study the timing and evolution of brain injury.  Neonates born with congenital heart disease (CHD) have a higher incidence of neurocognitive impairment.  DCS can potentially offer doctors constant, noninvasive bedside monitoring of rCBF in high risk patients, such as neonates with CHD.  Our goal was to improve quantification of DCS instrumentation.  Methods include accounting for artifacts caused by blood flow changes in the skull/ scalp in DCS readings, designing a double layer phantom to model the skull/ scalp and brain, the addition of patient specific absolute properties in DCS computing, as well as correcting DCS probe/tissue interface boundary conditions.

 

Electric Field Alignment of Ion-Containing Block Copolymers
Alexa Kuenstler, University of Rochester
Winey Group, Materials Science and Engineering

Ion-containing block copolymers are intriguing materials for their potential uses as solid-state electrolytes.  However, little is known about the mechanism for ion conduction in these materials.  The aim of this project is to explore the method of aligning the nanostructured morphology of these materials using an applied electric field to provide a framework for investigating the relationship between morphology and conductivity.  Samples of PS-b-PMMA + EMIM-TFSI and PS-b-PAEBIm-TFSI were cast in toluene and exposed to varying field strengths during solvent evaporation.  Following electric field exposure, samples were evaluated for microdomain alignment using scanning electron microscopy (SEM).  In PS-b-PMMA + EMIM-TFSI, alignment of lamellae was seen for field strengths greater than 210 V/mm, demonstrating it is possible to align ion-containing block copolymers.  Microphase separation but no alignment was observed in PS-b-PAEBIm-TFSI exposed to a field strength of 50 V/mm however, it is believed that alignment could be achieved in this material at higher field strengths. Electric field alignment can be used to manipulate ion-containing block copolymer nanostructures, and this experimental tool can be used in future studies to investigate the effect of these nanostructures on conductivity. 

 

Synthesis of Functionalized Helical Protein-Protein Interaction Inhibitors for HIV-1 Antiretroviral Therapy
Brent Powell, Morgan State University
Winkler Group, Chemistry

Our initial investigation is concerned with synthesizing enantiomerically pure Hünlich base. Enantiopure Hünlich base monomers will be used in the stereo-selective synthesis and study of novel helical systems that will serve as platform for the development of inhibitors of protein-protein interactions (PPIs) for HIV-1 Antiretroviral Therapy. Previous work done in this area by the Winkler’s Research Group focused on the design of helical protein- protein interaction (PPI) inhibitors from Tröger’s Base derivatives which is structurally similar to these Hünlich base derivatives studied. Here we  proposed that these  compounds that we will design, which are larger than classical α-helix mimetics that have been previously been proposed and  are not protein based and therefore not subjected to proteolytic degradation, and so will be more effective in disturbing PPIs for HIV-1 antiretroviral therapy.

 

Chirality of Self-Assembling Supramolecular Dendrimers
Margaret Prendergast, University of Maryland
Percec Group, Chemistry

From drug delivery to electronics, self-assembling synthetic complexes such as supramolecular dendrimers offer many applications in chemistry, biology, physics, medicine and nanoscience. [1]. The aim of this study is to understand the effects of chirality on the dendronized cyclotriveratrylene (3,4)dm8*G1-1-CTV and  the dendronized perylene bismide (3,4,5)dm8*G1-1-PBI through the comparison of elongation temperatures and molar enthalpies of  R,S, racemic by mixing and racemic by synthesis CD and UV-vis spectra in solution. Cooling scans were taken of each molecule to determine elongation temperature and molar enthalpy. Spin coated thin film experiments were performed to compare with solution. Thin film results were in agreement with solution results of CTV molecules, while thin film experiments with PBI molecules provided mixed results. Chirality was found to affect the self-assembly of (3,4)dm8*G1-1-CTV but not (3,4,5)dm8*G1-1-PBI. Results are in agreement with solid state experiments previously performed in Percec Laboratory.

 

Construction and Characterization of Electrical Double Layer, Pseudo, and Hybrid Capacitors: Using Poly-(3,4-propylenedioxythiophene) and Various Carboneus Materials
Jaclyn Robustelli, Iona College
Santiago-Avilés Group, Electrical and Systems Engineering

Energy storage has been a topic of increasing interest with the increasing utilization of non-renewable resources.  It has been projected that there will be a significant increase in energy consumption by the year 2040.  Electrochemical capacitors are fairly new devices that achieve greater power density than conventional batteries.  Unfortunately, conventional capacitors lack in having high energy density.  Supercapacitor devices are technological improvements in electrical engineering that achieve higher energy densities than conventional capacitors.  Further advancements in increasing both the energy and power densities are significant areas of research. 
There are different types of supercapacitors: electrical double layer capacitors, pseudo-capacitors, and hybrid capacitors.  Electrical double layer capacitors, EDLC, have high power density while pseudo-capacitors have high energy density. A hybrid capacitor is the combination of an EDLC and a pseudo-capacitor, which will hopefully result in a device with both high energy and power density. 
Four different methods were tried to attempt to build a hybrid capacitor with activated carbon and conductive polymer, 3,4-propylenedioxythiophene (ProDOT).  One method was electropolymerization of poly-ProDOT on the electrodes and then adding a thin activated carbon film.  Another method was adding a thin activated carbon film with pinholes to the electrodes first and then electropolymerization of the electrode.  A more rudimentary method started with electropolymerization of poly-ProDOT on the electrodes and then subsequently rubbing together the polymerized electrode with the activated carbon film.  The last method that was used was drop casting activated carbon dispersed in propylene carbonate.  The most promising method that yielded the highest capacitance was the drop casting method.  However, due to time constraints, other methods were sought that were more time efficient.  The next most favorable method was rubbing the polymer and activated carbon film together.  This yielded a higher capacitance than the other methods previously mentioned.  However, this potential method of creating a hybrid capacitor must be further refined.

 

Mapping Actin’s Role on Cytoplasmic Viscoelasticity
Charles Roco, Virginia Tech
Composto Group, Materials Science and Engineering

A novel method in atomic force microscopy (AFM) has been developed that enables viscoelastic mapping across a soft tissue at the nanoscale. AMFM mode operates with a series of feedback loops while oscillating the cantilever at its resonant frequency.  Feedback loops collect information across both first and second order frequencies to output the appropriate signals used to calculate viscoelasticity.  Connective tissue cells comprised of fibroblasts are treated with the mycotoxin cytochalasin D to measure the effects of actin depolymerization on cellular viscoelasticity.  Actin filament retraction and cell softening at the cytoplasmic level are noticeable trends which further intensify as cytochalasin D concentration increases.  Thus, proving the capability of AMFM’s high resolution tracking on soft tissue, a goal not yet achieved until now.  Polyacrylamide gels with varying defined elastic moduli are created as means for a calibration method to confirm accuracy of AFM viscoelastic modeling calculations.  Quantified progression of cytochalasin D treated fibroblasts in conjunction with a proper calibration technique has established proof of concept for AMFM mode and has opened a gateway for simpler, yet more resolute viscoelastic measurements.


 

 

REU Class of 2010
Class of 2010

 

CLASS of 2010
Student (click name for abstract) Home university Lab placement
Charles Majdalani University of Texas at Austin Bau group (MEAM)
Rosa Santana-Carrrero University of Puerto Rico, Mayaguez Daldal group (Biology)
Priya Balasubramanian Duke University Yang group (MSE)
Peter Forzaglia Manhattan College Lee group (CBE)
Adrian Levine The University of Western Ontario Tsourkas group (BE)
Stephanie Cheung Grinnell College Jouille group (Chemistry)
Jorrell Fredericks Alabama State University Johnson group (Physics)

 

Heater Design For Loop- Mediated Isothermal Amplification (LAMP)

Charles Majdalani, University of Texas at Austin
Bau Group, Mechanical Engineering and Applied Mechanics

This study demonstrates the ability to produce a portable, chemical heater that does not require electrical power.  The heater provides the temperature required for DNA amplification using the loop-mediated isothermal amplification (LAMP) reaction.  The heater is integrated into a chip containing LAMP reagents.  When saliva is injected into the chip, the heater will activate the process.  After completion, an indicator will display the diagnostic results.  The chip requires a flameless, chemical heater to heat the reagents to the optimal reaction temperature.  The components of this chip are inexpensive, making it viable for use in impoverished regions without access to diagnostic laboratories.  Currently, the chip research is directed towards rapid detection of the Human Immunodeficiency Virus (HIV).  In the future, the chip will be able to identify other diseases such as malaria.
 

Determining the role of CcmI in the maturation of Cytochrome c2 in Rhodobacter capsulatus

Rosa Santana-Carrrero, University of Puerto Rico, Mayaguez
Daldal group, Biology

The maturation process of c type cytochromes has been studied extensively in recent years and Cytochrome maturation system I (Ccm), one of the three proposed systems, consists of approximately 10 genes that encode membrane-bound components such as CcmI. This is a bipartite membrane protein in R. capsulatus, thought to be a chaperone of the apocytochrome c that forms a heme ligation core complex with CcmF and CcmH. The role of CcmI in the maturation of the cytochrome c2 was analyzed by studying protein-protein interactions between CcmI and apocytochrome c2.
 

Fabrication of Superhydrophobic Surfaces Using Functionalized Silica Nanoparticles

Priya Balasubramanian, Duke University
Yang group, Materials Science and Engineering

A superhydrophobic surface is a phenomenon that can be characterized by the creation of a Cassie-Baxter wetting state indicated visually by high water repellency. The underlying mechanism to create a surface demonstrating the Cassie-Baxter wetting state is two-fold. The first mechanistic requirement necessitates roughness on the surface to allow for minimum contact of water with the surface. This requirement will be met through the self-assembly of silica nanoparticles on the substrate. The second mechanistic requirement is the use of a low surface energy material as a top surface coat to create chemically inherent water repellency. The presence of the Cassie-Baxter wetting state is measured through the contact angle of a five-microliter water droplet on the surface. A surface which has a static contact angle with a water droplet of 150 degrees or greater is labeled as a superhydrophobic surface. Through the application of functionalized silica nanoparticles to create dual scale roughness (two different sized nanoparticles coated as subsequent layers) followed by the deposition of a low surface energy coating on the surface of silicon wafers and fabric, the Cassie-Baxter wetting state was achieved. Two different varieties of functionalized nanoparticles were prepared and individually experimented with: aminopropyl-functionalized particles and fluorocarbon-functionalized particles. While the fluorocarbon-functionalized nanoparticles were hydrophobic by nature, the aminopropyl-functionalized nanoparticles necessitate a low surface energy top coating to allow for chemical hydrophobicity when fabricating the superhydrophobic surface. The cost-effectiveness and ease of coating the surface due to the silica particles, as well as the optical transparency that comes with the nano-scale roughness is beneficial in practical applications.

Layer-by-Layer Assembly of Functional Thin Films With an Application in Renewable Energy

Peter Forzaglia, Manhattan College
Lee group, Department of Chemical and Biomolecular Engineering

Layer-by-Layer assembly is a precisely tunable and versatile technique that can be used to form functional thin films. By varying the materials and assembly conditions, the range of functions of these films can also vary immensely. Mastery of this technique can have incredible implications in optics, biology, separations, and renewable energy. This research was conducted to find the optimal conditions for the assembly of TiO2 and carbon nanotube layers so that a composite film with photocatalytic properties can be formed. It was found that the addition of polymers (PSS and PEI) between the nanoparticle layers was critical for the adsorption of these particles. Salt-free solutions with a pH of 3 yielded the best results on the glass substrate for all attempted nanoparticle/polymer sequences. As a side project to the research, it was proven that LBL could not only be done in water, but also nonpolar solvents like toluene. This will widen the range of materials that can be assembled via LBL and make it even more valuable in even more fields.
 

Functionalization Of Glycol Chitosan Via The Hydroxyl Group With The Amine Group Protected

Adrian Levine, University of Western Ontario
Tsourkas group,
Bioengineering

The amine group on carbon 2 of glycol chitosan has an unusually low pKa, making it titratable at physiological pHs. This gives the polymer and its derivatives the potential to have pH dependent biological functions. However, to date, most functionalizations of glycol chitosan have been accomplished by reacting this amine group, resulting in the loss of this pH responsiveness. This paper delineates a facile protocol that allows for amination of the hydroxyl groups and conjugation of the created amine groups while the pH responsive amine group is protected with a pthalimide group.  This allows for the polymer to be functionalized with any amine reactive group while maintaining the original amine group, which is subsequently deprotected.
 

Second Generation Synthesis of Trichodermamides

Stephanie Cheung, Grinnell College
Jouille group, Chemistry

The trichodermamide family of natural products consists of three unique dipeptide compounds, trichodermamides A, B, and C, isolated from the marine-derived fungus Trichoderma virens. While trichodermamide A shows limited bioactivity, trichodermamides B and C show significant cytotoxicity against human colorectal carcinoma HCT-116 (IC50 of 0.32mg/ml). Due to the biological significance and structural novelty of the trichodermamides, two total syntheses have been reported: a racemic total synthesis of trichodermamide B by the Zakarian group, and a enantioselective total synthesis of trichodermamides A and B by the Joullié group. Although the Joullié synthesis successfully synthesizes trichodermamides A and B, it contains problematic factors that could be improved upon. Moreover, a total synthesis of trichodermamide C is yet to be reported. Therefore, we are interested in developing a second generation total synthesis of trichodermamides A and B as well as the first total synthesis of trichodermamide C. Herein is described the proposed synthetic plan as well as the current progress of the second generation synthesis.
 

Optimization of Carbon Nanotubes

Jorrell Fredericks, Alabama State University
Johnson group, Department of Physics and Astronomy

Carbon nanotubes, also known as CNTs, are allotropes of carbon with a cylindrical nanostructure. Nanotubes have been constructed with length-to-diameter ratio of up to 132,000,000:1. Since their discovery, carbon nanotubes (CNTs) have been widely studied due to their large potential applications. These cylindrical carbon molecules have novel properties that make them potentially useful in many applications in nanotechnology, electronics, optics and other fields of materials science as well as potential uses in architectural fields. They exhibit extraordinary strength and unique electrical properties, and are efficient thermal conductors. Nanotubes are categorized as single-walled nanotubes (SWNTs) and multi-walled nanotubes (MWNTs). First produced in arc-discharge process or by laser-ablation, the CNTs grown by catalytic chemical vapor deposition (CCVD) have been showing however a large expansion for the past decade. What is actually the role played by the catalyst in the CCVD of CNTs? In this paper, we will discuss the influence of the composition of the catalyst material, of the morphology of the catalyst nanoparticles, of the support, of the preparation method of the nanoparticles.
 

 

REU Class of 2009
Class of 2009
Front: Marc van der Rijin, Abdul-Rahman Raji, Nanette Jarenwattananon, Laura Tanebaum; Second row: Jennifer Winkler, Lianette Rivera, Oscar Beteta, Luis Reyes; Back: Jennifer Kay, Derek Lee, Jonathan Rosen, Swarnali Sengupta not pictured: Yewande Alade

 

CLASS of 2009
Student (click name for abstract) Home university Lab placement
Yewande Alade Swarthmore College Robert Carpick
Oscar Beteta Bucknell University Daniel A. Hammer
Ninnette Jarenwattananon Barnard College Joshua Wand
Jennifer Kay University of Pittsburgh Daeyeon Lee
Derek Lee Boston University Jorge Santiago-Avilés
Abdul-Rahman O. Raji Morgan State University Christopher B. Murray
Lianette Rivera Baez University of Puerto Rico, Mayaguez Fevzi Daldal
Luis E. Reyes Rowan University So-Jung Park
Jonathan Rosen Lehigh Univedrsity Ju Li
Swarnali Sengupta Johns Hopkins University Robert L. Mauck
Laura Tanenbaum Rice University Kathleen Stebe
Marc J. van de Rijn Stevens Institute of Technology Beth Winkelstein
Jennifer Winkler University of Rochester Gianluca Piazza

 

CLASS of 2008
Student Home university Lab placement
Ian Clark University of Oregon Degrado Group
Orielyz Flores University of Puerto Rico at Cayey Santiago Group
Kendrick Hernandez University of Puerto Rico-Mayaquez Carpick Group
Matthew Kraeutler University of Virginia Composto Group
Brenna Krieger Rutgers University Goldman Group
Elliot Nelson Wheaton College Chen Group
Laurent Palmatier University of California, San Diego Bau Group
Frances Rodriguez University of Puerto Rico at Cayey Dmochowski Group
Swarnali Sengupta Johns Hopkins University Mauch Group
Serina Woods Norfolk State University Yodh Group
Livia Zarnescu University of Arizona Bonnell Group

 

Read details of former REU student participants

Class of 2007

Manpreet Sen, George Washington University
Manipulations of the Oxygen Scavenger System for Optimal Fluorophore Activity (read abstract)
worked in Yale Goldman’s group

Ricardo Rivera, University of Puerto Rico, Cayey
Fabrication of Oriented Polyethylene Oxide Microfibers Through Electrospinning (read abstract)
worked in Jorge Santiago-Aviles’ group

Kelisha Kuykendall, University of South Texas
Synthesis of Metal Polypyridyl Based Porphyrin Supermolecule for Non-Linear Optical Studies (read abstract)
worked in Michael Therien’s group

Kelly McCarthy, Pennsylvania State University
Synthesis, Characterization, and Assembly of CdSe Nanorods (read abstract)
worked in Marija Drndic’s group

Evan Reed, The College of New Jersey
FEM Modeling of Contour-Mode RF Piezoelectric Resonators (read abstract)
worked in Gianluca Piazza’s group

Arelys Rosado, University of Puerto Rico, Rio Piedras
Temperature Dependence of Domain Polarization on BaTiO3 Thin Film and Single Crystal (read abstract)
worked in Dawn Bonnell’s group

Class of 2006

Gloriell M. Cardona, Mathematics, University of Puerto Rico at Cayey
Study of the Use of Ferrofluid & Ferro-Wax as a Pumping & Valving Mechanism (read abstract)
worked in Haim Bau’s group

Tyson Moyer, Materials Science and Engineering, Cornell University
Forced Unfolding of Actinin Visualized in Embryonic Cardiomyocytes (read abstract)
worked in Dennis Discher’s group

Jessica Ortiz, Chemistry, University of Puerto Rico at Cayey
Crack Free PZT films by Sol-Gel Synthesis (read abstract)
worked in Dawn Bonnell’s group

Josean Paulino Sustache, Physics, University of Puerto Rico at Humacao
Electrostatic Deposition of Nanofibers for Gas Sensors (read abstract)
worked in Jorge Santiago-Aviles’ group

Diana Tomezsko, Chemistry, LaSalle University
Studies toward the Use of PPES and PNES Polymers to Dissolve and Separate Nanotubes (read abstract)
worked in Michael Therien’s group

During the summer of 2006, six students from across the country and Puerto Rico participate in the 10-week research program.  Their research is highlighted in the following sections.  
If you would like to participate in the Summer 2007 program, click here.

NBIC REU, Class of 2007

REU Group, 2007
REU Students, 2007

 

Synthesis of Metal Polyridyl Based Porphyrin Supermolecule for Non-Linear Optical Studies

Kelisha Kuykendall, Texas Southern University
Advisor: Dr. Michael Therein

Porphyrins, a large class of deeply colored dyes, provide an interesting research opportunity because of their unique optical properties. Besides their biological significance, porphyrins have also been studied extensively from a materials scientific point of view. A unique class of supermolecular chromophore based on metal polypyridyl complexes and porphyrins have been developed in Therien lab. Completing the syntheses of these chromopores can be challenging. In this report the synthesis of RuPZn chromophore from commercially available reagents is discussed in detail.
 

Synthesis, Characterization, and assembly of CdSe-based nanorods

Kelly McCarthy,  Pennsylvania State University 
Advisor: Marija Drndić

Controlled alignment of semiconductor nanorods is desired for ongoing work involving individual nanorod luminescence, as well as transport measurements over an array of nanorods.  This paper documents the characterization of CdSe nanorods prepared by several methods of synthesis.  The concentration of solvents from which the nanorods are deposited on TEM grids has an effect on the assembly of nanorods before applying an electric field which has previously been found to influence the order within nanorod films, and to lead to nanorod alignment.  When dropcast on a carbon grid, a dilute solution of CdSe rods assemble relatively randomly, but showing small tracks about five rods.  However for a more concentrated solution of rods, multiple layers appear to form and track length increases to about fifty rods. An applied electric field during the drop-cast is expected to increase the order parameter further. 
 

Fabrication of Oriented Polyethylene Oxide Microfibers Through Electrospinning

Ricardo Rivera, University of Puerto Rico at Cayey
Advisor: Dr. Jorge Santiago

Polyethylene oxide (PEO) fibers with sub-micron scale diameters were synthesized through electrospinning.  The fibers were deposited in a near-parallel arrangement through the use of a custom-made electrospinning apparatus consisting of a rotating target anode and a linearly translating syringe cathode.  The fibers exhibited diameters ranging from 0.7 microns to 55 microns, and were characterized using optical microscopy and surface-enhanced Raman spectroscopy (SERS).  In addition, PEO fibers containing silver nanoflakes (5 weight percent, mean diameter of 100nm) were synthesized and characterized in the same fashion.  In both cases, the diameters of the fibers varied only with changes in the rate at which the polymer solution was pumped to the syringe cathode.  Samples of both types of fibers were also sintered in a vacuum oven at 200°C for 30 minutes and 180°C for 10 minutes, and were characterized via the aforementioned techniques.  Although the sintered fibers exhibited enhanced signals during SERS, they also fluoresced more than the unsintered samples and were thus less amenable to this type of characterization.
 

Manipulations Of The Oxygen Scavenger System For Optimal Fluorophore Activity

Manpreet Sen, The George Washington University
Advisor: Dr. Yale E. Goldman

Single molecule observations utilizing fluorescent probes are often plagued by short, intermittent light signals.  Fluorophores are essential to biological research, allowing researchers to observe molecular conformational changes and interactions with other molecules. Extended fluorophore lifetime is desirable and is currently achieved with the use of various anti-fade reagents. For each type of fluorescent probe different reagents were tested. Using the FIONA (Fluorescence Imaging with One Nanometer Accuracy) microscope, images of the fluorescent signals were captured under an assortment of conditions. Analysis of the images led to determination of the appropriate reagents and protocols for several types of fluorophores.

Note:  Ms Sen’s paper was recently published in journal of undergraduate research at The George Washington University called Inquiry, volume 5 (Spring 2008)

 

NBIC REU, Class of 2006

REU 2006
 

 
A Study of the Use of Ferrofluid and Ferro-Wax as a Pumping and Valving Mechanism

Gloriell M. Cardona
Mathematics, University of Puerto Rico at Cayey
Advisor:  Dr. Haim Bau

This research project is focused on studying the feasibility of using ferrofluid and ferro-wax as a pumping and valving mechanism in a microfluidic device.  The material used to create the chip was polycarbonate (PC).  Since it was found that controlling surface properties is necessary to create an effective pumping system, oxygen, and argon plasma treatment in addition to poly(vinyl pyrrolidone) or PVP solution application were used to make PC hydrophilic.  This is reflected by the water contact angle.  It decreased from ~ 45º to ~7º on all the treated samples.  In order to bond treated PC without reversing the plasma treatment, using a temperature less than 140 ºC, different bonding techniques using acetone and PVP were tested.  Dipping the PC in acetone and applying it using a pipe cleaner were the most effective techniques to use before using the thermal bonding press.  For future work, a further study of the use of ferro-wax as pump and valve is also necessary to determine at what parameter are these materials more effective.
 

Forced Unfolding of Actinin Visualized in Embryonic Cardiomyocytes

Tyson Moyer

Materials Science and Engineering, Cornell University
Advisor:  Dr. Dennis Discher

α-Actinin is a member of the spectrin family and known primarily for cross-linking actin proteins.  It is involved in the formation of the cytoskeleton and connection to the plasma membrane.  The structure of α-Actinin is comprised of four spectrin repeats, EF-hands, and an actin-binding domain.  Previous research has shown that α-Actinin unfolds under force from Atomic Force Microscopy (AFM), which leads to the possibility of force-dependent change in cells.  The work described in this paper is a study designed to determine whether the unfolding of α-Actinin occurs under force from within embryonic cardiomyoctes through the exposure of a mutated cysteine inside the protein.  Using mutagenesis, cysteines in the spectrin repeats of α-Actinin are replaced by alanine, without any change to the structure.  Then, one cysteine is mutated into the protein at the inside of one of the three helices in the fourth spectrin repeat, so that a cysteine dye will not fluoresce under normal conditions.  By transfecting the mutated Actinin protein in chicken cardiomyocytes, the presence of a conformation change can be determined.  Under the forces in the beating cardiomyocytes, the α-Actinin undergoes forces strong enough to create a change in conformation.  The change in protein shape can be determined by causing any exposed cysteines to fluoresce, since the cysteine that was previously hidden will become exposed after the protein has unfolded.  Evidence that α-Actinin unfolds can show that it is involved in a force-sensitive pathway within the cell. 
 

Crack Free PZT films by Sol-Gel Synthesis
 
Jessica Ortiz
Chemistry, University of Puerto Rico at Cayey

Advisor:  Dr. Dawn Bonnell

Ferroelectric films are the materials of great technological importance.  These films could be used as a storage media (Fe-RAM, for example).  The other reason attractive application of those films is the study of domain specific reaction.  For these applications high quality ferroelectric films are required.  The most common ferroelectric material is Pb(Zr, Ti)O3, a.k.a. PZT. Many groups are synthesizing PZT but procedure varies from group to group as well as film quality (multiphase composition and grain size). In this work we found an optimal condition for the synthesis of crack free PbTiO3 films with grain size smaller then 1 mm.
 

Electrostatic Deposition of Nanofibers for Gas Sensors

Josean Paulino Sustache
Physics, University of Puerto Rico at Humacao
Advisor:  Jorge Santiago

This work addresses the formation of nanofibers of tin oxide (SnO2) and carbon by using electrospinning aiming at application as gas sensors. The tin oxide (SnO2) fibers were electrospun from a precursor solution containing 100 mg poly (ethylene oxide) (molecular weight 900 000), 10 ml chloroform (CHCl3) and 5 ml dimethyldineodecanoate tin (C22H44O4Sn). After the deposition, the fibers were sintered in a furnace for 1 h at 250, 320 and 600 ◦C, respectively. The scanning electron microscope was used to characterize the sintered fibers. After this analysis we studied the electrical conductivity of a single fiber. The carbon nanofibers used in this work were derived from a polyacrylonitrile (PAN)/N, N-dimethyl formamide (DMF) precursor solution using electrospinning and vacuum furnace techniques. The carbon fibers were observed in the optical microscope and photographed.
 

Studies toward the Use of PPES and PNES Polymers to Dissolve and Separate Nanotubes
 
Diana Tomezsko
Chemistry, LaSalle University
Advisor:  Dr. Michael Therien

Single walled nanotubes (SWNTs) are carbon tubes with a wide range of novel thermal, mechanical, and opto-electrical properties that enable them to be such a functional material.  However, for any practical application of these properties, for example in the design of an electronic or optical device, a homogenous sample of SWNTs is needed.  When synthesized, SWNTs are a tangle of sizes, shapes, and chiralities.  In this project, new strategies for obtaining a homogenous sample of SWNTs are explored.
 


 

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