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research.shtml
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<!--#include virtual="header.html" -->
<body>
<!--Center for Molecular Modeling-->
<div id = "cmm">
<div class="row-fluid" align="center">
<h2>Center for Molecular Modeling - University of Pennsylvania</h2><br><br>
<div class="thumbnail span8 offset2">
<img src="assets/images/linkerzoom.jpg">
<div class="caption">
<p>Figure: Visualization of the coxsackie adenovirus receptor (CAR) and carbon nanotube simulation setup. The enlarged portion is a linker site in which the protein is covalently bonded to the nanotube.</p>
</div>
</div>
</div>
<p>
During the summer of 2007, I participated in the
Research Experience for Undergraduates (REU) program
at the University of Pennsylvania with the A T Charlie Johnson Group.
While I was there,
experiments on single walled carbon nanotube (SWNT) field effect transistors
(FET) functionalized with biomolecules were underway. These experiments
demonstrated that these devices possess extraordinary chemical sensing and
protein-binding detection applications.
Functionalizing SWNT field effect transistors with single stranded DNA create devices
with different electronic responses when exposed to various gases. <sup>1, 2</sup>
Hence, this work shows promise in "electronic nose" and/ or "electronic tongue" applications.
Moreover, other work within the group focuses the detection of proteins associated with human
infection of the adenovirus. Infection by adenovirus is initiated by the binding of two
proteins: CAR and Knob. This group was able to covalently functionalize CAR to SWNT FETs
and use these devices to detect CAR-knob binding<sup>3</sup>. This demonstrates that the biological
CAR- Knob can be immobilzed on the surface of a single walled carbon nanotube without
losing its biological functionality.
</p>
<p>
In addition to the experimental work, attention
has also been brought to computational simulation methods. In particular, my work entailed
performing a series of molecular dynamics (MD) simulations on biological-molecule / nanotube systems
in order to obtain a detailed atomic scale picture. More specifically, we investigated the
process in which the coxsackie adenovirus receptor (CAR) protein is immobilized on SWNT.
We conducted MD on an isolated, unbound
CAR in aqueous solution, the protein covalently linked to the nanotube, and the protein non-
specifically adsorbed to the nanotube. Furthermore, we also considered the possible linking sites
of the protein, the conformational changes of the protein, the maximum and average height of
the protein above the nanotube. The focus of this discussion will be on utilizing MD tools to
verify existing experimental data as well as obtaining atomic resolution picture of the
immobilization process between the CAR protein and a single walled carbon nanotube.
We have found that CAR does not undergo major conformational changes upon SWNT binding and retains
a low RMSD with respect to the unbound structure, reinforcing interpretations of recent
experiments that suggest that CAR in complex with SWNT retains its biologically active form.
We also report that four particuarly promising sites in which the protein can link to
the nanotube. The focus of my work was utilizing MD tools to verify existing
experimental data as well as obtaining atomic resolution picture of the immobilization
process between the CAR protein and a single walled carbon nanotube.
</p>
<p>
Click here for an abstract of my <a href="http://mrsec.org/highlights/2008/06/12/carbon-nanotube-biosensors">work</a>.
<br> This has also led to the following <a href="http://pubs.acs.org/doi/abs/10.1021/jp901999a">publication</a> (first appeared May 2009).
<br><a href="http://www.library.upenn.edu/scitech/engineering/featured.html">Featured Image</a>
</p>
<br>
<hr>
</div>
<!-- Columbia Research -->
<div id = "nec">
<br><br>
<div class="row-fluid" align="center">
<h2>Nanoscale Engineering Center - Columbia University</h2>
<div class="thumbnail span4 offset4">
<img src="assets/images/ntcolumbia1.jpg">
<div class="caption">
<p>
Figure: Scanning Electron Microscope image of a carbon nanotube device in which
the nanotubes align themselves with the 'floating' gold posts.
</p>
<p>Source:</font><a href="assets/docs/app_phys_a.pdf" >Banerjee, White, Huang, Rego, O'Brien, & Herman</a></p>
</div>
</div>
</div>
<p>
During the academic year at Columbia, I worked in Professor Herman's group on the assembly
of nano-electric devices. In particular, we were interested in creating single walled carbon
nanotube devices using dielectrophoresis. At a high level this means that
we used E-Fields to help align nanotubes. We used the property that nanotubes tend to allign with
an external electric field in order to align the nanotubes along our devices.
</p>
<p>
Our samples are typically two gold pads separated by either
3 or 10 nanometers. These pads are then contacted by electrodes using a probe station,
where a potential difference is applied. This creates an electric field across the gap, whose
value depends on the geometry of the gold. We have found that we can further enhance the field
across the gap by placing 'floating posts' within the gaps. An example of one of our samples
can be seen in the SEM image above. To read more about this work, see the publications section.
</p>
<p>
Additionally, we are also investigating methods on improving electrical properties of the devices
we create. So far, we have
examined methods such as annealing the samples, electrodepositing palladium compounds on the
samples, and shining UV light onto the samples. In my last semester, specifically, my main
tasks involved working on a probe station
electrodepositing a palladium compound onto the samples as well as performing before and after IV
measurements on the nano structures. From these measurements, we can monitor the change in
electrical resistance of the devices.
</p>
<div align="center">
<a href="cv.shtml#publications">See publications</a><br><br>
</div>
</div>
<hr>
<!-- LRSM Research -->
<div id="lrsm">
<div align="center">
<h2>The Laboratory for the Research and Structure of Matter <br>(LRSM):<br>
University of Pennsylvania<br></h2>
</div>
<p>
During the summer of 2006, I participated in a National Science Foundation (NSF) program called
Research Experience for Undergraduates in Professor Luzzi's Group. I worked on a project
investigating factors that lead to the controlled growth of single walled carbon
nanotubes. The concentration of the catalyst solution, the effect of fast-heating vs. slow-heating,
and the direction of the gas flow relative to tube growth were studied in respect to nanotube
densities (number of nanotubes per gap) and nanotube orientation in the growth of single
walled nanotubes across 4 µm gaps via chemical vapor deposition. Samples were characterized
through the use of scanning electron microscope imaging. In the growth of nanotubes formed from
iron/molybdenum nanoparticles, it is observed that the fast growth method produced a higher nanotube
density than does the slow growth method.
</p>
<p>
We also reported that as concentration of the catalyst
solution increases, the tendency of particles depositing on the substrate increases as well as the
particles’ tendency to agglomerate. Thus, the appropriate solution must have a catalyst
concentration high enough such that enough particles are deposited on the substrate,
but low enough such that agglomeration that causes surface diffusion does not have a dominant effect.
The catalyst solution concentration that produced the highest nanotube density yield was
10mg Fe(NO3)3: 100 mL 2-Proponal. Moreover, there is also a noticeable morphology difference between
the deposited catalyst particles from fast heating growth and particles from slow heating growth.
We believe this difference to be due to thermal fluctuations caused by the fast-heating method
as well as grain coarsening in the slow-heating method.
</p>
<p>
For the complete report, click <a href="assets/docs/REUFinal.pdf">here</a>.
</p>
</div>
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