(Committee: John Reif, Thom LaBean, Bruce Donald, Chris Dwyer)
Towards compact robust DNA self-assembly: modeling, simulation and experiments
Since our physical experiments showed that computational assemblies we developed error
correction techniques for increasing robustness in computational assemblies. We also developed a stochastic model for computing equilibrium yields and convergence rates of erroneous assemblies and error rates at near equilibrium.
Bachelor's of Technology Thesis, Spring 2003 - Spring 2004
(Supervisor, Sudeb Prasant Pal, IIT Kharagpur)
Quality of Service for internet, multimedia and other real time systems
We developed an analytical model for the top (application) layer of the internet in order to deliver better latency and QoS for various internet services and evaluated its
performance using simulation models. This also includes study of
dynamic schemes for resource management of memory and bandwidth in the
internet so that latency can be improved for the average case as well as the
worst case. The issue of real time and multimedia traffic is one step ahead of that
for networks. We incorporated parametric
decompression into the existing model to improve
the document retrieval latency for dynamic requests from huge databases.
Research Initiation Project
Fall 2005 - Spring 2006
(Committee: John Reif, Thom LaBean, Alex Hartemink, Chris Dwyer)
Self-Assembly across scales
We studied computational self-assembly processes in both nano and macro scales.
I was awarded the most outstanding Research Initiation Project, 2006 from the Department of Computer Science, Duke University for this project
.
Nanoscience Rotation Project
Fall 2007 - Spring 2008
(Committee: Thom LaBean and John Reif)
Meso-scale magnetic self-assembly capable of complex computation
We designed magnetic barcodes to encode computation in meso-scale tiles that can self-
assemble to perform computation when agitated.
Randomized Algorithms (under Prof John Reif, Spring 2006)
Probabilistic Models for Damage and Self-Repair in DNA Self-Assembly
We studied the extent of damage and inherent self-repairing capabilities of DNA-based self-assembled fragile nanostructures.
Computation Geometry (under Prof Pankaj Agarwal, Fall 2005)
Using Motion Planning to study Self-Assembly by shape recognition
We developed a framework for analyzing the dynamics of self-assembly of tiles by
shape recognition using probabilistic roadmaps.
Topics in Physical Chemistry (under Prof David Beratan, Fall 2005)
Molecular Dynamics (MD) Simulation of Holliday Junctions
We studied conformational changes in Holliday Junctions using Steered Molecular
Dynamics. This is a precurser to the MD simulations of the complex DNA-based nanostructures
that we build and characterize in our laboratory.
Foundations of Nanoscience (under Prof Chris Dwyer, Spring 2005)
Carbon Nanotube Biosensors
We did a SPICE Modeling (individual transistor and its potential device integration) and
experimentally demonstrated a single walled carbon nano-tube (SWNT) transistor. The
SWNT was prepared in a controllable way using an improved CVD method.
Design and Analysis of Algorithms (under Prof John Reif, Fall 2004)
Haplotype Inference
We studied different algorithmic and probabilistic approaches to the haplotype inference
problem.
Computational Biology (under Prof Alex Hartemink, Fall 2004)
Tool for Differential Genome Comparisons
Differential genome comparison is a method to search for the genes that are
responsible for an observed phenotype in a group of species. We developed software tool
to perform such differential genome comparisons.
