Urmi Majumder

Graduate Student

Office: D104 LSRC
Department of Computer Science
Duke University
P.O.Box 90129
Durham, NC 27708-0129 USA

Phone: 1-919-660-6504
Email: urmim@cs.duke.edu

Home

Research

Interests

Computational Nanotechnology
Computational Chemistry

Computational Biology
Algorithm Design and Analysis

Stochastic Analysis
Mathematical Modeling

Education

PhD Student, Computer Science Department, Duke University, Projected Graduation Date: May, 2009
Certificate, Graduate Nanoscience Program, Duke University, Graduation Date: April, 2008
Masters of Science , Computer Science Department, Duke University, Graduation Date: October, 2007
Bachelor of Technology, Computer Science and Engineering Department, Indian Institute Of Technology, Kharagpur, India, Graduation Date: May, 2004

Recent Research Experience

Department of Computer Science, Duke University, Durham, NC (May, 2005 - present)

Thesis topic: Towards Compact Robust DNA Self-Assembly based Computation: Modeling, Simulation and Experiments
Advisers: Prof John H. Reif & Thomas H. LaBean

Simulate a finite state automata by an isothermal Whiplash PCR machine.
Design and analyze a stochastic model for reversible assemblies.
Build a proof-of-concept system for robust tile assembly and provide probabilistic guarantees on its performance.
Design and simulate magnetic assembly capable of complex computation.
Design and simulate compact self-repairing DNA lattices for biomolecular computation.
Laboratory demonstration of binary counting using DNA macromolecules.

Selected Publications:

Urmi Majumder, Sudheer Sahu and John H. Reif, Stochastic Analysis of Self-Assembly Processes, Volume 5, Number 7, pp. 1289-1305, July 2008.
John Reif and Urmi Majumder, Autonomous Reactivating Whiplash PCR for Locally Programmable Molecular Computation, DNA 14, LNCS, invited for submission in Natural Computing, Springer-Verlag NY 2008.
Urmi Majumder and John Reif, A Framework for Designing Novel Magnetic Tiles Capable of Complex Computation, UC 2008, LNCS 5204, 0129-0146, Springer-Verlag, NY 2008.
Urmi Majumder, Probabilistic Models for Damage and Self-Repair in DNA Self-Assembly, NSTI Nanotech 2008, June 1-5, Boston, MA, invited for submission in Molecular Simulation, 2008.
Urmi Majumder, Thomas H. LaBean, and John. H. Reif, Activatable Tiles for Compact, Robust Programmable Assembly and other Applications, DNA 13, LNCS 4848, pgs: 15-25, Springer-Verlag, NY 2008.
Urmi Majumder, Sudheer Sahu, Thomas H. LaBean, John H. Reif, Design and Simulation of Self-Repairing DNA Lattices, DNA 12, LNCS 4287, pgs: 195-214, Springer-Verlag, NY 2007.

Selected Technical Presentations:

Oral Talks:

Towards Compact Robust DNA Self-Assembly based Computation: Modeling, Simulation and Experiments, GHC PhD Forum, GHC 2008.
A Framework for Designing Novel Magnetic Tiles Capable of Complex Computation, UC 2008.
Towards Compact Robust DNA Self-Assembly based Computation: Modeling, Simulation and Experiments/i>, Masters Defense Presentation, Duke, October 2007.

Activatable Tiles for Compact, Robust Programmable Assembly and other Applications, DNA 13.
Self-assembly across scales, Research Initiation Project Presentation, Duke, May 2005.

Poster Presentations:

Stochastic Analysis of Reversible Assembly, GHC Technical Poster Session, GHC 2008.
Probabilistic Models for Damage and Self-Repair in DNA Self-Assembly, NSTI Nanotech 2008.
Autonomous Reactivating Whiplash PCR for Locally Programmable Molecular Computation, FNANO 08.
Isothermal and autocatalytic Whiplash PCR machines for autonomous computing, Seventh Annual Graduate Research Day, Duke, April 2008.
Activatable DNA Tiles for Compact, Error-Resilient Algorithmic Assembly and Other Applications, inDUKE Frontiers 2007.
Activatable Tiles for Compact Error-Resilient Directional Assembly, FNANO 07
Reversible Self-Assembly of Squares as a Rapidly Mixing Markov Chain, FNANO 07.
Design and Simulation of Self-Repairing DNA Lattices, FNANO 06.
Design and Simulation of Self-Repairing DNA Lattices, Sixth Annual Graduate Research Day, Duke, April 2006.

Recent Industry Experience:

Nanorex Inc, Bloomfield Hills, MI (May 2008-August 2008)

Summer Intern: Developed CAD tools for DNA and protein nanotechnology

Teaching Experience:

Department of Computer Science, Duke University, Durham, NC

Teaching Assistant for Discrete Mathematics, Instructor: B. Maggs (August, 2007 - December 2007).
Teaching Assistant for Graduate Computational Complexity, Instructor: J. Reif (January, 2007 - May 2007).
Teaching Assistant for Graduate Algorithms, Instructor: H. Edelsbrunner (August 2005- December 2005).
Teaching Assistant for Mathematical Foundations of Computer Science, Instructor: S. Rodger (Jan. 2005 - May 2005).

Responsibilities included teaching recitation, creating and maintaining class webpage, designing and grading homeworks, labs and quizzes, occasionally teaching class, holding office hours and responding to student questions and needs.

Leadership Experience/ Service:

President of the Duke Chapter of ACM-W (Spring 2008 - present).
Organizer for Biomolecular Computation Journal Club, Duke CS (Fall 2006-present).
Organizer for biweekly lunches for women graduate students in Duke CS, since October 2007.
Assistant Organizer for FNANO Conference (April 2005, April 2006, April 2007, 2008).
Referee to the Reviewing Committee of DNA12, Natural Computing, BioSystems, DISC08, SODA09.
Assisted writing NSF EMT Grant CCF-0829798: EMT/NANO: Polymerase-Based Self-Activating and Reactivating DNA Systems, (PI John H. Reif with coPI Thomas H. La Bean), 09/01/2008-08/31/2009, $200,000, with expected continued support for 2009 and 2010 for $150,000/year.
Professional Affiliations: ACM, ACM-W, ISNSCE

Relevant Coursework:

Algorithms
Complexity Theory
Computational Geometry
Randomized Algorithms
Algorithms in Structural Molecular Biology
Computational Biology

Discrete Structures
Data Structures
Graph Theory
Automata Theory
Software Engineering
Probability

Numerical Analysis
Operation Research
Computer Networks
Database Theory
Operating Systems
Computer Architecture

Skills:

Programming: Python, PyQt, C, C++, HTML, CSS.
Scripting: Perl, Shell Programming
Operating Systems: Mac OSX, Linux, Windows XP
Interdisciplinary Skills: active learning, teamwork and ability to integrate methods from different fields.
Public speaking: experience gained from conference oral/poster presentations.
Technical writing and ability to meet deadlines: experience gained from writing conference / journal papers and writing research grants.
Multi-tasking: experience gained from balancing dry and wet lab research projects, professional service and sometimes teaching.
Mentoring: experience gained from teaching recitations as a CS teaching assistant and training new lab members in biomolecular computation wet lab.
Event organization: experience gained from helping run FNANO Conference (2005- 2008), organizing ACM-W events and Biomolecular Computation Journal Club presentations at Duke.

Selected Honors:

Full scholarship to present in GHC 2008 (awarded based on the merit).
Departmental as well as graduate school travel scholarship to present in UC 2008 (awarded to post-preliminary exam doctoral candidates).
Departmental as well as graduate school travel scholarship to present in NSTI Nanotech 2008 (awarded to post-preliminary exam doctoral candidates).
Full scholarship to attend Google Workshop, 2008.
Student Travel Scholarship for DNA13 Conference, 2007 (awarded based on the merit of the publication).
Outstanding Research Initiation Project Award, Comp. Sci. Dept., Duke University, Aug. 2005 - May 2006.

Non-Academic Interests:

Scrapbooking

Music

Literature

Yoga