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Arthi

Arthi Jayaraman

After completing my postdoctoral research with
Prof. Ken Schweizer at UIUC,
in August 2008 I will be joining the Department of Chemical and Biological Engineering at
University of Colorado-Boulder as assistant professor.




Ph.D. Chemical Engineering, January 2006
North Carolina State University

M.S. Chemical Engineering, December 2002
North Carolina State University

B.E. (Honors) Chemical Engineering, May 2000
BITS Pilani, India 


Thesis Title: Pattern Recognition by Biomimetic Polymers

Advisors: Carol K. Hall and Jan Genzer

Systems of Interest:

Methods:

  • Copolymer on heterogeneous surfaces

  • DNA microarrays

  • Lattice Monte Carlo Simulations

Abstract:

The overall aim of my research has been to understand the underlying molecular phenomena governing recognition in numerous biological processes such as antibody-antigen binding, transmembrane signaling, viral-inhibition, etc. Specifically, I have used computer simulation to study the thermodynamics of recognition and selective adsorption of biopolymer sequences.

1. Designing pattern recognition surfaces for selective adsorption of copolymer sequences : Most of the theoretical work in the area of the pattern recognition by biomimetic polymers has focussed on keeping the pattern on the heterogeneous surface fixed and allowing different types of copolymers to adsorb on the surface to determine the characteristics of the copolymer that can "recognize" the surface pattern. However, the question of how to design optimal surfaces or what pattern the surfaces should have for recognizing specific monomer sequences in copolymers, had not been answered yet. To address this issue, we have developed a novel simulation method to design surfaces for recognizing specific monomer sequences in copolymers. This work provides the foundation for future work in understanding many biological processes that rely on pattern recognition, such as transmembrane signaling, pathogen-host interactions, viral-inhibition, etc. (publication 1)

2. Pattern transfer in AB diblock copolymer film adsorbed on a heterogeneous surface: In this work we investigated how a pattern imposed in a copolymer film at a certain distance from the surface propagates through the film onto an adsorbing heterogeneous surface. We examined the effect of varying the copolymer chain length, the size of the target pattern, and the distance from the surface where the target pattern is applied, z', on the extent of pattern transfer. For each chain length, target pattern, and z' we compared the energy of the system when a pattern is applied in the bulk to the energy when no pattern is applied in order to understand why a certain pattern size is transferred to the surface with higher fidelity than the others. (publication 2)

3. Molecular recognition in model DNA microarrays : DNA microarrays has been widely adopted by the scientific community for a variety of applications to reconstruct the metabolic pathways for cell operation, to identify genes that are differentially expressed in healthy versus diseased cells, etc. In order to improve performance and to design next generation microarrays there is a need for a fundamental understanding of the interplay between the various factors that affect microarray performance. To gain such a fundamental understanding we study the thermodynamics and the kinetics of hybridization of single stranded "target" genes in solution with complimentary immobilized "probe" DNA molecules on a microarray surface using a coarse-grained lattice model. We use Monte Carlo simulations to examine how various parameters affect the extent of hybridization and the kinetics of the hybridization process. This work should give a fairly broad physical picture of molecular recognition in DNA microarrays and eventually provide a set of general guidelines for maximizing microarray sensitivity and specificity. (publications 4-6)


Publications :

1. A. Jayaraman, C. K. Hall, and J. Genzer, 'Designing Pattern-Recognition Surfaces for Selective Adsorption of Copolymer Sequences Using Lattice Monte Carlo Simulation' ,
Physical Review Letters, 94,
078103 (2005)
This also appears in Virtual Journal of Biological Physics

News release about our Physical Review Letters publication

2. A. Jayaraman, C. K. Hall, and J. Genzer, 'Computer simulation study of pattern transfer in AB diblock copolymer film adsorbed on a heterogeneous surface'  J. Chem. Phys., 123 124702 (2005)

3. A. Striolo, A. Jayaraman, C. K. Hall, and J. Genzer, 'Adsorption of comb copolymers on weakly-attractive solid surfaces' J. Chem. Phys., 123, 064710 (2005)
This also appears in Virtual Journal of Biological Physics

4. A. Jayaraman, C. K. Hall, and J. Genzer, 'Computer Simulation Study of Molecular Recognition in Model DNA Microarrays' Biophys. J., 91, 2227 (2006)

5. A. Jayaraman, E. E. Santiso, C. K. Hall and J. Genzer, 'Theoretical study of kinetics of zipping phenomena in biomimetic polymers'
Phys. Rev. E., 76(1), 011915 (2007)
This also appears in Virtual Journal of Biological Physics

6. A. Jayaraman, C. K. Hall and J. Genzer, `Computer simulation study of probe-target hybridization in model DNA microarrays: Effect of probe surface density and target concentration' J. Chem. Phys., 127, 144912(2007)
Presentations :

A. Jayaraman*, `Computer Simulation Studies of Pattern Recognition in Biomimetic Polymers' oral presentation at Dept. of Chemical Engineering, University of California, Berkeley, March 21, 2006

A. Jayaraman*, `Computer Simulation Studies of Pattern Recognition in Biomimetic Polymers' oral presentation at The Center for Engineering in Medicine, Harvard Medical School, February 22, 2006

A. Jayaraman*, C. K. Hall and J. Genzer, `Computer Simulation Studies of Pattern Recognition in Biomimetic Polymers' oral presentation at the Edward M. Schoenborn Competition, Dept. of Chemical and Biomolecular Engineering, NC State University, January 24, 2006

A. Jayaraman*, C. K. Hall and J. Genzer, 'Molecular Recognition in Model DNA Microarrays: A Computer Simulation Study' oral presentation at the AIChE Conference, October 31, 2005, Cincinnati, OH

A. Jayaraman*, C. K. Hall and J. Genzer, 'Computer Simulation Studies of Pattern Recognition in Biomimetic Polymers' poster presentation at the AIChE Conference, October 30, 2005, Cincinnati, OH

A. Jayaraman*, C. K. Hall and J. Genzer, 'Pattern Recognition in Biomimetic Polymers' poster presentation at Thermo 2005, College Park, MD

A. Jayaraman*, C. K. Hall and J. Genzer, 'Designing pattern recognition surfaces for copolymers using computer simulation' oral presentation at the AIChE Conference, November 10, 2004, Austin, TX

A. Striolo*, A. Jayaraman, C. K. Hall and J. Genzer, 'Adsorption of comb copolymers on solid surfaces ' oral presentation at the AIChE Conference, November 10, 2004, Austin, TX

A. Jayaraman*, C. K. Hall and J. Genzer, 'Designing pattern recognition surfaces using computer simulation' poster presentation at the 10th PPEPPD Conference, May 18, 2004, Snowbird, UT.

A. Jayaraman*, C. K. Hall and J. Genzer, 'Designing pattern recognition surfaces for copolymers using computer simulation' poster presentation at the Richard D. Gilbert Award Symposium, ACS Polymer Discussion Group, February 12, 2004, Raleigh, NC.

A. Jayaraman*, C. K. Hall and J. Genzer, 'Designing pattern recognition surfaces for copolymers using computer simulation' oral presentation at the AIChE Conference, November 20, 2003, San Francisco, CA.






 








Last updated : July 2007
ajayara@uiuc.edu