(6aq) Computational and Theoretical Studies of Soft Materials and Biological Systems

Authors: 
Jayaraman, A., University of Colorado at Boulder
Schweizer, K. S., University of Illinois at Urbana-Champaign
Hall, C. K., North Carolina State University


My research is aimed at understanding molecular phenomena at the interface between materials science and biology using computational and theoretical methods.

During my doctoral work with Prof. Carol Hall and Prof. Jan Genzer at North Carolina State University, I used computer simulations to study the thermodynamics of molecular recognition in bio-mimetic polymer systems, specifically, in the following two areas:

1.1. Designing pattern recognition surfaces for selective adsorption of copolymer sequences: We developed a novel simulation method to design surfaces for recognizing specific monomer sequences in copolymers [1]. The order parameter characterizing the surface pattern, and the surface selectivity were determined as a function of polymer-surface and polymer-polymer interactions, and the blockiness of the monomer sequence. The highlight of this work was that the designed surfaces recognize specific monomer sequences with higher selectivity than the standard checker board surfaces of sizes commensurate with the monomer sequence.

1.2. Molecular recognition in model DNA microarrays : We studied 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 [2]. We used Monte Carlo simulations to examine how various parameters affect the extent of hybridization and the kinetics of the hybridization process. This work provided a set of general guidelines for maximizing microarray sensitivity and specificity.

In my post-doctoral work with Prof. Kenneth Schweizer at University of Illinois, Urbana- Champaign, I use theoretical methods to study soft materials. Currently, I am investigating:

2.1 Structure and phase behavior of melts and dense solutions of polymer tethered nanoparticles: We have applied microscopic Polymer Reference Interaction Site Model (PRISM) theory to study dense solutions and melts of polymer tethered spherical nanoparticles. The complex interplay of entropy (translational, conformational and packing) and enthalpy (particle-particle attraction) leads to different spatial arrangements with distinctive scattering signatures. The tethered particles prefer to organize themselves in a specific geometry that is dictated by particle radius, length of the tethered polymer, number and positions of the tethered polymers, total fluid packing fraction and interfacial attraction strengths.

My future research plan is the following: (a) apply theory and simulation to study thermodynamics and kinetics in multi-component self-assembling mixtures, including polymers, colloids, and nanoparticles; (b) apply multi-scale modeling and simulation to study molecular recognition in bio-inspired systems: In particular, I plan to use multi-scale modeling and simulations to study recognition and repair of DNA damage, and investigate the role of damage repair in the development of resistance against anti-cancer drugs.

References:

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)

2. A. Jayaraman, C. K. Hall, and J. Genzer, 'Computer simulation study of molecular recognition in model DNA microarrays', Biophys. J., 91, 2227 (2006)