Research Area

Molecular Recognition in Microarrays: A Computer Simulation Study

Systems of Interest

  • ssDNA
  • DNA Microarrays

Methods

  • Discontinuous Molecular Dynamics (DMD) Simulations

Abstract

DNA microarrays have revolutionized the way biological research is done, enabling scientists to measure the expression patterns of thousands of genes in a single experiment. Current and potential applications of this technology include identification of gene expression in cells, identification of genes that are differentially expressed in healthy versus diseased cells, and tracking changes in a cell's expression profile to infer which genes regulate which stages of a cell's development, enabling disease diagnosis and the development of drugs that can exploit this difference. A fundamental understanding of the principles that govern the interplay between the various factors that affect microarray performance is needed to fully exploit their incredible potential.

We will perform discontinuous molecular dynamics (DMD) simulations of intermediate-resolution model DNA molecules immobilized on microarray surfaces to discover how molecular sequence, the presence of the microarray surface, and temperature affect the configurational properties of DNA molecules on microarray surfaces and the dynamics of the hybridization process.

BDNABDNAtop
Figure1: Atomistic representation 10 base pair BDNA molecule. Side (Left) and top (Right) views. 1DB0 file from Protein Data Bank.


Publications

J.R. Maury-Evertsz and G.E. Lopez, "Studies on the behavior of nanoconfined homopolymers with cyclic chain architecture"  J. Chem. Phys. 123 (2005) 054903

J.R. Maury-Evertsz, L.A. Estevez and G.E. Lopez, "Effect of branching and confinement on star-branched polymeric systems" J. Chem. Phys. 121 (2004) 8652

J.R. Maury-Evertsz, L.A. Estevez and G.E. Lopez, "Equilibrium properties of confined single-chain homopolymers" J. Chem. Phys. 119 (2003) 9925

M. Ocasio, J. Maury-Evertsz, B. Pastrana-Rios and G. E. Lopez, "Exploring repulsive interactions in a model helical peptide: A parallel tempering Monte Carlo study"  J. Chem. Phys. 119 (2003) 9274

V. Ortiz, J. Maury-Evertsz and G. E. Lopez, "Parallel tempering-cavity-bias algorithm in the Gibbs ensemble"  Chem. Phys. Lett. 368 (2003) 452

Presentations

J.R. Maury-Evertsz, L.A. Estevez and G.E. Lopez, 'Effect of branching and chain size on the equilibrium properties of confined star polymes' Sigma Xi Poster Day, March 19, 2004, Mayaguez, PR.

J.R. Maury-Evertsz, L.A. Estevez and G.E. Lopez, 'Molecular Simulation of the Thermodynamic Behavior of Confined Polymers' - oral presentation at the AIChE Conference, November 20, 2003, San Francisco, CA.