Ph.D., Chemical and Biomolecular Engineering, University of Pennsylvania, 2007.
B.S.E, Chemical Engineering, University of Puerto Rico, Mayagüez Campus, 2002.
Our primary research interests reside in the development and application of advanced multi-scale computational modeling techniques for the study of biological macromolecules. The goal is to provide insight into the molecular mechanisms that drive assembly in biology, thereby providing guidance for development of better and more efficient biomedical and environmental sensing technologies.
A multi-scale computational approach for the study of nucleic-acid-based systems
From an engineering point of view, the deregulation of epigenetics has been recognized as an important mechanism in the pathogenesis of various cancers and other diseases. Here the term epigenetics refers to changes in phenotype (appearance) or gene expression caused by mechanisms other than changes in the underlying DNA sequence. As such, basic research in the field of epigenetics has dramatically increased throughout the past decade, and some of the first epigenetic drugs have recently been approved for clinical use. These discoveries have also lead to the development of efficient nucleic-acid-based methods for sensing and the treatment of diseases, which have already started to revolutionize the way medicine is practiced and applied. On the other hand, the use of nucleic acids for templating directed organization of nanomaterials, including biomolecules, templating of inorganics, and approaches combining preformed and template materials has placed nucleic acids in a starring role in the areas of nanotechnology and materials.
These new discoveries have great potential to solve many problems that we currently face in areas as diverse as biology and medicine and materials science but, for some of them, development is hindered by a lack of understanding of the molecular level interactions that drive the mechanisms on which these new technologies are based. We use a multi-scale hierarchical modeling approach, rooted in the use of advanced, state-of-the-art sampling methods, to investigate the behavior of nucleic acids in solution and when in contact with other macromolecules (proteins, nanotubes), surfaces or assemblies (membranes). Results from these studies will address a range of problems that these technologies face, and predict and suggest ways to improve and make them more efficient.
Ortiz V, Sambriski EJ, and de Pablo JJ, "Effects of sequence on DNA kinking and flexibility", Physical Review Letters, submitted (2010)
Loverde SM, Ortiz V, Kamien RD, Klein ML, and Discher DE, "Curvature-driven molecular demixing in the budding and breakup of mixed component worm-like micelles", Soft Matter, 6 1419 (2010)
Sambriski EJ, Ortiz V, and de Pablo JJ, "Sequence effects in the melting and renaturation of short DNA oligonucleotides: structure and mechanistic pathways", Journal of Physics: Condensed Matter, 21 034105 (2009)
Ortiz V, Nielsen SO, Discher DE, and Klein ML, Lipowsky R, and Shillcock J, "Dissipative particle dynamics simulations of polymersomes", Journal of Physical Chemistry B, 109 17708 (2005)
Nielsen SO, Ensing B, Ortiz V, Moore PB, and Klein ML, "Lipid bilayer perturbations around a transmembrane nanotube: A coarse grain molecular dynamics study", Biophysical Journal, 88 3822 (2005)
Ortiz V, Nielsen SO, Klein ML, and Discher DE, "Unfolding a linker between helical repeats", Journal of Molecular Biology, 349 638 (2005)