Research Topics
  • Processes and properties of bio-nano interfaces
    • DNA functionalized surfaces
    • Interactions of gold nanoparticle with DNA
    • RNA nanoparticles
  • Structure and processing of polymer nanocomposites
    • Magnetically-Driven Orientation of Multiphase Polymer Systems
    • Morphology formation of polymer nanocompostes for organic photovoltaics
  • Three dimensional structure prediction of biomolecules
    • Structure of cellulose synthase protein
    • Tertiary RNA stucture prediction
  • Visualization and analysis tools for biomolecular structure exploration
  • Role of ionic liquids properties on enzymatic reactions

Processes and properties of bio-nano interfaces
    Ongoing Projects:
  • DNA functionalized surfaces
  • Interactions of gold nanoparticle with DNA
  • RNA nanoparticles

Nucleic acids, such as RNA and DNA molecules, are used for assembly of natural and synthetic materials due to their versatility in function and structure and molecular recognition properties of base pairing. Our goal is to develop a fundamental understanding of the processes driving the self-assembly of nucleic acids that will ultimately lead to the development of novel functional materials. Moreover, further investigation of molecular self-assembly mechanisms will allow us to build a more complete picture of the structures and functions of natural NAs.

Recent Publications:

  • M. A. Pasquinelli, Y. G. Yingling, "Molecular dynamics simulaitons of bio-nano materials" Encyclopedia of Nanotechnology (2011) submitted.
  • A. Singh, H. Eksiri, Y. G. Yingling, "Theoretical perspective on properties of DNA-functionalized surfaces" Journal of Polymer Science B: Polymer Physics (2011) ASAP.
  • A. Singh, L. Sethaphong, Y. G. Yingling,"Interactions of cations with RNA loop-loop complexes" Biophysical Journal 101 (2011) 727.
  • A. Singh, Y. G. Yingling, "Simulations of stretching single stranded DNA", Mater. Res. Soc. Proc. (2011).
  • A. Singh, S. Snyder, L. Lee, A. P. R. Johnston, F. Caruso, Y. G. Yingling, Effect of Oligonucleotide Length on the Assembly of DNA Materials: Molecular Dynamics Simulations of Layer-by-Layer DNA Films, Langmuir 26 (2010) 17339-17347.
  • L. Sethaphong, A. Singh, A. E. Marlowe, Y. G. Yingling, The sequence of HIV-1 TAR RNA helix controls cationic distribution, J. Phys. Chem. C, 114 (2010) 5506-5512.
  • A. V. Semichaevsky, A. E. Marlowe, Y. G. Yingling, Comparing ion distributions around RNA and DNA helical and loop-loop motifs, Mater. Res. Soc. Symp. Proc. Vol. 1130 (2009) W05-05.

Structure and processing of polymer nanocomposites 
  • Magnetically-Driven Orientation of Multiphase Polymer Systems
We are investigating how interactions between ligand functionalized nanoparticles and polymers affect the morphology of the system.

Funded by CBET NSF, in collaboration with Prof. Tracy and Prof. Spontack

  • Morphology formation of polymer nanocompostes for organic photovoltaics

Three dimensional structure prediction of biomolecules
Knowledge of biomolecular three dimensional structure and dynamics is crucial to understanding its function and mechanism in the cell.
  • Structure of cellulose synthase protein
We are using a combination of bioinformatics and molecualr dynamics methods to predict 3D structure of cellulose synthase for various plants. Funded through DOE EFRC "Center for Lignocellulose Structure and Formation".
  • Tertiary RNA stucture prediction
We have developed a molecular modeling approach for the first-order RNA tertiary structure prediction and successfully applied it to predict structures of the wild-type telomerase RNA pseudoknot domain and other viral RNAs. We are using our method to predict structure of RNA and RNA-RNA interactions in RCNM plant virus in collaboration with T. Sit and S. Lommel (NCSU).

Selected Publications:

  • V. A. Stupina, A. Meskauskas, J. C. Mccormack, Y. G. Yingling, B. A. Shapiro, J. D. Dinman, A. E. Simon, The 3' Proximal Translational Enhancer of Turnip Crinkle Virus Binds to 60S Ribosomal Subunits, RNA 14 (2008) 2379-2393.
  • J. C. McCormack, X. Yuan, Y. G. Yingling, W. Kasprzak, R. E. Zamora, B. A. Shapiro, A. E. Simon Structural Domains Within the 3' UTR of Turnip Crinkle Virus, Journal of Virology 82 (2008) 8706-8720.
  • B. A. Shapiro, Y. G. Yingling, W. Kasprzak, E. Bindewald, Bridging the gap in RNA structure prediction, Current Opinion in Structural Biology 17 (2007) 157-165.
  • Y. G. Yingling, B. A. Shapiro, The Prediction of the Wild-type Telomerase RNA Pseudoknot Structure and the Pivotal Role of a Bulge in its Formation, J Mol Graph Model 25 (2006) 261-274.

Visualization and analysis tool for biomolecular structure exploration
Protein tertiary structure analysis provides valuable information on their biochemical functions. The structure-to-function relationship can be directly addressed through three dimensional structure exploration and comparison. We are developing a visual analysis tool for 3D biomolecular structure exploration that will allow a clear comparison between similar structures from various species, elucidation of structural effects of mutations, and assessment of snapshots from molecular dynamics trajectories.

Funded by Renaissance Computing Institute (RENCI) and in collaboration with Dr. Hong Yi (RENCI)

Publications: H. Yi, A. Singh, Y. G. Yingling, "X3DBio: A Visual Analysis Tool for Biomolecular Structure Exploration", (2011) submitted


Role of ionic liquid properties on enzymatic reactions

in collaboration with Prof. Y.-M. Koo (Inha University, Korea)

We are investigating the role of various ionic liquids on structure and functions of enzymes

Publications: H. S. Kim, R. Pani, S. H. Ha, Y.-M. Koo, Y. G. Yingling, "The role of hydrogen bonding in water-mediated glucose solubility in ionic liquids" (2011) submitted.

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