All Publications


  • The proto-Nucleic Acid Builder: a software tool for constructing nucleic acid analogs NUCLEIC ACIDS RESEARCH Alenaizan, A., Barnett, J. L., Hud, N., Sherrill, C., Petrov, A. S. 2021; 49 (1): 79–89

    Abstract

    The helical structures of DNA and RNA were originally revealed by experimental data. Likewise, the development of programs for modeling these natural polymers was guided by known structures. These nucleic acid polymers represent only two members of a potentially vast class of polymers with similar structural features, but that differ from DNA and RNA in the backbone or nucleobases. Xeno nucleic acids (XNAs) incorporate alternative backbones that affect the conformational, chemical, and thermodynamic properties of XNAs. Given the vast chemical space of possible XNAs, computational modeling of alternative nucleic acids can accelerate the search for plausible nucleic acid analogs and guide their rational design. Additionally, a tool for the modeling of nucleic acids could help reveal what nucleic acid polymers may have existed before RNA in the early evolution of life. To aid the development of novel XNA polymers and the search for possible pre-RNA candidates, this article presents the proto-Nucleic Acid Builder (https://github.com/GT-NucleicAcids/pnab), an open-source program for modeling nucleic acid analogs with alternative backbones and nucleobases. The torsion-driven conformation search procedure implemented here predicts structures with good accuracy compared to experimental structures, and correctly demonstrates the correlation between the helical structure and the backbone conformation in DNA and RNA.

    View details for DOI 10.1093/nar/gkaa1159

    View details for Web of Science ID 000610552100013

    View details for PubMedID 33300028

    View details for PubMedCentralID PMC7797056

  • Streamwise localization of traveling wave solutions in channel flow PHYSICAL REVIEW E Barnett, J., Gurevich, D. R., Grigoriev, R. O. 2017; 95 (3): 033124

    Abstract

    Channel flow of an incompressible fluid at Reynolds numbers above 2400 possesses a number of different spatially localized solutions that approach laminar flow far upstream and downstream. We use one such relative time-periodic solution, which corresponds to a spatially localized version of a Tollmien-Schlichting wave, to illustrate how the upstream and downstream asymptotics can be computed analytically. In particular, we show that for these spanwise uniform states the asymptotics predict the exponential localization that has been observed for numerically computed solutions of several canonical shear flows but never properly understood theoretically.

    View details for DOI 10.1103/PhysRevE.95.033124

    View details for Web of Science ID 000399149600013

    View details for PubMedID 28415376