The Pierce Lab

Journal Publications

  • Programming biomolecular self-assembly pathways P. Yin, H.M.T. Choi, C.R. Calvert, N.A. Pierce Nature, 451:318-322, 2008.
  • An autonomous polymerization motor powered by DNA hybridization S. Venkatarman, R.M. Dirks, P.W.K. Rothemund, E. Winfree, N.A. Pierce Nature Nanotech, 2(8):490-494, 2007. (pdf) (supp info)
  • Thermodynamic analysis of interacting nucleic acid strands R.M. Dirks, J.S. Bois, J.M. Schaeffer, E. Winfree and N.A. Pierce SIAM Rev, 49(1):65-88, 2007. (pdf)
  • Topological constraints in nucleic acid hybridization kinetics J.S. Bois, S.Venkataraman, H.M.T. Choi, A.J. Spakowitz, Z.-G. Wang and N.A. Pierce Nucleic Acids Res, 33(13):4090-4095, 2005. (pdf)
  • Triggered amplification by hybridization chain reaction R.M. Dirks and N.A. Pierce Proc Natl Acad Sci, 101(43):15275-15278, 2004. (pdf)
  • A synthetic DNA walker for molecular transport J.-S. Shin and N.A. Pierce J Am Chem Soc, 126:10834-10835, 2004. (pdf) (supp info)
  • Rewritable memory by controllable nanopatterning of DNA J.-S. Shin and N.A. Pierce Nano Lett, 4(5):905-909, 2004. (pdf) (supp info)
  • An algorithm for computing nucleic acid base-pairing probabilities including pseudoknots R.M. Dirks and N.A. Pierce J Comput Chem, 25:1295-1304, 2004. (pdf)
  • Adjoint and defect error bounding and correction for functional estimates N.A. Pierce and M.B. Giles J Comput Phys, 200:769-794, 2004. (pdf)
  • Paradigms for computational nucleic acid design R.M. Dirks, M. Lin, E. Winfree and N.A. Pierce Nucleic Acids Res, 32(4):1392-1403, 2004. (pdf) (supp info text) (supp info sequences)
  • A partition function algorithm for nucleic acid secondary structure including pseudoknots R.M. Dirks and N.A. Pierce J Comput Chem, 24(13):1664-1677, 2003. (pdf) (supp info)
  • Exact rotamer optimization for protein design D.B. Gordon, G.K. Hom, S.L. Mayo and N.A. Pierce J Comput Chem, 24(2):232-243, 2003. (pdf)
  • Algorithm developments for discrete adjoint methods M.B. Giles, M.C. Duta, J.-D. Mueller and N.A. Pierce AIAA J, 41(2):198-205, 2003. (pdf)
  • Protein design is NP-hard N.A. Pierce and E. Winfree Protein Engineering, 15(10):779-782, 2002. (pdf)
  • Analytic adjoint solutions for the quasi-one-dimensional Euler equations M.B. Giles and N.A. Pierce J Fluid Mech, 426:327-345, 2001. (pdf)
  • Conformational splitting: a more powerful criterion for dead-end elimination N.A. Pierce, J.A. Spriet, J. Desmet and S.L. Mayo J Comput Chem, 21(11):999-1009, 2000. (pdf)
  • Adjoint recovery of superconvergent functionals from PDE approximations N.A. Pierce and M.B. Giles SIAM Rev, 42(2):247-264, 2000. (pdf)
  • An introduction to the adjoint approach to design M.B. Giles and N.A. Pierce Flow Turb Comb, 65:393-415, 2000. (pdf)
  • Optimum aerodynamic design using the Navier-Stokes equations A. Jameson, L. Martinelli and N.A. Pierce Theor Comput Fluid Dyn, 10:213-237, 1998. (pdf)
  • Efficient computation of unsteady viscous flows by an implicit preconditioned multigrid method N.A. Pierce and J.J. Alonso AIAA J, 36(3):401-408, 1998. (pdf)
  • Preconditioned multigrid methods for compressible flow calculations on stretched meshes N.A. Pierce and M.B. Giles J Comput Phys, 136:425-445, 1997. (pdf)