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. (pdf) (supp info)
  • 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)

Chapters & Proceedings

  • Nanoscale molecular transport by synthetic DNA machines J.-S. Shin and N.A. Pierce In Nanotechnology: Science and Computation (In honor of Ned Seeman), Eds J. Chen, N. Jonoska, and G. Rozenberg, Springer, 2006. (pdf)
  • Adjoint and defect error bounding and correction for functional estimates N.A. Pierce and M.B. Giles AIAA Paper 2003-3846, In 16th Computational Fluid Dynamics Conference Proceedings, Orlando, FL, 2003. (pdf)
  • Adjoint error correction for integral outputs M.B. Giles and N.A. Pierce In Lecture Notes in Computer Science & Engineering: Error Estimation and Adaptive Discretization Methods in Computational Fluid Dynamics, Vol. 25, Springer-Verlag, 2002. (ps.gz)
  • Superconvergent lift estimates through adjoint error analysis M.B. Giles and N.A. Pierce In Innovative methods for numerical solutions to partial differential equations (In honor of Phil Roe), Eds M. Hafez and J.J. Chattot, World Scientific, 2001. (ps.gz)
  • Improved lift and drag estimates using adjoint Euler equations M.B. Giles and N.A. Pierce AIAA Paper 99-3293, In 14th Computational Fluid Dynamics Conference Proceedings, Norfolk, VA, 1999. (ps.gz)
  • On the properties of solutions of the adjoint Euler equations M.B. Giles and N.A. Pierce In Numerical Methods for Fluid Dynamics VI, M. Baines, ed., ICFD, Oxford, UK, 1998. (ps.gz)
  • Adjoint equations in CFD: duality, boundary conditions and solution behavior M.B. Giles and N.A. Pierce AIAA Paper 97-1850, In 13th Computational Fluid Dynamics Conference Proceedings, Snowmass, CO, 1997. (ps.gz)
  • Accelerating three-dimensional Navier-Stokes calculations N.A. Pierce, M.B. Giles, A. Jameson and L. Martinelli AIAA Paper 97-1953, In 13th Computational Fluid Dynamics Conference Proceedings, Snowmass, CO, 1997. (ps.gz)
  • A preconditioned implicit multigrid algorithm for parallel computation of unsteady aeroelastic compressible flows N.A. Pierce and J.J. Alonso AIAA Paper 97-0444, 35th Aerospace Sciences Meeting and Exhibit, Reno, NV, 1997. (ps.gz)
  • Optimum aerodynamic design using the Navier-Stokes equations A. Jameson, N.A. Pierce and L. Martinelli AIAA Paper 97-0101, 35th Aerospace Sciences Meeting and Exhibit, Reno, NV, 1997. (ps.gz)
  • Preconditioning compressible flow calculations on stretched meshes N.A. Pierce and M.B. Giles AIAA Paper 96-0889, 34th Aerospace Sciences Meeting and Exhibit, Reno, NV, 1996. (ps.gz)

Reports

  • Algorithm developments for discrete adjoint methods M.B. Giles, M.C. Duta, J.D. Mueller and N.A. Pierce Oxford University Computing Laboratory Report NA 01/15, 2001. (ps.gz)
  • Analysis of adjoint error correction for superconvergent functional estimates M.B. Giles and N.A. Pierce Oxford University Computing Laboratory Report NA 01/14, 2001. (ps.gz)
  • An introduction to the adjoint approach to design M.B. Giles and N.A. Pierce Oxford University Computing Laboratory Report NA 00/04, 2000. (ps.gz)
  • Analytic adjoint solutions for the quasi-1D Euler equations M.B. Giles and N.A. Pierce Oxford University Computing Laboratory Report NA 00/03, 2000. (ps.gz)
  • Improved lift and drag estimates using adjoint Euler equations M.B. Giles and N.A. Pierce Oxford University Computing Laboratory Report NA 00/02, 2000. (ps.gz)
  • Adjoint recovery of superconvergent functionals from approximate solutions of partial differential equations N.A. Pierce and M.B. Giles Oxford University Computing Laboratory Report NA 98/18, 1998. (ps.gz)
  • Preconditioning on stretched meshes N.A. Pierce and M.B. Giles Oxford University Computing Laboratory Report NA 95/10, 1995. Presented at the 12th AIAA Computational Fluid Dynamics Conference, San Diego, CA, 1995. (ps.gz)

Theses

  • Preconditioned multigrid methods for compressible flow calculations on stretched meshes N.A. Pierce DPhil thesis, Oxford University, 1997. (ps.gz)
  • Characteristic-based dissipative schemes and characteristic time stepping for the Euler equations N.A. Pierce Qualifying dissertation for DPhil status, Oxford University, 1994. (ps.gz)