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)