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1

An Introduction to the Adjoint Approach to Design

Michael B. Giles, Niles A. Pierce

Journal:

Flow, Turbulence and Combustion

Year:

2000

Language:

english

File:

PDF, 180 KB

english, 2000

2

Preconditioned Multigrid Methods for Compressible Flow Calculations on Stretched Meshes

Niles A. Pierce, Michael B. Giles

Journal:

Journal of Computational Physics

Year:

1997

Language:

english

File:

PDF, 911 KB

english, 1997

3

Programming biomolecular self-assembly pathways

Yin, Peng, Choi, Harry M. T., Calvert, Colby R., Pierce, Niles A.

Journal:

Year:

2008

Language:

english

File:

PDF, 1.32 MB

english, 2008

4

An autonomous polymerization motor powered by DNA hybridization

Venkataraman, Suvir, Dirks, Robert M., Rothemund, Paul W. K., Winfree, Erik, Pierce, Niles A.

Journal:

Nature Nanotechnology

Year:

2007

Language:

english

File:

PDF, 721 KB

english, 2007

5

Selective Nucleic Acid Capture with Shielded Covalent Probes

Vieregg, Jeffrey R., Nelson, Hosea M., Stoltz, Brian M., Pierce, Niles A.

Journal:

Journal of the American Chemical Society

Year:

2013

Language:

english

File:

PDF, 2.65 MB

english, 2013

6

A Synthetic DNA Walker for Molecular Transport

Shin, Jong-Shik, Pierce, Niles A.

Journal:

Journal of the American Chemical Society

Year:

2004

Language:

english

File:

PDF, 175 KB

english, 2004

7

Efficient Computation of Unsteady Viscous Flows by an Implicit Preconditioned Multigrid Method

Pierce, Niles A., Alonso, Juan J.

Journal:

Year:

1998

Language:

english

File:

PDF, 2.50 MB

english, 1998

8

Algorithm Developments for Discrete Adjoint Methods

Giles, Michael B., Duta, Mihai C., M-uacute, Jens-Dominik, ller,, Pierce, Niles A.

Journal:

Year:

2003

Language:

english

File:

PDF, 258 KB

english, 2003

9

Exact rotamer optimization for protein design

D. Benjamin Gordon, Geoffrey K. Hom, Stephen L. Mayo, Niles A. Pierce

Journal:

Journal of Computational Chemistry

Year:

2003

Language:

english

File:

PDF, 180 KB

english, 2003

10

A partition function algorithm for nucleic acid secondary structure including pseudoknots

Robert M. Dirks, Niles A. Pierce

Journal:

Journal of Computational Chemistry

Year:

2003

Language:

english

File:

PDF, 471 KB

english, 2003

11

An algorithm for computing nucleic acid base-pairing probabilities including pseudoknots

Robert M. Dirks, Niles A. Pierce

Journal:

Journal of Computational Chemistry

Year:

2004

Language:

english

File:

PDF, 270 KB

english, 2004

12

NUPACK: Analysis and design of nucleic acid systems

Joseph N. Zadeh, Conrad D. Steenberg, Justin S. Bois, Brian R. Wolfe, Marshall B. Pierce, Asif R. Khan, Robert M. Dirks, Niles A. Pierce

Journal:

Journal of Computational Chemistry

Year:

2011

Language:

english

File:

PDF, 68 KB

english, 2011

13

Nucleic acid sequence design via efficient ensemble defect optimization

Joseph N. Zadeh, Brian R. Wolfe, Niles A. Pierce

Journal:

Journal of Computational Chemistry

Year:

2011

Language:

english

File:

PDF, 1.21 MB

english, 2011

14

Progress in adjoint error correction for integral functionals

Michael B. Giles, Niles Pierce, Endre Süli

Journal:

Computing and Visualization in Science

Year:

2004

Language:

english

File:

PDF, 834 KB

english, 2004

15

Adjoint and defect error bounding and correction for functional estimates

Niles A. Pierce, Michael B. Giles

Journal:

Journal of Computational Physics

Year:

2004

Language:

english

File:

PDF, 416 KB

english, 2004

16

Programmable in situ amplification for multiplexed imaging of mRNA expression

Choi, Harry M T, Chang, Joann Y, Trinh, Le A, Padilla, Jennifer E, Fraser, Scott E, Pierce, Niles A

Journal:

Nature Biotechnology

Year:

2010

Language:

english

File:

PDF, 932 KB

english, 2010

17

Progress in adjoint error correction for integral functionals

Michael B. Giles, Niles Pierce, Endre Süli

Journal:

Computing and Visualization in Science

Year:

2004

Language:

english

File:

PDF, 727 KB

english, 2004

18

[Lecture Notes in Computer Science] DNA Computing Volume 3892 || Designing Nucleotide Sequences for Computation: A Survey of Constraints

Carbone, Alessandra, Pierce, Niles A.

Year:

2006

Language:

english

File:

PDF, 345 KB

english, 2006

19

[American Institute of Aeronautics and Astronautics 35th Aerospace Sciences Meeting and Exhibit - Reno,NV,U.S.A. (06 January 1997 - 09 January 1997)] 35th Aerospace Sciences Meeting and Exhibit - A preconditioned implicit multigrid algorithm for parallel computation of unsteady aeroelastic compressible flows

Pierce, Niles, Alonso, Juan, Pierce, Niles, Alonso, Juan

Year:

1997

Language:

english

File:

PDF, 1.42 MB

english, 1997

20

[American Institute of Aeronautics and Astronautics 14th Computational Fluid Dynamics Conference - Norfolk,VA,U.S.A. (01 November 1999 - 05 November 1999)] 14th Computational Fluid Dynamics Conference - Improved lift and drag estimates using adjoint Euler equations

Giles, Michael, Pierce, Niles

Year:

1999

Language:

english

File:

PDF, 1.07 MB

english, 1999

21

[American Institute of Aeronautics and Astronautics 16th AIAA Computational Fluid Dynamics Conference - Orlando, Florida ()] 16th AIAA Computational Fluid Dynamics Conference - Adjoint and Defect Error Bounding and Correction for Functional Estimates

Pierce, Niles, Giles, Michael

Year:

2003

Language:

english

File:

PDF, 3.61 MB

english, 2003

22

Conditional Dicer Substrate Formation via Shape and Sequence Transduction with Small Conditional RNAs

Hochrein, Lisa M., Schwarzkopf, Maayan, Shahgholi, Mona, Yin, Peng, Pierce, Niles A.

Journal:

Journal of the American Chemical Society

Year:

2013

Language:

english

File:

PDF, 2.93 MB

english, 2013

23

Next-Generation in Situ Hybridization Chain Reaction: Higher Gain, Lower Cost, Greater Durability

Choi, Harry M. T., Beck, Victor A., Pierce, Niles A.

Journal:

Year:

2014

Language:

english

File:

PDF, 4.30 MB

english, 2014

24

Sensitive and Selective Nucleic Acid Capture with Shielded Covalent Probes

Vieregg, Jeffrey R., Nelson, Hosea, Stoltz, Brian, Pierce, Niles A.

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 83 KB

english, 2012

25

Elucidation and Control of the Hybridization Chain Reaction

Beck, Victor A., Bois, Justin S., Dirks, Robert M., Pierce, Niles A.

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 69 KB

english, 2011

26

Selective Oligonucleotide and MRNA Pull-Down with Shielded Covalent Probes

Vieregg, Jeffrey R., Pierce, Niles A.

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 33 KB

english, 2013

27

Selective Nucleic Acid Capture with Shielded Covalent Probes

Vieregg, Jeffrey, Pierce, Niles A.

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 40 KB

english, 2014

28

Thermodynamic Analysis of Interacting Nucleic Acid Strands

Robert M. Dirks, Justin S. Bois, Joseph M. Schaeffer, Erik Winfree and Niles A. Pierce

Journal:

Year:

2007

Language:

english

File:

PDF, 2.48 MB

english, 2007

29

Adjoint Recovery of Superconvergent Functionals from PDE Approximations

Niles A. Pierce and Michael B. Giles

Journal:

Year:

2000

Language:

english

File:

PDF, 1.18 MB

english, 2000

30

Developmental Self-Assembly of a DNA Tetrahedron

Sadowski, John P., Calvert, Colby R., Zhang, David Yu, Pierce, Niles A., Yin, Peng

Journal:

Year:

2014

Language:

english

File:

PDF, 6.78 MB

english, 2014

31

Rewritable Memory by Controllable Nanopatterning of DNA

Shin, Jong-Shik, Pierce, Niles A.

Journal:

Year:

2004

Language:

english

File:

PDF, 246 KB

english, 2004

32

Exquisite Sequence Selectivity with Small Conditional RNAs

Sternberg, Jonathan B., Pierce, Niles A.

Journal:

Year:

2014

Language:

english

File:

PDF, 2.79 MB

english, 2014

33

Multiplexed In Situ Hybridization Using Hybridization Chain Reaction

Choi, Harry M.T., Beck, Victor A., Pierce, Niles A.

Journal:

Year:

2014

Language:

english

File:

PDF, 176 KB

english, 2014

34

Thermodynamic Analysis of Interacting Nucleic Acid Strands

Dirks, Robert M., Bois, Justin S., Schaeffer, Joseph M., Winfree, Erik, Pierce, Niles A.

Journal:

Year:

2007

Language:

english

File:

PDF, 656 KB

english, 2007

35

Adjoint Recovery of Superconvergent Functionals from PDE Approximations

Pierce, Niles A., Giles, Michael B.

Journal:

Year:

2000

Language:

english

File:

PDF, 421 KB

english, 2000

36

[Lecture Notes in Computer Science] DNA Computing Volume 3892 || Towards Practical Biomolecular Computers Using Microfluidic Deoxyribozyme Logic Gate Networks

Carbone, Alessandra, Pierce, Niles A.

Year:

2006

Language:

english

File:

PDF, 736 KB

english, 2006

37

Selective cell death mediated by small conditional RNAs

Suvir Venkataraman, Robert M. Dirks, Christine T. Ueda and Niles A. Pierce

Journal:

Proceedings of the National Academy of Sciences

Year:

2010

Language:

english

File:

PDF, 2.10 MB

english, 2010

38

Sequence Design for a Test Tube of Interacting Nucleic Acid Strands

Wolfe, Brian R., Pierce, Niles A.

Journal:

ACS Synthetic Biology

Year:

2014

Language:

english

File:

PDF, 1.75 MB

english, 2014

39

[Lecture Notes in Computer Science] DNA Computing Volume 3892 || Photo- and Thermoregulation of DNA Nanomachines

Carbone, Alessandra, Pierce, Niles A.

Year:

2006

Language:

english

File:

PDF, 905 KB

english, 2006

40

[Lecture Notes in Computer Science] DNA Computing Volume 3892 ||

Carbone, Alessandra, Pierce, Niles A.

Year:

2006

Language:

english

File:

PDF, 10.23 MB

english, 2006

41

[Lecture Notes in Computer Science] DNA Computing Volume 3892 || Design of Autonomous DNA Cellular Automata

Carbone, Alessandra, Pierce, Niles A.

Year:

2006

Language:

english

File:

PDF, 1.59 MB

english, 2006

42

[Lecture Notes in Computer Science] DNA Computing Volume 3892 || Analysis and Simulation of Dynamics in Probabilistic P Systems

Carbone, Alessandra, Pierce, Niles A.

Year:

2006

Language:

english

File:

PDF, 1.12 MB

english, 2006

43

Combinatorial Analysis of mRNA Expression Patterns in Mouse Embryos Using Hybridization Chain Reaction

Huss, David, Choi, Harry M.T., Readhead, Carol, Fraser, Scott E., Pierce, Niles A., Lansford, Rusty

Journal:

Cold Spring Harbor Protocols

Year:

2015

Language:

english

File:

PDF, 678 KB

english, 2015

44

Analytic adjoint solutions for the quasi-one-dimensional Euler equations

GILES, MICHAEL B., PIERCE, NILES A.

Journal:

Journal of Fluid Mechanics

Year:

2001

Language:

english

File:

PDF, 546 KB

english, 2001

45

Multiplexed miRNA northern blots via hybridization chain reaction

Schwarzkopf, Maayan, Pierce, Niles A.

Journal:

Nucleic Acids Research

Year:

2016

Language:

english

File:

PDF, 2.40 MB

english, 2016

46

Single-molecule RNA detection at depth via hybridization chain reaction and tissue hydrogel embedding and clearing

Shah, Sheel, Lubeck, Eric, Schwarzkopf, Maayan, He, Ting-fang, Greenbaum, Alon, Sohn, Chang ho, Lignell, Antti, Choi, Harry M. T., Gradinaru, Viviana, Pierce, Niles A., Cai, Long

Journal:

Development (The Company of Biologists)

Year:

2016

Language:

english

File:

PDF, 2.88 MB

english, 2016

47

[American Institute of Aeronautics and Astronautics 34th Aerospace Sciences Meeting and Exhibit - Reno,NV,U.S.A. (15 January 1996 - 18 January 1996)] 34th Aerospace Sciences Meeting and Exhibit - Preconditioning compressible flow calculations on stretched meshes

Pierce, Niles, Giles, Michael

Language:

english

File:

PDF, 1.41 MB

english

48

Constrained Multistate Sequence Design for Nucleic Acid Reaction Pathway Engineering

Wolfe, Brian R., Porubsky, Nicholas J., Zadeh, Joseph N., Dirks, Robert M., Pierce, Niles A.

Journal:

Journal of the American Chemical Society

Year:

2017

Language:

english

File:

PDF, 1.46 MB

english, 2017

49

Multidimensional quantitative analysis of mRNA expression within intact vertebrate embryos

Trivedi, Vikas, Choi, Harry M. T., Fraser, Scott E., Pierce, Niles A.

Journal:

Development (The Company of Biologists)

Year:

2018

Language:

english

File:

PDF, 4.13 MB

english, 2018

50

Third-generation in situ hybridization chain reaction: multiplexed, quantitative, sensitive, versatile, robust

Choi, Harry M. T., Schwarzkopf, Maayan, Fornace, Mark E., Acharya, Aneesh, Artavanis, Georgios, Stegmaier, Johannes, Cunha, Alexandre, Pierce, Niles A.

Journal:

Development (The Company of Biologists)

Year:

2018

Language:

english

File:

PDF, 4.63 MB

english, 2018