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stsaft's thermodynamics [33 articles]

Recent papers added to stsaft's library classified by the tag thermodynamics. You can also see everyone's thermodynamics.
  • On-chip non-equilibrium dissociation curves and dissociation rate constants as methods to assess specificity of oligonucleotide probes
    Nucleic Acids Research, Vol. 34, No. 3. (2006), pp. e26-e26.
    by Lukas M Wick, Jean M Rouillard, Thomas S Whittam, Erdogan Gulari, James M Tiedje, Syed A Hashsham
    posted to thermodynamics probe microarray design corrections by stsaft on 2008-06-06 19:11:52 as **
  • Free energy of DNA duplex formation on short oligonucleotide microarrays
    Nucleic Acids Research, Vol. 35, No. 3. (February 2007), pp. e18-e18.
    by Zhang, Li, Wu, Chunlei, Carta, Roberto, Zhao, Haitao
    posted to thermodynamics probe microarray design by stsaft on 2008-06-06 19:06:20 as ** along with 1 person bertelsen
  • Modeling DNA shuffling.
    Journal of computational biology : a journal of computational molecular cell biology, Vol. 6, No. 1. (1999), pp. 77-90.
    by F Sun
    posted to vitro thermodynamics shuffling mutagenesis model in evolution by stsaft on 2008-05-23 06:10:04 as **
  • eCodonOpt: a systematic computational framework for optimizing codon usage in directed evolution experiments.
    Nucleic acids research, Vol. 30, No. 11. (1 June 2002), pp. 2407-2416.
    by GL Moore, CD Maranas
    posted to thermodynamics shuffling kinetics crossover by stsaft on 2008-05-23 06:06:30 as **
  • Computational and experimental analysis of DNA shuffling.
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 100, No. 6. (18 March 2003), pp. 3071-3076.
    by N Maheshri, DV Schaffer
    posted to thermodynamics shuffling kinetics crossover by stsaft on 2008-05-23 06:05:40 as **
  • Predicting crossover generation in DNA shuffling.
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 98, No. 6. (13 March 2001), pp. 3226-3231.
    by GL Moore, CD Maranas, S Lutz, SJ Benkovic
    posted to thermodynamics shuffling crossover by stsaft on 2008-05-23 06:05:04 as **
  • The Fidelity of the Tag-Antitag System
    DNA Computing (2002), pp. 138-149.
    by John Rose, Russell Deaton, Masami Hagiya, Akira Suyama
    posted to universal_microarrays thermodynamics simulation by stsaft on 2008-04-22 20:54:25 as **
  • The Fidelity of the Tag-Antitag System III. Robustness in the Excess Limit: The Stringent Temperature
    Knowledge-Based Intelligent Information and Engineering Systems (2004), pp. 40-49.
    by John A Rose
    posted to universal_microarrays thermodynamics simulation by stsaft on 2008-04-22 20:53:21 as **
  • The fidelity of the tag-antitag system II: reconciliation with the stringency picture
    Evolutionary Computation, 2003. CEC '03. The 2003 Congress on, Vol. 4 (2003), pp. 2740-2747 Vol.4.
    by JA Rose, M Hagiya, A Suyama
    posted to universal_microarrays thermodynamics simulation by stsaft on 2008-04-22 20:52:35 as **
  • Statistical thermodynamic analysis and designof DNA-based computers
    Natural Computing, Vol. 3, No. 4. (December 2004), pp. 443-459.
    by John Rose, Russell Deaton, Akira Suyama
    posted to thermodynamics simulations codeword_design by stsaft on 2008-04-22 20:42:42 as **
  • On the specificity of DNA-protein interactions.
    Proc Natl Acad Sci U S A, Vol. 83, No. 6. (March 1986), pp. 1608-1612.
    by PH von Hippel, OG Berg
    posted to thermodynamics simulation protein dna by stsaft on 2008-04-22 20:41:44 as ** along with 3 people and 1 group jjray cisevol lambda cis-regulatory-evolution
  • The fidelity of the tag-antitag system: Characterization of the stringent temperature for robustness in the excess limit
    Int. J. Know.-Based Intell. Eng. Syst., Vol. 9, No. 4. (December 2005), pp. 285-292.
    by John A Rose
    posted to universal_microarrays thermodynamics by stsaft on 2008-04-22 20:40:14 as **
  • Coupled Equilibrium Model of Hybridization Error for the DNA Microarray and Tag–Antitag Systems
    NanoBioscience, IEEE Transactions on, Vol. 6, No. 1. (2007), pp. 18-27.
    by John A Rose, Russell J Deaton, Masami Hagiya, Akira Suyama
    posted to universal_microarrays thermodynamics microarrays codeword_design by stsaft on 2008-04-22 20:38:30 as **
  • A Competitive Kinetic Model of Nucleic Acid Surface Hybridization in the Presence of Point Mutants
    Biophys. J., Vol. 90, No. 3. (1 February 2006), pp. 831-840.
    by J Bishop, S Blair, AM Chagovetz
    posted to kinetics microarrays modeling simulation thermodynamics by stsaft on 2008-03-31 03:52:42 as **
  • Modeling of DNA hybridization kinetics for spatially resolved biochips
    Analytical Biochemistry, Vol. 317, No. 2. (15 June 2003), pp. 186-200.
    by David Erickson, Dongqing Li, Ulrich J Krull
    posted to hybridization kinetics microarrays model simulation thermodynamics by stsaft on 2008-03-31 03:49:32 as **
  • Statistical mechanics of base stacking and pairing in DNA melting
    Physical Review E, Vol. 70, No. 5. (16 November 2004), 051907.
    by Vassili Ivanov, Yan Zeng, Giovanni Zocchi
    posted to dna hybridization melting model simulation thermodynamic thermodynamics by stsaft on 2008-03-28 22:10:53 as ****
  • Self-Assembly of DNA-like Structures In Silico
    Genetic Programming and Evolvable Machines, Vol. 4, No. 2. (14 June 2003), pp. 185-200.
    by Max Garzon, Derrel Blain, Kiran Bobba, Andrew Neel, Michael West
    posted to computing dna efficiency hybridization memories simulation thermodynamics by stsaft on 2008-03-27 20:16:48 as **
  • Thermodynamic parameters for DNA sequences with dangling ends
    Nucl. Acids Res., Vol. 28, No. 9. (1 May 2000), pp. 1929-1934.
    by Salvatore Bommarito, Nicolas Peyret, John S Jr
    posted to model parameters thermodynamics by stsaft on 2008-03-07 06:12:41 as **
  • DNA Modeling within Ab Initio and Empirical Methods
    pp. 349-383.
    by I Cozmuta
    posted to dna kinetics model simulation thermodynamics by stsaft on 2008-02-05 00:47:46 as ****
  • Design automation for DNA self-assembled nanostructures
    (2006), pp. 919-924.
    by Constantin Pistol, Alvin R Lebeck, Chris Dwyer
    posted to codeword_design self-assembly thermodynamics by stsaft on 2008-01-24 23:42:09 as ** along with 1 person Kiarostami
  • Sequence Design for Stable DNA Tiles
    DNA Computing (2006), pp. 172-181.
    by Naoki Iimura, Masahito Yamamoto, Fumiaki Tanaka, Atsushi Kameda, Azuma Ohuchi
    posted to codeword_design self-assembly thermodynamics by stsaft on 2008-01-24 23:38:02 as **
  • Untitled
    posted to codeword codeword_design dna dna_computing hybridization kinetics thermodynamic thermodynamics by stsaft on 2007-10-08 07:03:22 as **
  • A dimensionless number analysis of the hybridization process in diffusion- and convection-driven DNA microarray systems
    Journal of Biotechnology, Vol. 123, No. 4. (10 June 2006), pp. 381-396.
    by Kris Pappaert, Gert Desmet
    posted to hybridization kinetics microarray simulation thermodynamics by stsaft on 2007-04-30 21:28:44 as *****
  • Untitled
    posted to thermodynamics kinetics folding dna by stsaft on 2007-01-19 22:47:45 as *****
  • Parallel multiplex thermodynamic analysis of coaxial base stacking in DNA duplexes by oligodeoxyribonucleotide microchips
    Nucl. Acids Res., Vol. 29, No. 11. (1 June 2001), pp. 2303-2313.
    by Vadim A Vasiliskov, Dmitry V Prokopenko, Andrei D Mirzabekov
    posted to thermodynamics microarrays kinetics dna by stsaft on 2007-01-19 22:44:11 as *****
  • Prediction of hybridization and melting for double-stranded nucleic acids.
    Biophys J, Vol. 87, No. 1. (July 2004), pp. 215-226.
    by RA Dimitrov, M Zuker
    posted to thermodynamics kinetics dna by stsaft on 2007-01-19 22:38:28 as *****
  • DNA probes: applications of the principles of nucleic acid hybridization
    Crit Rev Biochem Mol Biol, Vol. 26, No. 3-4. (1991), pp. 227-259.
    by JG Wetmur
    posted to dna thermodynamics by stsaft on 2006-03-07 05:23:24 as ** along with 1 person flying98
  • Improved nearest-neighbor parameters for predicting DNA duplex stability
    Biochemistry, Vol. 35, No. 11. (19 March 1996), pp. 3555-3562.
    by J Santalucia, HT Allawi, PA Seneviratne
    posted to dna thermodynamics by stsaft on 2006-03-07 04:57:45 as read along with 2 people davidng yoanjacquemin
  • Nearest-neighbor thermodynamics and NMR of DNA sequences with internal A.A, C.C, G.G, and T.T mismatches
    Biochemistry, Vol. 38, No. 12. (23 March 1999), pp. 3468-3477.
    by N Peyret, PA Seneviratne, HT Allawi, J Santalucia
    posted to dna thermodynamics by stsaft on 2006-03-07 00:11:40 as read
  • A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics
    Proc Natl Acad Sci U S A, Vol. 95, No. 4. (17 February 1998), pp. 1460-1465.
    by J Santalucia
    posted to dna kinetics thermodynamics by stsaft on 2006-02-28 20:58:06 as ** along with 2 people davidng talponer
  • Statistical thermodynamic analysis and design of DNA-based computers
    Natural Computing, Vol. 3, No. 4. (2004), pp. 443-459.
    by John A Rose, Russell J Deaton, Akira Suyama
    posted to bibtex-import dna kinetics simulation thermodynamics by stsaft on 2006-02-28 20:55:36 as **
  • Predicting oligonucleotide affinity to nucleic acid targets
    RNA, Vol. 5, No. 11. (November 1999), pp. 1458-1469.
    by DH Mathews, ME Burkard, SM Freier, JR Wyatt, DH Turner
    posted to dna kinetics thermodynamics by stsaft on 2006-02-28 20:52:18 as ** along with 1 person Hosna
  • The thermodynamics of DNA structural motifs
    Annu Rev Biophys Biomol Struct, Vol. 33 (2004), pp. 415-440.
    by J Santalucia, D Hicks
    posted to dna santalucia thermodynamics by stsaft on 2006-02-28 00:00:28 as read along with 1 person balajis
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