Research Articles

1. Sanbonmatsu KY, Joseph S, Tung CS.
Simulating movement of tRNA into the ribosome during decoding.
Proc Natl Acad Sci U S A. 2005 Oct 25. PDF. pubmed
Supplementary Data and Movies

2. Tung CS, Sanbonmatsu KY.
Atomic model of the Thermus thermophilus 70S ribosome developed in silico.
Biophys J. 2004 Oct;87(4):2714-22. pubmed
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3. Gnanakaran S, Nymeyer H, Portman J, Sanbonmatsu KY, Garcia AE.
Peptide folding simulations.
Curr Opin Struct Biol. 2003 Apr;13(2):168-74. pubmed
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4. Sanbonmatsu KY, Joseph S.
Understanding discrimination by the ribosome: stability testing and groove measurement of codon-anticodon pairs.
J Mol Biol. 2003 Apr 18;328(1):33-47. pubmed
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5. Tung CS, Joseph S, Sanbonmatsu KY.
All-atom homology model of the Escherichia coli 30S ribosomal subunit.
Nat Struct Biol. 2002 Oct;9(10):750-5. pubmed
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6. Garcia AE, Sanbonmatsu KY.
Alpha-helical stabilization by side chain shielding of backbone hydrogen bonds.
Proc Natl Acad Sci U S A. 2002 Mar 5;99(5):2782-7. Epub 2002 Feb 26. pubmed
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7. Sanbonmatsu KY, Garcia AE.
Structure of Met-enkephalin in explicit aqueous solution using replica exchange molecular dynamics.
Proteins. 2002 Feb 1;46(2):225-34. pubmed
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8. Sanbonmatsu KY, Murillo MS.
Shear viscosity of strongly coupled Yukawa systems on finite length scales.
Phys Rev Lett. 2001 Feb 12;86(7):1215-8. pubmed
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9. Garcia AE, Sanbonmatsu KY.
Exploring the energy landscape of a beta hairpin in explicit solvent.
Proteins. 2001 Feb 15;42(3):345-54. pubmed
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10. Sanbonmatsu, KY; Newman, DL; Goldman, MV.
Quasi-linear Zakharov simulations of Langmuir turbulence at rocket altitudes in the auroral ionosphere.
Journal of Geophysical Research; 1 June 2001; vol.106, p.10519-35. PDF

11. Sanbonmatsu, KY; Vu, HX; DuBois, DF; Bezzerides, B.
Quantitative comparison of reduced-description particle-in-cell and quasilinear-Zakharov models for parametrically excited Langmuir turbulence.
Physics of Plasmas; July 2000; vol.7, no.7, p.2824-41 SearchPlus

12. Sanbonmatsu, KY; Vu, HX; Bezzerides, B; DuBois, DF.
The effect of kinetic processes on Langmuir turbulence.
Physics of Plasmas; May 2000; vol.7, no.5, p.1723-31. SearchPlus

13. Vu, HX; Sanbonmatsu, KY; Bezzerides, B; DuBois, DF.
Laying a foundation for laser-plasma modeling for the national ignition facility.
Computer Physics Communications; May 2000; vol.127, no.1, p.71-90. pubmed

14. Sanbonmatsu, KY; Thode, LE; Vu, HX; Murillo, MS.
Comparison of molecular dynamics and particle-in-cell simulations for strongly coupled plasmas.
JOURNAL DE PHYSIQUE IV; MAR 2000; v.10, no.P5, p.259-262. SearchPlus

15. Sanbonmatsu, KY; Vu, HX; DuBois, DF; Bezzerides, B.
New paradigm for the self-consistent modeling of wave-particle and wave-wave interactions in the saturation of electromagnetically driven parametric instabilities.
Physical Review Letters; 1 Feb. 1999; vol.82, no.5, p.932-5. SearchPlus

16. Sanbonmatsu, KY; Doxas, I; Goldman, MV; NEwman, DL.
Non-Markovian electron diffusion in the auroral ionosphere at high Langmuir-wave intensities.
Geophysical Research Letters; 1 April 1997; vol.24, no.7, p.807-10. SearchPlus

17. SANBONMATSU, KY; GOLDMAN, MV; NEWMAN, DL.
Nonlinear coupling of lower hybrid waves to the kinetic low-frequency plasma response in the auroral ionosphere.
Geophysical Research Letters; 1 Sept. 1995; vol.22, no.17, p.2397-400. SearchPlus

18. SANBONMATSU, KY; HELFAND, DJ.
A distance determination for the supernova remnant G27.4+0.0 and its central X-ray source.
Astronomical Journal; Dec. 1992; vol.104, no.6, p.2189-92. PDF