Selected Publications

Machine Learning and Data Science

SP Mielke. Extracting meaningful models directly from data: a review of machine-learning approaches to data-driven equation discovery. In preparation.

Protein Bioinformatics and Structure Prediction

(See Repository for selected project files.)

SP Mielke and VV Krishnan (2008) Characterization of protein secondary structure from NMR chemical shifts. Progress in NMR Spectroscopy 54, 141–165.

SP Mielke and VV Krishnan (2005) Estimation of protein secondary structure content directly from NMR spectra using an improved empirical correlation with averaged chemical shift. Journal of Structural and Functional Genomics 6, 281–285.

SP Mielke and VV Krishnan (2004) An evaluation of chemical shift index-based secondary structure determination in proteins: Influence of random coil chemical shifts. Journal of Biomolecular NMR 30, 143–153.

SP Mielke and VV Krishnan (2003) Protein structural class identification directly from NMR spectra using averaged chemical shifts. Bioinformatics 19, 2054–2064.

SP Mielke and VV Krishnan (2003) Chemical shift-based identification of protein structural classes. Biophysical Journal 84, 460A. (Abstract)

Modeling and Analysis of DNA Structure and Dynamics

(See Repository for selected project files.)

SP Mielke, CJ Benham, and N Grønbech-Jensen (2009) Persistence lengths of DNA obtained from Brownian dynamics simulations. Journal of Physical Chemistry A 113, 4213–4216.

H Tanaka, SP Mielke, CJ Benham, T Kawai (2008) Visualization of the detailed structure of plasmid DNA. Journal of Physical Chemistry B 112, 16788–16792.

SP Mielke, N Grønbech-Jensen, and CJ Benham (2008) Brownian dynamics of double-stranded DNA in periodic systems with discrete salt. Physical Review E 77, 031924-1–11.

SP Mielke and CJ Benham (2007) Brownian dynamics of superhelical DNA. Journal of Biomolecular Structure and Dynamics 24, 736–737. (Abstract)

SP Mielke (2006) Computational approaches to the structure and dynamics of biomolecules. UC Davis, dissertation.

SP Mielke and VV Krishnan (2006) Superhelical denaturation of DNA: A theoretical perspective. Research Trends: Trends in Chemical Physics 13, 29–40.

SP Mielke, N Grønbech-Jensen, VV Krishnan, WH Fink, and CJ Benham (2005) Brownian dynamics simulations of sequence-dependent duplex denaturation in dynamically superhelical DNA. Journal of Chemical Physics 123, 124911–124921.

CJ Benham and SP Mielke (2005) DNA mechanics. Annual Review of Biomedical Engineering 7, 21–53.

SP Mielke, WH Fink, VV Krishnan, N Grønbech-Jensen, and CJ Benham (2004) Transcription-driven twin supercoiling of a DNA loop: A Brownian dynamics study. Journal of Chemical Physics 121, 8104–8112.

SP Mielke, CJ Benham, N Grønbech-Jensen, WH Fink, and VV Krishnan (2004) A dynamic model of localized denaturation in superhelical, closed-circular DNA. Biophysical Journal 86, 415A. (Abstract)

Photosynthetic Energy-Storage

D Mauzerall and SP Mielke (2014) Energy changes in photosynthetic electron transport: Probing photosynthesis by pulsed photoacoustics. In The Biophysics of Photosynthesis, JH Golbeck, A van der Est, Eds. Springer, Amherst.

SP Mielke, NY Kiang, RE Blankenship, and D Mauzerall (2013) Photosystem trap energies and spectrally-dependent energy-storage efficiencies in the Chl d-utilizing cyanobacterium, Acaryochloris marina. Biochim. Biophys. Acta 1827, 255–265.

SP Mielke, NY Kiang, RE Blankenship, MR Gunner, and D Mauzerall (2011) Efficiency of photosynthesis in a Chl d-utilizing cyanobacterium is comparable to or higher than that in Chl a-utilizing oxygenic species. Biochim. Biophys. Acta 1807, 1231–1236.

Atomic Structure

SP Mielke (2000) A nonlinear least-squares fitting program for atomic energy parameters along the argon isoelectronic sequence. U Toledo, thesis.