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] . Coulombic free energy and salt ion association per phosphate of all-atom models of DNA oligomer: dependence on oligomer size. Soft Matter. 2012;8:9345-9355.
. Mechanism of bacterial transcription initiation: RNA polymerase - promoter binding, isomerization to initiation-competent open complexes, and initiation of RNA synthesis. J Mol Biol. 2011;412(5):754-71.
. Nonspecific DNA Binding and Bending by HU(alpha beta): Interfaces of the Three Binding Modes Characterized by Salt-Dependent Thermodynamics. Journal of Molecular Biology. 2011;410:241-267.
. Protein Diffusion in the Periplasm of E-coli under Osmotic Stress. Biophysical Journal. 2011;100:22-31.
. Quantifying why urea is a protein denaturant, whereas glycine betaine is a protein stabilizer. Proc Natl Acad Sci U S A. 2011;108(41):16932-7.
. Separation of preferential interaction and excluded volume effects on DNA duplex and hairpin stability. Proceedings of the National Academy of Sciences of the United States of America. 2011;108:12699-12704.
. Contributions of the Histidine Side Chain and the N-Terminal alpha-Amino Group to the Binding Thermodynamics of Oligopeptides to Nucleic Acids as a Function of pH. Biochemistry. 2010;49:2018-2030.
. One-step DNA melting in the RNA polymerase cleft opens the initiation bubble to form an unstable open complex. Proceedings of the National Academy of Sciences of the United States of America. 2010;107:10418-10423.
. Preferential Interactions between Small Solutes and the Protein Backbone: A Computational Analysis. Biochemistry. 2010;49:1954-1962.
. Preferential Interactions between Small Solutes and the Protein Backbone: A Computational Analysis. Biochemistry. 2010;49:1954-1962.
. Probing DNA Binding, DNA Opening, and Assembly of a Downstream Clamp/Jaw in Escherichia coil RNA Polymerase-lambda P-R Promoter Complexes Using Salt and the Physiological Anion Glutamate. Biochemistry. 2010;49:4361-4373.
. Why Hofmeister effects of many salts favor protein folding but not DNA helix formation. Proceedings of the National Academy of Sciences of the United States of America. 2010;107:7716-7721.
. Cytoplasmic Protein Mobility in Osmotically Stressed Escherichia coli. Journal of Bacteriology. 2009;191:231-237.
. Evidence for a Tyrosine-Adenine Stacking Interaction and for a Short-lived Open Intermediate Subsequent to Initial Binding of Escherichia coli RNA Polymerase to Promoter DNA. Journal of Molecular Biology. 2009;385:339-349.
. Interactions of the Osmolyte Glycine Betaine with Molecular Surfaces in Water: Thermodynamics, Structural Interpretation, and Prediction of m-Values. Biochemistry. 2009;48:10372-10379.
. Quantifying the roles of water and solutes (denaturants, osmolytes, and Hofmeister salts) in protein and model processes using the solute partitioning model. Methods Mol Biol. 2009;490:179-93.
. Using Surface Tension Data to Predict Differences in Surface and Bulk Concentrations of Nonelectrolytes in Water. Journal of Physical Chemistry C. 2009;113:2171-2174.
. DNA Binding Mode Transitions of Escherichia coli HU alpha beta: Evidence for Formation of a Bent DNA - Protein Complex on Intact, Linear Duplex DNA. Journal of Molecular Biology. 2008;383:324-346.
. Formation of a wrapped DNA-protein interface: Experimental characterization and analysis of the large contributions of ions and water to the thermodynamics of binding IHF to H ' DNA. Journal of Molecular Biology. 2008;377:9-27.
. Late steps in the formation of E-coli RNA Polymerase-lambda P-R promoter open complexes: Characterization of conformational changes by rapid [Perturbant] upshift experiments. Journal of Molecular Biology. 2008;376:1034-1047.
. Quantifying accumulation or exclusion of H+, HO-, and Hofmeister salt ions near interfaces. Chemical Physics Letters. 2008;467:1-8.
. Thermodynamic origin of Hofmeister ion effects. Journal of Physical Chemistry B. 2008;112:9428-9436.
. Thermodynamics and Folding Pathway of Tetraloop Receptor-Mediated RNA Helical Packing. Journal of Molecular Biology. 2008;384:702-717.
. Hofmeister salt effects on surface tension arise from partitioning of anions and cations between bulk water and the air-water interface. Journal of Physical Chemistry B. 2007;111:5411-5417.
. Methods of changing biopolymer volume fraction and cytoplasmic solute concentrations for in vivo biophysical studies. 2007:487-504.
. Real-time footprinting of DNA in the first kinetically significant intermediate in open complex formation by Escherichia coli RNA polymerase. Proceedings of the National Academy of Sciences of the United States of America. 2007;104:7833-7838.
. Urea-amide preferential interactions in water: Quantitative comparison of model compound data with biopolymer results using water accessible surface areas. Journal of Physical Chemistry B. 2007;111:9675-9685.
. Crowding and confinement effects on protein diffusion in vivo. Journal of Bacteriology. 2006;188:6115-6123.
. Do sigma factors need help with a meltdown?. Cell. 2006;127:256.
. Interactions of cationic ligands and proteins with small nucleic acids: analytic treatment of the large coulombic end effect on binding free energy as a function of salt concentration. Biochemistry. 2006;45(27):8411-26.
. Partitioning of atmospherically relevant ions between bulk water and the water/vapor interface. Proceedings of the National Academy of Sciences of the United States of America. 2006;103:14278.
. Solute probes of conformational change in open complex formation by E coli RNA polymerase at the lambdaPR promoter: evidence for unmasking of the active site in the isomerization step and for largescale coupled folding in the subsequent conversion to RPo. Biochemistry. 2006;45(7):2161-77.
. Solute probes of conformational changes in open complex (RPo) formation by Escherichia coli RNA polymerase at the lambda PR promoter: Evidence for unmasking of the active site in the isomerization step and for large-scale coupled folding in the subsequent. BiochemistryBiochemistry. 2006;45:2161-2177.
. Thermodynamic expressions relating different types of preferential interaction coefficients in solutions containing two solute components. Journal of Physical Chemistry B. 2006;45:2161-2177.
. The effects of upstream DNA on open complex formation by Escherichia coli RNA polymerase. Proceedings of the National Academy of Sciences of the United States of America. 2005;102:285-290.
. Use of urea and glycine betaine to quantify coupled folding and probe the burial of DNA phosphates in Lac repressor - Lac operator bindings. Biochemistry. 2005;44:16896-16911.
. Use of urea and glycine betaine to quantify coupled folding and probe the burial of DNA phosphates in lac repressor-lac operator binding. Biochemistry. 2005;44(51):16896-911.
. Application of the local-bulk partitioning and competitive binding models to interpret preferential interactions of glycine betaine and urea with protein surface. Biochemistry. 2004;43(28):9276-88.
. Application of the local-bulk partitioning and competitive binding models to interpret preferential interactions of glycine betaine and urea with protein surface. BiochemistryBiochemistry. 2004;43:9276-9288.
. Effect of the number of nucleic acid oligomer charges on the salt dependence of stability (Delta G degrees(37)) and melting temperature (T-m): NLPB analysis of experimental data. BiochemistryBiochemistry. 2004;43:7090-7101.
. Effect of the number of nucleic acid oligomer charges on the salt dependence of stability (DeltaG 37degrees) and melting temperature (Tm): NLPB analysis of experimental data. Biochemistry. 2004;43(22):7090-101.
. The exclusion of glycine betaine from anionic biopolymer surface: why glycine betaine is an effective osmoprotectant but also a compatible solute. Biochemistry. 2004;43(46):14732-43.
. The exclusion of glycine betaine from anionic biopolymer surface: Why glycine betaine is an effective osmoprotectant but also a compatible solute. BiochemistryBiochemistry. 2004;43:14732-14743.
. Gibbs-Duhem-based relationships among derivatives expressing the concentration dependences of selected chemical potentials for a multicomponent system. Biophysical ChemistryBiophysical Chemistry. 2004;112:165-175.
. Gibbs-Duhem-based relationships among derivatives expressing the concentration dependences of selected chemical potentials for a multicomponent system. Biophys Chem. 2004;112(2-3):165-75.
. Interactions of the KWK6 cationic peptide with short nucleic acid oligomers: demonstration of large Coulombic end effects on binding at 0.1-0.2 M salt. Nucleic Acids ResearchNucleic Acids Res. 2004;32:3271-3281.
. Interactions of the KWK6 cationic peptide with short nucleic acid oligomers: demonstration of large Coulombic end effects on binding at 0.1-0.2 M salt. Nucleic Acids Res. 2004;32(11):3271-81.
. Large changes in cytoplasmic biopolymer concentration with osmolality indicate that macromolecular crowding may regulate protein-DNA interactions and growth rate in osmotically stressed Escherichia coli K-12. Journal of Molecular RecognitionJournal of Molecular Recognition. 2004;17:488-496.
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