BOOKS

JA McCammon and SC Harvey, "Dynamics of Proteins and Nucleic Acids" (1987) Cambridge University Press, London (ISBN 0521356520).

 

RD Wells and SC Harvey, Eds. "Unusual DNA Structures" (1987) Springer-Verlag, New York.

RECENT PUBLICATIONS

2018

N.D. Keul, K. Oruganty, E.T. Schaper Bergman, N.E. Beattie, W.E. McDonald, R. Kadirvelraj, M.L. Gross, R.S. Phillips, S.C. Harvey and Z.A. Wood, "The Entropic Force Generated by Intrinsically Disordered Segments Can Tune Protein Function", Nature (2018) in press.

KA Sharp, X-J Lu, G Cingolani & SC Harvey "Simulations and Electrostatic Analyses Suggest an Active Role for DNA Conformational Changes During Genome Packaging by Bacteriophages". bioRxiv (2018).  Link to supplementary material.

2016

JT Waters, HD Kim, JC Gumbart, X-J Lu & SC Harvey "DNA Scrunching in the Packaging of Viral Genomes", J Phys Chem B 120:6200-6207   PMID 27214211.

JT Waters, X-J Lu, R Galindo-Murillo, JC Gumbart, HD Kim, TE Cheatham III and SC Harvey "Transitions of Double-Stranded DNA Between the A- and B-Forms", J Phys Chem B 120:8449-8456   

 PMID 27135262.

2015

SC Harvey "The Scrunchworm Hypothesis: Transitions Between A-DNA and B-DNA Provide the Driving Force for Genome Packaging in Double-Stranded DNA Bacteriophages," J Struct Biol 189:1-8   PMC 4357361.

 

RF Garmann, A Gopal, SS Athavale, CM Knobler, WM Gelbart & SC Harvey, "Visualizing the Global Secondary Structure of a Viral RNA with Cryo-Electron Microscopy," RNA 21:1-10 PMC 4408795.

 

AS Petrov, B Gulen, AM Norris, NA Kovacs, CR Bernier, KA Lanier, GE Fox, SC Harvey, RM Wartell, NV Hud & LD Williams, "The History of the Ribosome and the Origin of Translation," Proc Natl Acad Sci USA 112:15396-15401 PMID 26621738.

 

SC Harvey "Productivity: Social Impacts of Science Metrics", Nature 524:35 PMID 26245571.

 

2014

S.C. Harvey, "Comment on the Article by A. Ben-Shaul: 'Entropy, Energy and Bending of DNA in Viral Capsids'," Biophys J 106, 489-492 (2014) PMC 3907254.

 

A.S. Petrov, C.R. Bernier, B. Gulen, C.C. Waterbury, E. Hershkovits, C. Hsiao, S.C. Harvey, N.V. Hud, G.E. Fox, R.M. Wartell & L.D. Williams, "Secondary Structures of rRNAs from all Three Domains of Life," PLoS ONE 9: e88222 (2014) PMC 3914948.

 

A.S. Petrov, C.R. Bernier, C. Hsiao, A.M. Norris, N.A. Kovacs, C.C. Waterbury, V.G. Stepanov, S.C. Harvey, G.E. Fox, R.M. Wartell, N.V. Hud & L.D. Williams, "Evolution of the Ribosome at Atomic Resolution," Proc Natl Acad Sci USA 111: 10251-10256 (2014) PMC 4104869.

 

C.R. Bernier, A.S. Petrov, C. Waterbury, J. Jett, F. Li, L.E. Freil, X. Xiong, L. Wang, B.L.R. Migliozzi, E. Hershkovitz, Y. Xue, C. Hsiao, J.C. Bowman, S.C. Harvey, M.A. Grover, Z.J. Wartell & L.D. Williams, "Ribovision: Visualization and Analysis of Ribosomes," Faraday Disc. 169:195-107 (2014) PMID 25340471.

 

2013

S.S. Athavale, J.J. Gossett, J.C. Bowman, N.V. Hud, L.D. Williams and S.C. Harvey, "In vitro Secondary Structure of the Genomic RNA of Satellite Tobacco Mosaic Virus", PLoS ONE 8, e54384 (2013) PMC 3551766.

 

C. Hsiao, T.K. Lenz, J.K. Peters, P.-Y. Fang, D.M. Schneider, E.J. Anderson, T. Preeprem, J.C. Bowman, E.B. Oneill, S.S. Athavale, J.J. Gossett, L. Lie, C. Trippe, J. Murray, Petrov, A.S., R. Wartell, S.C. Harvey, N.V. Hud and L.D. Williams, "Molecular Paleontology: A Biochemical Model of the Ancestral Ribosome," Nucleic Acids Res 41:3373-3385 (2013) PMC 3597689.

 

E.D. Horowitz, K.S. Rahman, B.D. Bower, D.J. Dismuke, M.C. Falvo, J.D. Griffith, S.C. Harvey and A. Asokan, "Biophysical and Ultrastructural Characterization of Adeno-Associated Viral Capsid Uncoating and Genome Release," J Virol 87, 2994-3002 (2013) PMC 3592113.

 

A.S. Petrov, S.S. Douglas and S.C. Harvey, "Effects of Pulling Forces, Osmotic Pressure, Condensing Agents and Viscosity on the Thermodynamics and Kinetics of DNA Ejection from Bacteriophages to Bacterial Cells: A Computational Study," J Phys Condensed Matter 25, 115101 (2013) PMC 3705564.

 

S.C. Harvey, Y. Zeng and C.E. Heitsch, "The icosahedral RNA Virus as a Grotto: Organizing the Genome as Stalagmites and Stalactites" J Biol Phys 39, 163-172 (2013) PMC 3662420.

 

C. Hsiao, I.-C. Chou, C.D. Okafor, J.C. Bowman, E.B. O'Neill, S.S. Athavale, A.S. Petrov, N.V. Hud, R.M. Wartell, S.C. Harvey and L.D. Williams, "Iron(II) as a Cofactor Folds RNA and Confers the Ability to Catalyze Electron Transfer," Nature Chemistry 5, 525-528 (2013) PMID 23695635.

 

A.S. Petrov, C.R. Bernier, E. Hershkovits, Y. Xue, C.C. Waterbury, C. Hsiao, V.G. Stepanov, E.A. Gaucher, M.A. Grover, S.C. Harvey, N.V. Hud, R.M. Wartell, G.E. Fox and L.D. Williams, "Secondary Structure and Domain Architecture of the 23S and 5S rRNAs," Nucleic Acids Res 41, 7522-7535 (2013) PMC 3753638.

 

K.S. Rahman, G. Cui, S.C. Harvey and N.A. McCarty, "Modeling the Conformational Changes Underlying Channel Opening in CFTR," PLoS ONE 8, e74574 (2013) PMC 3785483.

 

2012

S.S. Athavale, J.J. Gossett, C. Hsiao, J.C. Bowman, E. O’Neill, E. Hershkovitz, T. Preeprem, N.V. Hud, R.M. Wartell, S.C. Harvey and L.D. Williams, “Domain III of the Thermus thermophilus 23S Ribosomal RNA Folds Independently to a Near-Native State,” RNA 18,752-758 (2012) PMC 3312562.

 

S.S. Athavale, A. Petrov, C. Hsiao, D. Watkins, C.D. Prickett, J.J. Gossett, L. Lie, J.C. Bowman, E. O’Neill, C.R. Bernier, N.V. Hud, R.M. Wartell, S.C. Harvey and L.D. Williams, “RNA Folding and Catalysis Mediated by Iron(II),” PLoS ONE 7(5): e38024 (2012) PMC 3365117.

 

M.S. Swenson, J. Anderson, A. Ash, P. Gaurav, Z. Sukosd, D.A. Bader, S.C. Harvey and C.E. Heitsch, "GTfold: Enabling Parallel RNA Secondary Structure Prediction on Multi-Core Desktops," BMC Res Notes 5:341 (2012) PMC 3748833  GTfold webpage   Download GTfold from GitHub.

 

L. Rishishwar, N. Varghese, E. Tyagi, S.C. Harvey, I.K Jordan and N.A. McCarty, "Relating the Disease Mutation Spectrum to the Evolution of the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR)," PLoS ONE 7(8): e42336 (2012) PMC 3413703.

 

A.S. Petrov, C. Bernier, C. Hsiao, C.D. Okafor, E. Tannenbaum, J. Stern, E. Gaucher, D. Schneider, N.V. Hud, S.C. Harvey and L.D. Williams, “RNA-Magnesium-Protein Interactions in the Large Ribosomal Subunit,” J Phys Chem B 116, 8113-8120 (2012) PMID 22712611.

 

M.R. Smyda and S.C. Harvey, “The Entropic Cost of Polymer Confinement,” J Phys Chem B 116, 10928-10934 (2012) PMC 3471378.

 

Y.Y. Zeng, S.B. Larson, C.E. Heitsch, A. McPherson and S.C. Harvey, “A Model for the Structure of Satellite Tobacco Mosaic Virus,” J Struct Biol 180, 110-116 (2012) PMC 3466382.