S.C. Harvey and P. Hoekstra

Dielectric Relaxation Spectra of Water Absorbed on Lysozyme

J. Phys. Chem. 76, 2987-2994 (1972)

.

S.C. Harvey and H.C. Cheung

Computer Simulation of Fluorescence Depolarization Due to Brownian Motion

Proc. Natl. Acad. Sci. USA 69, 3670-3672 (1972)

.

K.E. Thames, H.C. Cheung, and S.C. Harvey

Binding of 1,N6-Ethenoadenosine Triphosphate to Actin

Biochem. Biophys. Res. Commun. 60, 1252-1261 (1974)

.

S.C. Harvey and H.C. Cheung

Fluorescence Studies of 1,N6-Ethenoadenosine Triphosphate Bound to G-Actin: The Nucleotide Base is Inaccessible to Water

Biochem. Biophys. Res. Commun. 73, 865-868 (1976)

.

S.C. Harvey, H.C. Cheung, and K.E. Thames

Cooperativity in F-Actin Filaments on Binding of Myosin Subfragments, Demonstrated by Fluorescence of 1,N6-Ethenoadenosine Diphosphate

Arch. Biochem. Biophys. 179, 391-396 (1977)

.

S.C. Harvey and H.C. Cheung

Fluorescence Depolarization Studies on the Flexibility of Myosin Rod

Biochemistry 16, 5181-5187 (1977)

.

S.C. Harvey

Diffusion of Hinged Particles:  An Exception to the Einstein Relation

J. Chem. Phys. 69, 3426-3427 (1978)

.

S.C. Harvey

Experimental Detection of Macromolecular Flexibility by Observation of Time-Dependent Diffusion Coefficients

J. Chem. Phys. 71, 4221-4226 (1979)

.

S.C. Harvey

Transport Properties of Particles with Segmental Flexibility. I. Hydrodynamic Resistance and Diffusion Coefficients of a Freely Hinged Particle

Biopolymers 18, 1081-1104 (1979)

.

S.C.  Harvey and H.C. Cheung

Transport Properties of Particles with Segmental Flexibility. II. Decay of Fluorescence Polarization Anisotropy from Hinged Macromolecules

Biopolymers 19, 913-930 (1980)

.

S.C. Harvey and J. Garcia de la Torre

Coordinate Systems for Modeling the Hydrodynamic Resistance and Diffusion Coefficients of Irregularly Shaped Rigid Macromolecules

Macromolecules 13, 960-964 (1980)

.

S.C. Harvey and J.A. McCammon

Intramolecular Flexibility in Phenylalanine Transfer RNA

Nature 294, 286-287 (1981)

.

S.C. Harvey and J.A. McCammon

Macromolecular Conformational Energy Minimization: An Algorithm Varying Pseudodihedral Angles

Comput. Chem. 6, 173-179 (1982)

.

S.C. Harvey, P. Mellado, and J. Garcia de la Torre

Hydrodynamic Resistance and Diffusion Coefficients of Segmentally Flexible Macromolecules with Two Subunits

J. Chem. Phys. 78, 2081-2090 (1983)

.

S.C. Harvey

DNA Structural Dynamics:  Longitudinal Breathing as a Possible Mechanism for the B to Z Transition

Nucleic Acids Res. 11, 4867-4878 (1983)

.

M. Prabhakaran, S.C. Harvey, B. Mao, and J.A. McCammon

Molecular Dynamics of Phenylalanine Transfer RNA

J. Biomol. Struct. Dyns. 1, 357-369 (1983)

.

S.C. Harvey, M. Prabhakaran, B. Mao, and J.A. McCammon

Phenylalanine tRNA:  Molecular Dynamics Simulation

Science 223, 1189-1191 (1984)

.

C.S. Tung and S.C. Harvey

A Molecular Mechanical Model to Predict the Helix Twist Angles of B-DNA

Nucleic Acids Res. 12, 3343-3356 (1984)

.

C.S. Tung, J.A. McCammon, and S.C. Harvey

Large Amplitude Bending Motions in Phenylalanine Transfer RNA

Biopolymers 23, 2173-2193 (1984)

.

S.C. Harvey, M. Prabhakaran, and J.A. McCammon

Molecular Dynamics Simulation of Phenylalanine Transfer RNA:  I.  Methods and General Results

Biopolymers 24, 1169-1188 (1985)

.

M. Prabhakaran, S.C. Harvey, and J.A. McCammon

Molecular Dynamics Simulation of Phenylanine Transfer RNA:  II.  Amplitudes, Anisotropies and Anharmonicities of Atomic Motions

Biopolymers 24, 1189-1204 (1985)

.

D.S. Kang, S.C. Harvey, and R.D. Wells

Diepoxybutane Forms a Monoadduct with B-form (dG-dC)n.(dG-dC)n and a Crosslinked Diadduct with the Left-Handed Z-form

Nucleic Acids Res. 13, 5645-5656 (1985)

.

M. Prabhakaran and S.C. Harvey

Molecular Dynamics Anneals Large-Scale Deformations of Model Macromolecules:  Stretching the DNA Double Helix to Form an Intercalation Site

J. Phys. Chem. 89, 5767-5769 (1985)

.

S.C. Harvey

Conformational Dynamics of Transfer RNA

Comments Mol. Cell. Biophysics 3, 219-239 (1986)

.

C.S. Tung and S.C. Harvey

Computer Graphics Program to Reveal the Dependence of the Gross Three-Dimensional Structure of the B-DNA Double Helix on Primary Structure

Nucleic Acids Res. 14, 381-387 (1986)

.

C.S. Tung and S.C. Harvey

Base Sequence, Local Helix Structure, and Macroscopic Curvature of A-DNA and B-DNA

J. Biol. Chem. 261, 3700-3709 (1986)

.

S.C. Harvey and M. Prabhakaran

Ribose Puckering: Structure, Dynamics, Energetics, and the Pseudorotation Cycle

J. Amer. Chem. Soc. 108, 6128-6136 (1986)

.

C.D. Bell and S.C. Harvey

Comparison of Free Energy Surfaces for Extended Atom and All-Atom Models of n-Butane

J. Phys. Chem. 90, 6595-6597 (1986)

.

C.S. Tung and S.C. Harvey

A Common Structural Feature in Promoter Sequences in E. coli

Nucleic Acids Res. 15, 4973-4985 (1987)

.

M. Prabhakaran and S.C. Harvey

Asymmetric Oscillations in Cyclodextrin:  A Molecular Dynamics Study

Biopolymers 26, 1087-1096 (1987)

.

S.C. Harvey and M. Prabhakaran

Umbrella Sampling:  Avoiding Possible Artifacts and Statistical Biases

J. Phys. Chem. 91, 4799-4801 (1987)

.

R.K.Z. Tan and S.C. Harvey

A Comparison of Six DNA Bending Models

J. Biomol. Struct. Dyns. 5, 497-512 (1987)

.

R.K.Z. Tan, M. Prabhakaran, C.S. Tung, and S.C. Harvey

AUGUR:  A Program to Predict, Display and Analyze the Tertiary Structure of B-DNA

Comput. Applics. Biosci. 4, 147-151 (1988)

.

M. Prabhakaran and S.C. Harvey

Molecular Dynamics of Structural Transitions and Intercalation in DNA

Biopolymers 27, 1239-1248 (1988)

.

S.C. Harvey, J. Luo, and R. Lavery

DNA Stem-Loop Structures in Oligopurine-Oligopyrimidine Triplexes

Nucleic Acids Res. 16, 11795-11809 (1988)

.

R.K.Z. Tan and S.C. Harvey

Molecular Mechanics Model of Supercoiled DNA

J. Mol. Biol. 205, 573-591 (1989)

.

S.C. Harvey

Treatment of Electrostatic Effects in Macromolecular Modeling

Proteins 5, 78-92 (1989)

.

M. Prabhakaran and S.C. Harvey

Models for Two tRNAs Bound to Successive Codons on mRNA on the Ribosome

J. Biomol. Struct. Dyns. 7, 167-179 (1989)

.

J.L. Lopez-Lacomba, M. Guzman, M. Cortijo, P.L. Mateo, R. Aguirre, S.C. Harvey, and H.C. Cheung

Differential Scanning Calorimetric Study of the Thermal Unfolding of Myosin Rod, Light Meromyosin, and Subfragment 2

Biopolymers 28, 2143-2159 (1989)

.

K.A. Sharp, B. Honig, and S.C. Harvey

Electrical Potential of Transfer RNAs: Codon-Anticodon Recognition

Biochemistry 29, 340-346 (1990)

.

A. Malhotra, R.K.Z. Tan, and S.C. Harvey

Prediction of the Three-Dimensional Structure of Escherichia coli 30S Ribosomal Subunit: A Molecular Mechanics Approach

Proc. Natl. Acad. Sci. USA 87, 1950-1954 (1990)

.

N.R. Krishna, B.Y. Choe, M. Prabhakaran, G.C. Ekborg, L. Rodén, and S.C. Harvey

Nuclear Magnetic Resonance and Molecular Modeling Studies on O-b-D-Galactopyranosyl-(1Ý4)-O-b-D-Xylopyranosyl-(1ÝO)-L-Serine, A Carbohydrate-Protein Linkage Region Fragment from Connective Tissue Protoglycans

J. Biol. Chem. 265, 18256-18262 (1990)

.

H. De Loof, S.C. Harvey, J.P. Segrest, and R.W. Pastor

Mean Field Stochastic Boundary Molecular Dynamics Simulation of a Phospholipid in a Membrane

Biochemistry 30, 2099-2113 (1991)

.

B.Y. Choe, G.C. Ekborg, L. Rodén, S.C. Harvey, and N.R. Krishna

High-Resolution NMR and Molecular Modeling Studies on O-b-D-Gal-(1Ý3)-O-b-D-Gal-(1Ý4)-O-b-D-Xyl-(1ÝO)-L-Ser, A Carbohydrate-Protein Linkage Region Fragment from Connective Tissue Proteoglycans

J. Amer. Chem. Soc. 113, 3743-3749 (1991)

.

D. Sprous and S.C. Harvey

A Three Dimensional Model for Nodule DNA

J. Biol. Chem. 267, 5502 (1992)

.

M.H. Hao and S.C. Harvey

A Lattice Theory for Counterion Binding on Polyelectrolytes

Macromolecules 25, 2200-2208 (1992)

.

H.A. Gabb, M.E. Harris, N.B. Pandey, W.F. Marzluff, and S.C. Harvey

Molecular Modeling to Predict the Structural and Biological Effects of Mutations in a Highly Conserved Histone mRNA Loop Sequence

J. Biomol. Struct. Dyns. 9, 1119-1130 (1992)

.

M.H. Hao and S.C. Harvey

Analyzing the Normal Mode Dynamics of Macromolecules by the Component Synthesis Method

Biopolymers 32,1393-1405 (1992)

.

S.C. Harvey and R.K.Z. Tan

Teaching Macromolecular Modeling

Biophys. J. 63, 1683-1688 (1992)

.

R. Lavery, K. Zakrzewska, J.S. Sun, and S.C. Harvey

A Comprehensive Classification of Nucleic Acid Structural Families Based on Strand Direction and Base Pairing

Nucleic Acids Res. 20, 5011-5016 (1992)

.

R.K.Z. Tan and S.C. Harvey

Yammp: Development of a Molecular Mechanics Program Using the Modular Programming Method

J. Comp. Chem. 14, 455-470 (1993)

.

T.J. You and S.C. Harvey

Finite Element Approach to the Electrostatics of Macromolecules with Arbitrary Geometries

J. Comp. Chem. 14, 484-501 (1993)

.

A. Malhotra, H.A. Gabb, and S.C. Harvey

Modeling Large Nucleic Acids

Curr. Opin. Struct. Biol. 3, 241-246 (1993)

.

H.A. Gabb and S.C. Harvey

Conformational Transitions in Potential and Free Energy Space for Furanoses and 2'-Deoxynucleosides

J. Amer. Chem. Soc. 115, 4218-4227 (1993)

.

S.C. Harvey and H.A. Gabb

Conformational Transitions Using Molecular Dynamics with Minimum Biasing

Biopolymers 33, 1167-1172 (1993)

.

L.L. Pearce and S.C. Harvey

Langevin Dynamics Studies of Unsaturated Phospholipids in a Membrane Environment

Biophys. J. 65,1084-1092 (1993)

.

J.P. Segrest, D.W. Garber, C.G. Brouillette, S.C. Harvey and G.M. Anantharamaiah

The Amphipathic a Helix: A Multi-Functional Structural Motif in Plasma Apolipoproteins

Advances in Protein Chemistry: Lipoproteins, Apolipoproteins and Lipases, (V.N. Schumaker, Ed.) Vol. 45, pp 303-369 (1994)

.

A. Malhotra, R.K.Z. Tan and S.C. Harvey

Utilization of Shape Data in Molecular Mechanics Using a Potential Based on Spherical Harmonic Surfaces

J. Comp. Chem. 15, 190-199 (1994)

.

W.R. Rudnicki, B. Lesyng and S.C. Harvey

Lagrangian Molecular Dynamics Using Selected Conformational Degrees of Freedom, With Application to the Pseudorotation Dynamics of Furanose Rings

Biopolymers 34, 383-392 (1994)

.

A. Malhotra, R.K.Z. Tan and S.C. Harvey

Modeling Large RNAs and Ribonucleoprotein Particles using Molecular Mechanics Techniques

Biophys. J. 66, 1777-1795 (1994)

.

A. Malhotra and S.C. Harvey

A Quantitative Model of the Escherichia coli 16S RNA in the 30S Ribosomal Subunit

J. Mol. Biol. 240, 308-340 (1994)

.

P.H. Konstant, L.L. Pearce and S.C. Harvey

Langevin Dynamics of the Choline Head Group in a Membrane Environment

Biophys. J. 67, 713-719 (1994)

.

M.E. Harris, J.M. Nolan, A. Malhotra, J.W. Brown, S.C. Harvey and N.R. Pace

Use of Photoaffinity Crosslinking and Molecular Modeling to Analyze the Global Architecture of Ribonuclease P RNA

EMBO J. 13, 3953-3963 (1994)

.

T.R. Easterwood, F. Major, A. Malhotra and S.C. Harvey

Orientations of Transfer RNA in the Ribosomal A and P Sites

Nucleic Acids Res. 22, 3779-3786 (1994)

.

M.H. Hao and S.C. Harvey

Active Transport of Ions Across Membranes: Energetic Role of Electrostatics and Binding Site Asymmetry

Biochim. Biophys. Acta 1234, 5-14 (1995)

.

D. Sprous, W. Zacharias, Z.A. Wood and S.C. Harvey

Dehydrating Agents Sharply Reduce Curvature in DNAs Containing A Tracts

Nucleic Acids Res. 23, 1816-1821 (1995)

.

J.A. Schellman and S.C. Harvey

Static Contributions to the Persistence Length of DNA and Dynamic Contributions to DNA Curvature

Biophys. Chem. 55, 95-114 (1995)

.

P. Chartrand, S.C. Harvey, G. Ferbeyre, N. Usman and R. Cedergren

An Oligodeoxyribonucleotide that Supports Catalytic Activity in the Hammerhead Ribozyme Domain

Nucleic Acids Res. 23, 4092-4096 (1995)

.

S.C. Harvey, M. Dlakic, J. Griffith, R. Harrington, K. Park, D. Sprous and W. Zacharias

What is the Basis of Sequence-Directed Curvature in DNAs Containing A Tracts?

J. Biomol. Struct. Dyns. 13, 301-307 (1995)

.

T.R. Easterwood and S.C. Harvey

Modeling the Structure of the Ribosome

Biochem. Cell Biol. 73, 751-756 (1995)

.

D. Sprous and S.C. Harvey

Action at a Distance in Supercoiled DNA: Effects of DNA Sequence on Slither, Branching, and Intramolecular Concentration

Biophys. J. 70, 1893-1908 (1996)

.

R.K.Z. Tan, S.C. Harvey, E. DiMauro, G. Camilloni and P. Venditti

DNA Topological Context Affects Access to Eukaryotic DNA Topoisomerase I

J. Biomol. Struct. Dyns. 13, 855-872 (1996)

.

S.R. Sanghani, K. Zakrzewska, S.C. Harvey and R. Lavery

Molecular Modeling of (A4T4NN)n and (T4A4NN)n:  Sequence Elements Responsible for Curvature

Nucleic Acids Res. 24, 1632-1637 (1996)

.

M. Dlakic, K. Park, J.D. Griffith, S.C. Harvey and R.E. Harrington

The Organic Crystallizing Agent MPD Reduces DNA Curvature by Means of Structural Changes in A-tracts

J. Biol. Chem. 271, 17911-17919 (1996)

.

D. Sprous, R.K.Z. Tan and S.C. Harvey

Molecular Modeling of Closed Circular DNA Thermodynamic Ensembles

Biopolymers 39, 243-258 (1996)

.

R.K.Z. Tan, D. Sprous and S.C. Harvey

Molecular Dynamics Simulations of Small DNA Plasmids: Effects of Sequence and Supercoiling on Intramolecular Motions

Biopolymers 39, 259-278 (1996)

.

S.C. Harvey

Slipped Structures in DNA Triplet Repeat Sequences: Entropic Contributions to Genetic Instabilities

Biochemistry 36, 3047-3049 (1997)

.

T.R. Easterwood and S.C. Harvey

Ribonuclease P RNA: Models of the P15/16 Bulge Junction

RNA 3, 577-585 (1997)

.

A. Bacolla, R. Gellibolian, M. Shimizu, S. Amirhaeri, S. Kang, K. Ohshima, J.E. Larson, S.C. Harvey, B.D. Stollar, and R.D. Wells

Flexible DNA: Genetically Unstable CTG•CAG and CGG•CCG from Human Hereditary Neuromuscular Disease Genes

J. Biol. Chem. 272, 16783-16792 (1997)

.