Scientific Publications of Dr. Scott H. Northrup

Department of Chemistry, Tennessee Technological University

 1. Northrup, SH; Hynes, JT. Coupling of translational and reactive
 dynamics for a simple lattice model. J Stat Phys. 1978; 18: 91,105. 

 2. Northrup, SH; Hynes, JT. Coupling of translational and reactive 
dynamics for a fokker-planck model. J Chem Phys. 1978; 68: 
3203,3216.

 3. Northrup, SH; Hynes, JT. On the description of reactions in 
solution. Chem Phys Let. 1978; 54: 244,247.

 4. Northrup, SH; Hynes, JT. On reaction rate constants and kernels. 
Chem Phys Let. 1978; 54: 248,252.

 5. Northrup, SH; Hynes, JT. Reactive dynamics for diffusive barrier 
crossing. J Chem Phys. 1978; 69: 5246,5260.

 6. Northrup, SH; Hynes, JT. Initial condition effects for diffusive 
barrier crossing. J Chem Phys. 1978,; 69: 5261,5266.

 7. Northrup, SH; Hynes, JT. Short range caging effects for reactions 
in solution. I. reaction rate constants and short range caging 
picture. J Chem Phys. 1979; 71: 871,883.

 8. Northrup, SH; Hynes, JT. Short range caging effects for reactions 
in solution. II. escape probability & time dependent 
reactivity. J Chem Phys. 1979; 71: 884,893.

 9. Northrup, SH. Theoretical studies of reaction dynamics in 
solution. Ph.D. Thesis. 1978

 10. Northrup, SH; McCammon, JA. Simulation methods for protein 
structure fluctuations. Biopolymers. 1980; 19: 1001,1016. 

 11. McCammon, JA; Northrup, SH; Karplus, M.; Levy, R. Helix-coil 
transitions in a simple polypeptide model. Biopolymers. 1980; 
19: 2033,2045.

 12. Northrup, SH; McCammon, JA. Efficient trajectory, simulation 
methods for diffusional barrier crossing processes. J Chem 
Phys. 1980; 72: 4569,4578.

 13. Northrup, SH; Hynes, JT. The stable states picture of chemical 
reactions. I. Formulation for rate constants and initial 
condition effects. J Chem Phys. 1980; 73: 2700,2714.

 14. Northrup, SH; Pear, MR; McCammon, JA; Karplus, M. Molecular 
dynamics of ferrocytochrome c. Nature. 1980; 286: 304,305. 

 15. Pear, MR; Northrup, SH; McCammon, JA. Diffusional correlations 
in polymer dynamics. J Chem Phys. 1980; 73: 4703,4704.

 16. Pear, MR; Northrup, SH; McCammon, JA; Karplus, M.; Levy, R. 
Correlated helix-coil transitions in polypeptides. 
Biopolymers. 1981; 20: 629,632.

 17. Northrup, SH; Pear, MR; McCammon, JA; Karplus, M.; Takano, T. 
Internal mobility of ferrocytochrome c: theory & experiment. 
Nature. 1980; 287: 659,660.

 18. Northrup, SH; Pear, MR; Morgan, JD; McCammon, JA; Karplus, M. 
Molecular dynamics of ferrocytochrome c: magnitude and anisotropy of atomic displacements. J Mol Biol. 1981; 153: 1087,1109.

 19. Northrup, SH; Pear, MR; Morgan, JD; McCammon, JA. Molecular 
dynamics of ferrocytochrome c: fluctuation anisotropy. Proc 
6th Annual Taniguchi Symposium. 1980;

 20. Northrup, SH; Pear, MR; Lee, C.; McCammon, JA; Karplus, M. 
Dynamical theory of activated processes in globular proteins. 
Proc Nat Acad Sci USA. 1982; 79: 4035,4039.

 21. Mao, B.; Pear, MR; McCammon, JA; Northrup, SH. Repulsive 
interactions between polar & apolar atoms in globular 
proteins. J Mol Biol. 1981; 151: 199,202.

 22. Mao, B.; Pear, MR; McCammon, JA; Northrup, SH. Molecular 
dynamics of ferrocytochrome c: anharmonicity of atomic 
displacements. Biopolymers. 1982; 21: 1979,1989.

 23. McCammon, JA; Northrup, SH. Gated binding of ligands to 
proteins. Nature. 1981; 293: 316,317.

 24. Northrup, SH; Zarrin, F.; McCammon, JA. Rate theory for gated 
diffusion-influenced ligand binding to proteins. J Phys Chem. 
1982; 86: 2314,2321.

 25. Szabo, A.; Shoup, D.; Northrup, SH; McCammon, JA. Stochastically 
gated diffusion-influenced reactions. J Chem Phys. 1982; 77: 
4484,4493. 

 26. Morgan, JD; McCammon, JA; Northrup, SH. Molecular dynamics of 
ferrocytochrome c: time dependence of the atomic 
displacements. Biopolymers. 1983; 22: 1579,1593.

 27. Northrup, SH; McCammon, JA. Saddle-point avoidance in 
diffusional reactions. J Chem Phys. 1983; 78: 987,989.

 28. McCammon, JA; Lee, CY; Northrup, SH. Sidechain rotational 
isomerization in proteins: a mechanism involving gating and 
transient packing defects. J Amer Chem Soc. 1983; 105: 
2232,2237.

 29. Berkowitz, M.; Morgan, JD; McCammon, JA; Northrup, SH. 
Diffusion-controlled reactions. A variational formula for the 
optimum reaction coordinate. J Chem Phys. 1983; 79: 
5563,5565. 

 30. Northrup, SH; McCammon, JA. Gated reactions. J Amer Chem Soc. 
1984; 106: 930,934.

 31. Northrup, SH; Allison, SA; McCammon, JA. Brownian dynamics 
simulation of diffusion-influenced biomolecular reactions. J 
Chem Phys. 1984; 80: 1517,1524.

 32. Northrup, SH. Molecular mechanics of kink formation in lipid 
monolayers. J Phys Chem. 1984; 88: 3441,3446.

 33. Allison, SA; Srinivasan, N.; McCammon, JA; Northrup, SH. 
Diffusion controlled reactions between a spherical target and 
dumbell dimer by brownian dynamics simulation. J Phys Chem. 
1984; 88: 6152,6157.

 34. Northrup, SH. Chemistry through models. J Amer Chem Soc. 1984; 
106: 7656.

 35. Allison, SA; McCammon, JA; Northrup, SH. Dynamics of 
macromolecular interactions. J Amer Chem Soc. 1986; 302: 
216,231.

 36. McCammon, JA; Allison, SA; Northrup, SH. Theoretical molecular 
biology: some recent developments. J Mol Sci. 1985; 3: 
193,204.

 37. McCammon, JA; Northrup, SH; Allison, SA. Diffusional dynamics 
of ligand-receptor association. J Phys Chem. 1986; 90: 
3901,3905.

 38. Allison, SA; Northrup, SH; McCammon, JA. Extended brownian 
dynamics of diffusion controlled reactions. J Chem Phys. 
1985; 83: 2894,2899.

 39. Allison, SA; Northrup, SH; McCammon, JA. Simulation of 
biomolecular diffusion and complex formation. Biophys J. 
1986; 49: 167,175.

 40. Northrup, SH; Curvin, MS. Molecular dynamics simulation of 
disorder transitions in lipid monolayers. J Phys Chem. 1985; 
89: 4707,4713.

 41. McCammon, JA; Lybrand, TP; Allison, SA; Northrup, SH. Ligand 
binding: new theoretical approaches to molecular recognition. 
Biomolecular Stereodynamics. 1986; 0: 4707,4713.

 42. Northrup, SH; Curvin, M.; Allison, SA; McCammon, JA. 
Optimization of brownian dynamics methods for diffusion-
influenced rate constant calculations. J Chem Phys. 1986; 84: 
2196,2203. 

 43. Northrup, SH; Smith, J.; Boles, J.; Reynolds, J. The effect of 
dipole moment on diffusion-controlled bimolecular reaction 
rates. J Chem Phys. 1986; 84: 5536,5544.

 44. Northrup, SH; Reynolds, JCL; Miller, CM; Forrest, KJ; Boles, JO. 
Diffusion controlled association rate of cytochrome c and 
cytochrome c peroxidase in a simple electrostatic model. J 
Amer Chem Soc. 1986; 108: 8162,8170.

 45. Northrup, SH. Diffusion-controlled ligand binding to multiple 
competing cell-bound receptors. J Phys Chem. 1988; 92: 
5847,5850.

 46. McCammon, JA; Bacquet, RJ; Allison, SA; Northrup, SH. 
Trajectory simulation studies of diffusion-controlled 
reactions. Faraday Disc. 1987; 83: 213,222.

 47. Northrup, SH; Boles, JO; Reynolds, JCL. Electrostatic effects in 
the brownian dynamics of association and orientation of 
heme proteins. J Phys Chem. 1987; 91: 5991,5998.

 48. Northrup, SH; Luton, JA; Boles, JO; Reynolds, JCL. Brownian 
dynamics simulation of protein association. J Computer-aided 
Mol Design. 1988; 1: 291,311.

 49. Northrup, SH; Boles, JO; Reynolds, JCL. Brownian dynamics of 
cytochrome c and cytochrome c peroxidase association. 
Science. 1988; 241: 67,70.

 50. Herbert, RG; Northrup, SH. Brownian simulation of cytochrome 
c551 association and electron self-exchange. J Mol Liq. 1989; 
41: 207,222.

 51. Northrup, SH; Wensel, TG; Meares, CF; Wendoloski, JJ; Matthew, 
JB. Electrostatic field around cytochrome c: theory and 
energy transfer experiments. Proc Nat Acad Sci USA. 1990; 87: 
9503,9507.

 52. Northrup, SH. Theoretical simulation of protein-protein 
interactions. Cytochrome C: A Multidisciplinary Approach. 
1996; 543,570.

 53. Reynolds, JCL; Cooke, KF; Northrup, SH. Electrostatics and 
diffusional dynamics in the carbonic anhydrase active site 
channel. J Phys Chem. 1990; 94: 985,991.

 54. Eltis, LD; Herbert, RG; Barker, PD; Mauk, AG; Northrup, SH. 
Reduction of horse heart ferricytochrome c by bovine liver 
ferrocytochrome b5. Experimental and theoretical anaylsis. 
Biochemistry. 1991; 30: 3663,3674.

 55. Northrup, SH; Erickson, HP. Kinetics of protein-protein 
association explained by brownian dynamics computer 
simulation. Proc Nat Acad Sci USA. 1992; 89: 3338,3342.

 56. Northrup, SH; Herbert, RG. Brownian simulation of protein 
association and reaction. Int J Quant Chem. 1990; 17: 55,71. 

 57. Northrup, SH; Thomasson, KA; Miller, CM; Barker, PD; Eltis, LD; 
Guillemette, JG; Mauk, AG. Effects of charged amino acid 
mutations on the bimolecular kinetics of reduction of yeast 
iso-1-ferricytochrome c by bovine ferrocytochrome b. 
Biochemistry. 1993; 32: 6613,6623.

 58. Andrew, SM; Thomasson, KA; Northrup, SH. Simulation of 
electrons transfer self-exchange in cytochrome c and b5. J 
Amer Chem Soc. 1993; 115: 5516,5521.

 59. Northrup, SH. Hydrodynamic motions of larger molecules. Current 
Opinion Str Bio. 1994; 4: 269,274.

 60. Thomasson, KA; Northrup, SH. Free energy of nonspecific binding 
of cro repressor protein to DNA. J Phys Chem. 1997; 101: 9127,9136.

 61. Northrup, SH. Computer modeling of protein-protein interactions. 
Protein Electron Transfer. 1996; 69,94.

 62. Northrup, SH. Molecular graphics and simulation of proteins and 
nucleic acids. Using Computers in Chemistry and Chemical Education. 
1997; 283,308.

 63. Mauk, AG; Mauk, MR; Moore, GR; Northrup, SH. Experimental and theoretical
analysis of the interaction between cytochrome c and cytochrome b5.
J Bioenerg Biomem. 1995; 27: 311,330.

 64. Northrup, SH. Activation of an enzyme simulated by explicit dynamics of an 
active site lid. Biophysical J. 1996; 71: 3.

 65. Castro, G; Boswell, CA; Northrup, SH Dynamics of protein-protein docking;
cytochrome c and cytochrome c peroxidase revisited. J. Biomolecular
Structure & Dynamics.  1998; 16: 413.