678 References
Chipot, C.and Pohorille, A. (eds) (2007).Free Energy Calculations. Springer–Verlag,
Berlin, Heidelberg, New York.
Ciccotti, G., Jacucci, G., and McDonald, I. R. (1976). Transport properties of molten
alkali-halides.Phys. Rev. A, 13 , 426.
Ciccotti, G., Jacucci, G., and McDonald, I. R. (1979). Thought experiments by
molecular dynamics.J. Stat. Phys., 21 , 1.
Ciccotti, G., Pierleoni, C., and Ryckaert, J. P. (1992). Theoreticalfounadtion and
rheological application of nonequilibrium molecular dynamics. InMicroscopic Sim-
ulations of Complex Hydrodynamic Phenomena(ed. M. Marechal and B. L. Holian),
p. 25. Plenum Press, New York.
Coker, D. F., Berne, B. J., and Thirumalai, D. (1987). Path integralMonte-Carlo
studies of the behavior of excess electrons in simple fluids. J. Chem. Phys., 86 ,
5689.
Cornell, W. D., Cieplak, P., Bayly, C. I., Gould, I. R., Merz, K. M., Jr., Ferguson,
D. M., Spellmeyer, D. C., Fox, T., Caldwell, J. W., and Kollman, P. A. (1995). A
2nd generation force-field for the simulation of proteins, nucleic-acids, and organic-
molecules.J. Am. Chem. Soc., 117 , 5179.
Craig, I. R. and Manolopoulos, D. E. (2004). Quantum statistics and classical
mechanics: Real time correlation functions from ring polymer molecular dynamics.
J. Chem. Phys., 121 , 3368.
Crooks, G. E. (1998). Nonequilibrium measurements of free energy differences for
microscopically reversible Markovian systems.J. Stat. Phys., 90 , 1481.
Crooks, G. E. (1999). Entropy production fluctuation theorem and the nonequilib-
rium work relation for free energy differences.Phys. Rev. E, 60 , 2721.
Cuendet, M. A. (2006). Statistical Mechanical derivation of Jarzynski’s identity for
thermostatted non-Hamiltonian dynamics.Phys. Rev. Lett., 96 , 120602.
Darve, E. (2007). Thermodynamic integration using constraintedand unconstrained
dynamics. InFree Energy Calculations(ed. C. Chipot and A. Pohorille), pp. 119–
- Springer-Verlag, Berlin, Heidelberg, New York.
Darve, E. and Pohorille, A. (2001). Calculating free energies using avearge force.J.
Chem. Phys., 115 , 9169.
Darve, E., Rodriguez-Gomez, D., and Pohorille, A. (2008). Adaptivebiasing force
method for scalar and vector free energy calculations.J. Chem. Phys., 128 , 144120.
Darve, E., Solomon, J., and Kia, A. (2009). Computing generalized Langevin equa-
tions generalized Fokker–Planck equations. Proc. Natl. Acad. Sci. U.S.A., 106 ,
Davisson, C. and Germer, L. H. (1927). Reflection of electrons bya crystal of nickel.
Nature, 119 , 558.
De Leon, N., Mehta, M. A., and Topper, R. Q. (1991). Cylindrical manifolds in phase
space as mediators of chemical reaction dynamics and kinetics I. Theory.J. Chem.
Phys., 94 , 8310.
Delbuono, G. S., Rossky, P. J., and Schnitker, J. (1991). Model dependence of quan-
tum isotope effects in liquid water.J. Chem. Phys., 95 , 3728.
Dellago, C., Bolhuis, P. G., Csajka, F. S., and Chandler, D. (1998). Transition path
sampling and the calculation of rate constants.