Herman

G. T. Herman, Image Reconstruction from Projections, Academic Press, NY, 1980... 

Altschuler M.D and Herman G. Fully three-dimensional image reconstruction using series expansion methods., A Review of Information Processing in Medical Imaging, Oak Ride National Lab., Oak Ride, TN, 1977, p.124-142. 

Herman G.T. Image reconstruction from projections.. Computer Science and Applied Mathematics, New York Academic, 1980... 

Gordon R., Bender R., Herman G.T. Algebraic reconstruction techniques (ART) for three-dimensional electron micrographs and X-ray photography., J. Theor. Biol., V. 29, 1970, p. 471-481. 

Mathematical framework of cone beam 3D reconlruction via the first derivative of the Radon transform, in Herman, Louis, Natterer (eds.). Mathematical Methods in Tomography, Springer, 1991... 

Herman M A and Sitter H 1996 Moiecuiar Beam Epitaxy Fundamentais and Current Status (Berlin Springer)... 

Yvon J 1935 Actualities Scientifiques et Industriel Pans Herman et Cie)... 

Herman B and Jacobsen K 1990 Optical Microscopy for Biology (Wiley)... 

Deuflhard P, Hermans J, Leimkuhler B, Mark A E, Reich S and Skeel R D (ed) 1998 Computational Molecular Dynamics Challenges, Methods, Ideas vol 4 Lecture Notes in Computational Science and Engineering (Berlin Springer)... 

Herman M F, Bruskin E J and Berne B J 1982 On path integral Monte Carlo simulations J. Chem. Phys. 76 5150-5... 

Herman M F and Kluk E 1984 A semiclassical justification for the use of non-spreading wavepackets in dynamics calculations Chem. Phys. 91 27... 

Herman M F, Kluk E and Davis H L 1986 Comparison of the propagation of semiclassical frozen Gaussian wave functions with quantum propagation for a highly excited enharmonic oscillator J. Chem. Phys. 84 326... 

Herman P R, LaRooque P E and Stoioheff B P 1988 Vaouum ultraviolet laser speotrosoopy 5 rovibrational speotra of Ar2 and oonstants of the ground and exoited states J. Chem. Phys. 89 4535-49... 

Berendsen, H.J.C., Postma, J.P.M., Van Gunsteren, W.F. Statistical mechanics and molecular dynamics The calculation of free energy, in Molecular Dynamics and Protein Structure, J. Hermans, ed.. Polycrystal Book Service, PO Box 27, Western Springs, 111., USA, (1985) 43-46. 

Experimental techniques based on the application of mechanical forces to single molecules in small assemblies have been applied to study the binding properties of biomolecules and their response to external mechanical manipulations. Among such techniques are atomic force microscopy (AFM), optical tweezers, biomembrane force probe, and surface force apparatus experiments (Binning et al., 1986 Block and Svoboda, 1994 Evans et ah, 1995 Israelachvili, 1992). These techniques have inspired us and others (see also the chapters by Eichinger et al. and by Hermans et al. in this volume) to adopt a similar approach for the study of biomolecules by means of computer simulations. 

We assume that the unbinding reaction takes place on a time scale long ( ompared to the relaxation times of all other degrees of freedom of the system, so that the friction coefficient can be considered independent of time. This condition is difficult to satisfy on the time scales achievable in MD simulations. It is, however, the most favorable case for the reconstruction of energy landscapes without the assumption of thermodynamic reversibility, which is central in the majority of established methods for calculating free energies from simulations (McCammon and Harvey, 1987 Elber, 1996) (for applications and discussion of free energy calculation methods see also the chapters by Helms and McCammon, Hermans et al., and Mark et al. in this volume). 

Zhang and Hermans, 1996] Zhang, L., and Hermans, J. Hydrophilicity of cayities in proteins. Proteins Struc. Pune, and Genetics. 24 (1996) 433-438... 

Hermans, J., Subramaniam, S. The free energy of xenon binding to myoglobin from molecular dynamics simulation. Isr. J. Chem. 27 (1986) 225-227... 

Hermans, J. A simple analysis of noise and hysteresis in free energy simulations. J. Phys. Chem. 95 (1991) 9029-9032... 

Hermans, J., Yun, R. H., Anderson, A. G. Precision of free-energies calculated by molecular dynamics simulations of peptides in solution. J. Comp. Chem. 13 (1992) 429-442... 

Hermans, J., Wang, L. Inclusion of loss of translational and rotational freedom in theoretical estimates of free energies of binding. Application to a complex of benzene and mutant T4-lysozyme. J. Am. Chem. Soc. 119 (1997) 2707-2714... 

Hermans, J. Sigma documentation. University of North Carolina. (1994) http //femto.med.unc.edu/SIGMA... 

Leech, J., Prins, J., Hermans, J. SMD Visual steering of molecular dynamics for protein design. IEEE Computational Science Engineering 3(4) (1996) 38-45... 

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