Brooks, Harvey

Brooks, Harvey. 1967. Dilemmas of Engineering Education. IEEE Spectrum 4, no. 2 (February) 89-91. 

Breeii Robert, 146 Brooks, Harvey, 52, 54, 62, 132 Brown, Gordon S., 24, 179 Brown, J. Douglas, 27 Bucciarelli, Louis, 182 Buckley, William E, Jr., 102 Buhl, Harold R., 127 Burnham, Donald, 74 Burriss, Stanley W, 34, 96 Bush, Vannevai 29... 

Brooks, Harvey, 1994, The Relationship Between Science and Technology, Research Policy 12>, All... 

In combination, the book should serve as a useful reference for both theoreticians and experimentalists in all areas of biophysical and biochemical research. Its content represents progress made over the last decade in the area of computational biochemistry and biophysics. Books by Brooks et al. [24] and McCammon and Harvey [25] are recommended for an overview of earlier developments in the field. Although efforts have been made to include the most recent advances in the field along with the underlying fundamental concepts, it is to be expected that further advances will be made even as this book is being published. To help the reader keep abreast of these advances, we present a list of useful WWW sites in the Appendix. 

Good reviews of the application of dynamic simulation methods to biomolecules can be found in the books by Brooks et al. [1] and McCammon and Harvey [2]. Good short reviews on this topic can also be found in Refs. 3-5. More detailed discussions of dynamic simulation methodologies can be found in books by Allen and Tildesley [6], Frenkel and Smit [7], and Rapaport [8] and in the review by van Gunsteren [9]. 

CL Brooks, M Karplus, M Pettitt. Proteins. Adv Chem Phys, Vol 71. New York Wiley, 1988. JA McCammon, SC Harvey. New York Cambridge Univ Press, 1987. 

A number of books and journal articles reviewing computational methods relevant to biophysical problems have been published in the last decade. Two of the most popular texts, however, were published more than ten years ago those of McCammon and Harvey in 1987 and Brooks, Karplus, and Pettitt in 1988. There has been significant progress in theoretical and computational methodologies since the publication of these books. Therefore, we feel that there is a need for an updated, comprehensive text including the most recent developments and applications in the field. 

McCammon, J.A., Harvey, S.C. (1987), Dynamics of proteins and nucleic acids. Cambridge, UK Cambridge University Press. Brooks III, C. L., Karplus, M., Pettitt, B.M. (1988), Proteins. A theoretical perspective of dynamics, structure, and thermodynamics. New York Wiley. 

Leonard, K.S., Harvey, B.R., Woodhead, R.J., Brooks, T. and McCubbin, D. (1994) Assessment of an ultrafiltration technique for the fractionation of radionuclides associated with humic material./. Radioanal. Nucl. Chem. Articles, 181, 309-320. 

The change in velocity vt is equal to the integral of acceleration over time. In MolD, one numerically and iteratively integrates the classical equations of motion for every explicit atom N in the system by marching forward in time by tiny time increments, At. A number of algorithms exist for this purpose (Brooks et al., 1988 McCammon and Harvey, 1987), and the simplest formulation is shown below ... 

Since the late 1970 s, molecular dynamics simulation (MDS) has been proven a powerful tool for the study of protein intermolecular dynamics (McCommon et al., 1977, McCommon and Harvey, 1987 Brooks et al., 1988 Karplus and McCammon, 1986 Karplus and Petsko, 1990 and references therein). 

Since the first work describing a molecular dynamics simulation of a small protein was published (McCammon et al. 1977), there has been explosive growth in research concerned with theoretical studies of proteins and enzymes (McCammon and Harvey 1987 Brooks, et al 1988 Warshel 1991). Most of the studies have used empirical energy functions. This chapter describes the nature of the empirical energy function, its use in molecular mechanics calculations and molecular dynamics simulations and... 

The botulinum neurotoxins (BoNTs) comprise a family of seven distinct neurotoxic proteins (A-G) produced by immunologically discrete strains of the anaerobic bacterium Clostridium botulinum and in rare cases by Clostridium baratii and Clostridium butyricum (Habermann and Dreyer, 1986 Harvey et ah, 2002 Simpson, 2004). These toxins act on peripheral cholinergic synapses to inhibit spontaneous and impulse-dependent release of acetylcholine (ACh) (Brooks, 1956 Kao et al., 1976). Intoxication by BoNT results in muscle weakness, which can be fatal when the diaphragm and intercostal muscles become sufficiently compromised to impair ventilation (Dickson and Shevky, 1923). The BoNTs are the most potent substances in nature, and exposure to as httle as 1-3 ng/kg may be sufficient to cause human lethahty (GUI, 1982 Middlebrook and Franz, 1997 Amon et al., 2001). 

J. A. McCammon and S. C. Harvey, Dynamics of Proteins and Nucleic Acids, Cambridge University Press, 1987 C. L. Brooks, M. Karplus, and B. M. Pettitt, Proteins A Theoretical Perspective of Dynamics, Structure and Thermodynamics, Wiley, New York, 1988. 

It is of interest that two additional papers on the subject of Reactor Dynamics in this volume include problems involving expansions in space dependent modes, first, the paper on Tem perature coefficients and stability by Harvey Brooks, and, second, the paper on System kinetics by T. A. Welton. Brooks is also interested in representations of the neutron density with the aid of a multi-mode analysis, but his problem is more complicated than that of this section because of feedback considerations. However, he confines his detailed analysis to a case in which the fundamental mode is dominant and where the effect of higher modes can be treated by a perturbation method. Welton s multi-mode analysis is peculiar to the aqueous homogeneous reactor and bears little resemblance to the corresponding problems treated by Brooks and this writer. Neither Brooks nor Welton appear to be interested in graphical representations of their results. 

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